101
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Karmakar A, Chandra A. Dynamics of vibrational spectral diffusion in water: Effects of dispersion interactions, temperature, density, system size and fictitious orbital mass. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.11.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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102
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Dohn AO, Jónsson EÖ, Levi G, Mortensen JJ, Lopez-Acevedo O, Thygesen KS, Jacobsen KW, Ulstrup J, Henriksen NE, Møller KB, Jónsson H. Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex. J Chem Theory Comput 2017; 13:6010-6022. [PMID: 29083921 DOI: 10.1021/acs.jctc.7b00621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.
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Affiliation(s)
- A O Dohn
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland
| | - E Ö Jónsson
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland
| | - G Levi
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - J J Mortensen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - O Lopez-Acevedo
- Department of Applied Physics, Aalto University , 02150 Espoo, Finland
| | - K S Thygesen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - K W Jacobsen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - J Ulstrup
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - N E Henriksen
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - K B Møller
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - H Jónsson
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland.,Department of Applied Physics, Aalto University , 02150 Espoo, Finland
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103
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Holmes JD, Otero-de-la-Roza A, DiLabio GA. Accurate Modeling of Water Clusters with Density-Functional Theory Using Atom-Centered Potentials. J Chem Theory Comput 2017; 13:4205-4215. [DOI: 10.1021/acs.jctc.7b00624] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jake D. Holmes
- Department
of Chemistry and ‡Faculty of Management, The University of British Columbia, 3247
University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- Department
of Chemistry and ‡Faculty of Management, The University of British Columbia, 3247
University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Gino A. DiLabio
- Department
of Chemistry and ‡Faculty of Management, The University of British Columbia, 3247
University Way, Kelowna, British Columbia, Canada V1V 1V7
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104
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Galib M, Duignan TT, Misteli Y, Baer MD, Schenter GK, Hutter J, Mundy CJ. Mass density fluctuations in quantum and classical descriptions of liquid water. J Chem Phys 2017; 146:244501. [DOI: 10.1063/1.4986284] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Mirza Galib
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Timothy T. Duignan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Yannick Misteli
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Gregory K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Jürg Hutter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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105
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Vibrational echo spectral observables and frequency fluctuations of hydration shell water around a fluoride ion from first principles simulations. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1313-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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106
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Gao L, Bu Y. Protonation-modulated localization of excess electrons in histidine aqueous solutions revealed by ab initio molecular dynamics simulations: anion-centered versus cation-centered localization. Phys Chem Chem Phys 2017; 19:13807-13818. [PMID: 28508903 DOI: 10.1039/c7cp01847a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we present an ab initio molecular dynamics simulation study on the interaction of an excess electron (EE) with histidine in its aqueous solution. Two different configurations of histidine (imidazole group protonated or not) are considered to reflect its different existing forms in neutral or slightly acidic surroundings. The simulation results indicate that localizations of EEs in different aqueous histidine solutions are quite different and are strongly affected by protonation of the side chain imidazole group and are thus pH-controlled. In neutral aqueous histidine solution, an EE localizes onto the carboxyl anionic group of the amino acid backbone after a relatively lengthy diffuse state, performing just like in an aliphatic amino acid solution. But in weakly acidic solution in which the side chain imidazole group is protonated, an EE undergoes a short lifetime diffuse state and finally localizes on the protonated imidazole group. We carefully examine these two different localization dynamics processes and analyze the competition between different dominating groups in their corresponding electron localization mechanisms. To explain the difference, we investigate the frontier molecular orbitals of these two systems and find that their energy levels and compositions are important to determine these differences. These findings can provide helpful information to understand the interaction mechanisms of low energy EEs with amino acids and even oligopeptides, especially with aromatic rings.
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Affiliation(s)
- Liang Gao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.
