1
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Drost DA, Merten C. Vibrational circular dichroism spectra of proline in water at different pH values. Phys Chem Chem Phys 2024; 26:17753-17759. [PMID: 38873734 DOI: 10.1039/d4cp01768d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Recording VCD spectra of aqueous solution poses a particular challenge as water is a strong infrared absorber. Likewise, the computational analysis of VCD spectra by means of DFT-based spectral calculations requires the consideration of explicit solvent molecules, thus posing an even greater challenge. Several studies suggested that by modeling the solvent environment with a few water molecules in a micro-solvation approach would be sufficient to describe experimental spectra. For example, using proline at different pH values, we herein show that a change in the relative spatial orientation of a single water molecule in five-fold solvated structures strongly affects the computed VCD spectral signatures and that Boltzmann-weighted spectra do not correctly reproduce the experiment. We thus explored an approach based on molecular dynamics and subsequent DFT-calculations, in which we considered 30 water molecules (about 1.5 solvation shells). Once again, it was found that the Boltzmann-weighted spectra obtained on the basis of several hundred structures did not correctly reproduce experimental signatures, and a simple averaging scheme resulted in well-matching spectra with comparable bandwidths. The rationale behind the procedure was that sampling the configurational space of the solvent molecules is as equally important as the conformational sampling of the solute. For conformationally more flexible molecules, it is assumed that a much larger set of structures will have to be computed in order to properly sample the conformational space of both solute and solvent.
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Affiliation(s)
- Deborah A Drost
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Organic Chemistry II, Universitätsstraße 150, 44801 Bochum, Germany. www.mertenlab.de
| | - Christian Merten
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Organic Chemistry II, Universitätsstraße 150, 44801 Bochum, Germany. www.mertenlab.de
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2
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Schreder L, Luber S. Chiral Spectroscopy of Bulk Systems with Propagated Localized Orbitals. J Chem Theory Comput 2024; 20:3894-3910. [PMID: 38661175 DOI: 10.1021/acs.jctc.4c00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
We present approaches for the simulation of electronic circular dichroism, Raman, and Raman optical activity (ROA) spectra for isolated and periodic systems as well as subsystem analysis thereof. The method is based on the use of time-dependent maximally localized Wannier functions in the CP2K package and accounts for origin dependencies inherent to the Gaussian and plane wave with pseudopotentials approach as well as the origin dependence of the magnetic dipole and electric quadrupole operators. Tests on the H-bonded enantiomers of alanine by harmonic normal-mode analysis and on an aqueous solution of l-alanine by ab initio molecular dynamics obeying periodic boundary conditions (PBCs) are presented as total and subsystem-resolved spectra. To our knowledge, this is the first instance of an ROA spectrum derived from real-time propagation obeying PBCs and the first ROA simulation considering off-, pre-, and on-resonance effects within PBCs.
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Affiliation(s)
- Lukas Schreder
- University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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3
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Bowles J, Jähnigen S, Agostini F, Vuilleumier R, Zehnacker A, Calvo F, Clavaguéra C. Vibrational Circular Dichroism Spectroscopy with a Classical Polarizable Force Field: Alanine in the Gas and Condensed Phases. Chemphyschem 2024; 25:e202300982. [PMID: 38318765 DOI: 10.1002/cphc.202300982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/07/2024]
Abstract
Polarizable force fields are an essential component for the chemically accurate modeling of complex molecular systems with a significant degree of fluxionality, beyond harmonic or perturbative approximations. In this contribution we examine the performance of such an approach for the vibrational spectroscopy of the alanine amino acid, in the gas and condensed phases, from the Fourier transform of appropriate time correlation functions generated along molecular dynamics (MD) trajectories. While the infrared (IR) spectrum only requires the electric dipole moment, the vibrational circular dichroism (VCD) spectrum further requires knowledge of the magnetic dipole moment, for which we provide relevant expressions to be used with polarizable force fields. The AMOEBA force field was employed here to model alanine in the neutral and zwitterionic isolated forms, solvated by water or nitrogen, and as a crystal. Within this framework, comparison of the electric and magnetic dipole moments to those obtained with nuclear velocity perturbation theory based on density-functional theory for the same MD trajectories are found to agree well with one another. The statistical convergence of the IR and VCD spectra is examined and found to be more demanding in the latter case. Comparisons with experimental frequencies are also provided for the condensed phases.
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Affiliation(s)
- Jessica Bowles
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
| | - Sascha Jähnigen
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Anne Zehnacker
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay UMR8214, 91405, Orsay, France
| | - Florent Calvo
- Université Grenoble Alpes, CNRS, LIPhy, 38000, Grenoble, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
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4
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Tao Z, Qiu T, Bhati M, Bian X, Duston T, Rawlinson J, Littlejohn RG, Subotnik JE. Practical phase-space electronic Hamiltonians for ab initio dynamics. J Chem Phys 2024; 160:124101. [PMID: 38526114 DOI: 10.1063/5.0192084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024] Open
Abstract
Modern electronic structure theory is built around the Born-Oppenheimer approximation and the construction of an electronic Hamiltonian Ĥel(X) that depends on the nuclear position X (and not the nuclear momentum P). In this article, using the well-known theory of electron translation (Γ') and rotational (Γ″) factors to couple electronic transitions to nuclear motion, we construct a practical phase-space electronic Hamiltonian that depends on both nuclear position and momentum, ĤPS(X,P). While classical Born-Oppenheimer dynamics that run along the eigensurfaces of the operator Ĥel(X) can recover many nuclear properties correctly, we present some evidence that motion along the eigensurfaces of ĤPS(X,P) can better capture both nuclear and electronic properties (including the elusive electronic momentum studied by Nafie). Moreover, only the latter (as opposed to the former) conserves the total linear and angular momentum in general.
