X-Message-Number: 13747
Date: Fri, 19 May 2000 09:30:30 -0400
From: Jeffrey Soreff <>
Subject: CryoNet #13726 - #13731

Thomas Donaldson wrote:

>If I properly understand just what you're saying, it still won't
>work. Chemical compounds consist of atoms linked together; that
>linkage is by electrons. If you can use X-rays to identify atoms
>from carbon onward, you still need some way to work out which atom
>is chemically attached to which other atoms. Physical nearness isn't
>enough evidence.

While I have other concerns about X-ray probes, ambiguity about
bonding isn't a major concern.  If one knew the positions of all
of the atoms (really the center of electron density from X-ray
structure, which is close to the positions of the nucleii, but
not quite...), yes it is true that there is still ambiguity about
chemical bonding, but it is only important in rare cases.
If we could guarantee that the electrons were in the ground state
for the specific positions of the nucleii, then there _wouldn't_
be ambiguity.  That is the reason that one can represent molecular
mechanics reasonably well by potential energy surface calculations.
Specifying the positions of nucleii and requiring the electrons to
be in the ground state almost always (barring things like spin
orientation in free radicals) gives a unique electronic state.
Now electronically excited states _do_ have different electron
distributions and different potential energy surfaces, and they
are important during transition states of reactions, but I doubt
that a significant number of molecules in a biological system
are in electronically excited states at any given time.  The
cases of electronically excited states that I am aware of in
biological systems are things like singlet oxygen, which is toxic.
Does anyone know of any persistent electronically excited
molecule in a biological system which is required for normal
function?
                                      Best wishes,
                                      -Jeffrey Soreff

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