1
|
Ono J, Matsumura Y, Mori T, Saito S. Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events. J Phys Chem B 2024; 128:20-32. [PMID: 38133567 DOI: 10.1021/acs.jpcb.3c05307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Proteins exhibit conformational fluctuations and changes over various time scales, ranging from rapid picosecond-scale local atomic motions to slower microsecond-scale global conformational transformations. In the presence of these intricate fluctuations, chemical reactions occur and functions emerge. These conformational fluctuations of proteins are not merely stochastic random motions but possess distinct spatiotemporal characteristics. Moreover, chemical reactions do not always proceed along a single reaction coordinate in a quasi-equilibrium manner. Therefore, it is essential to understand spatiotemporal conformational fluctuations of proteins and the conformational change processes associated with reactions. In this Perspective, we shed light on the complex dynamics of proteins and their role in enzyme catalysis by presenting recent results regarding dynamic couplings and disorder in the conformational dynamics of proteins and rare but rapid enzymatic reaction events obtained from molecular dynamics simulations.
Collapse
Affiliation(s)
- Junichi Ono
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Yoshihiro Matsumura
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Toshifumi Mori
- Institute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - Shinji Saito
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585, Japan
| |
Collapse
|
2
|
Takahashi H, Tanimura Y. Discretized hierarchical equations of motion in mixed Liouville-Wigner space for two-dimensional vibrational spectroscopies of liquid water. J Chem Phys 2023; 158:044115. [PMID: 36725520 DOI: 10.1063/5.0135725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A model of a bulk water system describing the vibrational motion of intramolecular and intermolecular modes is constructed, enabling analysis of its linear and nonlinear vibrational spectra as well as the energy transfer processes between the vibrational modes. The model is described as a system of four interacting anharmonic oscillators nonlinearly coupled to their respective heat baths. To perform a rigorous numerical investigation of the non-Markovian and nonperturbative quantum dissipative dynamics of the model, we derive discretized hierarchical equations of motion in mixed Liouville-Wigner space, with Lagrange-Hermite mesh discretization being employed in the Liouville space of the intramolecular modes and Lagrange-Hermite mesh discretization and Hermite discretization in the Wigner space of the intermolecular modes. One-dimensional infrared and Raman spectra and two-dimensional terahertz-infrared-visible and infrared-infrared-Raman spectra are computed as demonstrations of the quantum dissipative description provided by our model.
Collapse
Affiliation(s)
- Hideaki Takahashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| |
Collapse
|
3
|
Ariga K. Liquid Interfacial Nanoarchitectonics: Molecular Machines, Organic Semiconductors, Nanocarbons, Stem Cells, and Others. Curr Opin Colloid Interface Sci 2022. [DOI: 10.1016/j.cocis.2022.101656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
4
|
Jung KA, Markland TE. 2D spectroscopies from condensed phase dynamics: Accessing third-order response properties from equilibrium multi-time correlation functions. J Chem Phys 2022; 157:094111. [DOI: 10.1063/5.0107087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The third-order response lies at the heart of simulating and interpreting nonlinear spectroscopies ranging from two dimensional infrared (2D-IR) to 2D electronic (2D-ES), and 2D sum frequency generation (2D-SFG). The extra time and frequency dimensions in these spectroscopies provides access to rich information on the electronic and vibrational states present, the coupling between them, and the resulting rates at which they exchange energy that are obscured in linear spectroscopy, particularly for condensed phase systems that usually contain many overlapping features. While the exact quantum expression for the third-order response is well established it is incompatible with the methods that are practical for calculating the atomistic dynamics of large condensed phase systems. These methods, which include both classical mechanics and quantum dynamics methods that retain quantum statistical properties while obeying the symmetries of classical dynamics, such as LSC-IVR, Centroid Molecular Dynamics (CMD) and Ring Polymer Molecular Dynamics (RPMD) naturally provide short-time approximations to the multi-time symmetrized Kubo transformed correlation function. Here, we show how the third-order response can be formulated in terms of equilibrium symmetrized Kubo transformed correlation functions. We demonstrate the utility and accuracy of our approach by showing how it can be used to obtain the third-order response of a series of model systems using both classical dynamics and RPMD. In particular, we show that this approach captures features such as anharmonically induced vertical splittings and peak shifts while providing a physically transparent framework for understanding multidimensional spectroscopies.