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Affiliation(s)
- Zhen Tao
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Tian Qiu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mansi Bhati
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xuezhi Bian
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Titouan Duston
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jonathan Rawlinson
- Department of Mathematics, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Robert G Littlejohn
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Joseph E Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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5
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Puente AR, Polavarapu PL. Influence of microsolvation on vibrational circular dichroism spectra in dimethyl sulfoxide solvent: A Bottom-Up approach using Quantum cluster growth. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123231. [PMID: 37562213 DOI: 10.1016/j.saa.2023.123231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/09/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Chiroptical spectroscopic measurements serve as routine methods to assign the absolute configuration of chiral compounds and interpret their conformational behavior in solution. One common challenge is the use of strongly hydrogen-bonding solvents, which can significantly bias the conformational ensemble and affect the vibrational circular dichroism (VCD) active bands in solution. One such solvent is dimethyl sulfoxide (DMSO)-an excellent solvent for stubborn compounds-that must be explicitly considered in VCD analysis. Explicit consideration of solvent remains a critical challenge in chiroptical spectroscopy due to the need to explore solute-solvent conformational space and the computational expense in modeling these clusters. Interested in the recent development of the Quantum Cluster Growth (QCG) program by the Grimme lab, we set out to model and interpret previously reported VCD spectra for several molecules using their efficient program. Our purposes are two-fold: (1) to investigate the applicability of the QCG program to the problem of reproducing VCD spectra in DMSO solvent and (2) to identify limitations in using this approach. We find that we can conveniently model and analyze the VCD spectra of investigated molecules in DMSO. However, the final set of conformers used for VCD calculations are functional dependent and different sets of conformers can provide satisfactory quantitative agreement between experimental and predicted VCD spectra. We hope that this study provides guidance for future chiroptical studies in the challenging DMSO solvent.
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Affiliation(s)
- Andrew R Puente
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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6
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Jähnigen S. Vibrational Circular Dichroism Spectroscopy of Chiral Molecular Crystals: Insights from Theory. Angew Chem Int Ed Engl 2023; 62:e202303595. [PMID: 37071543 DOI: 10.1002/anie.202303595] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 04/19/2023]
Abstract
Chirality is a curious phenomenon that appears in various forms. While the concept of molecular (RS-)chirality is ubiquitous in chemistry, there are also more intricate forms of structural chirality. One of them is the enantiomorphism of crystals, especially molecular crystals, that describes the lack of mirror symmetry in the unit cell. Its relation to molecular chirality is not obvious, but still an open question, which can be addressed with chiroptical tools. Vibrational circular dichroism (VCD) denotes chiral infrared (IR) spectroscopy that is susceptible to both, the molecular as well as the intermolecular space by means of vibrational transitions. When carried out in the solid state, VCD delivers a very rich set of non-local contributions that are determined by crystal packing and collective motion. Since its discovery in the 1970s, VCD has become the method of choice for the determination of absolute configurations, but its applicability reaches beyond towards the study of different crystal forms and polymorphism. This brief review summarises the theoretical concepts of crystal chirality and how computations of solid-state VCD can shed light into the intimate connection of chiral structure and vibrational optical activity.
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Affiliation(s)
- Sascha Jähnigen
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
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7
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Perera AS, Carlson CD, Cheramy J, Xu Y. Infrared and vibrational circular dichroism spectra of methyl β-D-glucopyranose in water: The application of the quantum cluster growth and clusters-in-a-liquid solvation models. Chirality 2023; 35:718-731. [PMID: 37162747 DOI: 10.1002/chir.23576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
The infrared (IR) and vibrational circular dichroism (VCD) spectra of methyl β-D-glucopyranose in water were measured. Both implicit and explicit solvation models were utilized to explain the observed spectra. The vast body of existing experimental and theoretical data suggested that about eight explicit water molecules are needed to account for the solvent effects, supported by the current Quantum Cluster Growth (QCG) analysis. Extensive manual and systematic conformational searches of the molecular target and its water clusters were carried out by using a recently developed conformational searching tool, conformer-rotamer ensemble sampling tool (CREST), and the microsolvation model in the associated QCG code. The Boltzmann averaged IR and VCD spectra of the methyl β-D-glucopyranose-(water)n (n = 8) conformers in the PCM of water provide better agreement with the experimental ones than those with n = 0, 1, and 2. The explicit solvation with eight water molecules was shown to greatly modify the conformational preference of methyl β-D-glucopyranose from its monomeric form. Further analyses show that the result is consistent with the existence of long-lived methyl β-D-glucopyranose monohydrates with the additional explicit water effects being accounted for with the quantum mechanical treatment of the other seven close-by water molecules in the PCM of water.
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Affiliation(s)
| | - Colton D Carlson
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Joseph Cheramy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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8
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Blasius J, Kirchner B. Selective Chirality Transfer to the Bis(trifluoromethylsulfonyl)imide Anion of an Ionic Liquid. Chemistry 2023; 29:e202301239. [PMID: 37341169 DOI: 10.1002/chem.202301239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 06/22/2023]
Abstract
Chirality transfer from the chiral molecule (R)-1,2-propylene oxide to the achiral anion of the 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid is observed. The chiral probe selectively affects one part of the binary ionic liquid, i. e., it has previously been shown experimentally and theoretically that this particular imidazolium cation can be affected by chirality transfer, but in the present system chirality is almost exclusively transferred to the anion and not to both parts of the solvent (anion and cation). This observation is of high relevance because of its selectivity and because anion effects are usually much more important in ionic liquid research than cation effects. From ab initio molecular dynamics simulations, a conformational analysis and dissected vibrational circular dichroism spectra are obtained to study the chirality transfer. While in the neat ionic liquid two mirror imaged trans conformers of the anion occur almost equally, we observe an excess of one of these conformers in the presence of the chiral solute, causing optical activity of the anion. Although the cis conformers are not tremendously affected by the chirality transfer, they gain in total population when (R)-1,2-propylene oxide is dissolved in the ionic liquid.
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Affiliation(s)
- Jan Blasius
- Mulliken Center for Theoretical Chemistry, Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4-6, D-53115, Bonn, Germany
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4-6, D-53115, Bonn, Germany
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9
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Bowles J, Jähnigen S, Vuilleumier R, Calvo F, Clavaguéra C, Agostini F. Influence of the environment on the infrared spectrum of alanine: An effective mode analysis. J Chem Phys 2023; 158:094305. [PMID: 36889973 DOI: 10.1063/5.0135608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000-2000 cm-1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.
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Affiliation(s)
- Jessica Bowles
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Sascha Jähnigen
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Florent Calvo
- Université Grenoble Alpes, CNRS, LIPhy, F-38000 Grenoble, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
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10
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Jähnigen S, Le Barbu-Debus K, Guillot R, Vuilleumier R, Zehnacker A. How Crystal Symmetry Dictates Non-Local Vibrational Circular Dichroism in the Solid State. Angew Chem Int Ed Engl 2023; 62:e202215599. [PMID: 36441537 PMCID: PMC10107176 DOI: 10.1002/anie.202215599] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 11/29/2022]
Abstract
Solid-State Vibrational Circular Dichroism (VCD) can be used to determine the absolute structure of chiral crystals, but its interpretation remains a challenge in modern spectroscopy. In this work, we investigate the effect of a twofold screw axis on the solid-state VCD spectrum in a combined experimental and theoretical analysis of P21 crystals of (S)-(+)-1-indanol. Even though the space group is achiral, a single proper symmetry operation has an important impact on the VCD spectrum, which reflects the supramolecular chirality of the crystal. Distinguishing between contributions originating from molecular chirality and from chiral crystal packing, we find that while IR absorption hardly depends on the symmetry of the space group, the situation is different for VCD, where completely new non-local patterns emerge. Understanding the two underlying mechanisms, namely gauge transport and direct coupling, will help to use VCD to distinguish polymorphic forms.
