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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.

Structure of Amines

Structure of Amines

The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’ carbon–carbon bond (154 pm). These aspects are illustrated in Figure...

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...

VSEPR Theory

VSEPR Theory

Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...

VSEPR Theory and the Basic Shapes

VSEPR Theory and the Basic Shapes

Overview of VSEPR Theory

Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.

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Related Experiment Video

Updated: Jun 14, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

The PubChem chemical structure sketcher.

Wolf D Ihlenfeldt¹, Evan E Bolton, Stephen H Bryant

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA. bryant@ncbi.nlm.nih.gov.

Journal of Cheminformatics

|March 20, 2010

Summary

PubChem now offers a web-based chemical structure editor for searching compounds. This tool avoids complex technologies like Java applets, ensuring broad accessibility for chemical structure drawing and querying.

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Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

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Last Updated: Jun 14, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Area of Science:

Chemical Informatics
Bioinformatics
Web Technologies

Background:

PubChem is a vital public resource for chemical and bioactivity data.
Efficient chemical structure searching requires interactive sketching tools.
Existing web-based sketchers often rely on problematic technologies like Java applets or platform-specific plugins.

Purpose of the Study:

To develop a universally accessible web-based chemical structure sketching tool for PubChem.
To overcome limitations of existing sketchers, particularly their reliance on complex or platform-dependent technologies.
To enable convenient structure-based querying of the PubChem compound database.

Main Methods:

Developed a chemical structure editor utilizing Common Gateway Interface (CGI) server processing.
Implemented client-side JavaScript functions for interactive sketching.
Employed image sequence streaming for rendering the drawing interface.
Ensured no reliance on specific runtime libraries or browser configurations on the client-side.

Main Results:

The developed sketcher is completely platform-independent.
It functions effectively across all major web browsers, including older versions.
The tool eliminates the need for Java applets or plug-ins, enhancing accessibility.
Successfully integrated into PubChem for structure-based searching.

Conclusions:

The new PubChem structure editor provides a robust, accessible solution for chemical structure searching.
Its platform-independent and plugin-free design significantly broadens user accessibility.
This advancement facilitates more convenient and widespread use of PubChem's chemical information resources.