The Journal of Chemical Physics
Articles in this Issue
Electrochemical investigation of Donnan exclusion mechanisms in molecular layer-by-layer membranes
Membrane-based separations play a central role in water purification, energy generation, and resource recovery, and their performance is strongly influenced by ion transport through steric, dielectric...
Parquet theory for molecular systems: Formalism and static kernel parquet approximation
The GW approximation has become a method of choice for predicting quasiparticle properties in solids and large molecular systems, owing to its favorable accuracy–cost balance. However, its accuracy is...
Load-balanced diffusion Monte Carlo method with lattice regularization
Ab initio quantum Monte Carlo (QMC) is a stochastic approach for solving the many-body Schrödinger equation without resorting to one-body approximations. QMC algorithms are readily parallelizable via...
Dynamic insights into the structural evolution of ACE2–RBD interactions through molecular dynamics simulation, Markov state modeling, and large language model mutation prediction
The viral Spike protein of SARS-CoV-2 is responsible for virus–host recognition, in which the receptor-binding domain (RBD) binds to the host receptor angiotensin-converting enzyme 2 (ACE2). Structura...
Numerically “exact” charge transport dynamics in a dissipative electron–phonon model rationalizing the success of the transient localization scenario
Optical conductivity in molecular semiconductors is suppressed in the terahertz region, featuring the displaced Drude peak that reflects carriers’ transient localization (TL) by slow intermolecular vi...
Master equation study of three-body recombination of nitrogen and oxygen in non-equilibrium hypersonic flows
This work aims to study the energy transfer and recombination processes in N2∑g+3 + NSu4 and O2∑g+3 + OP23 chemical systems when the system is suddenly cooled in a 0-D isothermal reactor thereby induc...
Excimer and non-photochemical quenching in LHCII
The light-harvesting complex of photosystem II (LHCII) plays the dual roles of photosynthetic energy capture and dissipation, where the excitation energy in excess is dissipated safely via non-photoch...
Electronic localization on the structural inhomogeneities formed due to Bi and Te deficiency in the MBE grown films of AF topological insulator MnBi2Te4: Evidence from spectroscopic ellipsometry and infrared studies
The intrinsic substitutional and antisite defects cause unintentional doping and a shift of the EF position above the conduction band minimum in the AF topological insulator MnBi2Te4. This prevents me...
Confinement-controlled selective CO2 insertion into a dicopper dihydride core: A multiscale mechanistic study
CO2 is an abundant C1 feedstock for fuel and chemical synthesis. We have previously demonstrated experimentally a stepwise insertion of CO2 into a [Cu2H2] core via a solid–gas in crystallo reaction, f...
Dynamic catalysts and the digital age: Synthetic consequences
The growing insight that interfacial catalysts are dynamic materials with continuously re-forming active sites is investigated here with respect to its consequences for their material science. The con...
Hypergraph-based models of random chemical reaction networks: Conservation laws, connectivity, and percolation
Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often redu...
Non-resonant elastic and inelastic x-ray scattering study of nitrous oxide
The non-resonant elastic and inelastic x-ray scattering technique has been employed to study the molecular structure and the K-shell excitations of N atoms for nitrous oxide (NT-NC-O). The elastic squ...
Determination of binding free energy shifts in protein complexes induced by single and double amino acid mutations using molecular dynamics simulations
Binding free energy between protein molecules strongly influences protein functions. In particular, shifts in binding free energy caused by amino acid mutations alter the conformational stability of t...
On the origin of hydrophilic interactions at alumina surfaces
Despite advances in understanding macroscopic wetting behavior, the atomistic mechanisms underlying hydrophilicity at solid–liquid interfaces remain only partially understood, particularly for chemica...
ABACUS: An electronic structure analysis package for the AI era
ABACUS (Atomic-orbital Based Ab initio Computation at USTC) is an open-source software for first-principles electronic structure calculations and molecular dynamics simulations. It mainly features den...
Cation–DNA outer sphere coordination in DNA polymorphism
There are two approaches to describing DNA–ion interactions. The physical approach is an analysis of electrostatic interactions between ions and charges on the DNA molecule. The coordination chemistry...
Ion transport in water film on silica and mica surfaces: Insights from microsecond molecular dynamics and logarithmic mean-force dynamics
Ion transport in water films on mineral surfaces is crucial for geophysical and engineering applications. However, probing these nanoscale phenomena is challenging for both experiments and conventiona...
Interplay of coil–globule transitions and aggregation in homopolymer aqueous solutions: Simulation and topological insights
We investigate the structural and topological properties of hydrophobic homopolymer chains in aqueous solutions using molecular dynamics simulations and circuit topology (CT) analysis. By combining ge...
Study of the properties of nanoconfined EMIMBF4 using polarizable molecular dynamics
We present a molecular dynamics study of the structure and dynamic behavior of the ionic liquid 1-ethyl-3-methylimidazolium tetrafluoroborate under nanoconfinement using a polarizable force field. Two...
Quantumness of classical-trajectory-based methods for vibrational spectroscopy
Classical-trajectory-based methods calculate the vibrational spectrum of a molecular system as the Fourier transform of an appropriate time correlation function. In this paper, we assess the quantumne...
Quantifying the transition from single file to Fickian diffusion
Single-file diffusion occurs when diffusing particles are confined to a narrow tube, which prohibits particles from passing one another. Observed in a variety of natural and engineered systems, single...
Illuminating non-equilibrium multi-step reaction dynamics with stochastic Marcus state model
Modeling the stochastic reaction dynamics is a significant task to explain the modern measurements of non-equilibrium processes at mesoscopic scales. Marcus’s transition-state theory describes the rea...
Mesoscale particle-based simulations of flow in expansion–contraction microchannels at low Reynolds number
We computationally study the flow of Newtonian fluids through sinusoidal expansion–contraction microchannels at low Reynolds numbers. We first use a perturbation method to analytically derive series s...
Pressure-dependent structure of neat liquid methanol, CH3OH: Molecular dynamics simulations with various united atom-type potentials
Molecular dynamics computer simulations have been conducted on neat liquid methanol, using three different “united atom” (three site) interatomic potentials: TraPPE [Chen et al., J. Phys. Chem. B 105,...
Efficient optimization of low-rank antisymmetric product of geminals wavefunction using the direct Givens rotation method
In our previous study [Kawasaki and Nakatani, Mol. Phys. 123(16), e2449186 (2025)], we proposed the low-rank antisymmetric product of geminals (APG) method, which reconstructs the wavefunction by extr...