101
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Simon A, Spiegelman F. Water clusters adsorbed on polycyclic aromatic hydrocarbons: Energetics and conformational dynamics. J Chem Phys 2013; 138:194309. [DOI: 10.1063/1.4805015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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102
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Lilienfeld OAV. Force correcting atom centred potentials for generalised gradient approximated density functional theory: Approaching hybrid functional accuracy for geometries and harmonic frequencies in small chlorofluorocarbons. Mol Phys 2013. [DOI: 10.1080/00268976.2013.793834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- O. Anatole von Lilienfeld
- Argonne Leadership Computing Facility, Argonne National Laboratory , Argonne, IL, 60439, USA
- Department of Chemistry, University of Basel , Basel, Klingelbergstr, 80, 4056, Switzerland
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103
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Sulpizi M, Salanne M, Sprik M, Gaigeot MP. Vibrational Sum Frequency Generation Spectroscopy of the Water Liquid-Vapor Interface from Density Functional Theory-Based Molecular Dynamics Simulations. J Phys Chem Lett 2013; 4:83-87. [PMID: 26291216 DOI: 10.1021/jz301858g] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The vibrational sum frequency generation (VSFG) spectrum of the water liquid-vapor (LV) interface is calculated using density functional theory-based molecular dynamics simulations. The real and imaginary parts of the spectrum are in good agreement with the experimental data, and we provide an assignment of the SFG bands according to the dipole orientation of the interfacial water molecules. We use an instantaneous definition of the surface, which is more adapted to the study of interfacial phenomena than the Gibbs dividing surface. By calculating the vibrational (infrared, Raman) properties for interfaces of varying thickness, we show that the bulk spectra signatures appear after a thin layer of 2-3 Å only. We therefore use this value as a criterion for calculating the VSFG spectrum.
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Affiliation(s)
- Marialore Sulpizi
- †Department of Physics, Johannes Gutenberg Universitat, Staudingerweg 7, 55099, Mainz, Germany
| | - Mathieu Salanne
- ‡UPMC Université Paris 06, CNRS, ESPCI, UMR 7195, PECSA, F-75005 Paris, France
| | - Michiel Sprik
- §Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Marie-Pierre Gaigeot
- ∥LAMBE CNRS UMR8587, Université d'Evry val d'Essonne, Boulevard F. Mitterrand, Bât Maupertuis, 91025 Evry, France
- ⊥Institut Universitaire de France, 103 Boulevard St. Michel, 75005 Paris, France
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104
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Roy TK, Gerber RB. Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications. Phys Chem Chem Phys 2013; 15:9468-92. [DOI: 10.1039/c3cp50739d] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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105
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Pincu M, Brauer B, Gerber RB. When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:15382-91. [DOI: 10.1039/c3cp52220b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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106
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Ivanov SD, Witt A, Marx D. Theoretical spectroscopy using molecular dynamics: theory and application to CH5+ and its isotopologues. Phys Chem Chem Phys 2013; 15:10270-99. [DOI: 10.1039/c3cp44523b] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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107
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Jiao T, Gao L, Chen X, Fang W. The Folding Dynamics and Infrared Spectra of a Photocleaved Tetrapeptide Predicted by Theoretical Simulations. J Phys Chem B 2012. [DOI: 10.1021/jp311286k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tiantian Jiao
- Key Laboratory of Theoretical and
Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and
Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xuebo Chen
- Key Laboratory of Theoretical and
Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Weihai Fang
- Key Laboratory of Theoretical and
Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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108
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Sieffert N, Bühl M, Gaigeot MP, Morrison CA. Liquid Methanol from DFT and DFT/MM Molecular Dynamics Simulations. J Chem Theory Comput 2012; 9:106-18. [DOI: 10.1021/ct300784x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nicolas Sieffert
- Université Joseph Fourier Grenoble I, CNRS UMR-5250 Département de Chimie Moléculaire, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| | - Michael Bühl
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Marie-Pierre Gaigeot
- Université d’Evry val d’Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Blvd F. Mitterrand, Bat Maupertuis, 91025 Evry, France
- Institut Universitaire de France (IUF), 103 Blvd St Michel, 75005 Paris, France
| | - Carole A. Morrison
- EaStCHEM School of Chemistry, University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh, EH9 3JJ, United Kingdom
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109
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Zen A, Zhelyazov D, Guidoni L. Optimized Structure and Vibrational Properties by Error Affected Potential Energy Surfaces. J Chem Theory Comput 2012; 8:4204-4215. [PMID: 24093004 DOI: 10.1021/ct300576n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The precise theoretical determination of the geometrical parameters of molecules at the minima of their potential energy surface and of the corresponding vibrational properties are of fundamental importance for the interpretation of vibrational spectroscopy experiments. Quantum Monte Carlo techniques are correlated electronic structure methods promising for large molecules, which are intrinsically affected by stochastic errors on both energy and force calculations, making the mentioned calculations more challenging with respect to other more traditional quantum chemistry tools. To circumvent this drawback in the present work, we formulate the general problem of evaluating the molecular equilibrium structures, the harmonic frequencies, and the anharmonic coefficients of an error affected potential energy surface. The proposed approach, based on a multidimensional fitting procedure, is illustrated together with a critical evaluation of systematic and statistical errors. We observe that the use of forces instead of energies in the fitting procedure reduces the statistical uncertainty of the vibrational parameters by 1 order of magnitude. Preliminary results based on variational Monte Carlo calculations on the water molecule demonstrate the possibility to evaluate geometrical parameters and harmonic and anharmonic coefficients at this level of theory with an affordable computational cost and a small stochastic uncertainty (<0.07% for geometries and <0.7% for vibrational properties).
