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

Reaction Mechanisms03:06

Reaction Mechanisms

29.7K
Chemical reactions often occur in a stepwise fashion, involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs.
For instance, the decomposition of ozone appears to follow a mechanism with two steps:
29.7K
Multi-Step Reactions02:31

Multi-Step Reactions

8.3K
Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...
8.3K
Temperature Dependence on Reaction Rate02:55

Temperature Dependence on Reaction Rate

87.2K
The Collision Theory
Atoms, molecules, or ions must collide before they can react with each other. Atoms must be close together to form chemical bonds. This premise is the basis for a theory that explains many observations regarding chemical kinetics, including factors affecting reaction rates.
The collision theory is based on the postulates that (i) the reaction rate is proportional to the rate of reactant collisions, (ii) the reacting species collide in an orientation allowing contact between...
87.2K
Introduction to Chemical Reactions01:23

Introduction to Chemical Reactions

11.3K
All chemical reactions begin with a reactant, the general term for one or more substances entering the reaction. Sodium and chloride ions, for example, are the reactants in the production of table salt. One or more substances produced by a chemical reaction are called the product. Chemical reactions follow the law of conservation of mass, which means that matter cannot be created nor destroyed in a chemical reaction. The components of the reactants—the number of atoms and the...
11.3K
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

9.5K
Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
9.5K
Radical Reactivity: Overview01:11

Radical Reactivity: Overview

2.5K
Radicals, the highly reactive species, gain stability by undergoing three different reactions. The first reaction involves a radical-radical coupling, in which a radical combines with another radical, forming a spin‐paired molecule. The second reaction is between a radical and a spin‐paired molecule, generating a new radical and a new spin‐paired molecule. The third reaction is radical decomposition in a unimolecular reaction, forming a new radical and a spin‐paired...
2.5K

You might also read

Related Articles

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

Sort by
Same author

LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations.

Journal of chemical information and modeling·2024
Same author

Type Label Framework for Bonded Force Fields in LAMMPS.

The journal of physical chemistry. B·2024
Same author

Evolution of Glassy Carbon Derived from Pyrolysis of Furan Resin.

ACS applied engineering materials·2023
Same author

Molecular Dynamics Modeling of Interfacial Interactions between Flattened Carbon Nanotubes and Amorphous Carbon: Implications for Ultra-Lightweight Composites.

ACS applied nano materials·2022
Same author

Internal circulation and mixing within tight-squeezing deformable droplets.

Physical review. E·2021
Same author

Voxelized Atomic Structure Potentials: Predicting Atomic Forces with the Accuracy of Quantum Mechanics Using Convolutional Neural Networks.

The journal of physical chemistry letters·2020

Related Experiment Video

Updated: Dec 2, 2025

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

4.9K

Chemical Reactions in Classical Molecular Dynamics.

Jacob R Gissinger1, Benjamin D Jensen2, Kristopher E Wise2

  • 1Materials Science and Engineering Program, University of Colorado, Boulder, CO 80309-0424, USA.

Polymer
|November 5, 2020
PubMed
Summary
This summary is machine-generated.

A new algorithm, fix bond/react, enables multi-step chemical reactions in atomistic molecular dynamics (MD) simulations. This method accurately models polymerization and crosslinking processes using LAMMPS.

More Related Videos

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

13.1K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.7K

Related Experiment Videos

Last Updated: Dec 2, 2025

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

4.9K
Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

13.1K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.7K

Area of Science:

  • Computational Chemistry
  • Materials Science
  • Polymer Science

Background:

  • Atomistic molecular dynamics (MD) simulations are crucial for understanding chemical processes at the atomic level.
  • Simulating chemical reactions, especially multi-step mechanisms, within traditional MD frameworks using fixed-valence force fields presents significant challenges.
  • Existing methods often struggle to accurately capture dynamic bond changes during complex reaction pathways.

Purpose of the Study:

  • To introduce a novel algorithm, fix bond/react, for incorporating multi-step reaction mechanisms into atomistic MD simulations.
  • To enable dynamic bonding topology modifications within the LAMMPS simulation environment.
  • To demonstrate the algorithm's capability in simulating complex polymerization and crosslinking reactions.

Main Methods:

  • Developed and implemented the fix bond/react algorithm within LAMMPS.
  • Utilized pre- and post-reaction bonding templates to define specified chemical transformations.
  • Employed interatomic separation and a generalized topology matching algorithm to identify reactants.
  • Incorporated topology conversion and dynamic relaxation to manage reaction intermediates and products.

Main Results:

  • Successfully simulated the condensation polymerization of nylon 6,6.
  • Demonstrated the algorithm's ability to model the formation of a highly-crosslinked epoxy system.
  • Validated the robustness, stability, and computational efficiency of the fix bond/react algorithm.

Conclusions:

  • The fix bond/react algorithm provides a powerful tool for integrating complex chemical reactions into MD simulations.
  • This method enhances the capability of atomistic simulations for studying polymer formation and network development.
  • Further improvements could expand the algorithm's applicability to a wider range of chemical systems.