Transcription Activity Guide 3d Molecular Designs

Purpose: When we first consider the structure of organic molecules, most of us realize that three-dimensional structure is both supremely important and sometimes hard to visualize. Once upon a time, every organic chemistry student was encouraged to buy a small set of molecular models (wood, metal or plastic) to help learn the characteristic shapes of all those curious combinations of sp² and sp³ hybridizations. Biochemists built elaborate (and sometimes quite lovely) 3D models of their favorite proteins. Nowadays, molecular modeling software is available for the same purposes.

Molecular viewing software should allow you to easily create molecules (or load them from a variety of file formats), optimize the geometry if needed, then display the structures in a variety of formats: "ball and stick" and "wire frame" mimic some of the older wooden and metal models, while semi-transparent electron density formats provide information not available from physical model kits. Most packages also allow the color coding or labeling of atoms (or residues) and automatic rotation of the image to fool the eye into seeing 3 dimensions on a flat display screen.

Recommended: For building, optimizing and displaying small molecules quickly, the ACD/3D viewer software from Advanced Chemistry Development is hard to beat. It is an 'add-on' to their invaluable ChemSketch 12.0 molecular drawing software, which is why they are downloaded from the same page. Switching between drawing (2D) and viewing (3D) modes is quick and painless, and the viewer offers six customizable display formats, automatic rotation, and (limited) imports of other file formats. Strongly recommended for students of organic chemistry who are still learning to see molecules in their mind's eye. A short demonstration video is available for download below. ACD/3D viewer, like ChemSketch, runs in Windows and Linux but not on the MacOS.

On the other hand, if you want to look at larger molecules, the Molegro Molecular Viewer from Molegro Bioinformatics is a good choice. Like ChemSketch, the Molegro viewer is commercial freeware with an easy-to-use interface and good quality graphics. It cannot be used to build molecules, but macromolecules can be imported using a variety of file formats, including MDL, Sybyl and protein data bank (.pdb). Since the viewer is designed to help analyze interactions between small molecules (ligands) and macromolecules, it should be especially useful for drug interactions and docking. The Molegro viewer is available for Windows, Mac and Linux operating systems.

Two other programs which may be useful to more advanced students are the open source molecular viewer and editor Avogadro and the more advanced commercial freeware program Discovery Studio Visualizer. Additional information on these programs can be found in the Resource pdf attachment (below).

Last updated July 18,2011