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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Vermeyen T, Brence J, Van Echelpoel R, Aerts R, Acke G, Bultinck P, Herrebout W. Exploring machine learning methods for absolute configuration determination with vibrational circular dichroism. Phys Chem Chem Phys 2021; 23:19781-19789. [PMID: 34524304 DOI: 10.1039/d1cp02428k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The added value of supervised Machine Learning (ML) methods to determine the Absolute Configuration (AC) of compounds from their Vibrational Circular Dichroism (VCD) spectra was explored. Among all ML methods considered, Random Forest (RF) and Feedforward Neural Network (FNN) yield the best performance for identification of the AC. At its best, FNN allows near-perfect AC determination, with accuracy of prediction up to 0.995, while RF combines good predictive accuracy (up to 0.940) with the ability to identify the spectral areas important for the identification of the AC. No loss in performance of either model is observed as long as the spectral sampling interval used does not exceed the spectral bandwidth. Increasing the sampling interval proves to be the best method to lower the dimensionality of the input data, thereby decreasing the computational cost associated with the training of the models.
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Affiliation(s)
- Tom Vermeyen
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium. .,Department of Chemistry, Ghent University, Krijgslaan 281, B-9000 Ghent, Belgium.
| | - Jure Brence
- Department of Knowledge Technologies, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Robin Van Echelpoel
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Roy Aerts
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Guillaume Acke
- Department of Chemistry, Ghent University, Krijgslaan 281, B-9000 Ghent, Belgium.
| | - Patrick Bultinck
- Department of Chemistry, Ghent University, Krijgslaan 281, B-9000 Ghent, Belgium.
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
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3
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Kirchner B, Blasius J, Esser L, Reckien W. Predicting Vibrational Spectroscopy for Flexible Molecules and Molecules with Non‐Idle Environments. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000223] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Barbara Kirchner
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Beringstr. 4+6 D‐53115 Bonn Germany
| | - Jan Blasius
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Beringstr. 4+6 D‐53115 Bonn Germany
| | - Lars Esser
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Beringstr. 4+6 D‐53115 Bonn Germany
| | - Werner Reckien
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Beringstr. 4+6 D‐53115 Bonn Germany
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4
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Blasius J, Kirchner B. Cluster-Weighting in Bulk Phase Vibrational Circular Dichroism. J Phys Chem B 2020; 124:7272-7283. [DOI: 10.1021/acs.jpcb.0c06313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Blasius
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4+6, D-53115 Bonn, Germany
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4+6, D-53115 Bonn, Germany
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5
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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6
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Hope M, Šebestík J, Kapitán J, Bouř P. Understanding CH-Stretching Raman Optical Activity in Ala–Ala Dipeptides. J Phys Chem A 2020; 124:674-683. [DOI: 10.1021/acs.jpca.9b10557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marius Hope
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
- Norwegian University of Science and Technology NO-7491 Trondheim, Norway
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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7
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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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8
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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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9
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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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10
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Rode JE, Górecki M, Witkowski S, Frelek J. Solvation of 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol revealed by circular dichroism: a case of chromane helicity rule breaking. Phys Chem Chem Phys 2018; 20:22525-22536. [PMID: 30140796 DOI: 10.1039/c8cp02491j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The primary goal of this work is to clarify why 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol {(S)-TMChM} deviates from the chromane helicity rule under solvent change. The rule, applicable to determining the absolute configuration of molecules containing the chromane chromophore, binds the sign of the 1Lb Cotton effect (CE) with the helicity of the dihydropyran ring. In case of TMChM, however, this CE exhibits extreme solvent dependence: it is negative in non-coordinating solvents and positive in coordinating ones, irrespective of the helicity of the heterocyclic ring. TD-DFT calculations using PCM and hybrid solvation models were performed to explain origin of this phenomenon. It turned out that the 1Lb CE sign directly depends on the position of the phenolic OH group at carbon atom C6 (OHC6). In the absence of interactions with solvents (as in CCl4 or nC6H14) or when a solvent plays proton donor role (as in CHCl3), the OHC6 lies in the phenyl plane and the 1Lb CE sign follows the P/M helicity rule. In contrast, in proton acceptor solvents, like DMSO, CH3OH or CH3CN, the OHC6 group is deflected from the phenyl plane, and the 1Lb CE sign of individual (S)-TMChM conformers depends on the sector in which the OHC6 is located. Thus, in solution, the 1Lb CE sign is an average over different orientations of the OHC6 group and can be positive (as in DMSO and CH3OH) or negative (as in CH3CN) which means that it does not follow the chromane helicity rule. The impact of OHC6 on the 1Lb CE sign and thus the conclusions for the stereochemistry of chromans are demonstrated here for the first time. Additionally, a comparison of experimental and simulated ECD spectra, supported by VCD data, allowed to determine the geometry of intermolecular clusters formed in different solvents.
