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Chemistry research that matters
Van ’t Hoff Institute for Molecular Sciences
Valorisation at HIMS
Chemistryresearchthat matters
Van 't Hoff Institute for Molecular Sciences
The Van 't Hoff Institute for Molecular Sciences (HIMS) is one of eight research institutes of the Faculty of Science (FNWI) of the University of Amsterdam. HIMS houses 135 staff members from 34 nationalities. Together they publish over 180 peer reviewed scientific articles, 18 PhD theses and on average 4 patents per year. The institute focuses on top-quality chemistry research and at the same time has an open eye to technological applications and innovations. HIMS is organized in four strong research themes: Sustainable Chemistry, Analytical Chemistry, Computational Chemistry and Molecular Photonics.
Knowledge transfer to industry and society is in the DNA of our organization. On top of the four science themes we indicated several utilisation areas. These areas stimulate the collaboration between groups within the institute and are important for the visibility of the institute.
Researchers from HIMS contribute to several large national programs on conversion of sun light into electricity, fuels, or base chemicals like SOLARDAM, CatchBio or BioSolarCell. We participate in the Institute QuantiVision that aims to develop medical (imaging) devices and protocols for quantitative analysis of medical images to guide therapy and facilitate therapeutic interventions, with a focus on oncology and neurology. HIMS is also one of the academic partners of the Advanced Research Center for Nanolithography (ARCNL) that focuses on the fundamental physics involved in current and future key technologies in nanolithography, primarily for the semiconductor industry.
Science for Arts is an interdisciplinary research theme on art history, art conservation and science. Chemists from HIMS collaborate with physicists, researchers from the faculty of Humanities and the Rijksmuseum and Cultural Heritage Agency.
The Co van Ledden Hulsebosch Center (CLHC) is the interdisciplinary center of expertise for forensic scientific and medical research in Amsterdam and has its headquarters within HIMS. The CLHC serves to bundle the forensic experience, knowledge and expertise of the University of Amsterdam's Faculty of Science, the Academic Medical Center (AMC-UvA) and the Netherlands Forensic Institute (NFI).
On top of collaborations with third parties we sometimes develop our fruitful results into spin-off companies. Examples are catalysis company InCatT and bioplastic company Plantics.
At HIMS we are always looking for partnerships with industry to identify research questions that matter, transfer our knowledge and turn innovative ideas into reality. Maybe this brochure with posters on valorisation of our research inspires you to contact us via [email protected].
Joost Reek Director HIMS
Add name Research group
Phone: +31 (0)20 – 525 ****
Email: ****@uva.nl
URL: hims.uva.nl/***
Name
The Sustainable Chemistry theme is focused on the development of new technologies that enable efficient and sustainable chemical transformations. Efficient production of chemicals is crucial to ensure a sustainable society with a growing world population increasingly facing problems associated with scarcity of materials, energy and feedstock. Catalysis is the key enabling technique to ensure atom & energy efficient synthesis and to store and release chemical energy.
The theme works on the development of new (cheap and sustainable) catalysts to improve the efficiency of chemical transformations and to efficiently convert solar/electrical energy to fuels (electocatalysis, photocatalysis) and vice versa (fuel cells), thus contributing to solving energy and sustainability problems.
The strengths of the Sustainable Chemistry team are in catalyst design, synthesis, kinetics, (spectroscopic) characterization, modeling and testing catalysts under applied conditions. The team consists of a group of highly interdisciplinary and world-renowned top-researchers. The theme is strong in both fundamental research and applied catalysis, and was recently appointed as a university Research Priority Area.
On the fundamental side, the Sustainable Chemistry team collaborates with several top-scientists and renowned scientific institutes all over the world. Applied research is performed in close collaboration with several industrial partners and in spin-off companies.
Transition(base) metal catalysisKinetic DFT studies & spectroscopy
Fuel cell technology & electrochemistryHomo-, hetero-, organo- and bio-catalysis
Biomass conversion to fuels and chemicalsBio-inspired (supramolecular & metalloradical) catalysis
Short-cuts & new methods in (enantio)selective synthesis
Homogeneous and supramolecular catalysis
Homogeneous andsupramolecular catalysis
Key expertise:
HydroformylationAsymmetric hydrogenationC-C and C_X bond formationWater oxidation/proton reductionLigand synthesisCombinatorial approachesLead optimizationKinetics/mechanism
Industrial application of newly developed catalystsSolar to fuel devices (not on the poster)Phone: +31 (0)20 – 5256437
Email: [email protected]
URL: hims.uva.nl/***
Prof dr. JNH Reek
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One-pot Metallo-Radical Approach to 2H-Chromenes
Homogeneous, Supramolecular& Bio-Inspired Catalysis
2H-Chromenes are important structural motifsthat exist in numerous natural products (e.g.tannins and polyphenols found in teas, fruits, andvegetables) and medicines possessing interestingbiological activities (Figure 1).
Figure 1. Bio- and photo-active 2H-chromenes.
2H-chromenes are crucial substructure of a widevariety of known pharmaceutical agents and drugcandidates, and find applications as photochromicmaterials and dyes. However, all previouslydeveloped synthetic methods involve waste-generating multistep reactions, use complicatedpre-functionalized starting materials, have a limiteddegree of functional group tolerance and/or lead toformation of regioisomeric product mixtures.Therefore, the development of shorter, moreefficient and broadly applicable synthetic routestowards 2H-chromenes is in demand. Building onour ‘carbene-radical’ chemistry (Figure 2), werecently developed a novel metallo-radical route to2H-chromenes.
Figure 2. ‘Carbene-radicals’ in catalysis.
Figure 3. One-pot metallo-radical synthesis of 2H-chromenes fromalkynes and salicyl-N-tosylhydrazones.
Cobalt(III)–carbene radicals, generated bymetalloradical activation of salicyl N-tosylhydrazones by cobalt(II) complexes ofporphyrins readily undergo radical addition toterminal alkynes to produce salicyl-vinyl radicalintermediates (Figure 3). Subsequent hydrogenatom transfer leads to the formation of 2H-chromenes in a one-pot reaction. The processtolerates various substitution patterns and producesthe corresponding 2H-chromene products in goodisolated yields.
The successful development of this new catalyticreaction is expected to trigger further developmentsin catalytic radical-induced cyclization processes forselective syntheses of heterocycles that are difficultto prepare otherwise.
Developing new synthetic methodologies for (fine-chemical) organic synthesis based on cobalt metallo-radical chemistry.
A Metalloradical Approach to 2H-ChromenesPaul, N.D.; Mandal, S. Otte, M. Cui. X. Zhang, X.P.; de Bruin, B., J. Am. Chem. Soc., 2014, 136, 1090–1096
Phone: +31 (0)20 – 525 6495
Email: [email protected]
URL: hims.uva.nl/HomKat
Bas de Bruin
Functional Polymers via ‘Carbene Polymerization’
Homogeneous, Supramolecular& Bio-Inspired Catalysis
Non-functionalised polyolefins (e.g. polyethene)have found their way in many commodityapplications due to their outstanding properties,such as solvent resistance and thermal stability.Nowadays, these materials can easily be obtainedin large scales and at low cost with very highprecision of the polymer microstructures. However,due to their lack of functional groups they generallyhave poor surface chemistry properties.
Synthetic methods that allow controlledincorporation of polar functionalities into apolymeric carbon-chain are rather scarce. Themost widely-applied commercial approach toobtain functionalised polyolefins is post-functionalization reactions of existing polyolefinchains, requiring harsh reaction conditions withlimited control.
Over the past few years we developed a novelsynthetic method to prepare functionalized carbon-chain polymers; Rhodium-mediated ‘stereoregularpolymerization of functionalized carbenes’ proveda versatile new polymerization methodology(Figure 1).
Figure 1. ‘Rhodium-mediated ‘carbene-polymerization’.
The method involves an unusual carbenemigratory insertion chain-growth process whichelongates the polymeric carbon-chain with one‘carbene carbon’ unit in each insertion step. Thisallows formation of highly substituted and highlystereoregular (syndiotactic) carbon-chain polymerswith unusual properties.
