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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

Molecular Shapes

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...

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The pV diagram, which is a graph of pressure versus volume of the gas under study, is helpful in describing certain aspects of the substance. When the substance behaves like an ideal gas, the ideal gas equation describes the relationship between its pressure and volume. On a pV diagram, it is common to plot an isotherm, which is a curve showing p as a function of V with the number of molecules and the temperature fixed. Then, for an ideal gas, the product of the pressure of the gas and its...

Molecular Kinetic Energy

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The word "gas" comes from the Flemish word meaning "chaos," first used to describe vapors by the chemist J. B. van Helmont. Consider a container filled with gas, with a continuous and random motion of molecules. During collisions, the velocity component parallel to the wall is unchanged, and the component perpendicular to the wall reverses direction but does not change in magnitude. If the molecule’s velocity changes in the x-direction, then its momentum is changed.

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Related Experiment Video

Updated: Mar 14, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Mol* web molecular graphics engine.

Alexander S Rose¹, Gianluca Tomasello², Áron Samuel Kovács³

¹Research Collaboratory for Structural Bioinformatics (RCSB), San Diego Supercomputer Center, University of California San Diego, San Diego, California, USA.

Protein Science : a Publication of the Protein Society

|March 13, 2026

Summary

This summary is machine-generated.

The Mol* toolkit

Keywords:

GPU accelerated global illumination immersive AR/VR mesoscale molecular models web molecular graphics

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Area of Science:

Computational biology
Molecular visualization
Web technologies

Background:

Web-based molecular graphics utilize modern web technologies for interactive visualization.
High-performance frameworks are essential for handling complex molecular data.

Purpose of the Study:

To present the graphics engine powering the Mol* toolkit.
To highlight its capabilities for high-fidelity molecular visualization.

Main Methods:

Developed a graphics engine with a comprehensive styling system and optimized rendering primitives.
Implemented level-of-detail management, GPU instancing, and spatial acceleration for large scenes.
Integrated screen-space global illumination and AR/VR support.

Main Results:

Achieved efficient handling of large-scale molecular scenes.
Delivered high-quality, real-time visualization with flexibility and visual fidelity.
Enabled immersive molecular exploration across various scales.

Conclusions:

The Mol* graphics engine offers a powerful, web-native solution for molecular visualization.
Its capabilities support diverse applications in academia and industry.
Facilitates engaging and high-fidelity exploration of molecular systems.