Scientific Report 2013-2014

Physical Chemistry Institute

RocasolanoSpanish National Research Council

Editors: Clara Gómez, José M. Pérez Cañadillas and Lourdes Infantes

Composition and layout:José Luis Rojo Marco, Producción Gráfica Multimedia PGM

The editors would like to thank all the staff of the Institute who have contributed to the realization of this Scientific Report.

Table of Contents

Department of Crystallographyand Structural Biology 7

Department of Structure, Energy and Chemical Reactivity 30

Department of BiologicalPhysical Chemistry 61

Department of LowDimensional Systems, Surfaces and Condensed Matter 115

Research SupportServices 153

ANNEX 1. Singular Instrumentation 174

ANNEX 2.IQFR Facts and Figures 181

Direction. Presentation 3

Scientific Report 2013/2014 3

PresentationThe “Rocasolano” Institute of Physical Chemistry (IQFR) continues the scientific tradition of the National Institute of Physics and Chemistry, whose building it still occupies. The original Institute, which was part of the Board of Extension of Studies and Scientific Research (JAE), was opened in 1932, thanks to a generous grant from the Rockefeller Foundation. This donation was made on the condition that the building be exclusively dedicated to research, after the Rockerfeller Foundation had detected a group of competent scientists doing their work in precarious conditions. It was the first modern research center in Spain both in terms of the building design and its operating rules which were comparable to the best modern day centers. Let us note, for example, the criteria for the forming a new section: “A new section will not created until a qualified person is identified who is recognized as an authority in his/her research field”. This Institute’s first years witnessed the advances made by Blas Cabrera, Miguel Catala, Enrique Moles and Julio Palacios, and the level of its international connections is illustrated by renowned visitors such as Arnold Sommerfeld, William Bragg or Marie Curie. This glorious period was cut short by the Spanish Civil War.

Later, in 1946, the Spanish National Scientific Research Council (CSIC), which inherited the tasks and responsibilities of the JAE, created the “Rocasolano” Institute of Physical Chemistry (IQFR). Antonio Rius was the first director. Since then, the IQFR has been a national reference in research in Pure and Applied Physical Chemistry. Its generalist vocation is evidenced by the fact that for decades it spawned many more specialized research institutes within the CSIC as well as a number of university departments throughout Spain.

Since the days of the National Institute of Physics and Chemistry, the research has evolved and changed. Some lines of research have become extinct or are continued in other centers which originated from the IQFR. Other lines have become international benchmarks. At present,

the Institute focuses its research in various fields of Physical Chemistry, emphasizing its strong multidisciplinary nature at the border between Chemistry, Physics, Biology and Materials Science. It is known for its set of advanced techniques that enhance the capabilities of the center and permit our research to span many different fields. In this era of overly specialized institutes, the IQFR is one of the few institutes which maintain a generalist nature that can incorporate new research fields that share the physicochemical methodologies, among which we highlight Atmospheric Chemistry or Biological Chemistry. In the first case, the recent addition of a dedicated Atmospheric Chemistry group benefits from the previous experience of other groups in photolysis, chemical reactivity and surface reactivity. In the second case, the application of chemical and physical techniques to solve problems of biological interest has developed considerably. We take advantage our own unique instrumentation such as the High Field Nuclear Magnetic Resonance Laboratory, home to the CSIC’s highest field nuclear magnetic resonance spectrometer (one of only three in Spain of its kind), fluorescence techniques, high resolution mass spectrometry and the Laboratory for X-ray diffraction of proteins. The experience of researchers in using unique instrumentation has made them frequent users of the ALBA synchrotron in Barcelona.

In short, the IQFR covers topics related to

Juan de la Figuera Bayón Douglas Vinson Laurents Juan Zenón Dávalos PradoDirector Scientist vice-director Technical vice-director

Juan de la Figuera Bayón

fundamental Physical Chemistry, the study of energy and chemical reactivity (Ion-Molecule Reactions, Thermochemistry, Computational Chemistry, Reactions at Surfaces), which complement the interdisciplinary research in Science and Technology of Materials and Nanotechnology, the study of the molecular basis of biological function in systems with increasing levels of organization, and the impact of chemical processes on Climate Change and pollution.

The Institute has specialized support units in electronics, mechanics and glass blowing, which are vital to much of the experimental work carried out in the IQFR. The same is true of the Stockroom and also the Library, which is a direct descendant of the original library of the National Institute of Physics and Chemistry. It is the best Chemistry and Physics library in Spain and one of the top scientific libraries in Europe with an impressive subscription to hundreds of journals and an important historical collection. In the current digital age, our Library is a major source for loans to other institutions.

However during 2013 and 2014, the economic crisis and the management of its impact on research and development in Spain, and more specifically in the CSIC, have been a significant

burden on the Institute’s work. The IQFR, due to the fundamental nature of much of its research, has been funded mainly by competitive projects in local, national and international calls. The erratic national policy with unpredictable timing of the calls and sharp cuts in past years has been a major problem. Although IQFR has maintained the highest levels of scientific productivity in its history, the uncertainty and the feeling of a lack of support for research has led two excellent research groups to move out of the CSIC and Spain, respectively. Moreover, the staff has suffered from the retirements of scientific and technical personnel, the absence of new positions and the drastic decrease in our ability to hire trainees. As for the equipment, the Institute has worked hard in an emergency mode to keep the equipment in operation; in the case of the High Field Nuclear Magnetic Resonance Laboratory, the Institute received vital support from the CSIC.

Despite these difficulties the Institute maintains an excellent research level and outstanding technical ability. It is thus positioned to take advantage of any improvement in the research climate in Spain and to contribute to the development of Physical Chemistry in its many facets.

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Rafael Notario• Energetics, Structure and Molecular Interactions Group• Photolysis and Chromatography Group• Atmospheric Chemistry and Climate Group

Departments

Department of Crystallographyand Structural Biology

Armando Albert

Department of Biological Physical Chemistry

Marta Bruix• NMR of Protein Structure, Dynamics and Interactions

Group • Protein Bioconformatics and Assamblies Group • Structural Bioinformatics Group • Fluorescence and Molecular Biophysics Group• Protein Structure and Thermodynamics Group• NMR of Nucleic Acids Group

Department of Low DimensionalSystems, Surfaces and Condensed Matter

Department of Structure, Energyand Chemical Reactivity

José F. Marco• Lasers, Nanostructures and Materials Processing Group• Laser Materials and Laser-Materials Interaction Group• Statistical Mechanics and Condensed Matter Group• Surface Analysis and Mössbauer Spectroscopy Group

Scientific Report 2013/2014 5

Department of Crystallography and Structural Biology

Scientific Report 2013/2014 Department of Crystallography 8 and Structural Biology

IntroductionThe members of the Department constitute the Group of Protein Crystallography and Molecular Recognition in Biological Processes and focus their research to understand the biological functions of macromolecules in terms of their 3D structure at atomic, molecular and supramolecular levels. This provides information on their functionality and ability to recognize other molecular partners or a substrate, or to develop their activity in a particular environment. To achieve these objectives, we combine chemical, physical-chemical and biological approaches. Among them, crystallography occupies a preferential place since it is the most powerful technique to characterize single proteins or large stable macromolecular complexes at atomic level. Such knowledge provides the basis for new medical treatments and many biotechnological applications. In addition, our Department is also involved in the development of novel and efficient methods and strategies for phasing structures that make possible the solution of protein structures.

The Department is equipped with the state of the art technologies to develop our research. Our molecular biology laboratory is perfectly set up and equipped with all the modern technologies to produce recombinant proteins at milligram scale. The diffraction laboratory includes a new rotating anode generator equipped with two area detectors and a micro source generator for testing crystals. We also provide X-ray facilities for the crystallographic community through the RedLab network, which coordinates all the technological platforms of the Madrid Regional Government. In addition, we have established an automated crystallization platform which offers the newest and fastest tools for the screening of crystallization conditions using a minimum amount of protein sample. The platform includes two crystallization robots and a “crystal farm” for storage and analysis of the experiments. All these facilities are available for all CSIC researchers and for those coming from other institutions.

Group of Protein Crystallography and Molecular Recognition in Biological Processes

Tenured Staff ScientistsArmando Albert de la Cruz (Associate Professor) ReID ORCID SCOPUSBeatriz González Pérez (Assistant Professor) ReID ORCID SCOPUSJuan Antonio Hermoso Domínguez (Professor) ReIDLourdes Infantes San Mateo (Assistant Professor) ReID ORCID SCOPUSJosé Miguel Mancheño Gómez (Assistant Professor) ReID ORCID SCOPUSMartin Martínez Ripoll (Professor) ReID ORCID María José Sánchez-Barrena (Ramón y Cajal) ReID SCOPUSJulia Sanz Aparicio (Associate Professor) ReID ORCID SCOPUS

Non-tenured Scientists Sergio Galán Bartual (Juan de la Cierva)Iván Acebrón Avalos (Contract, from 1/12/2013)Antonio Chaves Sanjuán (Contract, from 01/10/2014)Lisandro Otero (Contract, until 30/06/2013)

Doctoral StudentsIvan Acebrón Avalos (Fellowship, until 31/7/2013)

Yanaisis Álvarez Sánchez (Fellowship, until 15/01/2014)Cecilia Artola Recolons (Fellowship, until 30/06/2014)Jose Ignacio Baños Sanz (Fellowship, until 31/08/2013) Noelia Bernardo García (Contract)Alejandra Carriles Linares (Contract, from 09/09/2014)Antonio Chaves Sanjuán (Fellowship, until 30/08/2013)Teresa Domínguez Gil-Velasco (Fellowship)Elsa Franco Echevarría (Contract, from 01/07/2013)Javier Gutierrez Fernandez (Contract)Mercedes Ramírez Escudero (Contract)María Ángela Sainz Polo (Fellowship)

Technical StaffJuana María González RubioAinhoa Erce Llamazares (Contract, until 01/07/2014)Rocío Benavente Rubio (Contract, from 01/02/2013)Mª Mar Esteban-Torres (Contract, 21/04/2014-20/06/2014Alzoray Rojas Altube (Contract, until 28/02/2014)

Scientific Report 2013/2014 Department of Crystallography 9 and Structural Biology

Strategic Aims• Characterization of the mechanisms of bacterial infection and the development of new

therapeutic tools against multiresistant pathogens.

- Structural and functional characterization of pivotal proteins involved in bacterial virulence.

- To assess the role of pneumococcal surface-exposed proteins in pathogen-host interactions.

- To identify the molecular basis of bacterial cell wall remodeling and its implications in antibiotics resistance.

- To develop new lead compounds and enzybiotics against bacterial infections.

• Molecular basis of substrate recognition and structure-based design of enzymes for biotechnology.

- Unravel the molecular mechanisms involved in biologically relevant carbohydrates recognition and processing.

- Enzymatic degradation of plant cell-walls.

- Structure-based design of enzymes: production of prebiotic oligosaccharides and glycosilation of bioactive products.

- Structural enzymology of lipases and esterases from the lactic acid bacterium Lactobacillus plantarum.

- Structural basis of the specificity of fungal lectins: applications of β-trefoil lectins as fusion tags.

• The structural analysis of the cell signaling components in mammals and plants. Signal regulation through protein-protein interactions.

- Structural Biology of Inositide Signalling and Inositide regulation and synthesis. Design of inhibitors of the pathway with application in cell biology and cancer biomedicine.

- Structure and inhibition of UDG, a protein invoved in DNA repair

- Structure and function of Frequenin: synaptic function control

- Structural basis of abiotic stress plant cell response: The auxin and abcisic mediated pathway. The development mimicking compounds with biotechnological applications.

• Education and public outreach activities

Scientific Report 2013/2014 Department of Crystallography 10 and Structural Biology

ResultsStructural biology of bacterial pathogenesisAntimicrobial resistance is one of the most serious health threats. Cell-wall remodeling processes are tightly regulated to warrant bacterial survival and most of them are directly linked to antibiotic resistance. The main goal of Hermoso’s team is to generate the knowledge, based on an integrative study of some critical bacterial cell wall remodeling processes, to provide new pharmacological targets in the fight against some of the most dangerous multidrug-resistant pathogens. We focus on five main general objectives: (i) the study of the virulence mechanisms mediated by pneumococcal surface proteins, (ii) the molecular characterization of the pneumococcal divisome, (iii) Cell-wall recycling and antibiotics resistance in G(-) pathogens, (iv) The multidrug resistance mechanisms in MRSA, (v) Synthesis and regulation of cell

wall mediated by non-canonical D-amino acids (NCDAA).

Inside these objectives, some of the main achievements during 2013-2014 were:

Antibiotics resistance in bacterial pathogensWe have discovered that resistance in Methicillin-resistant S. aureus (MRSA) is related with the existence of a distant allosteric site that regulates activity of critical PBP2a enzyme (Otero et al. 2013; Fishovitz et al. 2014). We have also recently used a combination of structural and biophysical techniques to study the link between some cell-wall recycling enzymes (AmpDh2, AmpDh3 and MltC, Figure 1) and antibiotic resistance in Gram(-) organisms (Martínez-Caballero et al. 2013; Lee et al. 2013; Artola-Recolons et al. 2014).

Figure 1: Three-dimensional structures of MltC, AmpDh2 and AmpdH3 involved in peptidoglycan (black sticks) recycling and antibiotics resistance in G(-) pathogens.

Scientific Report 2013/2014 Department of Crystallography 11 and Structural Biology

Pneumococcal surface-proteins and virulenceWe characterized at physiological, functional and structural levels two novel surface-exposed thioredoxin-family lipoproteins, Etrx1 and Etrx2 (Saleh et al. 2013). The impact of both Etrx proteins and their redox partner methionine sulfoxide reductase MsrAB2 on pneumococcal pathogenesis was assessed in mouse virulence studies and phagocytosis assays. The results demonstrate that loss of function of either both Etrx proteins or MsrAB2 dramatically attenuated pneumococcal virulence in the acute mouse pneumonia model and that Etrx proteins compensate each other. Our results describe for the first time the complete extracellular

oxidative-stress resistance mechanism in S. pneumoniae (Figure 2) (see movie in http://bit.ly/1uOvIOB). Identification of this system and its target proteins paves the way for the design of novel antimicrobials.

The Divisome machinery in PneumococcusWe have very recently provided the structural and functional characterization of the essential PcsB protein. Combined study by X-ray crystallography, SAXS, Analytical ultracentrifugation and protein engineering allowed us to propose a mechanism of cell division mediated by PcsB (Bartual et al. 2014).

Figure 2: The complete extracellular oxidative-stress resistance system in Streptococcus pneumoniae is composed by two integral membrane proteins (CcdA1 and CcdA2), two

thioredoxin-like lipoproteins (Etrx1 y Etrx2) and a methionine sulfoxide reductase (MsrAB2).

Scientific Report 2013/2014 Department of Crystallography 12 and Structural Biology

Figure 3. An experimental model for IP3 3-K (green and brown) regulation by calmodulin (blue) obtained by combination of X-ray structures and SAXS data.

Structural Basis for Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor SIGN-R1The classical pathway is one of the major complement activation mechanisms and is required for innate protection against pathogenic microorganisms. SIGN-R1 receptor mediates a novel complement activation strategy in splenic marginal zone macrophages and prevents encapsulated pathogens such as S. pneumoniae from escaping C3 opsonization. Structural determination SIGN-R1 revealed two binding sites allowing SIGN-R1 to simultaneously bind both immune glycoproteins and microbial polysaccharide components, accommodating SIGN-R1’s ability to relate the recognition of microbes to the activation of the classical complement pathway (Silva-Martín et al. 2014).

Inositol phosphates: synthesis, regulation and functionOur group is focused on the structural biology of enzymes involved in the Inositol phosphates (IP) metabolism. IPs are small molecules that

present multiple functions in cells; they act as second messengers or participate in crucial events as DNA repair and edit, RNA export, vesicle trafficking etc. Several proteins are able to synthesize different IPs, and many others are able to bind them to carry out their function. Our last work has been focused on the activation of an IP kinase (IP3 3K) by calmodulin. IP3 3K is an essential enzyme that binds an IP (IP3) to yield other IP (IP4). During the last decades, plenty of work has been done on this enzyme since its substrate (IP3) is a second messenger involved in Ca2+ signalling and its product IP4 is necessary for lymphocyte development. In turn, recent studies show a role for IP3 3K in the metastatic potential of lung cancer cells. We have recently determined the crystallographic structures of a protein-protein complex between calmodulin and the CAM binding domain present in IP3 3K. This structure in combination with SAXS data allowed us to propose a complete structural model of IP3 3K-CAM complex (Figure 3). The results reveal essential features about the mechanism of regulation of IP3 3K and a novel example of how CAM recognise its targets. In conclusion, the structure obtained represents a key piece for the IP metabolism understanding (Franco-Echevarria et al. 2014).

Scientific Report 2013/2014 Department of Crystallography 13 and Structural Biology

Inhibition of UDG, an enzyme involved in DNA repair In collaboration with Prof. Margarita Salas group (CBM-CSIC) we have made the structural study of Uracil DNA glycosilase (UDG enzyme). Uracil DNA glycosylases (UDGs) are a family of key enzymes that initiate the base scission repair (BER) pathway detecting uracil and removing it from DNA. Some viral bacteriophages encode proteins that are able to inhibit this enzyme, ensuring that way they genome is replicated in host cells. P56 is one of those proteins, which is encoded by f29, a Bacillus subtilis phage, and inhibits UDG with high affinity. We have solved the crystal structure of a complex between UDG

and a dimer of p56 at atomic resolution, as well as the structure of UDG in free state.

The complex structure has revealed that the binding between both proteins is very specific, presenting multiple polar and hydrophobic interactions. This high specificity arises from p56 ability to mimic UDG and DNA binding. On one hand, both subunits of p56 grab the UDG residue responsible of UDG insertion into the DNA (Phe191). On the other hand, p56 blocks the UDG active site impeding the uracil binding and its cleavage. This work allowed us to understand the structural bases of UDG inhibition and the ability of p56 to mimic the DNA binding to UDG (Baños-Sanz et al. 2013).

Figure 4. Structure of the complex between UDG (cream surface) and p56 (cartoon representation, each p56 subunit shown in different colour).

Scientific Report 2013/2014 Department of Crystallography 14 and Structural Biology

Figure 5. Details on the molecular surface of dFrq2 and schematic representation of the activity of the new drugs.

Frequenin/NCS-1 as a pharmacological target for synapse regulation in X-linked mental retardation and autismThe conserved Ca2+-binding protein Frequenin/Neuronal Calcium Sensor 1 (Frq/NCS-1) is involved in pathologies such as X-linked mental retardation and autism, which result from abnormal synapse number and probability of neurotransmitter release per synapse. Both synaptic features are likely co-regulated but the intervening mechanisms remain poorly understood. Thus, we have conducted a multidisciplinar approach including biochemical, crystallographic and cell biological studies to shed light into this issue.

We found that Frq has to interacts with Ric8, an activator of G protein complexes, to regulate

synapse number and neurotransmitter release. To understand the structural determinants of Frq-Ric8 binding, we have solved the structure of dFrq2 and compared it with dFrq1, which is 95% identical and does not bind Ric8. Site directed mutagenesis on Frq1 followed by pull-down assays showed that the differential amino acids R94 and T138 account for this specificity. Human NCS-1 and Ric8a reproduce the binding and maintain the structural requirements at these key positions. These results expose the Frq2-Ric8a interacting surface as a potential pharmacological target for NCS-1 related diseases and provide key data towards the corresponding drug design (Baños-Mateos et al. 2014 and Romero-Pozuelo et al. 2014). Our on-going research is focused in the finding of new drugs that target NCS-1 and disrupt Ric8 interaction to re-establish synapse function in Fragile X Syndrome and autism.

Scientific Report 2013/2014 Department of Crystallography 15 and Structural Biology

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complexWe are interested in understanding how Pygo PHD domains, that are histone code readers, have evolved to recognize different methylation histone marks that permit the activation of ß-Catenin/Armadillo dependent transcription of Wnt signaling genes. Inappropriate activation of this pathway often leads to cancer, especially in the intestinal epithelium, thus, it is essential to understand the mechanism of action of Pygo protein and its protein-protein interaction interfaces, which constitute farmacological targets against colon cancer. In a previous work, we showed that human and Drosophila Pygo PHD fingers associate with their cognate HD1 domains from BCL9/Legless to bind specifically to the histone H3 tail methylated at lysine 4 (H3K4me) (Fiedler et al. 2008).

Intriguingly, Drosophilid Pygo orthologs exhibit a tryptophan>phenylalanine substitution in their histone pocket-divider which reduces their affinity for histones. Here (Miller et al. 2013), we used X-ray crystallography and NMR, to discover a novel groove bordering this phenylalanine in the Drosophila PHD-HD1 complex – a semi-aromatic cage recognizing asymmetrically-methylated arginine 2 (R2me2a) of the histone H3 tail, a chromatin mark of silenced genes. Our structural model of the ternary complex reveals a new mode of di-methylarginine recognition, involving a polar interaction between R2me2a and its groove whose structural integrity is crucial for normal tissue patterning. Notably, humanizing fly Pygo enables it to derepress Notch targets, implying an inherent Notch-related function of classical Pygo orthologs – disabled in Drosophilid Pygo orthologs, which thus appear to be dedicated to Wnt signaling.

Figure 6. Recognition of the histone H3 methylated at Arginine 2 and Lisine 4 (H3R2me2aK4me2) by the Drosophila Pygo-BCL9/Armadillo PHD1-HD1 complex.

Scientific Report 2013/2014 Department of Crystallography 16 and Structural Biology

Structural biology of carbohydrate-active enzymesOur goal is to unravel de concerted molecular mechanism of recognition in carbohydrate-processing enzymes, and their sophisticated regulatory strategies controlling specificity. These knowledge is crucial to understand many biologically relevant process and to undertake protein engineering for biotechnological purposes. Our main feats during 2013-14 were focussed on:

Molecular mechanism involved in plat cell-wall deconstructionThe plant cell-wall is a highly complex and heterogeneous network of polymers recalcitrant to enzymatic attack. Its deconstructions is a

central event in carbon cycle but, also, is of great interest for the transformation of lignocelluloses into biofuel and added-value products through a sustainable industrial activity. The plant cell-wall degrading enzymes are frequently modular and contain non-catalytic domains that are revealed as very interesting tools regulating specificity and catalytic efficiency. However, modularity confers flexibility making them a difficult target for crystallographic studies. Our group has reported a detailed analysis of Xyn30D, a full modular enzyme, which has revealed novel features of its supplementary domain previously unobserved. By analysis of both, the complete enzyme and its isolated domains, we have unravelled the key role of Xyn30D modularity in deconstruction of highly substituted xylans (Sainz-Polo et al. 2014).

Figure 7. Xyn30D is a modular enzyme with a very unusual GH35-CBM35 domain architecture presenting a moderate domain flexibility. Out results assign a key role to Xyn30D in

deconstructing highly substituted xylans through an oriented recognition pattern with its target substrate (Sainz-Polo et al. 2014)

Scientific Report 2013/2014 Department of Crystallography 17 and Structural Biology

Enzymes producing prebioticsFructooligosaccharides (FOS) are polymers made from fructose units that present prebiotic activity. Prebiotics are indigestible food ingredients that selectively stimulate the growth and maintenance of beneficial gut microbiota, contributing to prevent cardiovascular disease, colon cancer and osteoporosis. Different types of FOS may present enhanced activity profiles and, therefore, exists an increasing interest in the development of new compounds with novel prebiotic efficiency directed to a future preventive medicine adapted to patient. In this context, we have improved the transglycosylation

activity of a Ffase from yeast to produce a new enzyme with a 5.5-fold improvement in fructose transferase activity over the parental type and greater selectivity for the synthesis of 6-kestose (Abreu et al. 2013). We have also reported on the structure of Saccharomyces invertase, which catalyzes the hydrolysis of the disaccharide sucrose into glucose and fructose and also produces prebiotics. Although invertase is a fundamental enzyme for sugar metabolism in yeast and a classical model in early biochemical studies, its structure was still unkown (Sainz-Polo et al. 2013). Our results were disclosed to the media (see below).

Figure 8. Left: Phaffia rhodozyma β-fructofuranosidase is a highly glycosylated enzyme presenting a novel dimeric structure, mediated by a 100-residues segment inserted at its C-term

and one of the glycan chains. Through molecular analysis of its complexes we have found a potential activity in producing a broad range of bioconjugates. Right:

Swannyomyces occidentalis Ffase was improved by directed evolution producing a new variant with enhanced FOS producing activity (Abreu et al. 2013)

Scientific Report 2013/2014 Department of Crystallography 18 and Structural Biology

Structural analysis of protein-lipid interactions in enzymatic systems from Lactobacillus plantarumProtein-lipid interactions occur in a wide range of physiologically relevant contexts: from those appearing in biological membranes both involving integral membrane proteins and proteins that interact transiently with these structures, to different enzymatic systems with lipidic substrates. During the period 2013-2014 the group of José M. Mancheño has focused on the structural characterization of proteín-lipid interactions appearing in different enzymatic systems from the lactic acid bacteria Lactobacillus plantarum, particularly esterases/

carboxylesterases and glycerophosphodiester phosphodiesterases. The most relevant results obtained were:

Characterization of a novel carboxylesterase (LpEst1) from L. plantarum related to the mammalian hormone-sensitive lipase

The crystal structure of LpEst1 (Álvarez, Esteban-Torres et al. 2014) has revealed novel topological features within the αβ-hydrolase superfamily, as well as a new dimerization mechanism. Analysis of the active site has permitted the design of variants with altered specificity.

Figure 9. The structure of the esterase LpEst1 from Lactobacillus plantarum revealed new topological features within the α/β hydrolase superfamily as well as a new dimerization mode.

Scientific Report 2013/2014 Department of Crystallography 19 and Structural Biology

Structural analysis and study of the associative behavior of the esterase Cest-2923

The combination of crystallographic information with hydrodynamic data of the enzyme Cest2923 has permitted to understand the complex pleomorphic behavior of this protein. We have shown the existence of pH-dependent equilibria between monomeric, dimeric and tetrameric species (Benavente et al. 2013).

Functional analysis of a wide array of esterases from L. plantarumThe objective of the functional characterization of different esterases from this lactic acid bacterium is the determination of the optimum experimental conditions of activity (Esteban-Torres et al. 2013, 2014a, 2014b, 2014c). The perspective of these studies is the potential application of these enzymes in food industry.

Structural basis of the control of abiotic stress in plants

Plants have to endure adverse environmental conditions, among them, drought and salinity constrain agricultural productivity most

dramatically. Many of the plant adaptive responses take place at cell membrane where it is required the regulation o a variety of ion channels and transporters. This adjusts the intracellular ion concentration necessary for cell live. From a molecular point of view, the levels of abscisic acid (ABA) and calcium encode the information to orchestrate cell response to stress. We have discovered and characterized a new family of proteins, CAR for C2-domain ABA-related, which target ABA recognition machinery to the cell membrane. The joined structural and biochemical analyses has provided a working model that illustrates how CAR proteins anchor to plasma membrane and specifically bind the ABA receptors (Rodriguez et al. 2014). As the activity of these proteins is dependent of calcium, they represent a central hub decoding ABA and calcium stimuli and provide a target for biotechnological work for the use of plants in our benefit. In additiom, we have also studied the CIPK family of twenty-six protein kinases that regulates the function of several ion transporters at the cell membrane to restore ion homeostasis under stress situations. Our analyses provide an explanation on how the CIPKs are differentially activated to coordinate the adequate cell response to a particular stress (Chaves-Sanjuan et al. 2014).

Figure 10. CIPK inactivation inhibits the growth of Arabidopsis thaliana model plant in presence of salt.

Scientific Report 2013/2014 Department of Crystallography 20 and Structural Biology

Scientific outreach and distance teaching of crystallographyThe CBE researchers pay special attention not only to disseminate their work through a departmental web page (http://www.xtal.iqfr.csic.es/) but also to approach the fundamentals of crystallography to the society at different levels including both students and the general scientific community. This program, presented in terms of a web page (http://www.xtal.iqfr.csic.es/Cristalografia/) and offered in both Spanish and English, has become an international reference for crystallographic teaching.

Although according to Google Analytics, OneStat.com, o ClustrMaps it receives between 1,000 and 1,500 visits a day, distributed by all countries, but especially from the US, Europe, India and Latin American countries. This tutorial has been selected by the International Union of Crystallography as one of the web sites of interest for learning crystallography (http://bit.ly/1zCsBOX); it has been included as such in the commemorative website of the International Year of Crystallography (http://bit.ly/1AvTc0d), and is offered as one of the best online learning tools by several US universities (see for example: http://bit.ly/guMQax).

Figure 11. Snapshot of the welcome web page of the crystallographic tutorial shown in http://www.xtal.iqfr.csic.es/Cristalografia/. On the right column, the number of user long

sessions during a three weeks period and their most significant countries are shown.

Scientific Report 2013/2014 Department of Crystallography 21 and Structural Biology

Abdullah, M.R.; Gutiérrez-Fernández, J.; Pribyl, T.; Gisch,N.; Saleh, M.; Rohde, M.; Petruschka, L.; Burchhardt, G.; Schwudke, D.; Hermoso, J.A. and Hammerschmid, S. (2014). Structure of the pneumococcal L,D-carboxypeptidase DacB and pathophysiologi-cal effects of disabled cell wall hydrolases DacA and DacB. Molecular Microbiology 93 (6), 1183-1206

Albert, A. (2014). Capítulo de libro: “Co-municación celular a escala atómica” en A través del cristal. Cómo la cristalografía ha cambiado la visión del mundo (2014). (M. Martínez-Ripoll, J.A. Hermoso y Armando Albert, coord.), CSIC-Catarata, pp. 171-182, ISBN: 978-84-00-09800-1

Alvarez, L.; Espaillat, A.; Hermoso, J.A.; De Pedro, M.A. and Cava, F. (2014). Peptidogly-can remodeling by the coordinated action of multispecific enzymes. Microbial Drug Re-sistance 20, 1-9

Alvarez, Y.; Esteban-Torres, M.; Cortés-Ca-brera, A.; Gago, F.; Acebrón, I.; Benavente, R.; Mardo, K.; de Las Rivas, B.; Muñoz, R.; Mancheño, J.M. (2014). Esterase LpEst1 from Lactobacillus plantarum: a novel and atypical member of the α/β hydrolase superfamily of enzymes. PLoS ONE 9(3):e92257

Artola-Recolons, C.; Lee, M.; Bernardo-García, N.; Blázquez, B.; Hesek, D.; Bartual, S.; Mahasenan, K.V.; Lastochkin, E.; Pi, H.; Meindl, K.; Boggess, W.; Uson, I.; Fisher, J.F.; Mobashery, S. & Hermoso, J.A. (2014). Struc-ture and Cell Wall Cleavage by Modular Lytic Transglycosylase MltC of Escherichia coli. ACS Chemical Biology 9 (9), 2058–2066

Baños-Mateos, S., Chaves-Sanjuán, A., Man-silla, A., Ferrús, A., Sánchez-Barrena, MJ. (2014) Frq2 from Drosophila melanogaster: cloning, expression, purification, crystalli-zation and preliminary X-ray analysis. Acta Cryst. Section F 70, 530-534

Bartual, S.G.; Straume, D.; Stamsås, G.A.; Muñoz, I.G.; Alfonso, C.; Martínez-Ripoll, M.; Håvarstein, L.S. & Hermoso, J.A. (2014). Structural basis of PcsB-mediated cell sepa-ration in Streptococcus pneumoniae. Nature Communications 5, Article number 3842

Bernardo, N. and Hermoso J.A. (2014). Capí-tulo de libro: “Una ventana hacia las enferme-dades infecciosas”. En A través del Cristal. Cómo la cristalografía ha cambiado la vision del mundo. (Martín Martínez-Ripoll, Juan A. Hermoso and Armando Albert co-ord.), CSIC-Catarata, (2014). ISBN: 978-84-00-09800-

Bortolotti, A.; Sánchez-Azqueta, A.; Maya, C.M.; Velázquez, A.; Hermoso, J.A.; Medina, M.; Cortez, N. (2014). The C-terminal exten-sion of bacterial flavodoxin-reductases: in-volvement in the hydride transfer mechanism from the coenzyme. BBA - Bioenergetics 1837, 33–43

Brabcova, J., Carrasco-Lopez, C., Bavaro T., Hermoso, J.A., Palomo, J.M. (2014). Escheri-chia coli LacZ β-galactosidase inhibition by monohydroxy acetylated glycopyranosides: Role of the acetyl groups. J Mol Cata B: En-zym. 107, 31-38

Chaves-Sanjuán A, Sánchez-Barrena MJ, González-Rubio JM, Albert A. (2014) Prelimi-nary crystallographic analysis of the ankyrin-repeat domain of Arabidopsis thaliana AKT1: identification of the domain boundaries for protein crystallization. Acta Crystallograph-ica F70, 509-512

Chaves-Sanjuan, A.; Sanchez-Barrena, M.J.; Gonzalez-Rubio, J.M.; Moreno, M.; Ragel, P.; Jimenez, M.; Pardo, J.M.; Martinez-Ripoll, M.; Quintero, F.J.; Albert, A. (2014) Structural ba-sis of the regulatory mechanism of the plant CIPK family of protein kinases controlling ion homeostasis and abiotic stress. Proceedings of the National Academy of Sciences, PNAS 111, 4532-4541

Chioua, M.; Samadi, A.; Soriano, E.; Infantes, L.; Marco-Contelles, J. (2014) Silver Triflate-Catalyzed Cyclization of 2-Amino-6-propargyl-amineazines Leading to Iminoimidazoazines. Adv. Synth. Catal. 356, 1235-1241

Espaillat, A.; Carrasco-López, C.; Bernardo-García, N.; Pietrosemolli, N.; Otero, L.H.; Alvarez, L.; de Pedro, M.A.; Pazos, F.; Davis, B.M.; Waldor, M.K.; Hermoso, J.A. and Cava, F. (2014). Structural bases for the broad speci-ficity of a new family of amino acid racemases. Acta Cryst. D 70, 79-90

Publications

Scientific Report 2013/2014 Department of Crystallography 22 and Structural Biology

Esteban-Torres, M.; Barcenilla, J.M.; Manche-ño, J.M.; de las Rivas, B.; Muñoz, R. (2014b). Characterization of a versatile arylesterase from Lactobacillus plantarum active on wine esters. J. Agric. Food Chem. 62, 5118-5125

Esteban-Torres, M.; Mancheño, J.M.; de las Rivas, B.; Muñoz, R. (2014c). Characteriza-tion of a cold-active esterase from Lactobacil-lus plantarum suitable for food fermentations. J. Agric. Food Chem. 62, 5126-5132

Esteban-Torres, M.; Mancheño. J.M.; de las Rivas, B.; Muñoz, R. (2014a). Production and characterization of a tributyrin esterase from Lactobacillus plantarum suitable for cheese lipolysis. J. Dairy Sci. 97, 6737-6744

Ferreira, P.; Villanueva, R.; Martínez-Júlvez, M.; Herguedas, B.; Marcuello, C.; Fernandez-Silva, P.; Cabon, L.; Hermoso, J.A.; Lostao, A.; Susin, S.; Medina, M. (2014). Structural insights into the coenzyme mediated mon-omer-dimer transition of the pro-apoptotic Apoptosis Inducing Factor. Biochemistry 53, 4204–4215

Fishovitz, J.; Hermoso, J.A.; Chang, M. & Mobashery, S. (2014). Penicillin-binding Pro-tein 2a of Methicillin-resistant Staphylococcus aureus. UBMB Life 66, 572-577

Fishovitz, J.; Rojas-Altuve, A.; Otero, L.H.; Dawley, M.; Carrasco-López, C.; Chang, M.; Hermoso, J.A. & Mobashery, S. (2014). Dis-ruption of Allosteric Response as an Unprec-edented Mechanism of Resistance to Antibiot-ics. J. Am. Chem. Soc. 136, 9814–9817

Franco-Echevarria, E., Baños-Sanz, J.I., Mon-terroso, B., Round A, Sanz-Aparicio, J., Gon-zalez, B* (2014). A new calmodulin binding motif for inositol 1,4,5-trisphosphate 3-kinase regulation. Biochem J. 463, 319-328

Fulde, M.; Bernardo-García, N.; Rohde, M.; Nachtigall, N.; Frank, R.; Preissner, K. T.; Klett, J.; Morreale, A.; Chhatwal, G. S.; Her-moso, J. A. & Bergmann, S. (2014). Pneumo-coccal phosphoglycerate kinase interacts with plasminogen and its tissue activator. Throm-bosis and Haemostasis 111 3, 401-416

Gonzalez-Guzman, M.; Rodriguez, L.; Loren-zo-Orts, L.; Pons, C.; Sarrion-Perdigones, A.; Fernandez, M.A.; Peirats-Llobet, M.; Forment, J.; Moreno-Alvero, M.; Cutler, S.R.; Albert, A.;

Granell, A.; Rodriguez, P.L. (2014) Tomato PYR/PYL/RCAR abscisic acid receptors show high expression in root, differential sensitivity to the abscisic acid agonist quinabactin, and the capability to enhance plant drought resist-ance. Journal of Experimental Botany 65, 4451-4464

Gutiérrez-Fernández, J.; Vaquero, M.E.; Prieto, A.; Barriuso, J.; Martínez, M.J. and Hermoso, J.A. (2014). Crystal Structures Of Ophiostoma Piceae Sterol Esterase: Activation Mechanism And Product Release. Journal of Structural Biology 187, 215-222. (portada de la revista)

Hermoso J.A. (2014). Getting CAD in Shape: The Atomic Structure of Human Dihydrooro-tase Domain. Structure 22, 179-181

Hermoso, J.A. (2014). Aportaciones de la cris-talografía a la medicina. De la comprensión de las armas moleculares de los patógenos al desarrollo de fármacos contra enfermedades infecciosas. Investigación y Ciencia Julio, Nº. 454, 11-14

Jiménez, N.; Esteban-Torres, M.; Mancheño, J.M.; de Las Rivas, B.; Muñoz, R. (2014). Tan-nin degradation by a novel tannase enzyme present in some Lactobacillus plantarum strains. Appl. Environ. Microbiol. 80, 2991-2997.