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Affiliation(s)
- Sascha Jähnigen
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, CNRS, PSL University, Sorbonne Université, 75005, Paris, France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, CNRS, PSL University, Sorbonne Université, 75005, Paris, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
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11
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Galimberti DR. Vibrational Circular Dichroism from DFT Molecular Dynamics: The AWV Method. J Chem Theory Comput 2022; 18:6217-6230. [PMID: 36112978 PMCID: PMC9558311 DOI: 10.1021/acs.jctc.2c00736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The paper illustrates the Activity Weighted Velocities
(AWV) methodology
to compute Vibrational Circular Dichroism (VCD) anharmonic spectra
from Density Functional Theory (DFT) molecular dynamics. AWV calculates
the spectra by the Fourier Transform of the time correlation functions
of velocities, weighted by specific observables: the Atomic Polar
Tensors (APTs) and the Atomic Axial Tensors (AATs). Indeed, AWV shows
to correctly reproduce the experimental spectra for systems in the
gas and liquid phases, both in the case of weakly and strongly interacting
systems. The comparison with the experimental spectra is striking
especially in the fingerprint region, as demonstrated by the three
benchmark systems discussed: (1S)-Fenchone in the
gas phase, (S)-(−)-Propylene oxide in the
liquid phase, and (R)-(−)-2-butanol in the
liquid phase. The time evolution of APTs and AATs can be adequately
described by a linear combination of the tensors of a small set of
appropriate reference structures, strongly reducing the computational
cost without compromising accuracy. Additionally, AWV allows the partition
of the spectral signal in its molecular components without any expensive
postprocessing and any localization of the charge density or the wave
function.
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Affiliation(s)
- Daria Ruth Galimberti
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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12
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Villaseco Arribas E, Agostini F, Maitra NT. Exact Factorization Adventures: A Promising Approach for Non-Bound States. Molecules 2022; 27:molecules27134002. [PMID: 35807246 PMCID: PMC9267945 DOI: 10.3390/molecules27134002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Modeling the dynamics of non-bound states in molecules requires an accurate description of how electronic motion affects nuclear motion and vice-versa. The exact factorization (XF) approach offers a unique perspective, in that it provides potentials that act on the nuclear subsystem or electronic subsystem, which contain the effects of the coupling to the other subsystem in an exact way. We briefly review the various applications of the XF idea in different realms, and how features of these potentials aid in the interpretation of two different laser-driven dissociation mechanisms. We present a detailed study of the different ways the coupling terms in recently-developed XF-based mixed quantum-classical approximations are evaluated, where either truly coupled trajectories, or auxiliary trajectories that mimic the coupling are used, and discuss their effect in both a surface-hopping framework as well as the rigorously-derived coupled-trajectory mixed quantum-classical approach.
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Affiliation(s)
| | - Federica Agostini
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, 91405 Orsay, France;
| | - Neepa T. Maitra
- Department of Physics, Rutgers University, Newark, NJ 07102, USA;
- Correspondence:
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13
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Berrones-Guerrero JD, Frausto-Reyes C, De la Torre-I MH, Ortiz-Morales M, M López-T J. Impact on the Raman spectra of liquids when a polarized light source is used. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 272:121001. [PMID: 35158137 DOI: 10.1016/j.saa.2022.121001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
The polarization state of the excitation light used in two Raman systems was controlled to study its effect in the unpolarized Raman spectra of unstructured samples. Both systems work in different regions of the electromagnetic spectrum (NIR and visible). Four polarization states (linear, linear at 45° and 90°, and circular) were used to excite liquid samples (ethanol, acetone, and their mixture). The results show that the Raman peaks intensities' ratio varies according to the polarization state of the excitation light. Peaks related to functional groups and C-H stretching modes increase their intensity when circular polarization (CP) is applied. The latter may help to study liquid mixtures with low concentrations. Different polarizing light states give a more detailed spectroscopic analysis since it gathers more structural information of the samples tested in this work with an undefined structure.
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Affiliation(s)
- J D Berrones-Guerrero
- Centro de Investigaciones en Óptica, A.C., Unidad Aguascalientes, Prol. Constitución 607, Fracc. Reserva Loma Bonita Aguascalientes 20200, Mexico.
| | - C Frausto-Reyes
- Centro de Investigaciones en Óptica, A.C., Unidad Aguascalientes, Prol. Constitución 607, Fracc. Reserva Loma Bonita Aguascalientes 20200, Mexico.
| | - Manuel H De la Torre-I
- Centro de Investigaciones en Óptica, A.C., Unidad Aguascalientes, Prol. Constitución 607, Fracc. Reserva Loma Bonita Aguascalientes 20200, Mexico
| | - M Ortiz-Morales
- Centro de Investigaciones en Óptica, A.C., Unidad Aguascalientes, Prol. Constitución 607, Fracc. Reserva Loma Bonita Aguascalientes 20200, Mexico
| | - Juan M López-T
- Centro de Investigaciones en Óptica, A.C., Unidad Aguascalientes, Prol. Constitución 607, Fracc. Reserva Loma Bonita Aguascalientes 20200, Mexico
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14
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Ditler E, Zimmermann T, Kumar C, Luber S. Implementation of Nuclear Velocity Perturbation and Magnetic Field Perturbation Theory in CP2K and Their Application to Vibrational Circular Dichroism. J Chem Theory Comput 2022; 18:2448-2461. [PMID: 35363490 DOI: 10.1021/acs.jctc.2c00006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the implementation of nuclear velocity perturbation theory (NVPT), using a pioneering combination of atom-centered (velocity-dependent) Gaussian basis functions and plane waves in the CP2K package. The atomic polar tensors (APTs) and atomic axial tensors (AATs) are evaluated in the velocity representation using efficient density functional perturbation theory. The presence of nonlocal pseudopotentials, the representation of potentials on numerical integration grids, and effects arising from the basis functions being centered on the atoms have been considered in the implementation. The Magnetic Field Perturbation Theory (MFPT) using gauge-including atomic orbitals is implemented in the same code and compared to the NVPT. Our implementation is the first to compare both approaches (MFPT and NVPT) in the same code. The implementation has been verified via sum rules and by investigating the gauge origin dependence of the AATs for a set of small molecules, oxirane, and fluoro-oxirane. We also present vibrational circular dichroism spectra that are related to the APTs and AATs, applying both theories.
