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Unformatted text preview: Calculate Energy command, except the result is listed in kcal/mol instead of kJ/mol.
A geometry optimization calculation begins by determining the energy of the current geometry of the molecule.
Then the calculation continues by varying the geometrical parameters and recalculating the energy until a minimum
in the energy is achieved. The geometry at the minimum energy is said to be the optimized geometry or a stable
structure. To perform a geometry optimization calculation, select "Extensions → Optimize Geometry" from the
menu at the top of the screen. The energy of the optimized structure may be viewed by clicking on the "Messages"
tab at the bottom of the screen; the final energy shown is in kcal/mol. You should always make sure that the
geometry optimization is complete by repeating the calculation and making sure that the final energy is converged to
0.01 kcal/mol. 7
Appendix 4: Measuring and Adjusting Geometrical Parameters with A vogadro
It is sometimes useful to be able to measure and also change the bond lengths, bond angles, and torsional angles of a
molecular structure using Avogadro. MEASURING G EOMETRICAL P ARAMETERS
To measure geometrical parameters, use the Measure Tool, . Clicking with the left mouse button on two atoms will display the distance between them.
Clicking on three atoms in sequence will display distances 1-2 and 2-3 along with angle 1-2-3.
Finally, clicking on four atoms in sequence will display the associated distances and angles as well as the dihedral (or
torsional) angle 1-2-3-4. ADJUSTING G EOMETRICAL P ARAMETERS
To make adjustments to geometrical parameters, use the Bond Manipulation tool, . To adjust a bond length, left click on the bond to select it (a plane will be displayed that contains the bond). Then,
right click on one of the atoms and drag the mouse to change the bond length (the value is displayed at the bottom of
To adjust a bond angle, left click on one of the bonds that comprises the bond angle to select it and move the mouse
so that the plane that appears is rotated into the plane of the display. This is illustrated in Figure A5 for the water
molecule. Then, left click and drag the mouse to change the bond angle. Figure A5. Preparing to adjust the bond angle using the Bond Manipulation tool....
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This document was uploaded on 03/04/2014 for the course CHEM 380.37 at Illinois State.
- Fall '13