Martínez-Caballero, S.; Cano-Sánchez, P.; Mares-Mejía, I.; Díaz-Sánchez, A.; Macías-Ru-balcava, M.; Hermoso, J.; Rodríguez-Romero, A. (2014). Comparative study of two GH19 chitinase-like proteins from Hevea brasilien-sis, one exhibiting a novel carbohydrate-bind-ing domain. FEBS Journal 281(19):4535-54

Martínez-Ripoll, M; López Sancho, J.M.; More-no Gómez, E. (2014) El CSIC cumple 75 años. Revista Española de Física 28, 25-27

Martínez-Ripoll, M. (2014). Capítulo de libro: “Una historia con claroscuros plagada de lau-reados Nobel”. En A través del Cristal. Cómo la cristalografía ha cambiado la vision del mundo. (Martín Martínez-Ripoll, Juan A. Her-moso and Armando Albert coord.), CSIC-Cata-rata, (2014). ISBN: 978-84-00-09800-1

Martínez-Ripoll, M.; Hermoso, J.A. & Albert, A. (2014). Capítulo de libro: “A través del cristal y más allá”. En A través del Cristal. Cómo la cristalografía ha cambiado la vision del

Scientific Report 2013/2014 Department of Crystallography 23 and Structural Biology

mundo. (Martín Martínez-Ripoll, Juan A. Her-moso and Armando Albert coord.), CSIC-Cat-arata. ISBN: 978-84-00-09800-1

Mesa-Torres, N.; Yunta, C.; Fabelo-Rosa, I.; Gonzalez-Rubio, J.M.; Sanchez-Ruiz, J.M.; Salido, E.; Albert, A.; Pey, A.L. (2014) The consensus-based approach for gene/enzyme replacement therapies and crystallization strat-egies: the case of human alanine:glyoxylate aminotransferase. Biochemical Journal 462, 453-463

Rico-Díaz, A., Vizoso-Vázquez, A-, Cerdán, M.A., Becerra, M., Sanz-Aparicio, J. (2014). Crystallization and preliminary X-ray diffrac-tion data of β-galactosidase from Aspergillus niger. Acta Crystallogr. F70, 1529-1531

Riveron, J.M.; Yunta, C.; Ibrahim, S.S.; Dj-ouaka, R.; Irving, H.; Menze, B.D.; Ismail, H.M.; Hemingway, J.; Ranson, H.; Albert, A.; Wondji, C.S. (2014) A single mutation in the GSTe2 gene allows tracking of metabolically based insecticide resistance in a major ma-laria vector. Genome Biology 15, R27

Rodriguez, L.; Gonzalez-Guzman, M., Diaz, M.; Rodrigues, A.; Izquierdo-Garcia, A.C.; Peirats-Llobet, M.; Fernandez, M.A.; Antoni, R.; Fer-nandez, D.; Marquez, J.A.; Mulet, J.M., Albert, A.; Rodriguez, P.L. (2014) C2-Domain Abscisic Acid-Related Proteins Mediate the Interaction of PYR/PYL/RCAR Abscisic Acid Receptors with the Plasma Membrane and Regulate Abscisic Acid Sensitivity in Arabidopsis. The Plant Cell 12, 4802-4820

Romero-Pozuelo, J., Dason, J.S., Mansilla, A., Baños-Mateos, S., Sardina JL, Chaves-Sanjuán, A,, Jurado-Gómez, J,, Santana, E., Atwood, H.L., Hernández-Hernández, A., Sánchez-Barrena, M.J., Ferrús, A. (2014) The binding of a Calcium sensor to a guanine-ex-change factor mediates the regulation of syn-apse number and probability of release. Jour-nal of Cell Science 127(19), 4246-4259

Sainz-Polo, M.A; Valenzuela, S.; González-Pé-rez, B.; Pastor, F.J.; Sanz-Aparicio, J. (2014). Structural analysis of glucuronoxylan specific Xyn30D and its attached CBM35 domain give insights into the role of modularity in specific-ity. J. Biol. Chem. 289, 31088-31101

Sainz-Polo, M.A., González-Pérez, B., Pastor, F.J., Sanz-Aparicio, J. (2014). Crystallization

and preliminary X-ray diffraction analysis of the N-terminal domain of Paenibacillus barci-nonensis xylanase 10C containing the CBM22-1--CBM22-2 tandem. Acta Crystallogr. F71, 136-140

Sainz-Polo, M.A.Valenzuela, S., Pastor, F.J., Sanz-Aparicio, J. (2014). Crystallization and preliminary X-ray diffraction analysis of Xyn30D from Paenibacillus barcinonensis. Acta Crystallogr. F70, 963-6

Sammito, M.; Meindl, K.; de Ilarduya, I.; Mil-lán, C.; Artola-Recolons, C.; Hermoso, J. & Usón, I. (2014). Structure solution with AR-CIMBOLDO using fragments derived from dis-tant homology models. FEBS Journal 281, 4029-4045

Sanz-Aparicio, J. (2014). Capítulo de libro: “El arma secreta de la biotecnología” en A través del cristal. Cómo la cristalografía ha cambiado la visión del mundo (2014). (M. Martínez-Ripoll, J.A. Hermoso y Armando Albert, coord.), CSIC-Catarata, pp. 155-170, ISBN: 978-84-00-09800-1

Silva-Martín, N.; Bartual, S.G.; Ramírez-Aportela, E.; Chacón, P.; Park, C.G. and Hermoso, J.A. (2014). Structural Basis for Selective Recognition of Endogenous and Mi-crobial Polysaccharides by Macrophage Recep-tor SIGN-R1. Structure 22 1595–1606. (por-tada de la revista)

Silva-Martín, N.; Retamosa, G.; Maestro, B; Bartual, S.G.; Rodes, M.J.; García, P.; Sanz, J.M. & Hermoso, J.A. (2014). Crystal struc-tures of CbpF complexed with atropine and ip-ratropium reveal clues for the design of novel antimicrobials against Streptococcus pneumo-niae. BBA - General Subjects 129-135

Stelter, M.; Molina, R.; Jeudy, S.; Kahn, R.; Abergel, C. and Hermoso, J.A. (2014). A com-plement to the modern crystallographer’s toolbox: caged gadolinium complexes with versatile binding modes. Acta Cryst. D 70, 1506-1516

Abreu, M., Alvaro-Benito, M., Sanz-Aparicio, J., Plou, F.J., Fernandez-Lobato, M., Alcalde, M. (2013). Synthesis of 6-kestose using a highly efficient β-fructofuranosidase engineered by directed evolution. Adv. Synth. Catal. 1698-1702

Scientific Report 2013/2014 Department of Crystallography 24 and Structural Biology

Baños-Sanz, J.I., Mojardín, L., Sanz-Aparicio, J., Lázaro, J.M., Villar, L., Serrano-Heras, G., González, B., and Salas, M., (2013) Crystal structure and functional insights into uracil-DNA glycosylase inhibition by phage ϕ29 DNA mimic protein p56. Nucleic Acids Re-search 41, 6761-6773

Benavente, R.; Esteban-Torres, M.; Acebrón, I.; de Las Rivas, B.; Muñoz, R.; Alvarez, Y.; Mancheño, J.M. (2013). Structure, biochemi-cal characterization and analysis of the pleo-morphism of carboxylesterase Cest-2923 from Lactobacillus plantarum WCFS1. FEBS J. 280, 6658-6671

Bouit, P.A.; Infantes, L.; Calbo, J.; Viruela, R.; Ortí, E.; Delgado, J.L.; Martín, N. (2013) Efficient Light Harvesters based on the 10-(1,3-Dithiol-2-ylidene)anthracene core. Org. Lett. 15, 4166-4169

Chioua, M.; Soriano, E.; Infantes, L.; Jimeno, M.L.; Marco-Contelles, J.; Samadi, A. (2013) The Silver-catalyzed Cyclization of N-(prop-2-yn-1-yl)pyridin-2-amines. Eur. J. Org. Chem. 35-39

Durante-Rodríguez, G.; Mancheño, J.M.; Ri-vas, G.; Alfonso, C.; García, J.L.; Díaz, E.; Car-mona, M. (2013). Identification of a missing link in the evolution of an enzyme into a tran-scriptional regulator. PLoS ONE 8(3):e57518

Engel, H.; Gutiérrez-Fernández, J.; Flückiger, C.; Martínez-Ripoll, M.; Mühlemann, K.; Her-moso, J.A.; Hilty, M.; Hathaway, L.J. (2013). Heteroresistance to fosfomycin is predominant in Streptococcus pneumoniae and depends on murA1 gene. Antimicrobial Agents and Chemotherapy 57 (6), 2801-1808

Esteban-Torres, M.; Reverón, I.; Mancheño, J.M.; de Las Rivas, B.; Muñoz, R. (2013). Characterization of a feruloyl esterase from Lactobacillus plantarum. Appl. Environ. Mi-crobiol. 79, 5130-5136

Fernández de la Pradilla, R.; Simal, C.; Bates, R.H.; Viso, A.; Infantes, L. (2013) Sulfoxide-Directed Enantioselective Synthesis of Func-tionalized Tetrahydropyridines. Org. Lett. 15, 4936-4939

Infantes, L.; García, M.A.; López, C.; Clara-munt, R.M.; Elguero, J. (2013) The Struc-ture and Dynamic Properties of 1H-Pyrazole-

4-carboxylic acids in the Solid State. Z. Phys. Chem. 227, 841-856

Lee, M.; Artola-Recolons, C.; Carrasco-López, C.; Martínez-Caballero, S.; Hesek, D.; Spink, E.; Lastochkin, E.; Zhang, W.; Hellman, L.; Boggess, B.; Hermoso, J.A. & Mobashery, S. (2013). Cell-Wall Remodeling by the Zinc-Pro-tease AmpDh3 from Pseudomonas aerugino-sa. J. Am. Chem. Soc. 12605-12607

Martínez-Caballero, S.; Lee, M.; Artola-Reco-lons, C.; Carrasco-López,C.; Hesek, D.; Spink, E.; Lastochkin, E.; Zhang, W.; Hellman, L.M.; Boggess, B.; Mobashery, M. and Hermoso, J.A. (2013). Reaction products and the X-ray structure of AmpDh2, a virulence determinant of Pseudomonas aeruginosa. J. Am. Chem. Soc. 135; 10318-10321

Martínez-Ripoll, M. (2013). ¿Cómo aprendi-mos a “ver” los átomos? En El CSIC en la Es-cuela, Investigación sobre la enseñanza de la ciencia en el aula, 9, pp. 9-34, e-ISBN (n. 9): 978-84-00-09659-5

Mesa-Torres, N.; Fabelo-Rosa, I.; Riverol, D.; Yunta, C.; Albert, A.; Salido, E.; Pey, A.L. (2013) The role of protein denaturation ener-getics and molecular chaperones in the aggre-gation and mistargeting of mutants causing primary hyperoxaluria type I. PLoS ONE 8, e71963

Miller, T.C.R., Mieszczanek, J., Sánchez-Bar-rena, M.J., Rutherford, T.J., Fiedler, M., Bienz, M. (2013) Evolutionary Adaptation of the Fly Pygo PHD Finger toward Recognizing Histone H3 Tail Methylated at Arginine 2. Structure 21(12), 2208-2220

Otero, L.H.; Rojas-Altuve, A., Llarrull, L.I.; Kumarasiri, M.; Lastochkin, E.; Fishovitz, J.; Dawley, M.; Hesek, D.; Lee, M.; Johnson, J.W.; Fisher, J.F.; Chang, M.; Mobashery, S. and Hermoso, J.A. (2013). How allosteric con-trol of Staphylococcus aureus penicillin-bind-ing protein 2a enables methicillin-resistance and physiological function. PNAS 110, 16808-16813

Pérez-Dorado I., Bortolotti A., Cortez N., Her-moso, J.A. (2013) Structural and Phylogenetic Analysis of Rhodobacter capsulatus NifF: Un-covering General Features of Nitrogen-fixation (nif)-Flavodoxins. International Journal of Molecular Sciences 14(1):1152-1163

Scientific Report 2013/2014 Department of Crystallography 25 and Structural Biology

Pérez-Faginas, P.; Aranda, M.T.; García-López, M.T.; Infantes, L.; Fernández-Carvajal, A.; González-Ros, J.M.; Ferrer-Montiel, A.; González-Muñiz, R. (2013) Highly functional-ized β,γ–diamino compounds through reduc-tive amination of amino acid-derived β–keto esters. PLoS ONE 8(1), e53231

Pey, A.L.; Albert, A.; Salido, E. (2013) Pro-tein homeostasis defects of alanine-glyoxylate aminotransferase: new therapeutic strategies in primary hyperoxaluria type I. Biomed Re-search International 2013:687658

Pizzio, G.A.; Rodriguez, L.; Antoni, R.; González-Guzman, M.; Yunta, C.; Merilo, E.; Kollist, H.; Albert, A.; Rodriguez, P.L. (2013) The PYL4 A194T mutant uncovers a key role of PYR1-LIKE4/PROTEIN PHOSPHATASE 2CA in-teraction for abscisic acid signaling and plant drought resistance. Plant Physiology 163, 441-55

Sainz-Polo, M.A., Ramírez, M., Lafraya, A., González, B., Marín-Navarro, J., Polaina, J., Sanz-Aparicio, J. (2013). The three-dimen-sional structure of Saccharomyces invertase: role of a non-catalytic domain in oligomeriza-tion and substrate specificity. J. Biol. Chem. 288, 9755-9766

Saleh, M.; Bartual, S.G.; Abdullah, M.R.; Jensch, I.; Asmat, T.M.; Petruschka, L.; Prib-yl, T.; Hermoso, J.A. and Hammerschmidt S. (2013). Molecular architecture of Streptococ-cus pneumoniae surface thioredoxin-fold li-poproteins crucial for extracellular oxidative stress resistance and maintenance of viru-lence. EMBO Molecular Medicine 5, 1852-1870 (portada de la revista)

Sánchez-Barrena, M.J.; Martínez-Ripoll, M.; Albert, A. (2013) Structural Biology of a Major Signaling Network that Regulates Plant Abiotic Stress: The CBL-CIPK Mediated Pathway. Int. J. Mol. Sci. 14, 5734-5749

Scientific Report 2013/2014 Department of Crystallography 26 and Structural Biology

COMPETITIVE FUNDING

Principal Investigator Title Reference

Juan A. Hermoso Maquinas moleculares de remodelado de pared I-LINK0864 bacteriana en patógenos multiresistentes: aplicaciones al desarrollo de nuevos fármacos

Juan A. Hermoso Bases estructurales de los mecanismos bacterianos I-LINK0319 de patogenicidad y resistencia a antibióticos

Principal Investigator Title Reference

Juan A. Hermoso Biologia estructural de proteinas de la pared celular BFU2011-25326 bacteriana: implicaciones en las interacciones hospedador-patogeno

Beatriz González Pérez Structural biology of inositol phosphates signalling: BFU2011-24982 regulation by kinases and function in mrna export.

Jose Miguel Mancheño Biología estructural de enzimas lipolíticas y gdpds BFU2010-17929 de la bacteria láctica lactobacillus plantarum wcfs1

Armando Albert Biologia estructural de la tolerancia hidrica y salina BFU2011-25384 en plantas. Papel del calcio y del acido abcisico

CSIC

MINECO

National Grants: individual

Scientific Report 2013/2014 Department of Crystallography 27 and Structural Biology

Principal Investigator Title Reference

Federico Gago Plataforma integrada de bioinformática para S2010/BMD-2457Juan A. Hermoso el descubrimiento de nuevos fármacos basado (PI grupo IQFRRX) en la estructura del receptor- BIPEDD2Armando Albert (PI Laboratorio DRX)

Principal Investigator Title Reference

María José Sánchez Barrena Structural biology of SCF(SKP2A) E3 ligase INSTRUCT-388 complexes of the ubiquitin/ proteasome pathway in plants: Auxin perception for cell division control

Principal Investigator Title Reference

Mayland Chang (PI) Novel Oxadiazols for the Treatment of Drug- 1R01AI090818-01Juan A. Hermoso (PI WP) Resistant Gram-Positive Bacteria

Principal Investigator Title Reference

María José Sánchez Barrena Biología estructural de complejos SCF(SKP2A) BIO2011-28184-C02-02 de la ruta ubiquitina/proteasoma en plantas

Juliana Sanz Aparicio Analisis cristalografico de los determinantes BIO2013-48779-C4-2-R moleculares de la especificidad en nuevas enzimas de interes biotecnológico

Juliana Sanz Aparicio Mecanismos moleculares de reconocimiento e BIO2010-20508-C04-03. hidrólisis de carbohidratos: estructura de glicosidasas modulares y de sus complejos con oligosacáridos mediante cristalografía de proteínas.

Government of Madrid

European Union

National Institutes of Health USA (NIH)

MINECO

National Grants: coordinated

International Grants: individual

International Grants: coordinated

Scientific Report 2013/2014 Department of Crystallography 28 and Structural Biology

Memoria 2013/2014 Department of Crystallography 30 and Structural Biology

Department of Structure, Energy and Chemical Reactivity

IntroductionThe Department of Structure, Energy and Chemical Reactivity has been formed during the biennium 2013-2014 by 8 research scientists:

• Professor: Rafael Notario Bueno.

• Associate Professors: Rosa Becerra Arias and Alfonso Saiz-López.

• Assistant Professors: Juan Z. Dávalos Prado, Pablo Echenique Robba, Rosa Lebrón Aguilar, Josep M. Oliva Enrich and Jose María Santiuste Bermejo.

The Department carries out different research lines exposed in the memories of the groups. The main objectives are: the study of the reactivity (by proton-interchange processes), structural effects on the gas phase acidity/basicity and thermodynamic stability of species with biological activity and/or technological and environmental relevance; the study of the dynamics of photodissociation (energy ranges of UV and X-ray) of organic species with heteroatoms of N, S and Cl; the development of methodologies; the study of the chemistry of heteroborane clusters, and their interactions with biomolecules; the studies of new reaction kinetic of silicon and germanium containing heavy carbenes of interest in the materials industry; the development and characterization of new stationary phases for gas chromatography based on ionic liquids; the determination

of chromatographic and thermodynamic parameters by gas chromatography; the development of advanced analytical methods by chromatography and mass spectrometry; the exploration of the interactions between anthropogenic and natural emissions, the chemical and physical climate system, and the biosphere, within a changing climate context; and the evaluation and improvement of molecular simulation methods.

We have in the Department different experimental techniques: combustion calorimetry with rotatory, static and semimicro bombs; combustion microcalorimetry (CMRT); diferential scanning calorimetry (DSC); Knudsen efussion technique; FT-ICR (Fourier transform ion cyclotron resonance) high resolution mass spectrometry of 4.7 T and 7.0 T (with ESI and MALDI sources); laser flash photolysis; gas chromatographs for capillary and packed columns, with flame ionization detectors; gas chromatograph coupled to a quadrupolar mass spectrometer, fitted with sample introduction systems for liquids and gases; diffferential Optical Absorption Spectroscopy (DOAS)/on-ground, ship, airborne and satellite based instrument; resonance and off resonance fluorescence by lamp excitation (ROFLEX)/on-ground, airborne; Incoherent Broadband Cavity Enhanced Absorption Spectroscopy (IBBCEAS); chemiluminiscence NOx.

Scientific Report 2013/2014 Department of Structure, Energy and 31 Chemical Reactivity

Groups Structure Energetics, Structure and Molecular Interactions 33

Photolysis and Chromatography 42

Atmospheric Chemistry and Climate 51

Scientific Report 2013/2014 Department of Structure, Energy and 32 Chemical Reactivity

Energetics, Structure and Molecular Interactions Group

Tenured Staff scientists

Juan Z. Dávalos Prado (Assistant Professor) ReID ORCID

Rafael Notario Bueno (Professor) ReID ORCID

Josep M. Oliva Enrich (Assistant Professor)

Doctoral students

Francisco Javier González (until 08/2014)

Technical Staff

Rocío Ramos Novillo (JAE Tec) (until 01/2013)

Scientific Report 2013/2014 Department of Structure, Energy and 33 Chemical Reactivity

Summary We study chemical reactivity, energetic properties, interactions and structure of neutral and ionic species – in the gas phase- of fundamental, biological and technological relevance. For this purpose we use a variety of experimental (Linear Triple Quadrupole TQ /Fourier Transform Ion Cyclotron Resonance FT-ICR Mass Spectrometer with ESI/MALDI sources; calorimetry of combustion; Knudsen’s effusion; photoelectron-photoion coincidence spectroscopy PEPICO) and theoretical techniques. The combination of the experimental

results with those obtained by means of quantum-mechanic calculations (ab-initio, DFT) allow us to: i) obtain quantitative information on thermodynamics and kinetics of a variety of ion-molecule reactions in the phase gas, ii) determine interesting and novel relationship of reactivity-chemical structure, iii) determine the thermodynamic stability of neutral and ionic species, iv) study the reactivity, energetic properties and fragmentation mechanisms of organic and organometallic species (from small to macromolecular fragments).

Strategic Aims Our research lines focus on the quantitative study of the energetic properties, structure, chemical reactivity and dynamics of dissociation of ions and molecules (organic, inorganic and organometallic) in the absence of the disturbing effect of the solvent.

The specific goals pursued are:

• Reactivity (by proton-interchange processes), structural effects on the gas phase acidity/basicity and thermodynamic stability of species such as amine-borane complexes, carboranes, phenolic acids, bisphenols and other compounds with biological activity, technological and environmental relevance.

• Study of the dynamics of photodissociation (energy ranges of UV and X-ray) of organic species with heteroatoms of N, S and Cl.

• Development of methodologies, using hybrid triple quadrupole and FT-ICR high-resolution mass spectrometry, to study: i/ the reactivity, energetic properties and fragmentation mechanisms of thermolabile molecules, ii/ the interactions among macromolecules and several organic and organometallic species, iii/ characterization of macromolecule fragments and analysis of complex-mixtures (including metabolites), iv/ elucidation of fine details in problems of sequenciation of biomolecules.

• Electronic structure of heteroborane clusters (HBC) in their ground and excited states.

• Construction of molecular architectures based on HBCs in different dimensions, computational and experimental studies of their properties.

• Theoretical and experimental studies of the interaction HBC·and·biomolecules.

Scientific Report 2013/2014 Department of Structure, Energy and 34 Chemical Reactivity

ResultsGas phase acidity measurement of local acidic groups in multifunctional speciesWe have determined the acidity GA -in the gas phase- of the hydroxyl and carboxyl local groups of the hydroxycinnamic acids, applying the kinetic method (EKM) in a mass spectrometer with electrospray (ESI)-source. Hydroxycinnamic acids are natural compounds found in several biological sources mostly in the plant kingdom either as esters of organic acids or glycosides, bound to proteins or as free acids

The most important contribution of this work has been to show that is possible to determine gas-phase acidities (GAs) or basicities (GBs) of different deprotonation or protonation sites of a same molecule, only by a careful control of the ESI-experimental conditions; since the measurement of GA or GB of monofunctional molecules not offer a new scientific challenge.

This work opens the implementation of new experimental methodologies (e.g. using ESI-MS) to extract and quantify reliable thermodynamic properties, such as GA or GB, of different local groups within a multifunctional molecule.

Energetics and Structural Properties of bisphenols in the gas phaseWe have carried out studies of the energetics, structure, and thermophysical properties (phase equilibria thermodynamics) of bisphenols A, E, F, AP and S. In particular, the standard enthalpies of sublimation and the standard enthalpies of formation in the gas phase, ∆fHm

0(g), for all these species were experimentally determined. A computational study, through M05-2X Density Functional Theory, of the various species shed light on structural effects and further confirmed, by means of isodesmic reactions scheme, the excellent consistency of the experimental results. Our results reflect also the fact that energetic substituent effects are transferable from diphenylalkanes to bisphenols.

Scientific Report 2013/2014 Department of Structure, Energy and 35 Chemical Reactivity

Chemical reactivity and interactions of icosahedral closo-(car)boranesA Linear ESI-TQ-FT-ICR mass spectrometer combines the highest available mass accuracy with advanced MS/MS capabilities and is perfectly suited to study the interactions of icosahedral closo-(car)boranes Li2[B12H12] (I) and Li[CB11H12] (II). The experimental results are explained and rationalized by quantum-chemical studies, finding the most stable structures of I, II, and their derived cluster anions.

According to the experimental results, the dianion B12H12

2− shows a bigger affinity for lithium than the monoanion CB11H12

−. Signals of oligomer anions of singly and doubly charged have been detected which were identified, respectively, as [In−Li]− (n = 1, 2, 3, 4) and [In−2Li]2− (n = 1, 4, 5, 6, 7). As for II, only monomer and dimer singly charged anions [IIn−Li]− (n = 1, 2) were detected.

We have studied also, both experimentally and computationally, the gas-phase acidity (GA = 1325 kJ·mol−1) and liquid-phase acidity (pKa = 2.00) of the carborane acid closo-1-COOH-1,7-C2B10H11. The experimental GA was determined by using the extended Cooks kinetic method (EKM).

Comparison of the constants for protonation− deprotonation microscopic equilibria in the ortho, meta, and para isomers of carborane amino acids with those for the corresponding amino benzoic acids is given. A remarkable difference is found between the proportion of neutral versus zwitterion structures in water for glycine and the carborane derived amino acids.

Scientific Report 2013/2014 Department of Structure, Energy and 36 Chemical Reactivity

Photodissociation of organic molecules by Synchrotron Radiation (VUV range)Photoelectron photoion coincidence PEPICO measurements have been performed for the thiazole (C3H3NS) molecule in gas phase, using time-of-flight mass spectrometry in the electron-ion coincidence mode and vacuum ultraviolet synchrotron radiation. PEPICO spectra have been recorded as a function of the photon energy covering the valence range from 10 to 21eV. The resulting photoionization products as well as the dissociation pathways leading to the ionic species were proposed and discussed. We have also performed DFT and ab initio calculations for the neutral molecule, its cation and the ion fragments produced in order to determine their electronic and structural parameters.

Characterization and structural properties of metallic complexesA new silver–chloroquine (CQ–Ag) complex has been synthesized and characterized by using a combination of NMR (solution and solid-state), FTIR, molar conductivity and ESI/FT-ICR high resolution mass spectroscopy with DFT calculations. The CQ–Ag complex is formed by silver–CQ cations and nitrate counter anions, where the silver atoms are di-coordinated to chloroquines (CQ2Ag2+) through the quinoline sp2 N and diethylamino sp3 N nitrogen basic sites. These cations presumably form polymeric structures mainly as head–head catemers. The most important cationic fragments of the CQ–Ag complex, detected by ESI/FT-ICR, were CQAg+, CQ2Ag+, chloroquine singly (CQH+) and doubly protonated (CQH2

2+), whose formations are clearly favored by proton-displacement of the Ag+ cations.

Scientific Report 2013/2014 Department of Structure, Energy and 37 Chemical Reactivity

Thermochemical study of amino acids and derivativesFollowing the studies started in the last years, we have published in the last two-year period five new studies on amino acids and derivatives: cyclic anhydrides of glycine and alanine, sarcosine and its cyclic anhydride, N-acetyl-L-cisteine, proline, and selenocysteine. All the studies were experimental and theoretical, except that on selenocysteine, which was only theoretical.

The standard molar enthalpies of formation in the crystalline phase of the studied compounds were calculated from the standard molar energies of combustion in oxygen, measured by static bomb combustion calorimetry. The standard molar enthalpies of sublimation were derived from the Clausius-Clapeyron equation, from the vapor pressures measured as function of temperature by the Knudsen effusion mass-loss technique, except in the case of N-acetyl-L-cisteine, which enthalpy of sublimation could not be determined due to the decomposition of the compound during the experiments. From those experimental values, the standard molar enthalpies of formation in the gas phase of the studied compounds were calculated.

Theoretical studies for all the compounds were carried out at the G3 and G4 levels, doing conformational analyses and calculating their enthalpies of formation through atomization and/or isodesmic reactions, observing in all cases a good agreement between experimental and computational values.

Thermochemical study of nitrogen-containing heterocyclesFollowing a line of work launched some years ago, and in which we continue working, on the thermochemical study of nitrogen-containing heterocycles, we have carried out in this biennium two experimental and theoretical studies on barbituric acid derivatives: one on 1,3,5-trimethyl-, 1,5,5-trimethyl-, and 1,3,5,5-tetramethylbarbituric acids, and the other on 1,3-diethylbarbituric and 1,3-diethyl-2-thiobarbituric acids, as well as a computational study on 2-selenobarbituric acid, in which the intrinsic acidity and basicity have been calculated, resulting that this compound is a very strong Brønsted acid in the gas phase.

Another study was devoted to study three uracils: 5,6-dimethyl-, 1,3,5-trimethyl-, and 1,3,5,6-tetramethyluracils.

Combustion energies were measured using static bomb combustion calorimetry, and from them the standard molar enthalpies of formation in the crystalline state were obtained. Sublimation enthalpies were determined by the transference (transpiration) method in saturated nitrogen flow.

Theoretical calculations at the G3 and G4 levels were performed, and a study on molecular and electronic structures of the compounds has been carried out. Calculated enthalpies of formation are in very good agreement with the experimental values.

Thermochemical study of fluorene derivativesThis is a research line started in the previous biennium in which we study, experimentally and computationally, the thermochemistry of fluorene derivatives.

Two papers have been published in this biennium: First, we have studied fluorene-9-methanbol and fluorene-9-carboxylic acid, and then, 2-nitro- and 2-aminofluorene. Combustion enthalpies have been determined using static bomb calorimetry, and sublimation enthalpies from Knudsen effusion technique. The corresponding enthalpies of formation have been calculated at the G3 and G4 levels. There is a good agreement between experimental and theoretical values.

Computational study of reaction mechanismsTheoretical calculations at MP2 or DFT levels of theory have been carried out in order to explore the nature of the mechanism of the thermal decomposition reaction of two β-hydroxy alkenes: 3-buten-1-ol and 3-methyl-3-buten-1-ol in m-xylene solution. The mechanism proposed is a one-step process proceeding through a six-membered cyclic transition state. The progress of the decomposition reactions has been followed by means of the Wiberg bond indices, calculated using a population partition technique, the natural bond orbital (NBO) analysis.

Scientific Report 2013/2014 Department of Structure, Energy and 38 Chemical Reactivity

Santos, A.F.L.O.M.; Amaral, L.M.P.F.; Ribeiro da Silva, M.D.M.C.; Roux, M.V.; Notario, R. (2013). Experimental and Computational Study on the Energetics of the Cyclic Anhydrides of Glycine and Alanine. J. Chem. Thermodyn. 58, 29-35.

Amaral, L.M.P.F.; Santos, A.F.L.O.M.; Ribeiro da Silva, M.D.M.C.; Notario, R. (2013). Thermochemistry of Sarcosine and Sarcosine Anhydride: Theoretical and Experimental Studies. J. Chem. Thermodyn. 58, 315-321.

Notario, R.; Emel´yanenko, V.N.; Roux, M.V.; Ros, F.; Verevkin, S.P.; Chickos, J.S.; Liebman, J.F. (2013). Thermochemistry of Uracils. Experimental and Computational Enthalpies of Formation of 5,6-Dimethyl-, 1,3,5-Trimethyl-, and 1,3,5,6-Tetramethyluracils. J. Phys. Chem. A 117, 244-251.

Pabon, A.; Escobar, G.; Vargas, E.; Cruz, V.; Notario, R.; Blair, S.; Echeverri, F. (2013). Diosgenone Synthesis, Anti-Malarial Activity and QSAR of Analogues of This Natural Product. Molecules 18, 3356-3378.

Vegas, A.; Notario, R.; Chamorro, E.; Pérez, P.; Liebman, J.F. (2013). Isoelectronic and Isolobal O, CH2, CH3+ and BH3 as Electron Pairs; Similarities between Molecular and Solid-state Chemistry. Acta Cryst. B 69, 163-175.

Chamorro, E.; Duque-Noreña, M.; Notario, R.; Pérez, P. (2013). Intrinsic Relative Scales of Electrophilicity and Nucleophilicity. J. Phys. Chem. A 117, 2636-2643.

Oliveira, J.A.S.A.; Calvinho, M.M.; Notario, R.; Monte, M.J.S.; Ribeiro da Silva, M.D.M.C. (2013). A Combined Experimental and Computational Thermodynamic Study of Fluorene-9-methanol and Fluorene-9-carboxylic acid. J. Chem. Thermodyn. 62, 222-230.

Liebman, J.F.; Chickos, J.S.; Notario, R. (2013). Maria Victoria Roux, Colleague, Calorimetrist, and Friend. Struct. Chem. 24, 1785-1787.

Lopez, V.; Quijano, J.; Luna, S.; Ruiz, P.; Ríos, D.; Parra, W.; Zapata, E.; Gaviria, J.; Notario, R. (2013). Experimental and Computational Study of the Thermal Decomposition of 3-Buten-1-ol in m-Xylene Solution. Struct. Chem. 24, 1811-1816.

Notario, R.; Klapoetke, T.M.; Liebman, J.F. (2013). The Gas Phase Enthalpies of Formation

of Hydrazine, its Methylated Derivatives, and the Corresponding Values for Ammonia and its Methylated Derivatives. Struct. Chem. 24, 1817-1819.

Juaristi, E.; Notario, R. (2013). Computational Reexamination of the Eclipsed Conformation in cis-2-tert-butyl-5-(tert-butylsulfonyl)-1,3-dioxane. Struct. Chem. 24, 1855-1862.

Perisanu, S.; Contineanu, I.; Neacsu, A.; Rath, N.P.; Chickos, J.S.; Notario, R.; Liebman, J.F. (2013). Thermochemical and Structural Study of a Dibenzocycloheptane Cyanoenamine. Struct. Chem. 24, 1975-1980.

Dávalos, J.Z., González, J.; Guerrero, A.; Hnyk, D.; Holub, J.; Oliva, J.M. (2013). Anionic Oligomerization of Li2[B12H12] and Li[CB11H12]: An Experimental and Computational Study. J. Phys. Chem. C 117, 1495-1501.

Golon, A.; González, J.; Dávalos, J.Z.; Kuhnert, N. (2013). Investigating the Thermal Decomposition of Starch and Cellulose in Model Systems and Toasted Bread Using Domino Tandem Mass Spectrometry. J. Agric. Food Chem. 61, 674-684.

Dávalos, J.Z.; González, J.; Guerrero, A.; Valderrama-Negrón, A.C.; Aguirre Méndez, L.D.; Claramunt, R.M.; Santa María, D.; Alkorta, I.; Elguero, J. (2013). Silver complex of chloroquine: synthesis, characterization and structural properties. New J. Chem. 31, 1391-1401.

Guerrero, A.; Baer, T.; Chana, A.; González, J.; Dávalos, J.Z. (2013). Gas Phase Acidity Measurement of Local Acidic Groups in Multifunctional Species: Controlling the Binding Sites in Hydroxycinnamic Acids. J. Am. Chem. Soc. 135, 9681-9690.

Dávalos, J.Z.; Jiménez, P.; Roux, M.V.; Molina, M.T.; Filipova, T.; Lewars, E.; Liebman, J. (2013). Thermochemical and structural properties of anthraquinones”. Struct. Chem. 24, 2027-2034.

Oliva, J.M.; Alcoba, D.R.; Lain, L,; Torre, A. (2013). Electronic structure studies of diradicals derived from closo-carboranes. Theor. Chem. Acc. 132, 1329-1, 1329-6.

Saurí, V.; Oliva, J.M.; Hnyk, D.; Bould, J.; Braborec, J.; Merchán, M.; Kubát, P.; Císarová, I.; Lang, K.; Londesborough, M.G.S. (2013). Tuning the photophysical properties of anti-B18H22: Quantum hopping between excited singlet and triplet states in new anti-B18H20(SH)2. Inorg. Chem. 52, 9266-9274.

Oliva, J.M. (2013). Julio Palacios Martínez

Publications

Scientific Report 2013/2014 Department of Structure, Energy and 39 Chemical Reactivity

(1891-1970): Un científico entre la física y la química. An. Quim. 109, 106-109.

Oliva, J.M.; Rué, J.; Hnyk, D.; Kennedy, J.D.; Rosenfeld, V.R. (2013). Borane polyhedra as building blocks for unknown but potentially isolatable new molecules – Extensions based on computations of the known B18H22 isomers. Croat. Chem. Acta. 86, 485-494.

Notario, R.; Roux, M.V.; Santos, A.F.L.O.M.; Ribeiro da Silva, M.D.M.C. (2014). Experimental and Computational Study on the Energetics of N-Acetyl-L-cysteine. J. Chem. Thermodyn. 73, 57-61.

Temprado, M.; Notario, R.; Roux, M.V.; Verevkin, S.P. (2014). Thermochemistry of Methoxythiophenes: Measurement of their Enthalpies of Vaporization and Estimation of their Enthalpies of Formation in the Condensed Phase. J. Chem. Thermodyn. 73, 97-100.

Notario, R.; Chickos, J.S.; Liebman, J.F. (2014). The Enthalpy of Formation of Selenocysteine: A G3 and G4 Quantum Chemical Study. J. Chem. Thermodyn. 73, 134-139.

Notario, R.; Roux, M.V.; Ros, F.; Emel´yanenko, V.N.; Verevkin, S.P. (2014). Experimental and Computational Thermochemical Study of 1,3,5-Trimethyl-, 1,5,5-Trimethyl-, and 1,3,5,5-Tetramethyl-barbituric Acids. J. Chem. Thermodyn. 74, 144-152.

Quijano, J.; Ruiz, P.; Notario, R.; Zapata, E.; Gaviria, J. (2014). Experimental and Computational Study of the Thermal Decomposition of 3-Methyl-3-buten-1-ol in m-Xylene Solution. Int. J. Chem. Kinet. 46, 363-369.

Notario, R. (2014). A Computational Study of 2-Selenobarbituric Acid: Conformational Analysis, Enthalpy of Formation, Acidity and Basicity. Procedia Comput. Sci. 29, 1356-1365.

Oliveira, J.A.S.A.; Monte, M.J.S.; Notario, R.; Ribeiro da Silva, M.D.M.C. (2014). Experimental and Computational Study of the Thermodynamic Properties of 2-Nitrofluorene and 2-Aminofluorene. J. Chem. Thermodyn. 76, 56-63.

Notario, R.; Roux, M.V.; Ros, F.; Emel´yanenko, V.N.; Zaitsau, D.H.; Verevkin, S.P. (2014). Thermochemistry of 1,3-Diethylbarbituric and 1,3-Diethyl-2-thiobarbituric Acids: Experimental and Computational Study. J. Chem. Thermodyn. 77, 151-158.

Santos, A.F.L.O.M.; Notario, R.; Ribeiro da Silva, M.A.V. (2014). Thermodynamic and Conformational Study of Proline Stereoisomers.

J. Phys. Chem. B 118, 10130-10141.

Freitas, V.L.S.; Leirosa, S.; Notario, R.; Ribeiro da Silva, M.D.M.C. (2014). Thermochemical Insights on the Conformational Energetics of Azepan and its Azepan-1-ylacetonitrile Derivative. J. Org. Chem. 79, 11583-11591.

Rodríguez-Bencomo, J.J.; Andújar-Ortiz, I.; Moreno-Arribas, M.V., Simó, C.; González, J.; Chana, A.; Dávalos, J.Z.; Pozo-Bayón, M.A. (2014). Impact of Glutathione-Enriched Inactive Dry Yeast Preparations on the Stability of Terpenes during Model Wine Aging. J. Agric. Food Chem. 62, 1373-1383.

Dávalos, J.Z.; González, J.; Ramos, R.; Guerrero, A.; Lago, A.F. (2014). Intrinsic (gas-phase) acidity and basicity of paracetamol. Arkivoc (ii) 150-160.

Dávalos, J.Z.; González, J.; Ramos, R.; Hnyk, D.; Holub, J.; Santaballa, J.A.; Canle-L, M.; Oliva, J.M. (2014): Acidities of closo-1-COOH-1,7-C2B10H11 and Amino Acids Based on Icosahedral Carbaboranes. J. Phys. Chem. A 118, 2788-2793.

Dávalos, J.Z.; Herrero, R.; Costa, J.C.S.; Santos, L.M.N.B.F.; Liebman, J.F. (2014). Energetic and Structural Study of Bisphenols”. J. Phys. Chem. A 118, 3705-3709.

Costa, J.C.S.; Dávalos, J.Z; Santos, L.M.N.B.F. (2014). Phase Transition Thermodynamics of Bisphenols. J. Phys. Chem. A 118, 9712-9719.

Alkorta, I.; Cancedda, C.; Cocinero, E.J.; Dávalos, J.Z.; Écija, P.; Elguero, J.; González, J.; Lesarri, A.; Ramos, R.; Reviriego, F.; Roussel, Ch.; Uriarte, I; Vanthuyne, N. (2014). Static and Dynamic Properties of 1,1’-Bi-2-naphthol and Its Conjugated Acids and Bases. Chem. Eur. J. 20, 14816-14825.

Lago, A.F.; Januário, R.D.; Simon, M.; Dávalos, J.Z. (2014). VUV photodissociation of thiazole molecule investigated by TOF-MS and photoelectron photoion coincidence spectroscopy. J. Mass Spectrom. 49, 1163-1170.

Alcoba, D.R.; Torre, A.; Lain, L.; Oña, O.B.; Oliva, J.M. (2014). Determination of Heisenberg exchange coupling constants in clusters with magnetic sites: A local spin approach. Int. J. Quantum Chem. 114, 952-958.

Bhattacharya, D.; Klein, D.J.; Oliva, J.M.; Griffin, L.L.; Alcoba, D.R.; Massaccesi, G.E. (2014). Icosahedral symmetry super-carborane & beyond. Chem. Phys. Lett. 616-617, 16-19.

Scientific Report 2013/2014 Department of Structure, Energy and 40 Chemical Reactivity

COMPETITIVE FUNDING

Principal Investigator Title Reference

Rafael Notario Bueno Termoquímica Experimental y Computacional: CTQ2010-16402 Relación Estructura-Energía en Heterociclos Nitrogenados de Interés Biológico

Juan Z. Dávalos Prado Gas-phase reactivity, energetics, structure CTQ2009-13652 and interactions of neutral and ionic species of fundamental biological and technological relevance

Principal Investigator Title Reference

Josep M. Oliva Diseño de imanes moleculares en base al boro ICOOP-B20040 mediante técnicas computacionales

Ministerio de Ciencia e Innovación (MICIMM)

CSIC

National Grants: individual

International Grants: individual

Scientific Report 2013/2014 Department of Structure, Energy and 41 Chemical Reactivity

Photolysis and Chromatography Group

Tenured Staff scientists

María Rosa Becerra Arias (Associate Professor) ReID ORCID

Rosa Lebrón Aguilar (Assistant Professor) ReID ORCID SCOPUS

José María Santiuste Bermejo (Assistant Professor)

SummaryThe Group studies the reactivity and reaction mechanisms of the intermediate species of Si, Ge, and Sn known as heavy carbenes because of their high technological, industrial and theoretical interest. Absolute rates of the reactions of heavy carbenes are obtained by direct, time-resolved kinetic experiments using laser flash photolysis. Analysis of reaction products and stable intermediates by gas chromatography coupled to mass spectrometry (GC-MS) allows us to determine reaction mechanisms. Since chromatographic resolution of these complex mixtures is difficult, the Group

investigates the use of ionic liquids (ILs) as new GC stationary phases and also the development of the necessary technology for the preparation of capillary columns using ILs. At this point, the information provided by inverse gas chromatography (IGC) on molecular interactions and solvation properties is essential, as it allows the extension of the application of ILs, not only in the development of analysis methods in different areas (environment, food, etc.), but also in organic synthesis or extraction process, among others.

Strategic Aims• New reaction kinetic studies of silicon and germanium containing heavy carbenes of interest

in the materials industry.

• Development and characterization of new stationary phases for gas chromatography based on ionic liquids.

• Determination of chromatographic and thermodynamic parameters by gas chromatography.

• Development of advanced analytical methods by chromatography and mass spectrometry.

Scientific Report 2013/2014 Department of Structure, Energy and 42 Chemical Reactivity

ResultsReactivity of heavy carbenes of Si and Ge with sulfur dioxideHeavy carbenes are divalent compounds of Group 14. Heavy methylenes are specifically the hydrides of heavy carbenes. Heavy methylenes such as silylene (SiH2) and germylene (GeH2) are of importance as key intermediates in the processes of electronic materials manufacture. Other heavy carbenes are intermediates involved in ceramics production.

Sulfur dioxide is an intriguing molecule. It is important in the environment, as a cause of acid rain, but also of interest in combustion as a reactive gaseous component species. There is even still debate about the nature of its bonding.

Our interest arises for two reasons. First, as a part of wider study of reactive heavy carbenes with gaseous small molecules, and secondly and more specifically, because we had already studied the reaction of silylene (SiH2) with carbon dioxide, and we wanted to compare it with SiH2 + SO2.