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Affiliation(s)
- Edward Ditler
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Tomáš Zimmermann
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Chandan Kumar
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
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15
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Yang Y, Cheramy J, Brehm M, Xu Y. Raman Optical Activity of N-Acetyl-L-Cysteine in water and in methanol: the "clusters-in-a-liquid" model and ab initio molecular dynamics simulations. Chemphyschem 2022; 23:e202200161. [PMID: 35353934 DOI: 10.1002/cphc.202200161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/29/2022] [Indexed: 11/06/2022]
Abstract
Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water and in methanol to evaluate the solvent effects. Two different solvation approaches, i.e. the DFT based clusters-in-a-liquid solvent model and the ab initio molecular dynamics (AIMD) simulations, were applied to simulate the Raman and ROA spectra. Systematic conformational searches were carried out using a recently developed conformational searching tool, CREST, with the inclusion of polarizable continuum model of water and of methanol. The CREST candidates of NALC and the NALC-solvent complexes were re-optimized and their Raman and ROA simulations were done at the B3LYP-D3BJ/def2-TZVP and the B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD simulations , which includes some anharmonic effects and all intermolecular interactions in solution, were performed. By empirically weighting the computed Raman and ROA spectra of each conformer, good agreements with the experimental data were achieved with both approaches, while AIMD offered some improvements in the carbonyl and in the low wavenumber regions over the static DFT approach. The pros and cons of these two different approaches for accounting the solvent effects on Raman and ROA of this flexible chiral system will also be discussed.
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Affiliation(s)
| | | | - Martin Brehm
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg, Chemistry, GERMANY
| | - Yunjie Xu
- University of Alberta Faculty of Science, Chemistry Department, 11227 Saskatchewan Drive, T6G 2G2, Edmonton, CANADA
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16
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Scholten K, Merten C. Solvation of the Boc-Val-Phe- nPr peptide characterized by VCD spectroscopy and DFT calculations. Phys Chem Chem Phys 2022; 24:3611-3617. [PMID: 35103263 DOI: 10.1039/d1cp05457k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The conformational preferences of peptides are strongly determined by hydrogen bonding interactions. Intermolecular solute-solvent interactions compete with intramolecular interactions, which typically stabilize the secondary structure of the peptide. The analysis of vibrational circular dichroism (VCD) spectra can give insights into solvation-induced changes in the conformational distribution of small peptides. Here we describe the VCD spectroscopic characterization of the model peptide Boc-Val-Phe-nPr in chloroform as representative for a weakly interacting solvent and dimethyl sulfoxide (DMSO-d6) as a strongly hydrogen bonding solvent. We show that the conformational preferences of the peptide in chloroform are well-described by the computationally predicted distribution of the isolated molecule assuming only implicit solvation effects through a continuum solvation model. In order to simulate the spectra recorded in DMSO-d6, solvation was accounted for explicitly by computed microsolvated structures containing one to three solvent molecules. A good match of the computed spectra with the experimental data is obtained by this method. Comparing the conformational distributions in deuterated chloroform-d1 and DMSO-d6, structures with intramolecular hydrogen bonds such as the (δ,δ)-conformer family contribute to the conformational distribution only when there is no strong interaction with the solvent. This is in contrast to the results for the related Boc-Pro-Phe-nPr studied before, for which the intramolecular interaction was found to persist in DMSO-d6. Furthermore, we discuss the influence of hydrogen bonding to different numbers of solvent molecules on the spectral signatures and show that the structure of the peptide in DMSO-d6 is best described as a mixture of twofold-solvated (δ,β)- and threefold-solvated (β,β)-conformers.
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Affiliation(s)
- Kevin Scholten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Christian Merten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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17
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Kessler J, Bouř P. Classical Trajectory of Molecules in Electromagnetic Field: A Handy Method to Simulate Molecular Vibrational Spectra. J Chem Theory Comput 2022; 18:1780-1787. [PMID: 35138830 DOI: 10.1021/acs.jctc.1c01138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Within harmonic approximations, molecular vibrational spectra are simulated in a standard way through force field diagonalization and following transformation of Cartesian to normal-mode tensor derivatives. This may become tedious for large systems of many thousands of atoms and also not necessary because of a limited resolution required to interpret an experiment. We developed an algorithm based on the real-time real-field molecular dynamics, effectively at zero temperature, invoked in a molecule by the electromagnetic field of light. The algorithm is simple to implement and suitable for parallel computing, and it can be potentially extended to more complicated molecular-light interaction modes. It circumvents the diagonalization and is suitable to model vibrational optical activity (vibrational circular dichroism and, to a lesser extent, Raman optical activity). For large molecules, it becomes faster than diagonalization, but it also enables the assignment of vibrational spectral bands to local molecular motions.
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Affiliation(s)
- Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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18
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Le Barbu-Debus K, Zehnacker A. Competition between inter and intramolecular hydrogen bond evidenced by vibrational circular dichroism spectroscopy: The case of (1S,2R)-(-)-cis-1-amino-2-indanol. Chirality 2021; 33:858-874. [PMID: 34570370 DOI: 10.1002/chir.23362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 02/06/2023]
Abstract
The infrared (IR) absorption and vibrational circular dichroism (VCD) spectra of an intramolecularly hydrogen-bonded chiral amino-alcohol, (1S,2R)-(-)-cis-1-amino-2-indanol, are studied in DMSO-d6 . The spectra are simulated at the density functional theory (DFT) level within the frame of the cluster-in-the-liquid model. Both IR and VCD spectra show a clear signature of the formation of intermolecular hydrogen bonds at the detriment of the intramolecular OH … N interaction present in the isolated molecule. Two solvent molecules are necessary to reproduce the experimental spectra. Whereas the first DMSO molecule captures the main spectral modifications due to hydrogen bond formation between the solute and the solvent, the second DMSO molecule is necessary for a good description of the Boltzmann contribution of the different complexes, based on their Gibbs free energy.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, Orsay, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, Orsay, France
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19
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Johnson JL, Polavarapu PL. Chiral Molecular Structure Determination for a Desired Compound Just from Its Molecular Formula and Vibrational Optical Activity Spectra. J Phys Chem A 2021; 125:8000-8013. [PMID: 34478311 DOI: 10.1021/acs.jpca.1c06369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A novel proof-of-concept model for chiral molecular structure determination using just the molecular formula and vibrational optical activity (VOA) spectra is presented. To verify this concept, the molecular formula of a desired compound is used to generate all possible chiral structural isomers and their VOA spectra are predicted. The similarity analyses of predicted VOA spectra were then carried out in two different ways: (a) similarity between VOA spectrum of one structural isomer with those of the rest, referred to as cross-correlations; (b) similarity between VOA spectra of all chiral structural isomers with the experimental VOA spectra of the desired compound. Three different molecular formulae, C4H8O, C3H5ClO, and C6H10O, and their chiral structural isomers (6, 9, and 75 respectively), were investigated. In each case, the correct chiral molecular structure of the desired compound was identified without ambiguity. Cross-correlation analysis revealed the uniqueness of VOA spectra in deducing the chiral molecular structure solely from its molecular formula. Different chiral structural isomers associated with the molecular formula CH3NO2 were also found to have no significant cross-correlations between their VOA spectra, opening a pathway to detect and identify the elusive chiral N-hydroxyoxaziridine from its VOA spectra.
