Re: [ccp4bb] Negative density around C of COO-

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Date: 2008-05-05

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Subject: Re: Negative density around C of COO-
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2008-05-05

I don't mean to single anyone out, but the assignment of "free radicals"
as the species mediating radiation damage at cryo temperatures is a "pet
peeve" of mine. Free radicals have been shown to mediate damage at room
temperature (and there is a VERY large body of literature on this), but
there are a great many good reasons to think that free radicals do NOT
play a role in radiation damage under cryo.

This "assignment" of free radicals to damage is often made (flippantly)
in the literature, but I feel a strong need to point out that there is
NO EVIDENCE of a free radical diffusion mechanism for radiation damage
below ~130K. To the contrary there is a great deal of evidence that
water, buffers and protein crystals below ~130 K are in a state of
matter known as a "solid", and molecules (such as free radicals) do not
diffuse through solids (except on geological timescales). If you are
worried that the x-ray beam is heating your crystal to >130 K, then have
a look at Snell et. al. JSR 14 109-15 (2007). They showed quite
convincingly that this just can't happen for anything but the most
exotic situations.

There is evidence, however, of energy transfer taking place between
different regions of the crystal, but energy transfer does not require
molecular diffusion or any other kind of mass transport. In fact,
solid-state chemistry is generally mediated by cascading
neighbor-to-neighbor reactions that do not involve "diffusion" in the
traditional sense. Electricity is an example of this kind of chemistry,
and these reactions are a LOT faster than diffusion. The closest
analogy to "diffusion" is that the propagating reaction can be seen as a
"species" of sorts that is moving around inside the sample. Entities
like this are formally called quasiparticles. Some quasiparticles are
charged, but others are not. If you don't know what a quasiparticle is,
you can look them up in wikipedia.

Some have tried to rescue the "free radical" statements about radiation
damage by claiming that individual electrons are "radicals". I guess
this must come from the "pressure" of such a large body of free-radical
literature at room temperature. However, IMHO this is about as useful
as declaring that every chemical reaction is a "free radical" reaction
(since they involve the movement of electrons). I think it best that
we try to call the chemistry what it is and try to stamp out rumors that
mechanisms are known when in reality they are not.

Just my little rant.

-James Holton
MAD Scientist

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: question on how crystals form
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-05-05

Next message:
Subject: Re: HKL2000 and gcc4
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2008-05-05