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Affiliation(s)
- Andrea Zen
- Dipartimento di Fisica, La Sapienza-Università di Roma, P.le Aldo Moro 2, 00185 Roma, Italy
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110
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Tanzi L, Ramondo F, Guidoni L. Vibrational Spectra of Water Solutions of Azoles from QM/MM Calculations: Effects of Solvation. J Phys Chem A 2012; 116:10160-71. [DOI: 10.1021/jp3045059] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luana Tanzi
- Department of Physical
and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100
L’Aquila, Italy
| | - Fabio Ramondo
- Department of Physical
and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100
L’Aquila, Italy
| | - Leonardo Guidoni
- Department of Physical
and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100
L’Aquila, Italy
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111
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Rudić S, Xie HB, Gerber RB, Simons JP. Protonated sugars: vibrational spectroscopy and conformational structure of protonatedO-methyl α-D-galactopyranoside. Mol Phys 2012. [DOI: 10.1080/00268976.2012.660206] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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112
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Quarti C, Milani A, Civalleri B, Orlando R, Castiglioni C. Ab initio calculation of the crystalline structure and IR spectrum of polymers: nylon 6 polymorphs. J Phys Chem B 2012; 116:8299-311. [PMID: 22697809 DOI: 10.1021/jp303715v] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
State-of-the-art computational methods in solid-state chemistry were applied to predict the structural and spectroscopic properties of the α and γ crystalline polymorphs of nylon 6. Density functional theory calculations augmented with an empirical dispersion correction (DFT-D) were used for the optimization of the two different crystal structures and of the isolated chains, characterized by a different regular conformation and described as one-dimensional infinite chains. The structural parameters of both crystalline polymorphs were correctly predicted, and new insight into the interplay of conformational effects, hydrogen bonding, and van der Waals interactions in affecting the properties of the crystal structures of polyamides was obtained. The calculated infrared spectra were compared to experimental data; based on computed vibrational eigenvectors, assignment of the infrared absorptions of the two nylon 6 polymorphs was carried out and critically analyzed in light of previous investigations. On the basis of a comparison of the computed and experimental IR spectra, a set of marker bands was identified and proposed as a tool for detecting and quantifying the presence of a given polymorph in a real sample: several marker bands employed in the past were confirmed, whereas some of the previous assignments are criticized. In addition, some new marker bands are proposed. The results obtained demonstrate that accurate computational techniques are now affordable for polymers characterization, opening the way to several applications of ab initio modeling to the study of many families of polymeric materials.
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Affiliation(s)
- Claudio Quarti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica G. Natta, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
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113
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Hiratsuka M, Ohmura R, Sum AK, Yasuoka K. Molecular vibrations of methane molecules in the structure I clathrate hydrate from ab initio molecular dynamics simulation. J Chem Phys 2012; 136:044508. [PMID: 22299892 DOI: 10.1063/1.3677231] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm(-1) for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages.
