Now that you have a very good feel for
producing excellent results,
we'll take a look at the opposite situation - where you access an
external site, where you can do many calculation/visualization tasks at
no charge. Although many of these sites are available on the web,
we'll be focusing on Prof. Johann Gasteiger's incredible site at the
University of Erlangen. Prof. Gasteiger is one of the world's
experts on computational chemistry and visualization, having written
several books and many journal articles, and his making
all of the tools you'll see available to the chemistry community at no
charge is a wonderful act of generosity.
move up to a
browser with super features, like Mozilla or FireFox.
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
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
The main Gasteiger site is called TORVS (Techniques for Organic Reactions, Visualization, and Spectroscopy); once there, click
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.
- 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.
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.
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
- 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!
- 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.
- 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.
Translator -converts SMILES format (generator
included) to any of a large number of file formats.
Creator for Chemical Structures - from
Cactus (an NCI program), creates VRML files from an included SMILES
for 2D Plots of Chemical Structures - also
from Cactus, the NCI's
program for creating gif or png files from a SMILES string (SMILES
- 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!
FrontDoor - all kinds of galleries, animations, tutorials,
and more. Just go to the site; it's easier than trying to
everything on this large site.
Molecular Modeling - from Oxford Univ.; they call it a
"tutorial", but it does loads of calculations as well.
Resources on the WWW - the largest, most complete compilation of
WWW sites for computations, modeling, Java/VRML, and more.
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.
for Organic Chemistry - a course homepage from Imperial College, by
Prof. Henry Rzepa - one of the really active researchers in on-line
Molecular Models - a nice tutorial on all aspects of modeling,
including rendering (visualization) techniques. Really
Lastly, here are a few sites with useful information
- Free Molecular Modeling Programs
- a nice comparison of the 15 most popular free
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
Compression - incredibly, this site shrinks GIF
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
- JMol - a
replacement for Chime - it's faster, more sophisticated, and easier to
embed in web pages.
Home Page -
from the Univ. of MA, one of the very active modeling sites; covers
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!