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107
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Mouhat F, Sorella S, Vuilleumier R, Saitta AM, Casula M. Fully Quantum Description of the Zundel Ion: Combining Variational Quantum Monte Carlo with Path Integral Langevin Dynamics. J Chem Theory Comput 2017; 13:2400-2417. [DOI: 10.1021/acs.jctc.7b00017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Félix Mouhat
- IMPMC, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, 4 place Jussieu, 75252 Paris, France
| | - Sandro Sorella
- International
School for Advanced Studies (SISSA), Via Bonomea 26, 34136 Trieste, Italy
- INFM Democritos
National Simulation Center, 34151 Trieste, Italy
| | - Rodolphe Vuilleumier
- PASTEUR,
Département de chimie, École normale supérieure,
UPMC Univ Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, École normale supérieure, CNRS, Processus d’activation
sélective par transfert d’énergie uni-électronique
ou radiatif (PASTEUR), 75005 Paris, France
| | - Antonino Marco Saitta
- IMPMC, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, 4 place Jussieu, 75252 Paris, France
| | - Michele Casula
- IMPMC, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, 4 place Jussieu, 75252 Paris, France
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108
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Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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109
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Ruiz Pestana L, Mardirossian N, Head-Gordon M, Head-Gordon T. Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals. Chem Sci 2017; 8:3554-3565. [PMID: 30155200 PMCID: PMC6092720 DOI: 10.1039/c6sc04711d] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/24/2017] [Indexed: 01/23/2023] Open
Abstract
We have used ab initio molecular dynamics (AIMD) to characterize water properties using two meta-generalized gradient approximation (meta-GGA) functionals, M06-L-D3 and B97M-rV, and compared their performance against a standard GGA corrected for dispersion, revPBE-D3, at ambient conditions (298 K, and 1 g cm-3 or 1 atm). Simulations of the equilibrium density, radial distribution functions, self-diffusivity, the infrared spectrum, liquid dipole moments, and characterizations of the hydrogen bond network show that all three functionals have overcome the problem of the early AIMD simulations that erroneously found ambient water to be highly structured, but they differ substantially among themselves in agreement with experiment on this range of water properties. We show directly using water cluster data up through the pentamer that revPBE-D3 benefits from a cancellation of its intrinsic functional error by running classical trajectories, whereas the meta-GGA functionals are demonstrably more accurate and would require the simulation of nuclear quantum effects to realize better agreement with all cluster and condensed phase properties.
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Affiliation(s)
- Luis Ruiz Pestana
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , USA .
| | - Narbe Mardirossian
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
| | - Teresa Head-Gordon
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , USA .
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
- Departments of Chemistry , Bioengineering , Chemical and Biomolecular Engineering , University of California , Berkeley , USA
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110
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Vitale V, Dziedzic J, Albaugh A, Niklasson AMN, Head-Gordon T, Skylaris CK. Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory. J Chem Phys 2017; 146:124115. [DOI: 10.1063/1.4978684] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Valerio Vitale
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | - Alex Albaugh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | | | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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111
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Hirshberg B, Sagiv L, Gerber RB. Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications. J Chem Theory Comput 2017; 13:982-991. [DOI: 10.1021/acs.jctc.6b01129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Barak Hirshberg
- Institute
of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
| | - Lior Sagiv
- Institute
of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
| | - R. Benny Gerber
- Institute
of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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112
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Dettori R, Ceriotti M, Hunger J, Melis C, Colombo L, Donadio D. Simulating Energy Relaxation in Pump–Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids. J Chem Theory Comput 2017; 13:1284-1292. [DOI: 10.1021/acs.jctc.6b01108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Riccardo Dettori
- Dipartimento
di Fisica, Università di Cagliari, Cittadella Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Michele Ceriotti
- Laboratory
of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Claudio Melis
- Dipartimento
di Fisica, Università di Cagliari, Cittadella Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Luciano Colombo
- Dipartimento
di Fisica, Università di Cagliari, Cittadella Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Davide Donadio
- Department
of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
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113
