Re: [Ifeffit] Cu K edge XANES stds

[Latta, Drew E]

Hi Simon,

Since you are just looking for a sanity check (on what??) here are some Cu-S 
standards for you. They were published in DOI: 10.1021/es304736y.

The Cu-cys sample is not a pure phase, but probably a mixture of 
cysteine/cystine. But it is likely mostly Cu(I). Further discussion is 
available in the SI of the paper above.

The file is from an old, old version of Athena (0.8x)... hopefully it works for 
you.

Best,

Drew Latta
== 
Drew E. Latta, Ph.D.
Asst. Research Scientist

The University of Iowa
Civil and Environmental Engineering/IIHR
4105 Seamans Center
Iowa City, IA 52242

Ph. 319-936-0034
email. drew-la...@uiowa.edu
==



-Original Message-
From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of 
Simon James
Sent: Tuesday, February 26, 2019 3:18 PM
To: Ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Cu K edge XANES stds

Hi mailing list,

I am hoping someone is willing to share their Cu K-edge XANES spectra from 
biological Cu thiol complexes. I’m particularly interested in Cu(I/II)-GSH, 
Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am 
wrangling.

Can anyone help?

Best regards,

Simon


This mail was composed on the move via my phone. Apologies for any typos.

Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre
30 Royal Pde
Parkville, 3052 VIC


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Cu_Samples_athena.prj
Description: Cu_Samples_athena.prj
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Re: [Ifeffit] XANES spectra of Zn-organic references

[Latta, Drew E]

Dear Emmanuelle,

I worked with plants and metals a little in my post-doc as a collaboration. We 
found that ZnO-exposed wheat was binding Zn as a phosphate complex. Probably a 
Zn-phytate. But the coordination is close enough to the inorganic mineral 
hopeite for XANES fingerprinting. Data from the paper is attached here. The 
reference is a standard Zn foil reference.

https://link.springer.com/article/10.1007/s11051-012-1125-9

From my recollection, phytate-metal complexes are fairly ubiquitous in plants, 
but particularly so in the cereal grains. It is probably worth finding a 
Zn-phytate reference, but we never had the time and money to synthesize one.

Best regards,

Drew Latta

From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of 
emmanuelle Montarges-Pelletier
Sent: Friday, May 18, 2018 8:46 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] XANES spectra of Zn-organic references

Dear all
We have measured Zn XANES spectra within biological samples (seeds), in ambient 
conditions (room temperature). In order to interprete the spectra, we are 
searching for Zn-organic reference spectra (XANES only).
Indeed, we would be interested by Zn organic compounds with sulfur and/or 
nitrogen and/or oxygen in the first shell of coordination. On the joined graph 
are plotted the experimental spectra (microspectra on seeds), compared to 
Zn-citrate and Zn-cysteine. Energy calibration was checked for all spectra.
thanks in advance for your answers
best regards
Emmanuelle


Emmanuelle MONTARGES-PELLETIER
Chargée de Recherche CNRS


LIEC Laboratoire Interdisciplinaire des Environnements Continentaux
UMR 7360 CNRS Université de Lorraine
15 avenue du Charmois
F-54500 Vandœuvre-lés-Nancy - France
tel 33 (0)03 72 74 47 30
mob 33(0)6 31 33 10 30
attention changement de numéro de téléphone

tel 33 (0)3 72 74 47 30






ZnPO4.prj
Description: ZnPO4.prj
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Re: [Ifeffit] XAFS Analysis using Ifeffit

[Latta, Drew E]

Hi Ke,

Unfortunately, it looks like your data is showing the classic symptoms of 
self-absorption . The white line for UO2 is fairly pronounced, and should look 
like the attached picture.

Not sure on the setup at 12-BM-B, but next time ask if you could collect both 
fluorescence and transmission data at the same time. It can really save your 
behind.

You can dilute in whatever low Z compound you’d like, I think things like SiO2 
and boron nitride are common because of their low Z. Graphite might work also. 
Powder smears on tape are pretty common because you can fold/unfold to vary the 
amount of material in the beam. (though one can’t manipulate those at the 
beamline with a dispersible rad powder like UO2.)

Best,

Drew

From: Ke Yuan [mailto:key...@umich.edu]
Sent: Thursday, October 16, 2014 8:39 AM
To: ifeffit@millenia.cars.aps.anl.gov; Latta, Drew E
Subject: Re: XAFS Analysis using Ifeffit

Sorry here is the picture!

On Thu, Oct 16, 2014 at 9:37 AM, Ke Yuan 
mailto:key...@umich.edu>> wrote:
Hello Drew,

Thanks for your suggestions. I just checked my original data without 
normalization. The edge step is about 0.7 (see pic attached). I did the 
measurement in fluorescence mode at APS, beamline 12-BMB. What do you think 
about this pic?