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Affiliation(s)
- Joanna E Rode
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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11
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Scherrer A, Vuilleumier R, Sebastiani D. Vibrational circular dichroism from ab initio molecular dynamics and nuclear velocity perturbation theory in the liquid phase. J Chem Phys 2016; 145:084101. [DOI: 10.1063/1.4960653] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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12
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Bünnemann K, Merten C. Solvation of N,C-Protected Valine: Interactions with DMSO and a Chiral Solvating Agent. J Phys Chem B 2016; 120:9434-42. [DOI: 10.1021/acs.jpcb.6b05897] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Christian Merten
- Organische
Chemie 2, Ruhr Universität Bochum, 44801 Bochum, Germany
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13
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Almeida GG, Cordeiro JMM, Martín ME, Aguilar MA. Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures. J Chem Theory Comput 2016; 12:1514-24. [DOI: 10.1021/acs.jctc.5b00952] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Glauco G. Almeida
- Faculdade de Engenharia,
Universidade Estadual Paulista “Julio de Mesquita Filho″, Ilha Solteira 15385-000, Brasil
| | - João M. M. Cordeiro
- Faculdade de Engenharia,
Universidade Estadual Paulista “Julio de Mesquita Filho″, Ilha Solteira 15385-000, Brasil
| | - M. Elena Martín
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, Edif. José Ma Viguera
Lobo, 3a planta, Badajoz 06006, Spain
| | - Manuel A. Aguilar
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, Edif. José Ma Viguera
Lobo, 3a planta, Badajoz 06006, Spain
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14
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Thomas M, Kirchner B. Classical Magnetic Dipole Moments for the Simulation of Vibrational Circular Dichroism by ab Initio Molecular Dynamics. J Phys Chem Lett 2016; 7:509-513. [PMID: 26771403 DOI: 10.1021/acs.jpclett.5b02752] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a new approach for calculating vibrational circular dichroism spectra by ab initio molecular dynamics. In the context of molecular dynamics, these spectra are given by the Fourier transform of the cross-correlation function of magnetic dipole moment and electric dipole moment. We obtain the magnetic dipole moment from the electric current density according to the classical definition. The electric current density is computed by solving a partial differential equation derived from the continuity equation and the condition that eddy currents should be absent. In combination with a radical Voronoi tessellation, this yields an individual magnetic dipole moment for each molecule in a bulk phase simulation. Using the chiral alcohol 2-butanol as an example, we show that experimental spectra are reproduced very well. Our approach requires knowing only the electron density in each simulation step, and it is not restricted to any particular electronic structure method.
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Affiliation(s)
- Martin Thomas
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn , Beringstraße 4, 53115 Bonn, Germany
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn , Beringstraße 4, 53115 Bonn, Germany
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15
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Calvo F. Atomistic Modeling of IR Action Spectra Under Circularly Polarized Electromagnetic Fields: Toward Action VCD Spectra. Chirality 2015; 27:253-61. [DOI: 10.1002/chir.22421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 11/06/2014] [Accepted: 11/28/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Florent Calvo
- Laboratoire Interdisciplinaire de Physique; Université Joseph Fourier; Grenoble France
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16
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Choi JH, Cho M. Terahertz Chiroptical Spectroscopy of an α-Helical Polypeptide: A Molecular Dynamics Simulation Study. J Phys Chem B 2014; 118:12837-43. [DOI: 10.1021/jp508547y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun-Ho Choi
- Department
of Chemistry, Korea University, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 136-713, Korea
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17
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Carr JK, Zabuga AV, Roy S, Rizzo TR, Skinner JL. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations. J Chem Phys 2014; 140:224111. [PMID: 24929378 PMCID: PMC4187283 DOI: 10.1063/1.4882059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/26/2014] [Indexed: 02/04/2023] Open
Abstract
The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H(+) in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly (13)C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and (13)C(18)O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm(-1) for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.
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Affiliation(s)
- J K Carr
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - A V Zabuga
- Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - S Roy
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - T R Rizzo
- Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - J L Skinner
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
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18
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Parchaňský V, Kapitán J, Kaminský J, Šebestík J, Bouř P. Ramachandran Plot for Alanine Dipeptide as Determined from Raman Optical Activity. J Phys Chem Lett 2013; 4:2763-2768. [PMID: 26706714 DOI: 10.1021/jz401366j] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Accessible values of the φ and ψ torsional angles determining peptide main chain conformation are traditionally displayed in the form of Ramachandran plots. The number of experimental methods making it possible to determine such conformational distribution is limited. In the present study, Raman optical activity (ROA) spectra of Ac-Ala-NHMe were measured and fit by theoretical curves. This revealed the most favored conformers and a large part of the potential energy surface (PES) of this model dipeptide. Such experimental PES compares well to quantum chemical computations, whereas molecular dynamics (MD) modeling reproduces it less faithfully. The surface shape is consistent with the temperature dependence of the spectra, as observed experimentally and predicted by MD. Despite errors associated with spectral modeling and the measurement, the results are likely to facilitate future applications of ROA spectroscopy.