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Awoonor-Williams E, Rowley CN. The hydration structure of carbon monoxide byab initiomethods. J Chem Phys 2017; 146:034503. [DOI: 10.1063/1.4974164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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114
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Herrera C, de Carvalho Costa G, Atilhan M, Costa LT, Aparicio S. A theoretical study on aminoacid-based ionic liquids with acid gases and water. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.11.086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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115
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Cassone G, Creazzo F, Giaquinta PV, Sponer J, Saija F. Ionic diffusion and proton transfer in aqueous solutions of alkali metal salts. Phys Chem Chem Phys 2017; 19:20420-20429. [DOI: 10.1039/c7cp03663a] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report on a series of ab initio molecular dynamics investigations on LiCl, NaCl, and KCl aqueous solutions under the effect of static electric fields.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
| | - Fabrizio Creazzo
- Université d'Evry val d'Essonne-Université Paris-Saclay
- 91025 Evry
- France
| | - Paolo V. Giaquinta
- Università degli Studi di Messina
- Dipartimento di Scienze Matematiche e Informatiche
- Scienze Fisiche e Scienze della Terra
- 98166 Messina
- Italy
| | - Jiri Sponer
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
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116
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Hirshberg B, Gerber RB. Mean-Field Methods for Time-Dependent Quantum Dynamics of Many-Atom Systems. ADVANCES IN QUANTUM CHEMISTRY 2017. [DOI: 10.1016/bs.aiq.2017.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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117
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Atta-Fynn R, Bylaska EJ, de Jong WA. Strengthening of the Coordination Shell by Counter Ions in Aqueous Th4+ Solutions. J Phys Chem A 2016; 120:10216-10222. [DOI: 10.1021/acs.jpca.6b09878] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raymond Atta-Fynn
- Department
of Physics, The University of Texas at Arlington, Arlington, Texas 76006, United States
| | - Eric J. Bylaska
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Wibe A. de Jong
- Computational
Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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118
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Chen W, Ambrosio F, Miceli G, Pasquarello A. Ab initio Electronic Structure of Liquid Water. PHYSICAL REVIEW LETTERS 2016; 117:186401. [PMID: 27835004 DOI: 10.1103/physrevlett.117.186401] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Indexed: 05/26/2023]
Abstract
Self-consistent GW calculations with efficient vertex corrections are employed to determine the electronic structure of liquid water. Nuclear quantum effects are taken into account through ab initio path-integral molecular dynamics simulations. We reveal a sizable band-gap renormalization of up to 0.7 eV due to hydrogen-bond quantum fluctuations. Our calculations lead to a band gap of 8.9 eV, in accord with the experimental estimate. We further resolve the ambiguities in the band-edge positions of liquid water. The valence-band maximum and the conduction-band minimum are found at -9.4 and -0.5 eV with respect to the vacuum level, respectively.
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Affiliation(s)
- Wei Chen
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Francesco Ambrosio
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giacomo Miceli
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alfredo Pasquarello
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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119
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Pham TA, Ogitsu T, Lau EY, Schwegler E. Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations. J Chem Phys 2016; 145:154501. [DOI: 10.1063/1.4964865] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Tuan Anh Pham
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Tadashi Ogitsu
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Edmond Y. Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Eric Schwegler
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
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120
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Fischer JM, Mahlberg D, Roman T, Groß A. Water adsorption on bimetallic PtRu/Pt(111) surface alloys. Proc Math Phys Eng Sci 2016; 472:20160618. [PMID: 27843411 PMCID: PMC5095452 DOI: 10.1098/rspa.2016.0618] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/22/2016] [Indexed: 11/12/2022] Open
Abstract
The adsorption of water on bimetallic PtRu/Pt(111) surface alloys has been studied based on periodic density functional theory calculations including dispersion corrections. The Ru atoms of the PtRu surface alloy interact more strongly with water than Pt atoms, as far as both single water molecules and ice-like hexagonal structures are concerned. Within the surface alloy layer, the lateral ligand effect reducing the local reactivity of the surface atoms with increasing Ru content is more dominant than the opposing geometric effect due to the tensile strain. The structural preference for the Ru atoms also prevails at room temperature, as ab initio molecular dynamics simulations show.
