-
YRMS@2019 PROGRAM
-
MORNING 4TH APRIL
8:50 – 9:25 Registration and Welcome
9:25 – 9:30 Opening
9:30 – 10:00 CHRISTIAN MERTEN (Ruhr-University Bochum)
Matrix-isolation VCD spectroscopy: Towards the characterization of
chiral reactive intermediates
10:00 – 10:20 QIN YANG (Scuola Normale Superiore – Pisa)
Theoretical Investigations of the Optical Properties of
Helicene-Iridium Complexes
10:20 – 10:40 MARCO FUSÈ (Scuola Normale Superiore – Pisa)
Chiral properties of transition metal complexes: computational
approaches
10:40 – 11:00 MARTIN PIŽL (Czech Academy of Sciences)
Time-resolved vibrational spectra of Ru and Re 2iamine complexes:
Anharmonic calculations
11:00 – 11:20 Coffee Break
11:20 – 11:50 VINCENT LIÉGEOIS (University of Namur) New tools
to unravel the vibrational signatures of molecules – Application to
Raman optical activity and to sum-frequency generation
signatures
11:50 – 12:10 FUCSIA CREA (Freie Universität Berlin)
Photo-activation of mechanosensitive ion channels
12:10 – 12:30 MATTIA SAITA (Freie Universität Berlin) Giving
shape to protonated water clusters in membrane proteins with
polarized FTIR
12:30 – 12:50 SANDRA MÓNICA VIEIRA PINTO (Scuola Normale
Superiore – Pisa) In silico Infrared Spectroscopy of Protein Side
Chains
LUNCH
AFTERNOON 4TH APRIL
14:20 – 14:40 MARCO MENDOLICCHIO (Scuola Normale Superiore –
Pisa) Anharmonic vibrational treatment of linear, symmetric and
asymmetric molecules
14:40 – 15:10 LUCA EVANGELISTI (University of Bologna)
Challenges in Microwave Spectroscopy
15:10 – 15:30 THUY NGUYEN (LISA – Paris) Microwave spectroscopic
and quantum chemical investigations on 2-methylpyrrole
15:30 – 15:50 SILVIA ALESSANDRINI (Scuola Normale Superiore –
Pisa) Benchmark of quantum-chemical computations for molecules
containing second-row atoms
15:50 – 16:20 HA VINH LAM NGUYEN (LISA – Paris) Understanding
(coupled) large amplitude motions: The interplay of microwave
spectroscopy, spectral modeling, and quantum chemistry
16:20 – 16:40 MARIE-LUISE HEBESTREIT (Heinrich-Heine-University
– Düsseldorf) Position dependent study on 3-, 4-, and 5-Cyanoindole
via high resolution laser induced Stark spectroscopy
16:40 – 17:00 Coffee break
17:00 – 17:30 DANIELE LICARI (Istituto Italiano di Tecnologia)
Latest developments in VMS Draw
17:30 – 17:50 SURAJIT NANDI (Scuola Normale Superiore – Pisa) A
Modern-Fortran Program for Chemical Kinetics on top of Anharmonic
Vibrational Calculations
17:50 – 18:10 JACOPO LUPI (Scuola Normale Superiore – Pisa)
Quantum mechanical strategies for reactivity and kinetics of
atmospheric reaction pathways
18:10 – 18:30 BALASUBRAMANIAN CHANDRAMOULI (Scuola Normale
Superiore – Pisa) Examining molecular conformational landscape
using QM based stochastic approach
-
MORNING 5TH APRIL
9:00 – 9:30 ALBERTO BAIARDI (ETH Zurich) Efficient quantum
dynamics with the Time-Dependent Density Matrix Renormalization
Group
9:30 – 9:50 MATTHEW TURNER (University of Warwick) Indentifying
Secondary Species in Solution: A Combined Experimental and
Theoretical Approach
9:50 – 10:20 IKER LEÓN (University of Valladolid) Molecular
Spectroscopy: A Collaborative Effort
10:20 – 10:40 DRAGOS LUCIAN ISAC (Petru Poni Institute of
Macromolecular Chemistry – Iasi) Computational determination of the
charge transfer excited state in azobenzene maleimide
derivatives
10:40 – 11:00 SARA DEL GALDO (Scuola Normale Superiore – Pisa)
An effective integration of variational and perturbative QM/MM
approaches for computing UV-Vis spectra in condensed phases
11:00 – 11:20 Coffee break
11:20 – 11:50 ALFONSO PEDONE (University of Modena and Reggio
Emilia) Computational solid-state NMR spectroscopy as a tool for
the structure determination of oxide glasses and assessment of
classical Force-Fields
11:50 – 12:10 FEDERICA ROSSI (University of Turin) The accurate
1H-14N distance measurement by phase-modulated RESPDOR at
ultra-fast MAS
12:10 – 12:30 SIMONE BORDIGNON (University of Turin) 2D
solid-state NMR experiments to characterize the hydrogen bond
network in pharmaceutical cocrystals
12:30 – 12:50 SILVIA HRISTOVA (Bulgarian Academy of Sciences)
β-diketones based rotary switches: molecular spectroscopy and
computational chemistry playing together
CLOSING
LUNCH
-
BOOK OF ABSTRACTS
-
Matrix-isolation VCD spectroscopy:
Towards the characterization of chiral reactive
intermediates.
Dr. Christian Merten
Ruhr-Universität Bochum, Organische Chemie II,
Universitätsstraße 150, Bochum
[email protected]
Vibrational Circular Dichroism (VCD) spectroscopy measures the
small difference in the absorption of
left- and right circular polarized infrared light by a chiral
sample. It allows the unambiguous assignment of
absolute configurations by comparison of experimental and
computationally predicted spectra,[1] but it is
also highly sensitive to even very subtle differences in
structures, such as conformational changes induced by
solute-solvent interactions.[2] In our work, we take advantage
of this conformational sensitivity and use
VCD spectroscopy to probe intermolecular interactions of
interest in catalysis[3] and supramolecular
chemistry.[4]
After a short introduction to the technique itself, this talk
will focus on the implementation of a combined
setup of VCD spectroscopy and the matrix-isolation technique as
sample preparation method for the isolation
of small molecules and reactive intermediates. Highlighting some
recent results, we show that trapping chiral
molecules in solid rare gas matrices can help us understand
problems faced in the interpretation of solution
phase spectra. These challenges in the analysis are, for
instance, flat potential energy surfaces[5] or rapidly
rearranging photoisomerization products.[6] In addition, we will
discuss the use of liquid rare gases as inert
solvents for VCD measurements.[7]
References
[1] C. Merten, V. Smyrniotopoulos, D. Tasdemir, Chem. Commun. 51
(2015) 16217
[2] C. Merten PCCP 19 (2017) 18803
[3] a) C. Merten, C. H. Pollok, S. Liao, B. List, Angew. Chem.
Int. Ed. 54 (2015) 8841. b) N. Kreienborg, C. H. Pollok,
C. Merten, Chem. Eur. J. 22 (2016) 12455
[4] C. H. Pollok, Q. Zhang, K. Tiefenbacher, C. Merten,
ChemPhysChem 18 (2017) 1987
[5] C. H. Pollok, C. Merten, PCCP 18 (2016) 13496
[6] C. H. Pollok, T. Riesebeck, C. Merten Angew. Chem. Int. Ed.
56 (2017) 1925
[7] N. M. Kreienborg, J. Bloino, C. H. Pollok, T. Owoski, C.
Merten, Phys Chem Chem Phys 21 (2019) 6582
-
Theoretical Investigations of the Optical Properties of
Helicene-Iridium
Complexes
Qin Yang, Marco Fusè, Franco Egidi, Julien Bloino
Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa,
Italy
[email protected]
Iridium complexes are known for their bright phosphorescence,
which finds multiple applications, such
as organic light emitting diodes (OLEDs) and biomarkers. Their
basic optical properties and efficiency can
then be tuned by substituting the ligands of the metal center.
Recently a new family of molecules (KC and KD,
see Fig. 1) containing a helicene ligand (KB) was reported with
a long-lasting, bright phosphorescence[1].
However, the exact nature and origin of the enhancement have not
been fully identified. Further details can be
obtained with the help of computational chemistry.
The presence of two sources of chirality – the chiral center on
Ir and the chiral axis related to the helicene
ligand – demands a proper measurement and description of the
whole system. In view of the photo-emitting
properties of those complexes, electronic circular dichroism
(ECD) and circularly polarized phosphorescence
(CPP) have been chosen as reference spectroscopies. They can
provide complementary information on
transitions, ECD being an absorption technique, and CPP an
emission one. From a computational point of
view, their sensitivity requires the consideration of vibronic
effect to reach more accurate band-shape
predictions[2-3]. The presence of an Ir atom, coupled to the
phosphorescence process, makes the simulations
more complicated, since they require a proper consideration of
relativistic effect[4-5]. The setup of such
computational protocol is seriously hampered by the size of the
systems of interest (like KC and KD here). By
using smaller, prototypical systems (KA in this case) in
calculations, this problem can be alleviated and the
most suitable method chosen. Here, we will present a
cost-effective scheme able to reproduce the band-shapes
of KC and KD. In addition, the achieved results will also permit
us to analyze and discuss the origin and nature
of the enhancement supported by novel, graphical tools[6].
