Avogadro

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Avogadro

Avogadro is a free and open source, advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, material science, bioinformatics, etc.

Avogadro has features for high quality rendering, interactive tools, commands and powerful plug-in architecture. The features also include easy import of chemical files from Open Babel, multiple computational packages, crystals and biomolecules.

It is easy to install and source code is available under GNU GPL.


The Spoken Tutorial Effort for Avogadro has being contributed by Madhuri Ganapathi and Dr. Snehalatha Kaliappan.




Basic Level

1. Build Molecules

  • Import Molecules from chemical database
  • Rotate the molecules
  • Zoom in and zoom out the structures
  • Build molecules on the Panel using Draw tool
  • Set up force field and optimize the geometry using optimization tool
  • Measure bond lengths, bond angles and dihedral angles
  • Show fragment library
  • Build DNA/RNA molecules and peptides

2. Edit Molecules

  • Add and delete atoms
  • Add and delete bonds
  • Rotate bonds and change length of the bond
  • Change hydrogen to methyl group
  • Copy, paste and join structures.

3. Create Surfaces

  • View properties of the molecule
  • Label the atoms with partial charge
  • Create Van der waals surface
  • Color the surface according to the electrostatic potential energies.

4. Hydrogen Bonding

  • How to configure Avogadro
  • Show Intermolecular hydrogen bonding
  • Show Intramolecular hydrogen bonding
  • Measure length of hydrogen bonds
  • Show Force display type in water molecules
  • Show dipole moments in molecules

Intermediate Level

5. General Features in Avogadro

  • Proton transfer in compounds by changing pH values
  • Load crystal structures from Crystal library
  • Explain about Miller indices and planes
  • Show various Miller planes in crystal systems
  • Build super cell in three dimensions
  • Show geometries in coordination compounds
  • Build carbon nano tubes

6. Stereoisomerism

  • Define stereoisomerism
  • Define conformational isomerism
  • Show conformations of 1,2-dichloroethane
  • Show conformations of cyclohexane
  • Define geometrical isomerism
  • Demonstrate geomertical isomerism
  • Explain R S configuration priority rules
  • Demonstrate R-S configurations with examples

Advanced Level

6. File Extensions

  • Prepare input files for computational chemistry programmes such as: GAMESS, Gaussian, MOPAC, NWChem etc.
  • View Molecular orbitals and calculated IR spectrum using output files generated from GAMESS and Gaussian software.

Contributors and Content Editors

Madhurig, Snehalathak