Figure 2. Liquid-crystalline behavior of ‘poly-carbenes’
Variation of monomers & (co)polymersBesides a variety of different diazo compounds,
also sulfur yildes can be used as ‘carbene-monomer’ precursors. Copolymerization of different‘carbene monomers’ as well as copolymerization offunctionalized ‘carbenes’ with ethene provedpossible.
Figure 2. Co-polymerization of carbenes and ethene.
Developing new synthetic methodologies for functional, stereoregular polymer synthesis based on the rhodium-mediated ‘carbene polymerization’.
- B. de Bruin et. al. Chem. Eur. J., 2013, 19, 11577–11589.- B. de Bruin et. al. Angew. Chem. Int. Ed., 2012, 51, 5157-5161- B. de Bruin et. al. Chem. Soc. Rev., 2010, 39, 1706 - 1723
Phone: +31 (0)20 – 525 6495
Email: [email protected]
URL: hims.uva.nl/HomKat
Bas de Bruin
Smart Systems for Small Molecule Activation
Also actively involved inseveral projects related tocatalysis for sustainableenergy(e,g, electro- and photocatalytic H2 production, CO2 utilization)
Homogeneous, Bioinspired & Supramolecular Catalysis
Many challenges exist in (homogeneous) catalysis- direct conversion of C-H and C-C bonds,
formation of C-N and C-O bonds- selective functionalization of small molecules
(N2, NH3, H2O, CO2, P4 ...)- energy-related chemistry & biomass conversion
New concepts are required to induce paradigmshift in establishing such transformations- cooperative catalysis with smart (‘reactive’) and
adaptive ligands to activate substrates- bioinspired bimetallic catalysis- first row transition metal catalysis
Reactive ligand concepts are rapidly emerging asrelevant alternatives to ‘classical’ catalyticapproaches. We are actively pursuing thesestrategies, with the aim to unravel new low-energypathways for known reactions and to uncovertotally new reactivity and catalytic applications.
We have initiated a research program on first row& late transition metal chemistry with cooperativeand redox-active ligands.
Expertise & Interests
(Reactive) Ligand DesignSynthesis (Inorganic and Organometallic) Coordination ChemistryX-ray CrystallographySmall Molecule UtilizationCooperative CatalysisHydroaddition ReactionsPhotocatalysis & Energy
The group is highly interested in collaborative applied research[e..g. bilateral, TKI, STW, EU) on inorganic synthesis,ligand/catalyst screening, route scouting or analysis. Provenexperience with industrial projects (CatchBio, Aspect, Evonik,DSM)
JIvdV Angew. Chem. Int. Ed. 2009, 48,8832; Chem. Soc. Rev. 2010, 39, 2302;Chem. Eur. J. 2011, 17, 3850; Eur. J.Inorg. Chem. 2012, 363; Catal. Sci.Technol. 2013, 3, 1375; Inorg. Chem.2013, 32, 1682; J. Am. Chem. Soc.2014, 136, 11574; Angew. Chem. Int.Ed. 2014, in press
Phone: +31 (0)20 – 525 6459
Email: [email protected]
URL: http://www.homkat.nl/People
Dr.ir. Jarl Ivar van der Vlugt
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Understanding Catalysts and their Performance
Example: LiS Battery• Probing polysulfides and S-radical intermediates
during LiS battery cycling• Type of species and their rate of formation
depending on electrolyte solvent• Insights in battery deactivation mechanisms
Characterisation of Transition Metal Catalysts
The rational design of catalysts and materials isoften hampered by the lack of detailedunderstanding of their performance, i.e. theirchanging structural and electronic propertiesduring reaction to understand their reactionmechanism. We apply a breath of spectroscopytechniques, using different wavelengths andenergies, to provide complementary information onthe system under investigation. A special focus istowards X-ray spectroscopy methods.We do not only “just” apply available spectroscopytechniques, but also develop new techniques,including the required operando instrumentationand cells, as well as data analysis and theoreticalmethods.Application of the techniques to industriallyinteresting catalytic processes and materials hasbeen pursued, providing unprecedented insights incatalysts properties, reaction intermediates andmechanisms in the field of homogeneous andheterogeneous catalysis, photochemistry andphotocatalysis, electrochemistry and materialsscience. Example: Three Way Car
Exhaust Catalysts
Detailed understanding of reaction mechanisms and catalyst/material performance allow the rational design of new, better and more sustainable catalysts and materials and associated processes.
ACS Catalysis 2014, accepted for publication.J. Electrochem. 2014, submitted.Organometallics 2010, 29, 3085Angew. Chem. Int. Ed. 2007, 46, 5356AIP 2007, CP882, 858
Combined time/resolved UV-Vis/XAS set-up for homogeneous catalysis
Phone: +31 (0)20 – 525 6994
Email: [email protected]
URL: http://suschem.uva.nl/
Assoc. Prof. Dr. Moniek Tromp
X-rays Detection
S1 S2 S3
M1
M2D1
Exit
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S4
D2M2
UV: Light in
UV: Light out
Example: Industrial Ethene Trimerisation Catalyst• Activation: [CrCl3(decyl-SNS)] (5 mM) + 10 eq. AlMe3
– End state (~3 hrs): loss halide (methylation) and disproportionation– Catalytic Intermediate after 1 s: 4-coordinate Cr(II) with deprotonated NH
Spectro/electrochemical cell, allowing spatial resolved XAS on electrodes and electrolyte
Combined time-resolved XAS/DRIFTS/MS
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Inte
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, a.u
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Energy, eV
x=0.45 x=0.40 x=0.35 x=0.30 x=0.25 x=0.20 x=0.15
450 400 350 300 250 200 150 100
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x=0.45 x=0.30 x=0.15 x=0.00
High Throughput XAS/XRD/Raman/MS
Example: Pigments BiMoVOx• Doping oxidic materials - analyse structural and colouristic properties• Scrreening materials incl. UHV surface science and catalysis
Conversion of Biomass into High-value Chemicals
Ru nanoparticles areuniformly deposited onzirconia support andare resistant toagglomeration.
Heterogeneous Catalysis and Sustainable Chemistry
90% of chemicals are derived from crude oil now. Fluctuating prices and concerns over the environmental impact ofpetrochemical processes require developing sustainable and more environmentally-friendly alternatives. We research onconverting lignocellulosic biomass into high value chemicals using heterogeneous catalysts. Examples are conversion ofglycerol/lactic acid to acrylic acid, levulinic acid to -valerolactone and xylose to xylitol. The interaction of the catalysts withbiomass derived substrates and reaction environment are also studied by advanced spectroscopic and microscopictechniques.
Developing efficient heterogeneous catalytic routes tochemicals from biomass.Correlating structural properties of catalysts with activity.
(1) Bilge Coşkuner, Arturo Martínez-Arias, Gadi Rothenberg and N. RaveendranShiju, submitted to Green Chemistry.
(2) Carlos Hernandez Mejia, Heather Greer, Wuzong Zhou, GadiRothenberg, N. Raveendran Shiju, manuscript under preparation.
Phone: +31 (0)20 – 525 6515
Email: [email protected]
URL: hims.uva.nl/hcsc.
Shiju. N. R.
Levulinic acid-valerolactone
H2
H2
xylose
100% yield
Ru/ZrO2 catalyst
Ru/TiO2 rutile catalyst
Xylitol (>90% yield)
Ru/ZrO2 catalyst selectively converts levulinic acid to -valerolactone. The catalyst is not deactivated after several recycling tests.
Ru/TiO2 (rutile) catalyst selectively converts xylose to xylitol. The catalyst is stable and does not deactivate.
Activity of TiO2 supported Ru catalyst isstructure sensitive. Ru/TiO2-rutile catalystis more efficient than Ru/TiO2-anatase forconverting xylose to xylitol. TEM studiesshow that Ru nanoparticles are betterdispersed with small, uniform sizes onrutile TiO2. This may be due to the betterinteraction of RuO2 (rutile structure) withrutile TiO2.
