Biomedical Engineering Reference
In-Depth Information
6
Molecular Mechanics Examples
As a rough guide, molecular mechanics (MM) is used these days to study possible
equilibrium conformations of large molecules. In this chapter I will give an example of
what can be routinely done at this level of theory.
There are many packages on the market, and everyone has their favourite (or has
it imposed on them by their employer). My two favourite packages are Gaussian 03
(http://www.gaussian.com) and HyperChem v7 (http://www.hyper.com). The latest release
of HyperChem is actually v8. In my opinion, everything boils down to the graphical user
interface (GUI) for MM applications on large molecules and HyperChem has a first-class
integratedGUI.You do not need a third party package to input and visualize the calculations.
So for this chapter I am going to use HyperChem and treat the very simple molecule
phenylanine (Figure 6.1) discussed earlier in the topic.
HO
O
NH
2
Phenylanine
Figure 6.1
Structure of phenylanine
6.1 Geometry Optimization
Geometry optimization requires a starting structure. I mentioned the Z-matrix in Chapter 5,
and that is how molecules were input before the days of the GUI. We have moved along