Collapse
|
5
|
Mousavi SJ, Berger A, Hamm P, Shalit A. Low-frequency anharmonic couplings in bromoform revealed from 2D Raman-THz spectroscopy: from the liquid to the crystalline phase. J Chem Phys 2022; 156:174501. [DOI: 10.1063/5.0090520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Two-dimensional (2D) Raman-THz spectroscopy in the frequency up to 7 THz has been applied to study the crystalline beta-phase of bromoform (CHBr3). As for liquid CHBr3, cross peaks are observed, which however sharpen up in the crystalline sample and split into assignable sub-contributions. In the Raman dimension, the frequency positions of these cross peaks coincide with the intramolecular bending modes of the CHBr3 molecules, and in the THz dimension with the IR active lattice modes of the crystal. This work expands the applicability of this new 2D spectroscopic technique to solid samples at cryogenic temperatures. Furthermore, it provides new experimental evidence that the cross peaks indeed originate from the coupling between intra- and intermolecular vibrational modes.
Collapse
Affiliation(s)
| | - Arian Berger
- Physikalisch-Chemisches Institut, Universitaet Zuerich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Switzerland
| | | |
Collapse
|
6
|
Begušić T, Tao X, Blake GA, Miller TF. Equilibrium-nonequilibrium ring-polymer molecular dynamics for nonlinear spectroscopy. J Chem Phys 2022; 156:131102. [PMID: 35395895 DOI: 10.1063/5.0087156] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Two-dimensional Raman and hybrid terahertz-Raman spectroscopic techniques provide invaluable insight into molecular structures and dynamics of condensed-phase systems. However, corroborating experimental results with theory is difficult due to the high computational cost of incorporating quantum-mechanical effects in the simulations. Here, we present the equilibrium-nonequilibrium ring-polymer molecular dynamics (RPMD), a practical computational method that can account for nuclear quantum effects on the two-time response function of nonlinear optical spectroscopy. Unlike a recently developed approach based on the double Kubo transformed (DKT) correlation function, our method is exact in the classical limit, where it reduces to the established equilibrium-nonequilibrium classical molecular dynamics method. Using benchmark model calculations, we demonstrate the advantages of the equilibrium-nonequilibrium RPMD over classical and DKT-based approaches. Importantly, its derivation, which is based on the nonequilibrium RPMD, obviates the need for identifying an appropriate Kubo transformed correlation function and paves the way for applying real-time path-integral techniques to multidimensional spectroscopy.
Collapse
Affiliation(s)
- Tomislav Begušić
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Geoffrey A Blake
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|
7
|
Joonaki E, Hassanpouryouzband A, Heldt CL, Areo O. Surface Chemistry Can Unlock Drivers of Surface Stability of SARS-CoV-2 in a Variety of Environmental Conditions. Chem 2020; 6:2135-2146. [PMID: 32838053 PMCID: PMC7409833 DOI: 10.1016/j.chempr.2020.08.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The surface stability and resulting transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), specifically in indoor environments, have been identified as a potential pandemic challenge requiring investigation. This novel virus can be found on various surfaces in contaminated sites such as clinical places; however, the behavior and molecular interactions of the virus with respect to the surfaces are poorly understood. Regarding this, the virus adsorption onto solid surfaces can play a critical role in transmission and survival in various environments. In this article, we first give an overview of existing knowledge concerning viral spread, molecular structure of SARS-CoV-2, and the virus surface stability is presented. Then, we highlight potential drivers of the SARS-CoV-2 surface adsorption and stability in various environmental conditions. This theoretical analysis shows that different surface and environmental conditions including temperature, humidity, and pH are crucial considerations in building fundamental understanding of the virus transmission and thereby improving safety practices.