Kinetic studiesOur method is Laser Flash Photolysis, using Excimer photolysis at 193 nm of a suitable precursor to create SiH2 or GeH2 and an Argon Ion pumped dye laser to monitor the SiH2 or GeH2 species on a nanosecond timescale. This gives the desired gas-phase kinetic data for

reaction with the substrate over a pressure range of 1-100 Torr and temperature range of 300 -600 K.

Our results show that the reaction of silylene with sulfur dioxide in the gas phase is a fast process with no energy barrier, occurring at 71% of the maximum (collision) rate at 298 K. The rate coefficients show no pressure dependence and the reaction has a negative activation energy of -3.5 kJ mol-1.

The G3 calculated potential energy surface shows the presence of two stable low-energy cyclic molecules, but the lack of pressure dependence, predicted by RRKM theory, shows that these are not the end products. The most suitable candidates for these are H2SiO + 3SO. The reaction contrasts strongly with that of SiH2 + CO2, which is slow and has a positive activation energy. A comparison of the potential energy surfaces indicates that the π-bond in SO2 is weaker than that in CO2 thus making the initial addition easier.

Our further study of the reaction of germylene with sulfur dioxide in the gas phase shows similar kinetics, viz. a fast process with no energy barrier, occurring at 19% of the maximum (collision) rate at 298K. The rate coefficients are a little slower but again show no pressure dependence. The reaction has a negative activation energy of -4.6 kJ mol-1. The G3B3 calculated potential energy surface shows significant differences with that of SiH2 + SO2.

Figure 1. Reaction mechanism of SiH2 with SO2

Scientific Report 2013/2014 Department of Structure, Energy and 43 Chemical Reactivity

In particular, it shows the existence of a low energy pathway leading to the unexpected and, as yet, unsynthesised cyclo-GeO2S molecule via H2 elimination. Another novel and surprisingly stable species, Ge(OH)2··S, a cyclic five-membered ring comprising an S atom stabilised by dihydroxygermylene, was found on this

surface, although it appears not to be involved in the mechanism.

The heavy methylenes SiH2 and GeH2 are more reactive than most atmospheric intermediates and free radicals, and their chemistry, as revealed by these studies, is complex and diverse.

Figure 2. Potential Energy surface (low enthalpy pathways) for GeH2+ SO2.

Scientific Report 2013/2014 Department of Structure, Energy and 44 Chemical Reactivity

Anomalous behavior of the isothermal retention indices of alicyclic compoundsIsothermal Kováts retention indices (I) are essentially used in gas chromatography (GC) for identification purposes, but they are also useful in characterization of stationary phases (SPs) and for studying structural and physicochemical properties of both the analyte and the SP. Therefore, it is very important to have very accurate I values. Several years ago, our group developed a method for calculating I values with greater accuracy than the classical methods. Since then, we have been contributing to increase the isothermal retention index data in the NIST database.

During these two years, 670 I values of solutes belonging to 9 different chemical functions on a poly(100% dimethylsiloxane) SP have been obtained. For some solutes, they are reported for the first time on capillary columns. Moreover, we have found that I values increased with increasing column temperature, with the exception of the linear alcohols and the esters, which decreased with increasing temperature, and of cyclobutanol, 2-butanone, 2-pentanone, 1-butylamine and 1-pentylamine that showed a

well-defined minimum in the 358–377 K range.

On the other hand, linear relationships were found between I values and the number of carbon atoms (z) in the solute. A slope value around 100 was obtained, except for the alicyclic compounds, for which higher slope values were obtained. Moreover, a significant increase of the slopes with increasing temperature was also noticed for these compounds. This anomalous behavior was explained on basis of their structures. Alicyclic compounds have a larger surface area able to interact with the SP than the linear ones. The enlargement of the cycloalkane ring by the addition of a methylene group leads to a higher increase of its surface area with respect to that of the linear homologue. Consequently, the retention index increases considerably with the increasing cycle size. Furthermore, they are more affected by the easier solute insertion in the SP as temperature increases, due to their higher stiffness and surface area, this being more evident with increasing cycle size. As a result, for alicyclic solutes the slope of the I vs. z plot becomes steeper as temperature increases.

Finally, from the data of this work we have initiated the study of the relationship between I and thermodynamic magnitudes.

Figure 3. Slopes (m) of I vs. z plots for different chemical families: () 423 K and () 333–413 K; () y ( ) taken from the literature.

Scientific Report 2013/2014 Department of Structure, Energy and 45 Chemical Reactivity

Ionic liquids as stationary phases for gas chromatographyOver the past decade, ionic liquids (ILs) have generated great interest because of their unique and tunable physicochemical properties and their versatility for various applications. They are organic salts with melting points below 100 °C that typically possess negligible vapor pressure, high viscosity, good thermal stability and wide liquid ranges. All these properties make them ideal candidates as SPs for GC. In order to have a more specific idea of their potential, we have approached the problem from two different perspectives:

Characterization of the commercial columns based on ILs To date, only seven different ILs have been used to prepare commercial capillary columns. During these two years, in collaboration with the group of Dr. Mª Luz Sanz (IQOG, CSIC), we have carried out their characterization by means of the solvation parameter model (SPM), in order to better understand their retention mechanisms. They can be considered moderately hydrogen-bond acid and highly cohesive SPs, on which the dominant contributions to retention are the dipolar-type and hydrogen-bond base interactions, with barely significant π-π and n-π interactions. One of the most outstanding characteristics found for these ILs when

compared with other non-ionic SPs, is that they are hydrogen-bond acids. This acidity, along with their high polarity, confers on them unique separation properties, which clearly enhances the separation capacity of GC.

Evaluation of different ILs as new SPs for capillary columnsThe experimental set-up for fused silica capillary column preparation developed in the previous biennium has allowed us to prepare and characterize columns with 1-allyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide ([AMIM][NTf2]) ionic liquid. The columns obtained showed high polarity, acceptable efficiency and maximum allowable operating temperatures of 220 °C, which makes them very promising for further improvements. According to the SPM results, dipolar-type and hydrogen-bond base interactions were the dominant contributions to retention, while π-type interactions were barely significant. Moreover, [AMIM][NTf2] is a moderately hydrogen-bond acid and very cohesive SP. As a result of the different retention mechanisms involved, the new columns are highly versatile and have a noteworthy capacity to resolve complex mixtures. Thus, some of these columns have been used to develop a fast analytical method to control the PET (polyethylene terephthalate) manufacturing process.

Figure 4. Principal component analysis for the studied ILs and the most common SPs used in capillary GC: (1) Trifluoropropyl, (2) phenyl and (3) cyanopropyl siloxanes, and (4)

poly(ethylene glycols).

Scientific Report 2013/2014 Department of Structure, Energy and 46 Chemical Reactivity

Characterization by LC-MSn of sialylated oligosaccharides from ovine and caprine caseinomacropeptideCaseinomacropeptide (CMP), one of the major components of sweet whey, is produced by enzymatic cleavage of κ-casein during the primary stage of cheese making or during digestion in the stomach. The term CMP designates a heterogeneous group of polypeptides due to genetic variance and post-translational modifications, such as phosphorylation and glycosylation. Isolation and characterization of oligosaccharides from CMP are important in understanding their biological and functional properties. However, it is difficult to achieve this goal, due to the high degree of isomerism present in these types of compounds.

In this biennium, we have developed a new methodology for the detection and identification

of sialylated oligosaccharides from ovine and caprine CMP, based on graphitized carbon liquid chromatography-(ion trap) tandem mass spectrometry (LC-MSn). The optimized procedure allowed an exhaustive characterization of O-glycans of ovine and caprine CMP, four trisaccharides and four tetrasaccharides to be identified. The chromatographic method resolved linear and branched trisaccharides, as well as oligosaccharides of different polymerization degree, but not those having the same structure and differing only in the NeuAc or NeuGc units. However, results previously obtained by our group allowed a complete elucidation of the oligosaccharides studied even in case of coelution, using the information provided by their characteristics MSn spectra. Thus, the methodology developed using an ion trap-type mass analyzer could be used for unequivocal identification of short O-glycan oligosaccharides in other glycoproteins.

Figure 5. Chemical structures of O-glycans identified in ovine and caprine milk.

Scientific Report 2013/2014 Department of Structure, Energy and 47 Chemical Reactivity

Proanthocyanidins profile in plants by DI-ESI MSProanthocyanidins (PA) or condensed tannins are polymers of flavan-3-ol that are widely distributed in the plant kingdom and are among the most abundant polyphenols in our diet. Besides their participation in food quality attributes such as astringency, bitterness, aroma and color formation, PA consumption has been associated with numerous health benefits due their antioxidant, anti-carcinogenic, cardioprotective, antimicrobial and neuroprotective activities. Because of that, they are considered as functional ingredients in botanical and nutritional supplements. However, due to their structural diversity and complexity, the qualitative and quantitative analysis of PA is a difficult task.

Several years ago, we initiated a study in order to achieve a sound methodology to quantify and identify PA in different matrices by MS.

Reproducible mass spectra of proanthocyanidins in several nut skin extracts were obtained by direct injection-electrospray ionization mass spectrometry (DI-ESI MS), showing prevalence of monocharged ions, with no significant degradation, very good resolution and mass ranges up to 5000 u.

During this biennium, in collaboration with the group of Dr. Begoña Bartolomé (CIAL, CSIC), cranberry extracts have been successfully analyzed by DI-ESI MS. These results are significant because cranberry products are widely recommended in traditional American medicine for the prevention of urinary tract infections (UTI), and in recent years their popularity has considerably increased in the European market. With the aim of getting further insight into the establishment of the PA protective action against UTI, we have begun to analyze their content in incubations of PA with bacteria and in mouse feces after intake of cranberry extracts.

Figure 6. Direct injection mass spectrum of a cranberry extract.

Scientific Report 2013/2014 Department of Structure, Energy and 48 Chemical Reactivity

Casal, E.; Lebrón-Aguilar, R.; Y. Chuan-Lee, Y.; Noboru, T.; Quintanilla-López, J.E. (2013). Identification of sialylated oligosaccharides derived from ovine and caprine caseinomacropeptide by graphitized carbon liquid chromatography-electrospray ionization ion trap tandem mass spectrometry. Food Anal. Methods 6, 814-825.

Becerra R.; Cannady J.P.; Walsh R. (2013). Time-resolved gas-phase kinetic studies of the reaction of dimethylsilylene with triethylsilane-1-d: kinetic isotopic effect for the Si-H insertion process. Phys. Chem. Chem. Phys. 15, 5530-5538.

Becerra R.; Cannady J.P.; Goldberg N.; Walsh R. (2013). Reaction of silylene with sulfur dioxide: some gas-phase kinetic and theoretical studies. Phys. Chem. Chem. Phys. 15, 14748-14760.

Rodríguez-Sánchez, S.; Galindo-Iranzo, P.; Soria, A.C.; Sanz, M.L.; Quintanilla-López, J.E.; Lebrón-Aguilar, R. (2014). Characterization by the solvation parameter model of the retention properties of commercial ionic liquid columns for gas chromatography. J. Chromatogr. A 1326, 96-102.

Santiuste, J.M.; Quintanilla-López, J.E.; Becerra, R.; Lebrón-Aguilar, R. (2014). On the influence of column temperature on the isothermal retention indices of structurally different solutes on a poly(dimethylsiloxane) capillary column. J. Chromatogr. A 1365, 204-211.

Becerra R.; Cannady J.P.; Walsh R. (2014). Reaction of germylene with sulphur dioxide: gas-phase kinetic and theoretical studies. Organometallics 33, 6493-6503.

Publications

Scientific Report 2013/2014 Department of Structure, Energy and 49 Chemical Reactivity

COMPETITIVE FUNDING

Principal Investigator Title Reference

Begoña Bartolomé Sualdea Proantocianidinas de tipo A: AGL2010-17499 Estudio de su metabolismo por la microbiota intestinal y acción protectora frente a infecciones del tracto urinario

Principal Investigator Title Reference

Mª José González Carlos Metodologías analíticas innovadoras para S2009/AGR-1464 el control de la calidad y la seguridad de los alimentos

Mª Luisa Marina Alegre Estrategias avanzadas para la mejora y el S2013/ABI-3028 control de la calidad y la seguridad

Principal Investigator Title Reference

Rosa Becerra Arias Kinetic studies of the simplest Criegee intermediate

Ministry for Science and Innovation

Regional Government of Madrid

Royal Society of Chemistry (RSC)

National Grants: individual

National Grants: coordinated

International Grants: individual

Scientific Report 2013/2014 Department of Structure, Energy and 50 Chemical Reactivity

Atmospheric Chemistry and Climate Group

Tenured Staff scientists

Alfonso Saiz-López (Associate Professor) ReID

Non-tenured scientists

Carlos Alberto Cuevas Rodríguez (from 03/2013)

Rafael Pedro Fernández Cullen (03/2013 - 12/2013)

Cristina Prados Román (03/2013 - 09/2014)

Xavier Rodriguez Lloveras (06/2014 - 12/2014)

Technical Staff

Arturo Alonso de León (03/2013 - 08/2014)

Mónica Anguas Ballesteros (from 11/2014)

Chiara Cerruti (03/2013 - 10/2014)

Miguel Fernández Sánchez (03/2013 - 10/2014)

Scientific Report 2013/2014 Department of Structure, Energy and 51 Chemical Reactivity

Summary The Atmospheric Chemistry and Climate group (AC2) is a newly created research group within CSIC´s Institute of Physical Chemistry Rocasolano (IQFR). AC2 research efforts are directed at studying the role of atmospheric composition and chemistry in the climate system.

Within this scientific framework, AC2 provides an integrated research approach combining atmospheric measurements (satellite- and ground-based), modelling (microphysical to global chemistry-climate) and laboratory studies (photochemistry).

Strategic Aims• The goals are to explore the interactions between anthropogenic and natural emissions, the

chemical and physical climate system, and the biosphere, within a changing climate context.

Scientific Report 2013/2014 Department of Structure, Energy and 52 Chemical Reactivity

ResultsWe have implemented a state-of-the-art scheme of the atmospheric chemistry of bromine and iodine in the 3D chemistry climate model CAM-CHEM (Community Atmospheric Model with Chemistry, version 4.0), included into the CESM framework (Community Earth System Model, version 1.1.1).

Using this model we have calculated an annual average stratospheric injection of total bromine due to very short-lived (VSL) sources of about 5 pptv (parts per trillion by volume), ∼3 pptv entering the stratosphere as product gases (PGVSL) and ∼2 pptv as source gases (GVSL). The geographic distribution and partitioning of VSL bromine within the tropical tropopause layer (TTL), and its consequent stratospheric injection, indicate that atomic Br should be the dominant inorganic species in large regions of the tropical tropopause layer (TTL) during daytime, due to the low ozone and cold conditions of this region. We propose the existence of a “tropical ring of atomic bromine” located approximately between 15 and 19 km and between 30º N and 30º S. Daytime Br/BrO ratios of up to ~4 are predicted within this inhomogeneous ring in regions of highly convective transport, such as the tropical Western Pacific.

The ranges of inorganic iodine loading, partitioning and impact in the troposphere have also been studied. Our results show that the most abundant daytime iodine species throughout the middle to upper troposphere is atomic iodine, with an annual average tropical abundance of (0.15–0.55) pptv. We propose the existence of a “tropical ring of atomic iodine” that peaks in the tropical upper troposphere (∼11–14 km) at the equator and extends to the sub-tropics (30ºN–30ºS). Annual average daytime I/IO ratios larger than 3 are modelled within the tropics, reaching ratios up to ∼20 during vigorous uplift events within strong convective regions. We calculate that the integrated contribution of catalytic iodine reactions to the total rate of tropospheric ozone loss is 25 times larger than the combined bromine and chlorine cycles. Iodine loss represents an upper limit of approximately 27, 14 and 27% of the tropical annual ozone loss for the marine boundary layer (MBL), free troposphere (FT) and upper troposphere (UT), respectively, while the lower limit throughout the tropical troposphere is ~9 %. Our results indicate that iodine is the second strongest ozone-depleting family throughout the global marine UT and in the tropical MBL (Saiz-Lopez et al., 2014; Fernandez et al., 2014).

Figure 1. “Tropical rings of atomic halogens”: daytime levels of atomic Br and I increase significantly in the upper tropical troposphere until they become the dominant species for each halogen family, surpassing the abundance of the commonly targeted BrO and IO radicals. The

main drivers are the low ozone mixing ratios (O3 < 100 ppbv) and cold temperatures (T < 200K) that slows down the otherwise dominant Br/I + O3 → BrO/IO reaction. The tropical rings circle the tropics following the sun at different heights (11−15 km for iodine and 15−19 km for

bromine) due to their distinctive photochemistry.

Scientific Report 2013/2014 Department of Structure, Energy and 53 Chemical Reactivity

Naturally emitted from the oceans, iodine compounds efficiently destroy atmospheric ozone and reduce its positive radiative forcing effects in the troposphere. Emissions of inorganic iodine have been experimentally shown to depend on the deposition to the oceans of tropospheric ozone, whose concentrations have significantly increased since 1850 as a result of human activities. We have used the chemistry-climate model CAMCHEM to quantify the current ocean emissions of inorganic iodine and assess the impact that the anthropogenic increase of tropospheric ozone has had on the natural cycle of iodine in the marine environment since pre-industrial times. Our results indicate that the human-driven enhancement of tropospheric

ozone has doubled the oceanic inorganic iodine emissions following the reaction of ozone with iodide at the sea surface. The consequent build-up of atmospheric iodine, with maximum enhancements of up to 70% with respect to preindustrial times in continental pollution outflow regions, has in turn accelerated the ozone chemical loss over the oceans with strong spatial patterns. We suggest that this ocean-atmosphere interaction represents a negative geochemical feedback loop by which current ocean emissions of iodine act as a natural buffer for ozone pollution and its radiative forcing in the global marine environment. (Atmos. Chem. Phys., 15, 2215-2224, 2015).

Figure 2. Geochemical feedback mechanism. The anthropogenic increase in tropospheric ozone during the last two centuries (20-55%, Myhre et al., 2013) has led to an amplification

of the natural cycle of iodine emissions since pre-industrial times (PI cycle in yellow). This has consequently decreased the lifetime of ozone in the marine atmosphere and its associated

RF, thus closing a negative feedback loop and presenting the ocean emissions of iodine as a natural mitigating factor for anthropogenic RF in the marine environment (PD cycle in red).

Scientific Report 2013/2014 Department of Structure, Energy and 54 Chemical Reactivity

We have developed the first global data set of iodine oxide (IO) measurements in the open marine boundary layer (MBL), using a DOAS instruments during the Malaspina 2010 circumnavigation. Results show IO mixing ratios ranging from 0.4 to 1 pmol mol-1 (30% uncertainty) and, complemented with additional field campaigns, this data set confirms through observations the ubiquitous presence of reactive iodine chemistry in the global marine environment. We then use the global model CAMCHEM including organic (CH3I, CH2ICl, CH2I2 and CH2IBr) and inorganic (HOI and I2) iodine ocean emissions to investigate the contribution of the different iodine source gases to the budget of IO in the global MBL. In agreement with previous estimates, our results indicate that, globally averaged, the abiotic precursors contribute about 75% to the IO budget. However, this work reveals a strong geographical pattern

in the contribution of organic vs. inorganic precursors to reactive iodine in the global MBL. (Atmos. Chem. Phys., 15, 583-593, 2015).

We have studied the evolution of tropospheric nitrogen dioxide (NO2) over Spain, focusing on the densely populated cities of Barcelona, Bilbao, Madrid, Sevilla and Valencia, during 17 years, from 1996 to 2012. This data series combines observations from in-situ air quality monitoring networks and the satellite-based instruments GOME and SCIAMACHY. The results in these five cities show a smooth decrease in the NO2 concentrations of ∼2% per year in the period 1996–2008, due to the implementation of emissions control environmental legislation, and a more abrupt descend of ~7% per year from 2008 to 2012 as a consequence of the economic recession. In the whole Spanish territory the NO2 levels have decreased by ∼22% from 1996 to 2012 (Cuevas et al., 2014).

Figure 3. Iodine oxide observations in the global marine boundary layer. IO mixing ratios are shown for five different field campaigns: Malaspina (this work), CHARLEX (Gómez Martín et

al., 2013a), TransBrom (Großmann et al., 2013), HaloCAST-P (Mahajan et al., 2012) and Cape Verde (Read et al., 2008; Mahajan et al., 2010), as well as also for the MBL measurements

reported by Dix et al. (2013) during one research flight.

Scientific Report 2013/2014 Department of Structure, Energy and 55 Chemical Reactivity

Figure 4. Averaged tropospheric NO2 vertical column densities for different seasons during 1996 using the GOME resolution-corrected database (a, c and e), and 2011/2012 using

SCIAMACHY data (b, d, f). Top: annual averages. Middle: summer (Jun-Jul-Aug) averages. Bottom: winter (Dec-Jan-Feb) averages.

Mercury is a contaminant of global concern. It is transported in the atmosphere primarily as gaseous elemental mercury, but its reactivity and deposition to the surface environment, through which it enters the aquatic food

chain, is greatly enhanced following oxidation. Measurements and modelling studies of oxidised mercury in the polar to sub-tropical marine boundary layer (MBL) have suggested that photolytically produced bromine atoms are the

Scientific Report 2013/2014 Department of Structure, Energy and 56 Chemical Reactivity

Figure 5. Comparison of the average daily profile of reactive gaseous mercury (RGM) during October (grey area indicates the standard deviation of the data) with simulated profiles obtained by two different modelling approaches. (a) Modelled results from the original

chemistry scheme according to Goodsite et al. (2004) and Holmes et al. (2009) under four different scenarios. (b) Modelled results using an updated chemistry scheme according to

Goodsite et al. (2012) and Dibble et al. (2013).

primary oxidant of mercury. In this work we report year-round measurements of elemental and oxidised mercury, along with ozone, halogen oxides (IO and BrO) and nitrogen oxides (NO2), in the MBL over the Galápagos Islands in the equatorial Pacific. Elemental mercury concentration remained low throughout the year, while higher than expected levels of oxidised mercury occurred around midday. Our results show that the production of oxidised mercury in the tropical MBL cannot be accounted for by bromine oxidation only, or by the inclusion of ozone and hydroxyl. As a two-step oxidation mechanism, where the HgBr intermediate is further oxidised to Hg(II), depends critically on

the stability of HgBr, an additional oxidant is needed to react with HgBr to explain more than 50% of the observed oxidised mercury. Based on best available thermodynamic data, we show that atomic iodine, NO2, or HO2 could all play the potential role of the missing oxidant, though their relative importance cannot be determined explicitly at this time due to the uncertainties associated with mercury oxidation kinetics. We conclude that the key pathway that significantly enhances atmospheric mercury oxidation and deposition to the tropical oceans is missing from the current understanding of atmospheric mercury oxidation (Wang et al., 2014).

Scientific Report 2013/2014 Department of Structure, Energy and 57 Chemical Reactivity

Gómez Martín, J.C.; Mahajan, A.; Hay, T.D.; Prados-Román, C.; Ordóñez, C.; McDonald, S.M.; Plane, J.M.C.; Sorribas, M.; Gil, M.; Paredes Mora, F.; Agama Reyes, M.V.; Oram, D.E.; Leedham, E.; Saiz-Lopez, A. (2013). Iodine chemistry in the eastern Pacific marine boundary layer. JGR Atm. 118, 1-1454.

Gálvez, O.; Gómez Martin, J.C.; Gómez, P.C.; Saiz-Lopez, A.; Palacios, F. (2013). A theoretical study on the formation of iodine oxides aggregates and monohydrates. Phys. Chem. Chem. Phys. 15, 15572.

Hossaini, R.; Mantle, H.; Chipperfield, M.P.; Montzka, S.A. ; Hamer, P.; Ziska, F.; Quack, B.; Krüger, K.; Tegtmeier, S.; Atlas, E.; Sala, S.; Engel, A.; Bönisch, H.; Keber, T.; Oram, D.; Mills, G.; Ordoñez, C.; SaizLopez, A.; Warnick, N.; Liang, Q.; Feng, W.; Moore, F.; Miller, B.R.; Marécal, V.; Richards, N.A.; Dorf, M.; Pfeilsticker, K. (2013). Evaluating global emission inventories of biogenic bromocarbons. Atmos. Chem. Phys. 13, 11819-11838.

Wang, F.; Saiz-Lopez, A.; Mahajan, A. S.; Gómez Martín, J. C.; Armstrong, D.; Lemes, M.; Hay, T.; Prados-Roman, C. (2014). Enhanced production of oxidized mercury over the tropical Pacific Ocean: a key missing oxidation pathway. Atmos. Chem. Phys. 14, 1323-1335.

Lawler, M. J.; Mahajan, A. S.; Saiz-Lopez, A.; Saltzman, E. S. (2014). Observations of I2 at a remote marine site. Atmos. Chem. Phys. 14, 2669-2678.

Mahajan, A.S.; Prados-Roman, C.; Hay, T.D.; Lampel, J.; Pöhler,D.; Grossmann, K.; Tschritter,J.; Friess, U.; Platt, U.; Johnston, P.; Kreher, K.; Wittrock ,F.; Burrows, J.P.; Plane, J.M.C.; Saiz-Lopez, A. (2014). Glyoxal observations in the marine boundary layer. JGR. Atmos. 119, 6160-6169.

MacDonald, S.M.; Gómez Martín, J.C.; Chance, R.; Warriner, S.; SaizLopez, A.; Carpenter, L.J.; Plane, J.M.C. (2014). A laboratory characterization of inorganic iodine emissions from the sea surface: dependence on oceanic variables and parameterization for global modelling. Atmos. Chem. Phys. 14, 5841-5852.

Cuevas, C.A.; Notario, A.; Adame, J.A.; Hilboll, A.; Richter, A.; Burrows, J.P.; Saiz-Lopez, A. (2014). Evolution of NO2 levels in Spain from 1996 to 2012. Sci. Rep. 4, 5887.

Fernandez, R.P; Salawitch, R.J.; Kinnison, D.E; Lamarque, J.-F.; Saiz-Lopez, A. (2014).Bromine partitioning in the tropical tropopause layer: implications for stratospheric injection. Atmos. Chem. Phys. 14, 13391-13410.

Saiz-Lopez, A.; Fernandez, R.P.; Ordoñez, C.; Kinnison, D.E.; Gómez Martín, J.C.; Lamarque, J.-F.; Tilmes. S. (2014). Iodine chemistry in the troposphere and its effect on ozone. Atmos. Chem. Phys. 14, 13119-13143.

Boxe, C.S.; Francisco, J.S.; Shia, R.-L.; Yung, Y.L.; Nair, H.; Liang, M.C; Saiz-Lopez, A. (2014). New insights into martian atmospheric chemistry. Icarus 242, 97-104.

Garçon, V.C.; Bell, T.G.; Wallace, D.; Arnold, S.R.; Baker, A.; Bakker, D.C.E.; Bange, H.W.; Bates, N.R.; Bopp, L.; Boutin, J.; Boyd, P.W.; Bracher, A.; Burrows, J.P.; Carpenter, L.J.; de Leeuw, G.; Fennel, K.; Font, J.; Friedrich, T.; Garbe, C.S.; Gruber, N.; Jaeglé, L.; Lana, A.; Lee, J.D; Liss, P.S.; Miller, L.A.; Olgun, N.; Olsen, A.; Pfeil, B.; Quack, B.; Read, K.A.; Reul, N.; Rödenbeck, C.; Rohekar, S.S.; SaizLopez, A.; Saltzman, E.S.; Schneising, O.; Schuster, U.; Seferia, R.; Steinhoff, S.; Le Traon, P.Y.; Ziska, F. (2014) Ocean-Atmosphere Interactions of Gases & Particles, 2014, p247-306, 60p. Publisher: Springer Science & Business Media B.V.

Publications

Scientific Report 2013/2014 Department of Structure, Energy and 58 Chemical Reactivity

COMPETITIVE FUNDING

Principal Investigator Title Reference

Alfonso Saiz López FASE C/D del instrumento Ultraviolet and AYA2011-30475 Visible Atmospheric Sounder (UVAS) en SEOSAT/INGENIO

Principal Investigator Title Reference

Alfonso Saiz López Atmospheric MInor Species relevant to the Ozone AMISOC Chemistry at both sides of the subtropical jet.

Principal Investigator Title Reference

Alfonso Saiz López Quality Assurance for Essential Climate Variables QA4ECV

Principal Investigator Title Reference

Alfonso Saiz López Tecnologías innovadoras para la evaluación y TECNAIR mejora de la calidad del aire urbano

Principal Investigator Title Reference

Alfonso Saiz López DOAS measurements of Halogen oxides at Station DOASGREEN Nord (Greenland)

MINECO

INTA

EU

Comunidad de Madrid

Aarhus University

National Grants: individual

National Grants: coordinated

International Grants: coordinated

Scientific Report 2013/2014 Department of Structure, Energy and 59 Chemical Reactivity

Memoria 2013/2014 Department of Structure, Energy and 61 Chemical Reactivity

Department of Biological Physical Chemistry

Introduction http://qfbio.iqfr.csic.es

The research experience in our research Department covers the fields of Biochemistry, Molecular Biology, Structural Biology, Biophysics, Glycobiology, Bioinformatics and Biothermodynamics. The objective of our ongoing work is to understand the physical-chemical bases governing the structure, stability, dynamics and interactions of different biological molecules such as peptides, proteins, nucleic acids and carbohydrates. This investigation is conducted on systems with different levels of complexity, ranging from isolated molecules to macromolecular assemblies, membrane mimetics, cells and tissues. Many of these systems have biomedical, pharmacological or biotechnical importance.

We determine the structure and stability of nucleic acids and their complexes with proteins. The final aim is to characterise their relationship with the mechanisms of gen regulation at the transcriptional and post-transcriptional levels. We are also interested in the biophysical characterization of intrinsically disordered proteins, domains or protein fragments; and we are studying model systems in which this feature is essential for the biological function.

The Department also carries out research based on structural bioinformatics, and we are actively involved in the development of novel techniques for the simulation, analysis and modelling of large biomolecular systems.

We also study processes involved in the assembly and functional properties amyloids, the broad aim of which is to understand pathologies related to aberrant conformations, neurodegenerative disease, and in general, the process of aging. We also study the role of carbohydrates as recognition signals, their binding to ligands, and the structural organization of protein receptors for carbohydrate recognition. Other systems that we study include choline receptors, murein hydrolases, pneumococcal virulence factors and various allergens and toxins.

We have extensive experience in studying the mechanisms of protein folding and the design of peptides with a defined structure. Our work has contributed towards establishing structure-function relationships in proteins and protein-inhibitor complexes implicated in, for example, angiogenesis, immune response, and antiviral and antimicrobial activity.

Moreover, our research efforts have also been directed towards the determination of the structural organization and stability of membrane protein complexes, how the associated interactions alter the physical properties of cell membranes, and the mechanisms of action of anesthetics, anticancer and antiparasite drugs.Our Department is also actively involved in research aimed at developing methodology necessary for i) resolving problems related to molecular heterogeneity (isoforms, modifications and conformational heterogeneity), ii) enhancing the use and applicability of NMR Spectroscopy (development of new pulse sequences, reduced dimensionality and automatic assignment methods), iii) resolving molecular interactions in complex environments (fluorescence microspectroscopy or single cell spectroscopy), or whole-cell approaches (microarrays of design).

Experimental methods and equipmentThe Department has all of the necessary instrumentation for in-depth experimental studies of biological samples. Laboratories are well-equipped to carry out the basic techniques employed in isolating, cloning, expressing, purifying and concentrating proteins and nucleic acids; and have instrumentation necessary for their biophysical characterisation: immunochemical analysis, high-performance liquid chromatography, analytical ultracentrigugation, light scattering (MALLS), spectropolarimetry (CD), UV-visible spectroscopy, fluorescence spectroscopy, differential scanning calorimetry (DSC), isothermal titration calorimetry (ITC). A departmental microarray scanner, a manual microarrayer and a scanner for microarrays are also available. The Department is also well-equipped with instrumentation for advanced fluorescence methods required in high-resolution temporal (ps-ms) and spatial (mm-sub mm) studies of biological systems at different levels of organisation. We also have two high-field NMR spectrometers, a 600 MHz instrument and an 800 MHz one, each equipped with a gradient module and cryoprobe. All of the necessary software has been installed for processing and analyzing multidimensional NMR spectra, for calculations of macromolecular structures in solution, and for protein-protein and protein-ligand docking analyses.

Scientific Report 2013/2014 Department of Biological 62 Physical Chemistry

Group Structure

NMR of Protein Structure, Dynamics and Interactions 64

Protein Bioconformatics and Assemblies 75

Structural Bioinformatics 80

Fluorescence and Molecular Biophysics 88

Protein Structure and Thermodynamics 96

NMR of Nucleic Acids 104

Scientific Report 2013/2014 Department of Biological 63 Physical Chemistry

NMR of Protein, Structure, Dynamics and Interactions Group

Tenured Staff scientists

Manuel Rico Sarompas (Professor Ad honorem) († 01/12/2014)

Jorge Santoro Said (Professor)

Marta Bruix Bayes (Professor) ) ReID ORCID SCOPUS

María Ángeles Jiménez López (Associate Professor) ReID ORCID SCOPUS

Subramanian Padmanabhan (Associate Professor)

José Manuel Pérez Cañadillas (Assistant Professor) ReID ORCID

Non-tenured scientists

Mª Flor García Mayoral (until 15/11/2013)

Angélica Inés Partida Hanón (from 1/09/2014) ORCID

Aránzazu Gallego García (from 1/10/2014)

Doctoral students

Soraya Serrano Serrano (until 1/06/2014)

Hector Zamora Carreras

Santiago Martínez Lumbreras (until 31/12/2013)

Juán Manuel Ortíz Guerrero (until 31/12/2013)

Jesús Fernández Zapata (from 1/01/2014)

Technical Staff

David Pantoja Uceda (TSE)

Miguel Angel Treviño Avellaneda (TSE) ReID ORCID SCOPUS

Cristina López García (until 20/04/2014)

Luis de la Vega Serrada

Scientific Report 2013/2014 Department of Biological 64 Physical Chemistry

SummaryThis group (http://rmn.iqfr.csic.es), reputed nationally and internationally, is a pioneer in Spain in the application of NMR to the determination of the three-dimensional structure, dynamics and interactions of proteins and peptides, whose knowledge is essential for understanding the physicochemical bases of their biological functions and the regulatory mechanisms underlying their activities. Within this broad field, we study the structure and dynamics of a variety of biological systems. We also concurrently work on implementing and optimizing NMR methodology. This group and that of the “NMR of Nucleic Acids”, together manage and maintain the Manuel Rico NMR

Laboratory (http://rmn.iqfr.csic.es) that is equipped with advanced NMR instrumentation. The group has historically are been involved in studies of protein-lipid interactions involved in the cytotoxicity of specific ribonucleases and actinoporins, the structural and dynamic characterization of allergens and centrosomal proteins, proteins participating in mRNP formation and posttranscriptional control, and the structures and interactions of proteins regulating bacterial response to light. Peptide design and protein folding, and the structural characterization of intrinsically disordered, non-native states and folding intermediates continue to be subjects of study.

Strategic Aims• Development of new NMR methodology for fast and highly efficient determination of three-

dimensional structures of biomacromolecules and their complexes.

• New methods to study intrinsically disordered proteins.

• Design of peptides with well defined conformations. Structure-activity relationships.

• Structural study of proteins of biomedical relevance: applications in cancer and allergy.

• Structural study of protein-nucleic acid complexes: applications in the regulation of gene expression.

• Description of the molecular mechanisms of light sensing and response in bacteria and their exploitation in optogenetic applications.

Scientific Report 2013/2014 Department of Biological 65 Physical Chemistry

ResultsImplementation and optimization of NMR methodsTraditional NMR methods are rather ineffective with intrinsically disordered proteins (IDPs) given their peculariarities. Consequently, there is a considerable interest in the development of experimental NMR techniques for IDPs. We have developed pulse sequences that allow the assignment of the NMR spectra of IDPs by correlating the signals of two consecutive CO-N in the protein sequence. Of growing importance in NMR methodology is acquisition of spectra with nonuniform sampling. In recent years we have implemented and evaluated various methods of non-uniform sampling. Selecting the so-called Iterative soft thresholding method as most suitable for our work, we have developed over two dozen pulse sequences that enable an ~80% reduction in time for obtaining three-dimensional spectra.

Design and structure-function relationships in peptidesThe determination of the structure of biologically active peptides contributes to our understanding of their biological function and paves the way for the rational design of peptides with pharmaceutical applications. Recent research highlights from the group include the design and structure determination of peptides that block interactions between the protein VEGF and its receptors, of cyclic peptides derived from αMSH, of peptides corresponding to the choline binding repeats present in pneumococcal proteins, and of immunogenic peptides derived from the HIV-1 gp41 protein, which plays an important role in membrane fusion during viral entry to the host cell, and also contains several linear epitopes. Also ongoing are studies of peptide-lipid interactions aimed at a better understanding of the structure-activity relationships in antimicrobial peptides.

Figure 1. NMR structure of peptide MPERp from gp41 in the presence of hexafluoroisopropanol (left) and in dodecylphosphocholine micelles (right). The Trp side chains belonging to 2F5 (in green) and 4E10 (in magenta) epitopes are displayed. The amino-end is

indicated by an “N”.

Scientific Report 2013/2014 Department of Biological 66 Physical Chemistry

Molecular mechanisms of light sensingOur goal is to understand the molecular mechanisms of light sensing and response in bacteria. We combine high-resolution structural and biophysical studies with functional analyses (in collaboration with the Genetics group in the University of Murcia) of several protein factors that serve as receptors and transducers of the light signal, or are specific or global regulators of gene expression in the model bacterium, Myxococcus xanthus. Many of the factors that we study have turned out to be the prototypes

of novel and widespread protein families. Our studies have led to high-resolution, structural-functional insights of photosensory transcriptional factors that employ 5´-deoxyadenoylcobalamin (coenzyme B12) as the chromophore to act as a light-sensing allosteric switch, and how their actions can be downregulated by a protein with an SH3-domain topology that mimicks DNA. We have also uncovered a large family of bacterial RNA polymerase binding proteins with critical roles in the expression of essential genes, or of genes activated in response to specific stress signals such as light.

Figure 2. Structure of the M. xanthus CdnL in ribbon representation. CdnL is a member of the large CarD_CdnL_TRCF family of bacterial RNA polymerase binding proteins interaction that has been shown to be essential for cell growth and survival and is implicated in rRNA

transcription in M. xanthus and in mycobacteria, like Mycobacterium tuberculosis. The N-terminal, all-β (labeled) Tudor-like domain shown in cyan on the left is the RNA polymerase interaction domain with side-chains of contact residues indicated. The all-helical C-terminal

domain resembles some TPR (tetratricopepetide) domains, and the residues indicated form a solvent-accessible basic-hydrophobic patch crucial for function. The α-helices of these domains

are shown in red (α1), magenta (α2), yellow (α3), blue (α4) and green (α5).

Scientific Report 2013/2014 Department of Biological 67 Physical Chemistry

Structure and interactions of proteins involved in RNA metabolismWe continue research on several protein and protein domains involved in the biogenesis of different types of RNAs (mRNAs, snoRNAs,etc.). We have assigned the NMR spectra of a 20 KDa intrinsically disordered fragment of Tif4631 of the Pub1/Tif¡4631 system involved in the nucleation of stress granules, and characterized its molecular recognition features (MORFs). Our published structure and RNA binding mode

of part of the CCCH-type zinc finger region of Nab2, a critical factor for poly(A) tail length control, reveal remarkable features like the self recognition of the two histidine residues coordinating the zinc ions in fingers 3 and 4 (see figure 3). We have also obtained results for other systems including Gbp2/Hrb1, proteins involved in THO/TREX recruitment to nascent mRNA during transcription in collaborative work with the Bertrand Seraphin group (IGBMC/CNRS, France).

Figure 3. NMR structure of Nab2 zinc finger 3-4 tandem showing the atomic detail of the hydrogen bond network between His 355 and His 386. The degree of protection of Hδ1 of

these histidine residues is such that build up observable correlation peaks with their attached Nδ1 in the 1H-15N HSQC.

Scientific Report 2013/2014 Department of Biological 68 Physical Chemistry

Structure-function relationships in Anisakis alergensUnderstanding the function of biomolecules requires not only know the isolated structures, but also the interactions with other biomolecules. We are studying the principal allergens of Anisakis, at present one of the most important food-borne allergies. Ani s 5 belongs to the SXP / RAL-2 family of exclusively nematode origin. The function of this highly antigenic protein is

unknown. We have determined the structure of the principal regions involved in IgE and IgG4 binding, the first-ever structure resolved for an Anisakis allergen. Ani s 5 has the ability to bind divalent metals, which may be important for its function. The IgE /IgG4-binding regions are located linearly along the surface of the structure. The emerging structural data can help in the future design of new diagnostic tests and strategies for immunotherapy.

Figure 4. Ribbon representations of Ani s 5 with epitope mapping. A and B, Peptide segments representing the minimum unit necessary for IgE/IgG4 recognition are colored in cyan (E1,

7-18), purple (E2, 19-24), hot pink (E3, 31-36), blue (E4, 40-48), yellow (E7, 79-90), red (E8, 91-102), green (E9, 97-116) and dark green (E11, 109-128). The overlapping region 110-

116 is colored in pale green. C and D, Peptide segments recognized simultaneously by three different sera are colored in red (E5, 40-59), green (E6, 85-96) and cyan (E10, 103-122). Two

perspectives rotated 180º with respect to each other are shown in each panel.

