An On-Line Guide to Molecular Modeling - Part 2 - Dr. Howard Black - Dept. of Chemistry

As so often happens (and will continue until some generally-accepted standard for browser technology exists), many sites work much better with a certain browser than with others. The small table to the right provides links to the indicated browsers' home pages. The Gasteiger site seems to work best with either a late edition Netscape or any version of Mozilla (of course). Still struggling in the dark ages with IE? This is a great chance to

Links to Browser Sites

move up to a browser with super features, like Mozilla or FireFox.

The main Gasteiger site is called TORVS (Techniques for Organic Reactions, Visualization, and Spectroscopy); once there, click on "Services" from the link list on the left. There are many to choose from, so I'll highlight the ones most useful to organic chemists. Most applications can either read a file from your PC, or you can input the structure using a SMILES string generator. SMILES is a one line, text-only description of a structure; you just draw the structure using a basic drawing program, and it provides (and inputs) the SMILES description of the structure.

TeleSpek - a great IR spectra simulator. It requires Java, but you're probably running that now without knowing it. If not, you can get the latest version, free, via the icon to the right.
Gif Generator for Chemical Structures -can generate GIF or PNG format images, where you control most of the display parameters. It even provides the code to embed the structure in a web page.
VRML File Creator for Chemical Structures - (VRML - Virtual Reality Markup Language) creates WRL files, the standard format for virtual reality applications. To run VRML apps, you need a plugin; there are three that perform well and have been around for awhile: BS_Contact_VRML-X3D, Cortona, and Cosmo.
ComSpec3D - a wonderful IR spectrum generator that not only produces a detailed spectrum, but also a list of all peaks and their exact absorption; clicking the absorption produces an animated VRML image, in which the bonds responsible for the absorption you picked are slowly vibrating in the correct mode. Very cool!
OrbVis - input via SMILES, output is a calculation of every M.O. the molecule possesses. Click on one, and you get a VRML-based animated image of the MO. There's also a button to see the HOMO and LUMO together. Note - this program seems more browser-sensitive than usual, and often will run only on Netscape.
MolSurf - VRML visualization of surfaces, whose parameters you can adjust after the image is visible.

Of course, there are many other sites that do on-line calculations; I'll just highlight a few of the best.

Online SMILES Translator -converts SMILES format (generator included) to any of a large number of file formats.
VRML File Creator for Chemical Structures - from Cactus (an NCI program), creates VRML files from an included SMILES generator.
GIF/PNG-Creator for 2D Plots of Chemical Structures - also from Cactus, the NCI's program for creating gif or png files from a SMILES string (SMILES generator included).
Mol4D - Molecules in Four Dimensions - a great site in the Netherlands, it consists of a tutorial section where animations are used everywhere and a calculation site, where you can submit either a molecule or a reaction. The latter part, called CARP (Calculate and Animate a Reaction Pathway), is a quite sophisticated utility, and if the calculations contain a point near the transition state, it can construct the entire reaction path! Requires Chime.
Protein Explorer FrontDoor - all kinds of galleries, animations, tutorials, and more. Just go to the site; it's easier than trying to describe everything on this large site.
CAChe Molecular Modeling - from Oxford Univ.; they call it a "tutorial", but it does loads of calculations as well.
Computational Resources on the WWW - the largest, most complete compilation of WWW sites for computations, modeling, Java/VRML, and more.
3D Molecular Graphics on the WWW - excellent summary of VRML and how/where it's utilized on the web.
Modeling and Animation Links for Organic Chemists - the link collection of guess-who. Isn't as exhaustive as some link lists, but each link is described so that you know what each one does.
Molecular Modeling for Organic Chemistry - a course homepage from Imperial College, by Prof. Henry Rzepa - one of the really active researchers in on-line modeling.
Representation of Molecular Models - a nice tutorial on all aspects of modeling, including rendering (visualization) techniques. Really interesting.

Lastly, here are a few sites with useful information or calculations:

Free Molecular Modeling Programs - a nice comparison of the 15 most popular free modeling sites.
PDB to MultiGif Page - very useful utility that creates animations from PDF files. The animation slowly rotates in one direction (it made the two animations on my link library).
Spinwave - Graphics File Compression - incredibly, this site shrinks GIF or JPG files by up to 90%! In case you didn't know, GIF and JPG are already compressed as part of their standard protocol; removing 90% of the occupied space is almost to believe - except, there it is! You know, I'm sure, how large graphics files usually are; this is a decent solution.
JMol - a fairly new replacement for Chime - it's faster, more sophisticated, and easier to embed in web pages.
RasMol Home Page - from the Univ. of MA, one of the very active modeling sites; covers Protein Explorer, RasMol, Chime, and others.
About Graphics Software - a typical "About.com" page - full of great, well-organized information; has most of what you need to know.

I hope you enjoy exploring both your PC and the web as sources of free software, or on-line calculations, that will deepen your understanding of concepts that may be fuzzy. By the way, most of what we're dealing with is in the realm of physical chemistry, so now you can't go around saying how horrible p-chem is anymore!

to Part 1