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Affiliation(s)
- Jordan L Johnson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Prasad L Polavarapu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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20
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Jähnigen S, Sebastiani D, Vuilleumier R. The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution. Phys Chem Chem Phys 2021; 23:17232-17241. [PMID: 34369531 DOI: 10.1039/d1cp03106f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss the effect of the hydrogen bond network on the aggregation behaviour of the acid: while aggregates of the solute represent conditions encountered in a weakly interacting solvent, the presence of water drastically interferes with the clusters - more strongly than originally anticipated. For both scenarios we computed the VCD spectra by means of nuclear velocity perturbation theory (NVPT). The comparison with experimental data allows us to establish a VCD-structure relationship that includes the solvent network around the chiral solute. We suggest that fundamental modes with strong polarisation such as the carbonyl stretching vibration can borrow VCD from the chirally restructured solvent cage, which extends the common explanatory models of VCD generation in aqueous solution.
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Affiliation(s)
- Sascha Jähnigen
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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21
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Jähnigen S, Zehnacker A, Vuilleumier R. Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge. J Phys Chem Lett 2021; 12:7213-7220. [PMID: 34310135 DOI: 10.1021/acs.jpclett.1c01682] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We introduce a new theoretical formalism to compute solid-state vibrational circular dichroism (VCD) spectra from molecular dynamics simulations. Having solved the origin-dependence problem of the periodic magnetic gauge, we present IR and VCD spectra of (1S,2S)-trans-1,2-cyclohexanediol obtained from first-principles molecular dynamics calculations and nuclear velocity perturbation theory, along with the experimental results. Because the structure model imposes periodic boundary conditions, the common origin of the rotational strength has hitherto been ill-defined and was approximated by means of averaging multiple origins. The new formalism reconnects the periodic model with the finite physical system and restores gauge freedom. It nevertheless fully accounts for nonlocal spatial couplings from the gauge transport term. We show that even for small simulation cells the rich nature of solid-state VCD spectra found in experiments can be reproduced to a very satisfactory level.
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Affiliation(s)
- Sascha Jähnigen
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405 Orsay, France
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS,, 75005 Paris, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS,, 75005 Paris, France
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22
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Demarque DP, Kemper M, Merten C. VCD spectroscopy reveals that a water molecule determines the conformation of azithromycin in solution. Chem Commun (Camb) 2021; 57:4031-4034. [PMID: 33885696 DOI: 10.1039/d1cc00932j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the IR and VCD spectra of azithromycin, a macrolide antibiotic with a total of 18 stereogenic centers. The computational analysis of the spectra reveals that a single water molecule has to be considered in the conformational search. Its key role is the stabilization of an extended hydrogen bonding network and an otherwise unstable conformation that determines the VCD spectral signatures.
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Affiliation(s)
- Daniel P Demarque
- Ruhr-Universität Bochum, Organische Chemie 2, Stereochemistry and Chiroptical Spectroscopy, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Michael Kemper
- Ruhr-Universität Bochum, Organische Chemie 2, Stereochemistry and Chiroptical Spectroscopy, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Christian Merten
- Ruhr-Universität Bochum, Organische Chemie 2, Stereochemistry and Chiroptical Spectroscopy, Universitätsstraße 150, 44801 Bochum, Germany.
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23
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Giovannini T, Egidi F, Cappelli C. Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems. Phys Chem Chem Phys 2020; 22:22864-22879. [PMID: 33043930 DOI: 10.1039/d0cp04027d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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24
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Ghidinelli S, Abbate S, Koshoubu J, Araki Y, Wada T, Longhi G. Solvent Effects and Aggregation Phenomena Studied by Vibrational Optical Activity and Molecular Dynamics: The Case of Pantolactone. J Phys Chem B 2020; 124:4512-4526. [PMID: 32396357 PMCID: PMC8007093 DOI: 10.1021/acs.jpcb.0c01483] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Raman and Raman optical activity (ROA), IR, and vibrational circular dichroism (VCD) spectra of (R)- and (S)-pantolactone have been recorded in three solvents. ROA has been employed on water and DMSO solutions, VCD on DMSO and CCl4 solutions. In the last solvent, monomer-dimer equilibrium is present. Due to the low conformational flexibility of the isolated molecule and to the possibility of aggregation, this compound has been used here to test different protocols for computation of the spectroscopic responses taking into account solvent effects. Molecular dynamics (MD) simulations have been carried out together with statistical clustering methods based on collective variables to extract the structures needed to calculate the spectra. Quantum mechanical DFT calculations based on PCM are compared with approaches based on different representations of the solvent shell (MM or QM level). Appropriate treatment of the solvent permits obtaining of good band-shapes, with the added advantage that the MD analysis allows one to take into account flexibility of dimeric structures justifying the broadness of observed bands and the absence of intense VCD couplets in the carbonyl and OH stretching regions.