Ru/rutile-TiO2
Ru/anatase-TiO2 catalyst. Ru is non-homogeneously distributed and particlesize is bigger. Also, a mismatch betweenRuO2 and TiO2 structures is evident fromthe model. This indicates the importance ofknowing the structural details whendeveloping catalysts.
Levulinic acid to -valerolactone
Xylose to xylitol
Metal-organic frameworks as selective adsorbers
Heterogeneous Catalysis and Sustainable Chemistry
In the chemical, petrochemical and pharmaceutical industries separation technology is a key element inthe production of pure compounds. A large portion of the production costs are associated with purificationsteps, for instance using solvent extraction, adsorption, crystallization and distillation processes.Metal-organic frameworks (MOFs) are a new class of porous materials whose surface area, pore structureand thermal stability depend strongly on their individual components. This makes them interesting forselective molecular separations. MOFs can separate molecules through either physical sieving or on thebasis of chemical affinity and even chemical bonding.
Developing new adsorbers for highly efficient molecular separations.
R. Plessius et al., Chem. Eur. J., 2014.Doi: 10.1002/chem.201403241
Figure 1. 3D structure of [La(pyzdc)1.5(H2O)2]·2H2O. Non-coordinated water molecules wereremoved for clarity.
Phone: +31 (0)20 – 525 7245
Email: [email protected]
URL: hims.uva.nl/hcsc
Ştefania Grecea
100 200 300 400 500 600 70060
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Figure 2. TGA curves of the MOF as synthesized (black),activated at 200 ⁰C (red), after 24 h air exposure (black) andafter 72 h air exposure (green).
Figure 3. Water (circles) and methanol (square) adsorption isotherms of the MOF activated at 200 ⁰C .
We designed a new MOF built from lanthanumions and pyrazine-based linkers. This MOF ismicroporous, with 1D channels that easilyaccommodate water molecules. Its framework ishighly robust to dehydration/hydration cycles.Unusually for a MOF, it also features a highhydrothermal stability. This makes it an idealcandidate for air drying as well as for separatingwater/alcohol mixtures. : ****@uva.nlc
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water in LaMOF;T = 298 K;D/rc
2 = 3.5 x10--4 s-1
Figure 4. Kinetic water adsorption measured at 25 C. The continuous red line represents the model fit of the experimental data for transient uptake.
The robustness of the frameworks is confirmed by XRD and the water adsorption. The isotherms arepractically identical after three consecutive activation-uptake cycles. Transient uptake measurementexperiments indicate that the intra-crystalline diffusivities in LaMOF are of the order of 10-14 m2s-1.Transient breakthrough simulations for water/alcohol mixture confirm that water/alcohol mixtures can beseparated cleanly using our MOF.
Advanced Electrochemical Devices for Efficient Power Generation, Energy Storage and Chemicals Production
Sustainable Chemistry
Fundamental Principles
Diversify the application of electrocatalysts, particularly in industrial reaction processes.
Utilize electrochemical device as an alternative method for various purposes at a larger scale.
• N. Yan, et. al., J. Power Sources, 198(2012), 164-169.
• N. Yan, et. al., RSC Adv., 4(2014), 118-131.
• N. Yan, et. al., in: “Solid Oxide Fuel Cells: From Materials to System Modeling”, Chapter 10, ISBN: 978-1849736541, RSC Publishing.
Phone: +31 (0)20 - 525 - 6468
Email: [email protected]
URL: Suschem.uva.nl
Name: Ning Yan
Novel Materials Advanced Materials Processing
ConfigurationsAn advanced electrochemicaldevice usually has a sandwichstructure, which is consisted ofan anode, an electrolyte and acathode. (right, a schematic ofproton exchange membranefuel cells
Operation modesAdvanced electrochemical devices can work in either fuelcells mode to generate electricity and capture CO2; orelectrolysis cells mode to store energy. Both modes canbe used to produce chemicals
Active sites in electrodesTriple-phase boundary (TPB),where the electronic conductor,ionic conductor and open poresmeet, is the active site ofelectro-catalytic process, all theindividual phase must bephysically contiguous.
To Design Catalysts used in the device should be affordable, activeand stable. Herein, mixed ionic and electronic conductor(MIEC, e.g., La0.4Sr0.6TiO3) was used to maximize TPBand promote stability while active phases providesufficient electro-catalytic activity
To UseNovel materials developed aresimple but not simplistic, and arereadily available for industrialapplications.(right, coking resist-ant coatings on 3D complexstructures)
To Understand Fundamental studies provide us insights into materialsbehaviors under different conditions. The examplereveal BaZr0.1Ce0.7Y0.2O3 electrolyte degrade inambient air through a microcrucible mechanism.
State-of-the-artTo minimize the ohimc loss, electrodes and electrolytemembranes should be adequately thin. We use spin-coating or screen printing to fabricate these thin dense/porous films
VersatileTo adapt the proper-ties of different elec-trode catalysts, infilt-ration methods wasdeveloped
ScalableHigh performance electrocatalysts are synthesized via a variety of methods, some of which, e.g., combustion and spray pyrolysis are compatible with industrial processes
Power Generation Energy Storage Chemicals Production
(a) electrolysis cells use surplus electricity from the grid or renewable sources to convert stored CO2 into fuels; (b) fuel cells generate power while directly capture CO2
Coke formed only on (c) and (d) without coatings (collaboration with Vale Ltd.)
(left) combustion methods for catalyst synthesis; (right) nanoparticles of CuCrO2 dehydrogenation catalyst
with high efficiency ( up to 80 %) using diverse fuel sources including hydrocarbons
and sour gas (H2S containing natural gas) with combined heat and power supply co-producing value-added chemicals
Electrochemical device can produce value-added chemicals through:
When the electrochemical device is working under fuel cell mode, it can generate electricity:
(a) Mass spectroscopic signals from anode effluent as a function of fuelcells overpotential and (b) the corresponding polarization and powerdensity curves, when 0.5%H2S-CH4 fuelled the cell using La0.2Ce0.8O2-La0.4Sr0.6TiO3 anode at 800 °C. The potential scan rate was 0.2 mV s-1.
(de)hydrogenation, e.g., ethylene production; (de)oxygenation, e.g., oxygen purification; Electrocatalytic selective oxidation, e.g., CO
concentration from syngas;
Ethylene production through electro-dehydrogenation of ethane while cogenerating electricity using Cu-Cr2O3 catalysts. (in collaboration with NOVA chemicals)
When the electrochemical device is working under electrolysis cell mode, it can convert excess power from the grid into chemical fuels while consuming H2O and CO2 only.
Catalysts play vital roles in products selectivity, e.g., H2 prefers to form on Ni while CO prefers to form on Zn;
System efficiency is the key and challenging factor of CO2 reduction, e.g., the current density is usually several mA cm-2
(left) a schematic of the electrolysis cell (right) the potential required todrive each individual reactions
Bronsted acid organocatalysisEfficient catalytic asymmetric Pictet Spengler reactions of Nb-substituted tryptamines have been developed. Important biologically active indole alkaloids have been synthesized. Currently, the chemistry is expanded to the isoquinolinenatural compound class series.
Mission: The development of efficient and selective, diversity-oriented synthetic methodologies, in particular organocatalyticand biocatalytic procedures, and the target-oriented preparation of molecules of relevance in chemistry, biology and medicine.
Solanoeclepin A A biologically active compound isolated from the roots of the potato plant. It is a potent hatching agent of the potato cyst nematode. Its unique structural features makes it a challenging synthetic target. The retrosynthetic analysis of solanoeclepin A reveals two synthetic fragments, the right- and left-hand side.
Peptide RotaxanesMicrocin J25 is an example of a naturally occurring rotaxane (a so-current methods. A new strategy is required to synthesize these natural rotaxanes. The steps to bind the building blocks on the scaffold are based on robust reactions: oxime-ligation
-reactions.
Chan-Lam peptide activationC-terminal peptide elongation by traditional coupling
epimerization due to the formation of oxazoloneintermediates. We currently develop an epimerization-free approach to peptide aryl esters via the so called Chan-Lam reaction. This is a Cu(II)-mediated esterification of carboxylic acids with aryl boroxines.