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Affiliation(s)
- Julia M. Fischer
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - David Mahlberg
- Institute of Theoretical Chemistry, Ulm University, 89069 Ulm, Germany
| | - Tanglaw Roman
- Institute of Theoretical Chemistry, Ulm University, 89069 Ulm, Germany
| | - Axel Groß
- Institute of Theoretical Chemistry, Ulm University, 89069 Ulm, Germany
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121
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Borah S, Kumar PP. Ab initio molecular dynamics study of Se(iv) species in aqueous environment. Phys Chem Chem Phys 2016; 18:26755-26763. [PMID: 27711537 DOI: 10.1039/c6cp04725d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An ab initio molecular dynamics investigation is carried out on various water-borne Se(iv) species, H2SeO3, HSeO3- and SeO32-, in aqueous environment. Consistent with the reported acid dissociation constants, in neutral solution H2SeO3 exchanges protons with the surrounding water molecules establishing a dynamic equilibrium with HSeO3-. The SeO32- species is found to be stable only in basic environment, which is emulated in the present simulation through introducing a hydroxide ion, OH-, in the system. The hydration structure, hydrogen bonding and spectroscopic signatures of the species are comprehensively analyzed. The influence of the solute's hydration structure on the structural and dynamic response of the solvent is discussed. The correlation between the strength as well as the number of hydrogen bonds accepted by the solute on its vibrational properties are analyzed.
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Affiliation(s)
- Sangkha Borah
- Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
| | - P Padma Kumar
- Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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122
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Naderian M, Groß A. From single molecules to water networks: Dynamics of water adsorption on Pt(111). J Chem Phys 2016; 145:094703. [DOI: 10.1063/1.4961870] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Maryam Naderian
- Institute of Theoretical Chemistry, University of Ulm, Albert-Einstein-Allee 11, D-89069 Ulm, Germany
| | - Axel Groß
- Institute of Theoretical Chemistry, University of Ulm, Albert-Einstein-Allee 11, D-89069 Ulm, Germany
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123
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Structure and dynamics of solvated hydrogenoxalate and oxalate anions: a theoretical study. J Mol Model 2016; 22:210. [DOI: 10.1007/s00894-016-3075-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/27/2016] [Indexed: 11/26/2022]
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124
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Miceli G, Hutter J, Pasquarello A. Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets. J Chem Theory Comput 2016; 12:3456-62. [DOI: 10.1021/acs.jctc.6b00271] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giacomo Miceli
- Chaire
de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jürg Hutter
- Department
of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Alfredo Pasquarello
- Chaire
de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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125
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Brandt EG, Agosta L, Lyubartsev AP. Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations. NANOSCALE 2016; 8:13385-13398. [PMID: 27341183 DOI: 10.1039/c6nr02791a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.
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Affiliation(s)
- Erik G Brandt
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
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126
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Soniat M, Rogers DM, Rempe SB. Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration. J Chem Theory Comput 2016; 11:2958-67. [PMID: 26575733 DOI: 10.1021/acs.jctc.5b00357] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment.
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Affiliation(s)
- Marielle Soniat
- Department of Chemistry, University of New Orleans , 2000 Lakeshore Drive, New Orleans, Louisiana 70148, United States
| | - David M Rogers
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87123, United States.,Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87123, United States
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127
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Gor GY, Bernstein N. Adsorption-Induced Surface Stresses of the Water/Quartz Interface: Ab Initio Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5259-5266. [PMID: 27159032 DOI: 10.1021/acs.langmuir.6b00923] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Adsorption-induced deformation is expansion or contraction of a solid due to adsorption on its surface. This phenomenon is important for a wide range of applications, from chemomechanical sensors to methane recovery from geological formations. The strain of the solid is driven by the change of the surface stress due to adsorption. Using ab initio molecular dynamics, we calculate the surface stresses for the dry α-quartz surfaces, and investigate how these stresses change when the surfaces are exposed to water. We find that the nonhydroxylated surface shows small and approximately isotropic changes in stress, while the hydroxylated surface, which interacts more strongly with the polar water molecules, shows larger and qualitatively anisotropic (opposite sign in xx and yy) surface stress changes. All of these changes are several times larger than the surface tension of water itself. The anisotropy and possibility of positive surface stress change can explain experimentally observed surface area contraction due to adsorption.
