Journal ArticleDOI
Collective solvent coordinates for the infrared spectrum of HOD in D2O based on an ab initio electrostatic map.
TLDR
A collective coordinate response for the solvent effect is constructed by identifying the main electrostatic field and gradient components contributing to the line shape, which allows a realistic stochastic Liouville equation simulation of the line shapes which is not restricted to Gaussian frequency fluctuations.Abstract:
An ab initio MP2 vibrational Hamiltonian of HOD in an external electrostatic potential parametrized by the electric field and its gradient-tensor is constructed. By combining it with the fluctuating electric field induced by the D2O solvent obtained from molecular dynamics simulations, we calculate the infrared absorption of the O-H stretch. The resulting solvent shift and infrared line shape for three force fields (TIP4P, SPC/E, and SW) are in good agreement with the experiment. A collective coordinate response for the solvent effect is constructed by identifying the main electrostatic field and gradient components contributing to the line shape. This allows a realistic stochastic Liouville equation simulation of the line shapes which is not restricted to Gaussian frequency fluctuations.read more
Citations
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Journal ArticleDOI
Coherent Two-Dimensional Optical Spectroscopy
TL;DR: Although the optical analogs of 2D NMR do not provide an atomic resolution structure of complex molecules, optical domain multi-dimensional spectroscopy has certain advantages because of the dramatic gain in time resolution possible and the ability to directly observe and quantify the couplings between quantum states involved in molecular dynamical processes.
Journal ArticleDOI
Vibrational Spectroscopy as a Probe of Structure and Dynamics in Liquid Water
Huib J. Bakker,James L. Skinner +1 more
TL;DR: Water is, of course, a fascinating and important substance, but for such a simple molecule, its condensed phase properties are surprisingly complex: the many different solid phases, the higher density of the liquid as compared to ice Ih, and the density maximum in the liquid phase.
Journal ArticleDOI
Hydrogen bonding definitions and dynamics in liquid water.
TL;DR: A systematic procedure based on two-dimensional potentials of mean force for defining cutoffs for a given pair of distance and angular coordinates is developed and an electronic structure-based definition of hydrogen bonding in liquid water is developed, related to the electronic occupancy of the antibonding OH orbitals.
Journal ArticleDOI
IR and Raman spectra of liquid water: theory and interpretation.
B. M. Auer,James L. Skinner +1 more
TL;DR: The results demonstrate that the peak in the parallel-polarized Raman spectrum at about 3250 wavenumbers is collective in nature, and shows that while the coupling between chromophores is relatively modest, it nevertheless produces delocalization of the vibrational eigenstates over up to 12 Chromophores, which has a profound effect on the spectroscopy.
Journal ArticleDOI
Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule Perspectives
TL;DR: The chiral stationary phase for high-performance liquid chromatography shows good chiral recognition ability and can be synthesized by supramolecular chemistry techniques.
References
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Journal ArticleDOI
Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
Journal ArticleDOI
Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Journal ArticleDOI
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Journal ArticleDOI
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
TL;DR: In this article, the parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described, and the parameters for both torsional and non-bonded energy properties have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER force field.