[Ifeffit] Beryllium and EXAFS

Matthew Marcus mamarcus at lbl.gov
Tue Dec 18 12:39:15 CST 2012

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.

  ----- 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 Farquhar, Ph.D.
  Case Center for Synchrotron Biosciences
  Brookhaven National Lab
  NSLS, Building 725A-X3
  Upton, NY  11973
  efarquhar at bnl.gov

  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

  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

  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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  Ifeffit at millenia.cars.aps.anl.gov


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