Scientific Report 2013/2014 Department of Biological 69 Physical Chemistry

Structure and association of actinoporinsWe continue to study actinoporin protein family structure (of StnI) and association (of StnII) to membranes in solution and at the cell surface. A knowledge of these is fundamental for understanding their hemolytic and toxic activity through pore formation. Notably, our atomic level description of the interaction of Stn I with micelles provides insights into the initial stages of pore formation by these proteins.

RNases of therapeutical interestIn line with that described in the previous

Annual Report, we have worked on elucidating the structure and interactions of an Onconase zymogen with significant therapeutic potential (ONCFLG), as it can be selectively activated by the HIV-1 protease. Using NMR as a tool, we have conducted a comprehensive study and determined the three-dimensional structure of the native and activated zymogen, their internal dynamics and conformational stability. Structural and dynamic changes resulting from zymogen activation by the HIV-1 protease, allowed the description of the structure-activity relationships and the structural motifs responsible for the high conformational stability, which may be important from the standpoint of its possible therapeutic action.

Figure 5. Representation of the final structures of the ONCFLG zimógeno. On the left, superposition of the backbone atoms of the final 20 structures, the gray part represents the 16 residue insertion that blocks the active site. On the right, a ribbon representation of the

structures with the b-sheet regions in red.

Scientific Report 2013/2014 Department of Biological 70 Physical Chemistry

Interactions of centrosomal proteinsThe centrosome is an organelle that plays a key role in cell division, and whose dysfunction is the origin of many diseases. Our studies have proceeded in two ways. One involves the study of fragments. Human centrosomal proteins are rich in unstructured regions and coiled-coils, and we showed that these features allow favourable transitions between both conformations to facilitate intermolecular complex formation. Studies of the interactions of different fragments of centrosomal proteins using NMR and CD demonstrated that conformational polymorphism modulated by intermolecular contacts is a general property of these proteins.

These results might aid to improve oncologic therapies directed to block cell division, and

hence to decrease proliferation and migration of tumor cells.

Moreover, we participated in a study aimed at understanding the interactions that regulate the dynamic properties of microtubules and their organization during mitosis. We have characterized the molecular interaction between TACC3 and chTOG, key proteins in the formation of the intracellular scaffolding that enables and supports cell division and perpetuation. Using NMR we have identified the key residues crucial for the molecular interaction. These results could help in the improvement of cancer therapies aimed at blocking the processes of cell division, and thereby limit proliferation and expansion of tumor cells.

Scientific Report 2013/2014 Department of Biological 71 Physical Chemistry

Abellón-Ruiz, J., Bernal-Bernal, D., Abellán, M., Fontes, M., Padmanabhan, S., Murillo, F.J. and Elias-Arnanz, M. (2014). The CarD/CarG regulatory complex is required for the action of several members of the large set of Myxococcus xanthus extracytoplasmic function sigma factors. Environ. Microbiol. 16, 2475-2490.

Gallego-García, A., Mirassou, Y., García-Moreno, D., Elias-Arnanz, M., Jiménez, M.A. and Padmanabhan, S. (2014). Structural insights into RNA polymerase recognition and essential function of Myxococcus xanthus CdnL. PLoS One 9, e108946.

García-Linares, S., Richmond, R., García-Mayoral, M.F., Bustamante, N., Bruix, M., Gavilanes, J.G. and Martínez-Del-Pozo, A. (2014). The sea anemone actinoporin (Arg-Gly-Asp) conserved motif is involved in maintaining the competent oligomerization state of these pore-forming toxins. FEBS J. 281, 1465-1478.

García-Mayoral, M.F., Treviño, M.A., Pérez-Pinar, T., Caballero, M.L., Knaute, T., Umpierrez, A., Bruix, M. and Rodríguez-Pérez, R. (2014). Relationships between IgE/IgG4 epitopes, structure and function in Anisakis simplex Ani s 5, a member of the SXP/RAL-2 protein family. PLoS Negl. Trop. Dis. 8, e2735.

Jiménez, M.A. (2014). Design of Monomeric Water-Soluble beta-Hairpin and beta-Sheet Peptides. Methods Mol. Biol. 1216, 15-52.

Mortuza, G.B., Cavazza, T., García-Mayoral, M.F., Hermida, D., Peset, I., Pedrero, J.G., Merino, N., Blanco, F.J., Lyngso, J., Bruix, M., Pedersen, J.S., Vernos, I. and Montoya, G. (2014). XTACC3-XMAP215 association reveals an asymmetric interaction promoting microtubule elongation. Nat. Commun. 5, 5072.

Pantoja-Uceda, D. and Santoro, J. (2014). New 13C-detected experiments for the assignment of intrinsically disordered proteins. J. Biomol. NMR 59, 43-50.

Serrano, S., Araujo, A., Apellaniz, B., Bryson, S., Carravilla, P., de la Arada, I., Huarte, N., Rujas, E., Pai, E.F., Arrondo, J.L., Domene, C., Jiménez, M.A. and Nieva, J.L. (2014). Structure and immunogenicity of a peptide vaccine, including the complete HIV-1 gp41 2F5 epitope: implications for antibody recognition

mechanism and immunogen design. J. Biol. Chem. 289, 6565-6580.

Treviño, M.A., García-Mayoral, M.F., Jiménez, M.A., Bastolla, U. and Bruix, M. (2014). Emergence of structure through protein-protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteins. Biochim. Biophys. Acta. 1844, 1808-1819.

Aguado-Llera, D., Hamidi, T., Domenech, R., Pantoja-Uceda, D., Gironella, M., Santoro, J., Velázquez-Campoy, A., Neira, J.L. and Iovanna, J.L. (2013). Deciphering the binding between Nupr1 and MSL1 and their DNA-repairing activity. PLoS One 8, e78101.

Ardá, A., Blasco, P., Varon Silva, D., Schubert, V., Andre, S., Bruix, M., Canada, F.J., Gabius, H.J., Unverzagt, C. and Jiménez-Barbero, J. (2013). Molecular recognition of complex-type biantennary N-glycans by protein receptors: a three-dimensional view on epitope selection by NMR. J. Am. Chem. Soc. 135, 2667-2675.

Bermel, W., Bruix, M., Felli, I.C., Kumar, M.V.V., Pierattelli, R. and Serrano, S. (2013). Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins. J. Biomol. NMR 55, 231-237.

Callís, M., Serrano, S., Benito, A., Laurents, D.V., Vilanova, M., Bruix, M. and Ribó, M. (2013). Towards tricking a pathogen’s protease into fighting infection: the 3D structure of a stable circularly permuted onconase variant cleavedby HIV-1 protease. PLoS One 8, e54568.

Diez, A.I., Ortiz-Guerrero, J.M., Ortega, A., Elias-Arnanz, M., Padmanabhan, S. and de la Torre, J.G. (2013). Analytical ultracentrifugation studies of oligomerization and DNA-binding of TtCarH, a Thermus thermophilus coenzyme B12-based photosensory regulator. Eur. Biophys. J. 42, 463-476.

Diez-García, F., Pantoja-Uceda, D., Jiménez, M.A., Chakrabartty, A. and Laurents, D.V. (2013). Structure of a simplified beta-hairpin and its ATP complex. Arch. Biochem. Biophys. 537, 62-71.

Dos Santos, H.G., Abia, D., Janowski, R., Mortuza, G., Bertero, M.G., Boutin, M., Guarin, N., Méndez-Giráldez, R., Nuñez, A., Pedrero, J.G., Redondo, P., Sanz, M., Speroni, S., Teichert, F., Bruix, M., Carazo, J.M., González, C., Reina, J., Valpuesta, J.M., Vernos, I.,

Publications

Scientific Report 2013/2014 Department of Biological 72 Physical Chemistry

Zabala, J.C., Montoya, G., Coll, M., Bastolla, U. and Serrano, L. (2013). Structure and non-structure of centrosomal proteins. PLoS One 8, e62633.

García-Aranda, M.I., González-López, S., Santiveri, C.M., Gagey-Eilstein, N., Reille-Seroussi, M., Martín-Martinez, M., Inguimbert, N., Vidal, M., García-López, M.T., Jiménez, M.A., González-Muñiz, R. and Pérez de Vega, M.J. (2013). Helical peptides from VEGF and Vammin hotspots for modulating the VEGF-VEGFR interaction. Org. Biomol. Chem. 11, 1896-1905.

García-Heras, F., Abellón-Ruiz, J., Murillo, F.J., Padmanabhan, S. and Elias-Arnanz, M. (2013). High-mobility-group a-like CarD binds to a DNA site optimized for affinity and position and to RNA polymerase to regulate a light-inducible promoter in Myxococcus xanthus. J. Bacteriol. 195, 378-388.

García-Linares, S., Castrillo, I., Bruix, M., Menéndez, M., Alegre-Cebollada, J., Martínez-del-Pozo, A. and Gavilanes, J.G. (2013). Three-dimensional structure of the actinoporin sticholysin I. Influence of long-distance effects on protein function. Arch. Biochem. Biophys. 532, 39-45.

García-Mayoral, M.F., Canales, A., Díaz, D., López-Prados, J., Moussaoui, M., de Paz, J.L., Angulo, J., Nieto, P.M., Jiménez-Barbero, J., Boix, E. and Bruix, M. (2013). Insights into the glycosaminoglycan-mediated cytotoxic mechanism of eosinophil cationic protein revealed by NMR. ACS Chem. Biol. 8, 144-151.

Martínez-Lumbreras, S., Santiveri, C.M., Mirassou, Y., Zorrilla, S. and Pérez-Cañadillas, J.M. (2013). Two singular types of CCCH tandem zinc finger in Nab2p contribute to polyadenosine RNA recognition. Structure 21, 1800-1811.

Mirassou, Y., Elias-Arnanz, M., Padmanabhan, S. and Jiménez, M.A. (2013). (1)H, (13)C and (15)N assignments of CdnL, an essential protein in Myxococcus xanthus. Biomol. NMR Assign. 7, 51-55.

Morais, M., Oliveira, B.L., Correia, J.D., Oliveira, M.C., Jiménez, M.A., Santos, I. and Raposinho, P.D. (2013). Influence of the bifunctional chelator on the pharmacokinetic properties of 99mTc(CO)3-labeled cyclic alpha-melanocyte stimulating hormone analog. J. Med. Chem. 56, 1961-1973.

Pantoja-Uceda, D. and Santoro, J. (2013). Direct correlation of consecutive C’-N groups in proteins: a method for the assignment of intrinsically disordered proteins. J. Biomol. NMR 57, 57-63.

Pantoja-Uceda, D. and Santoro, J. (2013). A suite of amino acid residue type classification pulse sequences for 13C-detected NMR of proteins. J. Magn. Reson. 234, 190-196.

San Sebastián, E., Zimmerman, T., Zubia, A., Vara, Y., Martin, E., Sirockin, F., Dejaegere, A., Stote, R.H., López, X., Pantoja-Uceda, D., Valcárcel, M., Mendoza, L., Vidal-Vanaclocha, F., Cossio, F.P. and Blanco, F.J. (2013). Design, synthesis, and functional evaluation of leukocyte function associated antigen-1 antagonists in early and late stages of cancer development. J. Med. Chem. 56, 735-747.

Santiveri, C.M., García-Mayoral, M.F., Pérez-Cañadillas, J.M. and Jiménez, M.A. (2013). NMR structure note: PHD domain from death inducer obliterator protein and its interaction with H3K4me3. J. Biomol. NMR 56, 183-190.

Serrano, S., Callís, M., Vilanova, M., Benito, A., Laurents, D.V., Ribó, M. and Bruix, M. (2013). (1)H, (13)C and (15)N resonance assignments of the Onconase FL-G zymogen. Biomol. NMR Assign. 7, 13-15.

Scientific Report 2013/2014 Department of Biological 73 Physical Chemistry

COMPETITIVE FUNDING

Principal Investigator Title Reference

M.A. Jiménez Bases estructurales del reconocimiento entre CTQ2011-22514 biomoléculas mediante RMN: proteínas y lípidos

M. Bruix Red temática de estructura y función de proteínas BFU2011-15733-E

J.M. Pérez Cañadillas Papel de las interacciones proteína-proteína y CTQ2011-26665 proteina-RNA en la composición y dinámica De ribonucleoproteínas (RNPs)

Principal Investigator Title Reference

M.A. Jiménez Interactómica del centrosoma S2010/BMD-2305

Principal Investigator Title Reference

S. Padmanabhan Iyer The light response regulatory network and BFU2012-40184-CO2-02 connections to other regulatory networks in the bacterium Myxococcus xanthus: structural analyses

Ministerio de Economía y Competitividad

Comunidad de Madrid

Ministerio de Economía y Competitividad

National Grants: individual

National Grants: coordinated

Scientific Report 2013/2014 Department of Biological 74 Physical Chemistry

Bioconformatics and Assemblies Group

Tenured Staff scientists

María Gasset Vega (Associate Professor) ReID ORCID SCOPUS

Doctoral students

Javier Martínez Férnandez (until 31/08/2014)

Technical Staff

Silvia Lisa Ferrer

Rosa Sánchez Hereros (until 31/12/2013 and 15/03/2014-15/12/2014)

Scientific Report 2013/2014 Department of Biological 75 Physical Chemistry

SummaryWe aim to decipher the basic elements forming the protein conformational disease language and exploit them for therapeutic and biotechnological purposes. For such purpose we use molecular biology, cellular biology and

biophysical approaches and collaborate with the groups of Prof. A. Aguzzi (UZ, Switzerland), Ilia V. Baskakov (UM,USA), and V. Muñoz (IMDEA-CNB).

Strategic Aims• To determine the celular basis of the cytotoxicity of intracelular protein aggregates relevant

to neurodegenerative disorders (CtmPrP).

• To unveil the basis of PrP amyloid polymorphism and its relation to self-propagation.

• To generalize amiloidogenesis to other pathogens following oral route exposition.

Scientific Report 2013/2014 Department of Biological 76 Physical Chemistry

ResultsTo determine the celular basis of the cytotoxicity of intracelular protein aggregates relevant to neurodegenerative disorders (CtmPrP)Cellular expression of PrP artificial mutants

forming intracellular CtmPrP accumulative forms occurs with enhanced ER stress markers and high cell death. Using several modulators of intracellular redox has permitted the finding of PDI activity levels as key element for aggregates cytotoxicity (Figure 1).

Figure 1.BMC, a small molecule with PDI-like activity, abrogates CtmPrP cytotoxicity.

Scientific Report 2013/2014 Department of Biological 77 Physical Chemistry

To unveil the basis of PrP amyloid polymorphism and its relation to self-propagationThe structure and sequence of PrP β2-α2 loop dictates its conversion propensity and interspecies prion transmission. Using rHaPrP (23-231) with NN (wt, rigid loop), SN (Mo-like flexible loop) and NT (elk-like hyper rigid loop) in 170 y 174 sequence positions we have characterized the α-fold stability, fibril formation and the amyloid state. The obtained results support the hypothesis that the β2-α2 regulatory elements function through the amyloid state (Figure 2).

To generalize amiloidogenesis to other pathogens following oral route expositionBy virtue of the large environmental changes taking place during food digestion we have addressed the role of amyloid formation on the allergenic activity of type-I food allergens. Using as model Gad m1 (cod β-parvalbumin) and a sequence analysis searching for adhesive hexapeptides, a conformational characterization under gastro-intestinal conditions and the allergenicity evaluation we have found that IgE-binding activity is the amyloid assembly (Figure 3).

Figure 2. POM!-inmunoflurescence of amyloid fibrils formed by PrP NN, SN and NT chains.

Figure 3. the architecture of the IgE epitope on rGad m1 is its amyloid fibril.

Scientific Report 2013/2014 Department of Biological 78 Physical Chemistry

COMPETITIVE FUNDING

Principal Investigator Title Reference

M. Gasset Role of methionine redox cycle on protein BFU2009-07571 conformational diseases

M. Gasset PrPC processing as a risk factor for FCIEN Aβ-oligomer toxicity

M. Gasset SDS-resistant aggregates Raman Health

Ministerio de Ciencia e Innovación (MICINN)

National Grants: individual

Scientific Report 2013/2014 Department of Biological 79 Physical Chemistry

Structural Bioinformatics Group

Tenured Staff scientists

Pablo Chacón Montes (Assistant Professor) ReID ORCID SCOPUS

Non-tenured scientists

José Ramón López Blanco SCOPUS

Doctoral students

Erney Ramírez

Scientific Report 2013/2014 Department of Biological 80 Physical Chemistry

SummaryThe Structural Bioinformatics Group (http://chaconlab.org) is focused on developing innovative techniques for the modeling, analysis and simulation of molecular structures in close contact with experimental labs. We are particularly interested in large macromolecules of dynamic composition and conformation whose actions and interactions are essential for cellular function. To better understand such systems, we work on new bioinformatics tools for bridging the resolution gap between atomic structures with low to medium resolution experimental data from different biophysical techniques (e.g. X-ray crystallography, Electron microscopy, SAXS, etc). Our research lines include efforts

to deal with the analysis and prediction of molecular flexibility. We actively work to effectively address the study and simulation of the dynamics of large biomolecular systems with Normal-Mode Analysis (NMA), geometric algebra and other multiscale approximations. We also expand our interest to understand and forecast protein-protein and protein-ligand molecular interactions. Our group employs and develops computer-based methodologies (e.g. virtual screening) to aid the rational design of new compounds. The developed methodologies are available via software distributions and web servers.

Strategic Aims• Bridging the resolution gap with hybrid methods. We develop new hybrid methods for

combining multiresolution structural information in collaboration with several experimental labs.

• Multiscale dynamics of macromolecular biomachines. We address the study and simulation of the dynamics of large biomolecular systems with NMA and other multiscale approximations.

• Atomistic molecular simulations. Our group employs MD simulation methods to examine a variety of biological phenomena including protein interactions and macromolecular flexibility.

• Protein modeling. We develop tools for modeling protein structures and their interactions. This includes novel methods for protein-protein docking and loop modeling problems.

• Exploring new strategies for structure-based rational design. Our group employs and develops computer-based methodologies for drug discovery.

Scientific Report 2013/2014 Department of Biological 81 Physical Chemistry

ResultsHybrid methodsAdvances in modern biology and medicine depend on the understanding of the actions and interactions of large biomolecular complexes. The structural characterization of such macromolecules can be only tackled with coordinated application of complementary biophysical approaches. Computational hybrid methods bridge the gap between such experimental techniques (Lopez-Blanco et al. 2015). Fitting is the standard way of interpreting the information contained in electron-microscopy (EM) maps of macromolecular structures by means of the available atomic structural components. This is a complicated jigsaw puzzle in which the low-resolution 3D EM density map of a macromolecule complex

acts as a fuzzy frame to guide the assemblage of interlocking atomic-resolution pieces. When complete, this puzzle allows to characterize at near-atomic-detail different functional states of the macromolecules in solution, and hence to a better understanding of the inner workings of the central actors in the principal cellular processes. We develop several approaches to try to solve this puzzle. For example, we recent developed IMODFIT (Lopez-Blanco et al. 2013) a flexible fitting tool based on NMA in internal coordinates (see Figure 1). This and another hybrid tools developed by us permitted the characterization of intricate helix bundle that dictates the assembly of the 26S proteasome lid (Estrin et al. 2013).

Figure 1. Flexible fitting of the experimental map of thermosome. The initial pose was obtained by rigid body fitting between the initial open atomic structure (cyan, PDB 1A6D)

and the corresponding closed experimental EM map (transparent surface, EMDB 1396) using ADP_EM (). The final flexible fitted model based in a new approach using NMA in internal

coordinates is represented with a yellow ribbon.

Scientific Report 2013/2014 Department of Biological 82 Physical Chemistry

Multiscale simulationsStructural flexibility of biomolecules is closely coupled to function, as evidenced by many conformational changes observed on key cellular process. Following the basic principle if you know how it moves, you can infer how it works; the knowledge of structural flexibility offers a straight-line connection between structure and function. Thus, inferring the intrinsic molecular flexibility from a single conformation could offer a direct link to understand likely large scale rearrangements. We are addressing this problem by simulation of the dynamics of biomolecular

systems with Normal-Mode Analysis (NMA) (Lopez-Blanco et al. 2014a), geometric algebra and other multiscale approximations. For example, iMOD is a versatile toolkit to perform NMA in internal coordinates (torsional space) on both protein and nucleic acid atomic structures (Lopez-Blanco et al. 2011). Our server, iMODS (http://imods.chaconlab.org) facilitates the exploration of such collective motions in internal coordinates. Moreover, we developed computational tools to extent NMA towards very large systems (see Figure 2 and Lopez-Blanco et al. 2013b).

Figure 2. Illustrative actin filament bending motions calculated using, IMOD, our NMA in internal coordinates approach. The first three bending modes computed from the straight

experimental structure are shown.

Scientific Report 2013/2014 Department of Biological 83 Physical Chemistry

Protein modelingWe develop tools for modeling protein structures and their interactions. Predict how two (or more) proteins can interact from its individual unbound components can reveal new insights in the basic principles of molecular recognition and hence in the key process on cellular functioning. Moreover, the better understanding of protein-protein interactions can be useful for structure-based drug design and other applications. Our research interests include the development of tools to address this otherwise high demanding computational problem. Our first approximation, FRODOCK, is focused on an initial stage exhaustive docking (Garzón et al. 2007, see also http://frodock.chaconlab.org). This stage generates many potential predictions which will be then assessed in a second refinement stage or scoring step that we are currently developing. We are also exploring new interacting potentials

(Krüge et al. 2013) as well as developing new algorithms for protein-ligand docking using GPUs (García et al. 2014).

We have validated the use of geometric algebra (GA) in modeling macromolecular flexibility. We have created a complete GA framework based in a backward recursive approximation using spinors (Chys & Chacon 2012) for efficient chain manipulation. We are working now in the effective incorporation of such GA tools in our multiscale simulation approaches. We also explored inverse kinematics problems, such as local deformation and loop closure using GA principles. Random Coordinate Descent (RCD) is a versatile loop closure tool to generate efficiently loop ensembles. The algorithm solves loop closure by optimizing randomly selected bonds and updating loop conformations by spinor-matrices (see Figure 3, Chys & Chacon 2013 and check http://rcd.chaconlab.org ).

Figure 3. RCD loop closure solution of the protein test loop 1i0h.pdb (8-peptide, 145–152) with (red) and without (green) geometric filters. The inclusion of grid filters improves the

sampling towards more feasible and clash-free solutions.

Scientific Report 2013/2014 Department of Biological 84 Physical Chemistry

Structure-based drug discovery and design Structure-based drug design and protein ligand docking are effective and low cost strategies for drug discovery. Our group employs and develops computer-based methodologies to aid the structure rational design of new active compounds. As developers, we are particular interested in virtual screening (VS) in where the most interesting and promising ligand molecules are computationally selected from very large libraries of compounds. Our research lines include the development of fast VS approximations on GPUs. As users, we are actively collaborating in multidisciplinary drug discovery projects using the state of the art bioinformatics tools. We already have an ongoing successful collaboration in the rational drug design of the antibiotic target FtsZ (Schaffner-Barbero et al. 2012). In this context, we already identify new hits that we are currently optimizing (Artola et al. 2015, Ruiz-Avila 2013).

Atomistic molecular simulations Our group employs MD simulation methods to examine a variety of biological phenomena

including protein interactions and macromolecular flexibility. Very recently, we report a state of the art study of the FtsZ filament dynamics interpreted in the context of the assembly cycle of this essential cell division protein (Aportela et al. 2014). In contrast with all previous studies based on the inactive (not functional) closed-cleft FtsZ conformation studies, our large scale simulations studies disclose different filament curvatures supported by nucleotide-regulated interfacial dynamics. Moreover, we have monitored, for the first time, the relaxation from the active polymer conformation to the inactive conformation of FtsZ monomers by closing the cleft between the C-terminal domain and helix H7. In agreement with experimental data, these groundbreaking results unravel the natural mechanism of the FtsZ assembly switch. Integrating this assembly switch and the nucleotide-dependent interfacial filament stability, our work offers a detailed molecular interpretation of the assembly-disassembly FtsZ cycle and its inhibition. Recently an in-house collaboration, we also helped to interpret the selective recognition of microbial polysaccharides by macrophage receptor SIGN-R1 (Silva-Martín et al. 2014) using MD techniques.

Figure 4. Molecular model of compound 28 recognition by the FtsZ nucleotide binding site.

Scientific Report 2013/2014 Department of Biological 85 Physical Chemistry

Ramírez-Aportela E., López-Blanco J.R., Andreu J.M., and Chacón P. (2014). Understanding Nucleotide-Regulated FtsZ Filament Dynamics and the Monomer Assembly Switch with Large-Scale Atomistic Simulations. Biophys. J. 107, 2164–2176.

Silva-Martín N., Bartual S.G., Ramírez-Aportela E., Chacón P., Park C.G., and Hermoso J.A. (2014). Structural Basis for Selective Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor SIGN-R1. Structure 22, 1595–1606.

López-Blanco J.R., Miyashita O., Tama F. and Chacón P. (2014a) Normal mode analysis in structural biology (version 2.0). In: eLS. John Wiley and Sons, Ltd: Chichester.

López-Blanco J.R., Aliaga J., Quintana-Ortí E. and Chacón P. (2014b) iMODS: Internal Coordinates Normal Mode Analysis Server. Nucleic Acids Res. 42, W271-276

Krüger D.M., Garzón J.I., P. Chacon and H. Gohlke (2014) DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking. Plos One, 9(2):e89466

López-Blanco J.R. and Chacón P. (2013). iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates. J. Struct. Biol. 184, 261–270

Ruiz-Avila L., Huecas S., Artola M., Vergoñós A., Ramírez-Aportela E., Cercenado E., Barasoain I., Vazquez-Villa H., Martin-Fontecha M., Chacon P., Lopez-Rodriguez M.L. and Andreu JM (2013). Synthetic inhibitors of bacterial cell division targeting the GTP binding site of FtsZ. ACS Chem. Biol. 8, 2072-2083

Estrin E., J.R. López-Blanco, P. Chacón, A. Martin. (2013). Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid. Structure, 21, 1624–1635

López-Blanco J.R., R. Reyes, J.I. Aliaga, R.M Badia, P. Chacón, E.S. Quintana-Ortí (2013) Exploring Large Macromolecular Functional Motions on Clusters of Multicore Processors. J. Comp. 246, 275–288.

Chys P. and P. Chacón (2013). Random coordinate descent with spinor-matrices and geometric filters for efficient loop closure. J. Chem. Theory Comput. 9, 1821–1829

Publications

Scientific Report 2013/2014 Department of Biological 86 Physical Chemistry

COMPETITIVE FUNDING

Principal Investigator Title Reference

P. Chacón Enhancing Macromolecular Sampling BFU2013-44306P for Integrative Structural biology

Principal Investigator Title Reference

M. L. Rodríguez Discover and Validation of therapeutic targets: CM S2010/BMD-2353 development of the MHIT Platform.

Ministerio de Economía y Competitividad

Comunidad de Madrid

National Grants: individual

National Grants: coordinated

Scientific Report 2013/2014 Department of Biological 87 Physical Chemistry

Fluorescence and Molecular Biophysics Group

Tenured Staff scientists

Mª Pilar Lillo Villalobos (Assistant Professor) ReID ORCID SCOPUS

A. Ulises Acuña Férnandez (Professor Ad honorem)

Doctoral students

Sebastian Raja (until 08/10/2013)

Technical Staff

Carolina García Rodríguez (TSE) ReID ORCID SCOPUS

Scientific Report 2013/2014 Department of Biological 88 Physical Chemistry

SummaryThe overall objective of the Group is to understand how biological systems work under physiological conditions. With this aim we develop and implement both theoretical and experimental methods based on ps-resolved fluorescence spectroscopy and two-photon laser excitation microscopy, to provide the required temporal

(ps-s) and spatial (subµm- nm) resolution.

The applications include biomolecular conformational dynamics, organization and interactions of multiprotein complexes, and lipid microdomains distribution, in vitro, in living cells, and tissues.

Strategic Aims• Mechanism of action of bioactive compounds: Quantitative characterization of drug-target

interactions in the cell membrane and inside the cell.

• Detection, identification, localization and quantification of in vivo cell markers.

• Detection of lipid micro-domains in model membrane systems and living cells, induced by bioactive compounds.

• 3-D organization, conformational dynamics and stoichiometry of multicomponent complexes.

• Spectroscopic characterization of fluorescent materials for biotechnological applications.

• Fundamental Photophysics. Design, synthesis, characterization and applications of emitting molecular probes and fluorescent drugs.

Scientific Report 2013/2014 Department of Biological 89 Physical Chemistry

ResultsIdentification of antitumour drug targets at the plasma membrane and inside the cell. PharmaMar R & D ContractCharacterization of Aplidin® interactions in living cells.

Using fluorescence lifetime imaging (FLIM) and phasor analysis (FLIM-phasor), we have found three important molecular species in the mechanism of action of the antitumor compound Aplidin®, which are located in the plasma membrane (species A), in the inner leaf and/or very close to the plasma membrane regions (species B), and in the cytoplasm (species C) of sensitive (HeLa wt) and resistant (HeLa AplR) cells treated with the fluorescent analogue of Aplidin®, Apl-dmac (Figure 1).

We have detected complexes Apl-dmac/eEF1A1-EGFP and Apl-dmac/ eEF1A2-EGFP in the plasma membrane and inside the cell, using fluorescence lifetime imaging, Förster resonance energy transfer methods (FLIM-FRET), HeLa wt and HeLa AplR cells expressing the elongation factor labeled with the fluorescent protein eEGFP (eEF1A1-EGFP or eEF1A2-EGFP). The location and distribution of these complexes follow the same pattern as species B and C.

We have detected Apl-dmac/eEF1A-EGFP complexes in the plasma membrane, and close to the inner leaf of the plasma membrane at short times of interaction. At longer times these complexes are distributed all over the cytoplasm, accumulating in well-defined regions. These results support the importance of the elongation factor as a relevant target in the action mechanism of Aplidin®.

Figura 1. Identification of different molecular species of Aplidin® interacting with living cells, using the FLIM-phasor approach. At short times, species A (Orange) is located in the

plasma membrane. Green, Light Blue and Dark Blue represent species C, indicating increasing concentrations with time. λexc=750 nm (82MHz); λem=520/35 nm; T=37ºC.

Scientific Report 2013/2014 Department of Biological 90 Physical Chemistry

3D organization, dynamics and stoichiometries in homo- and hetero-associations. Collaboration Dr. A.Felipe (Univ. Barcelona)Kv1.3 is a tetrameric protein which forms a membrane channel leading K+ ions through the cell membrane, in response to changes in the membrane voltage. It has recently been proposed that Kv1.3 interacts with the regulatory protein KCNE4 with unknown stoichiometry.

We have studied the homo-association of Kv1.3 and its interaction with the regulatory protein KCNE4 using homo- FRET/ fluorescence anisotropy images, FRET and FLIM-FRET, combined with FLIM-phasor analysis in HEK293

living cells, expressing the fluorescent proteins EGFP, mApple and mCherry tagged to Kv1.3 and KCNE4.

Figure 2 shows FLIM and fluorescence anisotropy images of a representative HEK293 cell and a membrane region detail. An increase in the fluorescence anisotropy is observed when the cell is expressing a mixture of Kv1.3-EGFP and unlabeled Kv1.3, due to a decrease in homo-FRET because of the presence of unlabeled Kv1.3 in the Kv1.3 tetramers.

Using the [Kv1.3-EGFP]4 complex as homo-FRET and hetero-FRET controls, we have characterized the organization and stoichiometry of [Kv1.3]-[KCNE4] complexes in the cell membrane.

Figure 2. Fluorescence lifetime (<t>; FLIM) and fluorescence anisotropy (r) images of a representative HEK293 cell, expressing Kv1.3-EGFP or a mixture of Kv1.3-EGFP and Kv1.3.

λexc=850 nm (82MHz); λem=520/35 nm; T=37ºC.

Scientific Report 2013/2014 Department of Biological 91 Physical Chemistry

Detection of micro-domains and dynamic organization of lipids in the plasma membrane

The presence of ordered and disordered lipid micro-domains in the plasma membrane of HeLa cells was quantified using fluorescence anisotropy images and lipophilic fluorescent probes. The method used is based on the effects of changes in the composition/lipid organization

on the rotational mobility of the fluorescent probes inserted in the cell membranes. These studies are complemented by generalized polarization images (GP) of fluorescent probes as Laurdan with photophysical properties sensitive to the order and membrane fluidity.

Figure 3 shows how the average lipid order of the plasma membrane decreases with time, in a membrane detail of a HeLa cell treated with an antitumor compound.

Figure 3. Plasma membrane detail of a representative HeLa cell, treated with an antitumor compound, and labeled with the fluorescent probe TMA-DPH. Time variation of the lipid order

(0-1 min-max scale). λexc=750 nm (82MHz); λem=483/32 nm; T=37ºC.

Scientific Report 2013/2014 Department of Biological 92 Physical Chemistry

Fundamental photophysicsThe first quantum model of the Triplet-Triplet, diffusion-controlled energy transfer process, in liquid solution, was completed in this period (Zapata et al. 2014, J. Chem. Phys.), in collaboration with Drs. O. Castaño, J.M. Frutos and coworkers, from the Dept. of Physical Chemistry of Alcalá University. Since the reaction coordinate was defined as a function of the energy and conformation of the intervening electronic excited-states, it is now possible to predict the transfer efficiency of this process from spectroscopic information of the exchange partners.

In collaboration with the same group, we carried out a detailed ab initio computational study of energies and conformation of singlet and triplet states of fluorescent compounds, synthesized in our laboratories, which present a binary effect (0-1) on the fluorescence emission as a function of pH (Acuña et al. 2013, Phys.Chem.Chem.Phys.). Vertical excitation energies, computed by TD-DFT using the HSE06 functional and 6-311++G(d,p) basis set, and solvent effects, simulated with PCM approach, provided a robust model of the mechanism underlying this surprising quenching effect.

Finally, we collaborated with members of the IUPAC Photochemistry Group to produce a

document (Ameloot et al. 2013, Pure Appl. Chem.) recommending practices and reference materials to improve the accuracy of stationary and time-dependent fluorescence anisotropy measurements in solution.

Design, synthesis, characterization and applications of emitting molecular probes and fluorescent drugsIn this period novel fluorogenic reactions were discovered and optimized, directed to the fluorescent labelling of important neurochemicals as dopamine and DOPA. As a side-result of this investigation, similar fluorogenic labelling reactions were found applicable to antioxidants as hydroxytirosol and salvianic acid, which give rise to 100% fluorescent products.

In addition, we completed the study of key biophysical properties in a membrane environment of several fluorescent lipid drugs (alkyl-phosphocholines and lyso-phosphatidylcholines) synthesized in our laboratories. These compounds were also applied in this period to the search of therapeutic targets of the parent drug, to understand the antitumor or antiparasite activity mechanism at a molecular level.

Scientific Report 2013/2014 Department of Biological 93 Physical Chemistry

Martínez-Tong, D.E., Soccio, M., Sanz, A., García, C., Ezquerra, T.A., Nogales, A. (2013) Chain arrangement and glass transition temperature variations in polymer nanoparticles under 3D-confinement. Macromolecules 46, 4698-4705.

Acuña, A.U., Álvarez-Pérez, M., Liras, M., Coto P.B., Amat-Guerri, F. (2013). Synthesis and photophysics of novel biocompatible fluorescent oxocines and azocines in aqueous solution. Phys. Chem. Chem. Phys. 15, 16704-16712.

Castro, B.M., Fedorov, A., Hornillos, V., Delgado, J., Acuña, A.U., Mollinedo, F., Prieto. M. (2013). Edelfosine and miltefosine effects on lipid raft properties: Membrane biophysics in cell death by anti-tumor lipids. J. Phys. Chem. B 117, 7929-7940.

Cuesta-Marbán, A., Botet, J., Czyz, O., Cacharro, L. M., Gajate, C., Bitew, T., Hornillos, V., Delgado, J., Zhang, H., de la Iglesia-Vicente, J., Amat-Guerri, F., Acuña, A.U. McMaster, C.R., Revuelta, J.L., Zaremberg, V., Mollinedo, F. (2013). Drug uptake, lipid rafts and vesicle trafficking modulate resistance to an anticancer lysophosphatidylcholine analogue in yeast. J. Biol. Chem. 288, 8405-8418.

Ameloot, M., vande Ven, M., Acuña A.U., Valeur, B. (2013). Fluorescence anisotropy measurements: methods and reference materials. Pure Appl. Chem. 85, 589-608.

Acuña, A.U., Santiuste, J.M. (2013). M. J. Molera: cinética, fotoquímica y cromatografía en la España de 1940-1980. An. Quim. 109, 31-33.

Martínez-Tong, D.E., Cui, J., Soccio, M., García, C., Ezquerra, T.A., Nogales, A. (2014) Does the glass transition of polymers change upon 3D-confinement? Macromol. Chem. Phys. 215, 1620-1624.

Zapata, F., Maruzzi, M., Castaño, O., Acuña, A.U., Frutos, L.M. (2014). Definition and quantification of the Triplet-Triplet energy transfer reaction coordinate. J. Chem. Phys. 140, 34102-3411.

de la Torre, B.G. , Hornillos, V., Luque-Ortega, J.R. , Abengózar, M., Amat-Guerri, F., Acuña, A.U., Rivas , L., Andreu, D. (2014) A BODIPY-embedding miltefosine analogue linked to cell-penetrating Tat(48-60) peptide favors intracellular delivery and visualization of the antiparasitic drug. Amino Acids 46, 1047-1058.

Publications

Scientific Report 2013/2014 Department of Biological 94 Physical Chemistry

COMPETITIVE FUNDING

Principal Investigator Title Reference

M.P. Lillo Dinámica e Interacciones de Biomoléculas CTQ-2010-16457 mediante Espectroscopía de Fluorescencia Polarizada con resolución espacial

Principal Investigator Title Reference

M. P. Lillo Estudio de las interacciones de Aplidina e Irvalec 020101130001 con la membrana celular MTA: OTT20100279

Principal Investigator Title Reference

A.U. Acuña, (S. Marcos, I.P.) Implante de lentes intraoculares mediante FIS2013-49544- técnicas de “photobonding” EXPLORA

Ministerio de Ciencia e Innovación (MICINN)

R&D Contract CSIC-PharmaMar S.A.

Ministerio de Economía y Competitividad

National Grants: individual

Contracts and Agreements with Companies

Scientific Report 2013/2014 Department of Biological 95 Physical Chemistry

Protein Structure and Thermodynamic Group

Tenured Staff scientists

Margarita Menéndez Fernández (Associate Professor) ReID ORCID SCOPUS

Mª Dolores Solís Sánchez (Associate Professor) ReID ORCID SCOPUS

Non-tenured scientists

Mónica Álvarez Pérez ReID ORCID SCOPUS

Noemí Bustamante Spuch

Mª Asunción Campanero Rhodes (until 5/01/2014) ReID ORCID SCOPUS

Manuel Alberto Iglesias Bexiga

Begoña Morales Juanós (from 11/02/2013)

Doctoral students

Radoslaw Borowski (from 1/09/2013)

Cristina Gallego Páramo

Lara López Merino (until 31/10/2013)

Ioanna Kalograiaki

Palma Rico Lastres

Guadalupe García Medina (until 30/06/2014)

Technical Staff

Mª Victoria López Moyano

Scientific Report 2013/2014 Department of Biological 96 Physical Chemistry

SummaryKnowledge of the structure and energetics of proteins in solution provides information on the nature of forces governing structural stability or ligand recognition, among other properties. This information is particularly relevant for proteins of biomedical or technological interest, since it facilitates a rational design of ligands (drugs, vaccines, etc.), or the stabilization of proteins themselves. In our group we have recently

studied, among other systems, different lectins, pneumococcal cell wall hydrolases and other proteins of biomedical interest. In addition, we investigate the recognition of carbohydrates and other compounds by these and other proteins, with the final aim of elucidating their role in numerous processes of biomedical relevance and developing new diagnostic and/or therapeutic strategies.

Strategic Aims• Systematic characterization of the structural organization, stability and specificity in ligand

recognition of galectins and other human lectins.

• Unravelling of the structural and energetic basis for substrate recognition of pneumococcal cell wall hydrolases. Search of inhibitors and design of new optimized enzymes with antimicrobial activity.

• Development of novel designer microarrays.

Scientific Report 2013/2014 Department of Biological 97 Physical Chemistry

ResultsStudy of structure-function relationships in galectinsGalectins are a family of endogenous lectins that recognize β-galactosides in cellular glycoconjugates and translate glycan signals into cellular responses. They play important roles in immune and inflammatory responses, cancer and other biomedically relevant processes. Characterization of the structure/function relationships of galectins is a fundamental step for a rational design of new diagnostic and therapeutic strategies.

Galectins are divided into three structural subgroups. Proto-type galectins contain one or two (homodimeric) identical carbohydrate-recognition domains (CRD). The chimera-type galectin-3 consists in one CRD linked to a non-lectin N-terminal region composed of collagen-like repeats and an N-terminal peptide. Finally, tandem-repeat-type galectins contain two different CRDs covalently connected by a linker peptide. In collaboration with Prof. H-J Gabius (Ludwig-Maximilians-Universität), we have studied the structural organization, stability and binding properties of human galectins (hGal) of the three subtypes.

