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Unformatted text preview: create the carbon-carbon bonds. Using the Drawing Tool, connect the carbon atoms by drawing
line segments to connect them, as shown in Figure A3. Figure A3. Creating the carbon-carbon bonds for the n -butane molecule. The final step in creating an initial structure of the n-butane molecule is to add the hydrogen atoms. To do this,
select "Build → Add Hydrogens" from the menu at the top of the screen. Your final creation should appear similar
to that shown in Figure A4. 6 Figure A4. The completed initial structure of the n -butane molecule. Appendix 3 : P erforming M olecular M echanics C alculations w ith A vogadro
In order to perform a molecular mechanics calculation, a force field must be selected. Avogadro has a number of
force fields available, including MMFF94 (a force field primarily useful for organic and biological molecules) and
UFF (a multi-purpose force field that spans the periodic table). To designate the force field to be used, select
"Extensions → Molecular Mechanics → Setup Force Field" from the menu at the top of the screen. The force field
may then be selected from the pull-down menu in the window that pops up. For organic molecules, select MMFF94
as the force field to be used.
There are two basic types of molecular mechanics calculations that may be performed using Avogadro: single
point energy calculations and geometry optimization calculations.
A single point energy calculation determines the energy of the current geometry of the molecule as specified in
the current display window. No adjustments in bond lengths, bond angles, or other geometrical parameters are made.
To perform a single point energy calculation, select "Extensions → Molecular Mechanics → Calculate Energy" from
the menu at the top of the screen. The energy of the molecule will be displayed in kJ/mol. To redisplay the current
energy, you may also click on the "Messages" tab at the bottom of the screen; the Total Energy listed there is the
same as was displayed by the...
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This document was uploaded on 03/04/2014 for the course CHEM 380.37 at Illinois State.
- Fall '13