DFT calculations in solution systems: solvation energy, dispersion energy and entropy

SC Liu, XR Zhu, DY Liu, DC Fang - Physical Chemistry Chemical …, 2023 - pubs.rsc.org
DFT calculations of reaction mechanisms in solution have always been a hot topic,
especially for transition-metal-catalyzed reactions. The calculation of solvation energy is …

Design, parameterization, and implementation of atomic force fields for adsorption in nanoporous materials

D Dubbeldam, KS Walton, TJH Vlugt… - Advanced Theory and …, 2019 - Wiley Online Library
Molecular simulations are an excellent tool to study adsorption and diffusion in nanoporous
materials. Examples of nanoporous materials are zeolites, carbon nanotubes, clays, metal …

In silico identification of Tretinoin as a SARS-CoV-2 envelope (E) protein ion channel inhibitor

D Dey, S Borkotoky, M Banerjee - Computers in biology and medicine, 2020 - Elsevier
Viroporins are oligomeric, pore forming, viral proteins that play critical roles in the life cycle
of pathogenic viruses. Viroporins like HIV-1 Vpu, Alphavirus 6 K, Influenza M2, HCV p7, and …

Extraction of material properties through multi-fidelity deep learning from molecular dynamics simulation

M Islam, MSH Thakur, S Mojumder… - Computational Materials …, 2021 - Elsevier
Simulation of reasonable timescales for any long physical process using molecular
dynamics (MD) is a major challenge in computational physics. In this study, we have …

The impact of mechanical vibration at cathode on hydrogen yields in water electrolysis

P Purnami, NW Satrio, YK Sofi'i, ING Wardana - Journal of Power Sources, 2024 - Elsevier
This study investigates the utilization of mechanical vibration to enhance the hydrogen
evolution reaction (HER) in electrolysis processes. By varying the force magnitude and …

Computational investigation of Moringa oleifera phytochemicals targeting EGFR: molecular docking, molecular dynamics simulation and density functional theory …

MA Yousaf, SA Anwer, S Basheera… - Journal of Biomolecular …, 2024 - Taylor & Francis
Epidermal growth factor receptor (EGFR) is a prominent target for anticancer therapy due to
its role in activating several cell signaling cascades. Clinically approved EGFR inhibitors are …

The MolSSI driver interface project: A framework for standardized, on-the-fly interoperability between computational molecular sciences codes

TA Barnes, E Marin-Rimoldi, S Ellis… - Computer Physics …, 2021 - Elsevier
Abstract The MolSSI Driver Interface (MDI) Project provides a standardized API for fast, on-
the-fly communication between computational molecular sciences codes. This greatly …

[HTML][HTML] Prediction of Dielectric Constant in Series of Polymers by Quantitative Structure-Property Relationship (QSPR)

E Ascencio-Medina, S He, A Daghighi, K Iduoku… - …, 2024 - pmc.ncbi.nlm.nih.gov
This work is devoted to the investigation of dielectric permittivity which is influenced by
electronic, ionic, and dipolar polarization mechanisms, contributing to the material's capacity …

Inhibition of Monkeypox Virus DNA Polymerase Using Moringa oleifera Phytochemicals: Computational Studies of Drug-Likeness, Molecular Docking, Molecular …

MA Yousaf, S Basheera, S Sivanandan - Indian Journal of Microbiology, 2024 - Springer
The emergence of zoonotic monkeypox (MPX) disease, caused by the double-stranded
DNA monkeypox virus (MPXV), has become a global threat. Due to unavailability of a …

[HTML][HTML] SAMPL9 blind predictions for toluene/water partition coefficients using nonequilibrium alchemical approaches

P Procacci, G Guarnieri - The Journal of Chemical Physics, 2023 - pubs.aip.org
We present our blind prediction of the toluene–water partition coefficients in the context of
the SAMPL9 challenge. For the calculation of the solvation free energies in water, toluene …