Full-length hGal-3, eight trimmed variants produced by removal of collagen-like repeats (with/without the N-terminal stretch) and the isolated CRD have been characterized to define the structural and functional significance of the N-terminal region. Their secondary and tertiary structure has been investigated by circular dichroism (CD), showing similar features for all the variants and comparable lactose-induced changes. However, a general tendency for an increase in thermal stability with progressive trimming has been observed. In addition, dimerization is observed for some variants in the absence of a ligand, whereas all the proteins behave as monomers in the presence of lactose. Precipitation studies with the glycoprotein asialofetuin (ASF), a multivalent ligand for galectins, have also revealed differences in the crosslinking behaviour of the variants, in general precipitation increasing with protein length, evidencing that the presence of the N-terminal region influences the ligand binding avidity of the protein.

Similar studies have been carried out with the tandem-repeat type hGal-4 and a variant with shortened linker, hGal-4V. We have found that hGal-4, but not hGal-4V, dimerize under non-reducing conditions. Analysis of the three

possible C/S hGal-4 mutants has demonstrated linker-mediated dimerization via intermolecular disulphide bridging, and precipitation assays in the presence of ASF confirmed a significant increase in crosslinking activity upon dimerization.

Two different conformations have been detected for homodimeric prototype hGal-7, due to a trans/cis conformational switch of a proline residue. Using size-exclusion chromatography, CD-based assays and ITC, the impact of this duality on protein features and ligand binding has been examined. Of note, abrogation of trans/cis isomerization by Pro to Leu mutation results in a higher thermal stability of the protein. These results open the discussion on the functional relevance of hGal-7 conformational duality.

Studies on other galactose-specific binding proteinsWe have studied the structural organization and stability of the human macrophage Gal-specific lectin (hMGL), a type-II transmembrane protein formed by a cytoplasmic domain, a transmembrane region, and an extracellular domain (ECD) consisting of a neck fragment and a C-type (i.e. Ca+2-dependent) CRD specific for Gal/GalNAc. HMGL is a key receptor for the Tn carcinoma associated antigen. Clustering of carbohydrate-binding sites in this and other C-type receptors is crucial to increase binding avidity and to ensure efficient recognition of simple epitopes. We have found that the ECD of the isoform 1 of hMGL exhibits an outstanding oligomerization capacity, neck-mediated disulphide-bridging playing a key role in the formation of high-order multimers. CD studies are consistent with a coiled coil structure for the neck and reveal that the aromatic residues in the vicinity of the high-affinity Ca+2-binding sites within the CRD are unequivocal spectroscopic markers of Ca+2 binding at these sites. In addition, CD-based thermal denaturation experiments have confirmed that both ECD and CRD exhibit the same binding preferences, GalNAc inducing the largest increase in stability. Altogether the results indicate that the ECD is a well-structured and functional sugar-binding protein that forms high-order multimeric assemblies, with important functional implications.

The non-human Gal-α-(1-3)-Gal disaccharide epitope (or glycotope) is directly involved in the hyperacute rejection (HAR) of porcine organ xenografts. Although porcine organs could be

Scientific Report 2013/2014 Department of Biological 98 Physical Chemistry

suitable replacements for overcoming the critical shortage of human organs, they express a high proportion of the Gal-α-(1-3)-Gal epitope and elicit a vigorous anti-Gal-α-(1-3)-Gal antibody response. We have examined the recognition of α-3-O-galactobiose by three different scFv antibody fragments using CD. Similar β-secondary structures and environment of aromatic residues have been found for all scFvs, but addition of Gal-α-(1-3)-Gal-β-1-OMe induces scFv-specific changes in the CD spectra, their intensity being directly related to the binding affinity. Thermal denaturation experiments have confirmed binding by the three scFvs, while STD-NMR analysis carried out in parallel by Prof. F.J. Cañada (CIB-CSIC) have served to identify the recognized sugar epitopes.

Development of new designer’s microarraysWe have developed new designer’s microarrays for the study of probe features and recognition by different receptors. Using this technology, we can incorporate, and subsequently evaluate, different samples in a single chip, from glycoproteins, glycolipids, or bacterial lipopolysaccharides, up to intact bacteria and cells. A protocol for the preparation and validation of bacteria microarrays has been established using Klebsiella pneumoniae as model human pathogen, in collaboration with Dr. J.A. Bengoechea (Fundación Caubet-Cimera). The recognition of a set of defined mutants by anti-Klebsiella antibodies and by the complement subcomponent C1q, which binds K. pneumoniae in an antibody independent manner, has been demonstrated. Furthermore, the potential of the bacteria microarray for investigating specific features, e.g. glycosylation patterns, of the cell surface has been confirmed by examining the binding behavior of a panel of plant lectins with diverse carbohydrate binding specificities.

This approach has also been used for exploring the glycosylation profiles of wild-type and mutant strains of non typable-Haemophilus influenzae (NT-Hi), in collaboration with Dr. Junkal Garmendia (Institute of Agrobiotechnology, CSIC), of potential relevance to infectivity and pathogenicity. The results evidence the presence of β-galactosides on the bacterial surface and provide a rationale for carbohydrate-mediated recognition of NT-Hi by galectins.

Previous findings on the galectin- and strain-type dependent selectivity towards NT-Hi have prompted the study of galectin binding to newly designed mutants bearing lipooligosaccharide (LOS) trimming at selected positions. Wild

type and mutant LOS have been isolated and quantitated using optimized electrophoretic and colorimetric protocols. The entire bacteria and purified LOSs have been printed in the microarrays and the binding has been examined in the absence and presence of potential inhibitors. Remarkably, the results reveal that hGal-4 and hGal-8 recognize different LOS epitopes, an observation that could likely account for the differential recognition of other bacteria by these two galectins.

In addition, we have investigated the recognition of Streptococcus pneumoniae (with and without capsule) and other pathogens (S. mitis, S. pyogenes and Staphylococcus aureus) as well as different types of the cell walls (S. pneumoniae, E. coli and Micrococcus spp.), all of them incorporated in designer’ microarrays, by Cpl7, its cell wall binding domain C-Cpl7, the mutant R19A of C-Cpl7, and the protein variants without one (Cpl7Δ1) or two (Cpl7Δ2) repetitions of the cell wall binding domain. Among other results, it is noteworthy the strong decrease in the affinity of the R10A mutant of C-Cpl-7 for the bacteria and the isolated cell wall. These microarrays have been used also to investigate a possible recognition of these bacteria by different galectins, checking their binding specificity by inhibition assays with asialofetuin/lactose.

Finally, we have also adapted the microarray set-up for exploring the glycosylation patterns of microvesicles and exosomes present in circulating blood as well as those derived from THP-1 neutrophils, in collaboration with Prof. Edit Buzás (Semmelweis University). Specific markers for each vesicle type have been used for controlling immobilization and retention, and array quality and integrity of the printed vesicles has been assessed using an anti-GAPDH antibody. Binding assays using the panel of plant lectins have revealed different glycosylation motifs among vesicle types, what could be exploited for vesicle fractionation.

Study of structure-function relationships in pneumococcal murolytic enzymes. Development of new antimicrobialsStreptococcus pneumoniae, the pneumococcus, is the causative agent of opportunistic infections and severe invasive diseases that remain potentially life-threatening (mortality rates surpass those of any other human pathogen). The murein hydrolases encoded by the pneumococcus and its bacteriophages are potential targets for developing new therapeutic strategies because of their capacity to modify

Scientific Report 2013/2014 Department of Biological 99 Physical Chemistry

Figure 1. Binding of biotinylated plant lectins to different vesicle populations. Serial dilutions of pellet and supernatant (SN) of blood (1,3) and THP-1-derived (2,4) exosomes (1,2) and microvesicles (3,4) were printed as triplicates onto nitrocellulose-coated glass slides and incubated with biotinylated plant lectins at the indicated concentrations. The extent of lectin

binding was determined using streptavidin-AlexaFluor647®.

and disrupt the peptidoglycan network forming the bacterial cell wall, un structure essential for bacterial survival not shared by eukaryotic cells. In-depth knowledge of pneumococcal murein hydrolases can provide a rational to develop novel therapeutic approaches aimed at i) interfering the activity of the bacterial enzymes (involved in fundamental processes for bacterial survival and virulence) with specific inhibitors, and ii) identifying or designing new murolytic enzymes that, used in their purified form, can behave as effective antimicrobials in the specific control of pneumococcal infections. In collaboration with the group of Bacterial Genetics at the CIB (CSIC), our recent work on pneumococcal murein hydrolases have focussed on functional characterization of the glucosaminidase LytB, the Cpl-7 endolysin, and four chimeric lysins (Cpl-711, Cpl-771, Cpl-117 and Cpl177) built by interchange of modules between Cpl-1 and Cpl-7 endolysins.

In the search for determinants of substrate specificity in pneumococcal murein hydrolases, the catalytic residues of LytB, the minimal hydrolysable substrate, and the nature of the muropeptides hydrolyzed after treatment of cell-wall isolates from different pneumococcal strains with the enzyme have been characterized. Among other results, a plausible model of a tetrasaccharide-di-pentapeptide in complex with the catalytic region (LytBCAT) has been generated (Figure 2), and the hydrolysis mechanism, compatible with the structural features and substrate specificity, has been proposed. On the other hand, the study of cell wall recognition by the three fully conserved CW_7 motifs of C-Cpl-7,

carried out in parallel, has unveiled the key role of the arginine residues located at position 19 of each motif on cell-wall binding. The analysis was performed by NMR, in collaboration with Dr. Marta Bruix from the Department of Biological Physical-Chemistry, and using the microarray technology (see above), while the crystal structure of the triple R19A mutant of C-Cpl-7 was determined in collaboration with Dr. Juan Hermoso from the Department of Structural Biology.

In order to provide more effective and specific antimicrobials against S. pneumoniae and other pathogens, four functional chimeric lysozymes with different substrate range were constructed by swapping the structural domains of Cpl-7 and Cpl-1 endolysins, in collaboration with Dr. Pedro Garcia from the group of Bacterial Genetics (CIB-CSIC). The chimeras Cpl-711 and Cpl-771 contained the catalytic domain and the choline-binding domain of Cpl-7 and Cpl-1 endolysins, respectively, connected through the linker peptides of Cpl-1 (Cpl-711) or Cpl-7 (Cpl-771), whereas Cpl-117 and Cpl-177 comprised the catalytic domain of Cpl-1 and the cell wall binding domain of Cpl-7S (an improved variant of the Cpl-7 endolysin) joined, again, by the linker peptides of Cpl-1 or Cpl-7, respectively. As expected, the activity of Cpl-711 and Cpl-771 was choline dependent whereas Cpl-117 and Cpl-177 hydrolyzed the cell walls in a choline-independent way, and their specific activities on pneumococcal cell wall fragments were similar. However, the chimera Cpl-711 substantially improved the killing activity of the parental lysozymes against pneumococcal

Scientific Report 2013/2014 Department of Biological 100 Physical Chemistry

Figure 2. Model of the complex formed by the catalytic region of LytB and the dipentapeptide tetrasaccharide (NAG-

NAM-L-Ala-D-isoGln-L-Lys-D-Ala-D-Ala)2. The GH73 domain is represented in

red, SH3B in yellow and the WW-type domain in Green. The ligand (stick model) is

shown with the carbon atoms coloured in green, oxygens in red and nitrogens in blue. The

discontinuous lines indicate possible hydrogen bonds.

bacteria, including multiresistant strains, both in vitro and in vivo. The protection provided by a single intraperitoneal injection of Cpl-711 to mice challenged with the pneumococcal D39 strain was 50% greater than with Cpl-1. This makes of Cpl-711 the most powerful enzybiotic against pneumococci so far described and opens a promising therapeutic perspective for the treatment of multiresistant pneumococcal infections.

Finally, activity assays in the presence of compounds identified as potential ligands of the LytA autolysin in thermal-shift assays have allowed the identification of an inhibitor whose binding affinity and mechanism of action are currently under investigation.

Other systems of interestThe group activities also included collaborations with different research groups aimed to the structural and/orther modynamic characterization of biomolecules and their complexes. Because of their biological or biotechnological relevance we can point out the studies performed on the CPEB protein and its non-toxic, amyloid-like orthologue Orb2, in collaboration with Dr. Mariano Carrión (Cajal Institute, CSIC); the sugar recognition by the carboxy-terminal head domain of the fiber from different adenovirus, in collaboration with Dr. van Raaij (CNB, CSIC); and the self-association of the MgaSpn protein from Streptococcus pneumonaie, involved in virulence, in cooperation with Dr. Alicia Bravo (CIB, CSIC).

Scientific Report 2013/2014 Department of Biological 101 Physical Chemistry

Carrero, P., Arda, A., Alvarez, M., Doyaguez, E.G., Rivero-Buceta, E., Quesada, E., Prieto, A., Solís, D., Camarasa, M.J., Pérez-Pérez, M.J., Jiménez-Barbero, J., San-Felix, A. (2013). Differential recognition of mannose-based polysaccharides by tripodal receptors based on a triethylbenzene scaffold substituted with trihydroxybenzoyl moieties. European J. Org. Chem. 1, 65-76.

Garcia-Linares, S., Castrillo, I., Bruix, M., Menéndez M., Alegre-Cebollada, J., Martínez-del-Pozo, A., Gavilanes, J.G. (2013) Three-dimensional structure of the actinoporin sticholysin I. Influence of long-distance effects on protein function. Arch. Biochem. Biophys. 532, 39-45.

Ruiz, F.M., Fernández, I.S., López-Merino L., Lagartera, L., Kaltner, H., Menéndez, M., André, S., Solís D., Gabius, H.-J., Romero, A. (2013) Fine-tuning of prototype chicken galectins: Structure of CG-2 and structure-activity correlations. Acta Cryst. D: Biol. Cryst. 69, 1665-1676.

Diez-Martínez, R., De Paz, H., Bustamante, N., García. E., Menéndez M., García P. (2013) Improving the lethal effect of Cpl-7, a pneumococcal phage lysozyme with broad bactericidal activity, by inverting the net charge of its cell wall-binding module. Antimicrob. Agents. Chemother. 57, 5355-5365.

Ermakova, E., Miller, M.C., Nesmelova, I.V., López-Merino, L., Berbis, M.A., Nesmelov, Y., Tkachev, Y.V., Lagartera, L., Daragan, V.A., André, S., Cañada, F.J., Jiménez-Barbero, J., Solís, D., Gabius, H.-J., Mayo, K.H. (2013) Lactose binding to human galectin-7 (p53-induced gene 1) induces long-range effects through the protein resulting in increased dimer stability and evidence for positive cooperativity. Glycobiology 23, 508–523.

Ruiz, F.M., Scholz, B.A., Buzamet, E., Kopitz, J., André, S., Menéndez, M., Romero, A., Solís, D., Gabius, H-J. (2014) Natural single amino acid polymorphism (F19Y) in human galectin-8: Detection of structural alterations and increased growth-regulatory activity on tumor cells. FEBS J. 281, 1446-1464.

Moscoso, M., Esteban-Torres, M., Menéndez, M., García, E. (2014) In vitro bactericidal and bacteriolytic activity of ceragenin CSA-13 against planktonic cultures and biofilms of Streptococcus pneumoniae and other pathogenic streptococci. PLos ONE 9, e101037.

Solís, D., Bovin, N.V., Davis, A.P., Jiménez-Barbero, J., Romero, A., Roy, R., Smetana Jr. K., Gabius H.-J. (2014) A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. B.B.A (Epub 2014 Mar 28).

Publications

Scientific Report 2013/2014 Department of Biological 102 Physical Chemistry

COMPETITIVE FUNDING

Principal Investigator Title Reference

M. Menéndez Structural variability and substrate fine specificity BFU2009-10052 of two families of biomedical relevant proteins

M. Menéndez Exploring exogenous and endogenous factors as BFU2012-36825 tools for the control of infectious and immune processes

Principal Investigator Title Reference

F. Gago Bioinformatics integrative platform for structure S2010/BMD-2457 E-based drug discovery (BIPEDD2)

Principal Investigator Title Reference

L. Joshi Glycomics by High-throughput Integrated (FP7-Health 2010- Technologies: 260600) Development and validation of complementary and integrated technologies for glycomic analysis of serum in cancer, glycobiomarker discovery, diagnostics and glycotherapeutic monitoring (GlicoHIT)

M. Barboiu Dynamic interactive nanosystems (DYNANO) FP7-ITN-GA:289003

D. Solís The Sugar Code: from (bio)chemical concept to FP7-ITN-GA:317297 clinics (GLYCOPHARM)

MINECO

CAM

UE

National Grants: individual

National Grants: coordinated

International Grants: coordinated

Scientific Report 2013/2014 Department of Biological 103 Physical Chemistry

NMR Spectroscopy of Nucleic Acids Group

Tenured Staff scientists

Carlos González Ibáñez (Professor) ReID ORCID

Douglas Vinson Laurents (Assistant Professor) ReID ORCID

Non-tenured scientists

Irene Gómez Pinto

Doctoral students

Miguel Garavís Cabello

Nerea Martín Pintado (hasta 13/06/2013)

Miguel Mompean García

Technical Staff

David Pantoja Uceda (TSE)

Miguel Angel Treviño Avellaneda (TSE) ReID ORCID SCOPUS

Diana Velázquez Carreras (JAE-TEC)

Scientific Report 2013/2014 Department of Biological 104 Physical Chemistry

SummaryThe chief objective of our group is to contribute to the understanding of molecular recognition events involving nucleic acids. These events are implicated in a myriad of processes of interest for Biology, Nanoscience and Macromolecular Chemistry. Understanding these processes has a direct impact on the development of new drugs.

One key approach to comprehend these

molecular recognition processes is to know the 3D structure of nucleic acids (DNA, RNA and their derivatives) at the highest level of detail possible. To this end, our group is dedicated to the determination of oligonucleotide structures either alone or in complex with proteins and other ligands. We use a diverse set of spectroscopic techniques, principally Nuclear Magnetic Resonance (NMR) Spectroscopy.

Strategic Aims• Structural studies of nucleic acid analogs and non-canonical structures important in Biology

and Nanoscience.

• Structural studies of nucleic acids implicated in human diseases and their complexes with ligands.

• Contribute to the elucidation of hypothetical molecular recognition processes and co-evolution between RNA and proteins during the Origin of Life.

• Study the formation and stability of the products of abnormal RNA translation, such as amyloids.

Scientific Report 2013/2014 Department of Biological 105 Physical Chemistry

ResultsStudies of nucleic acid - ligand interactionsThe research on RNA - ligand interactions over these two years can be classified into two groups. First, we have continued our studies of the effects of aromatic ligands on the DNA sequences that form quadruplexes and we have

made notable advances in the study of several DNA-ligand conjugates. These conjugates are diverse and range from DNA double helices to quadruplexes. Second, we have undertaken the identification of new ligands for human telomeric RNA utilising innovative methods that we will describe in the next section.

Figure: Close up view of the interaction between a carbohydrate and a guanine quadruplex.

Scientific Report 2013/2014 Department of Biological 106 Physical Chemistry

New MethodsFrom the technical perspective, we have developed new protocols for the production and purification of relatively long molecules of RNA in quantities and purities sufficient for NMR structural studies. Using these new methods, we have produced telomeric RNAs (TERRAS) which contain 100 nucleotides. Our collaboration with the group of Alfredo Villasante (CBMSO-CSIC) has been fundamental for this task. We have characterised the TERRA RNAs using NMR, CD, and optical tweezers in collaboration with Ricardo Arias (IMDEA).

Working with Dr. Ramon Campos (CNIO), we have implemented 19F NMR based methodologies to detect weak interactions between large RNA molecules and ligands labeled with fluorine. This has permitted us to explore the affinity of a library of compounds for human telomeric RNA and to identify new ligands for RNA quadruplexes. We have also collaborated with Juan Luis Asensio (IQO-CSIC) to develop a new strategy for identifying the ligands derived from amino glycosides that bind the most effectively to RNA.

Cartoon illustrating the structure of a segment of human telomeric RNA (TERRA) the effect that its presence produces on the signal 19F NMR signal of fluorine labeled ligands.

Scientific Report 2013/2014 Department of Biological 107 Physical Chemistry

Studies of Chemically Modified Nucleic AcidsWe have continued our studies of the effect of fluorine at the 2’ position on the pentose sugar ring. We have carried out the structural determination of the self complementary chimeric duplexes 2F’-ANA/2F’-RANA in a number of diverse sequences. These studies aid our comprehension of the structural bases of the stabilisation afforded by fluorine substituted

ribose (2’F -RANA) and arabinose (2’F -ANA) sugars. Moreover, these results could be used to obtain better compounds for antisense therapy and RNA silencing.

Moreover, we have carried out structural studies on guanine quadruplexes containing fluorine labeled nucleotides. Our results with telomeric sequences indicate that the presence of a single fluorine labeled nucleotide is able to modify and markedly stabilise the quadruplex structure.

Figure: Structure of an RNA duplex modified with 2’F-ANA and 2’F-RNA. Dotted lines indicate the pattern of non conventional H-bonds in the sugar backbone provoked by the presence of

fluorine atoms.

Scientific Report 2013/2014 Department of Biological 108 Physical Chemistry

Amyloid beta sheets

We have aimed to characterize the first steps in the formation of amyloids using NMR. However, the low concentration of the key intermediates and their rapid evolution towards large aggregates makes it difficult to characterise them by NMR spectroscopy. For this reason, we have realised these studies using computational methods. Specifically, we have used long Molecular Dynamics simulations (up to half a microsecond) to characterise the smallest oligomers formed by the Sup35 amyloid (sequence GNNQQNY), and QM/MM calculations to quantify how much the intra-sheet H-bonds strengthenes as the sheet grows. The experience gained from studying this peptide has allowed us to tackle the identification and characterisation of the amyloid forming segment of TDP-43,

a 414 residue human protein implicated in Amyotrophic Lateral Sclerosis.

In collaboration with Dr. M. Carrión-Vázquez (Cajal Institute) we have studied the conformational diversity present in proteins and amyloidogenic peptides implicated in diverse neurodegenerative diseases, such as Alzheimer’s, Parkinson’s and Huntington´s. Despite their different sequences, all these proteins undergo a similar conformational change in which random coils adopt structures rich in beta sheet. These findings have lead us to propose that conformational changes in the monomer trigger the formation of amyloid. In many cases, this crucial conformational change can be blocked by the peptide inhibitor QBP1 (sequence: WKWWPGIF). As a first step towards developing more effective inhibitors, we have determined QBP1’s structure using NMR.

Cross-eyed stereo view of the preferred conformation of QBP1 (color code W, K, P, G, I, F)

Scientific Report 2013/2014 Department of Biological 109 Physical Chemistry

Putative prebiotic peptidesOver the last several years, we have studied different peptides composed of the small sub-set of amino acids that could have formed on the prebiotic Earth. Some of these peptides adopt a well folded tetrameric structure composed of four alpha helices. During 2013-2014, we set out to determine if other simple peptides could form beta hairpins, the fundamental building blocks of β-sheets. The general sequence of these peptides is HφIKIDGKφIKH, where φ is H, F or W. We found that only the peptide

with 2 Trps could adopt a high population of beta hairpin structure. Moreover, we found that KIA²W and KIA²F (the variant with 2 Phe) bind to ATP and with less affinity to GTP to form 1:1 complexes. The elucidation of the structure of the KIA²W·ATP complex revealed that the adenine base inserts between two Trp indole rings, and that the phosphates of ATP and the ammonium groups of the lysines associate through favorable electrostatic interactions. This structure is the first determination of an ATP·²-hairpin complex.

Cross-eyed stereo view of the ATP(maroon )+ KIAβW (W, K, H, D, I) complex.

Scientific Report 2013/2014 Department of Biological 110 Physical Chemistry

Hervás, R, Fernández-Ramírez, M.C., Abelleira, L.E., Laurents, D.V. and Carrión-Vázquez, M. (2014). Chapter 6: Nanomechanics of Neurotoxic Proteins: Insights at the Start of the Neurodegeneration Cascade. “Bio-nanoimaging: Protein Misfolding and Aggregation”. Pages 57-68. ISBN: 978-0-12-394431-3.

Benabou, S., Avino, A., Eritja, R., Gonzalez, C. and Gargallo, R. (2014). Fundamental aspects of the nucleic acid i-motif structures. RSC Advances 4, 26956-26980.

Benabou, S., Ferreira, R., Avino, A., Gonzalez, C., Lyonnais, S., Sola, M., Eritja, R., Jaumot, J. and Gargallo, R. (2014). Solution equilibria of cytosine- and guanine-rich sequences near the promoter region of the n-myc gene that contain stable hairpins within lateral loops. Biochim Biophys Acta 1840, 41-52.

Doluca, O., Hale, T.K., Edwards, P.J.B., González, C. and Filichev, V.V. (2014). Assembly-dependent fluorescence enhancing nucleic acids (AFENA) in sequence-specific detection of double-stranded DNA. ChemPlusChem 79, 58-66.

Garavis, M., Lopez-Mendez, B., Somoza, A., Oyarzabal, J., Dalvit, C., Villasante, A., Campos-Olivas, R. and Gonzalez, C. (2014). Discovery of selective ligands for telomeric RNA G-quadruplexes (TERRA) through 19F-NMR based fragment screening. ACS Chem Biol 9, 1559-1566.

Lucas, R., Penalver, P., Gomez-Pinto, I., Vengut-Climent, E., Mtashobya, L., Cousin, J., Maldonado, O.S., Perez, V., Reynes, V., Avino, A., Eritja, R., Gonzalez, C., Linclau, B. and Morales, J.C. (2014). Effects of sugar functional groups, hydrophobicity, and fluorination on carbohydrate-DNA stacking interactions in water. J Org Chem 79, 2419-2429.

Martinez-Montero, S., Deleavey, G.F., Kulkarni, A., Martin-Pintado, N., Lindovska, P., Thomson, M., Gonzalez, C., Gotte, M. and Damha, M.J. (2014). Rigid 2’,4’-difluororibonucleosides: synthesis, conformational analysis, and incorporation into nascent RNA by HCV polymerase. J Org Chem 79, 5627-5635.

Mompean, M., Buratti, E., Guarnaccia, C., Brito, R.M., Chakrabartty, A., Baralle, F.E. and Laurents, D.V. (2014). Structural characterization of the minimal segment of TDP-43 competent for aggregation. Arch Biochem Biophys 545, 53-62.

Mompean, M., Gonzalez, C., Lomba, E. and Laurents, D.V. (2014). Combining Classical MD and QM calculations to elucidate complex system nucleation: a twisted, three-stranded, parallel beta-sheet seeds amyloid fibril conception. J Phys Chem B 118, 7312-7316.

Ramos-Martin, F., Hervas, R., Carrion-Vazquez, M. and Laurents, D.V. (2014). NMR spectroscopy reveals a preferred conformation with a defined hydrophobic cluster for polyglutamine binding peptide 1. Arch Biochem Biophys 558, 104-110.

Escaja, N., Gomez-Pinto, I., Viladoms, J., Pedroso, E. and Gonzalez, C. (2013). The effect of loop residues in four-stranded dimeric structures stabilized by minor groove tetrads. Org Biomol Chem 11, 4804-4810.

Garavis, M., Bocanegra, R., Herrero-Galan, E., Gonzalez, C., Villasante, A. and Arias-Gonzalez, J.R. (2013). Mechanical unfolding of long human telomeric RNA (TERRA). Chem Commun (Camb) 49, 6397-6399.

Garavis, M., Gonzalez, C. and Villasante, A. (2013). On the origin of the eukaryotic chromosome: the role of noncanonical DNA structures in telomere evolution. Genome Biol Evol 5, 1142-1150.

Gomez-Pinto, I., Vengut-Climent, E., Lucas, R., Avino, A., Eritja, R., Gonzalez, C. and Morales, J.C. (2013). Carbohydrate-DNA interactions at G-quadruplexes: folding and stability changes by attaching sugars at the 5’-end. Chemistry 19, 1920-1927.

Hospital, A., Faustino, I., Collepardo-Guevara, R., Gonzalez, C., Gelpi, J.L. and Orozco, M. (2013). NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res 41, W47-W55.

Jimenez-Moreno, E., Gomez-Pinto, I., Corzana, F., Santana, A.G., Revuelta, J., Bastida, A., Jimenez-Barbero, J., Gonzalez, C. and Asensio, J.L. (2013). Chemical interrogation of drug/

Publications

Scientific Report 2013/2014 Department of Biological 111 Physical Chemistry

RNA complexes: from chemical reactivity to drug design. Angew Chem Int Ed Engl 52, 3148-3151.

Martin-Pintado, N., Deleavey, G.F., Portella, G., Campos-Olivas, R., Orozco, M., Damha, M.J. and Gonzalez, C. (2013). Backbone FC-H...O Hydrogen Bonds in 2’F-Substituted Nucleic Acids. Angew Chem Int Ed Engl 52, 12065-12068.

Martin-Pintado, N., Yahyaee-Anzahaee, M., Deleavey, G.F., Portella, G., Orozco, M., Damha, M.J. and Gonzalez, C. (2013). Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom. J Am Chem Soc 135, 5344-5347.

Santana, A.G., Jimenez-Moreno, E., Gomez, A.M., Corzana, F., Gonzalez, C., Jimenez-Oses, G., Jimenez-Barbero, J. and Asensio, J.L. (2013). A Dynamic Combinatorial Approach for the Analysis of Weak Carbohydrate/Aromatic Complexes: Dissecting Facial Selectivity in CH/pi Stacking Interactions. J Am Chem Soc 135, 3347-3350.

Serrano, S., Callis, M., Vilanova, M., Benito, A., Laurents, D.V., Ribo, M. and Bruix, M.

(2013). (1)H, (13)C and (15)N resonance assignments of the Onconase FL-G zymogen. Biomol NMR Assign 7, 13-15.

Amiri, R., Bordbar, A.K., Laurents, D.V. (2014) Gemini surfactants affect the structure, stability, and activity of ribonuclease Sa. J Phys Chem B. 118, 10633-42.

Gotte, G., Laurents, D.V., Merlino, A., Picone, D., Spadaccini, R. (2013) Structural and functional relationships of natural and artificial dimeric bovine ribonucleases: new scaffolds for potential antitumor drugs. FEBS Lett. 587(22), 3601-8.

Diez-García, F., Pantoja-Uceda, D., Jiménez, M.Á., Chakrabartty, A., Laurents, D.V. (2013). Structure of a simplified β-hairpin and its ATP complex. Arch Biochem Biophys. 537(1), 62-7.

Callís, M., Serrano, S., Benito, A., Laurents, D.V., Vilanova, M., Bruix, M., Ribó, M. (2013). Towards tricking a pathogen’s protease into fighting infection: the 3D structure of a stable circularly permuted onconase variant cleavedby HIV-1 protease. PLoS One 8(1):e54568.

Scientific Report 2013/2014 Department of Biological 112 Physical Chemistry

COMPETITIVE FUNDING

Principal Investigator Title Reference

Laurents, D.V. Structure, Stability and Optimization of SAF2013-49179-C2-2-R QBP1 + CPEB Prion Domain Complexes x and in Memory Consolidation

Laurents, D.V. Structure, solvation and ligand binding of RNAs CTQ2010-21567-C02-02 and Proteins with Aberrant Conformations by NMR

Principal Investigator Title Reference

Carlos González Ibáñez Estudios estructurales de oligonucleotidos PRI-AIBNZ-2011-0919 modificados ricos en guaninas mediante RMN Acción integrada con Nueva Zelanda

Ministerio de Economía y Competitividad

Ministerio de Economía y Competitividad

National Grants: coordinated

International Grants: coordinated

Scientific Report 2013/2014 Department of Biological 113 Physical Chemistry

Memoria 2013/2014 Department of Biological Physical 115 Chemistry

Department of Low Dimensional Systems, Surfaces and

Condensed Matter

Scientific Report 2013/2014 Department of Low Dimensional Systems, 116 Surfaces and Condensed Matter

IntroductionThe Department of low-dimensional systems, surfaces and condensed matter is composed by various groups of the Institute “Rocasolano” who share a common interest in Materials Science. The Department has well-defined lines of research devoted to the synthesis, characterization and modeling of materials with applications such as optoelectronics, photonics, biomedicine, magnetism, catalysis, electrocatalysis and energy conversion and storage (to name a few).

An important part of the investigation of this Department is dedicated to the study of laser-induced processes in molecules and materials. The use of laser ablation for the generation of nanostructures, the implementation of new laser techniques for processing and synthesizing materials or the study of new organic dyes for laser emission are just some of the many aspects developed in the Department.

Another major part of the Department activities comprises the theoretical and experimental study of surfaces and thin films, molecular aggregates and properties of condensed matter, at the atomic and molecular scales, with the ultimate aim of understanding phenomena of surface

reactivity such as adsorption, corrosion or electrocatalysis.

The Department investigation is not constituted only by the individual addition of the research of the different groups that compose it. In the biennium to which this report (2013-2014) is concerned, there have been a significant number of intra-departmental collaborations that have been reflected in a significant number of joint scientific publications.

In the last two years the Department has experienced a significant reduction in its potential. To the retirements occurred in the previous biennium (2011-2012) we have to add the leave of Dr. Angel Cuesta to the University of Aberdeen (UK) and that of the group of Prof. García de Abajo to the ICFO in Catalonia. In practice, this has meant, in the first case, the complete dismantling of the group of Electrochemistry and, in the second, the disappearance of the Nanophotonics group. The disappearance of the group of Electrochemistry group results particularly painful since it means the end of the dedication to a discipline that has been fundamental for decades in the work of “Rocasolano” Institute and that has provided a very prestigious reputation both at national and international levels.

Group Structure

Lasers, Nanostructures and Materials Processing 118

Laser Materials and Laser-Materials Interaction 129

Statistical Mechanics and Condensed Matter 138

Surface Analysis and Mössbauer Spectroscopy 145

Scientific Report 2013/2014 Department of Low Dimensional Systems, 117 Surfaces and Condensed Matter

Lasers and Nanostructures and Materials Processing Group

Tenured Staff scientists

Marta Castillejo Striano (Associate Professor) ReID ORCID SCOPUS

Margarita Martín Muñoz (Associate Professor) ReID

Rebeca de Nalda Mínguez (Assistant Professor) ReID ORCID SCOPUS

Non-tenured scientists

Esther Rebollar González (Ramón y Cajal) ReID ORCID SCOPUS

Mohamed Oujja Ayoubi ReID ORCID SCOPUS

Mikel Sanz Monasterio (Until 21/02/2014)

Doctoral students

Ignacio López Quintás

Technical Staff

Antonio Benítez Cañete (JAE-Tec. Until 16/10/2013)

Scientific Report 2013/2014 Department of Low Dimensional Systems, 118 Surfaces and Condensed Matter

SummaryThe activity of the Group has focused on the research on the physics and chemistry of micro- and nanofabrication processes using pulsed laser irradiation and ablation in the nanosecond and femtosecond temporal domains and wavelengths from UV to IR. We have concentrated on the controlled generation of a broad range of nanomaterials and nanostructures with specific functionalities based on polymers, semiconductors, oxides and polymer/inorganic composites. Our work has unravelled basic

laser interaction mechanisms allowing us to propose new experimental methods to control the composition, morphology and structure of the fabricated nanomaterials. We have also directed our efforts towards the development of new experimental methodologies to extract physicochemical information about the different types of nanostructures. Our results are of interest for applications in biomedicine, sensing, photovoltaics, photonics, electronics, magnetic materials and cultural heritage.

Strategic AimsWe aim at achieving controlled fabrication of nanomaterials and nanostructures with specific functionalities by laser irradiation through the fundamental understanding of the laser writing and ablation of materials and the study of the properties of the ablation plasma. The specific objectives are:

• To design and fabricate polymer nanostructures and polymer-based nanocomposites with tailored properties by superficial laser writing.

• To obtain, by laser ablation and deposition, nanostructured deposits with magnetic ordering based on iron oxides and to control the doping of II-VI semiconductors with transition metal atoms.

• To develop novel methodologies for in situ determination of the growth and self-assembly processes of the laser generated nanomaterials.

• To identify targets and ablation regimes yielding plasmas with high efficiency for harmonic generation.

• The development and application of laser-based methodologies for the analysis and conservation of substrates and objects of Cultural Heritage.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 119 Surfaces and Condensed Matter

ResultsGeneration of superficial nanostructures by laser irradiationWe have continued our studies on the generation of superficial periodic nanostructures by laser irradiation (laser induced periodic surface structures, LIPSS). Together with substrates constituted by films of synthetic polymers, we have demonstrated LIPSS generation in different materials such as biocompatible biopolymers and semiconductors.

To develop new strategies for the control of the morphology and superficial chemistry of the generated nanostructures, we have undertaken the generation of LIPSS with ultrashort laser pulses in the femtosecond scale, and different wavelengths from the UV to the IR. In this case, we have determined the dependence of the period with laser wavelength (Fig. 1).

Besides, with temporally shaped ultrashort laser pulses we have demonstrated an active control of the properties of the generated superficial nanostructures generated on biopolymer films.

Within this topic it is worth pointing out the application of the GISAXS (grazing incidence small angle X ray scattering) technique to monitor periodic structures in thin polymer films generated by LIPSS approach and also by NIL (nanoimprint lithography). We have undertaken an investigation on the use of polymer films endowed with LIPSS as substrates for cell growth, successfully demonstrating the adhesion and proliferation of mesenchymal cells on polyethylene terephthalate (PET) based substrates.

Part of the work here reported has taken place in collaboration with the group of Prof. T. Ezquerra, Instituto de Estructura de la Materia, CSIC.

Figure 1. AFM height images of films of polytrimethylene terephthalate (PTT) irradiated at the given fluences, number of pulse and wavelengths. The height profile along a 5 µm line

perpendicular to the ripples is shown below every image (height scale: 250 nm). The double arrow indicates the laser polarization direction. Adapted from Rebollar et al., 2013.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 120 Surfaces and Condensed Matter

Laser ablation for the fabrication of thin films and nanostructuresWe have used laser transfer techniques, based in the ablation of a solid target to fabricate thin films and nanostructures with specific functionalities. By pulsed laser deposition (PLD) using a nanosecond IR laser (1064 nm) we have determined the dependence with the type of substrates of the morphology, structure and magnetic properties of deposits grown from hematite targets. While on silicon substrates we have confirmed the growth of stoichiometric magnetite, on SrTiO3:Nb substrates we observe magnetite domains magnetized along the in-plane <100> directions (Fig. 2). Magneto-optical Kerr effect measurements show that the maxima of the remanence and coercivity are also along in-plane <100> film directions. This easy-axis orientation differs from bulk magnetite and films prepared by other techniques, establishing that the magnetic anisotropy can be tuned by film growth. These studies have been carried out with the collaboration of Drs Juan de la Figuera and J.F. Marco of IQFR.

By laser irradiation of ZnS/Co(2%) targets, with nanosecond pulses of 1064 nm, we have observed, for the first time reported in ablation plasmas, the presence Co substituted (ZnS)n clusters. Analysis by EDS and cross-sectional HRTEM of plasma species, deposited on a Si substrate, allow the identification of crystalline nanoparticles with average composition Zn0.96Co0.04S. These results open a possible

path of controlled synthesis, via PLD, based on the hypothesis that selected compositions of bimetallic clusters, ZnnComSk, are formed in the plasma, and behave as building blocks and self-assemble in nanostructures with magnetic functionality, maintaining the semiconductor transport properties.

In PLD, the structural and chemical characteristics of deposits depend of the properties of the ablation plume, composition and dynamics of species, in route from the target to the substrate, and to the nucleation processes on the substrate itself. By optical emission spectroscopy, time-of-flight mass spectrometry and low-order harmonic generation of a probe laser we have undertaken the characterization of laser ablation plasmas of targets constituted by SiO, ZnS-Co and TiO2, where we have identified neutral and ionized atomic species, clusters (as mentioned in the paragraph above, or nanoparticles.

A second laser transfer technique, such as pulsed laser ablation in liquid medium (PLAL), has served us to obtain colloidal Pt nanoparticle solutions which we have used to fabricate photoactive substrates. We have demonstrated, in collaboration with the group of Prof. Bruno Martínez-Haya, of Universidad Pablo de Olavide, Sevilla, a significant increase of sensitivity and response in the detection of using the techniques de nanoparticle-assisted laser desorption/ionization (NALDI), surface enhanced Raman scattering (SERS) and surface enhanced infrared absorption (SEIRA).

Figure 2. Magnetite on SrTiO3:Nb. a) Atomic Force Microscopy image. The thermal color height scale corresponds to 40 nm; b) Scanning Tunnelling Microscopy (STM) image acquired with It=0.7 nA and Vbias= 1 V. The image is 10 nm high; c) STM image acquired with It=0.5 nA and Vbias= 1.1 V showing the rows of atoms with different orientation in consecutive terraces.

Adapted from Monti et al., 2013.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 121 Surfaces and Condensed Matter

Harmonic generation in laser ablation plasmasOur research in this domain focusses on low-order harmonic generation (3th and 5th), of a probe laser that propagates through the ablation plume induced by a second laser, as a spatio-temporal diagnostics technique of the different plume populations. This method has been applied to carbon containing targets (graphite and boron carbide) and the nucleobases uracil and thymine.

We have also tackled investigations of high

harmonic generation (HHG) processes in ablation plumes using ultrashort femtosecond pulses as driving fundamental radiation in cooperation with Prof. J.P Marangos, Imperial College London and Prof. R.A. Ganeev. We have compared the efficiency of the HHG process in atomic and nanoparticle ablation plasmas and have demonstrated, in the case of metallic silver-based targets, the noticeable increase of efficiency in the presence of nanoparticles (Fig. 3). Besides, in the search for nonlinear media based on ablation plasmas, we have identified resonance effects in indium plasmas, which are responsible for the higly efficient HHG.