Collapse
Affiliation(s)
- Edris Joonaki
- TÜV SÜD UK National Engineering Laboratory, Scottish Enterprise Technology Park, East Kilbride, South Lanarkshire, G75 0QF, United Kingdom
| | - Aliakbar Hassanpouryouzband
- School of Geosciences, University of Edinburgh, King's Buildings, West Main Road, Edinburgh, EH9 3JW, United Kingdom
| | - Caryn L Heldt
- Health Research Institute, Michigan Technological University, Houghton, MI 49931, USA
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI 49931, USA
| | - Oluwatoyin Areo
- Health Research Institute, Michigan Technological University, Houghton, MI 49931, USA
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI 49931, USA
| |
Collapse
|
8
|
Sidler D, Hamm P. A Feynman diagram description of the 2D-Raman-THz response of amorphous ice. J Chem Phys 2020; 153:044502. [PMID: 32752676 DOI: 10.1063/5.0018485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 2D-Raman-THz response in all possible time-orderings (Raman-THz-THz, THz-Raman-THz, and THz-THz-Raman) of amorphous water ice is calculated in two ways: from atomistic molecular dynamics simulations and with the help of a Feynman diagram model, the latter of which power-expands the potential energy surface and the dipole and polarizability surfaces up to leading order. Comparing both results allows one to dissect the 2D-Raman-THz response into contributions from mechanical anharmonicity, as well as electrical dipole and polarizability anharmonicities. Mechanical anharmonicity dominates the 2D-Raman-THz response of the hydrogen-bond stretching and hydrogen-bond bending bands of water, and dipole anharmonicity dominates that of the librational band, while the contribution of polarizability anharmonicity is comparably weak. A distinct echo of the hydrogen-bond stretching band is observed for the THz-Raman-THz pulse sequence, again dominated by mechanical anharmonicity. A peculiar mechanism is discussed, which is based on the coupling between the many normal modes within the hydrogen-bond stretching band and which will inevitably generate such an echo for an amorphous structure.
Collapse
Affiliation(s)
- David Sidler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
9
|
Two-dimensional infrared spectroscopy of aqueous solutions from first principles simulations. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
10
|
Sun X. Hybrid equilibrium-nonequilibrium molecular dynamics approach for two-dimensional solute-pump/solvent-probe spectroscopy. J Chem Phys 2019; 151:194507. [DOI: 10.1063/1.5130926] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Xiang Sun
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China; Department of Chemistry, New York University, New York, New York 10003, USA; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China; and State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| |
Collapse
|
11
|
Jansen TLC, Saito S, Jeon J, Cho M. Theory of coherent two-dimensional vibrational spectroscopy. J Chem Phys 2019; 150:100901. [DOI: 10.1063/1.5083966] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas la Cour Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Jonggu Jeon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| |
Collapse
|
12
|
Imoto S, Marx D. Pressure response of the THz spectrum of bulk liquid water revealed by intermolecular instantaneous normal mode analysis. J Chem Phys 2019; 150:084502. [PMID: 30823759 DOI: 10.1063/1.5080381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The radial distribution functions of liquid water are known to change significantly their shape upon hydrostatic compression from ambient conditions deep into the kbar pressure regime. It has been shown that despite their eye-catching changes, the fundamental locally tetrahedral fourfold H-bonding pattern that characterizes ambient water is preserved up to about 10 kbar (1 GPa), which is the stability limit of liquid water at 300 K. The observed increase in coordination number comes from pushing water molecules into the first coordination sphere without establishing an H-bond, resulting in roughly two such additional interstitial molecules at 10 kbar. THz spectroscopy has been firmly established as a powerful experimental technique to analyze H-bonding in aqueous solutions given that it directly probes the far-infrared lineshape and thus the prominent H-bond network mode around 180 cm-1. We, therefore, set out to assess pressure effects on the THz response of liquid water at 10 kbar in comparison to the 1 bar (0.1 MPa) reference, both at 300 K, with the aim to trace back the related lineshape changes to the structural