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Affiliation(s)
- Simone Ghidinelli
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy.,Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, Via Branze 45, 25123 Brescia, Italy
| | - Jun Koshoubu
- JASCO Corporation, 2967-5 Ishikawa-machi, Hachioji, Tokyo 192-8537, Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy.,Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, Via Branze 45, 25123 Brescia, Italy
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25
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Blasius J, Elfgen R, Hollóczki O, Kirchner B. Glucose in dry and moist ionic liquid: vibrational circular dichroism, IR, and possible mechanisms. Phys Chem Chem Phys 2020; 22:10726-10737. [PMID: 32150178 DOI: 10.1039/c9cp06798a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ionic liquids and their mixtures with water show remarkable features in cellulose processing. For this reason, understanding the behavior of carbohydrates in ionic liquids is important. In the present study, we investigated three d-glucose isomers (α, β and open-chain) in 1-ethyl-3-methylimidazolium acetate in the presence and absence of water, through ab initio molecular dynamics simulations. In the complex hydrogen bonding network of these mixtures, the most interesting observation is that upon water addition every hydrogen bond elongates, except the glucose-glucose hydrogen bond for the open-chain and the α-form which shortens, clearly showing the beginning of the crystallization process. The ring glucose rearranges from on-top to in-plane and the open form changes from a coiled to a more linear arrangement when adding water which explains the contradiction that the center of mass distances of the glucose molecules with other glucose molecules grow while the hydrogen bonds shorten. The appearance of coiled open forms indicates that the previously suggested isomerization between these forms is possible and might play a role in the solubility of the related carbohydrates. The calculated IR and VCD spectra reveal insight into the intermolecular interactions, with good to excellent agreements with experimental spectra. Investigating the role of the cation, distances between the acidic carbon atom of the cation and the glucose carbon atom where ring closure and opening occurs are found, which are way shorter than dispersion-like interactions between aliphatic hydrocarbons.
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Affiliation(s)
- Jan Blasius
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4 + 6, D-53115 Bonn, Germany.
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26
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Brehm M, Thomas M, Gehrke S, Kirchner B. TRAVIS—A free analyzer for trajectories from molecular simulation. J Chem Phys 2020; 152:164105. [DOI: 10.1063/5.0005078] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- M. Brehm
- Institut für Chemie, Martin-Luther-Universität Halle–Wittenberg, von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany
| | - M. Thomas
- Institut für Chemie, Martin-Luther-Universität Halle–Wittenberg, von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany
| | - S. Gehrke
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4+6, D-53115 Bonn, Germany
| | - B. Kirchner
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4+6, D-53115 Bonn, Germany
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27
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Krupová M, Kessler J, Bouř P. Recent Trends in Chiroptical Spectroscopy: Theory and Applications of Vibrational Circular Dichroism and Raman Optical Activity. Chempluschem 2020; 85:561-575. [DOI: 10.1002/cplu.202000014] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/18/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Mathematics and PhysicsCharles University Ke Karlovu 3 12116 Prague 2 Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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28
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Nafie LA. Vibrational optical activity: From discovery and development to future challenges. Chirality 2020; 32:667-692. [DOI: 10.1002/chir.23191] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/13/2022]
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29
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Polavarapu PL, Santoro E. Vibrational optical activity for structural characterization of natural products. Nat Prod Rep 2020; 37:1661-1699. [DOI: 10.1039/d0np00025f] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review presents the recent progress towards elucidating the structures of chiral natural products and applications using vibrational optical activity (VOA) spectroscopy.
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30
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Weirich L, Blanke K, Merten C. More complex, less complicated? Explicit solvation of hydroxyl groups for the analysis of VCD spectra. Phys Chem Chem Phys 2020; 22:12515-12523. [DOI: 10.1039/d0cp01656j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With increasing size of the molecules, hydrogen bonding induced solvent effects on the IR and VCD spectra become more negligible.
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Affiliation(s)
- Luisa Weirich
- Ruhr-Universität Bochum
- Fakultät für Chemie und Biochemie
- Organische Chemie II
- 44801 Bochum
- Germany
| | - Katharina Blanke
- Ruhr-Universität Bochum
- Fakultät für Chemie und Biochemie
- Organische Chemie II
- 44801 Bochum
- Germany
| | - Christian Merten
- Ruhr-Universität Bochum
- Fakultät für Chemie und Biochemie
- Organische Chemie II
- 44801 Bochum
- Germany
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31
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Weirich L, Magalhães de Oliveira J, Merten C. How many solvent molecules are required to solvate chiral 1,2-diols with hydrogen bonding solvents? A VCD spectroscopic study. Phys Chem Chem Phys 2020; 22:1525-1533. [DOI: 10.1039/c9cp06030h] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A VCD spectroscopic analysis of selected model systems for solute–solvent interactions of chiral diols with hydrogen bonding solvents DMSO and ACN.
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Affiliation(s)
- Luisa Weirich
- Ruhr-Universität Bochum
- Fakultät für Chemie und Biochemie
- Organische Chemie II
- 44801 Bochum
- Germany
| | | | - Christian Merten
- Ruhr-Universität Bochum
- Fakultät für Chemie und Biochemie
- Organische Chemie II
- 44801 Bochum
- Germany
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32
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Le Barbu-Debus K, Bowles J, Jähnigen S, Clavaguéra C, Calvo F, Vuilleumier R, Zehnacker A. Assessing cluster models of solvation for the description of vibrational circular dichroism spectra: synergy between static and dynamic approaches. Phys Chem Chem Phys 2020; 22:26047-26068. [DOI: 10.1039/d0cp03869e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solvation effects are essential for defining the shape of vibrational circular dichroism (VCD) spectra.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Université Paris-Saclay
- F-91405 Orsay
- France
| | - Jessica Bowles
- Université Paris-Saclay
- CNRS
- Institut de Chimie Physique
- UMR8000
- 91405 Orsay
| | - Sascha Jähnigen
- PASTEUR
- Département de Chimie
- Ecole Normale Supérieure
- PSL University
- Sorbonne Université
| | - Carine Clavaguéra
- Université Paris-Saclay
- CNRS
- Institut de Chimie Physique
- UMR8000
- 91405 Orsay
| | - Florent Calvo
- Université Grenoble Alpes
- CNRS
- LiPhy
- F-38000 Grenoble
- France
| | - Rodolphe Vuilleumier
- PASTEUR
- Département de Chimie
- Ecole Normale Supérieure
- PSL University
- Sorbonne Université
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Université Paris-Saclay
- F-91405 Orsay
- France
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33
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Johnson J, Polavarapu PL. Chiral Molecular Structures of Substituted Indans: Ring Puckering, Rotatable Substituents, and Vibrational Circular Dichroism. ACS OMEGA 2019; 4:4963-4976. [PMID: 31459680 PMCID: PMC6648482 DOI: 10.1021/acsomega.8b03628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/21/2019] [Indexed: 05/06/2023]
Abstract
The chiral molecular structures of four different substituted indans, namely, (S)-1-methylindan, (R)-1-methylindan-1-d, (R)-1-aminoindan, and (S)-1-indanol, were investigated using experimental vibrational absorption and vibrational circular dichroism spectra and corresponding spectra predicted using quantum chemical (QC) calculations. All of these molecules possess two ring puckering conformations, with ring puckering leading to the pseudoequatorial substituent being approximately four times more abundant over that leading to the pseudoaxial substituent. The amino group in 1-aminoindan has three conformations arising from the rotation of NH2 group, for each ring puckering conformation, resulting in a total of six conformations. Whereas 1-indanol in the nonhydrogen-bonding solvent CCl4 also has six conformations similar to those of 1-aminoindan, 1-indanol in the hydrogen-bonding solvent DMSO-d 6 adopts numerous conformations, of which 30 conformers are considered to have at least ∼1% or more population. In DMSO solution, ring puckering leading to pseudoequatorial substituent accounts for 77% population and 23% for pseudoaxial substituent. The QC spectra predicted for the geometry optimized conformers are found to be in excellent quantitative agreement with corresponding experimental spectra in all of the molecules considered. The procedures suggested in this work are hoped to provide successful pathways for future chiral molecular structural analyses.
