Jul 2026· Journal of Physical Chemistry B· Vol 130, pp. 7180-7191· 0 citations· 28 references
Medicine
Abstract
An equimolar N-methylacetamide-water (NMA-W) mixture was re-examined by combining molecular dynamics (MD) simulations, DFT-based Natural Bond Orbital (NBO) and Atoms-in-Molecules (
Aim
analyses, and data-driven reconstruction of previously reported neutron scattering functions of the NMA-W liquid. MD simulations, using an AMBER-based force field for NMA and the SPC/E model for water, reproduce reasonably well the experimental structure factors and pair correlation functions of the liquid. In parallel, a Random Forest Regressor is employed as a nonparametric data-driven reconstruction tool, showing that the main features of the structural data can be represented as a continuous numerical representation of the scattering vector Q, providing a continuous numerical representation for comparison purposes. Three representative NMA-water clusters previously identified as the most probable local arrangements governing the liquid structure are further analyzed using NBO and Atoms-in-Molecules (
Aim
approaches. The analysis provides additional information on hydrogen-bond electronic structure, including charge-transfer effects, electron density at bond critical points, and topological characteristics of intermolecular interactions. Comparison with MD-derived lifetimes shows that stronger electronic interactions do not always correspond to longer-lived hydrogen bonds, reflecting the role of local network topology and dynamical fluctuations.
This work releases OpenGEM26 (Open Generated Ensemble of Molecules, 2026), a large-scale dataset comprising 200,000 unique molecules and 4.4 million conformations composed of H, C, N, O, S and Cl with up to ten heavy atoms, providing a high-quality resource and robust ML potential for efficient simulations of sulfur- a...
Accurate prediction of transition-metal hydride (TM-H) bond dissociation energies (BDEs) remains challenging because of strong electron correlation, relativistic effects, and nuclear quantum contributions. Here, we assess the performance of neural-network variational Monte Carlo (NN-VMC) based on the Psiformer ansatz f...
Aqsa Shaikh, L. Mitas, P. Ganesh et al.· 0 citations
The results demonstrate that GROMACS-GaMD provides a practical, GPU-enabled, collective-variable-free enhanced-sampling framework for biomolecular free-energy calculations, protein folding, and ligand-binding studies.
The GFN2-xTB semiempirical method performed better than all tested uMLIPs, proving the need for more off-equilibrium data in the parametrization of uMLIPs, where OMOL-1k-MD can be of high use.
Maximilian Bechtel, J. Steffen· npj Computational Materials· 0 citations
SALTED provides an open-source Python package for machine learning the quantum-mechanical electron density in molecular and condensed-phase systems based on input atomic coordinates and species, based on a linear atom-centered decomposition of the electron density.
Zekun Lou, Alan M. Lewis, T. Bernhard et al.· 0 citations
The present work revisits the methods within CP2K that turn electronic structure into dynamics, transport, and spectroscopic response, highlighting CP2K's unique capability to unify quantum chemistry with quantum and statistical mechanics within a versatile, holistic simulation environment.
Jan Wilhelm, Anna-Sophia Hehn, Hossam Elgabarty et al.· 1 citation· ⚡1
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