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Affiliation(s)
- Masaki Hiratsuka
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
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114
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Hanson-Heine MWD, George MW, Besley NA. Investigating the Calculation of Anharmonic Vibrational Frequencies Using Force Fields Derived from Density Functional Theory. J Phys Chem A 2012; 116:4417-25. [DOI: 10.1021/jp301670f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Michael W. George
- School of Chemistry, University of Nottingham, University Park, Nottingham
NG7 2RD, U.K
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham
NG7 2RD, U.K
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115
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Xie HB, Jin L, Rudić S, Simons JP, Gerber RB. Computational Studies of Protonated β-d-Galactose and Its Hydrated Complex: Structures, Interactions, Proton Transfer Dynamics, and Spectroscopy. J Phys Chem B 2012; 116:4851-9. [DOI: 10.1021/jp3028325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hong-bin Xie
- Key Laboratory of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - Lin Jin
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - Svemir Rudić
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - John P. Simons
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
- Institute of Chemistry
and The
Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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116
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Gaigeot MP, Sprik M, Sulpizi M. Oxide/water interfaces: how the surface chemistry modifies interfacial water properties. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:124106. [PMID: 22395098 DOI: 10.1088/0953-8984/24/12/124106] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The organization of water at the interface with silica and alumina oxides is analysed using density functional theory-based molecular dynamics simulation (DFT-MD). The interfacial hydrogen bonding is investigated in detail and related to the chemistry of the oxide surfaces by computing the surface charge density and acidity. We find that water molecules hydrogen-bonded to the surface have different orientations depending on the strength of the hydrogen bonds and use this observation to explain the features in the surface vibrational spectra measured by sum frequency generation spectroscopy. In particular, 'ice-like' and 'liquid-like' features in these spectra are interpreted as the result of hydrogen bonds of different strengths between surface silanols/aluminols and water.
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Affiliation(s)
- Marie-Pierre Gaigeot
- LAMBE UMR8587, Université d'Evry val d'Essonne, Boulevard F Mitterrand, Bâtiment Maupertuis, F-91025 Evry, France.
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117
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Cecchet F, Lis D, Caudano Y, Mani AA, Peremans A, Champagne B, Guthmuller J. Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:124110. [PMID: 22394554 DOI: 10.1088/0953-8984/24/12/124110] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular, DFT calculations have been carried out on three classes of models for the aliphatic chains. The first class of models consists of aliphatic chains, containing from 3 to 12 carbon atoms, in which only one methyl group can freely vibrate, while the rest of the chain is frozen by a strong overweight of its C and H atoms. This enables us to localize the probed vibrational modes on the methyl group. In the second class, only one methyl group is frozen, while the entire remaining chain is allowed to vibrate. This enables us to analyse the influence of the aliphatic chain on the methyl stretching vibrations. Finally, the dodecanethiol (DDT) molecule is considered, for which the effects of two dielectrics, i.e. n-hexane and n-dodecane, are investigated. Moreover, DDT calculations are also carried out by using different exchange-correlation (XC) functionals in order to assess the DFT approximations. Using the DFT IR vectors and Raman tensors, the SFG spectrum of DDT has been simulated and the orientation of the methyl group has then been deduced and compared with that obtained using an analytical approach based on a bond additivity model. This analysis shows that when using DFT molecular properties, the predicted orientation of the terminal methyl group tends to converge as a function of the alkyl chain length and that the effects of the chain as well as of the dielectric environment are small. Instead, a more significant difference is observed when comparing the DFT-based results with those obtained from the analytical approach, thus indicating the importance of a quantum chemical description of the hyperpolarizability tensor elements of the methyl group.
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Affiliation(s)
- F Cecchet
- Research Centre in Physics of Matter and Radiation (PMR), FUNDP-University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium.
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118
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Sulpizi M, Gaigeot MP, Sprik M. The Silica–Water Interface: How the Silanols Determine the Surface Acidity and Modulate the Water Properties. J Chem Theory Comput 2012; 8:1037-47. [DOI: 10.1021/ct2007154] [Citation(s) in RCA: 286] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Marialore Sulpizi
- Johannes Gutenberg University, Staudinger Weg.7, D 55099, Mainz, Germany
| | - Marie-Pierre Gaigeot
- LAMBE UMR8587, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bat Maupertuis, 91025 Evry, France
- Institut Universitaire de France (IUF), 103 Blvd St Michel, 75005 Paris, France
| | - Michiel Sprik
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United
Kingdom
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119
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Caleman C, van Maaren PJ, Hong M, Hub JS, Costa LT, van der Spoel D. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant. J Chem Theory Comput 2012; 8:61-74. [PMID: 22241968 PMCID: PMC3254193 DOI: 10.1021/ct200731v] [Citation(s) in RCA: 463] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Indexed: 12/15/2022]
Abstract
The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.
