A Simple Electron-Density Based Force Field Model for High-Energy Interactions between Atoms and Molecules.

J Phys Chem A

Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstraße 25, Innsbruck 6020, Austria.

Published: February 2024

In high-energy molecular dynamics or Monte Carlo simulations, standard force fields optimized for simulations at ambient temperatures are inadequate. This is largely because their repulsive parts have been regarded as not very significant, even well below zero interaction energies. It is, therefore, not obvious which force fields to resort to for simulating hot gases or plasmas. A force field model that uses the electronic densities of noninteracting atoms or molecules within the pair approximation is introduced. We start by deriving a naïve model that neglects any exchange and correlation effects between the electronic clouds and then correct this model by adding a term calibrated from calculations using the CCSD(T)/cc-pVTZ level of theory. The resulting expression for this term can be regarded as a simple exchange-correlation function. We compare the results for the repulsive part of the potential energy hypersurfaces with the force fields commonly used on some dimers of small molecules.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10875675PMC
http://dx.doi.org/10.1021/acs.jpca.3c06724DOI Listing

Publication Analysis

Top Keywords

force fields
12
force field
8
field model
8
atoms molecules
8
force
5
simple electron-density
4
electron-density based
4
based force
4
model
4
model high-energy
4

Similar Publications

Exposure to anthracene can cause skin and eye irritation, respiratory issues, and potential long-term health risks, including carcinogenic effects. It is also toxic to aquatic and human life and has the potential for long-term environmental contamination. This study aims to alleviate the adverse environmental effects of anthracene through fungal degradation, focusing on bioremediation approaches using bioinformatics.

View Article and Find Full Text PDF

Supramolecular polymers represent a distinctive class of polymers exhibiting similarities with covalent polymers, while also showcasing distinctive attributes such as responsiveness, reversibility, self-healing, and dynamism, which are conferred upon them by non-covalent interactions including hydrogen bonding, electrostatic interactions, van der Waals forces, π-π arrangements, and donor-acceptor interactions, among others. The noteworthy features of these supramolecular polymers have attracted considerable interest across diverse fields of science and technology, spanning electrochemistry, environmental science, drug delivery and tissue engineering. Nonetheless, the prevailing research focus in the realm of supramolecular polymers revolves around the advancement of novel methodologies aimed at synthesizing a broad spectrum of polymers characterized by diverse topologies.

View Article and Find Full Text PDF

This Extracorporeal Life Support Organization guideline describes early rehabilitation or mobilization of patients on extracorporeal membrane oxygenation (ECMO). The guideline describes useful and safe practices put together by an international interprofessional team with extensive experience in the field of ECMO and ECMO rehabilitation or mobilization. The guideline is not intended to define the delivery of care or substitute sound clinical judgment.

View Article and Find Full Text PDF

Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands.

J Chem Inf Model

January 2025

Schrödinger Incorporated, Cambridge, Massachusetts 02142, United States.

Article Synopsis
  • Predicting how well ligands bind to nucleic acids is challenging, which limits the development of small-molecule drugs for diseases like cancer and infections.
  • Recent advancements in computational methods, particularly free-energy perturbation (FEP), have improved predictions for protein-ligand binding affinities, but its effectiveness for nucleic acids was unclear.
  • This study found that using FEP+ software with the OPLS4 force field can accurately predict binding energies for over 100 ligands interacting with DNA/RNA, achieving predictions that closely match experimental data and could aid drug discovery.
View Article and Find Full Text PDF

Atomic force microscopy (AFM) has reached a significant level of maturity in biology, demonstrated by the diversity of modes for obtaining not only topographical images but also insightful mechanical and adhesion data by performing force measurements on delicate samples with a controlled environment (e.g., liquid, temperature, pH).

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!