Introduction

Molecular properties are highly dependent on molecular structures. For a very long time, models made of plastic or metal materials that one can hold and manipulate, are used to study the three-dimensional nature of molecules. But these are very crude and inadequate even for presenting bond angles and lengths. Molecular modeling based on quantum mechanics and molecular mechanics has been a powerful research tool in presenting and studying molecular structures and properties. Properties such as energies, bond lengths, bond angles, dihedral angles, dipole moments, conformations, and equilibrium distributions can be readily studied and predicted by computer molecular modeling. While limited to mainframe and workstations in the early years, this technique is now available to the powerful desktop PC’s of today. This technique is also well suited for teaching important concepts in organic chemistry in a hands-on and interactive manner.

This module is built around PC’s with Pentium II or III processors with Windows 95, 98 or 2000 and PCMODEL v7.5 from Serenasoft. Open PCMODEL and the Web site according to instructions from your professor. Put the PCMODEL screen and WEB instruction screen on the same screen (top & bottom) for easy reference. Screens can be moved and resized by the normal Windows maneuvers. The instructions in the lab exercises refer to commands found on the horizontal “Menu Bar” and the vertical “Tools Bar” and the submenus within these. Menu commands are colored “sky blue” and Tools command are colored “Red” for easy reference. The most useful structure view is stick figures with hydrogens and hetero atoms showing. You can return to this by clicking View, Stick Figures and View, Labels, and choose “Hydrogens and lone pairs” option. Structures can be rotated by right click on screen and drag or more precisely rotated, moved or resized by clicking on View, Control Panel and use arrows in the Dials Panel. To erase an old screen, click Edit, Erase, Yes. Additional useful links are in blue. And as you go through the exercises, fill in the Report sheet handout provided and print results and save files as directed by your instructor. Also build, whenever feasible, models of the molecules being examined with your modeling kit. Holding and manipulating models in your hands give you unique perspectives about structures.

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