Fig. 1: The structure of KA, KB, KC, and KD
References:
[1] N. Hellou, M. Srebro-Hooper, L. Favereau, F. Zinna, E.
Caytan, L. Toupet, V. Dorcet, M. Jean, N. Vanthuyne, J.G.
Williams, and L. Di Bari, J. Autschbach and J. Carassous, Angew.
Chemie. Int. Ed. 28, (2017) 8348.
[2] J. Bloino, A. Baiardi and M. Biczysko, Int. J. Quantum Chem.
116, (2016) 1543.
[3] J. Bloino, M. Biczysko, F. Santoro and V. Barone, J. Chem.
Theory Comput. 6, (2010) 1256.
[4] F. Egidi, S. Sun, J.J. Goings, G. Scalmani, M.J. Frisch and
X. Li, J. Chem. Theory Comput. 13, (2017) 2591.
[5] F. Egidi, M. Fusè, A. Baiardi, J. Bloino, X. Li and V.
Barone, Chirality 30, (2018) 850.
[6] M. Fusè, F. Egidi, J. Bloino. Phys. Chem. Chem. Phys. 21
(2019) 4224.
-
Chiral properties of transition metal complexes:
computational approaches
Marco Fusè1, Julien Bloino1, Vincenzo Barone1
1Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa,
Italy.
[email protected]
Figure 1 . VTCD spectra of Fe(III) complex
Enantiopure metal complexes play crucial roles in several fields
such as catalysis, materials and life science
[1]. Their chiral properties are commonly characterized through
spectroscopic methodologies, which can be
combined to get a fuller description of those systems. However
experimental spectra can seldom be interpreted
on a basis of classical or phenomenological models. Over the
years, vibrational analysis supported by Density
Functional Theory (DFT) calculations have gained considerable
successes in assigning the absolute
configuration and evaluating the conformational properties of
many molecular systems, organometallics
included [2,3]. In this contribution, we will show some
strategies to achieve accurate simulations of IR and
vibrational circular dichroism (VCD) spectra beyond the harmonic
approximation [4].
For large systems like metal complexes, very accurate
calculations are not feasible on the whole system due
to the computational costs, therefore a balance between required
computational resources and accuracy is
mandatory. A convenient approach is to reduce the dimension of
the system to a set of normal modes directly
related to the region of interest of the spectrum [5]. In fact,
a careful definition of the reduced dimensionality (RD) scheme can
lead to very good results in the reproduction of target features of
the spectrum, at a fraction
of the computational cost of the full calculations. Moreover,
visualization of the vibrational transition current
density (VTCD)[6] allows exploration of the physical origin of
the electronic contribution to the electric and
magnetic vibrational dipole transition moments [7]. This can
give insights on the nature of the chiroptical
properties and on the origin of the band-shape, information that
are generally lost when only numerical values
are considered.
References
[1] E. C. Constable, Chem. Soc. Rev. (2013), 42, 1637.
[2] J. Autschbach, Chirality (2009), 21, E116.
[3] M. F, G. Mazzeo, et al. , Chem. Commun. (2015), 51,
9385.
[4] J. Bloino, V. Barone J. Chem. Phys. (2012), 136, 124108.
[5] V. Barone, M. Biczysko, J. Bloino, et al. Int. J. Quantum
Chem. (2012), 112, 2185.
[6] L. A. Nafie, J. Phys. Chem. A (1997), 101, 7826
[7] M. F., F. Egidi, J. Bloino, Phys. Chem. Chem. Phys. 21
(2019) 4224.
-
Time-resolved vibrational spectra of Ru and Re diimine
complexes: Anharmonic
calculations
Martin Pižl1,2, Marco Fusé3, Nicola Tasinato3, Antonín Vlček1,4,
Vincenzo Barone3, Stanislav Záliš1
1 J. Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, Dolejškova 3,
182 23 Prague, Czech Republic. 2 Department of Inorganic
Chemistry, University of Chemistry and Technology, Prague 6,
Technická 5, 166 28, Czech Republic. 3 Scuola Normale Superiore,
Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
4 Queen Mary University of London, School of Biological and
Chemical Sciences, Mile End
Road, London E1 4NS, United Kingdom.
e-mail: [email protected]
Vibrational properties of Ru and Re complexes were used for
characterization of their photophysical
properties. Anharmonic calculations are important for better
understanding of time-resolved IR spectra and
detailed description of experimental data by calculated results
[1]. Anharmonic frequencies were calculated
by second-order perturbation theory (VPT2) [2] in the frame of
DFT methodology using Gaussian 16 program
package. Resonances were treated by generalized VPT2 procedure
[3] (GVPT2).
Figure 2 Structure of complexes under study.
The simulated harmonic and anharmonic difference IR spectra
between excited and ground state of
[Re(NCS)(CO)3(2,2’-bipyridine)] (1) describes changes in the
experimental TRIR spectrum. The second part
of this work is focused on an application of the anharmonic
approach for estimating of diagonal and off-diagonal
anharmonicities in 2DIR spectra of Ru complexes –
[Ru(4,4ꞌ-di-R-2,2ꞌ-bipyridine)2(NCS)2] (R= OMe (2) and
CO2Et (3)). Anharmonic vibration analysis also well interprets
shifts of (N-C) stretching frequencies upon the
excitation and oxidation/reduction of Ru complexes. Structures
of complexes 1-3 are depicted on Fig.1.
Acknowledgements This work was supported by the Czech Science
Foundation (GAČR) grant 17-011375 and the
MOLIM COST action.
References
[1] H. Kvapilová, Vlček A. Jr., V. Barone, M. Biczysko, S.
Záliš, J. Phys. Chem. A 119 (2015) 10137.
[2] V. Barone, M. Biczysko, J. Bloino, Phys.Chem. Chem. Phys. 16
(2014) 1759.
[3] M. Piccardo, J. Bloino, V. Barone, Int. J. Quant. Chem. 36
(2015) 321.
-
New tools to unravel the vibrational signatures of molecules –
Application to
Raman optical activity and to sum-frequency generation
signatures
Vincent Liégeois1, Conrard Giresse Tetsassi Feugmo2, Benoît
Champagne1
1 Unit of Theoretical and Structural Physico-Chemistry (UCPTS),
Institute of Structured Matter, University
of Namur (UNamur), Rue de Bruxelles 61, 5000, Namur, Belgium 2
SoftSimu Group, University of Western Ontario, London, N6A 5B7, ON
Canada.
[email protected]
Vibrational spectroscopies are powerful tools to study the
structures of molecules, polymers, self-assembled
monolayers, interfaces, … Indeed, each normal mode of vibration
provides information about their structure:
the composition, the configuration, the conformation, or the
supramolecular arrangement. Last but not least,
there exists a broad range of vibrational spectroscopies:
Infrared (IR), Raman, Vibrational Circular Dichroism
(VCD), Raman Optical Activity (ROA), Hyper-Raman, Resonant Raman
(RR), Sum Frequency Generation
(SFG), which all provide specific signatures.
In many cases, there is no simple relationship between the
structure and the pattern observed on the
experimental spectra or, for many new techniques like ROA,
simple rules of thumb still need to be worked out.
This is where theoretical chemistry can help by unraveling the
different signatures and by relating these to the
specific structure. That’s why I have recently developed a suite
of two new programs called DrawMol
(www.unamur.be/drawmol) and DrawSpectrum
(www.unamur.be/drawspectrum) that are available on sale on
the Mac App Store since November 2016. DrawMol is a
full-featured program to build molecular structures
from scratch (and to generate the input files for Gamess-US and
Gaussian quantum chemistry packages) as well
as to visualize molecular properties. In addition to the
visualization of the structures, the molecular orbitals and
the dipole moments that are commonly found in other programs,
DrawMol also represents the polarizability and
hyper-polarizability using the unit sphere representation, the
vibrational normal modes together with the IR
vectors, the Raman and ROA tensors, the NMR chemical shifts, and
the magnetically induced current density.
The decomposition scheme [1] introduced by Hug that divides the
intensity into group coupling matrices
(GCMs) or atomic contribution patterns (ACPs) and the interface
to analyze the coupling between normal modes
of two similar molecules [2, 3] has also been implemented into
DrawMol. DrawSpectrum is a program that
plots IR, Raman, VCD, ROA, UV, ECD as well as SFG spectra from
molecular properties calculated in a
quantrum chemistry package. Experimental data can be plotted as
well.
In this contribution, I will present some of these tools (old
and new ones) and I will demonstrate that
more insight on the ROA signatures can be gained from using
them. In addition, these tools have been used to
unravel the structure of functionalized surfaces using the SFG
spectroscopy. For instance, the SFG signatures
of 1-dodecene molecule covalently bonded to hydrogen-terminated
Si(111) [4] are compared to experiment and
more insights about the orientation of the molecule at the
surface are obtained.
References
[1] W. Hug, Chem. Phys. 264 (2001) 53. [2] W. Hug, M.
