The Journal of Chemical Physics
Articles in this Issue
Application of the aperiodic defect model to a negatively charged monovacancy in phosphorene
We apply the recently introduced aperiodic defect model (ADM) to a negatively charged monovacancy in a phosphorene monolayer. In contrast to conventional supercell approaches, the ADM treats a single...
Stochastic process description of lipid flip-flop
Since lipid bilayers are self-assembled macroscopic aggregates, their constituent lipid molecules can spontaneously transition between the two leaflets. This so-called “flip-flop” is almost universall...
TiDES: A time-dependent electronic structure code for real-time electron and spin dynamics
In this work, we present the TiDES (Time-Dependent Electronic Structure) code, an open-source real-time electronic structure theory package. The software is written in Python and interfaces with the P...
Double helix crookedness regulates the twist–stretch coupling: A quantitative molecular dynamics analysis
DNA conformation and twist–stretch coupling play a fundamental role in multiple biological processes. The contrasting elongation of DNA and shortening of RNA upon overwinding hint at a helix-related t...
On the single-Hessian Gaussian wavepacket dynamics
Single-Hessian Gaussian wavepacket dynamics (GWD) significantly reduces the computational burden of Heller’s local harmonic GWD while maintaining comparable accuracy in approximating vibronic spectra....
Predicting the hydrogen bond strength from water reorientation dynamics at short timescales
Path-integral molecular dynamics simulations and electronic structure-based energy decomposition analysis (EDA) are employed to connect hydrogen bond (H-bond) strength, its asymmetry, and the total de...
Development and application of external electric fields for advanced polarizable force fields
External electric fields can dramatically alter the structure and dynamics of molecules and materials. The electric field response involves both the direct electrostatics and the polarization of the m...
Coupling between phase separation and geometry on a closed elastic curve: Free energy minimization and dynamics
We study the free energy and dynamics of a closed elastic filament (a one-dimensional curve in two dimensions) coupled to a scalar concentration field representing, for example, an adsorbed species. T...
Configuration interaction extension of AGP for incorporating inter-geminal correlations
In this paper, we develop a class of antisymmetrized geminal power configuration interaction (AGP-CI) wave functions that extend the AGP framework by incorporating inter-geminal correlations through a...
Molecular dynamics simulation of high slip flow of water confined between graphene nanochannels at experimentally accessible shear rates
The transient time correlation function (TTCF) method has emerged as a powerful methodology for accurately probing systems at low shear rates. In the present study, TTCF was used to evaluate the shear...
Two-dimensional IR–Raman spectroscopy of vibrational polaritons: Role of dipole surfaces
Nonlinear spectroscopy provides a unique perspective to understand time-resolved molecular dynamics under vibrational strong coupling (VSC). Herein, equilibrium–nonequilibrium cavity molecular dynamic...
Generalized Einstein relations between absorption and emission spectra in the electric-dipole approximation
Recently, Ryu et al. showed that two broadened bands connected by a set of four Einstein-coefficient spectra for stimulated and spontaneous single-photon transitions will obey detailed balance at equi...
A new Fe(IV) superoxide: The perferrate isomerization re-examined
The perferrate anion [FeVIIO4]−, the elusive iron analog of permanganate, has been extensively investigated, yet key questions remain unresolved concerning its stability with respect to isomerization....
Thermodynamic properties of Lennard-Jones fluids residing in two to five spatial dimensions
The thermodynamic properties and the microscopic structure of Lennard-Jones fluids residing in two to five spatial dimensions are discussed. Complementing literature data for one to three dimensions,...
The low-field effect in radical pairs: A zero-field singlet–triplet basis picture
We present a new formulation of the low-field effect (LFE) in spin-correlated radical pairs based on a zero-field singlet–triplet basis for the isotropic spin Hamiltonian. The aim is to provide a desc...
Intrinsic structural factors and solvent effects on excited-state dynamics and photophysical properties of BIDP derivatives with dual-ESIPT units
When multiple excited-state intramolecular proton transfer (ESIPT) units are incorporated into a molecule, the excited-state dynamics become more complex and sensitive to both intrinsic structure and...
Solvation of the Ra2+ ion in ammonia and water. A hybrid density functional theory Born–Oppenheimer molecular dynamics study
We present a comprehensive theoretical investigation of Ra(II) solvation in water and ammonia micro-solvation environments using hybrid density functional theory Born–Oppenheimer molecular dynamics si...
SITH: A quantum-chemical framework for predicting bond destabilization in stretched molecules
Mechanical forces can selectively destabilize chemical bonds of molecular systems, particularly in biological and synthetic polymers. While experimental and theoretical methods have advanced our under...
Analytic gradients and geometry optimization for orbital-optimized pair coupled cluster doubles
We introduce a reusable geometry-optimization engine in PyBEST for analytic, gradient-driven molecular structure optimization, with particular emphasis on orbital-optimized pair coupled-cluster double...
Constrained Møller–Plesset perturbation theory for charge transfer states
We propose a constrained Møller–Plesset second-order perturbation theory (CMP2) that incorporates electron correlation into the constrained Hartree–Fock (CHF) framework. In CMP2, the CHF solution is e...
Binary colloidal mixtures in near-critical binary solvents
The phase behavior of a single type of colloid C suspended in near-critical solvents is known to be very rich. Motivated in part by recent experiments [Kodger et al., “Composite colloidal assembly by...
Fermionic mean-field dynamics for spin systems beyond free fermions
We introduce the fermionized time-dependent Hartree–Fock (fTDHF), a real-time quantum dynamics method for spin-1/2 Hamiltonians following their mapping to fermions via the Jordan–Wigner transformation...
How do diluent-aggregates interactions affect the structure of colloidal systems in solvent extraction?
The structure and dynamics of extractant-based aggregates strongly influence metal ion extraction and third-phase formation in liquid–liquid systems. Here, classical molecular dynamics simulations wer...
Efficient simulation of non-Markovian path integrals via imaginary time evolution of an effective Hamiltonian
Accurately simulating the non-Markovian dynamics of open quantum systems remains a significant challenge. While the recently proposed time-evolving matrix product operator (TEMPO) algorithm based on p...
Perspective of Fermi’s golden rule and its generalizations in chemical physics
This perspective provides a succinct history of Fermi’s golden rule (FGR), an overview of its derivation, assumptions, and representative forms. Major applications of FGR, mostly in the field of chemi...