For the sample preparation, I think I need to mix UO2 with some other materials 
to dilute it. Do you have any suggestions on the matrix materials?


Best,
Ke



--
Ke Yuan

PhD Candidate
Department of Earth and Environmental Sciences
1100 North University Ave
3021 C.C Little
University of Michigan, Ann Arbor
MI 48109-1005
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Re: [Ifeffit] Ke

[Latta, Drew E]

Hi Ke,

It sounds like you are putting a lot of UO2 in the beam, and I might be worried 
about self-absorption in fluorescence data. I’m not sure about transmission, if 
you have lots of absorption (edge step of >>1) then you’ll be doing EXAFS on 
pinholes and thin spots.

What are you getting for transmission edge steps on that sort of sample? “Good” 
UO2 data for me can have an edge-step in transmission of 0.10 or less.

In my personal experience as little as ~2 mg U /square cm in UO2 will result in 
good data. YMMV based on beamline.


Best,

Drew Latta



From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Ke Yuan
Sent: Wednesday, October 15, 2014 10:20 AM
To: bra...@bnl.gov; ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Ke

Hi Bruce,

Thanks for your comments! I studied Shelly's paper and found my data does looks 
different, especially the first peak at 1.9 A, seems it splits into two in my 
case.

I prepared this sample by pressing UO2 powder into a hole (2mm deep), which 
might have significant self-absorption effect, because it's not dilute and 
thin. Do you think this will change the peak amplitude?

Best,
Ke


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Re: [Ifeffit] Aligning EXAFS E0 to Theory

[Latta, Drew E]

Hi Carter,

My interpretation of (for example) Shelly Kelly's tutorial on varying 
experimental E0 to fit the theory was to do this with the background 
subtraction E0 in Athena. E.g. 
http://www.xafs.org/Tutorials?action=AttachFile&do=get&target=Basics_of_XAFS_analysis_2009.pdf

I believe that the idea is not to move the whole spectrum in energy, but to 
change E0 in the background removal routine. You vary the E0 in the background 
removal box (as well as Rbkg, probably) to make the experimental EXAFS spectrum 
more closely match the theoretical first shell. It sounds like you are trying 
move the whole spectrum with respect to energy calibration.

However, someone who knows better than I may say that these two things are 
equivalent... But I would think if you were trying to fit some Cu compound [I 
gather people that do EXAFS have some sort of thing for Cu ;-) ] you'd still 
want to leave the whole spectrum calibrated to Cu foil, and move the background 
subtraction E0 around to best fit the theoretical first shell.

I suspect there are also cases where you might not be inclined to think that 
deltaE0 should be close to 0. For example, if you use a quasi-reference for 
energy calibration. Arsenic and uranium are common cases in my research, where 
oxides or higher valence compounds serve as references.

Best,

Drew Latta

From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Carter Abney
Sent: Wednesday, June 04, 2014 3:19 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Aligning EXAFS E0 to Theory

Hello, Everyone -

This is my first time trying to work through EXAFS analysis of experimental 
data, and I've got what (I think) should be a fairly straightforward question.  
I'm trying to minimize my delta E0 by aligning the EXAFS data with my best fit 
(i.e. - align the k-grid of the data with the k-grid of the theory to obtain a 
small delta E0).  However, I have been unsuccessful in "reading the theoretical 
chi(k) spectrum into 
Athena"
 to accomplish this.

I assume the crux of the problem is the format in which I am exporting my 
theoretical chi(k) spectrum from Artemis.  The only way I have been able to 
export the data with Artemis so Athena can import it is to click the "Save next 
plot to a file" button, which then allows me to save the data as a text file.  
I know I need chi(k) data that is not 
k-weighted,
 so I plot the best fit with k-weight of 0 in k space with deltaE0 equal to 0.  
Considering the problems I've had, I'm assuming somewhere in this process is 
where I'm going wrong.

When I import this data, I have four columns: k, experimental data, fit, 
window.  Since k is the wavenumber of the photoelectron, I choose that as 
"Energy."  Then I select column 3, the best fit, as "Numerator," and change the 
data type to chi(k).  I then import the data.  I've attached two pngs to this 
e-mail which, assuming they come through, should display the Athena data import 
window and the corresponding plot of chi(k).  When I plot this data in k-space 
or R-space using Artemis, the resulting plots look appropriate.

When I try to align the experimental EXAFS data in Athena, I know it aligns the 
first derivative of E for the selected data to the first derivative of E for 
the standard.  I want my best fit to be the standard to which the data is 
aligned.  However, I cannot plot chi(k) data in E, which causes me to believe I 
shouldn't be able to align data to the first derivative of E.  True enough, 
when I try to auto align, I get impossible values for E0 adjustment.

