The Journal of Chemical Physics
Articles in this Issue
Is there anybody out there? Ultrafast Rydberg–valence interactions in the photodissociation of trimethylamine
Trimethylamine (TMA) is a tertiary aliphatic amine that stands as a potential marker for life beyond Earth due to only being naturally produced via biotic means. However, its propensity to undergo pho...
Calculation of thermodynamic properties using path integral Monte Carlo simulations in the canonical ensemble
The method of Lustig [J. Chem. Phys. 100, 3048–3059 (1994)] is applied to the path integral formulation of the quantum-mechanical canonical ensemble to derive equations for the calculation of all comm...
Detection of the tunneling-rotation transitions of malonaldehyde in the submillimeter-wave region and proton tunneling dynamics
The tunneling-rotation transitions of malonaldehyde, consisting of more than 200 a-type Q-branch lines along with 50 R- and P-branch lines, were observed in the submillimeter-wave region of 590–760 GH...
Hydrogen storage in novel Zn(II) and Cd(II) MRT MOFs: A study using grand canonical Monte Carlo simulations
The development of advanced hydrogen storage materials is essential for the adoption of hydrogen-powered vehicles as a sustainable alternative to fossil fuels. Metal–organic frameworks (MOFs) have eme...
A semiclassical nonequilibrium Green’s function approach to electron transport in systems exhibiting electron–phonon couplings
We formulate a semiclassical theory for electron transport in open quantum systems with electron–phonon interactions adequate for situations when the system’s phonon dynamics is comparable with the el...
The role of effective mass on semiconductor charge carrier localization as revealed by the split operator method
Charge carriers in a solid-state material are modeled as free particles with a variable “effective” mass that is derived from the curvature of the conduction/valence band. These effective masses of el...
Discriminant analysis optimizes progress coordinate in weighted ensemble simulations of rare event kinetics
Calculating the kinetics of rare-but-important conformational transitions in complex biomolecules is a significant challenge in computational biophysics. Because of the long timescales needed to obser...
Simulation of coupled fluid–ion transport through a biological nanopore on graphics processing units
Nanoscale fluid–ion transport is investigated in biophysical chemistry, drug delivery, protein sequencing, etc. Currently, fast three-dimensional models for fluid–ion transport through biological nano...
Interaction strength of carbon dioxide on graphene from periodic quantum diffusion Monte Carlo
Despite the importance of graphene based carbon capture devices, an accurate estimate of the interaction strength of a carbon dioxide molecule with graphene from periodic calculations is lacking. In t...
Taylor-mode automatic differentiation for constructing molecular rovibrational Hamiltonian operators
We present an automated framework for constructing Taylor series expansions of rovibrational kinetic and potential energy operators for arbitrary molecules, internal coordinate systems, and molecular...
HEroBM: A deep equivariant graph neural network for high-fidelity backmapping from coarse-grained to all-atom structures
Molecular simulations play a pivotal role in chemistry, biology, and material sciences, enabling the study of complex dynamic properties within systems. Coarse-grained (CG) techniques have emerged as...
Minimized reaction network method for the construction of combustion reaction mechanism: NH3/DME mixed combustion
In view of the shortcomings of the previous NH3/DME reaction mechanism, combustion reaction mechanisms of NH3, DME, and NH3/DME were constructed by using the minimized reaction network method under th...
Reaction dynamics for the [NNO] system from state-resolved and coarse-grained models
The dynamics for the NO(X2Π) + N(4S) ↔ N2(X1Σg+) + O(3P) reaction was followed in the 3A′ electronic state using state-to-state (STS) and Arrhenius-based rates from two different high-level potential...
The effect of hydration and dynamics on the mass density of single proteins
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hyd...
A model of protein folding with multiple native states: Metamorphicity, intrinsic disorderness, and folding upon binding of proteins
The sequence–structure–function paradigm in biology states that a protein’s amino acid sequence determines its unique folded state structure, which in turn dictates its unique biological function. Thi...
High-energy reaction dynamics of O3
The high-temperature atom exchange and dissociation reaction dynamics of the O(3P) + O2(Σg−3) system are investigated based on a new reproducing kernel-based representation of high-level multi-referen...
Non-linear Fourier analysis of aperiodic structures: Mass-density-waves in adsorbed monolayers
The adsorption of a “solid-like” monolayer on a crystalline substrate can produce distortions in the monolayer which are describable as mass-density-waves. These mass-density-waves can lead to a fixed...
Effect of thiophenol adsorption on the optical properties of Ag nanoparticles supported on graphene/Rh(111)
Single-layer graphene on a transition metal surface forms a moiré structure that has been used as a template to fabricate metal nanoparticle assemblies. Ag nanoparticles were grown on graphene/Rh(111)...
Nonconventional growth characteristics of tin silicon oxide grown by thermal atomic layer deposition using H2O as oxidant
Atomic layer deposition (ALD) of tin silicon oxide was performed via an ALD supercycle on an amorphous carbon (a-C) layer, which serves as the mandrel in self-aligned double patterning (SADP) techniqu...
Exotic Harmonium model: Exploring correlation effects of attractive Coulomb interaction
Simple few-body systems often serve as theoretical laboratories across various branches of theoretical physics. A prominent example is the two-electron Harmonium model, which has been widely studied o...
Hybrid coarse-grained and all-atom molecular dynamics simulation studies of binary biological lipid membranes containing chlorosulfolipids
Chlorosulfolipids are the main component of the polar lipid of the flagellar membrane in sea algae and are also known as the major cause of seafood poisoning. Despite the active research on the synthe...
Evaluation of interfacial affinity between surface-modified metal oxide and solvent mixture using molecular dynamics simulations
The industrial application of surface-modified nanoparticles requires controlling their colloidal stability by selecting suitable surface modifiers and solvents. Solvent mixtures can control the inter...
Structure and dynamics of ionic liquids under shear flow
We investigate the intrinsic behavior of ionic liquids under shear flow using a coarse-grained model of [C4mim]+ [PF6]− as a prototypical example. The importance of long-ranged electrostatics is asses...
Conjugate-dual clusters
Discovery of clusters with high symmetrical geometry, such as C60 fullerene, always attracts lots of interest because of their diverse nature. However, most of such interesting clusters were sporadica...
Spherical to Cartesian coordinates transformation for solid harmonics revisited: Construction of the Hartree potential
Spherical harmonic Gaussian-type orbitals and Slater functions can be expressed using spherical coordinates or linear combinations of the appropriate Cartesian functions. General expressions for the t...