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Affiliation(s)
- Václav Parchaňský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
- Department of Analytical Chemistry, Institute of Chemical Technology , Technická 5, 16628 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Jaroslav Šebestík
- 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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19
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Farag MH, Zúñiga J, Requena A, Bastida A. Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water. J Chem Phys 2013; 138:205102. [DOI: 10.1063/1.4805086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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20
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Carbonniere P, Thicoipe S, Pouchan C. Theoretical strategy to build structural models of microhydrated inorganic systems for the knowledge of their vibrational properties: the case of the hydrated nitrate aerosols. J Phys Chem A 2013; 117:3826-34. [PMID: 23544698 DOI: 10.1021/jp309785q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This study provides theoretical anharmonic calculations for microhydrated NaNO3-labeled (NaNO3, nH2O)x with a water-to-solute ratio (n) ranging from 1 to 3. A representative geometrical model of these forms was first investigated by simulating the molecular clusters as (NaNO3,1H2O)x with x = 1 to 4. The comparison between the calculated time independent anharmonic frequencies using the B3LYP-D/6-311+G(d,p) method and their experimental counterparts led to the choice of a supercluster model. The most probable structures of (NaNO3,nH2O)3 molecular system were investigated by using our global search algorithm we developed recently (GSAM code) both at the B3LYP/6-311+G(d,p) and the B3LYP-D/6-311+G(d,p) levels of theory. The quality of the structural model is illustrated by comparing the B3LYP/6-311+G(d,p) and B3LYP-D/6-311+G(d,p) anharmonic vibrational signatures with those obtained from IR experiments. While an average deviation of 16 cm(-1) is observed in the case of the B3LYP computations, the deviation is reduced to 7 cm(-1) for the B3LYP-D computations.
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Affiliation(s)
- Philippe Carbonniere
- Groupe de Chimie Théorique et Réactivité, IPREM/ECP UMR CNRS 5254, Université de Pau et des Pays de l'Adour , F-64000 Pau, France
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21
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Ghosh MK, Lee J, Choi CH, Cho M. Direct Simulations of Anharmonic Infrared Spectra Using Quantum Mechanical/Effective Fragment Potential Molecular Dynamics (QM/EFP-MD): Methanol in Water. J Phys Chem A 2012; 116:8965-71. [DOI: 10.1021/jp306807v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manik Kumer Ghosh
- Department of Chemistry
and
Green-Nano Materials Research Center, College of Natural Sciences, Kyungpook National University, Taegu 702-701, South
Korea
| | - Jooyong Lee
- Department of Chemistry, Korea University, Seoul 136-713, Korea
| | - Cheol Ho Choi
- Department of Chemistry
and
Green-Nano Materials Research Center, College of Natural Sciences, Kyungpook National University, Taegu 702-701, South
Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-713, Korea
- Multidimensional Spectroscopy
Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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Yu W, Wu Z, Chen H, Liu X, MacKerell AD, Lin Z. Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures. J Phys Chem B 2012; 116:2269-83. [PMID: 22260814 DOI: 10.1021/jp207807a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Thorough searches on the potential energy surfaces of five tripeptides, GGG, GYG, GWG, TGG, and MGG, were performed by considering all possible combinations of the bond rotational degrees of freedom with a semiempirical and ab initio combined computational approach. Structural characteristics of the obtained stable tripeptide conformers were carefully analyzed. Conformers of the five tripeptides were found to be closely connected with conformers of their constituting dipeptides and amino acids. A method for finding all important tripeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid and dipeptide conformers is thus proposed. Applying the method to another five tripeptides, YGG, FGG, WGG, GFA, and GGF, studied before shows that the new approach is both efficient and reliable by providing the most complete ensembles of tripeptide conformers. The method is further generalized for application to larger peptides by introducing the breeding and mutation concepts in a genetic algorithm way. The generalized method is verified to be capable of finding tetrapeptide conformers with secondary structures of strands, helices, and turns, which are highly populated in larger peptides. This show some promise for the proposed method to be applied for the structural determination of larger peptides.