Cinchona alkaloid-based organocatalysisCinchona alkaloids are well known for their antimalariaproperties. In our lab these privileged molecules are elaborated further for organocatalytic purposes.
Add name Research group
Phone: +31 (0)20 – 525 ****
Email: ****@uva.nl
URL: hims.uva.nl/***
Name
Synthesis, analysis, and computational understanding of molecular systems are key disciplines for advancing chemical sciences, but the ultimate proof of their value must come from ‘seeing’ them at work and ‘steering’ them to perform user-defined tasks. The interaction of Light and Matter is per se at the basis of such endeavours. Not only does it allow the passive observation and characterization of molecular systems (molecular spectroscopy) but also to obtain emerging properties from their synergy (molecular photonics).
While the 20th century has been labelled as the century of the electron, it is now clear that the 21st century will be the century of the photon. The Molecular Photonics group harbours a power house of photochemical and photophysical expertise. It is in many aspects unique as it covers the complete trajectory from designing and constructing novel molecular systems to their application in areas of primary importance to society such as energy, sustainability, and health.
This is reflected in the strong interactions the groups has within and outside HIMS, such as the in 2014 started Advanced Research Center for Nano-Lithography, the free electron laser facilities (FELIX, FELICE) at Radboud University in Nijmegen, and medical research with the AMC and several companies.
Luminescent labels and probesSolar energy conversion
Molecular machineryMedical nanophotonicsBiomolecular dynamics
Molecules and Photons at Work
Molecular Photonics
Photoactive Materials SciencesThe interaction between Light and Matter allows forthe passive observation and characterization ofmolecular systems (molecular spectroscopy), butalso to obtain emerging properties from theirsynergy (molecular photonics). Applications rangefrom molecular machinery to medical imaging.
Example: advancing healthcare technologies
Understanding the intrinsic properties of molecularsunscreens is critical to developing more efficacioussunscreen products. Gas-phase spectroscopy andmicrosolvation studies provide innovative solutions.
Develop photoactive materials with user-defined propertiesExtend areas of commercial application of chiroptical techniquesOptimize catalytic activity nanoclusters
http://www.uva.nl/over-de-uva/organisatie/medewerkers/content/b/u/w.j.buma/w.j.buma.htmlPhone: +31 (0)20 – 525 6973
Email: [email protected]
URL: hims.uva.nl/research/research-themes/molecular-photonics/overview.html
Wybren Jan Buma
Chiral Structure AnalysisChiroptical techniques are emerging as powerfulmeans to determine the absolute configurationand conformational structure of chiralcompounds.
Tailoring Catalytic Activity on a Nanoscale
Example: development VOA analysis toolbox (together with TheoreticalChemistry (VU), SCM, andBioTools)
V.P. Nicu, to be published
Example: novel methods to increase efficiency and utility Vibrational Circular Dichroism (together with Prof. S. Woutersen)
Nanoclusters are rapidly gaining commercial interest because of their unusual chemical reactivity. This reactivity finds its origin in the electronic properties of the clusters. Gas-phase studies of structure and substrate binding offer detailed insight and pave the way for optimizing these properties.
Example: structure and reactivity Co clusters (together with Dr. J. Bakker and Prof. J. Oomens (FELIX, RU))
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Multi-dimensional Infrared Spectroscopy
Molecular Photonics
Unraveling the causes of Parkinson’sWe study the aggregation into fibrils of the protein α-synuclein with infrared spectroscopy. This aggregation process is responsible for Parkinson’s
disease. The mechanism of amyloid formation is poorly understood, and the structure of the (pathogenic) intermediates and the final fibril are still largely unknown and difficult to determine with conventional techniques. The combination of 2D-IR spectroscopy and vibrational circular dichroismoffers a unique insight into the kinetics and structure of the aggregation of α-synuclein into pathogenic fibrils.
Since amyloid fibrils are believed to be the thermodynamically most stable state of many proteins and peptides, the best hope for therapies lies in preventing fibril growth. The results of this research project, which is focused on the fibril nucleation and growth, should make a substantial contribution of our understanding of these processes, and thus help in developing therapies.
Understanding amyloid formation to help developing therapiesOptimizing catalyst performance using mechanistic insights
Nature Chemistry 5, 929 (2013). Inorg. Chem. 52, 14294 (2013).JACS 136, 3530 (2014). Inorg. Chem. 53, 5373 (2014).
Phone: +31 (0)20 – 525 7091
Email: [email protected]
URL: www.science.uva.nl/trvs
Prof. dr. Sander Woutersen
Catalyst structure and optimizationCatalytic complexes often occur in several conformations that exchange rapidly (<μs) in solution, so that their structures are difficult to characterize. Using 2D-IR spectroscopy on the CO and Rh-H stretching modes we have determined the structure of each of the two rapidly exchanging solution conformations of the hydroformylationcatalyst (xantphos)Rh(CO)2H.
This result demonstrates how 2DIR makes it possible to determine the structure of rapidly evolving, or exchanging, catalyst structures at the level of specific chemical bonds, and so to optimize their reactivity in a rationalistic manner.
10 μm
t = 0 h
t = 30 h
30 h0 h
Fluorescence Microspectroscopy in Materials Science
Molecular Photonics
Using a fluorescence microscope we image samples with spatial and temporal resolution and detectfluorescence parameters such as intensity, decay time, spectrum, etc. We apply this to the study ofpolymer dynamics, film formation in coatings and contact mechanics. Much of the potential of fluorescencemicroscopy for materials science is yet to be explored.
In these projects we develop tools to enable betterunderstanding of the physical properties of industriallyrelevant materials
1. J. R. Siekierzycka, et al., J. Am. Chem. Soc., 2010, 132, 1240.2. T. N. Raja, et al. Colloid. Polym. Sci., 2012, 290, 541–552.3. T. Suhina et al.submitted, 2014.
Phone: +31 (0)20 – 525 5491
Email: [email protected]
URL: hims.uva.nl/molphot
Prof. dr. Fred (A.M.) Brouwer
Single molecule free volume probe
Compound 1 has the unexpected and uniqueproperty that it emits fluorescence when in apolymer at temperatures below the glass transition.Increasing the temperature above Tg leads to thedisappearance of the fluorescence. This providesan optical method to observe the glass transition.
Single nanoparticles visualize latex film formation
Water borne coatings made from latex dispersionsrequire coalescence of the particles in order for arobust film to be formed. We can observe thisprocess directly by labeling the polymer in someparticles with a fluorescent dye molecule.
Contact-sensitive fluorescent monolayer
190 °15 h
PMATg = 10 °C
singlemoleculesat T < Tg
No moleculesdetected at T > Tg
Mechanical contacts between objects controlmany phenomena, from avalanches to friction. Incollaboration with prof. Daniel Bonn (Institute ofPhysics) we develop methods to visualizecontacts using fluorescence microscopy.A viscosity sensitive molecule is in a monolayer ona glass surface, and a plastic bead is presseddown on it with controlled force. Due to thedeformation of the bead, a contact area is formed.
The contact is directly observed as around fluorescent spot. Its radius nicelyfollows Hertz’s theory (1881). We seedetailed structure inside the spot due tothe roughness of the surface of the bead.
PVAc
After heating overnight theoriginal particles can no longerbe recognized in the confocalimage due to diffusion of thefluorescently labeled polymer.
Fluorescence Microspectroscopy in Materials Science
Molecular Photonics
Using a fluorescence microscope we image samples with spatial and temporal resolution and detectfluorescence parameters such as intensity, decay time, spectrum, etc. We apply this to the study ofpolymer dynamics, film formation in coatings and contact mechanics. Much of the potential of fluorescencemicroscopy for materials science is yet to be explored.
In these projects we develop tools to enable betterunderstanding of the physical properties of industriallyrelevant materials
1. J. R. Siekierzycka, et al., J. Am. Chem. Soc., 2010, 132, 1240.2. T. N. Raja, et al. Colloid. Polym. Sci., 2012, 290, 541–552.3. T. Suhina et al.submitted, 2014.
