The vibrational motion of molecules in dissipative environments, such as solvation and protein molecules, is composed of contributions from both intermolecular and intramolecular modes. The existence of these collective modes introduces difficulty into quantum simulations of chemical and biological processes. In order to describe the complex molecular motion of the environment in a simple manner, we introduce a system-bath model in which the intramolecular modes with anharmonic mode-mode couplings are described by a system Hamiltonian, while the other degrees of freedom, arising from the environmental molecules, are described by heat bath. Employing a machine-learning based approach, we determine not only the system parameters of the intramolecular modes but also the spectral distribution of the system-bath coupling to describe the intermolecular modes, using the atomic trajectories obtained from molecular dynamics (MD) simulations. The capabilities of the present approach are demonstrated for liquid water using MD trajectories calculated from the SPC/E model and the polarizable water model for intramolecular and intermolecular vibrational spectroscopies (POLI2VS) by determining the system parameters describing the symmetric-stretch, asymmetric-stretch and bend modes with intramolecular interactions and the bath spectral distribution functions for each intramolecular mode representing the interaction with the intra-molecular modes. From these results, we were able to elucidate the energy relaxation pathway between the intramolecular modes and the intermolecular modes in a non-intuitive manner.
Using depolarized light scattering, we have recently shown that structural relaxation in a broad range of supercooled liquids follows, to good approximation, a generic line shape with high-frequency power law $ω^{-1/2}$. We now continue this study by investigating a systematic series of polyalcohols (PAs), frequently used as model systems in glass-science, i.a., because the width of their respective dielectric loss spectra varies strongly along the series. Our results reveal that the microscopic origin of the observed relaxation behavior varies significantly between different PAs: While short-…
The breakdown of the direct relation between the density scaling exponent and the intermolecular interaction potential for molecular systems with purely repulsive intermolecular forces
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-Wig…
Structure of Liquid Nitromethane: Comparison of Simulation and Diffraction Studies
模拟（分子动力学和Car-Parrinello [Phys. Rev. Lett. 55，2471（1985）]）和衍射（X射线和中子）研究进行比较，旨在确定液体结构。除此之外，描述液体结构的方法的能力进行了讨论。对于所研究的液体，衍射方法在测定分子内结构方面表现得很好，但它们不能给出分子间结构的详细结构信息。的衍射实验和分子动力学模拟的结果之间的良好的协议证明使用模拟更详细的描述的液体结构，使用部分径向分布函数和取向关联函数。液态硝基甲烷被描述为一种分子液体，没有强的分子间相互作用，如氢键，但与可检测的取向相关性，导致优先反平行顺序的相邻分子。
In this letter, we examine the virial and the potential energy correlation for the quasi-real model system. This correlation constitutes the framework of the theory of the isomorph in the liquid phase diagram commonly examined using simple-liquids. Interestingly, our results show that for the systems characterized by structural anisotropy and flexible bonds, the instantaneous values of total viral and total potential energy are entirely uncorrelated. It is due to the presence of the intramolecular interactions because the contributions to the virial and potential energy resulting from the inte…
Frequency-domain two-dimensional Raman signals, which are equivalent to coherent two-dimensional Raman scattering (COTRAS) signals, for liquid water and carbon tetrachloride were calculated using an equilibrium-nonequilibrium hybrid MD simulation algorithm. We elucidate mechanisms governing the 2D signal profiles involving anharmonic mode-mode coupling and the nonlinearities of the polarizability for the intermolecular and intramolecular vibrational modes. The predicted signal profiles and intensities can be utilized to analyze recently developed single-beam 2D spectra, whose signals are gener…
Electron-hole excitation theory is used to unveil the role of nuclear quantum effects on the X-ray absorption spectral signatures of water, whose structure is computed via path-integral molecular dynamics with the MB-pol intermolecular potential model. Compared to spectra generated from the classically modeled water, quantum nuclei introduce important effects on the spectra in terms of both the energies and line shapes. Fluctuations due to delocalized protons influence the short-range ordering of the hydrogen bond network via changes in the intramolecular covalence, which broaden the pre-edge …
Corrections for nuclear quantum effects (NQE) have been calculated for classical molecular dynamics (MD) simulation models of light (H2O), heavy (D2O) and null (H1.28D0.72O) water. New path integral molecular dynamics (PIMD) simulations have also been conducted for the same systems. NQEs have somewhat smaller influence on the O-D and D-D partial radial distribution functions of heavy water than on the O-H and H-H ones of light water. After correcting for NQEs the O-H bondlengths in light and heavy water have become different: the O-D ones are about 0.5 % shorter than the O-H ones. Following NQ…
The properties of the intramolecular vibrational excitation (vibron) in a quasi 1D macromolecular structure are studied. It is supposed that due to the vibron interaction with optical phonon modes, a vibron might form partially dressed small polaron states. The properties of these states are investigated in dependence on the basic system parameters and temperature of a thermal bath. We also investigate the process of damping of the polaron amplitude as a function of temperature and vibron-phonon coupling strength. Two different regimes of the polaron damping are found and discussed.
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics simulation of water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads required. In this work we introduce a method whereby PIMD can be incorporated into a DFT simulation with little extra cost and little loss in accuracy. The method is based …
