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Re: molecular interactions

  • To: mathgroup at
  • Subject: [mg22936] Re: molecular interactions
  • From: "Kai G. Gauer" <gauer at>
  • Date: Thu, 6 Apr 2000 02:04:52 -0400 (EDT)
  • References: <8ce920$>
  • Sender: owner-wri-mathgroup at

rafie at wrote:

> Hai,
> I'm looking for the software that can model and simulate the molecular
> interactions. Do you have any idea?

I don't know of any freeware mathematica notebooks where you have some
nice palettes that will "easily" attach, say a CH3 free radical to any one
particular side of a C6 carbon ring (with whatever else attached to the
other edges). This will probably need quite a bit of symmetry group theory
built in to the notebook as well, which I can't find all that much ease
for use with Mathematica (at least, there's very few built-in internals
that will call up what, say, a group table of U(prime) without first
writing with the modulus function to go with it... I'm surprised there
was'nt even a built in way of defining/computing/looking up orders of
certain elements) ....anyways, once you've gotten all the short premature
codings down to build to morphisms of other symmetry groups, you'll find
that you'd probably want a pallette full of common radicals, complete with
the pointing of their covalent, hydrogen and ionic bondings. This will
require assigning a 3D basis to set the scope of what sort of possible 3D
codomain that you would want your free radical most preferentially siting
at an one moment (BTW, but my chemistry failing me, would something like a
C2H4Cl2 molecule (with exactly one chlorine atom touching exactly one
carbon atom) be able spin about the main axis of the C-C through time
(like a propellor on an aeroplane)? If it did, these sorts of
subprocedures would also probably be wished to be built in). You could
also discuss how you might wish to call your function palette easily
enough so that you know where each bond should sit (and maybe, what the
probability of it remaining there stable for a long period of time ...
with respect to where the radical would 'prefer' to sit, because of
relative bonding energies needed). Then would come the pretty pictures and
sizing everything down to the relative atomic sizes, distances from one
another (colours too, maybe ;^) and trying to render a fast 3D picture/
animation that would be: easy enough to zoom in on and look at the
perspective from multiple angles possibly from the view of the interior of
a DNA strand out, with cutaways to see better, and probably, some better
way to render rotating an image when you would have no premature idea of
what perspective the molecule's shape should be when seen from that angle.
Of course, the BIG idea here is speed in generating the image and
computing the ideal shape. I know a little bit of other styles of planar
tilings (if you're trying to produce an image of graphite), a bit about
non-periodic tilings (penrose tiles, etc), but ask me about trying to
build algebra structures that may be describing those non-periodic 3D
shapes we see so mush of in Scientific American, I'm only beginning to see
the relationships to group theory, nevermind my trying to write
programming to emulate this morphism from algebra to symmetry groups!

You could also check out an article pertaining to geology crystalline
structures which I've found in the Mathematica Journal a few years ago:
its by Jorg Enderlein of LANL.  ---- could you reply to me if you find
better notebooks (for Mathematica, of course)?

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