Quantitative molecular simulations

Kernel-Based Minimal Distributed Charges: A Conformationally Dependent ESP-Model for Molecular Simulations

A kernel-based method (kernelized minimal distributed charge model (kMDCM)) to represent the molecular electrostatic potential (ESP) in terms of off-center point charges is introduced. The positions of the charges adapt to the molecular geometry and allow the description of intramolecular charge flow. Using Gaussian kernels and atom-atom distances as the features, the ESPs for water and methanol are shown to improve by at least a factor of 2 compared with point charge models fit to an ensemble of structures. The conformationally fluctuating molecular dipole moment of water is reproduced almost twice as accurately using kMDCM compared with static PCs, despite not fitting to the dipole directly. The role of hyperparameters in the kernelization is investigated and their implication on model performance and simulation stability is discussed. Combining kMDCM for the electrostatics and reproducing kernels for the bonded terms allows energy-conserving simulations of 2000 water molecules with periodic boundary conditions on the nanosecond time scale. These MD simulations sample geometries outside the training set but remain stable, which demonstrates the robustness of the model and its implementation.

Microcanonical treatment of HCl dissociative chemisorption on Au(111): Reactive dampening through inefficient translational energy coupling and an active surface

Microcanonical unimolecular rate theory is applied to Shirhatti and Wodtke's recent supersonic molecular beam experiments examining the activated dissociative chemisorption of HCl on Au(111). A precursor mediated microcanonical trapping (PMMT) model (where the surface vibrates and HCl rotations, vibration, and translation directed along the surface normal are treated as active degrees of freedom) gave dissociative sticking coefficient predictions that are several orders of magnitude higher than experimental values but in good accord with prior quantum and molecular dynamics simulations. Density functional theory (DFT) electronic structure calculations using the Perdew-Burke-Ernzerhof (PBE) functional served to fix the vibrational frequencies of the reactive transition state and the threshold energy for dissociation, E0 = 72.9 kJ/mol. To explore the possibilities of varying threshold energy, coupling to phonons, and dynamics, a three-parameter [E0, s, ɛn] dynamically biased (d-) PMMT model was fit to the experiments. A dynamical bias was introduced using an efficiency, ɛn, of normal translational energy to contribute to the active exchangeable energy capable of promoting reactivity. To achieve the low sticking probabilities observed in experiment, severe normal translational energy dampening (ɛn → 0.26) was imposed, leading to a large vibrational efficacy of ηv = εv/εn = 3.85. The optimal threshold energy for dissociation was E0 = 30.88 kJ/mol, some 40 kJ/mol below the PBE-DFT prediction, and the optimal number of Au surface oscillators was s = 1. The d-PMMT modeling indicates that HCl/Au(111) reactivity can be consistent with electronically adiabatic passage across a relatively low and late transition state that dynamically disfavors normal translational energy.

Two-dimensional infrared-Raman spectroscopy as a probe of water's tetrahedrality

Two-dimensional spectroscopic techniques combining terahertz (THz), infrared (IR), and visible pulses offer a wealth of information about coupling among vibrational modes in molecular liquids, thus providing a promising probe of their local structure. However, the capabilities of these spectroscopies are still largely unexplored due to experimental limitations and inherently weak nonlinear signals. Here, through a combination of equilibrium-nonequilibrium molecular dynamics (MD) and a tailored spectrum decomposition scheme, we identify a relationship between the tetrahedral order of liquid water and its two-dimensional IR-IR-Raman (IIR) spectrum. The structure-spectrum relationship can explain the temperature dependence of the spectral features corresponding to the anharmonic coupling between low-frequency intermolecular and high-frequency intramolecular vibrational modes of water. In light of these results, we propose new experiments and discuss the implications for the study of tetrahedrality of liquid water.

Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry

There has been an almost exponential increase in the use of molecular dynamics simulations in basic research and industry over the last 5 years, with almost a doubling in the number of publications each year. Many of these are focused on neurological membranes, and biological membranes in general, applied to the medical industry. A smaller portion have utilized membrane simulations to answer more basic questions related to the function of specific proteins, chemicals or biological processes. This review covers some newer studies, alongside studies from the last two decades, to determine changes in the field. Some of these are basic, while others are more profound, such as multi-component embedded membrane machinery. It is clear that many facets of the discipline remain the same, while the focus on and uses of the technology are broadening in scope and utilization as a general research tool. Analysis of recent literature provides an overview of the current methodologies, covers some of the recent trends or advances and tries to make predictions of the overall path membrane molecular dynamics will follow in the coming years. In general, the overview presented is geared towards the general scientific community, who may wish to introduce the use of these methodologies in light of these changes, making molecular dynamic simulations more feasible for general scientific or medical research.