Avogadro

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 outputfiles generated from GAMESS and

  Gaussian software.

Contributors and Content Editors

Madhurig, PoojaMoolya, Pratik kamble, Snehalathak