Fedorovsky, Theor. Chem. Acc. 119 (2008) 113. [3] M. Fedorovsky,
Computing Letters 2 (2006) 233. [4] C.G. Tetsassi Feugmo, V.
Liégeois, B. Champagne J. Phys. Chem. C 119 (2015) 3180.
mailto:[email protected]:[email protected]
-
Photo-activation of mechanosensitive ion channels
Fucsia Crea1, Johannes Morstein2, Joachim Heberle1, Dirk
Trauner2
1 Freie Universität Berlin, Berlin, 14195, Germany 2 New York
University, New York, 10003, USA
[email protected]
Mechanosensitive ion channels are present in all three domains
of life, archaea, bacteria and eukaryota, and
are responsible for a wide variety of functions, from osmotic
pressure control in bacteria and cell turgor in
plants, to touch and pain sensation in humans. The
mechanosensitive ion channel of large conductance MscL
from E. coli is a model system for studying ion channels that
react to the lateral pressure exerted in the lipid
membrane.
To gain information at a molecular level on structural changes,
lipids-protein interaction and the gating
mechanism of MscL, we are using FT-IR spectroscopy. To induce a
change in lateral pressure in the membrane,
synthetic photoswitchable lipids are inserted in the lipid
bilayer. Indeed, upon illumination, these azobenzene-
containing phospholipids isomerize and ocuppy a different volume
inducing a pressure, allowing for a light
control of the lateral pressure in the membrane and therefore of
the ion channel activity.
Preliminary results on the photoswitchable lipids show the
reproducibility and reversibility of the light switching
mechanism in the lipids. Polarized attenuated total reflection
IR spectra give an insight on the orientation and
reorientation of photoswitchable lipids in a multilayer
structure. The induced pressure change is measured in
the monolayer with a Langmuir trough. The insertion of the
protein in the photoswitchable lipid bilayer is our
next step.
This work, other than elucidating a particular mechanism of ion
channel gating, could contribute to opening
the way to new applications in the field of
photopharmacology.
-
Giving shape to protonated water clusters in membrane proteins
with polarized
FTIR
Mattia Saita1, Victor Lórenz Fonfría1,2, Jan Daldrop1, Ramona
Schlesinger1, Roland Netz1, Joachim
Heberle1
1 Freie Universität, Berlin, 14195, Berlin. 2 Universitat de
Valencia, Valencia, 46980, Spain.
[email protected]
Proton transfers are fundamental steps in the functional
mechanism of many proteins involved in
bioenergetics. Important players in proton translocation are
hydrogen-bonded networks of amino acids and
water molecules, and the protonation of such networks can be
detected as unusually broad transient signatures
in the infrared spectral range, called continuum bands [1].
Bacteriorhodopsin (BR) is a membrane protein that is able to
pump protons across the membrane and it has
been extensively studied as a model for the investigation of
protonatable hydrogen-bonded networks in proteins
[2].
The molecular origin of the continuum band in Bacteriorhodopsin
has been long debated and the involvement
of water molecules is not yet settled [3,4].
We characterized the continuum band in BR with time-resolved and
polarization-resolved FTIR [5,6].
With the help of the marker vibrational bands of the protonation
of a buffer molecule (MES) we were able to
trace proton release and uptake events and measure the kinetics
of the continuum band in the same experiment.
Our results confirm the accepted model of the continuum band
arising from the deprotonation of the hydrogen-
bonded network located at the extracellular side of the
protein.
With the polarization-resolved measurements we observed a strong
dichroism of the broad transient negative
absorption (the continuum band signal in a difference absorption
experiment, spectral range 1800-2100 cm-1)
measured in the membrane plane and its normal (Figure 1). A
small dichroism has also been observed in a
photoselection experiment in the membrane plane. The
interpretation of the dichroism is helped by the
anisotropy of the infrared spectra of protonated water clusters
of different shapes, calculated by ab initio
molecular dynamics simulations.
Figure 3 Experimental polarization-resolved spectra. a) In the
experimental set-up, the purple membranes are
oriented in the xy plane and the proton pumping direction is
along z. b) Experimental IR light-minus-dark
difference spectra calculated along the xy and z directions.
We were able to estimate the 3D shape and the time evolution of
the protonated hydrogen-bonded network
that transiently releases a proton during the protein
photoreaction and contribute in the identification of its
molecular origin.
References
[1] F. Garczarek, & K. Gerwert, Nature, 439 (2006) 109.
[2] K. Gerwert, E. Freier & S. Wolf, Biochimica et
Biophysica Acta (BBA)-Bioenergetics 1837 (2014) 606.
[3] S. Wolf, E. Freier, K. Gerwert, Biophysical journal 107
(2014) 174
[4] P. Phatak, N. Ghosh, H. Yu, Q. Cui, M. Elstner, Proceedings
of the National Academy of Sciences 105 (2008) 19672
[5] J.O. Daldrop, M. Saita, M. Heyden, V. A. Lorenz-Fonfria, J.
Heberle, R. Netz, Nature communications 9 (2018) 311
[6] V. A. Lorenz-Fonfria, M. Saita, T. Lazarova, R. Schlesinger,
J. Heberle, Proceedings of the National Academy of
Sciences 114 (2017) 10909
-
In silico Infrared Spectroscopy of Protein Side Chains
Sandra M. V. Pinto1,2, Nicola Tasinato1, Vincenzo Barone1,
Andrea Amadei3, Laura Zanetti-Polzi2,
Isabella Daidone2
1 Scuola Normale Superiore, Pisa, 56124, Italy 2 Department of
Physical and Chemical Sciences, University of L’Aquila, L’Aquila,
67010, Italy
3Department of Chemical and Technological Sciences, University
of Rome “Tor Vergata”, Rome, 00185,
Italy
[email protected]
Infrared spectroscopy (IR) has proven to be a powerful technique
for the study of protein-mediated processes,
e.g., folding and unfolding kinetics and ligand migration [1].
In particular, the amide I’ region (1600 – 1700
cm-1 in D2O), in which the absorbance is mainly due to the C=O
stretching of the backbone carbonyl, is
commonly measured for the characterization of secondary
structure of proteins. Due to structural fluctuations
of the polypeptide chain and complex molecular interactions, the
understanding of these processes at the
molecular level exclusively on a phenomenological basis can be
very challenging. Hence, it is crucial to use
state-of-the-art computational methods to aid in the
interpretation of the experimental data.
The existing computational methodologies mainly focus on
reproducing the amide I mode, however, they
usually neglect in spectra calculations the contribution of the
protein side chains that absorb in the amide I’
region and at nearby frequencies (Asp, Glu, Asn, Gln and Arg).
Thus, an opportunity of improvement arises
from the inclusion of these side chains into the spectral
calculations. For the purpose of reproducing the IR
spectra of protein side chains, our method of choice is based on
the perturbed matrix method (PMM) and
molecular dynamics (MD) simulations. Briefly, this approach aims
at keeping the complexity of the
configurational complexity of the system (biomolecule + solvent)
with a proper treatment of the quantum
degrees of freedom of a portion of the system (quantum center,
QC) which is explicitly treated at the electronic
level. The phase space sampling of the whole system is provided
by classical MD.
This methodology has already proven its good modelling
capabilities for the reconstruction of IR spectra
of the amide I mode [2] and in this work we employ it to also
reconstruct the IR signal of protonated aspartic
acid (ASPH) side chain, mainly due to the C=O stretching mode,
which is used to monitor the aspartic acid
protonation state in proton pumps [3]. Three different systems
are studied: aspartic acid with zwitterionic and protonated
backbone and a capped aspartic acid (Figure 1). The ASPH-zwitt
system allows to isolate the
carbonyl group side-chain signal, in the ASPH-prot system the
contribution of both the side chain and the
backbone carbonyl groups are considered and the ASPH-cap allows
to compare the side-chain carbonyl group
signal and the amide I signal (see caption of Figure 1). The
experimental IR absorption maxima of the aspartic
acid side chain are at 1712, 1722 and 1707 cm-1 for ASPH-zwit,
ASPH-prot and ASPH-cap [4,5], respectively.
The calculated spectra are in qualitative good agreement with
the experimental observations. In addition, the
experimental shift between the absorption maximum of ASPH-zwitt
and ASP-prot (i.e. a 10 cm-1 upshift) is
reproduced by the calculation and is demonstrated to depend on
the coupling between the side-chain and
backbone modes. By considering the excitonic coupling between
the two chromophores in ASPH-prot we were
indeed able to reproduce an upshift of ~ 6 cm-1, in good
agreement with the experimental observations.
Figure 4 Structure the three systems under study. The QCs used
for the electronic level calculations are herein
represented with red circles for the protonated aspartic acid
side chain (ASPH) and blue circles for the amide I.
References
[1] J. A. Ihalainen, B. Paoli, S. Muff, E. H. G. Backus, J.
Bredenbeck et. al., Proc. Natl. Acad. Sci. 105 (2008) 9588. [2] L.
Zanetti-Polzi, A. Amadei, M. Aschi and I. Daidone, J. Am. Chem.