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Affiliation(s)
- Wenbo Yu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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23
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Choi JH, Cho M. Direct Calculations of Mid- and Near-IR Absorption and Circular Dichroism Spectra of Chiral Molecules Using QM/MM Molecular Dynamics Simulation Method. J Chem Theory Comput 2011; 7:4097-103. [DOI: 10.1021/ct200660s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jun-Ho Choi
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 1360-713, Korea
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Cruz V, Ramos J, Martínez-Salazar J. Water-Mediated Conformations of the Alanine Dipeptide as Revealed by Distributed Umbrella Sampling Simulations, Quantum Mechanics Based Calculations, and Experimental Data. J Phys Chem B 2011; 115:4880-6. [DOI: 10.1021/jp2022727] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Víctor Cruz
- BIOPHYM, Instituto de Estructura de la Materia, CSIC, Serrano 113bis, 28006, Madrid, Spain
| | - Javier Ramos
- BIOPHYM, Instituto de Estructura de la Materia, CSIC, Serrano 113bis, 28006, Madrid, Spain
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25
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Amadei A, Daidone I, Zanetti-Polzi L, Aschi M. Modeling quantum vibrational excitations in condensed-phase molecular systems. Theor Chem Acc 2011. [DOI: 10.1007/s00214-010-0882-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Rhee H, Choi JH, Cho M. Infrared optical activity: electric field approaches in time domain. Acc Chem Res 2010; 43:1527-36. [PMID: 20931956 DOI: 10.1021/ar100090q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy provides detailed information about the absolute configurations of chiral molecules including biomolecules and synthetic drugs. This method is the infrared (IR) analogue of the more popular electronic CD spectroscopy that uses the ultraviolet and visible ranges of the electromagnetic spectrum. Because conventional electronic CD spectroscopy measures the difference in signal intensity, problems such as weak signal and low time-resolution can limit its utility. To overcome the difficulties associated with that approach, we have recently developed femtosecond IR optical activity (IOA) spectrometry, which directly measures the IOA free-induction-decay (FID), the impulsive chiroptical IR response that occurs over time. In this Account, we review the time-domain electric field measurement and calculation methods used to simultaneously characterize VCD and related vibrational optical rotatory dispersion (VORD) spectra. Although conventional methods measure the electric field intensity, this vibrational technique is based on a direct phase-and-amplitude measurement of the electric field of the chiroptical signal over time. This method uses a cross-polarization analyzer to carry out heterodyned spectral interferometry. The cross-polarization scheme enables us to selectively remove the achiral background signal, which is the dominant noise component present in differential intensity measurement techniques. Because we can detect the IOA FID signal in a phase-amplitude-sensitive manner, we can directly characterize the time-dependent electric dipole/magnetic dipole response function and the complex chiral susceptibility that contain information about the angular oscillations of charged particles. These parameters yield information about the VCD and VORD spectra. In parallel with such experimental developments, we have also calculated the IOA FID signal and the resulting VCD spectrum. These simulations use a quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) method and calculate the electric dipole/magnetic dipole cross-correlation function in the time domain. Although many quantum chemistry calculation approaches can only consider a limited number of geometry-optimized conformations of chiral molecules in a gas phase, this computational method includes the solute-solvent interactions and the inhomogeneous distributions of solute conformers in condensed phases. A subsequent Fourier transformation of the chiral response function produced a theoretical VCD spectrum in the entire mid-IR frequency range. Directly comparing theory and experiment, we demonstrate quantitative agreement between frequency-tunable femtosecond IOA measurements and QM/MM MD simulations of (1S)-β-pinene in CCl(4) solution. We anticipate that these direct IOA measurement and calculation methods will be applied to the studies of equilibrium chiroptical properties and structure determinations. These methods provide tools to investigate ultrafast structural dynamics of chiral systems with unprecedented time resolution.
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Affiliation(s)
- Hanju Rhee
- Korea Basic Science Institute, Seoul 136-713, Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Jun-Ho Choi
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Korea Basic Science Institute, Seoul 136-713, Korea
- Department of Chemistry, Korea University, Seoul 136-701, Korea
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27
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Pirc G, Stare J, Mavri J. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate. J Chem Phys 2010; 132:224506. [PMID: 20550407 DOI: 10.1063/1.3429251] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.
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Affiliation(s)
- Gordana Pirc
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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28
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Gaigeot MP. Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for P(II)/beta conformations. Phys Chem Chem Phys 2010; 12:10198-209. [PMID: 20539891 DOI: 10.1039/c003485a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Following our previous work [J. Phys. Chem. B. Lett., 2009, 113, 10059], DFT-based molecular dynamics (DFTMD) simulations of 2-Ala peptide (i.e. Ac-Ala-NHMe dialanine peptide analog with methyl group caps at the extremities) immersed in liquid water at room temperature are reported. Our goal here is the theoretical calculation of the infrared spectrum of aqueous 2-Ala, in order to provide a definitive understanding of the average conformation adopted by this peptide in the liquid phase, taking into account solute and solvent at the same theoretical level of representation. We find that the experimental Amide I-II band predominantly results from a mixture of partially unfolded P(II) and unfolded beta conformational equilibrium of aqueous 2-Ala at room temperature.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France.
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