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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...

Molecular Shape and Polarity

Molecular Shape and Polarity

Dipole Moment of a Molecule

VSEPR Theory and the Basic Shapes

VSEPR Theory and the Basic Shapes

Overview of VSEPR Theory

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...

Microbial Morphologies

Microbial Morphologies

Bacterial and archaeal cells exhibit remarkable diversity in shape and structure, critical in their adaptability and functionality. Among bacteria, the most commonly observed shapes include cocci and bacilli. Cocci are spherical and may exist singly or in groupings such as pairs (diplococci), chains (streptococci), clusters (staphylococci), or tetrads. Bacilli, in contrast, are rod-shaped and can also occur as single cells, in pairs, or chains, depending on their environmental and genetic...

Molecular Geometry and Dipole Moments

Molecular Geometry and Dipole Moments

The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:

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Related Experiment Video

Updated: Jun 3, 2026

Assembly and Characterization of Polyelectrolyte Complex Micelles

Assembly and Characterization of Polyelectrolyte Complex Micelles

Published on: March 2, 2020

PubChem3D: Diversity of shape.

Evan E Bolton¹, Sunghwan Kim, 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. bolton@ncbi.nlm.nih.gov.

Journal of Cheminformatics

|March 23, 2011

Summary

Molecular shape diversity grows uniformly with volume. A single reference shape can represent many chemical structures, with larger volumes describing 40-70% of smaller volumes

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Analysis of SEC-SAXS data via EFA deconvolution and Scatter

Analysis of SEC-SAXS data via EFA deconvolution and Scatter

Published on: January 28, 2021

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Last Updated: Jun 3, 2026

Assembly and Characterization of Polyelectrolyte Complex Micelles

Assembly and Characterization of Polyelectrolyte Complex Micelles

Published on: March 2, 2020

Analysis of SEC-SAXS data via EFA deconvolution and Scatter

Analysis of SEC-SAXS data via EFA deconvolution and Scatter

Published on: January 28, 2021

Area of Science:

Computational chemistry
Cheminformatics
Molecular modeling

Background:

Explored shape diversity of 16.4 million biologically relevant molecules.
Analyzed 1.46 billion molecular conformers from PubChem.
Investigated shape diversity as a function of molecular volume.

Purpose of the Study:

Quantify the relationship between molecular volume and shape diversity.
Determine the rate of growth in molecular shape space.
Assess the representational capacity of molecular volumes for shape diversity.

Main Methods:

Determined shape similarity thresholds to maximize reference shapes per unit conformer volume.
Analyzed the rate of shape space growth as a function of volume.
Examined the ability of larger volumes to describe the shape diversity of smaller volumes.

Main Results:

Shape space growth rate, indicated by a decreasing similarity threshold, is smooth with increasing volume.
No correlation found between conformer count per volume and diversity.
A single reference shape can represent diverse chemical structures.
Larger volumes describe 40-70% of the shape diversity of smaller volumes.

Conclusions:

Molecular shape diversity exhibits uniform growth relative to volume and shape similarity.
This analysis provides a conservative estimate of true shape space diversity.
Findings are relevant given the distribution of known vs. theoretically possible chemicals.