Soc. 133 (2011) 11414. [3] J. Wallerstein, U. Weininger, M. Khan,
S. Linse and M. Akke, J. Am. Chem. Soc. 137 (2015) 3093. [4] R. M.
Abaskharon, S. P. Brown, W. Zhang, J. Chen, A. B. Smith III et.al.,
Chem. Phys. Lett. 683 (2017) 193. [5] A. D. Roddick-Lanzilotta and
J. McQuillan, J. Colloid Interface Sci. 227 (2000) 48.
-
Anharmonic vibrational treatment of linear, symmetric and
asymmetric
molecules
Marco Mendolicchio, Julien Bloino, Vincenzo Barone
Scuola Normale Superiore, I-56126, Italy.
[email protected]
Spectroscopies, such as infrared and Raman, are powerful tools
for the investigation of the physical-chemical
properties of molecular systems, providing detailed information
related to the structure and dynamics. However,
experimental spectra are characterized by several intertwined
effects which can make their interpretation
challenging without the support of computational models,
required to obtain accurate predictions of the
transition energies and intensities leading to line-shapes
directly comparable to experiment [1]. As a matter of
fact, ongoing developments of hardware and algorithms, including
the underlying physical mathematical
models, have been essential to the improvement of the quality of
the simulations, which can then provide data
to analyze the underlying stereo-electronic, dynamic, and
environmental effects. Despite the unquestionable
success of static structure-property relationships and of the
basic rigid rotor harmonic oscillator model to
introduce dynamic effects, accurate results, directly comparable
with experiment, can be obtained only
employing more refined models, and, in particular, including
anharmonicity effects, must be employed. Among
the possible methods employable for the inclusion of anharmonic
effects in the simulation of vibrational spectra,
the second-order vibrational perturbation theory (VPT2) [2] has
shown to offer a good balance between
accuracy and computational cost, giving the possibility to
target even medium-to-large systems. Historically,
different formulations of VPT2 have been proposed based on the
type of molecules (linear, symmetric,
spherical, or asymmetric rotors) [3-5]. With the aim of building
a versatile computational platform able to
support other types of coordinates (e.g. internal) and to
combine perturbational and variational calculations, a
general formalism supporting different representations of the
vibrational wavefunction has been developed. The
latter offers the possibility to compute the full spectra up to
three quanta of a wide range of molecules. In this
contribution, the possibilities offered by this platform will be
illustrated through applications to different
molecules of astrochemical interest.
References
[1] V. Barone, Computational Strategies for Spectroscopy, from
Small Molecules to Nano Systems, John Wiley & Sons, Inc.,
2011.
[2] H.H. Nielsen, Rev. Mod. Phys. 23. (1951) 90. [3] J. Plìva,
J. Mol. Spectrosc. 139 (1990) 278. [4] A. Willetts, N. Handy, Chem.
Phys. Lett. 235 (1995) 286. [5] M. Piccardo, J. Bloino, V. Barone,
Int. J. Quantum Chem. 115 (2015) 1948.
-
Challenges in Microwave Spectroscopy
Luca Evangelisti1
1 Department of Chemistry “G. Ciamician”, University of Bologna,
via Selmi 2, Bologna, 40126, Italy
[email protected]
Several questions are usually addressed: which is the preferred
binding site, which type of interactions are
established, whether any conformational change takes place in
the monomers upon complexation. Another
important question is what are the driving forces of the
interactions and how they can be influenced. The nature
and driving forces of intermolecular interactions in
non-covalently bound molecular complexes can be studied
to a very high degree of accuracy by pulsed-jet microwave
spectroscopy. From the detailed structural and
dynamical data that can be obtained, the site and geometry of
the interaction and information on the binding
energy can be inferred without ambiguity.
So, answers to these questions allow insight into the molecular
interaction process at the molecular level,
bridging the gap between gas-phase and bulk properties.
Some chosen examples of published and unpublished results of
complexes of medium-size organic
molecules with different partners formed in a supersonic
expansion and characterized by rotational
spectroscopy will be discussed.
-
Microwave Spectroscopic and Quantum Chemical Investigations on
2-
Methylpyrrole
Thuy Nguyen1, Wolfgang Stahl2, Ha Vinh Lam Nguyen1, Isabelle
Kleiner1
1 Laboratoire Interuniversitaire des Systèmes Atmosphériques
(LISA), CNRS UMR 7583, Université
Paris-Est Créteil, Université Paris Diderot, Institut Pierre
Simon Laplace, 61 avenue du Général de
Gaulle, F-94010 Créteil, France 2 Institute of Physical
Chemistry, RWTH Aachen University, Landoltweg 2, D-52074
Aachen,
Germany
[email protected]
Pyrroles are nitrogen containing five-membered ring systems
which possess unique organoleptic properties
[1]. Some pyrroles are utilized as flavor additives. In the
mid-1906s, pyrroles became known to represent a
minor class of potentially significant flavor-associated
compounds that were found to be naturally occurring
in foods. Pyrrole and the substituted 2-methylpyrrole (2MP) are
found in fried chicken [2]. In this work, 2MP
was investigated by a combination of molecular jet Fourier
transform microwave spectroscopy and quantum
chemical calculations.
Figure 5. The molecular geometry of 2MP optimized at the
MP2/6-311++G(d,p) level of theory.
The calculations at the MP2/6-311++G(d,p) level of theory
yielded only one stable conformer (Fig. 1)
which was identified in the rotational spectrum.
The rotational spectrum of 2MP was recorded using two molecular
jet Fourier transform microwave
spectrometers operating in the frequency range from 2 to 40 GHz.
The splittings arising from the internal
rotation of the methyl group as well as the 14N nuclear
quadrupole coupling were successfully assigned. All
spectra of 2MP were analyzed using the XIAM [3] and the
Belgi-Cs-hyperfine codes [4]. With the fitted
parameters, the whole data set could be reproduced with a
root-mean-square deviation of approximately 3 kHz
which is close to the experimental accuracy.
From the torsional splittings due to the internal rotation of
the methyl group a barrier height of 279.7183(26)
cm-1 was deduced. The 14N quadrupole coupling constants were
accurately determined to be aa = 1.3345(20)
MHz and bb − cc = 4.3599(36) MHz. Due to the Cs symmetry of 2MP
the c axis is a principal axis of both
the inertia and the quadrupole coupling tensor, the value of cc
could be directly compared with other aromatic
five-membered rings. Different signs of the cc constant were
explained by the different chemical bond
situations.
References
[1] J.A. Maga, J. Agric. Food Chem. 29 (1981) 691.
[2] T. Jian, J.Q. Zhang, S.G. Hui, Ho. Chi Tang, C. Stephen S,
J. Agric. Food Chem. 31 (1983) 1287.
[3] H. Hartwig, H. Dreizler, Z. Naturforsch. 51a (1996) 923.
[4] R. Kannengießer, W. Stahl, H.V.L. Nguyen, I. Kleiner, J.
Phys. Chem. A 120 (2016) 3992.
mailto:[email protected]:[email protected]
-
Benchmark of quantum-chemical computations for molecules
containing second-row atoms
Silvia Alessandrini1, Jürgen Gauss2, Cristina Puzzarini3
1 Scuola Normale Superiore, Pisa, I-50126, Italy. 2 Universität
Mainz, Mainz, D-55099, Germany.
3 Alma Mater Studiorum – University of Bologna, Bologna,
I-40126, Italy.
[email protected]; [email protected]
Statistical analyses of computed spectroscopic parameters are
fundamental to assess the accuracy of the
predicted molecular properties and spectra. In the case of
rotational spectra, the transitions mainly depend on
the value of rotational constants and their accurate estimate is
crucial for the interpretation of experimental and
astronomical observations. The accuracy of rotational constants
obtainable from high-level quantum-chemical
calculations for molecules containing first-row atoms is well
addressed [1], while an extension to systems
bearing second-row atoms was still missing. To fill this gap. in
the work I will present, two new statistical
analyses have been carried out2. A first benchmark study
concerns sulfur-bearing species: by comparing 15
different computational approaches, all of them based on the
CCSD(T) method, the effects on computed
rotational constants due to (i) extrapolation to the complete
basis-set limit (see Figure 1), (ii) correlation of
core electrons, and (iii) vibrational corrections to rotational
constants, have been analyzed. To extend the
analysis to other molecules containing second-row elements as
well as to understand the effect of higher
excitations, a second benchmark study has been performed.
The accuracy obtainable will be then shown for some
sulfur-containing molecules of astrochemical interest,
like CCS. Here, results will be illustrated by direct comparison
of the experimental and computed spectra.
References [1] C. Puzzarini, M. Heckert and J. Gauss, J. Chem.
Phys. 128 (2008) 194108. [2] S. Alessandrini, J. Gauss and C.
Puzzarini, J. Chem. Theory Comput. 14 (2018) 5360.
-5.0 -3.0 -1.0 1.0 3.0 5.0Δ [%]
fc-CCSD(T)/cc-pVTZfc-CCSD(T)/cc-pVQZfc-CCSD(T)/cc-pV5Zfc-CCSD(T)/CBS(T,Q)fc-CCSD(T)/CBS(Q,5)
Figure 1 – Convergence to the complete basis set limit of the
CCSD(T) method for molecules containing
second-row atoms [2].