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Sidler D, Bleiziffer P, Riniker S. Beyond the Rosenfeld Equation: Computation of Vibrational Circular Dichroism Spectra for Anisotropic Solutions. J Chem Theory Comput 2019; 15:2492-2503. [PMID: 30802403 DOI: 10.1021/acs.jctc.8b01156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The difference in absorption of left and right circularly polarized light by chiral molecules can be described by the Rosenfeld equation for isotropic samples. It allows the assignment of the absolute stereochemistry by comparing experimental and computationally derived spectra. Despite the simple form of the Rosenfeld equation, its evaluation in the infrared regime remained challenging, as the contribution from the magnetic dipole operator is zero within the Born-Oppenheimer (BO) approximation. In order to resolve this issue, "beyond BO" theories had to be developed, among which Stephen's magnetic field perturbation (MFP) approach offers a computationally easily accessible form. In this work, optical activity is discussed for cylindrically symmetric solutions, which cannot be described anymore by Rosenfeld's equation due to broken spherical symmetry. Mathematical properties of natural and electric-field induced anisotropies are discussed on the basis of the gauge-independent theoretical framework of Buckingham and Dunn. The issue of achiral noise arising from external field perturbations is considered, and potential remedies are introduced. Natural anisotropic vibrational circular dichroism (VCD) equations are solved numerically by applying the MFP approach within the Hartree-Fock (HF) formalism. Properties of anisotropic VCD spectra are discussed for R-(+)-methyloxirane and (1 S,2 S)-cyclopropane-1,2-dicarbonitrile. In particular, by using a group theoretical argument, a gauge-independent lower bound for the quadrupole contribution of C2-symmetric molecules can be identified, which allows the importance of additional quadrupole terms in anisotropic VCD spectra calculation to be assessed.
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Affiliation(s)
- Dominik Sidler
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Patrick Bleiziffer
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
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35
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Weirich L, Merten C. Solvation and self-aggregation of chiral alcohols: how hydrogen bonding affects their VCD spectral signatures. Phys Chem Chem Phys 2019; 21:13494-13503. [DOI: 10.1039/c9cp01407a] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IR and VCD spectra of chiral alcohols in different solvents are analyzed with DFT spectra calculations. We show that for ACN or DMSO explicit solvation is needed to reproduce experimental spectra.
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Affiliation(s)
- Luisa Weirich
- Ruhr-Universität Bochum
- Fakultät für Chemie und Biochemie
- Organische Chemie II
- 44801 Bochum
- Germany
| | - Christian Merten
- Ruhr-Universität Bochum
- Fakultät für Chemie und Biochemie
- Organische Chemie II
- 44801 Bochum
- Germany
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Jähnigen S, Scherrer A, Vuilleumier R, Sebastiani D. VCD‐Verstärkung durch chirale Packungseffekte in molekularen Kristallen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sascha Jähnigen
- Martin-Luther-Universität Halle-Wittenberg Institut für Chemie von-Danckelmann-Platz 4 Halle 06120 Deutschland
| | - Arne Scherrer
- Martin-Luther-Universität Halle-Wittenberg Institut für Chemie von-Danckelmann-Platz 4 Halle 06120 Deutschland
| | - Rodolphe Vuilleumier
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS 75005 Paris Frankreich
| | - Daniel Sebastiani
- Martin-Luther-Universität Halle-Wittenberg Institut für Chemie von-Danckelmann-Platz 4 Halle 06120 Deutschland
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37
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Jähnigen S, Scherrer A, Vuilleumier R, Sebastiani D. Chiral Crystal Packing Induces Enhancement of Vibrational Circular Dichroism. Angew Chem Int Ed Engl 2018; 57:13344-13348. [DOI: 10.1002/anie.201805671] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/25/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Sascha Jähnigen
- Martin-Luther-Universität Halle-WittenbergInstitut für Chemie von-Danckelmann-Platz 4 Halle 06120 Germany
| | - Arne Scherrer
- Martin-Luther-Universität Halle-WittenbergInstitut für Chemie von-Danckelmann-Platz 4 Halle 06120 Germany
| | - Rodolphe Vuilleumier
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS 75005 Paris France
| | - Daniel Sebastiani
- Martin-Luther-Universität Halle-WittenbergInstitut für Chemie von-Danckelmann-Platz 4 Halle 06120 Germany
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38
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Perera AS, Cheramy J, Merten C, Thomas J, Xu Y. IR, Raman, and Vibrational Optical Activity Spectra of Methyl Glycidate in Chloroform and Water: The Clusters-in-a-liquid
Solvation Model. Chemphyschem 2018; 19:2234-2242. [DOI: 10.1002/cphc.201800309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Indexed: 11/09/2022]
Affiliation(s)
| | - Joseph Cheramy
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada T6G 2G2
| | - Christian Merten
- Ruhr-University Bochum; Faculty of Chemistry and Biochemistry; 44801 Bochum Germany
| | - Javix Thomas
- Department of Chemical and Material Engineering; University of Alberta; Edmonton Alberta Canada T6G 1H
| | - Yunjie Xu
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada T6G 2G2
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39
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Xia Y, Koenis MAJ, Collados JF, Ortiz P, Harutyunyan SR, Visscher L, Buma WJ, Nicu VP. Regional Susceptibility in VCD Spectra to Dynamic Molecular Motions: The Case of a Benzyl α-Hydroxysilane. Chemphyschem 2018; 19:561-565. [PMID: 29244237 DOI: 10.1002/cphc.201701335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 01/24/2023]
Abstract
Experimental and theoretical studies of the vibrational circular dichroism (VCD) spectrum of 3-methyl-1-(methyldiphenlsilyl)-1-phenylbutan-1-ol, whose absolute configuration is key to elucidating the Brook rearrangement of tertiary benzylic α-hydroxylsilanes, are presented. It is found that the entire OH-bending region in this spectrum-a region that provides important marker bands-cannot be reproduced at all by standard theoretical approaches even though other regions are well described. Using a novel approach to disentangle contributions to the rotational strength of these bands, internal coordinates are identified that critically influence the appearance of this part of the spectrum. We show that the agreement between experiment and theory is greatly improved when structural dynamics along these coordinates are explicitly taken into account. The general applicability of the approach underlines its usefulness for structurally flexible chiral systems, a situation that is more the rule rather than the exception.