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Affiliation(s)
- Carl Caleman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron Notkestraße 85, DE-22607 Hamburg, Germany
| | - Paul J. van Maaren
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Minyan Hong
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Jochen S. Hub
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Luciano T. Costa
- Departamento de Ciências Exatas, Federal University of Alfenas—MG Rua Gabriel Monteiro da Silva, 700 Alfenas—MG CEP:37130-000, Brazil
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
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120
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Xie HB, Gerber RB. Interaction and reaction of the hydroxyl ion with β-d-galactose and its hydrated complex: an ab initio molecular dynamics study. Phys Chem Chem Phys 2012; 14:12086-9. [DOI: 10.1039/c2cp41593c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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121
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Jin L, Gerber RB. Migration and chemical reaction of H+ in protonated β-galactose. Phys Chem Chem Phys 2012; 14:13522-6. [DOI: 10.1039/c2cp41766a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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122
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Van-Oanh NT, Falvo C, Calvo F, Lauvergnat D, Basire M, Gaigeot MP, Parneix P. Improving anharmonic infrared spectra using semiclassically prepared molecular dynamics simulations. Phys Chem Chem Phys 2012; 14:2381-90. [DOI: 10.1039/c2cp23101h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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123
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Calvo F, Van-Oanh NT, Parneix P, Falvo C. Vibrational spectra of polyatomic molecules assisted by quantum thermal baths. Phys Chem Chem Phys 2012; 14:10503-6. [DOI: 10.1039/c2cp41663h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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124
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Domin D, Benoit DM. Assessing Spin-Component-Scaled Second-Order Møller-Plesset Theory Using Anharmonic Frequencies. Chemphyschem 2011; 12:3383-91. [DOI: 10.1002/cphc.201100499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Indexed: 11/08/2022]
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125
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Shmilovits-Ofir M, Gerber RB. Proton Transfer and Dissociation of GlyLysH+ following O–H and N–H Stretching Mode Excitations: Dynamics Simulations. J Am Chem Soc 2011; 133:16510-7. [DOI: 10.1021/ja205634b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michaela Shmilovits-Ofir
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - R. Benny Gerber
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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126
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Bovi D, Mezzetti A, Vuilleumier R, Gaigeot MP, Chazallon B, Spezia R, Guidoni L. Environmental effects on vibrational properties of carotenoids: experiments and calculations on peridinin. Phys Chem Chem Phys 2011; 13:20954-64. [PMID: 21946923 DOI: 10.1039/c1cp21985e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Carotenoids are employed in light-harvesting complexes of dinoflagellates with the two-fold aim to extend the spectral range of the antenna and to protect it from radiation damage. We have studied the effect of the environment on the vibrational properties of the carotenoid peridinin in different solvents by means of vibrational spectroscopies and QM/MM molecular dynamics simulations. Three prototypical solvents were considered: cyclohexane (an apolar/aprotic solvent), deuterated acetonitrile (a polar/aprotic solvent) and methanol (a polar/protic solvent). Thanks to effective normal mode analysis, we were able to assign the experimental Raman and IR bands and to clarify the effect of the solvent on band shifts. In the 1500-1650 cm(-1) region, seven vibrational modes of the polyene chain were identified and assigned to specific molecular vibrations. In the 1700-1800 cm(-1) region a strong progressive down-shift of the lactonic carbonyl frequency is observed passing from cyclohexane to methanol solutions. This has been rationalized here in terms of solvent polarity and solute-solvent hydrogen bond interactions. On the basis of our data we propose a classification of non-equivalent peridinins in the Peridinin-Chlorophyll-Proteins, light-harvesting complexes of dinoflagellates.
