The Journal of Chemical Physics
Articles in this Issue
Molecular conical intersections with odd electron number are realizations of the topological Yang monopole
The two-level conical intersection of a molecule with an odd electron number in the absence of a magnetic field obeys time-reversal symmetry T2 = −1 (referred to as the T2 = −1 conical intersection) a...
Energy-dependent selective bond cleavage induced by low-energy electrons in DNA films deposited from buffered solutions: Insights from XPS
In this study, we investigated chemical modifications caused by low-energy electrons (LEEs) in DNA films deposited from Tris-EDTA (TE) buffered solutions, using x-ray photoelectron spectroscopy (XPS)....
Thermodynamics of hard-sphere plus square-well trimer fluids. A small mystery
The aim of this work is to show that the thermodynamics of some simple fluids, composed of molecules formed by only three atoms—trimers—presents a challenge when confronted with molecular simulation r...
Revealing the microhydration mechanisms of <i>α</i> -hydroxy carboxylic acids: Identification of large-amplitude torsional and librational motion
The molecular recognition mechanisms associated with the self-aggregation and microhydration processes of two different bifunctional α-hydroxy carboxylic acids, prototypical glycolic acid [CH2OHCOOH]...
Spin localization in intermolecular complexes: A challenge for semi-local approximants for the embedding potential
Regardless of how the electron correlation is treated, all methods based on frozen-density embedding theory rely on approximations to the non-additive kinetic potential bi-functional ṽtnad[ρA,ρB](r)≈...
On the importance of numerical integration details for homogeneous flow simulation
The Sllod equations of motion enable modeling of homogeneous flow at the atomic scale and are commonly used to predict fluid properties such as viscosity. However, few publicly available codes support...
Regional chemical potential analysis for material surfaces
We propose a local regional chemical potential (RCP) analysis method based on an energy window scheme to quantitatively estimate the selectivity of atomic and molecular adsorption on surfaces, as well...
sbml4md: A computational platform for system–bath modeling via molecular dynamics powered by machine learning
We introduce sbml4md, a newly developed algorithm implemented as a software package to extract parameters of multimode anharmonic Brownian models from molecular dynamics (MD) trajectories for simulati...
Physical mechanisms of nanoparticle–membrane interactions: A coarse-grained study
Nanoparticles are promising drug carriers for targeted therapies, diagnostic imaging, and advanced vaccines. However, their clinical translation is limited by complex biological barriers that reduce c...
Pressure-induced p <i>K</i> a variations influence conformations of pH-sensitive polymers
Conformations of aqueous macromolecules depend on a delicate balance of hydrophobic, electrostatic, and hydrogen-bonding interactions, all of which are influenced by environmental factors such as pres...
Deriving effective electrode–ion interactions from free-energy profiles at electrochemical interfaces
Understanding ion adsorption at electrified metal–electrolyte interfaces is essential for accurate modeling of electrochemical systems. Here, we systematically investigate the free energy profiles of...
Many roads to the seam: How conformational flexibility drives nonadiabatic relaxation in a prototypical tetrapyrrolic chromophore
Large and structurally flexible chromophores pose challenges for in silico modeling of photodeactivation due to the many vibrational modes that can funnel the system toward energy degeneracy. In this...
Sequence-encoded patterning of stickers modulates biomolecular condensate reconfiguration in IDP systems
Intrinsically disordered proteins (IDPs) exert pivotal roles in Phase Separation Coupled to Percolation (PSCP), a process that drives the formation of functional biomolecular condensates linked to div...
Simulating quadrupolar NMR dynamics in solid electrolyte Li <b>10</b> GeP <b>2</b> S <b>12</b>
Quadrupolar solid-state nuclear magnetic resonance (NMR) spectroscopy is an excellent tool to trace lithium (Li) ion diffusion in solid electrolytes due to its sensitivity to dynamics over timescales...
Simultaneous optimization of assembly time and yield in programmable self-assembly
Rational design strategies for self-assembly require a detailed understanding of both the equilibrium state and the assembly kinetics. While the former is starting to be well understood, the latter re...
MD-BAX: A general-purpose Bayesian design framework for molecular dynamics simulations with input-dependent noise
Molecular dynamics (MD) simulations are a powerful tool for understanding complex molecular behavior, but exhaustively exploring the large space of input parameters can be computationally prohibitive,...
SHarmonic: A fast and accurate implementation of spherical harmonics for electronic-structure calculations
The authors present SHarmonic, a new implementation of the spherical harmonics targeted for electronic-structure calculations. Their approach is to use explicit formulas for the harmonics written in t...
Diffusion crossover of protein molecules: Two-step coarse-graining and oscillating memory
A consistent treatment of anomalous diffusion requires a microcosmic framework that captures the underlying couplings between the relevant degrees of freedom. To this end, we employ a two-step coarse-...
The connection between network structure and terminal relaxation of unentangled vitrimer melts: A dynamic cross-linked Gaussian-strand model study
Vitrimers are flowable cross-linked polymer networks that have drawn significant attention as a platform for developing novel polymer materials. Here, we utilize a dynamic cross-linked Gaussian-strand...
Ultrafast radiation chemistry of glycine in aqueous solution
Investigating the ultrafast dynamics of primary biological compounds is crucial for gaining insights into radiation damage. We computationally investigate the ionization-induced dynamics of glycine in...
<tt>dynsight</tt> : An open Python platform for simulation and experimental trajectory data analysis
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful inform...
An interpretable molecular descriptor for machine learning predictions in atmospheric science
The study of aerosol formation and chemistry using machine learning is limited by the lack of molecular descriptors suited to atmospheric compounds. Interpretable models are particularly affected beca...
Shedding light on reactive sulfur species coordination to metmyoglobin by QM–MM TD-DFT simulations
Understanding how sulfur-containing ligands modulate the structure, electronic configuration, and spectroscopy of ferric heme proteins is essential for interpreting their reactivity and assigning expe...
Nonadiabatic ImF instanton rate theory
Semiclassical instanton theory captures nuclear quantum effects, such as tunneling in chemical reactions. It was originally derived from two different starting points, the flux correlation function an...
Branching ratios and mechanisms of the reactions of Ar+ with CH4 and C2H4 at cryogenic temperatures
Interest in interstellar noble gas chemistry has been stimulated by the recent detection of ArH+ and HeH+ in a variety of astrophysical environments ranging from diffuse clouds to supernova remnants....