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Affiliation(s)
- Gennady Y Gor
- NRC Research Associate, Resident at Center for Materials Physics and Technology, and ‡Center for Materials Physics and Technology, Naval Research Laboratory , Washington D.C. 20375, United States
| | - Noam Bernstein
- NRC Research Associate, Resident at Center for Materials Physics and Technology, and ‡Center for Materials Physics and Technology, Naval Research Laboratory , Washington D.C. 20375, United States
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128
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Nagata Y, Ohto T, Bonn M, Kühne TD. Surface tension of ab initio liquid water at the water-air interface. J Chem Phys 2016; 144:204705. [DOI: 10.1063/1.4951710] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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129
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Köster A, Spura T, Rutkai G, Kessler J, Wiebeler H, Vrabec J, Kühne TD. Assessing the accuracy of improved force-matched water models derived fromAb initiomolecular dynamics simulations. J Comput Chem 2016; 37:1828-38. [DOI: 10.1002/jcc.24398] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 04/08/2016] [Accepted: 04/14/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Andreas Köster
- Thermodynamics and Energy Technology; Department of Mechanical Engineering, University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Thomas Spura
- Dynamics of Condensed Matter, Department of Chemistry; University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Gábor Rutkai
- Thermodynamics and Energy Technology; Department of Mechanical Engineering, University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Jan Kessler
- Dynamics of Condensed Matter, Department of Chemistry; University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Hendrik Wiebeler
- Dynamics of Condensed Matter, Department of Chemistry; University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Jadran Vrabec
- Thermodynamics and Energy Technology; Department of Mechanical Engineering, University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Thomas D. Kühne
- Dynamics of Condensed Matter, Department of Chemistry; University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
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130
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Sakong S, Forster-Tonigold K, Groß A. The structure of water at a Pt(111) electrode and the potential of zero charge studied from first principles. J Chem Phys 2016; 144:194701. [DOI: 10.1063/1.4948638] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sung Sakong
- Institute of Theoretical Chemistry, Ulm University, 89069 Ulm, Germany
| | | | - Axel Groß
- Institute of Theoretical Chemistry, Ulm University, 89069 Ulm, Germany
- Helmholtz Institute Ulm (HIU), Electrochemical Energy Storage, 89069 Ulm, Germany
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131
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Brotzakis ZF, Groot CCM, Brandeburgo WH, Bakker HJ, Bolhuis PG. Dynamics of Hydration Water around Native and Misfolded α-Lactalbumin. J Phys Chem B 2016; 120:4756-66. [DOI: 10.1021/acs.jpcb.6b02592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Z. F. Brotzakis
- Van’t
Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
| | - C. C. M. Groot
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
| | - W. H. Brandeburgo
- Van’t
Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
| | - H. J. Bakker
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
| | - P. G. Bolhuis
- Van’t
Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
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132
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Lin X, Evers F, Groß A. First-principles study of the structure of water layers on flat and stepped Pb electrodes. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:533-43. [PMID: 27335744 PMCID: PMC4901556 DOI: 10.3762/bjnano.7.47] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 03/29/2016] [Indexed: 06/06/2023]
Abstract
On the basis of perodic density functional theory (DFT) calculations, we have addressed the geometric structures and electronic properties of water layers on flat and stepped Pb surfaces. In contrast to late d-band metals, on Pb(111) the energy minimum structure does not correspond to an ice-like hexagonal arrangement at a coverage of 2/3, but rather to a distorted structure at a coverage of 1 due to the larger lattice constant of Pb. At stepped Pb surfaces, the water layers are pinned at the step edge and form a complex network consisting of rectangles, pentagons and hexagons. The thermal stability of the water layers has been studied by using ab initio molecular dynamics simulations (AIMD) at a temperature of 140 K. Whereas the water layer on Pb(111) is already unstable at this temperature, the water layers on Pb(100), Pb(311), Pb(511) and Pb(711) exhibit a higher stability because of stronger water-water interactions. The vibrational spectra of the water layers at the stepped surfaces show a characteristic splitting into three modes in the O-H stretch region.
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Affiliation(s)
- Xiaohang Lin
- Institut für Theoretische Chemie, Universität Ulm, 89069 Ulm, Germany
| | - Ferdinand Evers
- Institut für Theoretische Physik, Universität Regensburg, 93040 Regensburg, Germany
| | - Axel Groß
- Institut für Theoretische Chemie, Universität Ulm, 89069 Ulm, Germany
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133
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Gillan MJ, Alfè D, Michaelides A. Perspective: How good is DFT for water? J Chem Phys 2016; 144:130901. [DOI: 10.1063/1.4944633] [Citation(s) in RCA: 478] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael J. Gillan
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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134
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John C, Spura T, Habershon S, Kühne TD. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics. Phys Rev E 2016; 93:043305. [PMID: 27176426 DOI: 10.1103/physreve.93.043305] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 06/05/2023]
Abstract
We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.