level. To this end, we employ the instantaneous normal mode approximation to rigorously separate the H-bonding peak from the large background arising from the pronounced librational tail. By exactly decomposing the total molecular dynamics into hindered translations, hindered rotations, and intramolecular vibrations, we find that the H-bonding peak arises from translation-translation and translation-rotation correlations, which are successively decomposed down to the level of distinct local H-bond environments. Our utmost detailed analysis based on molecular pair classifications unveils that H-bonded double-donor water pairs contribute most to the THz response around 180 cm-1, whereas interstitial waters are negligible. Moreover, short double-donor H-bonds have their peak maximum significantly shifted toward higher frequencies with respect to such long H-bonds. In conjunction with an increasing relative population of these short H-bonds versus the long ones (while the population of other water pair classes is essentially pressure insensitive), this explains not only the blue-shift of the H-bonding peak by about 20-30 cm-1 in total from 1 bar to 10 kbar but also the filling of the shallow local minimum of the THz lineshape located in between the network peak and the red-wing of the librational band at 1 bar. Based on the changing populations as a function of pressure, we are also able to roughly estimate the pressure-dependence of the H-bond network mode and find that its pressure response and thus the blue-shifting are most pronounced at low kbar pressures.
Collapse
Affiliation(s)
- Sho Imoto
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| |
Collapse
|
13
|
Jung KA, Videla PE, Batista VS. Inclusion of nuclear quantum effects for simulations of nonlinear spectroscopy. J Chem Phys 2018; 148:244105. [PMID: 29960352 DOI: 10.1063/1.5036768] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The computation and interpretation of nonlinear vibrational spectroscopy is of vital importance for understanding a wide range of dynamical processes in molecular systems. Here, we introduce an approach to evaluate multi-time response functions in terms of multi-time double symmetrized Kubo transformed thermal correlation functions. Furthermore, we introduce a multi-time extension of ring polymer molecular dynamics to evaluate these Kubo transforms. Benchmark calculations show that the approximations are useful for short times even for nonlinear operators, providing a consistent improvement over classical simulations of multi-time correlation functions. The introduced methodology thus provides a practical way of including nuclear quantum effects in multi-time response functions of non-linear optical spectroscopy.
Collapse
Affiliation(s)
- Kenneth A Jung
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
| | - Pablo E Videla
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
| |
Collapse
|
14
|
Carpenter WB, Fournier JA, Biswas R, Voth GA, Tokmakoff A. Delocalization and stretch-bend mixing of the HOH bend in liquid water. J Chem Phys 2018; 147:084503. [PMID: 28863511 DOI: 10.1063/1.4987153] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Liquid water's rich sub-picosecond vibrational dynamics arise from the interplay of different high- and low-frequency modes evolving in a strong yet fluctuating hydrogen bond network. Recent studies of the OH stretching excitations of H2O indicate that they are delocalized over several molecules, raising questions about whether the bending vibrations are similarly delocalized. In this paper, we take advantage of an improved 50 fs time-resolution and broadband infrared (IR) spectroscopy to interrogate the 2D IR lineshape and spectral dynamics of the HOH bending vibration of liquid H2O. Indications of strong bend-stretch coupling are observed in early time 2D IR spectra through a broad excited state absorption that extends from 1500 cm-1 to beyond 1900 cm-1, which corresponds to transitions from the bend to the bend overtone and OH stretching band between 3150 and 3550 cm-1. Pump-probe measurements reveal a fast 180 fs vibrational relaxation time, which results in a hot-ground state spectrum that is the same as observed for water IR excitation at any other frequency. The fastest dynamical time scale is 80 fs for the polarization anisotropy decay, providing evidence for the delocalized or excitonic character of the bend. Normal mode analysis conducted on water clusters extracted from molecular dynamics simulations corroborate significant stretch-bend mixing and indicate delocalization of δHOH on 2-7 water molecules.