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Affiliation(s)
- Daniele Bovi
- Dipartimento di Fisica, Università di Roma LA SAPIENZA, Rome, Italy
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127
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Benoit DM, Madebene B, Ulusoy I, Mancera L, Scribano Y, Chulkov S. Towards a scalable and accurate quantum approach for describing vibrations of molecule-metal interfaces. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2011; 2:427-447. [PMID: 22003450 PMCID: PMC3190614 DOI: 10.3762/bjnano.2.48] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 07/14/2011] [Indexed: 05/31/2023]
Abstract
We present a theoretical framework for the computation of anharmonic vibrational frequencies for large systems, with a particular focus on determining adsorbate frequencies from first principles. We give a detailed account of our local implementation of the vibrational self-consistent field approach and its correlation corrections. We show that our approach is both robust, accurate and can be easily deployed on computational grids in order to provide an efficient computational tool. We also present results on the vibrational spectrum of hydrogen fluoride on pyrene, on the thiophene molecule in the gas phase, and on small neutral gold clusters.
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Affiliation(s)
- David M Benoit
- Nachwuchsgruppe Theorie – SFB 569, Albert-Einstein-Allee 11, University of Ulm, D-89081 Ulm, Germany
- Department of Chemistry, The University of Hull, Cottingham Road, Kingston upon Hull HU6 7RX, United Kingdom
| | - Bruno Madebene
- L.A.D.I.R Boite 49, Bat F74, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris, France
| | - Inga Ulusoy
- Technische Universität München, Theoretical Chemistry, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Luis Mancera
- Theoretical Chemistry, Albert-Einstein-Allee 11, University of Ulm, D-89081 Ulm, Germany
| | - Yohann Scribano
- Laboratoire Interdisciplinaire Carnot de Bourgogne,UMR 5209 CNRS – Université de Bourgogne, 9 av. A. Savary, BP 47870, F-21078 Dijon Cedex, France
| | - Sergey Chulkov
- Nachwuchsgruppe Theorie – SFB 569, Albert-Einstein-Allee 11, University of Ulm, D-89081 Ulm, Germany
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128
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Pincu M, Cocinero EJ, Mayorkas N, Brauer B, Davis BG, Gerber RB, Simons JP. Isotopic Hydration of Cellobiose: Vibrational Spectroscopy and Dynamical Simulations. J Phys Chem A 2011; 115:9498-509. [DOI: 10.1021/jp112109p] [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)
- Madeleine Pincu
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Emilio J. Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, (UPV − EHU), Apartado 644, E-48940, Bilbao, Spain
| | - Nitzan Mayorkas
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Brina Brauer
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Benjamin G. Davis
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - John P. Simons
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, U.K
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129
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Bouteiller Y, Poully JC, Grégoire G. Evaluation of polarizable continuum model for the prediction of vibrational frequencies of biomimetic molecules in solution. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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130
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Ingrosso F, Monard G, Hamdi Farag M, Bastida A, Ruiz-López MF. Importance of Polarization and Charge Transfer Effects to Model the Infrared Spectra of Peptides in Solution. J Chem Theory Comput 2011; 7:1840-9. [DOI: 10.1021/ct2000588] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Francesca Ingrosso
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 SRSMC, CNRS-Nancy Université, BP 70239 Vandœuvre-lès Nancy, France
| | - Gérald Monard
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 SRSMC, CNRS-Nancy Université, BP 70239 Vandœuvre-lès Nancy, France
| | - Marwa Hamdi Farag
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Manuel F. Ruiz-López
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 SRSMC, CNRS-Nancy Université, BP 70239 Vandœuvre-lès Nancy, France
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131
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Tkatchenko A, Rossi M, Blum V, Ireta J, Scheffler M. Unraveling the stability of polypeptide helices: critical role of van der Waals interactions. PHYSICAL REVIEW LETTERS 2011; 106:118102. [PMID: 21469900 DOI: 10.1103/physrevlett.106.118102] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Indexed: 05/30/2023]
Abstract
Folding and unfolding processes are important for the functional capability of polypeptides and proteins. In contrast with a physiological environment (solvated or condensed phases), an in vacuo study provides well-defined "clean room" conditions to analyze the intramolecular interactions that largely control the structure, stability, and folding or unfolding dynamics. Here we show that a proper consideration of van der Waals (vdW) dispersion forces in density-functional theory (DFT) is essential, and a recently developed DFT+vdW approach enables long time-scale ab initio molecular dynamics simulations at an accuracy close to "gold standard" quantum-chemical calculations. The results show that the inclusion of vdW interactions qualitatively changes the conformational landscape of alanine polypeptides, and greatly enhances the thermal stability of helical structures, in agreement with gas-phase experiments.
