[Ifeffit] Beryllium and EXAFS

Tue Dec 18 14:50:30 CST 2012

A bit unrelated to the question at hand, but regarding #5, yes, people do neutron PX.  The focus is almost entirely on locating hydrogen atoms (e.g. for protonation state), so I wonder what the neutron PX guys would say about looking for a Be atom. The downside is that you usually need quite large crystals compared to X-ray PX and long data collection times.

Erik

________________________________
From: Matthew Marcus <mamarcus at lbl.gov>
To: Erik Farquhar <efarq at yahoo.com>; XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov> 
Sent: Tuesday, December 18, 2012 1:39 PM
Subject: Re: [Ifeffit] Beryllium and EXAFS

Just to stir the pot a little more:
1.    ALS has some beamlines which can go down as far as Li.  Work has been done on Li, but only on concentrated stuff.
2.    The sample is probably really dilute in Be.  The signal will be pathetic.
3.    Radiation damage will be a major issue, especially with X-ray Raman, which is a highly inefficient technique.  Even LHe cooling doesn't solve that problem.
4.    Are there model compounds available for proposed local structures of the Be center?  You'd need that to have any hope of making sense out of Be XANES.
5.    Is there such a thing as neutron PX?  That might see the Be.
    mam

----- Original Message ----- 
>From: Erik Farquhar 
>To: XAFS Analysis using Ifeffit 
>Sent: Tuesday, December 18, 2012 5:32 AM
>Subject: Re: [Ifeffit] Beryllium and EXAFS
>
>
>To add to Matt's last paragraph, you might also consider beamline 6-2 at SSRL (http://www-ssrl.slac.stanford.edu/beamlines/bl6-2/), as they do a fair amount of work with proteins and have an X-ray Raman setup. I think the beamline scientist occasionally posts to this list.
>
>
>Good luck,
>Erik
>
>
>--
>Erik Farquhar, Ph.D.
>Case Center for Synchrotron Biosciences
>Brookhaven National Lab
>NSLS, Building 725A-X3
>Upton, NY  11973
>efarquhar at bnl.gov
>+1-631-344-8174
>
>
>
>________________________________
>From: Matt Newville <newville at cars.uchicago.edu>
>To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov> 
>Sent: Tuesday, December 18, 2012 7:52 AM
>Subject: Re: [Ifeffit] Beryllium and EXAFS
>
>Hi Gina,
>
>On Mon, Dec 17, 2012 at 5:23 PM, Clayton, Gina <ClaytonG at njhealth.org> wrote:
>> Hi there
>>
>> I am trying to find out more about EXAFS. I am a protein crystallographer.
>>
>>
>> I want to identify the environment of a beryllium ion in the protein, I work with,  of which I have a crystal structure.  EXAFS was recommended as a good technique for identification of the beryllium site and species. The beryllium is an acidic pocket of the protein surrounded by oxygens from the protein, likely covalently bound. However I have had  zero result finding a beam line that can tune their setups to the Be edge at 111 eV. Also some EXAFS users say that EXAFS technique would be good for working out the environment of the Be but some say it would not . In particular  I have been advised that  Be EXAFS would not be useful since  the Be  EXAFS signal would have unacceptable interference from the carbon K-edge at 285 eV and the oxygen K edge signal at 535 eV.
>>
>> Would EXAFS work or something in a similar vein? Or, for instance,  could the acidic pocket be identified using EXAFS, by measuring the oxygens (instead of the Beryllium) using the protein with and without beryllium?
>>
>>
>> Thank you so much for any advice.
>>
>> Gina
>
>As you and as the person who advised you suspect, you face a number of
>challenges:
>
>1.  The extremely low energy (111 eV).  You might be able to find a UV
>source or x-ray beamline that can reach this energy , but often such
>work is done in vacuo, and so may not be suitable for proteins.  Using
>electrons (from a TEM, say) might be possible too -- these can
>sometimes do C and N edges either directly or looking at Electron
>Energy Loss (send in an electron of high energy E1, and look for
>electrons of energy E1 - E, and scan the analyzer for the loss energy
>E through the absorption edge).  Again, electron probes may not be
>what you want for your proteins.
>
>2. The C K-edge will limit your signal to "only" 175 eV.  I would say
>to not worry so much about this limitation.  You'll really be
>measuring NEXAFS (near-edge X-ray absorption ....)  but that's OK.
>People measure the B, C, N, and O K edges, all facing the same
>problem, especially for the O K edge: our planet is more or less
>covered with the stuff ;).  These spectra tend to be very rich and
>sensitive to ligands.
>
>3. Not much (zero?? I can almost believe that!) literature on Be XAFS.
>This is unfortunate because most NEXAFS is measure and compare to
>known spectra.  I think that might mean you have to spend effort to
>building up a spectral library for Be in organic phases.
>
>I think trying to measure the O K edge with and without Be is nearly
>hopeless.  All the X-ray spectroscopies average equally over all the
>atoms of the absorbing species.  In addition all the spectra are
>grossly the same (a step function from 0 below the edge to 1 above the
>edge).  These make it difficult to see changes below about 1%.    So I
>think you would just have too high of an O::Be ratio to see anything
>useful.
>
>One option to consider is using X-ray Raman scattering
>(http://en.wikipedia.org/wiki/X-ray_Raman_scattering).  Here, one hits
>the sample with high-energy X-rays (say, 10 keV), which are highly
>penetrating for reasonably sized protein sample.  One analyzes an
>energy loss (again, E1 - E, where here E1 is around 10 keV) to get the
>edge of interest.  I'm familiar with (been involved with) studies on
>B, C, and O using this technique (all in solids, mostly at high
>pressure).  See, for example,  S. K. Lee, et al "Probing of bonding
>changes in B2O3 glasses at high pressure with inelastic X-ray
>scattering",  Nature Materials 4, pp 851-854 (2005), and also the work
>of Simo Huotari.    I'm not aware of anyone doing Be K-edge this way,
>but it should definitely be possible. For the work I've been involved
>with, Be would be challenging because there are other excitations in
>solids that appear around 100 eV.  I believe that effect would be far
>suppressed in a protein, though I'm not sure.
>
>That's somewhat more exotic than straightfoward XAFS,, but it might be
>the best chance for measuring Be in a protein.    I'm not sure I know
>any beamlines that do X-ray Raman on proteins, but I'd suggest APS
>beamline 20-ID or ESRF beamline as places to start.    The next
>questions would be "how many Be atoms are in your protein?", and "how
>much material do you have?"....
>
>Hope that helps,
>
>--Matt Newville
>
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