Collapse
Affiliation(s)
- William B Carpenter
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph A Fournier
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rajib Biswas
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| |
Collapse
|
15
|
Perakis F, Camisasca G, Lane TJ, Späh A, Wikfeldt KT, Sellberg JA, Lehmkühler F, Pathak H, Kim KH, Amann-Winkel K, Schreck S, Song S, Sato T, Sikorski M, Eilert A, McQueen T, Ogasawara H, Nordlund D, Roseker W, Koralek J, Nelson S, Hart P, Alonso-Mori R, Feng Y, Zhu D, Robert A, Grübel G, Pettersson LGM, Nilsson A. Coherent X-rays reveal the influence of cage effects on ultrafast water dynamics. Nat Commun 2018; 9:1917. [PMID: 29765052 PMCID: PMC5953967 DOI: 10.1038/s41467-018-04330-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/19/2018] [Indexed: 11/13/2022] Open
Abstract
The dynamics of liquid water feature a variety of time scales, ranging from extremely fast ballistic-like thermal motion, to slower molecular diffusion and hydrogen-bond rearrangements. Here, we utilize coherent X-ray pulses to investigate the sub-100 fs equilibrium dynamics of water from ambient conditions down to supercooled temperatures. This novel approach utilizes the inherent capability of X-ray speckle visibility spectroscopy to measure equilibrium intermolecular dynamics with lengthscale selectivity, by measuring oxygen motion in momentum space. The observed decay of the speckle contrast at the first diffraction peak, which reflects tetrahedral coordination, is attributed to motion on a molecular scale within the first 120 fs. Through comparison with molecular dynamics simulations, we conclude that the slowing down upon cooling from 328 K down to 253 K is not due to simple thermal ballistic-like motion, but that cage effects play an important role even on timescales over 25 fs due to hydrogen-bonding.
Collapse
Affiliation(s)
- Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden.
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA.
| | - Gaia Camisasca
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden
| | - Thomas J Lane
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Alexander Späh
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden
| | - Kjartan Thor Wikfeldt
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden
| | - Jonas A Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, S-10691, Stockholm, Sweden
| | - Felix Lehmkühler
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Harshad Pathak
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden
| | - Kyung Hwan Kim
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden
| | - Katrin Amann-Winkel
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden
| | - Simon Schreck
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden
| | - Sanghoon Song
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Takahiro Sato
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Marcin Sikorski
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Andre Eilert
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Trevor McQueen
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Hirohito Ogasawara
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Dennis Nordlund
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Wojciech Roseker
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jake Koralek
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Philip Hart
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Yiping Feng
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Diling Zhu
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Aymeric Robert
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, CA, 94025, USA
| | - Gerhard Grübel
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lars G M Pettersson
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden
| | - Anders Nilsson
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91, Stockholm, Sweden.
| |
Collapse
|
16
|
Ojha D, Henao A, Kühne TD. Nuclear quantum effects on the vibrational dynamics of liquid water. J Chem Phys 2018; 148:102328. [PMID: 29544291 DOI: 10.1063/1.5005500] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Based on quantum-mechanical path-integral molecular dynamics simulations, the impact of nuclear quantum effects on the vibrational and hydrogen bond dynamics in liquid water is investigated. The instantaneous fluctuations in the frequencies of the O-H stretch modes are calculated using the wavelet method of time-series analysis, while the time scales of the vibrational spectral diffusion are determined from frequency-time correlation functions, joint probability distributions, and the slope of three-pulse photon echo. We find that the inclusion of nuclear quantum effects leads not only to a redshift of the vibrational frequency distribution by around 130 cm-1 but also to an acceleration of the vibrational dynamics by as much as 30%. In addition, quantum fluctuations also entail a significantly faster decay of correlation in the initial diffusive regime, which is in agreement with recent vibrational echo experiments.
