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Related Concept Videos

Chemical Symbols01:09

Chemical Symbols

A chemical symbol is an abbreviation that is used to indicate an element or an atom of an element. For example, the symbol for mercury is Hg. We use the same symbol to indicate one atom of mercury (microscopic domain) or to label a container of many atoms of the element mercury (macroscopic domain).
Some symbols are derived from the common name of the element; others are abbreviations of the name in another language. Most symbols have one or two letters, but three-letter symbols have been used...
Chemical Formulas02:52

Chemical Formulas

A chemical formula presents information about the proportions of atoms constituting a particular chemical compound or molecule, mainly using symbols of elements and numbers. At times other symbols, such as dashes, parentheses, brackets, commas, plus, and minus signs, are also used. A chemical formula can be one of three types – molecular, empirical, and structural.
Formula Mass and Mole Concepts of Compounds02:56

Formula Mass and Mole Concepts of Compounds

Formula Mass of Covalent Compounds
Molecular Comparison of Gases, Liquids, and Solids02:26

Molecular Comparison of Gases, Liquids, and Solids

Particles in a solid are tightly packed together (fixed shape) and often arranged in a regular pattern; in a liquid, they are close together with no regular arrangement (no fixed shape); in a gas, they are far apart with no regular arrangement (no fixed shape). Particles in a solid vibrate about fixed positions (cannot flow) and do not generally move in relation to one another; in a liquid, they move past each other (can flow) but remain in essentially constant contact; in a gas, they move...
Overview of Advanced Functional Groups02:22

Overview of Advanced Functional Groups


Functional groups are groups of atoms with specific chemical properties that occur within organic molecules and are sometimes denoted as “R”. Functional groups can “functionalize” a compound by enabling it to adopt different physical and chemical properties.
Types of Advanced Functional Groups
The table below summarizes some of the major functional groups in organic chemistry.
Experimental Determination of Chemical Formula02:37

Experimental Determination of Chemical Formula

The elemental makeup of a compound defines its chemical identity, and chemical formulas are the most concise way of representing this elemental makeup. When a compound’s formula is unknown, measuring the mass of its constituent elements is often the first step in determining the formula experimentally.

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Updated: May 19, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
05:34

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

Marcus D Hanwell1, Donald E Curtis, David C Lonie

  • 1Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA. marcus.hanwell@kitware.com.

Journal of Cheminformatics
|August 15, 2012
PubMed
Summary

Avogadro is an open-source software for molecular visualization and editing, enhancing chemical data accessibility. It provides a flexible platform for building, analyzing, and visualizing molecular structures across various scientific disciplines.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Bioinformatics
  • Materials Science

Background:

  • Avogadro is an advanced, cross-platform molecule editor and visualizer.
  • It features high-quality rendering and a plugin architecture for extensibility.
  • The software utilizes the Chemical Markup Language (CML) for semantic data accessibility.

Purpose of the Study:

  • Detail the Avogadro library and its application programming interface (API).
  • Highlight its utility in research and education across chemistry, physics, materials science, and biology.
  • Showcase the extensibility through C++ or Python plugins for diverse applications.

Main Methods:

  • Development of a code library and API with 3D visualization capabilities.
  • Implementation of a rich graphical interface using dynamically loaded plugins.
  • Creation of example extensions, including a genetic algorithm for crystal structure prediction and an interface with PackMol for molecular dynamics simulations.

Main Results:

  • The Avogadro library provides a framework for molecular visualization and manipulation.
  • The Avogadro application offers a user-friendly interface with plugin support.
  • Example plugins demonstrate advanced functionalities like crystal structure prediction and simulation preparation.

Conclusions:

  • Avogadro serves as a semantic chemical builder and platform for visualization and analysis.
  • It offers users easy structure building, database integration, and format compatibility.
  • Developers can extend Avogadro's capabilities through its plugin mechanism for various scientific applications.