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Affiliation(s)
- Christopher John
- Dynamics of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - Thomas Spura
- Dynamics of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Thomas D Kühne
- Dynamics of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany and Paderborn Center for Parallel Computing and Institute for Lightweight Design, Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
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135
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Daschakraborty S, Kiefer PM, Miller Y, Motro Y, Pines D, Pines E, Hynes JT. Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics. J Phys Chem B 2016; 120:2271-80. [PMID: 26879554 DOI: 10.1021/acs.jpcb.5b12742] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protonation by carbonic acid H2CO3 of the strong base methylamine CH3NH2 in a neutral contact pair in aqueous solution is followed via Car-Parrinello molecular dynamics simulations. Proton transfer (PT) occurs to form an aqueous solvent-stabilized contact ion pair within 100 fs, a fast time scale associated with the compression of the acid-base hydrogen-bond (H-bond), a key reaction coordinate. This rapid barrierless PT is consistent with the carbonic acid-protonated base pKa difference that considerably favors the PT, and supports the view of intact carbonic acid as potentially important proton donor in assorted biological and environmental contexts. The charge redistribution within the H-bonded complex during PT supports a Mulliken picture of charge transfer from the nitrogen base to carbonic acid without altering the transferring hydrogen's charge from approximately midway between that of a hydrogen atom and that of a proton.
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Affiliation(s)
- Snehasis Daschakraborty
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Philip M Kiefer
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Yair Motro
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Dina Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Ehud Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - James T Hynes
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States.,Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
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136
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Moors SLC, Brigou B, Hertsen D, Pinter B, Geerlings P, Van Speybroeck V, Catak S, De Proft F. Influence of Solvation and Dynamics on the Mechanism and Kinetics of Nucleophilic Aromatic Substitution Reactions in Liquid Ammonia. J Org Chem 2016; 81:1635-44. [PMID: 26800020 DOI: 10.1021/acs.joc.5b02794] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of the solvent and the influence of dynamics on the kinetics and mechanism of the SNAr reaction of several halonitrobenzenes in liquid ammonia, using both static calculations and dynamic ab initio molecular dynamics simulations, are investigated. A combination of metadynamics and committor analysis methods reveals how this reaction can change from a concerted, one-step mechanism in gas phase to a stepwise pathway, involving a metastable Meisenheimer complex, in liquid ammonia. This clearly establishes, among others, the important role of the solvent and highlights the fact that accurately treating solvation is of crucial importance to correctly unravel the reaction mechanism. It is indeed shown that H-bond formation of the reacting NH3 with the solvent drastically reduces the barrier of NH3 addition. The halide elimination step, however, is greatly facilitated by proton transfer from the reacting NH3 to the solvent. Furthermore, the free energy surface strongly depends on the halide substituent and the number of electron-withdrawing nitro substituents.
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Affiliation(s)
- Samuel L C Moors
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Ben Brigou
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Dietmar Hertsen
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Balazs Pinter
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Saron Catak
- Department of Chemistry, Bogazici University , Bebek 34342, Istanbul, Turkey
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
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137
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Choudhary A, Chandra A. Anisotropic structure and dynamics of the solvation shell of a benzene solute in liquid water from ab initio molecular dynamics simulations. Phys Chem Chem Phys 2016; 18:6132-45. [DOI: 10.1039/c5cp07352a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The anisotropic structure and dynamics of the hydration shell of a benzene solute in liquid water have been investigated by means of ab initio molecular dynamics simulations using the BLYP (Becke–Lee–Yang–Parr) and dispersion corrected BLYP-D functionals.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India 208016
| | - Amalendu Chandra
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India 208016
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138
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Wang H, Liu J, Xu H, Ma Z, Jia W, Ren S. Demulsification of heavy oil-in-water emulsions by reduced graphene oxide nanosheets. RSC Adv 2016. [DOI: 10.1039/c6ra18898b] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The purpose of this work is to investigate the relationship between the chemical structure of the GO materials and the demulsification performance.