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Affiliation(s)
- Yiyin Xia
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Mark A J Koenis
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Juan F Collados
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Pablo Ortiz
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Syuzanna R Harutyunyan
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling, Section Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Wybren J Buma
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Valentin P Nicu
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.,Lucian Blaga University of Sibiu, Faculty of Agricultural Sciences, Food Industry and Environmental Protection, 7-9 Ioan Ratiu Street, 550012, Sibiu, Romania
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Daugey N, De Rycke N, Brotin T, Buffeteau T. Chiroptical properties of 2,2'-bioxirane. Chirality 2018; 30:342-350. [PMID: 29315870 DOI: 10.1002/chir.22814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 02/06/2023]
Abstract
The two enantiomers of 2,2'-bioxirane were synthesized, and their chiroptical properties were thoroughly investigated in various solvents by polarimetry, vibrational circular dichroism (VCD), and Raman optical activity (ROA). Density functional theory (DFT) calculations at the B3LYP/aug-cc-pVTZ level revealed the presence of three conformers (G+ , G- , and cis) with Gibbs populations of 51, 44, and 5% for the isolated molecule, respectively. The population ratios of the two main conformers were modified for solvents exhibiting higher dielectric constants (G- form decreases whereas G+ form increases). The behavior of the specific optical rotation values with the different solvents was correctly reproduced by time-dependent DFT calculations using the polarizable continuum model (PCM), except for the benzene for which explicit solvent model should be necessary. Finally, VCD and ROA spectra were perfectly reproduced by the DFT/PCM calculations for the Boltzmann-averaged G+ and G- conformers.
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Affiliation(s)
- N Daugey
- Institut des Sciences Moléculaires, Bordeaux University, Talence, France
| | - N De Rycke
- Ecole Normale Supérieure de Lyon, Lyon 1 University, Lyon, France
| | - T Brotin
- Ecole Normale Supérieure de Lyon, Lyon 1 University, Lyon, France
| | - T Buffeteau
- Institut des Sciences Moléculaires, Bordeaux University, Talence, France
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41
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Le Barbu-Debus K, Scherrer A, Bouchet A, Sebastiani D, Vuilleumier R, Zehnacker A. Effect of puckering motion and hydrogen bond formation on the vibrational circular dichroism spectrum of a flexible molecule: the case of (S)-1-indanol. Phys Chem Chem Phys 2018; 20:14635-14646. [DOI: 10.1039/c8cp01695j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Vibrational circular dichroism spectra of (S)-1-indanol in DMSO and CCl4 are described by cluster-in-the-bulk static calculations and first principles molecular dynamics.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- F-91405 Orsay
| | - Arne Scherrer
- PASTEUR
- Département de chimie
- École normale supérieure
- PSL University
- Sorbonne Université
| | - Aude Bouchet
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- F-91405 Orsay
| | - Daniel Sebastiani
- Martin-Luther-Universität Halle-Wittenberg
- Institut für Chemie
- 06120 Halle
- Germany
| | - Rodolphe Vuilleumier
- PASTEUR
- Département de chimie
- École normale supérieure
- PSL University
- Sorbonne Université
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d’Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- F-91405 Orsay
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42
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Brehm M, Thomas M. Computing Bulk Phase Raman Optical Activity Spectra from ab initio Molecular Dynamics Simulations. J Phys Chem Lett 2017; 8:3409-3414. [PMID: 28685571 DOI: 10.1021/acs.jpclett.7b01616] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present our novel methodology for computing Raman optical activity (ROA) spectra of liquid systems from ab initio molecular dynamics (AIMD) simulations. The method is built upon the recent developments to obtain magnetic dipole moments from AIMD and to integrate molecular properties by using radical Voronoi tessellation. These techniques are used to calculate optical activity tensors for large and complex periodic bulk phase systems. Only AIMD simulations are required as input, and no time-consuming perturbation theory is involved. The approach relies only on the total electron density in each time step and can readily be combined with a wide range of electronic structure methods. To the best of our knowledge, these are the first computed ROA spectra for a periodic bulk phase system. As an example, the experimental ROA spectrum of liquid (R)-propylene oxide is reproduced very well.
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Affiliation(s)
- Martin Brehm
- Institut für Chemie - Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Martin Thomas
- Institut für Chemie - Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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43
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Merten C. Vibrational optical activity as probe for intermolecular interactions. Phys Chem Chem Phys 2017; 19:18803-18812. [DOI: 10.1039/c7cp02544k] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A detailed VCD spectroscopic analysis of well-selected chiral model systems can give valuable and unprecedented insights into intermolecular interactions such as solvation or reactant–substrate binding in catalysis.
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44
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Giovannini T, Olszòwka M, Cappelli C. Effective Fully Polarizable QM/MM Approach To Model Vibrational Circular Dichroism Spectra of Systems in Aqueous Solution. J Chem Theory Comput 2016; 12:5483-5492. [PMID: 27704812 DOI: 10.1021/acs.jctc.6b00768] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a methodology, based on the combination of classical Molecular Dynamics (MD) simulations with a fully polarizable Quantum Mechanical (QM)/Molecular Mechanics (MM)/Polarizable Continuum Model (PCM) Hamiltonian, to calculate Vibrational Circular Dichroism (VCD) spectra of chiral systems in aqueous solution. Polarization effects are included in the MM force field by exploiting an approach based on Fluctuating Charges (FQ). By performing the MD, the description of the solvating environment is enriched by taking into account the dynamical aspects of the solute-solvent interactions. On the other hand, the QM/FQ/PCM calculation of the VCD spectrum ensures an accurate description of the electronic density of the solute and a proper account for the specific interactions in solution. The application of our approach to (R)-methyloxirane and (l)-alanine in aqueous solution gives calculated spectra in remarkable agreement with their experimental counterparts and a substantial improvement with respect to the same spectra calculated with the PCM.
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Affiliation(s)
| | - Marta Olszòwka
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa , Via Moruzzi 13, 56124 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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