Phone: +31 (0)20 – 525 5491
Email: [email protected]
URL: hims.uva.nl/molphot
Prof. dr. Fred (A.M.) Brouwer
Single molecule free volume probe
Compound 1 has the unexpected and uniqueproperty that it emits fluorescence when in apolymer at temperatures below the glass transition.Increasing the temperature above Tg leads to thedisappearance of the fluorescence. This providesan optical method to observe the glass transition.
Single nanoparticles visualize latex film formation
Water borne coatings made from latex dispersionsrequire coalescence of the particles in order for arobust film to be formed. We can observe thisprocess directly by labeling the polymer in someparticles with a fluorescent dye molecule.
Contact-sensitive fluorescent monolayer
190 °15 h
PMATg = 10 °C
singlemoleculesat T < Tg
No moleculesdetected at T > Tg
Mechanical contacts between objects controlmany phenomena, from avalanches to friction. Incollaboration with prof. Daniel Bonn (Institute ofPhysics) we develop methods to visualizecontacts using fluorescence microscopy.A viscosity sensitive molecule is in a monolayer ona glass surface, and a plastic bead is presseddown on it with controlled force. Due to thedeformation of the bead, a contact area is formed.
The contact is directly observed as around fluorescent spot. Its radius nicelyfollows Hertz’s theory (1881). We seedetailed structure inside the spot due tothe roughness of the surface of the bead.
PVAc
After heating overnight theoriginal particles can no longerbe recognized in the confocalimage due to diffusion of thefluorescently labeled polymer.
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2050
2000
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Multi-dimensional Infrared Spectroscopy
Molecular Photonics
Unraveling the causes of Parkinson’sWe study the aggregation into fibrils of the protein α-synuclein with infrared spectroscopy. This aggregation process is responsible for Parkinson’s
disease. The mechanism of amyloid formation is poorly understood, and the structure of the (pathogenic) intermediates and the final fibril are still largely unknown and difficult to determine with conventional techniques. The combination of 2D-IR spectroscopy and vibrational circular dichroismoffers a unique insight into the kinetics and structure of the aggregation of α-synuclein into pathogenic fibrils.
Since amyloid fibrils are believed to be the thermodynamically most stable state of many proteins and peptides, the best hope for therapies lies in preventing fibril growth. The results of this research project, which is focused on the fibril nucleation and growth, should make a substantial contribution of our understanding of these processes, and thus help in developing therapies.
Understanding amyloid formation to help developing therapiesOptimizing catalyst performance using mechanistic insights
Nature Chemistry 5, 929 (2013). Inorg. Chem. 52, 14294 (2013).JACS 136, 3530 (2014). Inorg. Chem. 53, 5373 (2014).
Phone: +31 (0)20 – 525 7091
Email: [email protected]
URL: www.science.uva.nl/trvs
Prof. dr. Sander Woutersen
Catalyst structure and optimizationCatalytic complexes often occur in several conformations that exchange rapidly (<μs) in solution, so that their structures are difficult to characterize. Using 2D-IR spectroscopy on the CO and Rh-H stretching modes we have determined the structure of each of the two rapidly exchanging solution conformations of the hydroformylationcatalyst (xantphos)Rh(CO)2H.
This result demonstrates how 2DIR makes it possible to determine the structure of rapidly evolving, or exchanging, catalyst structures at the level of specific chemical bonds, and so to optimize their reactivity in a rationalistic manner.
10 μm
t = 0 h
t = 30 h
30 h0 h
We use (time resolved) spectroscopy, supra-molecular organization and synthesis to get insight into and develop new materials for: Primary in events in organic photovoltaics.We focus on thin films containing perylene dyes or low band gap polymers and use fs pump-probe spectroscopy. We probe (non-)geminate charge recombination to the triplet state as charge loss.Photosensitizers for water oxidation and proton reduction in organized nano-materials.PS: Metal porphyrines, Ir and Ru complexes.WOC: Ir and Co nanoparticles + complexes.HEC: Pt and CoP nanoparticles.
Metal organic frameworks containing perylene-bis(dicarboximides) for photocatalysis.We use N-pyridyl as well as N-carboxyphenylPDI compounds and focus on CO2 fixation.Photodynamic therapy. Using light to save lives.Anti-cancer, anti-bacterial, anti-inflammatory and immune-activating applications. NIR absorbing nanomaterials. H2020 ITN project in development, looking for extra industrial partner.
Photoinduced Electron and Energy Transfer in Molecular- Supramolecular- and Nano-systems:
from Solar Cells to Solar Fuels
Molecular Photonics grouproom C 2.240
Converting the energy of photons into usable energy, electricity and fuels.Using light to save lives.
DOI: 10.1021/jp402086pDOI: 10.1002/ejoc.201200886DOI: 10.1039/C0CP02867C
Phone: +31 (0)20 – 525 5477
Email: [email protected]
URL: hims.uva.nl/MolPhot
René M. Williams
Primary in events in organic photovoltaics
Photoinduced proton reduction.
Add name Research group
Phone: +31 (0)20 – 525 ****
Email: ****@uva.nl
URL: hims.uva.nl/***
Name
The Computational Chemistry theme is leading worldwide in the fields of molecular simulations and multiscale modelling. Its aim is to develop computational tools to model and predict, from first principles, the behavior of complex chemical, biological, and physical processes.
Over the past decade the group has developed a strong alliance, the Amsterdam Center for Multiscale Modeling (ACMM), with its counterpart at the VU science faculty. The ACMM, established in 2007, has developed a strong High Performance Computing infrastructure and an internationally recognized training program.
The ACMM is world reference center in the field of research, training, and valorisation in the field of molecular multiscale modeling. Top research in all important modelling disciplines at one location, with direct access to essential infrastructure like the Supercomputer Center(SURFSARA) and the eScience Center.
Knowledge valorisation will also be facilitated via scientific consultancy for industry and the establishment of the ACMM-Laboratory (High Performance Computing infrastructure) that will be a hands-on hosting environment for commercial partners to learn and apply computational methods to systems of technological and industrial interest.
Molecular simulationsBiochemical and biophysical phenomena
Computational catalysisNovel methodology development
Aqueous chemical processesNanostructured materials
Soft matter
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Development of simulation tools for studying kinetics of rare events such as protein folding
The Trp-cage miniproteinis a model system for protein folding. We elucidated the mechanism and kinetics of the folding and unfolding of this small protein, using advanced simulation methods.
Kinetics and mechanisms of protein folding
Atomistic insight in biomolecular processes
ChallengeUnderstanding protein function requires knowledge of the structure, energetics and kinetics of the different intermediate states a protein can visit. Molecular simulation can provide exactly such knowledge, complementary to experiments. Molecular dynamics (MD) provides the necessary temporal and spatial resolution, as protein conformational changes are highly dynamical processes, in which thermal fluctuations play an important role. While MD in general has been hugely successful, addressing processes that take place on the millisecond to second time scale still poses a huge challenge.
Solution:One way to overcome this challenge involves the use of effective bias potentials forcing the system to undergo the process of interest. Nevertheless, application of such potentials biases the outcome, especially in complex systems. Therefore, it is essential to obtain unbiased dynamics, which is possible by using transition path sampling, a computational framework that harvests MD trajectories that undergo reactions of interest.
Unravel kinetics and reaction mechanisms in biological processesGuide and assist in the interpretation of experimentsDevelop new efficient computational tools for the community
Dark state
Signaling state
fs-ns
μs-ms
ms-sec
Mechanism of photoreceptor function
Protein DNA binding
Photoactive Yellow Protein is a bacterial blue-light receptor. Blue light triggers a cascade of rearrangements in the protein.
Using advanced simulation methods, we were able to predict the structure and mechanism of formation of the signaling state.
Prediction of structure and mechanismInterpret and guide experiments
In bacteria, the Histone-like Nucleoid Structuring protein forms bridges between strands of duplex DNA.
Prediction of structure and recognition mechanismInterpret and guide experiments
Phone: +31 (0)20 – 525 6447
Email: [email protected]
Peter Bolhuis
Phone: +31 (0)20 – 525 6489
Email: [email protected]
Jocelyne Vreede
We have studied the DNA binding of H-NS at different length and time scales, resulting in the prediction of the mechanism of nucleotide sequence recognition and bridge formation.
