The Journal of Chemical Physics
Articles in this Issue
Impact of solvent polarity on the photoinduced dynamics of a push–pull molecular motor
Light-driven rotary molecular motors convert light energy into unidirectional rotational movement. In overcrowded alkene-based molecular motors, rotary motion is accomplished through consecutive cis–t...
Single file dynamics of tethered random walkers
We consider the single file dynamics of N identical random walkers moving with diffusivity D in one dimension (walkers bounce off each other when attempting to overtake). In addition, we require that...
Repeated interaction scheme for the quantum simulation of non-Markovian electron transfer dynamics
Quantum algorithms have the potential to revolutionize our understanding of open quantum systems in chemistry. In this work, we demonstrate that a repeated interaction model, which could serve as the...
What is a chemostat? Insights from hybrid dynamics and stochastic thermodynamics
At the microscopic scale, open chemical reaction networks are described by stochastic reactions that follow mass-action kinetics and are coupled to chemostats. We show that closed chemical reaction ne...
The topological way—A new methodology to construct symmetric sets of valence-bond structures
Classical valence bond (VB) theory has advanced significantly in recent years, evolving into a quantitative tool comparable to molecular orbital-based methods. A key advantage of VB is its high interp...
Variational functional in local density approximation for coulombic electrolyte correlations in the electric double layer
A classical coulombic correlation functional in one-loop (1L) and local-density-approximation (LDA) is derived for electrolyte solutions, starting from a first-principles many-body partition function....
Excited-state decay dynamics of endohedral metal–metal-bonding fullerenes
Endohedral metal–metal-bonding fullerenes, in which the endohedral metal atoms form covalent metal–metal bonds, are typical models for studying the confined metal–metal bonds. Herein, utilizing time-d...
Non-adiabatic dynamics simulations reveal the reversal of photoinduced electron transfer in zinc phthalocyanine/endohedral metallofullerene donor–acceptor complexes via substitution and solvent effects
Herein, we investigated the photoinduced dynamics of a zinc phthalocyanine N-pyridyl-substituted Sc3N@Ih-C80 (ZnPc-C80) donor–acceptor complex and its sulfonyl-substituted derivative ZnPcS-C80 with st...
Sublinear scaling method for indirect spin–spin coupling constant calculations at Hartree–Fock and density functional theory level
The spin–spin coupling (SSC) phenomenon in nuclear magnetic resonance (NMR) spectroscopy is useful for determining the structures of unknown compounds. The SSC constants (SSCCs) can be obtained via qu...
Simulating iron in oxygen-containing environments: An improved Fe–O interaction for density-functional tight-binding
The chemistry of iron in oxygen-containing and wet environments plays a central role in corrosion, (electro)catalytic reactions, and several biological processes. These processes hinge on the molecula...
A five-terminal ITO transistor enabling memory, artificial synaptic behaviors, and logic operations
The increasing complexity of fabrication and high transistor density is slowing down progress in integrated circuits. Simplified designs are now critical to boost circuit performance while reducing ma...
Density-matrix embedding based multi-reference perturbation theory approach to single-ion magnets
Multi-configurational wave-function theory (MC-WFT) that combines the complete active space self-consistent field (CASSCF) approach with subsequent state interaction treatment of spin–orbit coupling,...
Hydrogen-bond rearrangements in the self-association and microhydration of ethylene glycol: A combined infrared and theoretical conformational sampling investigation
The hydrogen-bond rearrangements involved in the self-association and microhydration of the simplest vicinal diol, ethylene glycol (EG), have been explored by low-temperature mid- and far-IR cluster s...
Scalable quantum simulations of molecular systems via improved optimization of neural quantum states
Quantum simulations of molecular systems hold transformative potential for computational chemistry, yet optimization inefficiencies and classical computational bottlenecks hinder practical implementat...
Universal structure of computing moments for exact quantum dynamics: Application to arbitrary system–bath couplings
We introduce a general procedure for computing higher-order moments of correlation functions in open quantum systems, extending the scope of our recent work on Memory Kernel Coupling Theory (MKCT) [Li...
Mixed quantum–classical dynamics yields anharmonic Rabi oscillations
We apply a mixed quantum–classical (MQC) approach to the quantum Rabi model, involving a classical optical field coupled self-consistently to a quantum two-level system. Under the rotating wave approx...
Efficient and scalable electrostatics via spherical grids and treecode summation
Evaluation of noncovalent electrostatic interactions is the dominant bottleneck in classical molecular dynamics simulations, and evaluation of Coulombic matrix elements similarly limits quantum mechan...
Exploring minimum free-energy pathway of GB1 dimerization in dilute and crowded solution
The intracellular crowded environment plays a major role in driving the protein–protein association reaction that entails large conformational fluctuations. A detailed understanding of the crowding in...
Photolysis of methyl nitrate (CH3ONO2) through the prism of <i>ab initio</i> simulations of transient-absorption pump–probe spectra
The photolysis of methyl nitrate (CH3ONO2) UV-excited to the optically bright state is scrutinized by on-the-fly trajectory surface hopping simulations of dynamic observables and transient-absorption...
Exact first-passage time distributions from time-dependent solutions of the chemical master equation. I. Nonlinear networks with bimolecular reactions and Poisson-product initial conditions
The first passage time (FPT) is a generic measure that quantifies when a random quantity reaches a specific state. We consider the FTP distribution in nonlinear stochastic biochemical networks, where...
Manipulating coherent vibrational relaxation in ethylene carbonate with isotope substitution
Two-dimensional infrared spectroscopy (2DIR) and linear IR spectroscopy investigate the behavior of coherent vibrational energy transfer between Fermi coupled vibrations in a series of ethylene carbon...
Nuclear magnetic resonance relaxation and diffusion properties of confined fluids in organic nanopores: A molecular dynamics study
A series of molecular dynamics (MD) simulations was conducted to investigate the nuclear magnetic resonance (NMR) relaxation properties of confined fluids in kerogen nanopores. We examined how the lon...
Exact first-passage time distributions from time-dependent solutions of the chemical master equation. II. Nonlinear networks with bimolecular reactions and arbitrary initial conditions
In biochemical reaction networks, the first passage time (FPT) of a reaction quantifies the time, from the initial state, that it takes for the reaction to first occur. While the mean FPT historically...
Gauss–Legendre-spherical- <i>t</i> (GLST) cubature-based factorization of long-range electrostatics in simulations
We develop a highly parallelizable algorithm to calculate long-range electrostatic interactions named the Gauss–Legendre-Spherical-t (GLST) cubature method. Motivated by our recent spherical grid and...
Chain conformations in adsorbed layer during polymer capillary imbibition
We conducted molecular dynamics simulations to investigate chain conformations in adsorbed layers during polymer capillary imbibition. While the imbibition length adheres to the classical Lucas–Washbu...