User`s guide

2. Building Molecules
Adjust Tool and Dihedral Angle Dialog Box
To adjust the order of a bond, ctrl-click the bond to bring up a bond order context menu, from
which the desired bond order (single, double, triple) may be chosen. To adjust the hybridization
of an atom, ctrl-click the atom to bring up a hybridization context menu, from which the desired
hybridization (sp, sp2, sp3, dsp3, d2sp3) may be chosen.
Bond Order and Atom Hybridization Context Menus
F. Cleaning-Up Structures
Cleaning-up a chemical structure adds missing hydrogen atoms and sets bond lengths and angles
to ideal values. The resulting structure is usually a good guess of the starting geometry for a
calculation, although one may need to manually adjust dihedral angles to achieve a specifically
desired conformation.
The clean-up procedure involves three steps using basic organic chemistry rules:
• Add Hydrogens: Empty valencies are filled with hydrogen atoms
• Hybridization: Each atom is assigned a hybridization
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