Collapse
Affiliation(s)
- Deepak Ojha
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Andrés Henao
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| |
Collapse
|
17
|
|
18
|
Joutsuka T, Morita A. Efficient Computation of Difference Vibrational Spectra in Isothermal–Isobaric Ensemble. J Phys Chem B 2016; 120:11229-11238. [DOI: 10.1021/acs.jpcb.6b07121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tatsuya Joutsuka
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Akihiro Morita
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
- Elements
Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Ito H, Hasegawa T, Tanimura Y. Calculating two-dimensional THz-Raman-THz and Raman-THz-THz signals for various molecular liquids: The samplers. J Chem Phys 2014; 141:124503. [PMID: 25273447 DOI: 10.1063/1.4895908] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hironobu Ito
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
| | - Taisuke Hasegawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
- Department of Physics, University of Hamburg, Centre for Free Electron Laser Science, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
| |
Collapse
|
21
|
Jeon J, Cho M. An Accurate Classical Simulation of a Two-Dimensional Vibrational Spectrum: OD Stretch Spectrum of a Hydrated HOD Molecule. J Phys Chem B 2014; 118:8148-61. [DOI: 10.1021/jp501182d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonggu Jeon
- Department
of Chemistry, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 136-701, Korea
| |
Collapse
|
22
|
Imoto S, Xantheas SS, Saito S. Ultrafast dynamics of liquid water: frequency fluctuations of the OH stretch and the HOH bend. J Chem Phys 2014; 139:044503. [PMID: 23901989 DOI: 10.1063/1.4813071] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Frequency fluctuations of the OH stretch and the HOH bend in liquid water are reported from the third-order response function evaluated using the TTM3-F potential for water. The simulated two-dimensional infrared spectra of the OH stretch are similar to previously reported theoretical results. The present study suggests that the frequency fluctuation of the HOH bend is faster than that of the OH stretch. The ultrafast loss of the frequency correlation of the HOH bend is due to the strong couplings with the OH stretch as well as the intermolecular hydrogen bond bend.
Collapse
Affiliation(s)
- Sho Imoto
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | | | | |
Collapse
|
23
|
Chen YC, Tang PH, Wu TM. Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view. J Chem Phys 2013; 139:204505. [PMID: 24289362 DOI: 10.1063/1.4829679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.
Collapse
Affiliation(s)
- Yu-Chun Chen
- Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan
| | | | | |
Collapse
|
24
|
Perakis F, Borek JA, Hamm P. Three-dimensional infrared spectroscopy of isotope-diluted ice Ih. J Chem Phys 2013; 139:014501. [DOI: 10.1063/1.4812216] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
25
|
Costard R, Elsaesser T. Femtosecond OH Bending Dynamics of Water Nanopools Confined In Reverse Micelles. J Phys Chem B 2013; 117:15338-45. [DOI: 10.1021/jp403559d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Str. 2 a,
D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Str. 2 a,
D-12489 Berlin, Germany
| |
Collapse
|
26
|
Yagasaki T, Saito S. Fluctuations and Relaxation Dynamics of Liquid Water Revealed by Linear and Nonlinear Spectroscopy. Annu Rev Phys Chem 2013; 64:55-75. [DOI: 10.1146/annurev-physchem-040412-110150] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many efforts have been devoted to elucidating the intra- and intermolecular dynamics of liquid water because of their important roles in many fields of science and engineering. Nonlinear spectroscopy is a powerful tool to investigate the dynamics. Because nonlinear response functions are described by more than one time variable, it is possible to analyze static and dynamic mode couplings. Here we review the intra- and intermolecular dynamics of liquid water revealed by recent linear and nonlinear spectroscopic experiments and computer simulations. In particular, we discuss the population relaxation, anisotropy decay, and spectral diffusion of the intra- and intermolecular motions of water and their temperature dependence, which play important roles in ultrafast dynamics and relaxations in water.
