The Geometry of Small Molecules

Although the fine details of molecular structure such as precise bond angles and bond lengths are important, our first mental impression of a molecule has to do with its general shape. Predicting the shape of a molecule, or of the bonds around a particular atom in a particular setting, is the second skill a chemist acquires, after learning to wash glassware. In this exercise, we’ll look at a collection of molecules containing single bonds to see how well we and the modelbuilder program can predict shapes.

Below are some of the standard molecular examples of the application of the Valence Shell Electron Pair Repulsion Model. The table contains an example of each of the possible combination of bond pairs and lone pairs. For each, determine the predicted VSEPR shape. Then construct the molecule and see how well the modelbuilder does at predicting the VSEPR shape.

Now, starting with the modelbuilder geometry for each molecule in the table and carry out a geometry optimization to see what a semi-empirical molecular orbital method such as AM1 can do to give more realistic result. In carrying out the calculations you must be aware of two problems. One is that if a geometry calculation starts from a very symmetric structure, it will remain symmetric since the forces on the atoms will also be symmetric. Another problem is that one may drift into a local minimum that is not the true minimum energy geometry.

To overcome this, start with several skewed geometries much different than the one presented by the modelbuilder. This can be done by selecting various angles and using the edit menu to set a bond angle. Another option is to take advantage of a rarely used feature of HyperChem to allow a translation of just a portion of the molecule: Go to the "preferences" item in the file menu of HyperChem, open up the submenu and click on "tools". On the tools display, uncheck the item which says "whole molecule translation". (Be certain to come back later and turn this item back on to prevent accidental destruction of your carefully constructed molecules.). Then select any atom, choose the translation cursor, and, holding down the right mouse button, move just the single atom. Use the resulting geometry as a starting point for a geometry optimization.

All of the example molecules chosen above are made of atoms for which AM1 parameters are available in HyperChem.

Raymond Chang, Chemistry, 4th ed., (McGraw-Hill, New York), 1991.