-
Understanding (coupled) large amplitude motions: The interplay
of microwave
spectroscopy, spectral modeling, and quantum chemistry
Lam Nguyen
1 Laboratoire Interuniversitaire des Systèmes Atmosphériques
(LISA), CNRS UMR 7583, Université Paris-
Est Créteil, Université Paris Diderot, 61 avenue du Général de
Gaulle, F-94010 Créteil, France
[email protected]
An enormous number of investigations using molecular jet based
Fourier Transform microwave spectroscopy
has come up since this technique was established almost a
century ago and has become more and more popular
in the last decade. The complexity of molecules studied by this
method also increased dramatically, and still
shows a great potential in the future towards even more complex
systems with applications in diverse research
fields. With the capability to observe the spectra of heavier
and larger molecules, microwave spectroscopy is
emphasizing and consolidating its key role in yielding precise
information on various physical and chemical
objectives.
The effects of intramolecular dynamics cause tunneling
splittings on the rotational energy levels. The two
prototypes of such Large Amplitude Motions (LAMs) are methyl
group internal rotation and inversion tunneling
involving a double minimum potential. These LAMs sometimes
complicate the spectra that much that their
assignments were inhibited. New theoretical tools involving
correct Hamiltonian have to be developed to
reproduce the experimental spectra.
Density functional theory and ab initio calculations implemented
in programs such as Gaussian or GAMESS
are commonly used today in the spectroscopic community to
predict the molecular equilibrium structures, the
conformational and tautomeric preferences from the potential
energy surfaces, electric field gradients, etc., and
to calculate trial values of the related spectroscopic
parameters, including barriers for different types of LAMs
The talk will give an overview of the general procedure for an
investigation on a molecular system by a
combination of microwave spectroscopy, spectral modeling, and
quantum chemical calculations. The focus is
on the molecular dynamics, which are described by the barriers
to internal rotation or inversion. These
experimental data were supplemented by potential curves and
two-dimensional potential energy surfaces
obtained by quantum chemistry.
-
Position dependent study on 3-, 4-, and 5-Cyanoindole via high
resolution laser
induced Stark spectroscopy
Marie-Luise Hebestreit1, Michael Schneider1, Hilda Lartian1,
Michael Schmitt1
1 Heinrich-Heine-University, Düsseldorf, 40225, Germany.
[email protected]
For indole and its derivatives exist two close lowest
electronically excited singlet states, labeled La and Lb
in the nomenclature of Platt [1,2]. These states can be
distinguished by the orientation of the transition dipole
moment and the magnitude of the permanent dipole moment. These
parameters were accessible via rotationally
resolved Stark spectroscopy for the lowest excited state. In
combination with ab initio calculations it is possible
to determine the electronic nature of these states. In this
contribution investigations of the electronic nature of
4-cyanoindole (4-CI) are presented and compared to previous
investigations on 3- and 5-cyanoindole in our
group [3,4]. The studies showed Lb character for the lowest
excited state of 3-CI while for 4- and 5-CI the
lowest excited state was determined to be an La state. Reasons
for this behavior are given by the influence of
the inductive and mesomeric effect of the cyano group and the
resulting electron density flow in the
chromophor, depending if the cyano group is attached at the
pyrrole ring or at the benzene ring.
Figure 6: Indole, 3-, 4- and 5-cyanoindole with the orientation
of the transition dipole moment and the
magnitude of the permanent dipole moment [3-6].
References
[1] J. R. Platt, J.Chem.Phys 17 (1949) 484.
[2] G. Weber, Biochem. J. 75 (1960) 335.
[3] M. Schneider et al, PCCP 20 (2018) 23441.
[4] J. Wilke et al, ChemPhysChem 17 (2016) 2736.
[5] Kang et al, J.Chem.Phys. 122 (2005) 174301.
[6] C. Brand et al, Phys.Chem.Chem.Phys. 12 (2010) 4968.
-
Latest developments in VMS Draw
Daniele Licari1
1 Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova,
Italy
[email protected]
The impressive advances of computer power, effective and
user-friendly software and graphical interfaces
are leading to the development of a new generation of virtual
tools able to deal effectively with the complex
systems and phenomena of current interest in the study of
molecular systems.
Going from collections of numbers for oversimplified models
toward vis-a-vis comparison between in
silico and in vitro outcomes for real systems together with 3D
renderings and graphical user interfaces should
finally overcome the residual diffidence of experimentalists for
computer simulations.
Among those virtual instruments, I will be concerned here with
the Virtual Multi-frequency Spectrometer
Draw (VMS-Draw) our group is developing in the last few years
[1], allowing vis-a-vis comparison of
experimental spectra with their simulated counterparts, and
interpretation of the results.
In this presentation, the status of VMS-Draw and the ongoing
efforts toward a synergistic use of computer-
and data-intensive algorithms has led to the development of new
strategies for handling complex problems in
molecular modeling and atomistic simulations [2].
Fig,1 Virtual Multifrequency Spectrometer (VMS) system provide
access to the latest developments in
computational spectroscopy to the non-specialized user.
References
[1] D. Licari et al., J. Comput. Chem. 36 (2015) 321.
[2] D. Licari et al., Phys. Chem. Chem. Phys. 20 (2018)
26034.
-
A Modern-Fortran Program for Chemical Kinetics on top of
Anharmonic
Vibrational Calculations
Surajit Nandi1, Sergio Rampino1, Vincenzo Barone1
1 Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, 56126,
Italy. [email protected]
We discuss the design and implementation of StarRate, a modern,
object-based Fortran program for the
calculation of chemical kinetics within anharmonic vibrational
perturbative model [1]. The program is written
in the F language, a carefully crafted subset of Fortran95.
StarRate is made up of three main modules handling
the involved molecular species, the elementary reaction steps,
and the whole reaction scheme. Input data are
accessed through an XML interface based on a cross-code
hierarchical data format granting interoperability
with popular electronic-structure packages and with the
graphical interface of the Virtual Multifrequency
Spectrometer developed in our group [2]. Data extraction from
the output of electronic-structure calculations is
performed through versatile Python scripts. Test calculations on
the isomerization reaction of C-
cyanomethanimine using anharmonic densities of states, obtained
with a development version of Gaussian, are
presented and discussed.
References
[1] V. Barone, J. Chem. Phys. 122 (2005) 14108. [2] D. Licari,
A. Baiardi, M. Biczysko, F. Egidi, C. Latouche, V. Barone, J.
Comput. Chem. 36 (2015) 321.
-
Quantum mechanical strategies for reactivity and kinetics of
atmospheric
reaction pathways
Jacopo Lupi1, Zoi Salta1, Nicola Tasinato1, Vincenzo Barone1
1 Scuola Normale Superiore, Pisa, 56126, Italy.
[email protected]
Understanding the reaction pathways that lead to the formation
and dissociation of species present in
planetary systems, on Earth as a special case and in the
interstellar medium (ISM), are of paramount
importance. The comprehension of processes ruling the evolution
of our atmosphere is essential since they are
related, for example, to global climate change or to the
building-up of chemical complexity in space.
On Earth, organic acids are found to be released from burning
biomass and fossil fuels, as well as from
other industrial emissions [1]. Photochemical reactions are
important sources of these acids [2]. Because of
their solubility properties they are involved in aerosol and
cloud formation and a major fraction of them is
washed out by physical processes, such as wet and dry deposition
of aerosols [3]. The remaining part of organic
acids in the atmosphere is thought to react mainly with hydroxyl
radicals to form various products [4]. These
compounds are highly important in atmospheric chemistry, since
they not only have a dominant impact on the
acidity within the precipitation in remote areas, but also
significantly influence the acidity in industrial regions.
The acidification in remote areas is mainly due to formic and
acetic acids and in more polluted areas, sulfuric
and nitric acid dominate rainwater pH.
Quantum chemical calculations represent unique tools to explore
the pathways leading to the
formation/decomposition of atmospheric molecules by either gas-
or condensed-phase (i.e. at the gas/solid or
gas/liquid interface) reactions. In fact, they can provide
precise thermochemical data, such as relative energies,
barrier heights, reaction enthalpies/exothermicities, and which
represent crucial parameters to be inserted into
the atmospheric models employed to explain the observed
abundances. Furthermore, in order to study the
feasibility of these reactions from a kinetic point of view,
reaction rate coefficients (k) must also be obtained
in different conditions (temperature and pressure).
The need for these data is particularly stringent, since for
modeling the complex networks of elementary
reactions taking place in different areas of the planetary
atmospheres, a number of experimental parameters is
required. However, an exploration of the available literature
reveals that much information is still lacking, and
only a small fraction of the necessary data has been
characterized in laboratory experiments [5]. In such cases,
the computational approach may become the only viable route to
obtain the required parameters, such as barrier
heights and adsorption dynamics.