Clearly I'm doing something wrong - possibly even several somethings wrong.  
Any guidance would be greatly appreciated.

Thanks,

- Carter

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Re: [Ifeffit] Itinerant vs localized XAFS

[Latta, Drew E.]

Curious... has anyone tackled the EXAFS problem you are describing with respect 
to the Verwey transition in magnetite (Fe3O4)? If anyone has tried it I'd 
suspect that to be the system where it has been done (given the many hundreds 
of papers that have been written on that one subject).

Since this is an EXAFS mailing list, I suppose I'm being a little pedantic in 
mentioning that what you're looking for might be resolved with a 57Fe 
Moessbauer measurement. The itinerant electrons phenomenon is well known (and 
perhaps understood) in the Moessbauer community.

Anyways, disregard this email if I'm telling you things you already know...

Best,

Drew Latta

From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Maurits Boeije
Sent: Monday, December 09, 2013 9:03 AM
To: 'ifeffit@millenia.cars.aps.anl.gov'
Subject: [Ifeffit] Itinerant vs localized XAFS

Dear XAFS specialists,

We've performed an experiment at the ESRF in Grenoble to find experimental 
evidence of an electronic change in our system. We suspect, from ab initio 
calculations, that there is a change in how electrons are allocated in our 
Mn/Fe system. Calculations show that some electrons change from being itinerant 
at high temperatures, to being localized at low temperatures.
We performed an XAFS experiment and hope to see a difference between the low 
and high temperatures measurements. There is always difference because the cell 
parameters change as function of temperature, and I used your Artemis program 
to investigate the influence of the cell parameters on the EXAFS signal. I can 
get a decent fit using the crystallographic data we have, but I'm not sure if 
I'm not throwing away any evidence of our electronic change. I can interpret a 
fitted interatomic distance of 2.1 A (compared to 2.0 A we got from 
diffraction) as being the mean interatomic distance in our sample, but I could 
also interpret it as a 0.1 A difference because of our suspected electronic 
change.
The challenge now lies in seeing an electronic difference despite the 
crystallographic change. What we would ideally do, is to keep the (known) 
atomic positions and cell parameters fixed, fit the EXAFS parameters and see if 
we can predict either the high or low temperature spectrum. Do you think this 
is possible? Are there any parameters which are calculated by IFEFFIT who are 
not precise enough for such a conclusion? It could be that the effect we are 
looking for is so small that they are nullified by the assumptions in the EXAFS 
equation.

I would appreciate any insight you could have in this particular problem.

With kind regards,

Drs. MFJ Boeije
Fundamental Aspects of Materials and Energy

TU Delft
T +31 (0)15 27 83793

No trees were killed to send this message, but a large number of electrons were 
terribly inconvenienced

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Re: [Ifeffit] Linear Combination Fitting using ATHENA

[Latta, Drew E.]

I would say that the Mossbauer isn't always quite straight forward, especially 
if the OP is working with nanoparticles. You have to find the right temperature 
where superparamagnetism is gone but the Verwey transition hasn't occurred to 
reliably fit the resulting Mossbauer spectra. (I'll assume from ignorance that 
that Mg-ferrites have Verwey transitions.)

I would think the two best end-members for the XAS LC fits are possibly 
magnetite (fully stoichiometric: Fe2+/Fe3+ = 0.5) and either maghemite 
(gamma-Fe2O3) or the fully oxidized Mg-ferrite. Which Fe2O3 are you using Teck 
Kwang Choo? If you are using the alpha-form (hematite) then I would suspect you 
might not get very good fits as the structural difference between maghemite and 
hematite significantly influence their XANES spectra.

I've had good success finding Fe2+/Fe3+ ratios in partially oxidized magnetites 
by using magnetite and maghemite as end-members in LC fits. So I think you 
should have reasonable success for the Mg-ferrites using the right end-members.

Contact me in person below, if you are interested in magnetite/maghemite 
standard spectra.

Best,

Drew Latta
---
Drew E. Latta, Ph.D.
Postdoctoral Associate

Molecular Environmental Science Group
Biosciences Division
Argonne National Laboratory
Building 203, Room E-105
9700 South Cass Avenue
Argonne, IL  60439

Phone: 1-630-252-3985
dla...@anl.gov<mailto:dla...@anl.gov>
http://www.mesg.anl.gov
---



From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Alexandre dos 
Santos Anastacio
Sent: Monday, August 12, 2013 9:01 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Linear Combination Fitting using ATHENA

Hello,

maybe that fingerprinting technique would be Mossbauer spectroscopy. The 
Fe(II)/Fe(III) ratio comes easily and also there are lots of papers about 
Mg-ferrite, an example:

10.1109/TMAG.2009.2018880<http://dx.doi.org/10.1109/TMAG.2009.2018880>

Alexandre.

