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Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Molecular Shapes

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Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...

Virtual Work for a System of Connected Rigid Bodies

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Virtual work is a powerful method used to solve problems involving several connected rigid bodies. When the system is in equilibrium, virtual work is zero. This allows the calculation of the resulting forces when a system undergoes a virtual displacement. When attempting to analyze such a system, first, use a free-body diagram, where an independent coordinate represents the configuration of the links, and mark its deflected position resulting from the positive virtual displacement.
Next,...

Induced-fit Model

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
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Electron Orbital Model

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Orbitals are the areas outside of the atomic nucleus where electrons are most likely to reside. They are characterized by different energy levels, shapes, and three-dimensional orientations. The location of electrons is described most generally by a shell or principal energy level, then by a subshell within each shell, and finally, by individual orbitals found within the subshells.
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Atoms and molecules interact with each other through intermolecular forces. These electrostatic forces arise from attractive or repulsive interactions between particles with permanent, partial, or temporary charges. The intermolecular forces between neutral atoms and molecules are ion–dipole, dipole–dipole, and dispersion forces, collectively known as van der Waals forces.

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Related Experiment Video

Updated: May 19, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

A collaborative molecular modeling environment using a virtual tunneling service.

Jun Lee¹, Jee-In Kim, Lin-Woo Kang

¹Department of Advanced Technology Fusion, Konkuk University, Seoul 143-701, Republic of Korea.

Journal of Biomedicine & Biotechnology

|August 29, 2012

Summary

This study introduces a novel networked virtual environment for collaborative molecular modeling, overcoming geographical limitations. The system integrates diverse molecular modeling tools, enabling seamless 3D structure research across different locations and platforms.

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Area of Science:

Computational chemistry
Structural biology
Virtual reality

Background:

Collaborative 3D molecular modeling is hindered by time zone and location differences.
Existing networked environments lack integration across diverse computing platforms and user roles.

Purpose of the Study:

To develop an integrated collaborative molecular modeling environment overcoming spatial and temporal barriers.
To enhance collaboration by integrating different molecular modeling systems.

Main Methods:

Proposed a virtual tunneling service for integrating disparate molecular modeling systems.
Integrated Co-Coot (collaborative crystallographic object-oriented toolkit) with VRMMS (virtual reality molecular modeling system) via a collaborative tunneling system.

Main Results:

The integrated system demonstrated reliable performance in pilot experiments.
Achieved both quantitative and qualitative validation of the collaborative environment.

Conclusions:

The proposed virtual tunneling approach effectively integrates different molecular modeling systems.
The developed environment facilitates robust collaborative 3D molecular modeling research.