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 Rate This Message: http://www.cryonet.org/cgi-bin/rate.cgi?msg=13747