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Affiliation(s)
- Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
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132
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Brauer B, Pincu M, Buch V, Bar I, Simons JP, Gerber RB. Vibrational Spectra of α-Glucose, β-Glucose, and Sucrose: Anharmonic Calculations and Experiment. J Phys Chem A 2011; 115:5859-72. [DOI: 10.1021/jp110043k] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brina Brauer
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Madeleine Pincu
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Victoria Buch
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - John. P. Simons
- Chemistry Department, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, U.K
| | - R. Benny Gerber
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Department of Chemistry, University of California, Irvine, California 92697, United States
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133
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Nicely AL, Lisy JM. Charge and Temperature Effects on Hydrated Tryptamine Cluster Ions. J Phys Chem A 2011; 115:2669-78. [DOI: 10.1021/jp1059648] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amy L. Nicely
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - James M. Lisy
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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134
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Gaigeot MP, Besley NA, Hirst JD. Modeling the infrared and circular dichroism spectroscopy of a bridged cyclic diamide. J Phys Chem B 2011; 115:5526-35. [PMID: 21344909 DOI: 10.1021/jp111140f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory based molecular dynamics simulations are used to study the structure, infrared (IR) spectroscopy, circular dichroism (CD) spectroscopy, and coupling between the amide I vibrations of a bridged cyclic diamide in the gas phase and in aqueous solution. IR spectra computed via the dipole moment time correlation function show a large red-shift of 30 cm(-1) in the amide I vibration in solution compared to the gas phase, and are in good agreement with experiment. Conformationally averaged CD spectra computed using the CIS(D) method are highly sensitive to the structures used, and structures sampled in the aqueous phase simulation are required to obtain qualitatively correct CD spectra. Analysis of the coupling between the amide I modes shows that in the aqueous phase there is an increased localization of the vibrations on the individual peptide groups and a reduction in the mode coupling parameter compared to the gas phase. Overall, the results illustrate the significance of incorporating molecular dynamics in the simulation of IR and CD spectra.
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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'Environment, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France
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135
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Simon A, Rapacioli M, Lanza M, Joalland B, Spiegelman F. Molecular dynamics simulations on [FePAH]+ π-complexes of astrophysical interest: anharmonic infrared spectroscopy. Phys Chem Chem Phys 2011; 13:3359-74. [PMID: 21243160 DOI: 10.1039/c0cp00990c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article, classical Born-Oppenheimer molecular dynamics (MD) simulations in the microcanonical ensemble are performed on neutral and cationic polycyclic aromatic hydrocarbon (PAH) species, focusing on [FePAH](+)π-complexes. Their anharmonic mid-infrared (mid-IR) spectra in the classical approximation are derived. This approach allows us to describe the influence of the energy of a system on its IR spectrum in terms of band-shifts and broadenings. The MD simulations are performed on a potential energy surface (PES) described at the self-consistent-charge density functional tight-binding level of theory. The PES is benchmarked on DFT calculations, showing the validity of the approach for complexes of Fe(+) with PAHs larger than coronene (C(24)H(12)) that are of astrophysical interest. MD simulations at high temperature show the occurrence of the diffusion of the Fe cation on the surface of the PAH. It proceeds through the edge of the carbon skeleton which is the lowest energy pathway presenting barriers smaller than 1 eV. Although only qualitative information on the band broadenings can be obtained, we show that the dependence of the computed positions of the main bands of [C(24)H(12)](0/+)and [FeC(24)H(12)](+)π-complexes on temperature can be fit by linear laws. The spectral trends determined for [FeC(24)H(12)](+) are compared to those of N-substituted [C(23)NH(12)](+)and [SiC(24)H(12)](+)π-complexes of astrophysical interest.
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Affiliation(s)
- Aude Simon
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université de Toulouse, UPS, LCPQ, 118 Route de Narbonne, F-31062 Toulouse, France.
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136
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Ramos-Cordoba E, Lambrecht DS, Head-Gordon M. Charge-transfer and the hydrogen bond: Spectroscopic and structural implications from electronic structure calculations. Faraday Discuss 2011; 150:345-62; discussion 391-418. [DOI: 10.1039/c1fd00004g] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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137
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Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared spectra of protonated neurotransmitters: dopamine. Phys Chem Chem Phys 2011; 13:2815-23. [DOI: 10.1039/c0cp02133d] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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138
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Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared spectra of the protonated neurotransmitter histamine: competition between imidazolium and ammonium isomers in the gas phase. Phys Chem Chem Phys 2011; 13:15644-56. [DOI: 10.1039/c1cp21681c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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139
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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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