Exercise 6 Return to Index

Introduction

The previous exercise demonstrated how to measure bond lengths, bond angles, and torsion angles with the VMK. That exercise involved a model of propanoic acid that was constructed using the Molecular Editor control panel. The VMK has the capability to display other molecular properties of propanoic acid when a model of that compound is loaded from the Pre-Assembled MM Library Menu, which is located on the Model Tools control panel. Three of those properties-partial charges, the van der Waals surface area, and electrostatic potentials-are illustrated in this exercise.

Instructions

Images of the partial charges, the van der Waals surface, and an electrostatic potential map (MEP) for propanoic acid are presented in Figure 6.1 for comparison purposes.

1. Activate the Model Tools control panel and load a model of propanoic acid from the Pre-Assembled MM Library Menu.

2. Click on the Atom Colors:partial charge link.

The partial charge of each atom in the molecule is displayed. These partial charges are calculated using an MMFF94 algorithm. Calculations using other algorithms produce different charge distributions.

3. Click the Clean Up:clear link to remove the partial charges.

4. Display the van der Waals surface using the Surfaces:vdW option.

Interactions between two molecules beyond distances greater than their van der Waals surface are minimal, while penetration of the surface of one molecule by the van der Waals surface of another molecule generates a repulsive interaction.

5. Clear the vdW surface.

6. Select Surfaces:MEP 100.

MEP stands for molecular electrostatic potential. Roughly speaking it is a color-coded map of the relative electron density along a surface that is a specific distance from the nuclei of the molecule. That distance is greater for MEP 100 than it is for MEP 80, the two options available in the VMK. By convention, areas of relatively high electron density are colored red, while those of relatively low electron density are shown in blue. Intermediate colors imply intermediate electron densities.

Figure 6.1

Three presentations of the electron distribution in propanoic acid

7. Clear the MEP 100 and display the MEP 80.

The introduction to Exercise 3 outlined the biosynthetic pathway from the amino acid tyrosine to the hormone norepinephrine. Let's take "Route 7" and drive on to tyrosine.