Collapse
Affiliation(s)
- Takuma Yagasaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, and
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, and
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| |
Collapse
|
27
|
Kim K, Saito S. Multiple length and time scales of dynamic heterogeneities in model glass-forming liquids: A systematic analysis of multi-point and multi-time correlations. J Chem Phys 2013; 138:12A506. [DOI: 10.1063/1.4769256] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
28
|
Ono J, Ando K. Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets. J Chem Phys 2012; 137:174503. [DOI: 10.1063/1.4762840] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
29
|
Kozai T, Yamashita S, Hirochi K, Miyagawa H, Tsurumachi N, Koshiba S, Nakanishi S, Itoh H. Molecular vibrational dynamics in polyvinyl alcohol studied by femtosecond coherent anti-stokes Raman spectroscopy. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.09.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
30
|
Qvist J, Mattea C, Sunde EP, Halle B. Rotational dynamics in supercooled water from nuclear spin relaxation and molecular simulations. J Chem Phys 2012; 136:204505. [DOI: 10.1063/1.4720941] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
|
31
|
Hamm P, Savolainen J. Two-dimensional-Raman-terahertz spectroscopy of water: Theory. J Chem Phys 2012; 136:094516. [DOI: 10.1063/1.3691601] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
32
|
Yang M, Skinner JL. Time-averaging approximation in the interaction picture: absorption line shapes for coupled chromophores with application to liquid water. J Chem Phys 2012; 135:154114. [PMID: 22029304 DOI: 10.1063/1.3654005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The time-averaging approximation (TAA), originally developed to calculate vibrational line shapes for coupled chromophores using mixed quantum/classical methods, is reformulated. In the original version of the theory, time averaging was performed for the full one-exciton Hamiltonian, while herein the time averaging is performed on the coupling (off-diagonal) Hamiltonian in the interaction picture. As a result, the influence of the dynamic fluctuations of the transition energies is more accurately described. We compare numerical results of the two versions of the TAA with numerically exact results for the vibrational absorption line shape of the OH stretching modes in neat water. It is shown that the TAA in the interaction picture yields theoretical line shapes that are in better agreement with exact results.
Collapse
Affiliation(s)
- Mino Yang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea.
| | | |
Collapse
|
33
|
Ye S, Ma S, Wei F, Li H. Intramolecular vibrational coupling in water molecules revealed by compatible multiple nonlinear vibrational spectroscopic measurements. Analyst 2012; 137:4981-7. [DOI: 10.1039/c2an35684h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
34
|
Yagasaki T, Saito S. Energy relaxation of intermolecular motions in supercooled water and ice: A molecular dynamics study. J Chem Phys 2011; 135:244511. [DOI: 10.1063/1.3671993] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
35
|
Yagasaki T, Saito S. A novel method for analyzing energy relaxation in condensed phases using nonequilibrium molecular dynamics simulations: Application to the energy relaxation of intermolecular motions in liquid water. J Chem Phys 2011; 134:184503. [DOI: 10.1063/1.3587105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
36
|
Garrett-Roe S, Perakis F, Rao F, Hamm P. Three-dimensional infrared spectroscopy of isotope-substituted liquid water reveals heterogeneous dynamics. J Phys Chem B 2011; 115:6976-84. [PMID: 21561076 DOI: 10.1021/jp201989s] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The dynamics of the hydrogen bond network of isotopically substituted liquid water are investigated with a new ultrafast nonlinear vibrational spectroscopy, three-dimensional infrared spectroscopy (3D-IR). The 3D-IR spectroscopy is sensitive to three-point frequency fluctuation correlation functions, and the measurements reveal heterogeneous structural relaxation dynamics. We interpret these results as subensembles of water which do not interconvert on a half picosecond time scale. We connect the experimental results to molecular dynamics (MD) simulations, performing a line shape analysis as well as complex network analysis.