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Re: [Ifeffit] New Demeter Win7 install (?) problems

[Latta, Drew E.]

Fred,

Doing as you say and creating the "demeter" folder in %appdata% works.  Now the 
Demeter applications run from my user account.

Thanks for the tip,

Drew

-Original Message-
From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of 
fred.mosselm...@diamond.ac.uk
Sent: Tuesday, April 24, 2012 12:47 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] New Demeter Win7 install (?) problems

Hi
i dont know if this is relevant but the problem sounds similar to one i had at 
Diamond with Demeter that was covered on the list about six weeks ago.

that was with XP hence i am not certain it's relevant.
what was missing is the demeter folder for the log file to write to in the 
%appdata% folder.
creating (for each user) a demeter folder in their %appdata% enables the log 
file to be written and the program to run.

for my windows 7  home pc this appears to be uesername/appdata/roaming

cheers
Fred

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Re: [Ifeffit] New Demeter Win7 install (?) problems

[Latta, Drew E.]

Bruce,

More information:

I don't have a folder named "C:\Users\\AppData\Roaming\demeter\".  I 
checked while looking at hidden files, and it isn't there.  On the other hand 
if I log in to the local admin account for my computer, Demeter programs run 
just fine. 

So it would appear that the install didn't make this folder in the user 
account, only in the admin account.

Thanks for the help,

Drew


-Original Message-
From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel
Sent: Monday, April 23, 2012 10:50 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] New Demeter Win7 install (?) problems

On Monday, April 23, 2012 10:57:41 am Latta, Drew E. wrote:
> I am having issues with getting the new Demeter release for Windows to 
> work on my Win7 machine.  The install program runs just fine and drops 
> shortcuts to Artemis, Athena, Atoms, and Hephaestus on my desktop.  
> However, when I click on the shortcuts to run these programs I get a 
> very quick flash of a command line window saying something to the 
> effect of: "The system cannot find the path specified."
> 
> The shortcuts on the desktop point to, for
> example:  "C:\demeter\perl\site\bin\dathena.bat" and there are batch 
> files in the specified location with what appears to be useful text in them.
> 
> Note that I get the same issue if I un-install and re-install to the 
> default C:\strawberry directory. Running the batch files from their 
> actual directory does the same thing, suggesting to me that the 
> problem lies somewhere deeper than I have the wherewithal to de-bug.
> 
> Did I miss a crucial step somewhere?

I don't think so.  But it does underscore two problems with the installer that 
I need to address.

Problem #1: It seems that I have not sufficiently well tested relocating the 
installation away from C:\strawberry.  For the time being, you will need to 
live with it being in that location.

Problem #2 is a symptom of problem #1.  Go to the location of the demeter.ini 
file.  On your Win 7 computer, it should be in

   C:\Users\\AppData\Roaming\demeter\

where  is your login name.  Delete the "demeter.ini" file.
Try firing up one the programs -- Athena, for example, again.  Let me know if 
that works.  If not, send me the "dathena.log" file that is in the same folder 
as "demeter.ini".


Thaks for your patience.  It is always challenging to get new software to a 
stable state.  It really helps that you are willing to report about your 
problems.

B

-- 

 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology  Synchrotron Methods Group at 
NSLS --- Beamlines U7A, X24A, X23A2  Building 535A  Upton NY, 11973

 My homepage:http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter
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[Ifeffit] New Demeter Win7 install (?) problems

[Latta, Drew E.]

Bruce:

I am having issues with getting the new Demeter release for Windows to work on 
my Win7 machine.  The install program runs just fine and drops shortcuts to 
Artemis, Athena, Atoms, and Hephaestus on my desktop.  However, when I click on 
the shortcuts to run these programs I get a very quick flash of a command line 
window saying something to the effect of: "The system cannot find the path 
specified."

The shortcuts on the desktop point to, for example:  
"C:\demeter\perl\site\bin\dathena.bat" and there are batch files in the 
specified location with what appears to be useful text in them.

Note that I get the same issue if I un-install and re-install to the default 
C:\strawberry directory. Running the batch files from their actual directory 
does the same thing, suggesting to me that the problem lies somewhere deeper 
than I have the wherewithal to de-bug.

Did I miss a crucial step somewhere?

Cheers,

Drew Latta

---
Drew E. Latta, Ph.D.
Postdoctoral Associate

Molecular Environmental Science Group
Biosciences Division
Argonne National Laboratory
Building 203, Room E-105
9700 South Cass Avenue
Argonne, IL  60439

Phone: 1-630-252-3985
dla...@anl.gov<mailto:dla...@anl.gov>
http://www.mesg.anl.gov
---

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