CBE 422 - Using Hyperchem

Using HyperChem

HyperChem is a package for performing Molecular Mechanics, Molecular Dynamics and ab initio calculations for chemical systems.

The first screen that one sees on startup looks as follows:

First, let's create a simple molecule, propane. This is done by selecting Carbon as the element of interest and then using the "Draw" tool to sketch out the backbone. Don't worry about the bond lengths, these will be set at their proper values at a later stage. At the end of the process, the screen should look like this:

The next step is to "add hydrogens," under "Build:"

This is followed by a "Geometry Optimization" step (under "Compute") that minimizes the energy of the structure using the selected force field (MM+ in this case):

The final, energy-minimized structure is shown below.

One can "select" specific atoms using the

button. For example, selecting the first two carbon atoms gives the bond distance:

One can obtain an energy plot for varying this distance by selecting "Compute" "Potential", which brings up a screen defining the limits:

The resulting 1-dimensional potential is shown below. Note that in order to obtain proper titles (esp. for the x axis), one needs to modify the graph properties.

Some of the parameters used in the calculations can be checked (and edited if necessary) by using "Setup" "Edit Parameters" - for example, the O atom Lennard-Jones parameters in the Charmm27 force field are \eps=0.1521 kcal/mol, and \sigma/2 = 1.7682 Å.

"Quantitative structure-activity properties" (QSAR) of a molecule in a specific conformation can be obtained through the following menu:

For example, the "solvent-accessible" surface area can be obtained by using a probe of a certain size and constructing a grid of points around the molecule of interest. For the case of ethane at the minimum-energy conformation we obtain a surface area of ~175 Å²:

This calculation was based on a probe radius of 1.4 Å, roughly corresponding to water. A larger probe will result in a larger surface area; the probe size is set through the "options" menu.