Figure 3. Comparison of HHG signal of atomic vs nanoparticle ablation plume of silver. Adapted from Ganeev, Witting et al., 2013.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 122 Surfaces and Condensed Matter

Ultrafast dynamics and control of molecular processesImportant progress has been made in these past years both in the real-time observation of fast photoinduced chemical reactions and in the subject of intense laser control of reaction dynamics. These are experiments performed in the CLUR facility (Center for Ultrafast Lasers) in collaboration with Prof. Luis Bañares, from the Complutense University, Madrid. The work methodology is based on the use of tuneable, ultrashort laser pulses, in either pump-probe schemes, or pump-control-probe schemes. Observation is made through detection of charged particles in time-of-flight spectrometers in velocity map imaging configuration, a technique which offers detailed information on available energies in the reaction channels and also on the angular character of the processes under study.

Regarding the subject of real-time observation of molecular dynamics, we would like to emphasize

the work done on the bond breaking dynamics of the carbon-iodine bond in a series of alkyl iodides, with both linear and branched chains. This work revealed the crucial role of the radical structure on the redistribution of energy, and in its turn, its effect on the reaction dynamics.

In 2013-14 we have contributed with high impact publications to the field of laser control of chemical reactions. These describe the possibility of control of observables like quantum yields, lifetimes or kinetic energy distributions in processes of molecular photodissociation. Control is exerted through the dynamic Stark effect, the creation of laser-induced conical intersections and the generation of laser-induced potentials. As target species, we have selected methyl iodide, with well-known photodissociation processes, and for this case we have been able to show experimentally, as well as simulate theoretically, how the application of a strong laser field, with tailored properties, is capable of changing the “landscape” where the reaction takes place and thus modify its outcome.

Figure 4. Depiction of laser control of molecular dynamics, represented as the strong oscillating electric field of the laser acting on the reaction and modifying its outcome. The

background is an Abel-inverted velocity map image of the methyl fragment resulting from UV dissociation of methyl iodide, under strong field irradiation with an infrared pulse.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 123 Surfaces and Condensed Matter

Laser methods for the conservation of Cultural heritageThe most relevant result concern the laser cleaning of pictorial substrates and biodeterioration layers on stone substrate s. In the first case we have identified the physicochemical modifications associated to the direct laser irradiation of pigments traditionally used in the artistic painting practise and its dependence with laser wavelength and pulse

duration, in the nanosecond- femtosecond range. In the second case we have shown that IR nanosecond laser pulses serve for the satisfactory elimination of lichenic coatings on dolostone samples of built heritage (Fig. 5). On the other hand, we have succeeded in analysing and fully characterize degradation pathologies of historical Roman glasses using laser induced breakdown spectroscopy (LIBS) in combination with other more conventional glass analysis techniques.

Figure 5. SEM-BSE images of Verrucaria nigrescens lichen thalli and microorganisms on dolostone substrates; a) hydrated control thalli showing algal cells (ac) and chloroplast (c) (white open arrows and box). The complete laser destruction of algal and fungal cells can be observed in b) with some fungal lipid body debris (black empty arrows). Adapted from

Speranza et al., 2013.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 124 Surfaces and Condensed Matter

Oujja, M.; Sanz, M.; Rebollar, E.; Marco, J.F.; Domingo, C.; Pouli, P.; Kogou, S.; Fotakis, C.; Castillejo, M. (2013). Wavelength and pulse duration effects on laser induced changes on raw pigments used in paintings. Spectrochim. Acta A 102, 7-14.

Pérez, S.; Rebollar, E.; Oujja, M.; Martín, M.; Castillejo. M. (2013). Laser induced periodic surface structuring of biopolymers. Appl. Phys. A 110, 683-690.

Sanz, M.; Rebollar, E.; Ganeev, R.A.; Castillejo, M. (2013). Nanosecond laser-induced periodic surface structures on wide band-gap semiconductors. Appl. Surf. Sci. 278, 325-329.

López-Quintás, I.; Oujja, M.; Sanz, M.; Martín, M.; Ganeev, R.A.; Castillejo, M. (2013). Low-order harmonic generation in nanosecond laser ablation plasmas of carbon containing materials. Appl. Surf. Sci. 278, 33-37.

Rebollar, E.; R. Vázquez de Aldana, J.; Martín-Fabiani, I.; Hernández, M.; Rueda, D.R.; Ezquerra, T.A.; Domingo, C.; Moreno, P.; Castillejo, M. (2013). Assessment of femtosecond laser induced periodic surface structures on polymer films. Phys. Chem. Chem. Phys. 15 (27) 11287-11298.

Sanz, M.; Oujja, M.; Rebollar, E.; Marco, J.F.; de la Figuera, J.; Monti, M.; Bollero, A.; Camarero, J.; Pedrosa, F.J.; García-Hernández, M.; Castillejo, M. (2013). Stoichiometric magnetite grown by infrared nanosecond pulsed laser deposition. Appl. Surf. Sci. 282, 642-651.

Speranza, M.; Sanz, M.; Oujja, M.; de los Ríos, A.; Wierzchos, J.; Pérez-Ortega, S.; Castillejo, M.; Ascaso, C. (2013). Nd:YAG laser irradiation damage to Verrucaria nigrescens. Inter. Biodeterior. Biodegrad. 84, 281-290.

Hutchison, C.; Ganeev, R.A.; Castillejo, M.; Lopez-Quintas, I.; Zaïr, A.; Weber, S.J.; McGrath, F.; Abdelrahman, Z.; Oppermann, M.; Martin, M.; Lei, D.Y.; Maier, S.A.; Tisch, J.W.G.; Marangos, J.P. (2013). Comparison of high-order harmonic generation in uracil and thymine ablation plumes. Phys. Chem. Chem. Phys. 15, 12308-12313.

Díaz, L.; Camacho, J.J.; Sanz, M.; Hernández, M.; Jandova, V.; Castillejo, M. (2013). Temporal evolution study of the plasma induced by CO2 pulsed laser on targets of titanium oxides. Spectrochimica Acta B. 86, 88-93.

Palomar, T.; Oujja, M.; García-Heras, M.; Villegas, M.A.; Castillejo, M. (2013). Laser induced breakdown spectroscopy for analysis and characterization of degradation pathologies of Roman glasses. Spectrochimica Acta B. 87, 114-120.

Jadraque, M.; Evtushenko, A.B.; Ávila-Brande, D.; López-Arias, M.; Loriot, V.; Shukhov, Y.G.; Kibis, L.S.; Bulgakov, A.; Martín, M. (2013). Co-doped ZnS clusters and nanostructures produced by pulsed laser ablation. J. Phys. Chem. C. 117, 5416–5423.

Ganeev, R.A.; Hutchison, C.; Lopez-Quintas, I.; McGrath, F.; Lei, D.Y.; Castillejo, M.; Marangos, J.P. (2013). Ablation of nanoparticles and efficient harmonic generation using 1 kHz laser. Phys. Rev. A. 88, 033803 (1-10).

Ganeev, R.A.; Witting, T.; Hutchison, C.; Strelkov, V.V.; Frank, F.; Castillejo, M.; Lopez-Quintas, I.; Abdelrahman, Z.; Tisch, J.W.G.; Marangos, J.P. (2013). Comparative studies of resonance enhancement of harmonic radiation in indium plasma using multi-cycle and few-cycle pulses. Phys. Rev. A. 88, 033838 (1-11).

de Buergo, M. A.; Gomez-Heras, M.; Fort, R.; Ascaso, C.; de los Ríos, A.; Ortega, S. P.; Sanz, M.; Oujja, M.; Speranza, M.; Wierzchos, J.; Castillejo, M. (2013). Assessment of laser treatment on dolostones colonized by microorganisms and lichens. Science and Technology for the Conservation of Cultural Heritage, 173.

Oujja, M.; Sanz, M.; Castillejo, M.; Pouli, P.; Fotakis, C.; García, A.; Romero, C.; Vázquez de Aldana, J.R.; Moreno, P.; Domingo, C. (2013). Effect of wavelength and pulse duration on laser cleaning of paints. Science and Technology for the Conservation of Cultural Heritage, 179.

Palomar, T.; Oujja, M.; Castillejo, M.; Sabio, R.; Rincón, J. M.; García-Heras, M.; Villegas, M. A. (2013). Roman glasses from Augusta Emerita: Study of degradation pathologies using LIBS. Science and Technology for the Conservation of Cultural Heritage, 251.

Oujja, M.; García, A.; Romero, C.; R. Vázquez de Aldana, J.; Moreno, P.; Castillejo, M. (2013). Analysis of varnish removal on tempera paints by nanosecond and femtosecond UV lasers, in Saunders D., Strlic M., Korenberg C., Luxford N., Birkhölzer K. (Eds.), Proceedings of 9th International Conference of Lasers in the Conservation of Artworks, Archetype Publications, p. 12-18.

Publications

Scientific Report 2013/2014 Department of Low Dimensional Systems, 125 Surfaces and Condensed Matter

Monti, M.; Sanz, M.; Oujja, M.; Rebollar, E.; Castillejo, M.; Pedrosa, F.J.; Bollero, A.; Camarero, J.; Nemes, N.M.; Mompean, F.J.; García-Hernández, M.; Nie, S.; McCarty, K.F.; N´Diaye, A.T.; Chen, G.; Schmid, A.K.; Marco, J.F.; de la Figuera, J. (2013). In-plane <100> magnetic easy axis for Fe3O4/SrTiO3(001):Nb grown by infrared PLD. J. Appl. Phys. 114, 223902 (1-5).

Corrales, M.E.; Balerdi, G.; Loriot, V.; de Nalda, R.; Bañares, L. (2013). Strong field control of predissociation dynamics. Faraday Discussions 163, 447-460.

Balerdi, G.; Corrales, M.E.; Gitzinger, G.; Gonzalez-Vazquez, J.; Sola, I.R.; Loriot, V.; de Nalda R.; Bañares, L. (2013). Dynamic Stark shift of the R-3(1) Rydberg state of CH3I. EPJ Web of Conferences 41, 02035.

Ossi, P.; Castillejo, M.; Zhigilei, L. (Eds.) (2014). Lasers in Materials Science, Springer Series in Materials Science, Vol. 191.

Castillejo, M.; Ezquerra, T.A.; Oujja, M.; Rebollar, E. (2014). Laser Nanofabrication of Soft Matter, in Lasers in Materials Science, Springer Series in Materials Science 191, 325-344.

Rebollar, E.; Mildner, J.; Götte, N.; Otto, D.; Sarpe, C.; Köhler, J.; Wollenhaupt, M.; Baumert, T.; Castillejo, M. (2014). Microstucturing of soft organic matter by temporally shaped femtosecond laser pulses. Appl. Surf. Sci. 302, 231-235.

Soccio, M.; Alayo, N.; Martín-Fabiani, I.; Rueda, D.R.; García-Gutiérrez, M.C.; Rebollar, E.; Martínez-Tong, D.E.; Pérez-Murano, F.; Ezquerra, T.A. (2014). On the assessment by Grazing Incidence Small Angle X-ray Scattering of replica quality in polymer gratings fabricated by nanoimprint lithography. J. Appl. Crystal. 47, 613-618.

Lopez-Quintas, I.; Oujja, M.; Sanz, M.; Benitez-Cañete, A.; Hutchison, C.; de Nalda, R.; Martin, M.; Ganeev, R.A.; Marangos, J.P.; Castillejo, M. (2014). Characterization of laser-induced plasmas of nucleobases: uracil and thymine. Appl. Surf. Sci. 302, 299-302.

Cueto, M.; Piedrahita, M.; Caro, C.; Martínez Haya, B.; Sanz, M.; Oujja, M.; Castillejo, M. (2014). Platinum Nanoparticles as Photoactive Substrates for Mass Spectrometry and Spectroscopy Sensors. J. Phys. Chem. C. 118 (21), 11432-11439.

Oujja, M.; Sanz, M.; Castillejo, M. (2014). Técnicas láser para análisis y conservación

del patrimonio construido. Durabilidad y conservación de geomateriales del patrimonio construido, I.S.B.N: 978-84-615-7005-8.

Rebollar, E.; Pérez, S.; Hernández, M.; Domingo, C.; Martín, M.; Ezquerra, T.A.; García-Ruiz, J.P.; Castillejo, M. (2014). Physicochemical modifications accompanying UV laser induced surface structures on poly(ethylene terephthalate) and their effect on adhesion of mesenchymal cells. Phys. Chem. Chem. Phys. 16, 17551-17559.

Diaz, L.; Camacho, J.J.; Cid, J.P.; Martin, M.; Poyato, J.M.L. (2014). Time evolution of the infrared laser ablation plasma plume of SiO. Appl. Phys. A. 117, 125-129.

Corrales, M.E.; González-Vázquez, J.; Balerdi, G.; Solá, I.R.; de Nalda, R.; Bañares, L. (2014). Control of ultrafast molecular photodissociation by laser-field-induced potentials. Nature Chemistry 6, 785-790.

McGrath, F.; Hawkins, P.; Simpson, E.; Siegel, T.; Diveki, Z.; Austin, D.; Zair, A.; Castillejo, M.; Marangos, J.P. (2014). Extending HHG spectroscopy to new molecular species. Proc. SPIE 8984, Ultrafast Phenomena and Nanophotonics XVIII, 89841B.

Gitzinger, G.; Loriot, V.; Bañares, L.; de Nalda, R. (2014). Pulse shaping control of CH3I multiphoton ionization at 540 nm. J. Mod. Opt. 61, 864-871.

Loriot, V.; Mendoza-Yero, O.; Pérez-Vizcaíno, J.; Mínguez-Vega, G.; de Nalda, R.; Bañares, L.; Lancis, J. (2014). Fresnel phase retrieval method using an annular lens array on an SLM. Appl. Phys. B 117, 67-73.

Corrales, M.E.; Loriot, V.; Balerdi, G.; Gonzalez-Vazquez, J.; de Nalda, R.; Bañares, L.; Zewail, A.H. (2014). Structural dynamics effects on the ultrafast chemical bond cleavage of a photodissociation reaction. Phys. Chem. Chem. Phys. 16, 8812-8818.

de Nalda, R.; Bañares, L. (Eds.) (2014). Ultrafast Phenomena in Molecular Sciences: Femtosecond Physics and Chemistry. Springer Series in Chemical Physics, vol. 107.

de Nalda, R.; Rubio-Lago L.; Loriot V.; Bañares L. (2014). Femtosecond photodissociation dynamics by velocity map imaging: the methyl iodide case, in Ultrafast Phenomena in Molecular Sciences: Femtosecond Physics and Chemistry. Springer Series in Chemical Physics 107, 61-97.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 126 Surfaces and Condensed Matter

COMPETITIVE FUNDING

Principal Investigator Title Reference

Marta Castillejo Striano Caracterización y control de nanoestructuras Hasta 31/12/2013 generadas por irradiación láser CTQ 2010-15680

Javier Aoiz Moleres Dinámica de procesos químicos: experimentos CTQ2008-02578/BQU fotoiniciados con láseres de nanosegundo y femtosegundo y métodos teóricos

Principal Investigator Title Reference

Cesáreo Sáiz Jiménez, Marta Red Temática de Ciencia y Tecnología para la HAR2010-11432-ECastillejo Striano (IQFR). Conservación del Patrimonio Cultural (TechnoHeritage)

Principal Investigator Title Reference

Felipe Criado-Boado, Marta Programa de Investigación en Tecnologías para la CSD2007-00058Castillejo Striano (IFR-CSIC) conservación y revalorización del Patrimonio Until 31/12/2013 Cultural (Proyecto Consolider-Ingenio)

Luis Roso Franco Ciencia y aplicaciones de los láseres ultrarrápidos CSD2007-00013, y ultraintensos (Proyecto Consolider Ingenio) Until 31/12/2013

Principal Investigator Title Reference

Marta Castillejo Striano Control de Nanoestructuras Generadas From 01/01/2014 por Láser: Interacción Láser-Material y CTQ2013-43086 Procesos en el Plasma.

Member: Rebeca de Dinámica de procesos moleculares con From 01/01/2013Nalda Mínguez láser y métodos teóricos CTQ2012-37404-C02-01IP: Francisco Javier AoizMoleres (UCM, Madrid)

Ministerio de Ciencia e Innovación

Ministerio de Ciencia e Innovación

Ministerio de Educación y Ciencia

Ministerio de Economía y Competitividad

National Grants: individual

National Grants: coordinated

Scientific Report 2013/2014 Department of Low Dimensional Systems, 127 Surfaces and Condensed Matter

Principal Investigator Title Reference

Rafael Fort, Durabilidad y conservación de S2009/MAT-1629, Marta Castillejo Striano IQFR-CSIC geomateriales del patrimonio Until 31/12/2013 construido

Rafael Fort, Marta Castillejo Striano Tecnologías y Conservación de S2013/MIT-2914IQFR-CSIC: Geomateriales del Patrimonio From 01/10/2014

Participant: Rebeca de Nalda Mínguez. Diseño multiescala de DIMMAT, S2013/MIT- Coordinator: María Teresa Pérez-Prado materiales avanzados 2775(Fundación IMDEA Materiales, Madrid) From 01/10/2014

Consejería de Educación, Juventud y Deporte de la Comunidad Autónoma de Ma-drid. Programas de Actividades de I+D entre grupos de investigación de la Co-munidad de Madrid

Principal Investigator Title Reference

Tiberio Ezquerra Analysis in situ of Laser Induced SC3748 Periodic Surface Structures (LIPSS) Formation on Spin-coated Polymer Films

Tiberio Ezquerra “In situ” monitoring of Laser Induced Periodic SC3977 Surface Structures on conjugated polymers of interest in Organic Photovoltaics

Principal Investigator Title Reference

Participant: Rebeca de Nalda XLIC: XUV/X-ray light and fast From 13/05/2013Mínguez. IP: Manuel Alcamí ions for ultrafast chemistry (COST Action CM1204)(Universidad Autónoma, Madrid)

Principal Investigator Title Reference

Mari Cruz García-Gutiérrez Effects of laser induced periodic surface Proposal 20140340 structures on chain alignment and phase segregation in conjugated polymer blends

European Synchrotron Radiation Facility

European Union

Swiss Light Source (SLS)

International Grants: individual

International Grants: individual coordinated

Scientific Report 2013/2014 Department of Low Dimensional Systems, 128 Surfaces and Condensed Matter

Laser Materials and Interaction Laser-Materials Group

Tenured Staff scientists

Ángel Costela González (Professor) ReID ORCID SCOPUS

Inmaculada García-Moreno Gonzalo(Professor)

Clara Gómez Hernández (Assistant Professor)

Non-tenured scientists

Luis Cerdán Pedraza (Project Contract from 01/03/2013) ReID

Doctoral students

Luis Cerdán Pedraza (Project Contract until 28/02/2013)

Mª Eugenia Pérez-Ojeda Rodríguez (JAE-Pre fellowship until 10/2013)

Gonzalo Durán Sampedro (FPI fellowship)

SummaryThe research of the group continues centered in the design and development of new photonic systems based on photosensitized and nanostructured materials for advanced devices. We have continued the study on the processes that control the synthesis, performance and properties of both organic and organic-inorganic hybrid materials with specific properties and applications in the fields of biomedicine and optoelectronics. In particular, we have studied in depth the processes governing the synthesis, behavior and properties of the new materials in relation to their structure and nanostructure. We have designed and synthesized new molecular dyes, based on BODIPYs, which have shown optimized laser emission in the wide spectral region from the blue to the red. In the field of optoelectronics, we have demonstrated remarkable improvements in the

laser properties of the new materials when they incorporate scattering particles of nanometer size, which under certain conditions improve the conventional laser action through feedback non-resonant processes, and that in appropriate disordered systems give rise to coherent effects that result in the so-called random laser emission without the need of using resonant cavities external to the laser medium. We have also progressed in the understanding of the laser operation based on energy transfer processes where the active molecules are encapsulated into polymeric nanoparticles contained in colloidal suspensions. In the field of biomedicine, we investigate the use of gold nanoparticles in Photodynamic Therapy and continued our studies of nanostructured systems for controlled drug release and on the interaction of laser radiation with biological tissues.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 129 Surfaces and Condensed Matter

Strategic Aims• Development of new organic dyes with efficient and stable emisison in the blue, red, and

near infrared spectral regions.

• Development of organic dyes in the red and near IR spectral regions for applications in photodynamic therapy.

• Design, synthesis and analysis of new photosensitized materials nanostructured by the incorportion to linear and crosslinked homo- and copolymers of nanometric silica (polyhedral oligomeric silsesquioxanes, POSS), oxide nanoparticles (TiO2, ZnO) or metal nanoparticles (gold and silver), both bare or coated with dye-doped polymers or oxide layer (SiO2, TiO2, ZnO).

• Design, syntjesis and analysis of systems based on processes of energy transfer between active molecules encapsulated into structured nanoparticles.

• Structural, morphological, optical, photophysical and photochemical characterization of the synthesized dyes in liquid phase, confined in and covalently bonded to nanoparticles (polymeric, POSS, metal), incorporated into polymeric matrix (bulk, thin films), and into nanochannels (zeolite L).

• Characterization of the new materials as laser systems, microlasers, photonic coatings and random lasers.

• Study of the use of nanostructured systems in biological aplications (photodynamic and photothermal therapies; controlled release of drugs).

• Development, in collaboration with the company LASING S.A., of commercial laser systems based on our materials.

• Study of the laser radiation-biological tissue interaction to maximize the applications of the laser tool in dentistry.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 130 Surfaces and Condensed Matter

ResultsPhotosensitized and nanostructured materials for laser applicationsDuring the years 2013 and 2014 we have continued with the study and development of nanostructured materials, sensitized with organic dyes, where the emission properties are determined by appropriate physical and structural modifications. We have also delved in the study of the so-called “random” laser emission as well as in the processes of energy transfer (FRET: Förster Resonance Energy Transfer) between dyes encapsulated into nanoparticles.

We have obtained new dyes, with emission covering the spectral range from the blue to the red by modifications in the core of dipyrromethene dyes (BODIPYs), either by replacement of one or both of the fluorine atoms or by functionalization at the 8 position. We have also synthesized and characterized cassettes composed of dyads of new BODIPY-rhodamine dyes, as well as rosamine dyes with emission at wavelengths longer than 600 nm. The new dyes were developed in collaboration with the groups of Dr. J.L.Chiara (Instituto de Química Orgánica, CSIC), Prof. Mª José Ortiz (Departamento de Química Orgánica I, Universidad Complutense de

Fluorescence response of 8-amino BODIPY dyes (solutions in ethyl acetate; excitation at 366 nm)

Scientific Report 2013/2014 Department of Low Dimensional Systems, 131 Surfaces and Condensed Matter

Madrid), Prof. I. López Arbeloa (Departamento de Química Física, Universidad del País Vasco), Prof. K. Burgess (Department of Chemistry, Texas A&M University, USA), Prof. E. Peña Cabrera (Departamento de Química, Universidad de Guanajuato, México), and Prof. Xiao (State Key Laboratory of Fine Chemicals, Dalian University of Technology, China).

The laser properties of the new dyes were first evaluated in liquid solution, to be subsequently incorporated into various polymeric, hybrid and/or nanostructured media. Thus, these new materials were evaluated as laser emitters in bulk cylindrical matrices (1×1 cm) and in thin films, as well as in colloidal solution of nanoparticles containing dye mixtures. We consistently demonstrated laser efficiencies higher than in the corresponding commercial

dyes while maintaining high photostability. With respect to the “random” laser emission, we have studied the dependence of its properties with the packing fraction of nanoparticles. We have also systematically analyzed the FRET assisted emission in polymeric nanoparticles doped with dyes in terms of their photophysical and laser properties, and have used FRET dynamics to study the diffusion of dyes inside core/shell nanoparticles.

Finally, we have developed hybrid systems based on POSS nanoparticles labeled with chromophoric groups from fluorescent dyes linked to the inorganic rigid nucleus. These systems of POSS nanoparticles to which functionalized organic dyes are covalently linked have demonstrated to be useful as fluorescent bioprobes.

a) Laser emission of commercial dyes PM567 and PM597 (first and third from the left) and their derivatives with trifluoroacetoxy groups (to the right of the corresponding commercial dye) in distributed feedback structured PMMA thin film. b) Output intensity as a function of

pump intensity for PM567 (hollow circles) and its derivative (filled circles).

Scientific Report 2013/2014 Department of Low Dimensional Systems, 132 Surfaces and Condensed Matter

Laser emission of a rosamine dye (structure shown at the right) in ethanol solution as a function of dye concentration

Efficiency of the laser emission of different BODIPY dyes meso-

substituted and 3,5-meso-substituted in ethyl acetate solution. The numbers under

the peaks identify the corresponding dye.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 133 Surfaces and Condensed Matter

Sketch of a waveguide random laser

A) Normalized laser emission from colloidal suspensions of polymeric nanoparticles doped with commercial dyes Nile blue and Rhodamine 6G with different relative concentrations. Laser spectrum in yellow correspond to nanoparticles incorporating just Rh6G. B) Contour plot of a) laser efficiency (fL), b) laser energy transfer efficiency (fLET), c) FRET efficiency(fFRET), as a

function of both donor and acceptor concentrations.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 134 Surfaces and Condensed Matter

Complementary application of laser radiation in Periodontics and OrthodonticsLow level laser therapy (or Laser Phototherapy LP) exhibits a broad range of possibilities for application in the dental field and specifically in Periodontics and Orthodontics.

In collaboration with the Department of Stomatology III (Faculty of Dentistry, UCM, Madrid), we conducted a study with patients with chronic periodontitis, evaluating clinical, anti-inflammatory and osteoimmunological benefits of LP applied in repeated doses in combination with conventional periodontal therapy of scaling and root planing (SRP), compared with SRP applied as monotherapy. The results obtained showed clinical improvement of the disease with the two types of treatments. Applying adjunctive LP resulted in improvement of the periodontal scores, decrease of the IL-1βand TNF-α levels and a reduction of the RANKL / OPG ratio in the

gingival crevicular fluid (GCF).

In collaboration with the Department of Stomatology IV (Faculty of Dentistry, UCM, Madrid), a study with patients suffering from malocclusion due to severe dental crowding in the upper arch was carried out. The treatment involved the extraction of the maxillary second premolars and placement of fixed multibrackets and Nance button as an anchorage to achieve distalization of the maxillary first premolars. Quadrant 1 received adjuvant treatment with LP applied in repeated doses. Differences in pain, speed of the movement of distalation and RANKL and OPG concentrations in the GCF between orthodontic treatment and the same treatment complemented by LP were evaluated. A decrease in the perception of pain, an increase in the speed of distalation movement and a slight increase in values RANKL as consequence of a high bone resorption due to a fast orthodontic movement in early stages, were observed after application of repeated doses of LP.

Periodontal probe composed of a disposable light-diffusing tip covering a stainless steel autoclave handpiece.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 135 Surfaces and Condensed Matter

Esnal, I.; Bañuelos, J.; López Arbeloa, I.; Costela, A.; García-Moreno, I.; Garzón, R.; Agarrabeitia, A.R.; Ortiz, M.J. (2013). Nitro and amino BODIPYs: crucial substituents to modulate their photonic behavior. RSC Adv. 3, 1547-1556.

Cerdán, L.; Costela, A.; Enciso, E.; García-Moreno, I. (2013). Random lasing in self-assembled dye-doped latex nanoparticles: packing density effects. Adv. Funct. Mater. 23, 3916-3924.

Durán-Sampedro, G.; Agarrabeitia, A.R.; Cerdán, L.; Pérez-Ojeda, M.E.; Costela, A.; García-Moreno, I.; Esnal, I.; Bañuelos, J.; López Arbeloa, I.; Ortiz, M.J. (2013). Carboxylates versus fluorines: boosting the emission properties of commercial BODIPYs in liquid and solid media. Adv. Funct. Mater. 23, 4195-4205.

Esnal, I.; Urías-Benavides, A.; Gómez-Durán, C.F.A.; Osorio-Martínez, C.A.; García-Moreno, I.; Costela, A.; Bañuelos, J.; Epelde, N.; López Arbeloa, I.; Hu, R.; Zhong Tang, B.; Peña-Cabrera, E. (2013). Reaction of Amines with 8-MethylthioBODIPY. Dramatic Optical and Laser Response to Amine Substitution. Chem. Asian J. 8, 2691-2700.

Gartzia, L.; Yu, H.; Bañuelos, J.; López-Arbeloa, I.; Costela, A.; García-Moreno, I.; Xiao, Y. (2013). Photophysical and Laser properties of Cassettes Based on BODIPY and Rhodamine Pair. Chem. Asian J. 8, 3133-3141.

Costela, A.; Cerdán, L.; García-Moreno, I. (2013). Solid state dye lasers with scattering feedback. Prog. Quantum Electron. 37, 348-382.

Cerdán, L.; Martínez-Martínez, V.; García-Moreno, I.; Costela, A.; Pérez-Ojeda, M.E.; López Arbeloa, I.; Wu, L.; Burgess, K. (2013). Naturally Assembled Excimers in Xanthenes as Singular and Highly Efficient Laser Dyes in Liquid and Solid Media. Adv. Opt. Mat. 1, 984-990.

Esnal, I.; Valois-Escamilla, I.; Gómez-Durán, C.F.A.; Urías-Benavides, A.; Betancourt-Mendiola, M.L.; López Arbeloa, I.; Bañuelos, J.; García-Moreno, I.; Costela, A.; Peña-Cabrera, E. (2013). Blue-to-orange wavelength tunable laser emission from BODIPYs tailored combining meso-substitutions and push-pull effects. ChemPhysChem. 14, 4134-4142.

Pérez-Ojeda, M.E.; Trastoy, B.; Rol, A.; Chiara,

M.D.; García-Moreno, I.; Chiara, J.L. (2013). Controlled Click-Assembly of Well.Defined Hetero-Bifunctional Cubic Silsesquioxanes and Their Applications in Targeted Bioimaging. Chem. Eur. J. 19, 6630-6640.

Calderín, S.; García-Núñez, J.A.; Gómez, C. (2013). Short-term clinical and osteoimmunological effects of scaling and root planing complemented by simple or repeated Laser Phototherapy in chronic periodontitis. Lasers Med. Sci. 28(1), 157-166.

Benito, M.; Martín, V.; Blanco, M.D.; Teijón, J.M.; Gómez, C. (2013). Cooperative effect of 5-aminolevulinic acid and gold nanoparticles for photodynamic therapy of cancer. J. Pharm. Sci. 102(8), 2760-2769.

Cerdán, L.; Gartzia-Rivero, L.; Enciso, E.; Bañuelos, J.; López Arbeloa, I.; Costela, A.; García-Moreno, I. (2014). Focusing on charge-surface effects to enhance the laser properties of dye-doped nanoparticles. Laser Phys. Lett. 11, 015901 (6 pages).

Durán-Sampedro, G.; Esnal, I.; Agarrabeitia, A.R.; Bañuelos, J.; Cerdán, L.; García-Moreno, I.; Costela, A.; López Arbeloa, I.; Ortiz, M.J. (2014). First highly efficient and photostable E- and C-BODIPYs as dye lasers in liquid phase, thin films and solid state rods. Chem Eur. J. 20, 2646-2653.

Cerdán L.; Gartzia-Rivero, L.; Enciso, E.; López Arbeloa, I.; Costela, A.; García-Moreno, I. (2014). A FRET analysis of free dye diffusion in core/shell polymer nanoparticles. RCS Adv. 4, 22115- 22122.

Gartzia-Rivero, L.; Cerdán, L.; Bañuelos, J.; Enciso, E.; López Arbeloa, I.; Costela, A.; García-Moreno, I. (2014). Förster Resonance Energy Transfer and Laser Efficiency in Colloidal Suspensions of Dye-Doped Nanoparticles: Concentration Effects. J. Phys. Chem. C 118, 13107-13117.

Martínez-González, M.R.; Urías-Benavides, A.; Alvarado-Martínez, E.; Cristobal-Lopez, J.; Gómez, A.M.; del Rio, M.; García, I.; Costela, A.; Bañuelos, J.; Arbeloa, T.; López Arbeloa, I.; Peña-Cabrera, E. (2014). Convenient Access to Carbohydrate-BODIPY Hybrids by Two Complementary Methods Involving One-Pot Assembly of “Clickable” BODIPY Dyes. Eur. J. Org. Chem. 5659-5663.

Domínguez, A.; Gómez, C.; Palma, J.C. (2014). Efecto de la radiación láser de baja energía en la velocidad del movimiento dentario y en los niveles de RANKL y OPG en pacientes con tratamiento ortodóncico. Ortod. Esp. 52(2), 9-20.

Publications

Scientific Report 2013/2014 Department of Low Dimensional Systems, 136 Surfaces and Condensed Matter

COMPETITIVE FUNDING

Principal Investigator Title Reference

Angel Costela González New photonic systems based on dye-sensitized MAT2010-20646-C04 nanostructured materials for advanced devices. Design, synthesis and characterization

Principal Investigator Title Reference

M.H. Delville, Institut de Rational design of hybrid organic- COST Action MP1202Chimie de la Matière inorganic interfaces: the next stepCondensée de Bordeaux, towards advanced functionalUniversité Bordeaux, Francia materials

Ministerio de Ciencia e Innovación (MICINN)

European Commission Framework Programmes

National Grants: coordinated

International Grants: coordinated

Scientific Report 2013/2014 Department of Low Dimensional Systems, 137 Surfaces and Condensed Matter

Statistical Mechanics and Condensed Matter Group

Tenured Staff scientists

Noé García Almarza

(Assistant Professor) ReID ORCID

Eva González Noya

(Assistant Professor) ReID

Enrique Lomba García

(Professor) ReID ORCID SCOPUS

Claudio Martín Álvarez

(Assistant Professor. Until 10/24/2013)

Non-tenured scientists

Carl McBride (01/05/2013 - 01/10/2013)

Doctoral students

Cecilia Bores Quijano

Alberto Gallardo Sanz

Vicente Sánchez Gil

Scientific Report 2013/2014 Department of Low Dimensional Systems, 138 Surfaces and Condensed Matter

SummaryThe research carried out for the last two year focuses on the application of statistical mechanics and condensed matter theory tools in conjunction with simulation approaches in order to analyse problems of physico-chemical interest, basically in connection to phase transitions in bulk and under confinement, as well as adsorption processes in nanostructured

porous materials, in this latter instance, including the structural elucidation at the atomic level of newly synthesized materials. Our main contributions can be cast into three main complementary lines: methodology, systems of fundamental interest, and systems of experimental interest.

Strategic Aims• Development of new methodologies for the study of phase transitions.

• Study of phase transitions in complex fluids (water, liquid crystals, anomalous liquids)

• Self-assembly phenomena in simple models.

• Simulation and modelling of adsorption in disordered porous media (carbons, pillared interlayered clays) and ordered porous media (zeolites).

Scientific Report 2013/2014 Department of Low Dimensional Systems, 139 Surfaces and Condensed Matter

ResultsSystems with competitive interactionsUsing theoretical and simulation approaches we have studied phase equilibria in various systems with competitive interactions (Short range attractive-long range repulsive). This sort of interaction gives rise to the formation of a rich variety of mesophases (patters) at low temperature: clusters, lamellar phases, … Using Monte Carlo approaches enabled for the first time the determination of the complete phase diagram for a system with these characteristics. In collaboration with Gerhard Kahl (TUW), these systems were also studied under confinement in controlled pore glasses, providing a an explicit spatial description of the adsorbate structure by means of a new integral equation approach.

Phase equilibria under confinementUsing Monte Carlo methods, we managed to determine the phase diagram of a system with strongly anisotropic interaction (Lebwohl-Lasher model) under confinement. Effects of confinement and low dimensionality at low temperatures (where a vapour-liquid transition is present) and at high temperatures, in which an isotropic-nematic transition characteristic of liquid crystals occurs.

Self-assembled systems and microheterogeneityAnother of the main research lines in our group focuses on the simulation study of self-assembly processes of anisotropic colloidal particles. Our aim here is to further our knowledge and in the last instance predict the most stable crystalline structures emerging from the self-assembly process as a function of particle geometry. This is an extremely relevant topic in materials engineering for the bottom-up approach to the design of new materials. By means of crystal structure optimization procedures and free energy calculations, our studies in collaboration with the group of G. Kahl (TUW), have dealt with particles with heterogenous surface charges. We have found that this type of topology of the interactions stabilizes multiple crystalline phase, including a lamellar phase with interesting optical and mechanical properties. From a more

theoretical perspective, we have studied in a joint work with the group of M.M. Telo da Gama (U. Lisboa) a lattice version of the so called “Lisbone model” for colloidal particles with active sites. Using computer simulation we have determined its phase diagram, which turned out to exhibit rather exotic topologies: liquid-vapour equilibria with two critical temperatures, liquid phases with densities characteristic of a vapour phase, etc … Additionally, in collaboration with the group of Marcia Barbosa (UFRGS), Aurélien Perera (UPMC) and Diego Salgado (U. Vigo), we have started a full scale study of mixtures alcohol/water, in order to characterize thermodynamic and structural singularities, as well as the topology of the microheterogeneous structures, which can be thought as precursors of micellar systems. In line with these studies on microheterogeneity, we have also initiated a work in collaboration with Lev Sarkisov (U. Edinburgh) on ionic liquids under confinement, which represent promising materials both in the field of energy storage and carbon dioxide capture.

Adsorption in disordered porous materialsIn 2014 we publish an extensive work (Gallardo et al., 2014) in which we have collected all our experimental work -from adsorption experiments in collaboration with J.M. Guil (IQFR), J.Pires (U. Lisboa) D, to neutron scattering experiments (C. Cabrillo, IEM)- and simulation studies to investigate the behaviour of probe molecules adsorbed into pillared interlayered clays (PILCS). Our simulation results enable the interpretation of the anomalous behaviour of some of the samples studied. The core of this work was an essential part of the PhD thesis of Alberto Gallardo (defended in February 2015). Also, in collaboration with J.M. Guil, we have carried adsorption experiments of aromatic molecules, noble gases and methane into pure silica ZSM11. He it was detected for some of the compounds anomalous jumps in the adsorption volumetric and calorimetric curves (approximately at half filling). In order to get a microscopic insight into the origin of this behaviour, we have carried synchrotron X ray diffraction experiments at the ALBA facility (Barcelona) and neutron scattering experiments art he ISIS facility (Didcot, UK). Analysis of the diffraction patterns with an in-

Scientific Report 2013/2014 Department of Low Dimensional Systems, 140 Surfaces and Condensed Matter

house designed Reverse Monte Carlo code, together with Grand Canonical Monte Carlo simulations of the adsorption isotherms, indicate that the flexibility of the zeolite plays a crucial role in the adsorption process. The jump in the

adsorption curves could then be interpreted as a result of an spatial reordering of the adsorbate as a consequence of the flexibility of the zeolite framework during the loading process.

Figure 1. Neutron diffraction experiments of argon and methane adsorption into a ZSM11 zeolite carried at the ISIS facility (Dicot, UK).

Scientific Report 2013/2014 Department of Low Dimensional Systems, 141 Surfaces and Condensed Matter

Scientific Report 2013/2014 Department of Low Dimensional Systems, 142 Surfaces and Condensed Matter

Figure 2. Density map illustrating clustering effects for a system with competing interactions adsorbed in a controlled pore glass.

Figure 3. Clustering of [1-butyl, 3-metyl imidazolio]+ cations and [PF6]- inside a graphitic carbonaceous material.

Aragones, J.L.; Noya, E.G.; Valeriani, C.; Vega, C. (2013). Free energy calculations for molecular solids using GROMACS. J. Chem. Phys. 139, 034104.

Ashton, D.J.; Sánchez-Gil, V.; Wilding, N.B. (2013). Monte Carlo methods for estimating depletion potentials in highly size-asymmetrical hard sphere mixtures. J. Chem. Phys. 139, 144102.

McBride, C.; Noya, E.G.; Vega, C. (2013). A computer program to evaluate the NVM propagator for rigid asymmetric tops for use in path integral simulations of rigid bodies. Comp. Phys. Comm. 184, 885-890.

Pokalski, J.; Ciach, A.; Almarza, N.G. (2013). Periodic ordering of clusters in a one-dimensional lattice model. J. Chem. Phys. 138, 144903.

Lomba, E. (2014). Simple water-like lattice models in one dimension. Trans. R. Norw. Soc. Sci. Lett. 3, 63-74.

Almarza, N.G.; Pokalski, J.; Ciach, A. (2014). Periodic ordering of clusters and stripes in a two-dimensional lattice model. II. Results of Monte Carlo simulation. J. Chem. Phys. 140, 164708.

Gallardo, A.; Guil, J.M.; Lomba, E.; Almarza, N.G.; Khatib, S.J.; Cabrillo, C.; Sanz, A.; Pires, J. (2014). Adsorption of probe molecules in pillared interlayered clays: Experiment and computer simulation. J. Chem. Phys. 140, 224701.

Lomba, E.; Bores, C.; Kahl, G. (2014). Explicit spatial description of fluid inclusions in porous matrices in terms of an inhomogeneous integral equation. J. Chem. Phys. 141, 164704.

Lomba, E.; Høye, J.S. (2014). Critical region of D-dimensional spins: extension and analysis of the hierarchical reference theory. Mol. Phys. 112, 2892–2905.

