Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Valence Bond Theory02:45

Valence Bond Theory

50.5K
Overview of Valence Bond Theory
50.5K
Valence Bond Theory02:42

Valence Bond Theory

11.4K
Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
11.4K
Chemical Bonds02:40

Chemical Bonds

23.0K

Atoms participate in a chemical bond formation to acquire a completed valence-shell electron configuration similar to that of the noble gas nearest to it in atomic number. Ionic, covalent, and metallic bonds are some of the important types of chemical bonds. Bond energy and bond length determine the strength of a chemical bond.
Types of Chemical Bonds
An ionic bond is formed due to electrostatic attraction between cations and anions. Often, the ions are formed by the transfer of electrons...
23.0K
MO Theory and Covalent Bonding02:40

MO Theory and Covalent Bonding

14.2K
The molecular orbital theory describes the distribution of electrons in molecules in a manner similar to the distribution of electrons in atomic orbitals. The region of space in which a valence electron in a molecule is likely to be found is called a molecular orbital. Mathematically, the linear combination of atomic orbitals (LCAO) generates molecular orbitals. Combinations of in-phase atomic orbital wave functions result in regions with a high probability of electron density, while...
14.2K
Bond Energies and Bond Lengths02:49

Bond Energies and Bond Lengths

31.6K
Stable molecules exist because covalent bonds hold the atoms together. The strength of a covalent bond is measured by the energy required to break it, that is, the energy necessary to separate the bonded atoms. Separating any pair of bonded atoms requires energy — the stronger a bond, the greater the energy required to break it.
31.6K
Covalent Bonds01:08

Covalent Bonds

12.0K
Overview
When two atoms share electrons to complete their valence shells, they create a covalent bond. An atom's electronegativity—the force with which shared electrons are pulled towards an atom—determines how the electrons are shared. Molecules formed with covalent bonds can be either polar or nonpolar. Atoms with similar electronegativities form nonpolar covalent bonds; the electrons are shared equally. Atoms with different electronegativities share electrons unequally,...
12.0K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Two-dimensional Sc2N MXenes as efficient solid catalysts for CO2 adsorption and conversion: a density functional theory study.

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences·2026
Same author

The Impact of Ageing on Fibrillar Collagens.

Sub-cellular biochemistry·2026
Same author

A density functional theory study of thermally activated water splitting on the CuWO4 (010) surface.

The Journal of chemical physics·2025
Same author

Vacancy Ordering in Fe-Deficient Iron Sulfide with the NiAs-Type Structure.

The journal of physical chemistry. C, Nanomaterials and interfaces·2025
Same author

Thermodynamics of hydrogen adsorption on ruthenium <i>fcc</i> surfaces: a density functional theory study.

Physical chemistry chemical physics : PCCP·2025
Same author

Water Is Cool: Advanced Phonon Dynamics in Ice Ih and Ice XI via Machine Learning Potentials and Quantum Nuclear Vibrations.

Journal of chemical theory and computation·2025

Related Experiment Video

Updated: Feb 17, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

5.1K

ForceGen: atomic covalent bond value derivation for Gromacs.

Anthony Nash1, Thomas Collier2, Helen L Birch3

  • 1Department of Physiology, Genetics, and Anatomy, University of Oxford, Oxford, UK. anthony.nash@dpag.ox.ac.uk.

Journal of Molecular Modeling
|December 8, 2017
PubMed
Summary

ForceGen is a new Java tool that extracts atomic bond force values from quantum mechanical calculations. This enables more accurate computational models for proteins, ligands, and post-translational modifications in molecular simulations.

Keywords:
Force valuesGromacsHessianLaplacian bond orderMolecular dynamics

More Related Videos

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.7K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.0K

Related Experiment Videos

Last Updated: Feb 17, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

5.1K
Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.7K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.0K

Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Biophysics

Background:

  • Crystallographic protein structures often contain ligands, small molecules, and post-translational modifications.
  • Standard simulation software lacks readily available atomic bond force values for these components.
  • Accurate force field parameters are crucial for reliable molecular simulations.

Purpose of the Study:

  • To present ForceGen, a Java tool for extracting bond stretch and angle force constants.
  • To generate parameters compatible with common computational chemistry force fields.
  • To facilitate the inclusion of diverse molecular entities in atomistic simulations.

Main Methods:

  • Utilizing Gaussian vibrational frequency analysis to obtain the Hessian matrix.
  • Extracting bond stretch and bond angle force constants and equilibrium values from the Hessian.
  • Formatting output for compatibility with Gromacs topology.
  • Deriving Laplacian bond orders to correlate with quantum mechanical models.

Main Results:

  • ForceGen successfully extracts force field parameters from quantum mechanical calculations.
  • Parameters were derived for an organic solvent (toluene), a post-translational modification (protein crosslink), and amino acid ligands of a zinc ion.
  • Molecular Mechanics simulations of toluene validated the generated parameters, showing good agreement with quantum mechanical structures and experimental density.

Conclusions:

  • ForceGen provides a method to generate essential force field parameters for non-standard molecular components.
  • The tool enhances the accuracy and applicability of computational models in structural biology and drug discovery.
  • Accurate parameterization is key to advancing molecular simulations of complex biological systems.