Amyloid fibril formationAggregation of the insulin derived LVEALYL peptide occurs via the lock-dock mechanism.
Locked
Docked
Solvated
Insight in protein aggregationRole of water; control of growth
URL: http://www.acmm.nl URL: http://www.acmm.nl
linear chainsdilute networksnetwork of
micelles
Development of simulation tools for studying kinetics of rare events such as crystal nucleation
Predicting reaction coordinates of crystal nucleation
Understanding soft matter
Challenge
Soft materials such as colloids, emulsions, polymers, and surfactants, can have exceptional mechanical, optical or functional properties that find applications in both industry and society. Examples are found in consumer products such as shampoo, shaving cream, paint, plastics and food, but also in drug delivery systems. Soft matter easily deforms under external forces because forces and interactions act on mesoscopic scales. The components often self-organize into complex structures with striking mechanical, or functional properties. The key question is: How can we understand their structural, mechanical and (physico-) chemical properties from the building blocks and their interactions?Together with experimental groups we attack this problem using advanced molecular simulation methods.
Understand and predict soft matter self-assembly processesGuide and assist in the interpretation of experiments anddevelopment of devicesProvide control over material properties
Self-assembly of polymer networks
Anisotropic self-assembly of colloidal particles
Prediction of structure and mechanismInterpret and guide experimentsDevelopment of tools for analysis of networks
Isotropic particles can self-assemble into anisotropic structures.Acting as nanofiller in polymer nanocomposites, lead to special mechanical properties
Understanding and prediction of colloidal self assembly processes.Interpret and guide experiments
Phone: +31 (0)20 – 525 6447
Email: [email protected]
Peter Bolhuis
Phone: +31 (0)20 – 525 6485
Email: [email protected]
Christopher Lowe
Active matter
Active matter is a class of soft matter in which self propulsion plays an important role
Understanding of active matter properties
URL: http://www.acmm.nl URL: http://www.acmm.nl
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We predict the poorly understood structural nature of the critical nucleus and the involved reaction coordinates, and explain the observed kinetically favored meta stable crystal phases.
Telechelic polymers form complex networks depending on the functionality of the end-group. Asymmetric telechelicpolymers can be triggered separately. Together with WUR researchers we investigate dependence on the order of the trigger sequence on the final network properties.
We develop algorithms that identify a percolating network, e.g. if a polymer forms a gel. In this lattice model our algorithm proves the largest connected grouping (red) fails to connect over all space when repeated periodically. If just the points marked blue were connected it would.
We develop dynamics of microscopic filaments in fluids (micro-fluidics). In a circularly polarized field a initially misaligned fiber will align along the filed axis in a spiral motion.
Examples of active matter on different scales: birds, fish, bacteria, people.
We investigated in dense colloidal suspension (61% volume fraction) how activity enhances crystallization and suppresses the glass transition.
Inspiration
InterpretationGuidance
z
Molecular Simulation
- Screening of Compounds and Materials - Predictive Modeling for a Wide Range of Conditions
- Rational Design of Novel Processes and Compounds
- A. Pavlova and E.J. Meijer, Chem. Phys. Chem. 13, 3492 (2012) - A. Pavlova, T.T. Trinh, R. van Santen, E.J. Meijer, Phys.Chem.Chem.Phys. 15, 1123 (2013).
+31 (0)20–525 5054/6448 [email protected] molsim.chem.uva.nl
Evert Jan Meijer
Molecular Simulation
VUA 10-12
10-9
Fluid Dynamics Reactors
Polymers, Membranes Course Graining
High Accuracy Method Development
WFT, DMFT
Materials, Membranes MD & MC
Solvent Reactions AIMD Biomolecules
(DNA, Pharma, Solar) MD & Hybrid
Reactivity, Catalysis, Spectroscopy
DFT
UvA
Time
Siz
e
DFT (Ab Initio) Interactions Empirical Force Fields Statistical Thermodynamics
(Ab Initio) Molecular Dynamics Monte Carlo Methods Rare Event Sampling Methods
Solvent Effects in Chemical Reactions Transfer Hydrogenation
Metal-Catalyzed Transfer Hydrogenation
Reactive Pathways of Solvent Mediated Mechanism
Ionic Hydration and Protons Mobility HCl/MgCl Solution
Aqueous Solutions Important Factors
Ionic Size – Structure Making/Breaking – Proton Mobility
Ions Co-Factor in Aqueous Chemistry
Silica Oligomerization
First Step in Zeolite Synthesis
Important Factors: pH of solution
Structure Directing Agents (Ions)
Kinetic Network
IR Spectra
Important Factors: Ligands
Nature of Solvent
Proton transfer
Multiscale Modeling
Ru
H
C
Ab Initio Model Reaction Free Energy
Reaction Mechanism in Solution: Water and Ion Effects
Multiscale Modelling of Complex Materials
Computational Chemistry
Large polymer and biomolecularsystems are simulated withforcefield based MD or the hybrid QM(DFT)/MM and coarse-grain/atomistic methods. Wherenecesary, forcefields are fittedagainst accurate electronicstructure calculations.
Our multiscale modeling approach is widely applicable to:- Unravel and optimize reaction mechanisms- Predict structure and dynamics of molecular systems- Interpret experimental spectra and measurements
G. Díaz Leines and B. EnsingPhys. Rev. Lett. 109 (2012), 020601
M. Kılıç and B. EnsingJ. Chem. Theory Comput. 9 (2013), 3889
M. Kılıç and B. EnsingPhys. Chem. Chem. Phys. 16 (2014), 18993
Phone: +31 (0)20 – 525 5067
Email: [email protected]
URL: www.acmm.nl
Bernd Ensing
In-house developed simulation methods allow us to study larger molecular systems and longer time-scales. We use advanced sampling techniques to probe activated transitions and reaction dynamics.
By combining Electronic Structure Calculationswith Molecular Dynamics Simulations, we unravelcomplex molecular phenomena in catalysis, bio-chemistry, and material science.
Acidity / proton transfer
Reaction mechanics& dynamics
Polymer structure
Polymer dynamics
Enzyme catalysis
Bio-photo-sensing
Spectroscopyinterpretation
Redox propertieselectron transfer
Electronic structure
Development of theory, algorithms and computer code, allows us to calculate specificproperties and observables thatare not available in commercial modelling programs.
Proton and electron transfer processes are simulated withDFT-MD in different molecularenvironments to compute forexample conductivity, pKa, andredox potentials.
The free energy landscape gives direct insight in the reactionmechanisms and reaction rates. With our metadynamicssimulations, we probe catalyticreactions in solution, at interfaces, and in biomolecules.
Computational Polymer Chemistry
Crosslinking polymerization, that is known toproduces polymers with complicated branched topology dueto crosslinking reaction mechanism:
has been studied by means of a four-dimensional populationbalance model accounting for chain length x, free pendingdouble bonds y, crosslinks c, and radicals z as dimensions.The model, for the first time and to a full extent resolves thecrosslinking problem as formulated by Shiping Zhu twodecades ago, and covers both pre-gel and gel regimes in astraightforward manner.
The model has been validated with data from anexperimental crosslinking polymerization, Methyl Methacrylatewith Ethylene Glycol Dimethacrylate. Non-trivial patterns inthe time evolution of average quantities like crosslinkdensities, partly observed in prior studies, are naturallyemerging from the model by computing marginal of the four-dimensional distribution possessing an interesting multimodalstructure.
The work described here was financed by the
I. Kryven et al in:
• Polymer 55(16), 3475–3489, 2014• MTS 23, 7-14, 2014• Polymer, 54(14), 3472–3484, 2013• MRE 7 (5), 205-220, 2013
Phone: +31 (0)20 – 525 – 6484
Email: [email protected]
Ivan Kryven and Piet Iedema
Gelation in crosslinking polymerization:multiple radical sites that matter
Evolution of multiradicals
Concentration of moleculeswith various numbers ofradical sites as the reactionpasses the gelation point.A significant number ofmultiradicals is presenttemporary around the gelpoint.