To that end, the Potential Energy Surface (PES) of two
atmospherically important reaction pathways were
examined; the formation of methanesulfenic (CH3SOH) and
methanesulfinic acids (CH3S(O)OH) from the H-
abstaction reaction of dimethyl sulfide (CH3SCH3) with the OH
radical, and the H-abstraction reaction of
formic acid (HCOOH) with Cl atoms. All possible reactants,
pre-reactive complexes, intermediates, transition
states and products were characterized both structurally and
energetically with the use of high level
computational methodologies, and rate constants (k) for some of
the reactions were obtained, in order to
provide an overall assesment on the feasibility of the
aforementioned reaction pathways.
References
[1] J. Kesselmeier and M. Staudt, Journal of Atmospheric
Chemistry 33 (1999) 23.
[2] D. B. Millet et al., Atmospheric Chemistry and Physics 15
(2015) 6283.
[3] B. Radola, S. Picaud, D. Vardanega, and P. Jedlovszky, The
Journal of Physical Chemistry C 121 (2017) 13863.
[4] S. So, U. Wille, and G. da Silva, Environmental Science
& Technology 48 (2014) 6694.
[5] S. Frka, M. Šala, A. Kroflič, M. Huš, A. Čusak, and I.
Grgić, Environmental Science & Technology 50 (2016) 5526.
-
Examining molecular conformational landscape using QM based
stochastic approach
B. Chandramouli1,2, S. del Galdo2, G. Mancini2,3, V.
Barone2,3
1Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30,
I-16163 Genova, Italy 2Scuola Normale Superiore di Pisa, Piazza dei
Cavalieri 7 I-56126, Pisa, Italy
3Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa,
Largo Bruno Pontecorvo 3,
56127 Pisa, Italy
[email protected]
The search for stationary points in the molecular potential
energy surfaces (PES) is a problem of major
importance in computational chemistry1. In spectroscopic
applications, the minima conformers, thus obtained,
permit to correlate the properties estimated by QM calculations
to the experimental counterparts, thereby
facilitating the structural interpretation to the spectroscopic
signatures2. A complete characterization of the
lowest lying states of even relatively simple molecules can be
difficult due the high number of possible
structures to be evaluated and the presence of very shallow
minima that are hard to detect. MM based
simulations or systematic searches3, due to their very good
balance between computational cost and accuracy
are often used but such an approach may be of limited use if the
force field is unavailable (or not accurate)4.
Herein, we present a procedure that employs a very cheap and yet
accurate level of chemical theory combined
with a simple stochastic search protocol to efficiently sample
the conformational space of small molecules
without relying on MM force fields. Considering a set of well
studied showcase systems of varying complexity,
we show the reliability of the method in probing the
conformational landscape and solvent effects on the
conformational equilibria.
References
[1] Computational Biochemistry and Biophysics; CRC Press,
2001.
[2] J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López and S.
Blanco Phys. Chem. Chem. Phys. 11 (2009) 617.
[3] T. Hansson, C. Oostenbrink and W. van Gunsteren Curr. Opin.
Struct. Biol. 12 (2002) 190.
[4] B. Chandramouli, S. Del Galdo, G. Mancini, N. Tasinato and
V. Barone Biopolymers 109 (2018) e23109.
-
Efficient quantum dynamics with the Time-Dependent Density
Matrix
Renormalization Group
Alberto Baiardi1, Markus Reiher1
1 ETH Zürich, Laboratorium für Physikalische Chemie,
Vladimir-Prelog-Weg 2, Zürich, 8093, Switzerland
[email protected]
Thanks to the design of more and more accurate and powerful
ultrafast spectroscopic techniques, it is
nowadays possible to resolve the dynamics of a molecule under
non-equilibrium conditions on the natural time
scales of both electronic and nuclear motions. The most accurate
algorithms available in the literature to perform
quantum dynamics simulations on molecular systems encode the
wavefunction with a full configuration
interaction (CI) expansion. The exponential increase of the
computational cost of CI-based schemes with the
system size hinders, however, their application to molecules
with more than 10 atoms.
This unfavorable scaling can be limited by parametrizing the
wavefunction as a matrix product state and by
simulating its time evolution with the time-dependent (TD)
extension of the well-known density matrix
renormalization group algorithm (DMRG). In the present
contribution, we combine a recently developed TD-
DMRG algorithm [1] with our general framework for performing
DMRG calculations on vibrational- [2-3] and
electronic-structure [4] quantum-chemical Hamiltonians. We apply
the resulting theory to simulate both the
nuclear and the electronic dynamics, possibly coupled together,
of molecules with several dozens of degrees of
freedom [5] that are challenging to target with most full
quantum dynamics algorithms available in the literature.
Moreover, we demonstrate how TD-DMRG can be employed as a
cost-effective alternative to the standard time-
independent formulations of DMRG for calculating high-order
response properties or for simulating molecular
spectra in regions with a high density of excited states.
References
[1] J. Haegeman, C. Lubich, I. Oseledets and B. Vandereycken and
F. Verstraete, Phys. Rev. B 94 (2016) 1.
[2] A. Baiardi, C. J. Stein, V. Barone and M. Reiher, J. Chem.
Theory Comput. 13 (2017) 3764.
[3] A. Baiardi, C. J. Stein, V. Barone and M. Reiher, J. Chem.
Phys. 150 (2019) 094113.
[4] S. Keller, M. Dolfi, M. Troyer and M. Reiher, J. Chem. Phys.
143 (2015) 244118.
[5] A. Baiardi, M. Reiher, in preparation.
-
Indentifying Secondary Species in Solution: A Combined
Experimental and
Theoretical Approach1
M. A. P. Turner1,2,*, M. D. Horbury1, V. G. Stavros1, N. D. M.
Hine2,*
1 Department of Chemistry, University of Warwick, Coventry, CV4
7AL, UK 2 Department of Physics, University of Warwick, Coventry,
CV4 7AL, UK
*[email protected]; [email protected]
The measured electronic excitations of a given species in
solution are often the superimposed electronic
excitations of various equilibrium species of that
molecule.[2,3] These species can arise through many different
mechanisms, for example, a proportion of the species could
deprotonate in solution, or form a tautomeric
equilibrium. Equilibrium species may result in unwanted effects,
for instance, in the case of medicine where
potentially dangerous side products could be formed;[4] or in
dyes or paints whose colour may be affected by
properties which influence the equilibrium, such as solvent, pH,
or temperature.[5] Determining the identity
of the various species present is the first step towards
controlling them. In this talk I will discuss the application
of a combination of state-of-the-art experimental and
theoretical techniques used to deconvolve the spectrum
of a widely studied exemplar dye, alizarin, see Figure 1
(left).
Figure 1 left: Primary (A) and secondary (B−D) structures
considered within this work: (A) alizarin-a
tautomer; (B) alizarin-b tautomer; (C) alizarin monoanion-a; (D)
alizarin monoanion-b. Right:
Comparative theoretically predicted and experimentally obtained
UV-Vis spectra for alizarin.
Alizarin in methanol has an isosbestic point between the two
dominant excitations at 435 and 540 nm when
studied at different temperatures and pH values. The peak at 435
nm has been attributed to alizarin in previous
work [6]; the peak at 540 nm, however, more likely results from
a species in equilibrium with alizarin. In this
work, we were able to use both experimental and computational
techniques to selectively examine electronic
properties of both alizarin and its secondary species in
equilibrium. This was achieved through use of transient
electronic absorption spectroscopy, following selective
photoexcitation of the specific species in equilibrium.
This was compared to the spectra of alizarin in buffered
solution which allowed us to determine that the
secondary species was likely an anion of alizarin and not a
tautomer. Further to this, the ground state absorption
spectra associated with each species in equilibrium were
predicted using linear-scaling time-dependent density
functional theory with an explicitly modeled solvent and
compared to the experimental result, this is shown in
Figure 1 (right). This suggests that the excitation at 540 nm
arises from a specific monoanionic form of
alizarin: the “monoanion-b” form shown in Figure 1(left) -
species D.
References
[1] M. A. P. Turner, M. D. Horbury, V. G. Stavros, N. D. M.
Hine, J. Phys. Chem. A. 123 (2019) 873.
[2] L. Antonov, D. Nedeltcheva, Chem. Soc. Rev. 29 (2000)
217.
[3] L. Antonov, G. Gergov, V. Petrov, M. Kubista, J. Nygren,
Talanta 49 (1999) 99.
[4] M. Günther, E. Wagner, M. Ogris, J. Cell. Mol. Med. 12
(2008) 2704.
[5] D. Magde, G. E. Rojas, P. G. Seybold, Photochem. Photobiol.
70 (1999) 737.
[6] C. Miliani, A. Romani, G. Favaro, J. Phys. Org. Chem 13
(2000) 141.
-
Molecular Spectroscopy: A Collaborative Effort
Iker León1
1 Grupo de Espectrocopía Molecular (GEM), Edificio Quifima,
Laboratorios de Espectroscopia y
Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa,
Universidad de Valladolid, 47011,
Valladolid, Spain.
[email protected]
There exists a plethora of tools and techniques to investigate
the fundamental aspects of molecular physics.
Among them, spectroscopy is one of the most powerful techniques.
