The Journal of Chemical Physics
Articles in this Issue
Cesium exhibits different mesoscale segregation and ion pairing than lithium, sodium, or potassium in concentrated alkaline aqueous nitrite solutions
Understanding ion pairing in concentrated alkaline electrolytes facilitates the prediction and control of chemical processes in nuclear waste. While sodium is the dominant alkali metal in such systems...
Structural insights into nitrile–methanol hydrogen-bonded complexes based on mass-selected infrared spectroscopy and theoretical calculations
Hydrogen bonds, crucial for the formation and stabilization of complex organic molecules, present intriguing possibilities for the existence of such molecular complexes in extraterrestrial environment...
Adsorption of benzene on graphene studied by ML-accelerated <i>ab initio</i> molecular dynamics simulations
Periodic ab initio molecular dynamics simulations accelerated by machine learning were conducted to investigate the adsorption of benzene on graphene at a coverage of 0.11 ML and a temperature of 150 ...
High kinetic stability and high density of Ir(ppy)3 doped organic semiconductor glasses
Glasses prepared by physical vapor deposition (PVD) can have advantageous material properties, such as highly enhanced thermal stability and denser molecular packing, and thin glassy films prepared by...
Matching correlations matters: Modeling friction in a hydrophobic folding transition
The generalized Langevin equation provides a powerful framework for modeling and interpreting the conformational dynamics of (macro)molecules in solution. However, recent studies have shown that the s...
Investigation of ionic activity behavior in aqueous solutions containing heavy metal salts at 298.15 K
Modeling ionic activity is essential for understanding ion-specific effects in environmental and industrial systems. The microscopic interactions of heavy metal salts in aqueous solutions become incre...
Recovering hidden degrees of freedom using Gaussian processes
Dimensionality reduction represents a crucial step in extracting meaningful insights from Molecular Dynamics (MD) simulations. Conventional approaches, including linear methods such as principal compo...
The solubilities of water in liquid CO2 coexisting with water or hydrate
We investigate the solubilities of water in liquid CO2 in the presence and absence of coexisting clathrate hydrate from theoretical calculations of the chemical potentials of water and CO2 in the aque...
Learning collective variables that respect permutational symmetry
In addition to translational and rotational symmetries, clusters of identical interacting particles possess permutational symmetry. Coarse-grained models for such systems are instrumental in identifyi...
Origin of 4′,6-diamidino-2-phenylindole (DAPI) fluorescence dynamics in solution and DNA minor groove binding: Unveiled by femtosecond broadband fluorescence, transient absorption, and theoretical calculations
4′,6-Diamidino-2-phenylindole (DAPI) is a widely utilized DNA sensor, renowned for its strong affinity for the AT minor groove. Despite its essential role as a fluorescent probe in molecular biology a...
Computing dielectric spectra in molecular dynamics simulations: Using a cavity to disentangle self and cross correlations
Dielectric spectra are typically obtained in molecular dynamics (MD) simulations by analyzing the fluctuations, in the absence of an applied electric field, of the total dipole moment of the simulatio...
In search of mechanism of aggregation-induced emission in carbazole and triphenylamine substituted ethenes: An approach based on spin-flip time dependent density functional theory and optimally tuned range-separated hybrid functional
Aggregation-induced emission (AIE) has emerged as a groundbreaking advancement in the field of photoluminescence behavior. A thorough understanding of the AIE mechanism is essential for the rational d...
Electronic conduction in copper–graphene composites with functional impurities
Coal-derived graphene-like material and its addition to FCC copper are investigated using ab initio plane wave density functional theory (DFT). We explore ring disorder in the sp2 carbon and functiona...
Molecular dynamics investigation of polymer-decorated nanoparticles with co-nonsolvent: Structural transitions from isotropic layers to heterogeneous patches
With the assistance of molecular dynamics simulations, we systematically investigate the conformations of polymer-decorated nanoparticles (PDNP), making use of the co-nonsolvency effect, which dramati...
Blockwise optimization for projective variational quantum dynamics (BLOP-VQD): Algorithm and implementation for lattice systems
We present an efficient approach to simulate real-time quantum dynamics using projected variational quantum dynamics, where the computational cost is reduced by strategically optimizing only a subset...
Deciphering the molecular mechanisms of startle disease: The role of the Asn46Lys mutation in the glycine receptor
The glycine receptor (GlyR) is a pentameric ligand-gated ion channel that plays important physiological roles in the nervous system. Its malfunction is related to neurological disorders, including sta...
Mechanical characterization of intermediates of Ag+–DNA complex: An atomic force study
Silver ions (Ag+) are known to interact with DNA through nonspecific and specific mechanisms, inducing conformational and mechanical changes in the double helix. In this study, we investigate how vary...
Kinetic energy release distributions of multiply charged NOq+ (q = 2–7) molecular ions produced in collisions with 1.6 MeV Ar8+ ion beam
We report the fragmentation dynamics of multiply charged molecular ions of NO under the impact of highly charged Ar8+ ions in the intermediate velocity (vp ≈ 1 a.u.) range. Coincidence measurements of...
Exploring “Fano resonance”-assisted trapping of core–shell hybrid nanoparticles under femtosecond pulsed excitation using the generalized Lorenz–Mie theory
The core–shell type structure of metal-dielectric nanoparticles has great applications in the fields of nanophotonics and biomedical sciences due to the plasmonic properties of metals and field enhanc...
Photoelectron spectroscopy and formation mechanism of Ta2N3−: Activation of N2 by Ta2N−
This work investigated the reaction mechanism of N2 on Ta2N− via the photoelectron spectroscopy study of Ta2N3−, focusing on the activation of nitrogen molecules (N2) by Ta2N−. The vertical detachment...
Investigating reactive oxygen species triggered damage to cell teichoic acid via molecular dynamics
In this study, we investigated the mechanisms by which reactive oxygen species (ROS) cause oxidative damage to wall teichoic acid (WTA) and lipoteichoic acid (LTA) in two bacterial species: Staphyloco...
Generalized spin in the variational determination of two-electron reduced density matrices within the doubly occupied configuration interaction framework
This work extends the variational determination of two-electron reduced density matrices to the generalized spin formulation within the doubly occupied configuration interaction treatment. We describe...
Structure and adsorption properties of Cu–Au nanoparticles in harsh reactive environments
The reactivity of nanoparticles is governed by their surface composition, which tends to vary significantly under reactive conditions. In this study, the impacts of temperature and the presence of a C...
Ion selectivity in uncharged tapered nanoslits through heterogeneous water polarization
We employ molecular dynamics simulations to investigate ion and water transport driven by an electric field through quasi-two-dimensional nanoslits with a tapered geometry. Despite the absence of surf...
Dynamic correlations in a polar fluid: Confronting stochastic density functional theory to simulations
Understanding the dynamic behavior of polar fluids is essential for modeling complex systems such as electrolytes and biological media. In this work, we develop and apply a stochastic density function...