GPC chain length distributions at the gelpoint obtained in each radical class z areshown as solid lines. The values of theoverall distribution, depicted by a dashedline, are scaled by a factor 4 for comparison
FPDB distribution obtained from models with differentmaximum number of radical sites per molecule. Thedashed line depicts an asymptote of the tail of an FPDBdistribution with no restrictions on radical sites number:an algebraic decay proportional to x−2.5
Sol molecules can be separated accordingto number of FPDB they posses. Chainlength/crosslinks distributions for classesof molecules with a fixed number of FPDB,emerge as narrow peaks
Url: hims.uva.nl/compchem
Prediction of the topologies of branched polymer architectures and segment lengths from kinetics.
Add name Research group
Analytical Chemistry is forensic science at the molecular level. Analytical Scientists are involved in establishing which types of molecules are present, how many of them there are and, increasingly, what they are – or have been – doing. Thus, we are naturally involved with forensics, but also with chemistry, materials, art, food and medicine. In all these areas the analytical-chemistry group within HIMS collaborate with leading companies and institutions.
The Amsterdam universities are recognized as a unique national centre for Analytical Sciences in The Netherlands. We develop, improve and optimize analytical (separation) methods and technologies. We develop advanced software (‘chemometrics’)
to turn large amounts of data into useful information. We work together with world-leading high-tech-instrument companies to make our findings accessible to other scientists.
Phone: +31 (0)20 – 525 ****
Email: ****@uva.nl
URL: hims.uva.nl/***
Name
One- and two-dimensional separation techniquesGas and liquid chromatography
Mass spectrometryElectro-migration techniques
Field-flow fractionationData analysis and chemometricsBiomolecular systemsTransition
Towards HYPERformance liquid chromatography
Analytical Chemistry
During the last decade liquid chromatography has developed from a high-performance or high-pressure level (commonly known as HPLC) to what is known as ultra-high-performance liquid chromatography (HPLC). While UHPLC technology (smaller particles, smaller system volumes, higher pressures) definitely entails progress, it does not constitute a great leap forward. In contrast, progressing from conventional one-dimensional liquid chromatography to comprehensive two-dimensional liquid chromatography (LC×LC) and eventually “spatial” chromatography allows
the separation of many more components in a much shorter time. Several projects in our group are aimed at taking LC to a next level, identified as HYPERformance liquid chromatography and conveniently abbreviated as HPLC. Our objectives are to
Increase the peak capacity (the number of peaks that can be separated) by at least an order of magnitudeIncrease the peak production rate (peak capacity per unit time) buy at least an order of magnitudeEnhance the linear range of detection by at least an order of magnitude
• To develop and implement new or greatly improved separation methods• To greatly enhance the applicability of advanced separation methods
(such as LCxLC) in industry• To solve very complex separation problems
• E. Uliyanchenko, Sj. van der Waland P.J. Schoenmakers, Polym. Chem. 3 (2012) 2313-2335.
• P.J. Schoenmakers and P.J. Aarnoutse, Anal.Chem. 86 (2014) 6172-6179.
+31 2 5256642
Peter Schoenmakers
One-and-a-half-dimensional LC
Ultra-performance LC×LC Elena Uliyanchenko has decreased the required analysis time for LC×LC separation of copolymers according to composition (horizontal direction) and size (vertical direction) down from a typical 4 hours to some 20 minutes, making application of the technique in industry much more attractive.
E. Uliyanchenko, P.J.C.H. Cools, Sj. van der Wal andP.J. Schoenmakers, Anal.Chem. 84 (18) (2012) 7802-7809
with modulationwithout modulation
LC×LC modulator technology can be used to decrease the detection limits in LC-MS, as is illustrated in this example for the determination of testosterone in cow urine.Anna Baglai with RIKILT
Three-dimensional “spatial” LC
The concept of spatial LC×LC×LC promises peak capacities up to one million within a reasonable time.
With Sebatiaan Eeltink (VU Brussel)Patent application numbers 20120171086, 20120164744, 20120162637
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E. Davydova, P.J. Schoenmakers and G. Vivó-Truyols,J.Chromatogr.A 1271 (2013) 137-143.
Separation methods for macromolecules and particles
Analytical Chemistry
Phone: +31 (0)20 – 525 6539
Email: [email protected]
Dr. Wim Th. Kok
Glycerin based EO/PO polyols
• capillary electrophoresis (CE)
• separation based on functionality (OH end-groups)
• Kathalijne Oudhoff, 2005
Professional educationIn-house courses can be given on various levels (MBO/HBO/acad, NL/Eng), on:
• Basic statistics for analytical chemists• HPLC: principles and optimization• Capillary Electrophoresis
The conventional separation method for polymers/macromolecules is Size-Exclusion Chromatography (SEC). In SEC, the separation is according to molecular size. However, several other techniques have been developed in recent years that extend the size range of SEC, or that give other selectivities. Techniques studied within the Analytical Chemistry group of HIMS are:
• Capillary Electrophoresis (CE). This technique is suitable for water-soluble synthetic or natural macromolecules. CE can be used to study size distributions, functionality (end groups) or, e.g., the degree of substitution of modified polymers.
• Asymmetrical Flow Field-Flow Fractionation (AF4). Like SEC, AF4 separates according to size. However, its size range is much larger. AF4 can be applied to study supramolecular complexes, the aggregation of proteins, and to measure the size-distribution of particles.
• Hydrodynamic Chromatography (HDC). This technique can be especially suited for the analysis of solid particles, vesicles and liposomes. It has inherently a very high separation efficiency.
Lipoprotein characterization
• field-flow fractionation (AF4)
• separation based on size
• HDL – LDL – VLDL
• cholesterol and triglycerides
• Rashid Qureshi, 2010
sepsispatient
controlserum
Aggregation of fullerenes
• field-flow fractionation (AF4)
• aggregation behaviour
• relation with environmental fate
• Alina Astefani, 20140
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Microfluidics
Various research projects have been / are carried out on the development of microfluidic separation devices. Pillar-structured channels have been fabricated and evaluated that give excellent separation efficiency for Hydrodynamic Chromatography. The microfluidic channels will be tested for the HDC separation of vesicles and liposomes.
Carboxy Methyl Cellulose
• capillary electrophoresis• determination of the degree of
substitution
Url: hims.uva.nl/AnalChem
Bayesian statistics to deal with data analysis automation
Analytical chemistry(chemometrics cluster)
We are witnessing a tremendous explosion of the data sizes produced by analytical instrumentation. For example, a single injection of a sample in a GCxGC-MS instrument produces around 15 GB/hour or data. Often, the processing of this data into information becomes the major bottleneck of the analysis. In our group we are investigating methods to automate this proces.The classical approach to data analysis automation:
Developing a global software package for automated data treatment from chromatography using Bayesian statistics.
M. Lopatka, G. Vivó-Truyols, M. Sjerps, Anal. Chim. Acta, 817 (2014) 9-16.M. Woldegebriel, G. Vivó-Truyols, J. Chromatogr. A, submited.
Phone: +31 (0)20 – 525 6531
Email: [email protected]
Url: hims.uva.nl/analchem
Dr. Gabriel Vivó-Truyols
Our new approach approach to data analysis automation:
In this way, the user (and not the algorithm) takes the decision: the algorithm just helps the end user in taking this decision by delivering a collection of (ranked) possible answers.
Just an example: application to toxicology screening with NFI (Dutch forensic institute):
A list of ~500 compounds have to be identified in a huge data set (LC-MS): how to distinguish them (from noise, isotopes, etc.?)
Chemical noise Compound
Bayesian statistics provides an elegant way to provide the probability of a compound being present (rather than a binary anser of a peak being present/absent)
The method is able to scan high resolution LC-MS and looking for more than 500 compounds.Takes into account:
- Retention times- m/z values- Relative isotope ratios.
Sensitivity and specificity are better than commercial software packages (e.g. Mass hunter from Waters). It scans 0.5 Gb of data in ~ 6 min.
Mass Spectrometry Powered Biomolecular Systems Analysis
During the steps from discovery to validation each step must be optimised for each new project, and each sample. Methods must be sensitive, scalable, and enable translational research from bench to clinic and patient material to model systems.
