[Ifeffit] Debye Waller factors for Water Molecules

[Frenkel, Anatoly]

Paul,
 
In addition to my previous email, before you decide whether to set and fix the Zn-O DWF or not, I suggest that you look for a spread in reported values of DWF in Zn2+ -O in aqueous solutions - most of them were done at room temperature, but to get an idea about the spread it only matters that the temperature is the same between different publications, so RT would be fine. Irit Sagi and James Penner Hahn published many papers on Zn2+ complexes, so that could give you a good starting point. If you find that the spread is significant, it is either because the amount of static disorder differs between these cases, or the Einstein model doesn't work, or both... - but it is important to know before you decide whether to keep it fixed or not in your fit.
 
As far as keeping things fixed. Some things, like E0 or coord. numbers may be fixed if you analyze a series of compounds where you do not expect them to change between the samples. Sometimes, DWF of a certain bond is not expected to vary between different samples especially if they are all mixtures of different complexes of the same element, with the mixing fraction varied between the samples, common in time-resolved experiments with reaction intermediates. In many cases, DWF of the same bond varies from sample to sample. It is really not possible to say what's best to do in your case without knowing much detail. However, if you don't have a room for varying this parameter independently, as I assume you don't since you have a mixed first shell, it may be a good idea to fix it to something reasonable (e.g., as discussed in previous emails) and see if you get a reasonable fit.
 
Anatoly

________________________________

From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of Paul Fons
Sent: Mon 7/30/2007 6:31 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Debye Waller factors for Water Molecules


Hi Matt,
I took a look at the paper you mentioned and as in my case, the water is appears to be pretty much only bonded to the Zn at 1.96 Angstroms for the isolated enzyme.  I guess this implies that Anatoly's idea of using a Zn+2 solution as a starting point might make sense.  I have no idea how much the DW varies for water in these types of systems.  Is the usual idea to just set it at some "reasonable" value (e.g. from the idea of Anatoly) and then keep it fixed?


Paul



On Jul 30, 2007, at 3:51 PM, Paul Fons wrote:


	  Thanks everyone (Shelly, Matt, and Anatoly) for the info.   I thought it would be fun to learn while trying to work out a (relatively) simple system.  I have EXAFS data about a Zn site.  The Zn is bonded to three cystedines so I have the DW pretty much under control, but for the water molecules.  I will investigate the approaches mentioned here and see which one the data is most consistent with (I did have the foresight to choose a system for which I have high resolution x-ray crystallography data).

	Thanks
	

	Paul
	

	On Jul 29, 2007, at 12:57 AM, Matt Newville wrote:


		Hi Paul,

		A. Vogel et al (Biochemistry 43, p10379, 2004) report a Zn water (or
		OH) at 2.0Ang with sigma2=0.007Ang^2 for data collected at 30K.

		This is for a binuclear Zn compound, and the OH is a bridging ligand
		(with the other ligands being dominated by histidine-like rings), so I
		don't know how close it is to your structure.  But it might be a good
		place to start.

		Also, the results came from EXCURVE.  That's not to suggest that the
		results are not reliable, but you might want to check carefully the
		meaning of sigma2.  I'm not 100% sure of this (or what the Vogel et al
		paper is reporting), but I think the EXCURVE sigma2 might be a factor
		of 2 bigger than the Ifeffit sigma2.

		I'd be a little wary of using an Einstein model for "water"  ligands
		down to 30K.  It would be interesting to hear how well an Einstein
		model compares to the DFT modeling for any ligands in a bio-molecule.

		--Matt
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