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Affiliation(s)
- Huanjiang Wang
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Juan Liu
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Haiyan Xu
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Zhanwei Ma
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Weihong Jia
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Sili Ren
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
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139
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Cassone G, Creazzo F, Giaquinta PV, Saija F, Marco Saitta A. Ab initio molecular dynamics study of an aqueous NaCl solution under an electric field. Phys Chem Chem Phys 2016; 18:23164-73. [DOI: 10.1039/c6cp03926j] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations of salty water under an electric field reveal two regimes of the relative mobilities of chlorine and sodium ions. When water dissociation and proton transfer are actived at strong field intensities, the presence of the ions hinders the efficiency of the proton transfer mechanism.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics – Czech Academy of Sciences
- 61265 Brno
- Czech Republic
| | - Fabrizio Creazzo
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environment
- UMR8587 (CHARMMMAT)
- Université d'Evry val d'Essone
- 91025 Evry
- France
| | - Paolo V. Giaquinta
- Università degli Studi di Messina
- Dipartimento di Scienze Matematiche e Informatiche
- Scienze Fisiche e Scienze della Terra
- 98166 Messina
- Italy
| | | | - A. Marco Saitta
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie
- 75005 Paris
- France
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140
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Natarajan SK, Behler J. Neural network molecular dynamics simulations of solid–liquid interfaces: water at low-index copper surfaces. Phys Chem Chem Phys 2016; 18:28704-28725. [DOI: 10.1039/c6cp05711j] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulation of the water–copper interface have been carried out using high-dimensional neural network potential based on density functional theory.
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Affiliation(s)
| | - Jörg Behler
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- D-44780 Bochum
- Germany
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141
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Partanen L, Murdachaew G, Gerber RB, Halonen L. Temperature and collision energy effects on dissociation of hydrochloric acid on water surfaces. Phys Chem Chem Phys 2016; 18:13432-42. [DOI: 10.1039/c6cp00597g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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142
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Krueger RA, Vilčiauskas L, Melchior JP, Bester G, Kreuer KD. Mechanism of Efficient Proton Conduction in Diphosphoric Acid Elucidated via First-Principles Simulation and NMR. J Phys Chem B 2015; 119:15866-75. [DOI: 10.1021/acs.jpcb.5b09684] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rachel A. Krueger
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Linas Vilčiauskas
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Department
of Chemical Engineering, University of Texas, Austin, Texas 78712, United States
| | - Jan-Patrick Melchior
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
| | - Gabriel Bester
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
- Department
of Chemistry, University of Hamburg, D-20146 Hamburg, Germany
| | - Klaus-Dieter Kreuer
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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143
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Del Ben M, Hutter J, VandeVondele J. Probing the structural and dynamical properties of liquid water with models including non-local electron correlation. J Chem Phys 2015; 143:054506. [PMID: 26254660 DOI: 10.1063/1.4927325] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.
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Affiliation(s)
- Mauro Del Ben
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Joost VandeVondele
- Department of Materials, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich, Switzerland
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144
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Ikeda T, Boero M. Role of van der Waals corrections in first principles simulations of alkali metal ions in aqueous solutions. J Chem Phys 2015; 143:194510. [DOI: 10.1063/1.4935932] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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145
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Titantah JT, Karttunen M. Hydrophobicity: effect of density and order on water's rotational slowing down. SOFT MATTER 2015; 11:7977-7985. [PMID: 26327528 DOI: 10.1039/c5sm00930h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ab initio molecular dynamics (AIMD) simulations of over 4.5 ns were performed in the temperature range of T = 260-350 K with van der Waals corrections to investigate the relationship between local water density and tetrahedral order in bulk water and in the presence of a hydrophobe, tetramethylurea (TMU). We demonstrate that in bulk water, defects consisting of 5- and higher coordinated water are a major contributor to dynamics. Close to a hydrophobe, 3-coordinated defects take over. The co-existence of these defects gives rise to very different local densities. We propose that the slowing down of rotational motion close to a hydrophobe is induced by an interplay between density and order with the slowing down decreasing in the following order: (i) low-density ordered-water, (ii) normal-density ordered-water, (iii) high-density ordered-water and (iv) disordered-water. The proportions of these water environments vary with temperature. These local environments also support the idea of water's polymorphism, i.e., the existence of the high- and low-density states in supercooled water.