It is based on the study of the interaction
between matter and electromagnetic radiation to extract
information about the composition, and the physical
and electronic structure of matter at atomic, molecular, or
macro scales, and over a range of distances that go
from nanometers to astronomical distances.
Among the existing techniques, absorption/emission spectroscopy
is probably the most widely used one. For
example, rotational, vibrational, electronic and time-resolved
spectroscopies are well-known techniques that
yield particular information about the molecules. Combining
these studies with supersonic expansions permits
to greatly simplify the spectra, and provide an ultra-cold
molecular collision-free environment, which is ideal
to form clusters. Furthermore, it permits their study without
the interfering effects of a condensed medium.
These isolated conditions also enable direct comparison between
the experimental observables and those
provided in silico and in vacuo by DFT and ab initio
calculations. While rotational spectroscopy provides
accurate structural information, the molecular size manifests as
a limitation. On the other hand, vibrational and
electronic spectroscopies yield a more limited structural
information, but offer additional data and can be applied
to larger molecular systems. For molecular sizes ranging in
between, the combination of such spectroscopies
results in wealth of information and overcome their separated
particular drawbacks. Some examples will be
provided to highlight the complementarity of these
spectroscopies.
Additionally, theoretical models and computational chemistry are
essential. The symbiosis between theory
and experiment is the key to refine each other allowing
researchers to take a step forward into solving,
understanding and modelling larger molecular systems. Some
examples of the necessity of theoretical research
will be provided.
Figure 7 Electronic, rotational, vibrational and time-resolved
spectroscopies provide unique and complementary
information.
-
Computational determination of the charge transfer excited state
in azobenzene
maleimide derivatives
Dragos Lucian Isac1, Anton Airinei1, Corneliu Cojocaru1, Andrei
Neamtu1, Francesca Mocci2, Aatto
Laaksonen1, Mariana Pinteală1
1 “Petru Poni” Institute of Macromolecular Chemistry Iasi,
Grigore Ghica Voda Al. No. 41A, 700487 Iasi,
Romania. 2 Department of Chemical and Geological Sciences,
University of Cagliari, Monserrato, I-09042 Italy.
[email protected]
Azobenzene molecule belongs to the multiphotochromic molecular
systems family because it can be
activated by photo irradiation becoming a photochromic compounds
[1,2]. Photoisomerization can interconvert
the azobenzene structure between its trans (E)- and cis (Z)-
isomers via UV light irradiation. When the stationary
state is attained, this process is reversible by two pathways,
namely when the molecule is irradiated with visible
light or thermal isomerization occurs in the darkness. Each
conformation presents electronic distinct spectral
and geometric properties that allow of these molecules to serve
as ideal model systems for molecular motors
or as the optical switch devices [1,2]. In the azobenzene
derivatives two well-separated absorption bands in
the UV-Vis range have been identified. The strong absorption
band in near-UV region corresponds to a π →
π* symmetry-allowed transition (S0 → S2), whereas the absorption
band located in the visible region, much
weaker in intensity, arises from an n → π* forbidden transition
(S0 → S1). However, some aspects concerning
the electronic structures, spectra and the interconversion
mechanism of azobenzene systems after isomerization
remain questionable and open for discussion. The presences of
maleimide structure in the azobenzene structure
results in low energy transitions, changing the order of the
main transitions due to the charge transfer. A suite
of calculations TD-DFT (PBE0, CAM-B3LYP and ab initio (CIS,
CIS(D) and CASSCF-NEVPT2) were
performed in order to elucidate the relationship between their
electronic structure and the type of charge transfer
mechanism. The results show that a charge transfer occurs from
the azo moiety that acts as a donor to the maleimide
group (acts as acceptor). We find that the presence of charge
transfer states modifies the order of main electronic
transition of azobenzene, and the energy of these states depends
on the orientation of maleimide fragments. The
charge transfer mechanism in azobenzene maleimide derivatives
can occur via two pathways: planar and
twisted.
Figure 8 Structure of azobenzene maleimide derivatives
References
[1] A. Fihey, A. Perrier; W. R Browne, and D. Jacquemin, Chem.
Soc. Rev. 44 (2015) 3719.
[2] H. M. D. Bandara, and S. C. Burdette, Chem. Soc. Rev. 41
(2012) 1809.
-
An effective integration of variational and perturbative QM/MM
approaches for
computing UV-Vis spectra in condensed phases
Sara Del Galdo1,2, Balasubramanian Chandramouli2,3, Giordano
Mancini2,4
and Vincenzo Barone2,4
1 Consiglio Nazionale delle Ricerche (ICCOM-CNR), UOS di Pisa,
Area della Ricerca CNR, Via G.
Moruzzi 1, I-56124 Pisa, Italy. 2 Scuola Normale Superiore di
Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy.
3 Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego
30, I-16163 Genova, Italy. 4 Istituto Nazionale di Fisica Nucleare
(INFN) sezione di Pisa, Largo Bruno Pontecorvo 3,
56127 Pisa, Italy.
[email protected], [email protected]
The accurate reproduction of the spectroscopic properties of
molecular systems in condensed phase is among
the main aims of contemporary theoretical-computational
chemistry[1,2]. Currently, multi-scale approaches are
the methods of choice to achieve the goal, allowing reliable yet
feasible calculations. We computed the
electronic absorption spectrum of two differently featured
systems by means of different Quantum Mechanics
(QM) Molecular Mechanics (MM) methods[2,3]. In brief, the
well-known ONIOM/EE[2,3,4] method was
firstly applied, thus extracting from the MM sampling a huge
number of configurations to be employed for the
following QM calculations. Next, the Perturbed Matrix Method
[5,6] (aka PMM) was applied. The latter,
exploiting a perturbative approach, requires a tiny number of QM
calculations, but suffers from poor
convergence for configurations strongly different from the
reference one. We posit a combined approach in
which, provided a robust cluster analysis of the MM sampling,
the full ONIOM/EE method is used for a single
representative configuration of each cluster whilst the PMM is
employed to treat the in-cluster fluctuations
with respect to the references. Hence, paying attention to the
juxtaposition of accuracy and computational cost,
we aimed at providing a comparative analyses of different
methods to furnish guiding insights for users
suggesting the choice and application of suitable tools.
References
[1] Barone, V.; Wiley Interdisciplinary Reviews: Computational
Molecular Science 6 (2016) 86. [2] Morzan, U. N.; et al; Chemical
Reviews 118 (2018) 4071. [3] Chung, L. W.; et al ; Chemical Reviews
115 (2015) 5678. [4] Brunk, E.; Rothlisberger, U.; Chemical Reviews
115 (2015) 6217. [5] Aschi, M.; Spezia, R.; Di Nola, A.; Amadei,
A.; Chem. Phys. Lett. 344 (2001) 374. [6] Carrillo-Parramon, O.; et
al.; J. Chem. Theory Comput. 13 (2017) 5506.
-
Computational solid-state NMR spectroscopy as a tool for the
structure
determination of oxide glasses and assessment of classical
Force-Fields
Alfonso Pedone
Dipartimento di Scienze Chimiche e Geologiche, Università degli
Studi di Modena e Reggio Emilia, Via G.
Campi 183, 41125 Modena (Italy)
[email protected]
In this communication a computational approach which couples
molecular dynamics and DFT simulations
for the calculation of NMR parameters, line widths and shapes of
the spectra of oxide glasses will be
presented.[1,2] Emphasis is given to the decisive role of this
approach as i) interpretative tool for a deeper
understanding of the spectral behavior of complex systems, ii)
as predictive instrument to map NMR data into
a distribution of structural parameters and backwards and iii)
as a tool to evaluate the reliability of force-fields
for oxide glasses.
This approach will be applied to ‘simple’ network former glasses
and more complex silicates,
aluminosilicate, phosphosilicate and borosilicate glasses of
scientific relevance. [3-6]
References
[1] A. Pedone, T. Charpentier and M. C. Menziani Phys. Chem.
Chem. Phys. 12 (2010) 6054.
[2] T. Charpentier, P. Kroll and F. Mauri J. Phys. Chem. C 113
(2009) 7917.
[3] A. Pedone, T. Charpentier, G. Malavasi and M. C. Menziani
Chem. Mater. 22 (2010) 5644
[4] A. Pedone, T. Charpentier and M. C. Menziani J. Mater. Chem.
22 (2012) 12599.
[5] A. Pedone, E. Gambuzzi, G. Malavasi, and M. C. Menziani
Theor. Chem. Acc. 131 (2012) 1147.
[6] A. Pedone, E. Gambuzzi, M. C. Menziani J. Phys. Chem. C 115
(2012) 14599.
-
The accurate 1H-14N distance measurement
by phase-modulated RESPDOR at ultra-fast MAS
Federica Rossi,1 Nghia Tuan Duong,2 Amir Goldbourt,3 Michele R.