Gonzalez, M.A.; Sanz, E.; McBride, C.; Abascal, J.L.F.; Vega, C.; Valeriani, C. (2014). Nucleation free-energy barriers with Hybrid Monte-Carlo/Umbrella Sampling. Phys. Chem. Chem. Phys. 16, 24913.

Mompeán, M.; González, C.; Lomba, E.; Laurents, D.V. (2014). Combining Classical MD and QM Calculations to Elucidate Complex System Nucleation: A Twisted, Three Stranded, Parallel β-sheet Seeds Amyloid Fibril Conception. J. Phys. Chem. B. 118, 7312.

Pokalski, J.; Ciach, A.; Almarza, N.G. (2014). Periodic ordering of clusters and stripes in a two-dimensional lattice model. I. Ground state, mean-field phase diagram and structure of the disordered phases. J. Chem. Phys. 140, 114701.

Sánchez-Gil, V.; Noya, E.G.; Lomba, E. (2014). Reverse Monte Carlo modeling in confined systems. J. Chem. Phys. 140, 024504.

Tavares, J.M.; Almarza, N.G.; da Gama, M.M.T. (2014). Three-dimensional patchy lattice model: Ring formation and phase. J. Chem. Phys. 140, 044905.

Almarza, N.; Martín, C.C.; Lomba, E. (2014). Phase behaviour of the confined lattice gas Lebwohl-Lasher model. Condens. Matter Phys. (Ukraine). 16, 43602.

Publications

Scientific Report 2013/2014 Department of Low Dimensional Systems, 143 Surfaces and Condensed Matter

COMPETITIVE FUNDING

Principal Investigator Title Reference

Noé García Almarza Theory and simulation in complex systems FIS2013-47350-C5-4-R

Enrique Lomba Garcia Physical processes under confinement: FIS2010-15502 adsorption, self-assembly and phase transitions

Principal Investigator Title Reference

Enrique Lomba Garcia Modelling and simulation in complex systems: S2009ESP-1691 MODELICO-CM.

Principal Investigator Title Reference

Enrique Lomba García Anomalous behavior and emerging 2011BR0046 structures in self-assembly systems

Ministerio de Economía y Competitividad

Comunidad de Madrid

CSIC/CNPQ

National Grants: individual

National Grants: coordinated

International Grants: coordinated

Scientific Report 2013/2014 Department of Low Dimensional Systems, 144 Surfaces and Condensed Matter

Surface Analysis and Mossbauer Spectroscopy Group

Tenured Staff scientists

José Francisco Marco Sanz (Associate Professor) ReID ORCID

Juan de la Figuera Bayón (Assistant Professor) ReID ORCID SCOPUS

Non-tenured scientists

Raquel Gargallo (Contract from 01/03/2014)

Doctoral students

Matteo Monti (until 01/09/2014)

Laura Martín García (from 01/01/2014)

Technical Staff

Carlos Alonso González

Scientific Report 2013/2014 Department of Low Dimensional Systems, 145 Surfaces and Condensed Matter

SummaryThe scientific activity of this research group focuses on the study and characterization of surface processes of very different nature through the use of microscopy and spectroscopy techniques in ultrahigh vacuum (including nanospectroscopic techniques based on synchrotron radiation). In particular, in the period 2013-2014 our interest has been centered on the study of the growth dynamics of thin films of oxides on different substrates and the study of surface and interfacial magnetism. Another important line of research of this group is the chemical, structural and magnetic characterization of transition metal oxides with different structures (spinel, perovskite...) and

with potential applications in the field of energy conversion and storage. A notable aspect of our activity is the construction of instrumentation for surface analysis. We note that this group is one of the few spanish groups that has full Mossbauer spectroscopy capabilities in its different modes (transmission, integral conversion electron, integral low energy electron), and that is the reference group in Spain for low-energy electron microscopy (LEEM), performed in collaboration with the groups of Lucia Aballe (Alba synchrotron, Barcelona), Kevin F. McCarty (Sandia National Laboratories, USA) and Andreas K. Schmid (Berkeley National Laboratory, USA).

Strategic Aims• Understanding the dynamics and growth mode of thin films (a few atomic layers thick) of

metal oxides on metal and oxide substrates. Determination of the structural and magnetic properties of these films.

• Modification of the magnetic properties of thin films of metal oxides by changing their growth parameters. Eventually, the design of devices and sensors based on the modification of these properties.

• Determination of the influence that the stoichiometry and the method of preparation have on the cation distribution and the magnetic properties of complex transition metal oxides.

• Construction and implementation of instrumentation for surface analysis.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 146 Surfaces and Condensed Matter

ResultsControlling the growth of high quality thin films and heterostructuresWork has been carried out to determine the conditions for growing high quality thin and ultrathin films of various oxides. This has been performed combining many different growing techniques.

Molecular beam epitaxy (MBE-O2) and oxidation of metallic films (MBE + O2)The MBE growth experiments have been carried out both at the XPS/STM/LEED system of the group in Madrid, and at several LEEM microscopes. In the former case, an auxiliary UHV chamber for sample preparation has been mounted on the main system. In that chamber, iron oxides have been grown on Ru either by deposition of iron in an oxygen atmosphere (MBE-O2) or by Fe deposition in UHV followed by a subsequent step of oxidation of the deposited metal film in an oxygen atmosphere (MBE+O2). In the latter case, we have started to explore the phase space of mixed Co and Fe oxides on Ru (0001) determining that, in the initial stages, the growth proceeds through the formation of one or two layers of an Fe-Co mixed monoxide, and that, in a later stage, three-dimensional islands of a spinel phase appear.

Electron gun evaporation (evapE)In collaboration with Dr. P. Prieto from the Department of Applied Physics of the UAM, and within the current research project, we have grown thin iron oxide films by evaporating iron metal in a reactive atmosphere varying the O2 partial pressure, substrate temperature (300-400ºC) and the growth rate. We have obtained nonstoichiometric Fe3O4 films on glass and MgO substrates which show biaxial magnetic anisotropy. It has been confirmed that the assistance with ions during the growth process produces amorphization of the films.

Ion beam assisted deposition by reactive sputtering (sputt-O2) Also in collaboration with the group of P. Prieto we have grown and characterized thin iron oxides films made by reactive sputtering from

a metallic Fe target. We have also grown films with the assistance of a second beam of ions with variable ion energy and O2

+ content. We used three types of substrate: MgO, glass and Si wafers, and temperatures > 300 ° C. We have optimized the growth conditions to obtain films with biaxial magnetic anisotropy on MgO substrates, what is characteristic of epitaxial growth. Apart from iron oxides, we have also tried the growth of cobalt ferrite films carrying out a comparative study of the use of a CoFe2 metal target and an insulator target of CoFe2O4. We have found that the use of a “buffer” layer of TiN optimizes the crystal growth on Si, which enables the integration of magnetite in Si-based devices. We have started the growth of thin films of BiFeO3 as well as oxide/metal (CoFe2O4/ CoFe2) and oxide/oxide (CoFe2O4/ Fe3O4) bilayers on silicon substrates.

Growth by pulsed laser deposition (PLD)In collaboration with the group of M. Castillejo of the IQFR we have added a PLD growth chamber directly connected to the main surface characterization system of our lab. We have grown up to 20 nm thick layers of monocrystalline FeO having a low vacancy concentration, something which is quite unusual in the bulk form of FeO.

Sol-Gel (SLG)In collaboration with the Surface Science Group of the UCM we have synthesized and characterized Fe oxide nanoparticles embedded in a silica thin film grown on a Si substrate. Experimental evidence has been obtained for the synthesis of hematite (α-Fe2O3), maghemite (γ- Fe2O3), β- Fe2O3 and magnetite (Fe3O4). The β phase is a rare Fe3+ oxide polymorph being this the first time that has been synthesized by sol-gel techniques and its Raman spectrum identified. We are working on optimizing the conditions to favor the β single-phase synthesis, trying to grow thinner and more homogeneous layers than the current ones. Remarkably so, we want to state that we have optimized the synthesis of ε-Fe2O3 particles, a metastable phase volume, in a silica matrix on Si substrates, obtaining samples with a low concentration of other phases. The particles are nano-sized as well as (and this is unusual for this phase) micrometric allowing therefore its detailed characterization by Raman spectroscopy.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 147 Surfaces and Condensed Matter

Figure 1. Surface analysis system with the new chamber to prepare samples by PLD

Structural, electronic and magnetic properties of oxide surfaces both from thin films and bulk single crystals. Thickness and surface effectsAn important part of the work has been directed to identify the phases of Fe oxides obtained by the techniques described in the previous section, as well as to study the behaviour of magnetite surfaces of bulk crystals. Mössbauer spectroscopy has been applied to films made by all methods as well as to complex oxides of the perovskite family (this work in collaboration with the Department of Chemistry, University of Birmingham, UK).

The Fe (Fe-Co) oxide films grown by MBE-O2,

MBE+O2 have been specifically studied by STM, LEED, XPS,LEEM, PEEM and XMCD. This has allowed to identify that the films correspond to Fe3O4 (Fe3-xCoxO4) islands onto a FeO (FexCo1-xO) layer. By LEEMwe have investigated the influence of the Fe flux and oxygen pressure in MBE-O2-grown oxides, finding a strong dependence on the relative composition and morphology of the FeO/Fe3O4 combination. In the case of cobalt-iron mixed oxides, we have detected polarization circular dichroism of magnetic origin in the oxygen atoms, and we have measured the spin and orbital magnetic moments of both the Fe and the Co atoms of the oxides. A study combining MFM ex-situ and XMCD-PEEM in-situ in the same micrometric islands is currently under way. Finally, we have characterized CoFe2O4 thin films on TiN / Si (100), and determined its degree of

Scientific Report 2013/2014 Department of Low Dimensional Systems, 148 Surfaces and Condensed Matter

crystallinity by channeling in RBS. These layers show a surprisingly high coercive field> 6KOe.

Characterization of magnetite films grown by evapE has been carried out by XRD. MOKE and reflectance, transmittance, resistivity and, in some samples, Seebeck coefficient measurements. We have observed a correlation between the lattice parameter, coercive field and the Seebeck coefficient in evapE / glass and n-type conductivity. Characterization of films grown by sputt-O2 has been ccarried out by MOKE, XRD, and resistivity measurements. We have correlated the low O2 content in the assistance beam with the existence of tensions in the magnetite films. The SLG / glass samples were characterized by XRD, Raman spectroscopy-microscopy, AFM and magnetic measurements, Mössbauer, SQUID and VSM.

Special attention has been paid to the study of the magnetic anisotropy of magnetite, comparing the results obtained on single crystal samples with those obtained on the thin films. The films exhibit properties usually assigned to the presence of antiphase boundaries, as well as a biaxial symmetry along the easy magnetization axes within the plane of the film. This has been determined by MOKE and, in some cases, FMR and SPLEEM. These directions do not match neither those of the volume nor those most frequently reported by other groups in thin films. Besides, polycrystalline samples grown by sputt-O2 on Si have no anisotropy, whereas those grown on glass show uniaxial magnetic anisotropy within the plane. We are currently studying the origin of these discrepancies, in order to control the magnetic anisotropy in applications. Given the

dominant role of antiphase boundaries in the magnetic properties of iron and iron-cobalt spinel films, it is highly relevant to be able to grow crystals or films free of antiphase-boundaries. In this area we are using the combination of MBE-O2 growth with real time observation of the growth front by LEEM microscopy to obtain films with well defined microstructure that includes highly perfect spinel 3-dimensional islands with lack antiphase boundaries as each island arises from a single nucleation event.

For reference purposes, and also due to their intrinsic interest, we have caracterized the surface of magnetite bulk single crystals, in particular the (100) orientation. We have observed the ferroelastic Verwey transition on the magnetite surface for the first time, and we have discovered a novel surface order-disorder transition at high temperatures. Exposure to oxygen at high temperatures produces the formation of more magnetite at the surface, while oxidation takes place at macroscopically separared regions. This effect has implications in the use of magnetite as a catalyst. Finally, we have measured the magnetic moment at the surface together with the micromagnetism by XMCD-PEEM and SPLEEM, respectively. In the first case, the observation of a reduced spin moment is explained in terms of a surface reconstruction, and has been reported in the first publication of the LEEM/PEEM station of the Alba synchrotron. In the second case, the surprising finding of the temperature evolution of the magnetic domains has been related with the strong changes in the magnetocrystalline anisotropy of magnetite, and its competition with the shape anisotropy.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 149 Surfaces and Condensed Matter

de la Figuera J.; McCarty K.F. (2013). Low-energy electron microscopy, in Surface Science Techniques, Eds. G. Bracco and B. Holst, Springer Series in Surface Sciences, 51, 531.

de la Figuera J.; Vergara L.; N’Diaye, A.T; Quesada A.; Schmid, A. K. (2013). Micromagnetism in (001) magnetite by spin-polarized low-energy electron microscopy. Ultramicroscopy 130, 77-81.

Gautier, J.L.; Monrás, J.P.; Osorio-Román, I.O.; Vásquez, C.C.; Bravo, D.; Herranz, T.; Marco, J.F.; Pérez-Donoso, J.M. (2013). Surface characterization of GSH-CdTe quantum dots. Mat. Chem. Phys. 140, 113-118.

Alcázar, G.A.P.; Zamora, L.E.; Tabares, J.A.; Piamba, J.F.; González, J.M.; Grenèche , J.M.; Martínez, A.; Romero J.J.; Marco, J.F. (2013). Evidence of magnetic dipolar interaction in micrometric powders of the Fe50Mn10Al40 system: melted alloys. J. Magn. Magn. Mater. 327, 137-145.

Whitaker, M.J.; Marco, J.F.; Berry, F.J.; Taith, C.; Blackburn, E.; Greaves, C. (2013). Structural and magnetic characterisation of the pryrochlores Bi2-xFex(FeSb)O7, (x=0.1, 0.2, 0.3), Nd1.8Fe0.2(FeSb)O7 and Pr2(FeSb)O7. J. Solid State Chem. 198 316-322.

Prieto, P.; de la Figuera, J; Sanz, J.M.; Marco, J.F. (2013). Effects of low energy ion bombardment on the formation of cubic iron mononitride thin films. Thin Solid Films 539, 35-40.

Oujja, M.; Sanz, M.; Rebollar, E.; Marco, J.F.; Castillejo, M.; Domingo, C.; Pouli, P.; Kogou, S.; Fotakis, C. (2013). Wavelength and pulse duration effect on laser induced changes on raw pigments used in paintings. Spectrochim. Acta A: Mol. Biomol. Spec. 102, 7-14.

Gurushinge, N.N.M.; de la Figuera, J.; Marco, J.F.; Thomas, M.F.; Berry, F.J.; Greaves, C. (2013). Synthesis and characterisation of the Ruddlesden-Popper phases Ln2Sr(Ba)Fe2O7 (Ln=La, Nd, Eu). Mater. Res. Bull. 48, 3537-3544.

Sanz, M.; Oujja, M.; Rebollar, E.; Marco, J.F.; de la Figuera, J.; Monti, M.; Bollero,

A.; Camarero, J.; Pedrosa, F.J.; García-Hernández, M.; Castillejo, M. (2013). Stoichiometric magnetite grown by infrared nanosecond pulsed laser deposition. Appl. Surf. Sci. 282, 642-651.

Palacio, I.; Monti, M.; Marco, J.F.; McCarty K.F.; de la Figuera, J. (2013). Initial stages of FeO growth on Ru (0001). J. Phys.: Condens. Matter 25, 484001.

Marco, J.F.; Gancedo, J.R.; Monti, M.; de la Figuera, J. (2013). Mössbauer spectroscopy and surface analysis en Mössbauer Spectroscopy: Applications in Chemistry, Biology and Nanotechnology, First edition. Cap. 22, pp. 455-469. V.K. Sharma, G. Klingelhofer y T. Nishida, eds. John Wiley & Sons.

Nie, S.; Starodub, E.; Monti, M.; Siegel, D.A.; Vergara, L.; El Gabaly, F.; Bartelt, N.C.; de la Figuera, J.; McCarty, K.F. (2013). Insight into Magnetite’s Redox Catalysis from Observing Surface Morphology during Oxidation. J. Amer. Chem. Soc. 135, 10091-10098.

Monti, M.; Sanz, M.; Oujja, M.; Rebollar, E.; Castillejo, M.; Pedrosa, F. J.; Bollero, A.; Camarero, J.; Cuñado, J.L.F.; Nemes, N.M.; Mompean, F.J.; Garcia-Hernandez, M.; Nie, S.; McCarty, K.F.; N’Diaye, A.T.; Chen, G.; Schmid, A.K.; Marco, J.F.; de la Figuera, J. (2013). Room Temperature In-plane <100> Magnetic Easy Axis for Fe3O4/SrTiO3(001):Nb Grown by Infrared pulsed laser deposition. J. App. Phys. 114, 223902.

Siegel, D.A.; Chueh, W.C.; El Gabaly, F.; McCarty, K.F.; de la Figuera, J.; Blanco-Rey, M. (2013). Determination of the structure of CeO2(111) by low-energy electron diffraction. J. Chem. Phys. 139, 114703.

de la Figuera, J.; Novotny, Z.; Setvin, M.; Liu, T.; Mao, Z.; Chen, G.; N’Diaye, A.T.; Schmid, M.; Diebold, U.; Schmid, A.K.; Parkinson, G.S. (2013). Real Space Imaging of the Verwey Transition at the (100) Surface of Magnetite. Phys. Rev. B 88, 161410.

Porras-Vázquez, J.M.; Pike, T.; Hancock, C.A.; Marco, J.F.; Berry, F.J.; Slater, P.S. (2013). Investigation into the effect of Si doping on the performance of SrFeO3-δ SOFC electrode materials. J. Mater. Chem. A 1, 11834-11841.

Publications

Scientific Report 2013/2014 Department of Low Dimensional Systems, 150 Surfaces and Condensed Matter

Alfonso, J.E.; Olaya, J.J.; Pinzón, M.J.; Marco, J.F. (2013). Potentiodynamic polarization studies and surface chemical composition of bismuth titanate (BixTiyOz) films produced through radiofrecuency magnetron sputtering. Materials 6, 4441-4449.

Alfonso, J.E.; Cárdenas, M.; Marco, J.F. (2013). Influence of fabrication paameters on crystallization, microstructure, surface composition, and optical behavior of MgO thin films deposited by rf magnetron sputtering. J. Supercond. Nov. Magn. 26, 2463-2466.

Cubillos, G.I.; Olaya, J.J.; Bethencourt, M.; Cifredo, G.; Marco, J.F. (2013) “Producción y caracterización de películas de óxido de circonio por espray pirólisis”. Rev. LatinAm. Metal. Mat. 33, 116-130.

Garrido-Ramirez, E.G.; Mora, M.L.; Marco, J.F.; Ureta-Zañartu, M.S. (2013). “Characterization of nanostructured allophane clays and their use as support of iron species in a heterogeneous electro-Fenton system”. Applied Clay Science 86, 153-161.

Bartelt, N.C; Nie, S.; Starodub, E.; Bernal, I.; Gallego, S.; Vergara, L.; McCarty, K.F.; de la Figuera, J. (2013). “Order-disorder phase transition on the (100) surface of magnetite” Phys. Rev. B 88, 235436.

Cubillos, G.I.; Bethencourt, M.; Olaya, J.J.; Alfonso, J.E.; Marco, J.F. (2014). “The influence of deposition temperature on microstructure and corrosion resistance of ZrOxNy/ZrO2 coatings deposited using RF sputtering” App. Surf. Sci. 309, 181-187.

Berry, F.J.; de Laune , B. P; Greaves, C.; Whitaker, M.J.; Thomas, M.F.; Marco, J.F. (2014). “Mössbauer spectroscopy in the investigation of new mineral-related materials”. Hyperfine Interact. 226, 545-552.

Alburquenque, D.; Vargas, E.; Denardin, J.C.; Escrig, J.; Marco, J.F.; Ortiz, J.; Gautier, J.L. (2014). “Physical and electrochemical study of cobalt oxide nano- and microparticles”. Mat. Charac. 93, 191-197.

Gurushinge, N.N.M.; Fones, J.C.; Marco, J.F.; Berry, F.J.; Greaves, C. (2014). “Fluorine insertion in the Ruddlesden-Popper phase La2BaFe2O7: the structure and magnetic properties of La2BaFe2O5F4”, Dalton Trans. 43, 2038-2043

McCarty, K. F.; Monti, M.; Nie, S.; Siegel, D.A.; Starodub, E.; El Gabaly F.; McDaniel, A. H.; Shavorski, A.; Tyliszczak, T.; Blum, H.; Bartelt, N.C.; de la Figuera, J. (2014). “Oxidation of Magnetite (100) to Hematite Observed by In-situ Spectroscopy and Microscopy”, J. Phys. Chem C. 118, 19768-19777.

Gómez-Ferrer, B.; García-Cortés, I.; Marco, J.F.; Jiménez-Rey, D.; Vila, R. (2014). “Decoupling of defect and short range order contributions to resistivity recovery measurements in binary alloys”. Phys. Rev. B 90, 220102 (R).

Quesada, A.; Rubio-Marcos, F.; Marco, J.F.; Mompean, F.J.; García-Hernández, M.; Fernández, J.F. (2014). “On the origin of remanence enhancement in exchange-uncoupled CoFe2O4-based composites”. Appl. Phys. Lett. 105, 202405.

Scientific Report 2013/2014 Department of Low Dimensional Systems, 151 Surfaces and Condensed Matter

COMPETITIVE FUNDING

Principal Investigator Title Reference

Juan de la Figuera Ultrathin films for oxides-based electronics. MAT2012-38045-C04-01 Real time growth, interface effects and magnetism

Ministerio de Economía y Competitividad

National Grants: coordinated

Scientific Report 2013/2014 Department of Low Dimensional Systems, 152 Surfaces and Condensed Matter

Research Support Services

Chromatography and Mass Spectrometry Service 155

Library 159

Management and Administration 170

Stockroom 170

Reception 170

Technical Support Units 172

• Electronics Workshop 172

• Mechanics Workshop 172

• Glassblowing Workshop 172

• Computer Support 172

• Building Maintenance 172

Scientific Report 2013/2014 Research Support 153 Services

Chromatography and Mass Spectrometry Service

Chromatography and Mass Spectrometry Service

Scientific Director

Rosa Lebrón Aguilar (Assistant Professor) ReID ORCID SCOPUS

Technical Director

Plácido Galindo Iranzo (Specialized Technician)

Technician

Asunción de Diago Gómez (Research Assistant) (retired in October 2014)

IntroductionThe Chromatography and Mass Spectrometry Laboratory of the Institute of Physical Chemistry “Rocasolano” has been working since 2002. During this time, different mass spectrometers have allowed to analyze a large number of substances, ranging from small molecules to proteins and polymers. In the biennium 2013-2014, a matrix assisted laser desorption/ionisation-time of flight mass spectrometer (MALDI-TOF), model Voyager-DE PRO (Applied Biosystems), has been available.

The Laboratory work is mainly focused on the determination of molecular masses by MALDI-TOF of molecules with masses ranging from 1,000 to 300,000 u, especially intact proteins. The analyses are carried out by qualified technical personnel belonging to the IQFR, and the detailed rules of operation are collected on the web site of the Laboratory (http://serviciomasas.iqfr.csic.es/).

Scientific Report 2013/2014 Chromatography and Mass 156 Spectrometry Service

Strategic Aims• Supporting tool for the research carried out by the different Departments of the IQFR, as well

as external users.

• Integrate and adapt existing mass spectrometric methodologies to the specific needs of our users.

Figure 1: MALDI plate with some sample preparations using 2,5-DHB matrix. The left image shows part of spot 63 as seen on the TV screen of the ion source observation optics.

ResultsDuring the period 2013–2014, a total of 664 analyses have been carried out, almost the same number of samples than in the previous biennium. Of these analyses, 89% have been performed for the various departments of the IQFR, and the rest of them, for other CSIC institutes (Institute of Polymer Science and Technology, Institute of General Organic Chemistry, Institute of Medicinal Chemistry, and Institute of Food Science, Technology and Nutrition).

As usual, analyses to confirm the molecular mass (before and after different treatments) of proteins, peptides, carbohydrates, colorants and silsesquioxane, among others, have been

carried out. In particular, off-line monitoring of the degradation of muropeptides and oligosaccharides involved in hydrolysis protein reactions has been the most demanded. Synthetic polymers have also been studied by the standard procedures, in order to determine their molecular mass distributions, repetitive units and terminal polymer groups

Finally, the Service has continued organizing, preparing and giving three courses on “Liquid Chromatography coupled to Mass Spectrometry” (26 h/course) within the Training Program of the CSIC, which highlights our commitment to education and training.

Scientific Report 2013/2014 Chromatography and Mass 157 Spectrometry Service

Library “BIQFR”

IntroductionThe Rocasolano Institute of Physical Chemistry was set up in 1946 at same time as the Biqfr. Its holdings come from the “National Institute of Physics and Chemistry” created in 1932. Commonly known as the Rockefeller Institute, it was the cradle of all the research teams in the different disciplines of Chemistry, not only in Madrid, but throughout Spain. Three elements characterize the Biqfr: its Collection, Space and Management.

Collection: Among these old collections -unique in Spain- can be found famous titles such as: Annalen der Physik, Chemische Berichte, Annalen der Chemie. These are scientific journals in which the first advances in physics and chemistry are recorded. The Biqfr holds a valuable holding, mainly journals, of which 113 are complete starting from the first issue, 11 date from the 19th century to our days, and 16 start prior to 1920.

Space: Designed by the architects M. Sánchez Arcas and L. Lacasa (1932), innovators at the time, the library is arranged longitudinally with the rest of the building. It has an easy access from the main entrance and faces South with three large windows illuminating the two floors containing the reading room. This provides a silent and conducive reading environment, according to the architect Antonio Bonet Correa. The floors were communicated inside with original spiral staircase of the “flown boat” style, which was recently replaced by another wooden one. Subsequently, a basement has been added and their rooms refurbished, while retaining the original style. Because of its singular interest the library is the subject of visits by architects from various universities.

Management: At its genesis, the Biqfr was organized in a way that was revolutionary for those days, free access was permitted, and display stands facilitated access to the latest and the previous year’s issues of the journals. The main goal has always been the satisfaction of its users. The Biqfr is considered by the scientific community as the Reference Scientific Periodical Library, a historical landmark in the service of innovation, and is obviously one of the most outstanding scientific libraries in Europe. It is a rare example of 80 years of continuous service to Spanish researchers.

Einstein, A. (1905). Ist die Trägheit eines Körpers von seinem Energieinhalt abhängig? Ann. Phys. 18, 639-641. (The

equation E=mc2).

Scientific Report 2013/2014 Library “Biqfr” 160

Library “Biqfr”

Library Manager

Esperanza Iglesias Fernández

Technicians

Jorge Pariente Moronta

Adoración Urrea Salazar

Ángel González González (until 01/03/2104)

Ángel Alonso Fernández (until 09/2013)

Assistant

Santiago del Olmo Rodríguez

Strategic Aims• New technologies.

• Access to knowledge.

• Supply Documents.

• Economic implication.

• Standard management.

• Special activity.

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ResultsNew technologiesSince the beginning of technological age, in the 90s, the Biqfr has been aware that the technological changes, that were happening so quickly, provide an opportunity to the library to link it to the concept value. In recent years, this concept has been the mainstay of technical

work to ensure that the library is competitive, proactive and even co-creative. By knowing the researchers’ perception of the library in relation to the alternatives offered by its competitors (eg. Google), the Biqfr has developed links with scientists, to help researchers achieve their goals. Because of this, the Biqfr has an edge on its competitors.

Let’s put it on a timeline!

Scientific Report 2013/2014 Library “Biqfr” 162

The Blog & Social Networks Our blog remains a key tool for dissemination and visibility. It posts news from all areas of science and innovation. In the period 2013-2014, there have been changes in the editorial line to promote and disseminate the activities developed in IQFR: Seminars series, conferences, activities of the Center and the Biqfr. Always with the same purpose: trying to democratize “Science” and bring it to the public in a fun and an entertaining way.

The interest of our blog’s followers remains constant. During 2013-2014, 600 news items were published: an average of 2 per day! During this biennium, we achieved 257,369 visits to reach a total of 1,400,000 visits. The activity of our followers on the social networks Twitter and

Facebook is constant and stable, as is the case with the Blog.

The Biqfr Blog is not only considered a scientific dissemination source in America (Mexico, Colombia, United States and Argentina) and Germany, but we have also detected that it begins to attract followers from other European countries (Russia, France, Switzerland & Ukraine) and even in Lebanon.

Access to knowledge Over the last two years, a main goal has been the implementation of a smart tool to accelerate the search for scientific information, providing a competitive advantage to Biqfr over Google, while saving the user time and mouse clicks. Customization functionality has achieved a tool on demand: iLumina.

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All specialized databases in the fields of Chemistry, Physics and Biomedicine, to which users of the Biqfr have access, are brought together. Through a single search box, with one-click access to PDF or HTML, the user can access full-text content directly through the detailed record or from the result list preview pane. The AtoZ resource manager, can be utilized independently or through the iLumina system, where it is now incorporated.

iLumina leverages with discovery technology (EBSCO Discovery EDS) employing a multi-faceted relevance ranking methodology, moreover setting up a unified index with all the Biqfr information resources to offer their users an easy and powerful access to the Biqfr holdings with a single search interface. Metadata from internal sources (AtoZ) and external (supplier database) are managed, to create a large and

high speed index. The resulting collection is vast in size and in scope, but local indexing allows exceptionally fast response times.

Features:• Depth of indexing provides high-quality

metadata for the most viewed resources.

• Revelancy-ranked results speed users to the information.

• Searchable full text available.

• Rich Metadata (Author Abstracts, Author Keywords, Subject Headings, Full Text of Articles, etc.)

• Widgets for SciFinder, Reaxys, NIST, ICSD, Social Network, and more.

• Customization of the specialized databases in activity area of Biqfr to avoid noise.

At the end of 2013, the Biqfr project “iLumina” was launched as a single entry point to access to scientific information. Observing the results of the statistics, we find that many searches have been made with few queries, in addition,

the returned results were analyzed carefully by consulting the abstracts, and then the most relevant and applicable search results were downloaded.

Main Databases

arXiv Oxford

BioOne Online Journals Publisher Provided Full Text Searching File

Center for Research Libraries Research Starters

Directory of Open Access Journals SciELO

eArticle Science Citation Index

EDS Publication Finder ScienceDirect

J-STAGE Scopus®

MEDLINE Supplemental Index

Years Sessions Searches Abstracts Downloads

2013 816 24304 367 249

2014 2570 42951 2035 820

Scientific Report 2013/2014 Library “Biqfr” 164

iLuminaIt is available from the CSIC’s site to the whole Institution, and ubiquitously through the VPN to Biqfr users. Technology for mobile devices is offered.

AtoZ The resources AtoZ holds 30,654 journals & books. The Biqfr current subscriptions are available online.

Simultaneously, This tool (AtoZ) has been an access point to library’s electronic resources.

In 2013, the access for e-journals and for eBooks was brought together into a single interface, when the users were used to the application.

27,612 sessions were been made in 2013 and 15,812 in 2014. Whereas 15,747 researches have been achieved in 2013, with a decrease 10,798 in 2014.

Upon launching iLumina, at the end of 2013, a decline is seen in activity, which strongly suggests that users prefer iLumina as a knowledge manager, while they still use AtoZ for a particular citation.

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Document supply: Inter librarian loan (ILL)The wealth of the Biqfr’s holdings satisfies the needs of its direct users, which is verified by the small number of documents requested to other centers and the significant number documents supplied to external centers such as universities, laboratories, and other CSIC centers. As expected from modern science, 98% of document transactions were journal articles and only 2% were book loans. Remarkably, the Biqfr supplied 17% of all the shared journal articles within the whole CSIC Library Network.

The ILL is the key indicator of a library’s quality. The Biqfr has consolidated its position as the main supplier center at the CSIC. Over the last 14 years, the average Biqfr ratio of the supplied documents to requested documents is ten. That is to say, the Biqfr supplied 10 times more documents than we requested from other centers. In the last years, this value decreased to 7, due to the insertion at the Institute of research lines in the areas of “Life Sciences” whose resources are not directly available to our library. In contrast, on the whole, the

CSIC Library Network is slightly deficitory as it requests 1.03 documents for every document that it shares.

Over the last years, the flow of internal transactions among CSIC libraries has dropped 35% compared to 2001-2003, due to the advance of new technologies and the collective contracting by CSIC of the large packages of electronic resources, provided by the main publishers and other Institutions.

Nevertheless the number of documents supplied to other institutions, has slowly decreased with sight fluctuations. The level of total transactions increased by 2.1 % between 2009 and 2010. On the other hand, it decreased in 2011 by 5.8%, to then experience an increase of 6.3% in 2012. This level is similar to that of 2007. However, in 2013 the number of documents loaned dropped by 6.3% and in 2014, it fell a further 12.8%. In 2014, we should remark that there was a 21% decline in the number of Biqfr supplied documents to the CSIC centers, which could be reasonably explained by a putative decrease of the CSIC’s scientific activity and the closing of libraries at some CSIC centers.

Scientific Report 2013/2014 Library “Biqfr” 166

During 2013, the total number of document transactions was 3,978 (both supplied and requested.) Of these, 3,505 documents were delivered (-0.3 % lower than 2012) with 1,800 being sent to the CSIC’s library Network (-2.1% lower than 2012) and 1,705 to other institutions (1.6% higher than 2012). Regarding our

requests, 473 documents (14.1% lower than 2012); were obtained from other libraries, of which 219 (7.1% lower than 2012) came from CSIC’s network and 254 documents (11.8 lower than 2012) were sent by other institutions. 19.7 % documents requested from other libraries were supplied by Subito. Of these 3,505

Scientific Report 2013/2014 Library “Biqfr” 167

documents supplied, 3,366 came from journal articles and 31 were book loans.

During 2014 total number of items loaned or borrowed was 3,505, of which 3,055 documents were delivered (12.8 % lower than 2013) with 1,420 being supplied to CSIC’s library Network (21.1% lower than 2013) and 1,635 to other institutions (4.1% lower than 2013). On the other hand, 450 documents (4.8% lower than 2013) were requested from other libraries, of which 251 (14.6% higher than 2013) came from CSIC’s network and 199 (21.6 % higher than 2013) were sent by other institutions, with 25.6 % of these documents coming from Subito. Of these 3,055 documents supplied, 3,024 came from journal articles, while 31 were book loans.

The number of book loaned to users was 35 in 2013 and 38 in 2012. The number of book loaned showed a marked decrease of 53% compared with 2012.

Economic implicationsDuring the last two years of economic crisis, the human and financial resources of the Biqfr, like the rest of the CSIC, have been severely damaged:

Our staff has been reduced by one third with one technician retiring and a second on extended leave. The remainder of the staff has been forced to fill gaps while maintaining its activity. In many cases this has been a difficult and arduous task, surpassed only by the goodwill and enthusiasm its members. The situation is further aggravated if you consider that staff is aging and further retirements are planned. This situation cannot be extended for much more time without risking a possible closing of the library.

In 2010, Biqfr had a book acquisition budget of 46.430 €. Afterwards, a centralized office, the URICI (Unit of Information Resources for Research) was placed in charge of the acquisition of books for the libraries of the network, and

Biqfr has been uninvolved in the selection of books. Furthermore, since 2012 no funds have been allocated acquire new books or journal subscriptions. So, unfortunately, since 2013 no new books related to the IQFR’s activity have been incorporated.

Furthermore, most journals are no longer subscribed to in paper, but only in the electronic format. Hence many are unavailable in the print edition, as is the case for the International Journal of Chemical Kinetics, Chemistry Letters, Russian Chemical Reviews (devoted to reviews, this is the English version of the legendary Uspekhi Khimii, the flagship of Russian Chemistry) etc. In 2013, due to economic cuts, many electronic resources were not subscribed to by the CSIC Library Network. In 2014 some subscriptions were renovated but all. This change represents an impoverishment of our cultural heritage, because some publishers (IOP, Wiley, Springer, etc.) cut electronic access when the subscription is dropped, even to the years that the journals were purchased in paper.

Currently only 44 journals are subscribed to in print, compared with 169 journals in 2012.

Standard management The Biqfr has continued the work of technical process, collections control, organization of the holding and signaling, maintaining the reading room service, etc.

Collection improvement In 2013, a project aimed to improve the collection by reviewing the holdings located in various IQFR offices or departments was executed. This required locating each of the 1193 items in different departments, checking to ensure that the location in the network collective catalog was correct, error correction if necessary, and finally, cataloging and classification of issues not included in the catalog.

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Administration-Stockroom-Reception

Management and Administration

Manager

Isabel Cabo Chaves (until 14/02/2014)

Antonio Rubinos Pérez (from 15/02/2014)

Administration

Julia Cano García (Paymaster)

Sagrario Salado Rey

José Enrique García Ortega

Elvira Calviño López (until 01/11/2013)

Gloria Alonso Gómez

Pilar Ruiz Lafita

Mª Mar de la Torre Tante

Gloria Pinillos Pérez (from 01/11/2014)

Stockroom

Consuelo Martín de Loeches (Stockroom Manager)

Eva María Carpintero Vázquez

Reception

Mercedes Sanz Martín (until 01/08/2014)

Ángela Manso Asensio (until 11/02/2013)

José Luis Rodríguez Garro (from 12/02/2013)

Technical Support Units

Electronics Workshop

Pedro Durán Martín (Head)

Miguel Rodríguez Artigas

Pedro J. Navarrete Bodorrey

Mechanics Workshop

José Antonio Serna Ferrero

Ignacio Sanz Gómez

Glassblowing Workshop

Nicomedes San Román Prieto

Computer Support

Antonio Díaz Pozuelo

David Armenteros Escabias

Building Maintenance

Jesús López Mascaraque (Head)

José Antonio Mulero Bravo

Juan Luis Martínez García

Memoria 2013/2014 Department of Low Dimensional Systems, 174 Surfaces and Condensed Matter

Memoria 2013/2014 Instrumentación 174 Singular

Singular Instrumentation

Laboratory for single crystal X-ray diffraction (DRXM)

The services offered by the laboratory are aimed at obtaining: a) single crystals, b) X-ray diffraction patterns of single crystals from samples of any nature: inorganic, organic, organometallic, macromolecular

(proteins, enzymes) and polymer fibers, and c) if required, the three dimensional structure of the sample.

http://www.xtal.iqfr.csic.es/DRXM/

Scientific Manager: Armando Albert and Martín Martinez-Ripoll

Chromatography and Mass Spectrometry Laboratory for the determination of molecular masses by MALDI-TOF of molecules with masses ranging from 1,000 to 300,000 u, especially

intact proteins.

http://serviciomasas.iqfr.csic.es/

Scientific Manager: Rosa Lebrón Aguilar

CSIC High-Field NMR Laboratory

The High Field NMR Laboratory has cutting edge instrumentation and proven experience of over 40 years in the analysis of biomolecular structure and dynamics. We also offer technical support with unique experiments developed in our group, many designed to study intrinsically unstructured proteins (IDPs). The laboratory also provides scientific advice for studying nucleic acids,

small molecules and natural products.

http://rmn.iqfr.csic.es/

Laboratory Director: Prof. Marta Bruix

Technical Manager: Dr. David Pantoja

Scientific Committee: Prof. Jorge Santoro

Dra . Mª Angeles Jimenez

X-ray diffractometer #1

Rotating anode X-ray source (2,7 kW, MicroStar, Bruker), 100 μ micro-focus, brilliance 3 times higher than conventional rotating anodes. CuK α radiation through Helios mirrors (Bruker).

Four-circle Kappa goniometer and CCD detector (Bruker).

Cryoprotecting system (Oxford Cryosystems) with N2 stream in the range 350-100 K.

(Responsibles: Armando Albert and Martín Martinez-Ripoll)

X-ray diffractometer #2

This equipment shares the X-ray source with diffractometer #1

Imaging plate Mar345dtb (MarResearch).

Cryoprotecting system (Oxford Cryosystems) with N2 stream in the range 350-100 K.

(Responsibles: Armando Albert and Martín Martinez-Ripoll)

Crystallyztion robots

Liquid handler for crystallyzation purposes, Glison and Innovadine, for scaling from militers to nanoliters. Setup for 96 or 192

crystallization experiments per plate.

(Responsibles: Armando Albert and Martín Martinez-Ripoll)

Scientific Report 2013/2014 Singular 175 Instrumentation

Gas chromatograph coupled to a quadrupolar mass spectrometer, fitted with sample introduction systems for liquids and gases

(Responsible: Rosa Becerra Arias).

Gas chromatographs for capillary and packed columns, with flame ionization detectors

(Responsible: Rosa Lebrón Aguilar).

Diffferential Optical Absorption Spectroscopy (DOAS)/on-ground, ship, airborne and satellite based instrument.

(Responsible: Alfonso Saíz López)

X-ray diffractometer #3

X-ray micro-source IμS (Bruker) for CuKαX-ray radiation. Multilayer optics Elm3 (Bruker).

Four-circle goniometer with APEX II detector (Bruker).

Cryoprotecting system (Oxford Cryosystems) with N2 stream in the range 350-100 K.

(Responsibles: Armando Albert and Martín Martinez-Ripoll)

Scientific Report 2013/2014 Singular 176 Instrumentation

Incoherent Broadband Cavity Enhanced Absorption Spectroscopy (IBBCEAS).

Chemiluminiscence NOx.

(Responsible: Alfonso Saiz López).