Biomolecular Systems Analytics
This new HIMS group opens new areas of activity for the Institute by pursuing fundamental and applied research into the analysis of biomedical systems for health and disease as well as forensic science to aid crime investigation. A third area of activity concerns Science for Art*, that combines interdisciplinary research uniting art history, art conservation and science. * See Katrien Keune for more information
Our research uses mass spectrometers (MS) to characterise and quantify proteins in biological systems. Proteins are particularly interesting because they are critical for most biological processes and functions. The MS-based tools and allied technologies we develop enable the analysis of exquisite amounts of thousands of proteins that make up the molecular networks in cells, tissues and organs. Knowledge about the interplay and the molecular state of proteins is important to understand how cells respond to their environment and influence the emergent properties of living systems. This holistic approach to study biological systems from a molecular perspective requires multidisciplinary teams where chemistry and bioinformatics are key elements.
Technological advances have outstripped conceptual advances in biology. The days of one gene – one protein –one function are passed.
Networks of interacting molecules the key difference molecular between genotype and phenotype, where each node in a protein system represents a molecule of interest.
• To strategically underpin research in the Dutch biosciences community and to highlight the Netherlands as an important partner in research commercialisation.
• Developments of several analytical technologies for immediate spin off or though venture uptake.
• Kannaste et al., J Proteome Res. 13 (2014) 1957-68.
• Westermarck Jet al., Mol Cell Proteomics 12 (2013) 1752-63.
• Santos et al., Rapid CommunMass Spectrom. 26 (2012) 254-62.
New molecular information on potential therapeutic targets or tools for non-invasive diagnosis for endometriosis are important for patient care and treatment. From Vehmas et al. Ovarian Endometriosis Signatures Established through Discovery and Directed Mass Spectrometry Analysis, J Proteome Res. 2014
Phone +31 (0)20 - 525 5406
Email: [email protected]
Prof. Garry Corthals
To achieve our goals we develop Chemical procedures to aid preparation and
separation methods in line with MS Enabling technologies to quantitate proteins in
molecular networks in subcellular localities and in clinical tissues and their cellular substructures
Enabling technologies for post-translation modification interrogation
Bioinformatics that enables high-speed and high-accuracy proteome analysis
The analytical pathway from discovery to validation
Perturbation
Url: hims.uva.nl/AnalChem
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CS equation parameter values (%)
CS = 58%
Z- = 56%
Z+ = 98%
Z1 = 89%
Z2 = 69%
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CS equation parameter values (%)
CS = 63%
Z- = 63%
Z+ = 97%
Z1 = 85%
Z2 = 78%
2nd
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1st dimension
AO = 58%
AO = 63%
Asterisk equation parameter values (%)
Asterisk equation parameter values (%)
Current research directions
Corthals research group
The versatility and power of chromatographyChromatography is a versatile separation technique. Unlike other separation techniques, chromatography can separate based on variouschemical and physical properties of the sample components, such as size, shape, charge, hydrophobicity, hydrogen bonding ability, π-πinteractions, affinity for a particular ligand. With the appropriate selection of separation mechanisms it is now possible to separate 33 compounds per minute [1], making chromatography not only versatile but powerful.
The need for new technology and methodsDespite this the separation power of chromatography has not been exploited in sustainable chemistry or proteomics. This is partly due tolimitations in chromatographic technology. Our research aims to address this problem by developing methods and technology specificallyfor these application areas.
We are looking for interested industry partners in sustainable chemistry and protein analysis who face separation/characterisation problems to join us in tailoring methods and technology for their specific applications
Making method development clearer: The asterisk equations [2]
Aside from the asterisk equations the remaining projects are in the process of being launched, subject to funding.
[1] Stoll, D. R. et al. J. Chromatogr. A 2006, 1122, 123-137
[2] Camenzuli, M., Schoenmakers, P.J. Anal. Chim. Acta, 2014, 838, 93-101
[3] Selim, M., Soliven, A., Camenzuli, M. Dennis, G.R., Ritchie, H.J., Shalliker, R.A. Microchem J. 2014, 116, 87-91
[4] Camenzuli, M., Ritchie, H.J., Dennis, G.R., Shalliker, R.A. J. Chromatogr. A 2013, 1303, 62-65
Phone: +31 (0)20 – 525 7040
Name: Dr. Michelle CamenzuliAssistant Prof. Analytical Chemistry
Developing new chromatographic technology and methods for sustainable chemistry and proteomics
Email: [email protected]
Chromatography for sustainable chemistry:Two-dimensional chromatography forlignocellulosic biomass catalysisLignocellulosic biomass catalysis produces a vast variety of different compounds: sugars, aromatics, aliphatic compounds, phenols and other low molecular weight compounds which serve as important reagents in chemical synthesis. This makes for a complicated separation. To date, typical separation tools are predominantly one-dimensional. We are investigating the use of the increased power of two-dimensional chromatography to this application.
New chromatographic technology for proteinseparationsEfficient protein separations require stationary phases with high permeability, large pore size, high loadability yet chemically and mechanically stable. Core-shell stationary phases, while very efficient, have short lifetimes, reducedpermeability and reduced loading capacity. We aim to create a new stationaryphase which addresses the current limitations of existing technologyIn collaboration with: Prof Gadi Rothenburg and Prof Garry Corthals (HIMS)
Online reactions + separation = efficiency:Reaction flow chromatography [3,4]
Annular Frit encased in a flow
directing cap Reagent enters here
Column eluent + reagent to detector
Sealed with plugs
Figure 2: Diagram of reaction flow chromatography
In collaboration with:
In collaboration with:Reaction flow has
been used for online assays and
chemiluminescence
For maximum separation power in two-dimensional
chromatography, it is necessary to couple two selectivities which have
vastly different separation mechanisms.
The asterisk equations report metrics which
assesses the optimality separations mechanism
when combined. The equations are easily
used in Microsoft Excel.
Work has begun on extending the equations
to create a metric accounting for all
aspects of separation quality
Not all components adequately separated in 1D. Combining two selectivities can increase separation
power
In collaboration with: Dr. N. Raveendran Shiju (HIMS)
What happens in ageing oil paint?
• Evaluate effects of past and present approaches toconservation of painted surfaces
• Improve scientific basis to guide conservation strategies.
Hermans, J. J., Keune, K., van Loon, A., Corkery, R. W., & Iedema, P. D. (2014). Polyhedron, 81, 335–
340. Hermans, J. J., & Iedema, P. D. (2014). Journal of Molecular Structure, 1070, 43–44.Keune, K. and Boéve-Jones, G. (2014), In: Issues in Contemporary Oil Paints (ICOP), Proceedings from the Symposium, Amersfoort, The Netherlands, eds. K.J. van den Berg, et al., Springer
SynthesisModeling
Reconstructions Paint samples
.
nas (COO)
d (COO)
ns (COO)
CH2 progression bands
single crystal data Pb3O2(CH3COO)2
metal layer
8.53 Å
5.11 Å
chain angle
63°
84°
C: 24.12 % 24.10 %H: 3.85 % 3.87 %Pb: 62.4 % 62.15 %
PbO + C15H31COO-
1. Pb(C15H31COO)2
2. Pb3O2(C15H31COO)2
Calculating concentration profiles of relevant functional groups, and the cross-linked structure of the oil network
Mimicking paint composition and ageing to reproduce degradation phenomena and test conservation treatments
Studying paint samples from oil paintings to characterize paint composition and degradation phenomena
Understanding the reactions that take place in oil paint and providing a detailed characterization of reaction products
Couple aux têtes pleines de nuages, Salvador Dalí1936, Boijmansvan Beuningen
Collaboration with Rijksdienst Cultureel Erfgoed and Courtauld Institute of Art, London
paint degradation
PAinT team:Dr. Annelies van Loon Drs. Joen HermansDr. Katrien Keune Prof. dr. Piet IedemaDr. Maartje Stols-Witlox
Website: www.s4a-paint.uva.nl
Investigating & understanding these phenomena:
Valorisation goals:
