Avogadro

From Script | Spoken-Tutorial
Revision as of 11:26, 10 August 2016 by Snehalathak (Talk | contribs)

Jump to: navigation, search

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