Click on the menu Exploring, submenu Conformations for toolbar display
Example 1: pentane
Quick conformations by branch rotation
Interactions: list of examples, buttons E, R1, click on bond (branch
rotation)
Load pentane from the list of examples
Display energy (button E)
Switch to bond rotate mode (button R1)
Click on the second C-C bond for 60 degree branch rotation (observe
energy change and repeat)
Repeat with third C-C axis
Determine three configurations with the lowest energy
Conformations with branch rotation and display of the torsion angle
Interactions: list of examples, button E, click on atom (selection), buttons
T, R, table, x, y, z
Load pentane from the list of examples (make sure that R1 button is no
selected)
Display energy (button E)
Select four consecutive C atoms (click on atoms)
Display torsion angle for the selection (button T)
Click on the R button to rotate branch around the axis between 2nd and 3rd atom for 60
degrees (observe energy and dihedral angle change and repeat)
To rotate around a different axis, turn off selection (button X) and
repeat steps from 3
Instead of step 5 you can list all all the rotations (button table)
Additionally, during rotations you can change the view to make the
rotation axis horizontal (button x), vertical (y) or perpendicular to
the screen (z)
Determine three configurations with the lowest energy
Example 2: cyclohexane
Conformations with moving atoms and optimization
Interactions: list of examples, button E, button M, free rotation of the
model, dragging atoms, optimize button, center button
Load cyclohexane from the list of examples
Display energy (button E)
Switch to atom move mode (button M)
Rotate the structure so that two opposing C-C bonds are covered
Move the outward C atoms to the boat position
Optimize structure (observe energy change)
Center structure
Conformations with moving atoms and display of torsion angle
Interactions: click on atom (selection), button T
As above, between steps 2 and 3 add:
Select 4 atoms in the ring
Display torsion angle (observe change in torsion angle)
Example 3:
Conformations with bond inversion
Load methylcyclohexane from the list of examples
Display energy (button E)
Switch to bond invert mode (button I)
Click on the C ring atom with methyl (observe energy change)