Chierotti,1 Roberto Gobetto,1
Yusuke Nishiyama2,4
1 Department of Chemistry and NIS Centre, University of Torino,
Torino 10125, Italy 2 RIKEN-JEOL Collaboration Center, Yokohama,
Kanagawa 230-0045, Japan
3 School of Chemistry, Faculty of Exact Sciences, Tel Aviv
University, Ramat Aviv, Tel Aviv 69978, Israel 4JEOL RESONANCE
Inc., Musashino, Akishima, Tokyo 196-8558, Japan
[email protected]
The accurate determination of internuclear distances and from
these, of the geometry and conformation of
molecules, is of extremely interest in different fields such as
chemistry, biology, and pharmaceutical
science.[1,2] Despite X-ray and neutron diffraction techniques
are usually considered the best tools for structural
determination, the first can suffer from imprecise determination
of 1H positions and the latter requires
sufficiently large crystals and/or deuteration. Solid-state
nuclear magnetic resonance (SSNMR) spectroscopy
has been proved to be a valuable complementary method since it
has no restriction of sample morphology
(microcrystalline, disordered or amorphous samples) and it
directly provides the distances between two nuclei
via measurement of dipolar couplings. Unfortunately, the dipolar
coupling interaction is averaged out under the
magic angle spinning (MAS) condition, which is used for
high-resolution purpose. Over the past decades,
several methods, termed recoupling techniques,[3,4,5] have been
developed to recover the distance-encoding
interaction. Besides reintroducing the 1H-X heteronuclear
dipolar coupling, a recoupling sequence must also
suppress the intense 1H-1H homonuclear coupling interactions.
The latter requirement has been significantly
simplified by the advances in fast MAS probe technology, since
under such high spinning speeds the
aforementioned interactions are averaged out.[6] The major
drawback in the measurement of quantitative 1H-N
distances is the low natural abundance of 15N isotope (0.4%)
together with low transfer efficiency between 1H
and 15N magnetizations. On the other hand, the 14N isotope
benefits from a higher natural abundance (99.6%)
but, being an integer quadrupolar nucleus (spin number I = 1),
it suffers from quadrupolar interactions making
the 1H-14N distance measurement more challenging.
Here we report on the combination of phase-modulated (PM)
pulse[7] and resonance-echo saturation-pulse
double-resonance (RESPDOR) sequence[8] for determining 1H-14N
distances under ultra-fast MAS frequency
of 70 kHz. As the PM-pulse has not been demonstrated at such
high MAS frequencies, first its practicability
under this condition combined with the RESPDOR scheme was probed
by numerical simulations. Then, the
robustness of PM-RESPDOR sequence with respect to 14N
quadrupolar interaction and its application to a wide
range of d1H-14N were verified on the same modeled 1H-14N spin
system. Finally, the method was applied to two
different real samples, i.e. L-tyrosine∙HCl and
N-acetyl-L-alanine, with a small and large quadrupolar
constant,
respectively, to probe the feasibility of the sequence to
different systems. For the first time, multiple 1H-14N
heteronuclear dipolar couplings, and thus quantitative
distances, have been simultaneously and reliably
extracted by fitting the simulated curves to the experimental
build-up ones. The distances determined by the
employing of such SSNMR pulse sequence are in good agreement
with those derived from diffraction
techniques.
References
[1] W. T. Franks et al., Proceedings of the National Academy of
Sciences 105 (2008) 4621.
[2] L. Rajput, et al., IUCrJ 4 (2017) 466.
[3] G. De Paëpe, Annual Review of Physical Chemistry 63 (2012)
661.
[4] M. H. Levitt, eMagRes 9 (2007) 165.
[5] X. Zhao, J. L. Sudmeier, W. W. Bachovchin and M. H. Levitt,
Journal of the American Chemical Society 123 (2001)
11097.
[6] Y. Nishiyama, Solid State Nuclear Magnetic Resonance 78
(2016) 24.
[7] E. Nimerovsky, M. Makrinich, and A. Goldbourt, The Journal
of Chemical Physics, 146 (2017) 124202.
[8] Z. Gan, Chemical Communications (2006) 4712.
-
2D solid-state NMR experiments to characterize the hydrogen bond
network in
pharmaceutical cocrystals
S. Bordignon1, P. Cerreia Vioglio1, E. Priola1, D. Voinovich2,
R. Gobetto1, Y. Nishiyama3, M. R.
Chierotti1
1 Department of Chemistry and NIS Centre, University of Torino,
Via P. Giuria 7, 10125, Torino, Italy 2 Department of Chemical and
Pharmaceutical Sciences, University of Trieste, P.le Europa 1,
34127, Trieste,
Italy 3 JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo
196-8558, Japan.
[email protected]
Hydrogen bonds are among the main tools expendable to design
supramolecular adducts such as cocrystals.
A cocrystal is defined as a multi-component crystalline entity
in which two or more different molecules occupy
the same unit cell, linked by weak interactions [1].
Cocrystallization represents a strategy to successfully
modulate the physicochemical properties of the components, such
as mechanical properties, reactivity and
dissolution rate.
Despite many efforts, it is not uncommon to encounter drawbacks
in obtaining crystals suitable for X-ray
analysis. When this happens, solid-state NMR (SSNMR) can step in
to solve the issue. SSNMR has long proven
to be a powerful means to study and characterize hydrogen bonds
in supramolecular chemistry. In our case,
several 1D (1H MAS, 13C CPMAS and 15N CPMAS) and 2D (1H DQ MAS,
13C-1H HETCOR, 14N-1H J- and D-
HMQC) techniques were employed to investigate two samples: a
co-drug of indomethacin and caffeine and a
pharmaceutical cocrystal of ibuprofen and proline.
In the first case [2], single crystal X-ray diffraction analysis
was performed on a properly sized crystal, while
SSNMR spectra were acquired to evaluate the ionic or neutral
nature of the adduct which depends on the
position of the hydrogen atom along the N···H···O interaction.
As for the ibuprofen-proline cocrystal, owing to
the lack of X-ray data, the experiments provided the
stoichiometric ratio between the components, information
about the ionic or neutral nature of the cocrystal and the
hydrogen bond interactions at play in its crystal
structure.
References
[1] A. Author, B. Author and C. Author, Journal Volume (Year)
Firstpage. C. B. Aakeröy, D. J. Salmon, CrystEngComm
7 (2005) 439
[2] S. Bordignon, P. Cerreia Vioglio, E. Priola, D. Voinovich,
R. Gobetto, Y. Nishiyama, M. R. Chierotti, Cryst. Growth
Des. 17 (2017) 5744.
-
β-diketones based rotary switches: molecular spectroscopy and
computational
chemistry playing together
S. Hristova1, F. S. Kamounah2, A. Crochet3, P. E. Hansen4, K. M.
Fromm3 and L. Antonov1
1 Bulgarian Academy of Sciences, Institute of Organic Chemistry
with Centre of Phytochemistry, 1113
Sofia, Bulgaria,; 2University of Copenhagen, Department of
Chemistry, DK-2100 Copenhagen Ø, Denmark; 3 University of Fribourg,
Department of Chemistry, 1700 Fribourg, Switzerland; 4 Department
of Science
and Environment, Roskilde University, DK-4000, Roskilde,
Denmark.
[email protected]
The hydrazone functional group has found extensive the use in
medicine, supramolecular chemistry
(molecular switches and sensors) and in combinatory chemistry.
One important facet of hydrazone chemistry
is the fact that upon appropriate substitution they can exist in
solution as a mixture of isomers. For example
1,2,3 - tricarbonyl-2-arylhydrazones (TCAHs) exist in solution
as an equilibrated mixture of intramolecularly
H-bonded E and Z izomers. The position of the isomerization
equilibrium can be altered by catalytic amounts
of acid or base. However, this equilibration process is neither
selective nor optimal and only affords a mixture
of isomers (e.g., it can proceed from pure E to a mixture of E
and Z isomers) that cannot be controllably
switched back to the initial state [1,2].
We have studied compound 1, which
belongs to a series of arylhydrazones of
β-diketones, with molecular
spectroscopy (1H, 13C, 15N NMR and
UV-Vis) in DMSO and computational
methods. It has been found that the
studied compound exists as a mixture
of isomers of the hydrazone tautomer major (E’-oriented) and
minor conformer (Z’-oriented) in different
solvents. Also the OH group of the compound 1 deprotonates at
low concentrations and at high concentrations
(10-4 M and higher) linear (E’-E’) aggregates according to the
UV-Vis investigations and X-ray data [3,4].
References
[1] X. Su, I. Aprahamian, Chemical Society Reviews, 43(6) (2014)
1963.
[2] M. Landge, E. Tkatchouk, D. Benítez, A. Lanfranchi, M.
Elhabiri, A. Goddard, I. Aprahamian, Journal of the
American Chemical Society, 133(25) (2011) 9812.
[3] S. Hristova, F. S. Kamounah, N. Molla, P. E. Hansen, D.
Nedeltcheva, L. Antonov, Dyes Pigments 144 (2017) 249.
[4] V. Deneva, A. Lyčka, S. Hristova, A. Crochet, K.M. Fromm, L.
Antonov, Dyes Pigments, 165 (2019) 157.
Acknowledgements:
The financial support from the project DCOST01/5/2017 is
gratefully acknowledged.
mailto:[email protected]:[email protected]