Bruker AV-600 spectrometer

Cryoprobe TXI (1H,13C,15N)/Z gradients

Probe TXI (1H,13C,15N)/5 mm

Probe TBI (1H,13C, BB)/5 mm/gradients

Probe TXI (1H,13C,15N)/8 mm/Z gradients

Probe (1H-BB reverse)/10 mm

(Responsibles: D. Pantoja, M. Bruix)

Bruker AV-800 US2 spectrometer

Cryoprobe TCI (1H,13C,15N)/Z gradients

Probe TXI (1H,13C,15N)/5mm/ Z gradients

Probe QXI (1H, 13C, 15N, 31P)/5mm/ Z gradients

(Responsibles: D. Pantoja, M. Bruix)

Resonance and off resonance fluorescence by lamp excitation (ROFLEX)/on-ground, airborne.

(Responsible: Alfonso Saíz López)

Scientific Report 2013/2014 Singular 177 Instrumentation

Linear Triple Quadrupole TQ-high resolution FT-ICR Mass Spectrometer

FT-ICR (Fourier Transform Ion Cyclotron Resonance Spectrometry) a mass spectrometry based on the effect produced by an intense magnetic field (generated by superconducting solenoids) over the trajectories of charged particles (cyclotronic motion). As regards other spectrometries, FT-ICR presents the best sensitivity and resolution currently available.

Our spectromter is a hybrid tandem MS of a Triple quadrupole (TQ) Agilent/Varian 320 in line with high resolution FT-ICR Agilent/Varian-920 spectrometer, which is provided with a 7.0 T actively shielded superconducting magnet.

• TQ is equipped with an electrospray ionization (ESI) source. It also has a nano-ESI source. Its 2nd quadrupole is a CID chamber. TQ can be coupled to chromatographic interfaces (either gas GC or liquid HPLC). The mass range of this spectrometer is between 20 and 2 000 m/z unids.

• Resolution of FT-ICR is in order of ppm. In MS terms it can be better than 106. This spectrometer includes a MALDI (matrix-assisted laser desorption ionization) module, whose range is between 50 and 10 000 m/z unids. In FT-ICR is possible to isolate ions and perform a separated analysis of each of them. It is also possible to kinetically excite (by radio frequencies, SORI-CID), selectively activate some of their bonds by IR radiation (IRMPD) or non-selectively activate by electron capture (ECD).

• These options, lead to the fragmentation or controlled sequenciation of ions and provides valuable information about the structure. The resulting technique allows not only to perform identification and structural analysis of wide variety of species (from small to macromolecular fragments) but being a powerful tool for following reactivity, energetics and molecular interactions in the gas phase.

(Responsible: Juan Z. Dávalos Prado)

Scientific Report 2013/2014 Singular 178 Instrumentation

Fluorescence multi-photon microscope and confocal laser scanning (Olympus IX-71 / Micro-Time 200-PicoQuant).

Excitation: Laser Ti-Za (2-photons; 750-850 nm, 80 MHz, 100 fs) diodes (405 nm, 482 nm; 2.5-40 MHz; 100 ps). Detection of fluorescence polarization, time-resolved ps-s (TTTR-TCSPC). Temperature Control

(Responsible: M. Pilar Lillo)

Microarray platform

(Responsibles: Dolores Solís/María Asunción Campanero-Rhodes)

Mössbauer Spectroscopy

(Responsibles: J.F. Marco and J. de la Figuera)

Matrix assisted laser desorption/ionization-time of flight mass spectrometer

(Responsible: Rosa Lebrón Aguilar)

Scientific Report 2013/2014 Singular 179 Instrumentation

Scientific Report 2013/2014 Facts and 181 Figures

IQFR Facts and FiguresFormación Académica:

• PhD awardees 182

• PhD fellowship/contract holders 184

• Post-doctoral fellowship/contract holders 186

• Scientist exchange 187

• Courses and scientific meeting organization 192

• IQFR seminars cycles 194

Technology Transfer and Socio-Economic Impact:

• Patents 196

• Awards and distinctions 196

• Editorial and scientific committees 196

• Media coverage 199

Scientific Cloister 201

Board of Institute 203

Gender distribution of scientific staff according to professional category 204

Summary of economic data 205

Name Department Date University Thesis title

José Ignacio Crystallography and 23/09/2013 Universidad Biología Estructural deBaños Sanz Structural Biology Complutense Inositol Kinasas, de Madrid enzimas implicadas en la regulación de inositol fosfatos

Cecilia Artola Crystallography and 07/04/2014 Universidad Biología Estructural de Recolons Structural Biology Complutense Máquinas Moleculares de Madrid de Reciclaje de Peptidoglicano. Implicaciones en Mecanismos de Resistencias a Antibióticos

Iván Acebrón Crystallography and 01/07/2014 Universidad Búsqueda racional de Ávalos Structural Biology Complutense nuevas etiquetas de de Madrid fusión: aplicaciones biotecnológicas de los dominios lectina trébol beta

Antonio Crystallography and 15/10/2014 Universidad Bases estructurales de Chaves Sanjuan Structural Biology Internacional la homeostasis del Menéndez potasio en plantas: Pelayo Regulación del transportador AKT1 y de la quinasa CIPK23

Juan Manuel Biological Physical 31/05/2013 Universidad Papel de la vitamina Ortiz Guerrero Chemistry de Murcia B12 en la actividad de una familia de factores transcripcionales con una novedosa arquitectura de dominios

Fernando Díez Biological Physical 22/02/2013 Universidad Análisis conformacional García Chemistry Complutense de péptidos prebioticos de Madrid plausibles y su interacción con ácidos nucleicos, arenos y nucleótidos

Soraya Serrano Biological Physical 04/06/2014 Universidad Interacciones Serrano Chemistry Complutense proteína-membrana: de Madrid una aproximación estructural por RMN utilizando sistemas modelo

PhD awardees

Academic Training

Scientific Report 2013/2014 Facts and 182 Figures

Name Department Date University Thesis title

Santiago Biological Physical 19/11/2013 Universidad The role of Gbp2p,Martínez Chemistry Autónoma Nab2p and Pub1p along Lumbreras de Madrid the mRNA cycle: structural studies by NMR and other biophysical techniques

Silvia Lisa Biological Physical 04/09/2013 Universidad Interruptores Ferrer Chemistry Complutense moleculares en la de Madrid génesis de PrP patógenas: Metionilsulfósxidos y sus modelos

Sebastián Biological Physical 08/10/2013 Universidad ConformationalRaja Chemistry Autónoma Dynamics and Assembly de Madrid of the Ribosomal Stalk Proteins

Nerea Martín Biological Physical 06/2013 Universidad Study of the StructurePintado Chemistry Autónoma and Stability of Nucleic de Madrid Acids with Modified Furanoses Using NMR María Encina Low Dimensional 01/07/2013 Universidad Aplicaciones de plumasLópez Arias Systems, Surfaces Complutense de ablación de and Condensed de Madrid semiconductores en Matter óptica no lineal y síntesis de nuevos materiales

Grégory Low Dimensional 07/03/2013 Universidad Dinámica deGitzinger Systems, Surfaces Complutense predisociación y control and Condensed de Madrid de la fotoionización de Matter yoduro de metilo con pulsos láser de femtosegundos

Luis Cerdán Low Dimensional 08/02/2013 Universidad Láseres de colorante Systems, Surfaces Complutense en estado sólido: and Condensed de Madrid retroalimentación Matter por dispersión y dispositivos integrados

Mª Eugenia Low Dimensional 10/07/2014 Universidad Preparación yPérez-Ojeda Systems, Surfaces Complutense aplicaciones ópticas and Condensed de Madrid de sistemas híbridos Matter orgánicos-inorgánicos basados en silsesquioxanos oligoméricos poliédricos (POSS) funcionalizados con colorantes fluorescentes

Matteo Monti Low Dimensional 11/07/2014 Universidad Ultrathin iron oxide Systems, Surfaces Autónoma films on Ru (0001) and Condensed Matter de Madrid

Scientific Report 2013/2014 Facts and 183 Figures

Name Funding body Starting date Supervisor Javier Gutiérrez Fernández CSIC 2011-2014 Juan A. Hermoso Cecilia Artola Recolons MINECO 2010-2014 Juan A. Hermoso Noelia Bernardo García MINECO 2010 Juan A. Hermoso Teresa Domínguez Gil-Velasco MINECO 2012 Juan A. Hermoso Alejandra Carriles Linares CAM 2014 Juan A. Hermoso Elsa Franco Echevarría MINECO 2012 Beatriz González Pérez María Ángela Polo Sainz CSIC 2013 Juliana Sanz Aparicio Mercedes Ramírez Escudero MINECO 2012 Juliana Sanz Aparicio Iván Acebrón Ávalos MINECO 2011-2014 José Miguel Mancheño Yanaisis Álvarez Sánchez CSIC-CITMA 2010-2014 José Miguel Mancheño Martín Martinez Ripoll Ernesto Moreno Antonio Chaves Sanjuan MINECO 2010-2014 Armando Albert

Department of Crystallography and Structural Biology

Name Funding body Starting date Supervisor Francisco Javier González FPI, MINECO 01/09/2010 JZ Dávalos Prado

Department of Structure, Energy and Chemical Reactivity

Name Funding body Starting date Supervisor Soraya Serrano Serrano FPI, MINECO 01/11/2009 M. Bruix, M.A. Jiménez Héctor Zamora Carreras FPI, MINECO 01/12/2012 M. Bruix, M.A. Jiménez Juan Manuel Ortiz Guerrero JAE-pre, CSIC 01/09/2008 S. Padmanabhan Santiago Martínez Lumbreras CAM 01/01/2009 J.M. Pérez-Cañadillas Angélica Inés Partida Hanón Proyecto 01/09/2014 M. Bruix, M.A. Jiménez Jesús Fernández Zapata FPI, MINECO 01/01/2014 S. Padmanabhan Aránzazu Gallego García Proyecto 01/10/2014 S. Padmanabhan Javier Martínez Fernández MINECO 01/09/2010 M. Gasset Erney Ramírez JAE-Pre (CSIC) 01/05/2010 P. Chacón Palma Rico Lastres FPI, MINECO 21/06/2010 M. Menéndez Lara López Merino JAE-Pre (CSIC) 01/11/2009 Mª D. Solís

Department of Biological Physical Chemistry

PhD fellowship/contract holders

Scientific Report 2013/2014 Facts and 184 Figures

Name Funding body Starting date Supervisor Guadalupe García CIBERES 15/06/2012 M. Menéndez Moreno Ioanna Kalograiaki FP7-ITN- GA:289003 01/08/2012 Mª D. Solís Radoslaw Borowski FP7-ITN-GA:317297 01/09/2013 Mª D. Solís Miguel Mompean García FPI 11/2012 D.V. Laurents/ C. González Nerea Martín Pintado JAE 06/2009 C. González Miguel Garavís FPI (CBMSO) 10/2009 C. González A. Villasante

Name Funding body Starting date Supervisor Ignacio López Quintás FPI, MINECO 01/09/2011 Marta Castillejo Striano y Margarita Martín Muñoz Luis Cerdán Research Project 01/10/2012- Angel Costela e 28/02/2013 Inmaculada García-Moreno

Mª Eugenia Pérez-Ojeda JAE-Pre (CSIC) 01/09/2009 Inmaculada García-Moreno y José Luis Chiara

Gonzalo Durán FPI, MINECO 01/08/2011 Inmaculada García-Moreno y Mª José Ortiz

Cecilia Bores Quijano FPI, MINECO 01/12/2011 Enrique Lomba García Vicente Sánchez Gil CSIC 01/10/2011 Eva González Noya

Matteo Monti FPI, MINECO 01/09/2010- Juan de la Figuera 01/09/2014 y J.F. Marco

Laura Martín FPI, MINECO 01/01/2014 Juan de la Figuera y J.F. Marco

Department of Low Dimensional Systems, Surfaces and Condensed Matter

Scientific Report 2013/2014 Facts and 185 Figures

Name Funding body Starting date Supervisor

Lisandro Otero NIH 2011-2013 Juan A. Hermoso César Carrasco López CSIC 2013 Juan A. Hermoso Iván Acebrón Ávalos CSIC 2013 Juan A. Hermoso Sergio Galán Bartual MINECO 2012-2014 Juan A. Hermoso Antonio Chaves Sanjuán MINECO 01/10/2014 María José Sánchez Barrena

Department of Crystallography and Structural Biology

Name Funding body Starting date Supervisor Carlos Alberto Cuevas Rodríguez MINECO 03/2013 Alfonso Saiz López Rafael Pedro Fernández Cullen MINECO 03/2013 Alfonso Saiz López Cristina Prados Román MINECO 03/2013 Alfonso Saiz López

Department of Structure, Energy and Chemical Reactivity

Name Funding body Starting date Supervisor M. Flor García Mayoral Project M. Bruix

José Ramón López-Blanco CAM/MI P. Chacón

Mónica Álvarez Pérez EU-FP7 01/06/2012 Mª D. Solís (GlycoHIT project) CSIC 12/05/2014 Noemí Bustamante Spuch CIBERES 30/11/2009 M. Menéndez

Mª Asunción Campanero JAEDoc (CSIC) 16/09/2011 Mª D. Solís Rhodes

Manuel Iglesias Bexiga CAM (BIPPED-2) 15/07/2012 M. Menéndez CSIC 13/02/2014 CIBERES 10/09/2014

Irene Gómez Pinto JAE 01/01/11 C. González

Department of Biological, Physical Chemistry

Post-doctoral fellowship/contract holders

Scientific Report 2013/2014 Facts and 186 Figures

Name Funding body Starting date Supervisor

Luis Cerdán Research Project 01/03/2013 Angel Costela e Inmaculada García-Moreno

Raquel Gargallo Research Project 01/03/2014 Juan de la Figuera

Department of Low Dimensional Systems, Surfaces and Condensed Matter

Name Home Destination Dates Department institution institution Teresa IQFR/CSIC Univ. de Notre 28/04/14- Crystallography Domínguez Dame (USA) 25/07/14 and Structural Gil-Velasco Biology

Renee Bouley Univ. de Notre Dame IQFR/CSIC 26/05/14- Crystallography (USA) 01/07/14 and Structural Biology

Ángel Vizoso Univ. de La Coruña IQFR/CSIC O1/10/2013- Crystallography 31/12/2013 and Structural Biology

Lourdes Infantes IQFR/CSIC CCDC 01/10/2013- Crystallography Cambridge, UK 30/09/2014 and Structural Biology

Laura Salum CIHIDECAR- QFR/CSIC 16/12/2013- Structure, CONICET, 14/03/2014 Energy and Argentina Chemical Reactivity

Violeta Universidad IQFR/CSIC 01/12/2014- Structure, Romero Federico 31/12/2014 Energy and Villarreal, Chemical Lima-Perú Reactivity

Arminda Universidad IQFR/CSIC 01/12/2014- Structure, Tirado Federico 31/12/2014 Energy and Villarreal, Chemical Lima-Perú Reactivity

Anoop Indian Institute IQFR/CSIC 04/2014 Structure, Mahajan of Tropical Energy and meteorology Chemical Reactivity

Juan Carlos University of Leeds IQFR/CSIC 04/2014 Structure, Gómez Martín Energy and Chemical Reactivity

Scientist exchange

Scientific Report 2013/2014 Facts and 187 Figures

Name Home Destination Dates Department institution institution

Chistopher University of New-York IQFR/CSIC 04/2014 Structure, Blaszczack- Energy and Boxe Chemical Reactivity

Rafael Pedro CONICET IQFR/CSIC 05/2014 Structure, Fernández Energy and Cullen Chemical Reactivity

María Navarro University of Miami IQFR/CSIC 08/09/2014 Structure, Energy and Chemical Reactivity

Héctor Zamora IQFR/CSIC IBG-KIT center 01/08/2014- Biological Physical 20/11/2014 Chemistry

D. Soler U. Girona IQFR/CSIC 14/01/2013- Biological Physical 13/05/2013 Chemistry

Carlos A. U. Nova de Lisboa IQFR/CSIC 11-18/02/2013 Biological Physical Salgueiro 01-14/07/2013 Chemistry 11–19/02/2014

Joana Dantas U. Nova de Lisboa IQFR/CSIC 11–18/02/2013 Biological Physical 01–14/07/2013 Chemistry

Palma Rico IQFR/CSIC University of 02/09/2013 Biological Physical Lastres Newcastle 30/11/2013 Chemistry

Ioanna IQFR/CSIC Semelweis University 26/03/2013 Biological Physical Kalograiaki Faculty of Health Chemistry and Public Services (Budapest)

Ioanna IQFR/CSIC Instituto de 06/10/2013 Biological Physical Kalograiaki Agro- 10/11/2013 Chemistry biotecnología CSIC-UPNA (Pamplona)

Ioanna IQFR/CSIC Royal Institute 08/09/2014 Biological Physical Kalograiaki of Technology 26/09/2014 Chemistry (KHT)

Ioanna IQFR/CSIC ATTANA AB 28/09/2014 Biological Physical Kalograiaki (Estocolmo) 10/10/2014 Chemistry

Radoslaw IQFR/CSIC CIB/CSIC 06/10/2014 Biological Physical Borowski 05/12/2014 Chemistry

Paul University of IQFR/CSIC 01-04/2014 Biological Physical Fitzpatrick Texas, Chemistry San Antonio/ EEUU

Scientific Report 2013/2014 Facts and 188 Figures

Name Home Destination Dates Department institution institution Santiago Ruiz University of IQFR/CSIC 09-11/2014 Biological Physical Martínez Gerona Chemistry

Patrick J.B. Massey University, IQFR/CSIC 04/2013 Biological Physical Edwards Palmerston North, Chemistry Nueva Zelanda

Hala Abou Assi Mcgill University, IQFR/CSIC 09-11/2014 Biological Physical Montreal/ Chemistry Canada

Alfredo CBMSO/CSIC IQFR/CSIC 01/01/2013 Biological Physical Villasante 31/12/2014 Chemistry

Daniele Istituto di IQFR/CSIC 27/01/2014- Low Dimensional Cioffini Fisica Applicata 30/07/2014 Systems, “Nello Carrara” Surfaces and Consiglio Nazionale Condensed delle Ricerche, Matter Sesto Fiorentino, Italia

Marta IQFR/ CSIC Blackett 09/2012- Low Dimensional Castillejo Laboratory, 02/2013 Systems, Striano Imperial College Surfaces and London, Condensed Reino Unido Matter

Mª Eugenia IQFR/CSIC Lund University, 01/05/2013- Low Dimensional Pérez-Ojeda Lund, Suecia 01/07/2013 Systems, Surfaces and Condensed Matter

Vicente IQFR/CSIC Universidad 08/10/2013 Low Dimensional Sánchez Gil Federal 08/11/2013 Systems, Rio Grande Surfaces and do Sul (Brasil) Condensed Matter

Vicente IQFR/CSIC Institute of Solid 01/09/2014 Low Dimensional Sánchez Gil State Physics, 01/11/2014 Systems, Budapest Surfaces and Condensed Matter

Cecilia IQFR/CSIC Universidad 23/05/2014 Low Dimensional Bores Quijano Federal 23/06/2014 Systems, Rio Grande Surfaces and do Sul (Brasil) Condensed Matter

Cecilia Bores IQFR/CSIC Technische 01/04/2013 Low Dimensional Quijano Universität Wien 21/12/2013 Systems, Surfaces and Condensed Matter

Scientific Report 2013/2014 Facts and 189 Figures

Name Home Destination Dates Department institution institution

Cecilia Bores IQFR/CSIC Department of 03/09/2014 Low Dimensional Quijano Chemical 03/12/2014 Systems, Engineering, Surfaces and University of Condensed Edinbourgh Matter Jakub Pekalski Institute of IQFR/CSIC 04/05/2013 Low Dimensional Physical 28/06/2013 Systems, Chemistry Surfaces and (Polish Academy Condensed of Sciences) Matter Varsovia Alexandre Universidad IQFR/CSIC 12/03/2014 Low Dimensional Furlan Federal Rio 10/04/2014 Systems, Grande do Sul Surfaces and (Brasil) Condensed Matter Enrique IQFR/CSIC Universidad 17/09/2013 Low Dimensional Lomba García Federal Rio 01/10/2013 Systems, Grande do Sul Surfaces and (Brasil) Condensed Matter

Enrique IQFR/CSIC Université Pierre 01/10/2014 Low Dimensional Lomba García et Marie Curie 02/11/2014 Systems, Jussieu (Paris) Surfaces and Condensed Matter

Noe García IQFR/CSIC Universidad 20/04/2014 Low Dimensional Almarza Federal Rio 02/05/2014 Systems, Grande do Surfaces and Sul (Brasil) Condensed Matter Eva González IQFR/CSIC Universidad 15/07/2013 Low Dimensional Noya Federal 27/07/2013 Systems,, Rio Grande Surfaces and do Sul (Brasil) Condensed Matter

Eva González IQFR/CSIC Technische 24/09/2014 Low Dimensional Noya Universität 02/10/2014 Systems, Wien (Austria) Surfaces and Condensed Matter

Matteo IQFR/CSIC Berkeley National 15/08/2013 Low Dimensional Monti Labs (EEUU) 26/10/2013 Systems, Surfaces and Condensed Matter

Scientific Report 2013/2014 Facts and 190 Figures

Name Home Destination Dates Department institution institution

Juan de la IQFR/CSIC Berkeley National 15/07/2013 Low Dimensional Figuera Labs (EEUU) 16/08/2013 Systems, Surfaces and Condensed Matter

José F. Marco IQFR/CSIC Universidad de 22/06/2013 Low Dimensional Chile (Santiago, 14/07/2013 Systems, Chile) Surfaces and Condensed Matter

Laura Martín IQFR/CSIC Berkeley National 31/07/2014 Low Dimensional García Labs (EEUU) 09/09/2014 Systems, Surfaces and Condensed Matter

Juan de IQFR/CSIC Berkeley National 24/07/2014 Low Dimensional la Figuera Labs (EEUU) 02/09/2014 Systems, Surfaces and Condensed Matter

José F. Marco IQFR/CSIC Universidad de 06/11/2014 Low Dimensional Santiago de 27/11/2014 Systems, Chile (Chile) Surfaces and Condensed Matter

Scientific Report 2013/2014 Facts and 191 Figures

Organizer Class Title Date Place

Juan A. Scientific Congress XIV Congress 11-13/06/2014 Alcalá de Hermoso of The Spanish Henares Biophysical Society

Juan A. Scientific Congress 11th European 28-31/05/2013 Madrid Hermoso Meeting on the Molecular Biology of the Pneumococcus

Juan A. Workshop Macromolecular 6-10/05/2013 Madrid Hermoso Crystallography Armando School Albert

Juan A. Workshop Macromolecular 26-31/05/2014 Madrid Hermoso Crystallography Armando School Albert

José Miguel Course Protein 11-12/04/2013 TARTU Mancheño Crystallography (Estonia) Course Rosa Lebrón Specialization Cromatografía 25-28/11/2013 IQFR/CSIC Aguilar course de Líquidos acoplada a la Espectrometría de Masas Rosa Lebrón Specialization Cromatografía 13-16/10/2014 IQFR/CSIC Aguilar course de Líquidos acoplada a la Espectrometría de Masas: 1ª edición 2014

Rosa Lebrón Specialization Cromatografía 27-30/10/2014 IQFR/CSIC Aguilar course de Líquidos acoplada a la Espectrometría de Masas: 2ª edición 2014 Marta Bruix Organizer Congreso GERMN 22-25/09/2014 Alcalá de Committee Henares

Marta Bruix Organizer Congreso SBE 11-13/06/2014 Alcalá de Committee Henares

Courses and scientific meeting organization

Scientific Report 2013/2014 Facts and 192 Figures

Organizer Class Title Date Place

Dolores Solís Workshop DYNANO- 30/09/2013 Centre of GLYCOPHARM 02/10/2013 Biological Summer School Research (CIB-CSIC) Dolores Solís Course Chemical Glycobiology 06/06/2013 UCD School & Biomedicine. of Chemistry Principles of and Chemical the Sugar Code Biology University College (Dublin)

Douglas.V. Symposium First Symposium of 20/02/2014 IQFR/CSIC Laurents Young Researchers of the “Rocasolano” Institute of Physical Chemistry

Mohamed Oujja Workshop within Laser cleaning 11/2013 y IQFR/CSIC CSIC Science 11/2014 Week Marta Castillejo Symposium “Laser Materials 27-31/05/ Strasbourg, Striano Interactions for 2013 France Micro and Nano Applications” E-MRS Spring Meeting Marta Castillejo User’s 4th LASERLAB- 26-27/09/ Laboratoire Striano Meeting Europe III 2013 Lasers, User’s Meeting, Plasmas et “Using laser sources Procédés and secondary Photoniques sources as (LP3), diagnostic tools Marsella, for science Francia

Esther Rebollar Workshop Jornadas de 23-24/09/ Instituto de González microscopía AFM. 2014 Estructura Presentación de de la Materia la plataforma CSIC, Madrid AFM MultiMode 8 de Bruker Nano Surfaces. Estado del arte, soluciones y sesiones prácticas de manejo del microscopio MultiMode 8

Scientific Report 2013/2014 Facts and 193 Figures

Organizer Class Title Date Place

CSIC training Course: Scientific Creation of 21/03/2013 Royal Botanical office Culture and digital Identity: Garden. (Biqfr) Communication The Web 2.0. Madrid CSIC-MadrI+D Outreach: the Night El Rockefeller 27/09/2013 IQFR/CSIC (Biqfr) of the Researchers y el espíritu The Rockefeller Rockefelleriano Building and its Spirit

Biqfr Workshops Presentation of 06/02/2014 IQFR/CSIC iLumina

Speaker Title Date

María José Sánchez Frequenin/NCS-1 as a pharmacological 17/12/2014 Barrena target for synapse regulation in X-linked mental retardation and autism

María José Sánchez Bin2 is a membrane sculpting N-BAR 13/02/2013 Barrena protein that influences leucocyte podosomes, motility and phagocytosis Lourdes Infantes Structural Information in Chemistry 18/11/2014

William Seitz Entropy vs. Mixing: What 27/05/2014 Determines Complexity Alfonso Saiz López Atmospheric Chemistry and climate group 04/06/2013 Carlos Alberto Evolution of NO2 levels in Spain from 1996 12/03/2014 Cuevas Rodríguez to 2012 and UVAS retrieval algorithms

Cristina Prados Román A negative feedback between 23/04/2014 anthropogenic ozone pollution and enhanced ocean emissions of iodine

Lara López Merino The galectins: so similar, 27/06/2013 so different

Palma Rico Lastres Structural and functional characterization 26/03/2014 of the LytB glucosaminidase from Streptococcus pneumonia

Noemí Bustamante Study of substrate specificity of 30/04/2014 Spuch CW_7 cell-wall binding-motifs from the Cpl-7 endolysin

IQFR seminars cycles

Scientific Report 2013/2014 Facts and 194 Figures

Speaker Title Date

Ioanna Kalograiaki Exploring glycosylation patterns 11/06/2014 in pathogenic bacteria and extracellular vesicles as markers for endogenous receptors

Rubén Martínez-Buey Recognition mechanisms of +TIPS 06/06/2014 proteins (TIP interacting proteins)

Nerea Martín Pintado Interacciones no convencionales 04/2013 en ácidos nucleicos modificados

Miguel Garavís Estructuras no canónicas en ácidos 18/06/2014 nucleícos teloméricos y centroméricos

Rebeca de Nalda Mínguez Detener el tiempo: pulsos de luz 08/05/2014 para observar cambios ultrarrápidos

Marta Castillejo Striano Laser controlled fabrication 18/11/2014 of nanostructures

Cecilia Bores Quijano Dinámica y transiciones de fase de 09/04/2014 fluidos complejos adsorbidos en vidrios porosos

Scientific Report 2013/2014 Facts and 195 Figures

Authors Title Year Code

Alfonso Saiz López, Sonda atmosférica 2014 ES 201431130 Arturo Alonso, para detección Chiara Cerruti, remota a alta Tomás Belenguer resolución de Dávila gases traza

Pedro García, Improved bactericidal 2013 (Spain) P201330777 Margarita Menéndez, enzybiotics against 2014 (International) PCT/ES2014/070429 Ernesto García, the pneumococcus Roberto Díez, and other bacteria Héctor de Paz, Noemí Bustamante

Technology Transfer And Socio-Economic Impact

Patents

• Marta Bruix: The RSEQ NMR Group (GERMN) Bruker Prize, September 2014.

• Nerea Martín Pintado, Prize of the best PhD thesis award in the field of NMR, granted by RSEQ NMR Group (GERMN)

• Luis Cerdán was awarded the Innova Scientific Award 2013 (awarded by Innova Scientific) to the best-published work on experimental photonics, and Premio Extraordinario de Tesis Doctoral.

Awards and distinctions

Participant Committee/Journal Role

Martín Martínez Ripoll, Comité editorial Coordinators and Juan A. Hermoso and Colección Divulgación authors Armando Albert Eds. CSIC (2014) ISBN: 978-84-00-09800-1 Book “A través del Eds. Catarata (2014) Cristal. Cómo la ISBN: 978-84-8319-906-0 cristalografía ha cambiado la vision del mundo”.

Armando Albert Grupo Especializado de Treasurer Cristalografía y Crecimiento Cristalino- RSEQ

Editorial and scientific committees

Scientific Report 2013/2014 Facts and 196 Figures

Participant Committee/Journal Role Alfonso Saiz López Mission Advisory Group of Mission and the European Space Agency’s scientific requirements Earth Observation Satellite Sentinel-5 Precursor, TROPOMI

Alfonso Saiz López Scientific Steering Committee Definition of of the international strategic goals: Surface Ocean-Lower atmospheric chemistry Atmosphere Study (SOLAS)

Alfonso Saiz López Scientific Report Editorial Board Member

Alfonso Saiz López Science, Nature, PNAS, Reviewer JGR, Geophysical Research Letters, Atmos. Chem Phys., Environmental Chemistry, NASA, NSF, NRC, DFG, NERC

Alfonso Saiz López Tropospheric halogen Coordinator sesión at AGU 2014 and EGU 2013 and 2014 meetings

María A. Gasset PLosOne Editor

M. Pilar Lillo ISRN Biophysics Editor

A. Ulises Acuña IUPAC Photochemistry Group Project member

Douglas V. Laurents Arch. Biochem. Biophys. Editorial Board Member

Marta Castillejo Striano Elected Member as Monitoring of user access Chair of the Board of User’s to laser infrastructures Representatives and Member within LASERLAB Europe. of Management Committee LASERLAB Europe, of LASERLAB Europe III Participation in the (Integrated Initiative of European management of the Laser Infrastructures Consortium. From 01/2009 (7º EU Framework Program)

Marta Castillejo Striano International Conference LACONA Member of Permanent (Lasers in the Conservation Scientific Committee of Artworks) From 11/2003

Marta Castillejo Striano International Conference O3A, Member of Permanent Optics for Arts, Architecture Scientific Committee and Archaeology, SPIE International Symposium on Optical Metrology, Munich, Germany. 06/2013

Scientific Report 2013/2014 Facts and 197 Figures

Participant Committee/Journal Role Marta Castillejo Striano International Conference Member of Permanent TECHNART 2013, Analytical Scientific Committee Spectroscopy in Art and Archaeology at the Rijksmuseum, Amsterdam. 23-27/09/2013 Marta Castillejo Striano International Symposium Member of Scientific “Light-Matter Interactions and Committee of the Materials” within the Symposium Internacional Conference on Lasers and Electrooptics, CLEO 2013 y CLEO 2014, San Jose, California, USA

Marta Castillejo Striano Symposium “Light-Matter Member of Scientific Interactions and Materials” Committee of the within the Internacional Conference Symposium on Lasers and Electrooptics CLEO Europe 2013, Munich, Germany

Enrique Lomba García Condensed Matter Physics (Ukraine) Member of the Editorial Committee

José F. Marco Applications of the Mössbauer Effect Member of the International Advisory Board (05/2007-05/2013)

José F. Marco International Symposium on the Member of the Scientific Industrial Applications of the Executive Committee Mössbauer Effect

José F. Marco International Conference on the Member of the Applications of the Mössbauer International Effect. 2013, Opatija, Croacia Programme Committee

José F. Marco Mössbauer Effect Data Center Member of the International Advisory Board (from 2007)

Scientific Report 2013/2014 Facts and 198 Figures

Name Media and date

Juan A. Hermoso CSIC (08/05/2014) http://bit.ly/1Ca2GB3

Juan A. Hermoso RTVE (08/05/2014) http://bit.ly/1ECFPhE

Juan A. Hermoso Terra (08/05/2014) http://bit.ly/1AhBJVC

Juan A. Hermoso DOCSALUD.com (20/05/2014) http://bit.ly/1C8tqjH

Juan A. Hermoso El Universal (09/05/2014) http://bit.ly/1FRLOwt

Juan A. Hermoso IMPACTO.mx (08/05/2014) http://bit.ly/1B8mT32

Juan A. Hermoso ABC salud (08/05/2014) http://bit.ly/1GIKkIv

Juan A. Hermoso La Voz Digital (09/05/2014) http://bit.ly/1xgtLLt

Juan A. Hermoso Entorno Inteligente (09/05/2014) http://bit.ly/1wyrkc6

Juan A. Hermoso Vive Sana (09/05/2014) http://bit.ly/1GIKFuu

Juan A. Hermoso Diario de Yucatán (08/05/2014) http://bit.ly/1F2TTzH

Juan A. Hermoso El Diario Montañés (08/05/2014) http://bit.ly/1FRN7LH

Juan A. Hermoso EFE-Futuro (08/05/2014) http://bit.ly/1wyrJLs

Juliana Sanz Aparicio madri+d:(23/4/2013) http://bit.ly/1Ca45Yj

Juliana Sanz Aparicio La Razón (25/4/2013) http://bit.ly/1D9WWqJ

Juliana Sanz Aparicio CSIC (22/04/0143) http://bit.ly/1D9XkWj

Juliana Sanz Aparicio SoloCiencia.com (22/04/2013) http://bit.ly/1b4xTd1

Juliana Sanz Aparicio Química y Sociedad (23/04/2013) http://bit.ly/1GvIYNJ

Juliana Sanz Aparicio Negocio Tecnológico (30/04/2013) http://bit.ly/1Ca4olT

Juliana Sanz Aparicio Diario de Sevilla (29/04/2013) http://bit.ly/1Bvpx7K

Juliana Sanz Aparicio paperblog – Empresa (01/05/2013) http://bit.ly/1AhDceM

Juliana Sanz Aparicio Anales de Química (2013, 109(2): 161-166) http://bit.ly/18eBMu4

Juliana Sanz Aparicio fisicahoy (23/04/2013) http://bit.ly/1wysK6l

Media coverage

Scientific Report 2013/2014 Facts and 199 Figures

Juliana Sanz Aparicio Bitnavegantes (22/04/2013) http://bit.ly/1xgvpg1

Juliana Sanz Aparicio Sinc (22/04/2013) http://bit.ly/1L1LQsb

Juliana Sanz Aparicio Asaja (26/04/2013) http://bit.ly/1C8PM4K

Martín Martínez Ripoll La ONU declara 2014 Año Internacional de la Cristalografía. En Análisis Madri+d, 28 Enero 2014 http://bit.ly/1NScvXg

Clara Gómez Ortodoncia Española (2014, 52(3): 7-15) (Prize of the best article edited in Ortodoncia Española, 2014)

Biqfr Support document management for the preparation of the book dedicated to the 75th anniversary of CSIC. (2014)

Biqfr Has been involved with several holdings in the exhibition: The Generation of 1914. Science and Modernity. Organized by de National Library 14/03-01/06 (2014)

Biqfr Has been involved with several holdings in the exhibition: Marie Sklodowska Curie: a Polish Woman in Paris. Organized by Natural Sciences Museum. 05/03-15/10 (2014)

Biqfr Has been involved with several holdings in the exhibition: The internationalization of Spanish Culture. Organized by the Students´Residence (from 24/11/2014)

Name Media and date

Scientific Report 2013/2014 Facts and 200 Figures

Scientific Cloister

President: Enrique Lomba García (Professor) (Until 03/07/2013)

Juan de la Figuera Bayón (Assistant Professor) (From 04/07/2013)

Secretary: Armando Albert de la Cruz (Associate Professor)

Members: A. Ulises Acuña Fernández (Professor Ad honorem)

Manuel Rico Sarompas (Professor Ad honorem) († 01/12/2014)

Claudio Gutiérrez de la Fe (Professor Ad honorem)

Marta Bruix Bayés (Professor)

Ángel Costela González (Professor)

Francisco Javier García de Abajo (Professor) (Until 31/05/2013)

Inmaculada García-Moreno Gonzalo (Professor)

Carlos González Ibáñez (Professor)

Juan A. Hermoso Domínguez (Professor)

Enrique Lomba García (Professor)

Martín Martínez Ripoll (Professor)

Rafael Notario Bueno (Professor)

Jorge Santoro Said (Professor)

Armando Albert de la Cruz (Associate Professor)

Rosa Becerra Arias (Associate Professor)

Marta Castillejo Striano (Associate Professor)

Ángel Cuesta Ciscar (Associate Professor) (Until 30/06/2013)

María A. Gasset Vega (Associate Professor)

Mª Ángeles Jiménez López (Associate Professor)

José Francisco Marco Sanz (Associate Professor)

Margarita Martín Muñoz (Associate Professor)

Margarita Menéndez Fernández (Associate Professor)

Subramanian Padmanabhan (Associate Professor)

Alfonso Saiz-López (Associate Professor)

Juliana Sanz Aparicio (Associate Professor)

Mª Dolores Solís Sánchez (Associate Professor)

Ángel Vegas Molina (Associate Professor) (Until 31/10/13)

Scientific Report 2013/2014 Facts and 201 Figures

Members: Pablo Chacón Montes (Assistant Professor)

Juan Z. Dávalos Prado (Assistant Professor)

Pablo Echenique Robba (Assistant Professor)

Juan de la Figuera Bayón (Assistant Professor)

Noé García Almarza (Assistant Professor)

Clara Gómez Hernández (Assistant Professor)

Eva González Noya (Assistant Professor)

Beatriz González Pérez (Assistant Professor)

Lourdes Infantes San Mateo (Assistant Professor)

Douglas V. Laurents (Assistant Professor)

Rosa Lebrón Aguilar (Assistant Professor)

Mª Pilar Lillo Villalobos (Assistant Professor)

José Miguel Mancheno Gómez (Assistant Professor)

Claudio Martín Álvarez (Assistant Professor) (Until 24/10/2013)

Rebeca de Nalda Mínguez (Assistant Professor)

José Mª Oliva Enrich (Assistant Professor)

José Manuel Pérez Cañadillas (Assistant Professor)

José Mª Santiuste Bermejo (Assistant Professor)

Silvia Zorrilla López (Assistant Professor) (Until 15/06/2013)

Esther Rebollar González (Ramón y Cajal Contract)

Mª José Sánchez Barrera (Ramón y Cajal Contract)

Scientific Report 2013/2014 Facts and 202 Figures

Board of Institute

President: Enrique Lomba García (Director until 03/07/2013) Juan de la Figuera Bayón (Director from 04/07/2013)

Secretary: Isabel Cabo Chaves (Administrator until 14/02/2014) Antonio Rubinos Pérez (Administrator from 15/02/2014)

Members: Carlos González Ibáñez (Vice director until 03/07/2013)

Juan de la Figuera Bayón (Vice director until 03/07/2013)

Douglas V. Laurents (Vice director from 04/07/2013)

Juan Dávalos Prados (Vice director from 04/07/2013)

Armando Albert de la Cruz (Head of Department of Crystallography and Structural Biology)

Rafael Notario Bueno (Head of Department of Structure, Energy and Chemical Reactivity)

Marta Bruix Bayés (Head of the Department of Biological Physical Chemistry)

José Francisco Marco Sanz (Head of the Department of Low Dimensional Systems, Surfaces and Condensed Matter).

Mª Dolores Solís Sánchez (Personnel representative)

Mª Carmen Pérez Bécares (Personnel representative until 12/06/2014)

Antonio Rubinos Pérez (Personnel representative until 14/02/2014)

Jesús López Mascaraque (Personnel representative)

Scientific Report 2013/2014 Facts and 203 Figures

Category Women Men

Professors 2 11Associate Professors 8 6Assistant Professors 8 11Scientific Investigators OPI 0 0 Contract Investigators “Ramón y Cajal” programme 2 0 Other Contract Scientist 2 2Graduated Technicians CSIC 1 5Contract Technicians 2 1Specialized Technicians OPI 5 4Research Assistants 4 4Laboratory Assistants 0 0

Total 34 44

Gender distribution of scientific staff according to professional category

Professors

Men

Women

Associate ProfessorsAssistant ProfessorsOther Contract ScientistGraduated Technicians CSICContract TechniciansSpecialized Technicians OPIResearch Assistants

ProfessorsAssociate ProfessorsAssistant Professors

Other Contract ScientistGraduated Technicians CSICContract TechniciansSpecialized Technicians OPIResearch Assistants

Cont. Invest. “Ramón y Cajal” programme

Scientific Report 2013/2014 Facts and 204 Figures

Concept 2013 2014

Ordinary Budget 421 625.24 514 002.45

Support to Infrastructures 114 923.04 118 823.45

Projects and Contracts, Total 848 442.06 929 437.18

Total 1,384 990.34 1,562 263.08

Summary of economic data

2013

2014

Projects and Contracts, Total

Projects and Contracts, Total

Scientific Report 2013/2014 Facts and 205 Figures

Ordinary Budget andSupport to Infrastructures

Ordinary Budget andSupport to Infrastructures

CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS

SERRANO 11928006 MADRID