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Affiliation(s)
- John Tatini Titantah
- Department of Applied Mathematics, University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
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146
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Ohto T, Usui K, Hasegawa T, Bonn M, Nagata Y. Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function. J Chem Phys 2015; 143:124702. [DOI: 10.1063/1.4931106] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tatsuhiko Ohto
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kota Usui
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Taisuke Hasegawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
| | - Mischa Bonn
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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147
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Ojha D, Chandra A. Ultrafast Vibrational Echo Spectroscopy of Liquid Water from First-Principles Simulations. J Phys Chem B 2015; 119:11215-28. [PMID: 26161933 DOI: 10.1021/acs.jpcb.5b03109] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vibrational echo spectroscopy has become a powerful technique to study vibrational spectral diffusion in water and aqueous solutions. The dynamics of vibrational spectral diffusion is intimately related to the hydrogen bond fluctuations in liquid water and other hydrogen bonded liquids. Earlier theoretical calculations of vibrational echo spectroscopy of aqueous systems were based on classical molecular dynamics simulations involving empirical force fields of water. In the current work, we have employed the method of ab initio molecular dynamics simulation to calculate the spectral observables of vibrational echo and two-dimensional infrared (2D-IR) spectroscopy of liquid water at room temperature under Condon and cumulant approximations. The time scales extracted from the temporal decay of the frequency-time correlation function (FTCF), short-time slope of three pulse photon echo (SP3E), dynamic line width (DLW), and the slope of nodal line of 2D-IR spectra are found to be in reasonably close agreement with each other which reinforces the assertion that signatures of FTCF can be captured using three pulse photon echo and 2D-IR spectroscopy.
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Affiliation(s)
- Deepak Ojha
- Department of Chemistry, Indian Institute of Technology , Kanpur, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology , Kanpur, India 208016
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148
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Golze D, Hutter J, Iannuzzi M. Wetting of water on hexagonal boron nitride@Rh(111): a QM/MM model based on atomic charges derived for nano-structured substrates. Phys Chem Chem Phys 2015; 17:14307-16. [PMID: 25430062 DOI: 10.1039/c4cp04638b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The wetting of water on corrugated and flat hexagonal boron nitride (h-BN) monolayers on Rh(111) is studied within a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. Water is treated by QM methods, whereas the interactions between liquid and substrate are described at the MM level. The electrostatic properties of the substrate are reproduced by assigning specifically generated partial charges to each MM atom. We propose a method to determine restrained electrostatic potential (RESP) charges that can be applied to periodic systems. Our approach is based on the Gaussian and plane waves algorithm and allows an easy tuning of charges for nano-structured substrates. We have successfully applied it to reproduce the electrostatic potential of the corrugated and flat h-BN/Rh(111) known as nanomesh. Molecular dynamics simulations of water films in contact with these substrates are performed and structural and dynamic properties of the interfaces are analyzed. Based on this analysis and on the interaction energies between water film and substrate, we found that the corrugated nanomesh is slightly more hydrophilic. On a macroscopic scale, we expect a smaller contact angle for a droplet on the corrugated surface.
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Affiliation(s)
- Dorothea Golze
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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149
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Usui K, Hunger J, Sulpizi M, Ohto T, Bonn M, Nagata Y. Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution. J Phys Chem B 2015; 119:10597-606. [DOI: 10.1021/acs.jpcb.5b02579] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kota Usui
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Marialore Sulpizi
- Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz, Germany
| | - Tatsuhiko Ohto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
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150
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Yadav VK, Chandra A. First-Principles Simulation Study of Vibrational Spectral Diffusion and Hydrogen Bond Fluctuations in Aqueous Solution of N-Methylacetamide. J Phys Chem B 2015; 119:9858-67. [DOI: 10.1021/acs.jpcb.5b03836] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vivek Kumar Yadav
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
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