Collapse
Affiliation(s)
- Sean Garrett-Roe
- Institute of Physical Chemistry, University of Zurich, Zurich, Switzerland
| | | | | | | |
Collapse
|
37
|
Qvist J, Schober H, Halle B. Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations. J Chem Phys 2011; 134:144508. [DOI: 10.1063/1.3578472] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
38
|
Hasegawa T, Tanimura Y. A Polarizable Water Model for Intramolecular and Intermolecular Vibrational Spectroscopies. J Phys Chem B 2011; 115:5545-53. [DOI: 10.1021/jp111308f] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Taisuke Hasegawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| |
Collapse
|
39
|
Sakurai A, Tanimura Y. Does ℏ Play a Role in Multidimensional Spectroscopy? Reduced Hierarchy Equations of Motion Approach to Molecular Vibrations. J Phys Chem A 2011; 115:4009-22. [DOI: 10.1021/jp1095618] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Atsunori Sakurai
- Department of Chemistry, Graduate School of Science, Kyoto Universiy, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto Universiy, Kyoto 606-8502, Japan
| |
Collapse
|
40
|
Hattori T. Classical theory of two-dimensional time-domain terahertz spectroscopy. J Chem Phys 2010; 133:204503. [DOI: 10.1063/1.3507256] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
|
41
|
Yagasaki T, Saito S, Ohmine I. Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study. J Phys Chem A 2010; 114:12573-84. [PMID: 21077653 DOI: 10.1021/jp1084795] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.
Collapse
Affiliation(s)
- Takuma Yagasaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | | | | |
Collapse
|
42
|
Efremenko I, Poverenov E, Martin JML, Milstein D. DFT Study of the Structure and Reactivity of the Terminal Pt(IV)-Oxo Complex Bearing No Electron-Withdrawing Ligands. J Am Chem Soc 2010; 132:14886-900. [DOI: 10.1021/ja105197x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Irena Efremenko
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76000, Israel
| | - Elena Poverenov
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76000, Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76000, Israel
| | - David Milstein
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76000, Israel
| |
Collapse
|
43
|
Kim K, Saito S. Multi-time density correlation functions in glass-forming liquids: Probing dynamical heterogeneity and its lifetime. J Chem Phys 2010; 133:044511. [DOI: 10.1063/1.3464331] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
|
44
|
Nagata Y, Mukamel S. Vibrational sum-frequency generation spectroscopy at the water/lipid interface: molecular dynamics simulation study. J Am Chem Soc 2010; 132:6434-42. [PMID: 20394423 PMCID: PMC3151577 DOI: 10.1021/ja100508n] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sum-frequency generation (SFG) spectrum from the water/[1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine] (DMPC) interface in the OH stretching mode region of water is simulated and shows three spectral peaks which are assigned to different environments. The weak 3590 cm(-1) peak is attributed to a few water molecules coupled to the glycerol backbone of DMCP. The 3470 cm(-1) feature comes from the top water layer adjacent to the hydrophilic headgroup of DMPC. The 3290 cm(-1) peak arises from the near-bulk water nonadjacent to DMPC. The stretching mode corresponding to the 3290 cm(-1) peak is strongly coupled to the neighboring water molecules. In contrast, the 3470 cm(-1) mode is decoupled from the surrounding water molecules, and the orientation of water is governed by DMPC. This decoupling explains the slow relaxation dynamics of water measured in the time-resolved SFG experiment. Despite the similarity of the SFG spectra, the peak origins of water/lipid and water/vapor interfaces are different.
Collapse
Affiliation(s)
- Yuki Nagata
- University of California Irvine, Irvine, California, 92617, USA
| | - Shaul Mukamel
- University of California Irvine, Irvine, California, 92617, USA
| |
Collapse
|
45
|
Yagasaki T, Ono J, Saito S. Ultrafast energy relaxation and anisotropy decay of the librational motion in liquid water: A molecular dynamics study. J Chem Phys 2009; 131:164511. [DOI: 10.1063/1.3254518] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
|