Interpreting old XANES data with missing standards

Don Baker

8 Jun 2018 8 Jun '18

1:54 p.m.

Hello All, First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask. So, here is some background: I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available. Now for for my questions: 1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?) 2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling? And information, ideas, and suggestions that you may have will be appreciated. Wishing you all the best from a spring morning in Montreal, Don -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University

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Anatoly Frenkel

8 Jun 8 Jun

2:16 p.m.

Don, I am sure that Paul Northrup (northrup@bnl.gov) will help - he was the beamline scientist at X15B and is likely to have the standards you need. Anatoly ------------------------------------------------------------------- On Fri, Jun 8, 2018 at 9:54 AM, Don Baker wrote:

...

Hello All,

First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask.

So, here is some background:

I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available.

Now for for my questions:

1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?)

2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling?

And information, ideas, and suggestions that you may have will be appreciated.

Wishing you all the best from a spring morning in Montreal,

Don

-- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

Carlo Segre

2:45 p.m.

You might also ask the beamline scientist at APS Sector 9, Tianpin Wu carlo On Fri, 8 Jun 2018, Anatoly Frenkel wrote:

...

Don,

I am sure that Paul Northrup (northrup@bnl.gov) will help - he was the beamline scientist at X15B and is likely to have the standards you need.

Anatoly

-------------------------------------------------------------------

On Fri, Jun 8, 2018 at 9:54 AM, Don Baker wrote:

...
Hello All,

First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask.

So, here is some background:

I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available.

Now for for my questions:

1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?)

2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling?

And information, ideas, and suggestions that you may have will be appreciated.

Wishing you all the best from a spring morning in Montreal,

Don

-- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org

Ritimukta Sarangi

3:16 p.m.

Hi Don, I am sure you are aware but I would like to remind you that the sulfides that you are working with have serious potential for self absorption. Most spectra out there have different degrees of self absorption which can really mess up LCA type analysis. This is not a quick solution, but you might consider remeasuring the standards following a strict protocol of sample dilution, grinding and deposition on substrate to minimize any such artifacts. Best, Riti Sarangi Sent from my iPhone

...

On Jun 8, 2018, at 7:45 AM, Carlo Segre wrote:

You might also ask the beamline scientist at APS Sector 9, Tianpin Wu

carlo

...
On Fri, 8 Jun 2018, Anatoly Frenkel wrote:

Don,

I am sure that Paul Northrup (northrup@bnl.gov) will help - he was the beamline scientist at X15B and is likely to have the standards you need.

Anatoly

-------------------------------------------------------------------

...
On Fri, Jun 8, 2018 at 9:54 AM, Don Baker wrote:

Hello All,

First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask.

So, here is some background:

I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available.

Now for for my questions:

1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?)

2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling?

And information, ideas, and suggestions that you may have will be appreciated.

Wishing you all the best from a spring morning in Montreal,

Don

-- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

Don Baker

7:52 p.m.

Dear Carlo, Thank you so much for your suggestion. I shall! Have a wonderful weekend, Don On Fri, 2018-06-08 at 09:45 -0500, Carlo Segre:

...

You might also ask the beamline scientist at APS Sector 9, Tianpin Wu

carlo

On Fri, 8 Jun 2018, Anatoly Frenkel wrote:

...
Don,

I am sure that Paul Northrup (northrup@bnl.gov) will help - he was the beamline scientist at X15B and is likely to have the standards you need.

Anatoly

-------------------------------------------------------------------

On Fri, Jun 8, 2018 at 9:54 AM, Don Baker wrote:

...
Hello All,

First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask.

So, here is some background:

I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available.

Now for for my questions:

1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?)

2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling?

And information, ideas, and suggestions that you may have will be appreciated.

Wishing you all the best from a spring morning in Montreal,

Don

-- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University

Matthew Marcus

4:01 p.m.

Dear Don. Regarding yours of Fri, 08 Jun 2018 09:54:40 -0400: ESRF has a dbase of S XANES, but they're all pretty affected by overabsorption ("self-absorption"). I think the only reliable way to take such data is in TEY mode. There's a spectrum there for cinnabar (remember, there are multiple polymorphs of HgS) and three forms of Fe sulfide plus several more sulfides. Even the transmission spectra are subject to hole effect, which looks like overabsorption. Also, if you do take data on sulfides, beware of radiation damage. Does it really make sense that a silicate glass would have sulfide in it? I'd think that it would have mostly sulfate and maybe sulfite. Check the peak position; it's a pretty reliable indicator of sulfite vs. sulfate vs. other. Here are some spectra taken in TEY mode with the calibration gypsum = 2482.75eV. Sincerely, Matthew Marcus

...

Hello All,

First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask.

So, here is some background:

I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available.

Now for for my questions:

1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?)

2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling?

And information, ideas, and suggestions that you may have will be appreciated.

Wishing you all the best from a spring morning in Montreal,

Don

Don Baker

8:02 p.m.

Hi Matthew, Thanks for your ideas and even more for the spectra. I looked at the ESRF data base before, but forgot to mention it in my original email. We tried our best to avoid radiation damage and found little-to-no evidence of it in our samples when we compared our standards (a series of iron sulfides and alkali sulfites and sulfates) by comparison with previously measured spectra. The dominant sulfur species in our glasses is sulfide based upon both XANES and electron microprobe peak shift measurements. Wishing you a great weekend, Don On Fri, 2018-06-08 at 09:01 -0700, Matthew Marcus wrote:

...

Dear Don. Regarding yours of Fri, 08 Jun 2018 09:54:40 -0400:

ESRF has a dbase of S XANES, but they're all pretty affected by overabsorption ("self-absorption"). I think the only reliable way to take such data is in TEY mode. There's a spectrum there for cinnabar (remember, there are multiple polymorphs of HgS) and three forms of Fe sulfide plus several more sulfides. Even the transmission spectra are subject to hole effect, which looks like overabsorption. Also, if you do take data on sulfides, beware of radiation damage.

Does it really make sense that a silicate glass would have sulfide in it? I'd think that it would have mostly sulfate and maybe sulfite. Check the peak position; it's a pretty reliable indicator of sulfite vs. sulfate vs. other.

Here are some spectra taken in TEY mode with the calibration gypsum = 2482.75eV.

Sincerely, Matthew Marcus

...
Hello All,

First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask.

So, here is some background:

I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available.

Now for for my questions:

1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?)

2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling?

And information, ideas, and suggestions that you may have will be appreciated.

Wishing you all the best from a spring morning in Montreal,

Don

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University

Matt Newville

4:07 p.m.

HI Don, On Fri, Jun 8, 2018 at 8:55 AM Don Baker wrote:

...

Hello All,

First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask.

Great to hear from you, hope you're doing well. And, to be clear, this sort of question is completely appropriate here.

...

So, here is some background:

I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available.

Now for for my questions:

1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?)

There is also a good-sized set of S XANES from ESRF ID21 at http://www.esrf.eu/home/UsersAndScience/Experiments/XNP/ID21/php.html though I do not see CaS or MgS spectra there. We have lots of data that are not (yet?) in the CARS database, including quite a bit of data on S K edges, taken with various groups. Much of this data *should* be on the CARS XAFS database, but isn't yet. For CaS and MgS in particular, we have recently measured S XANES (in total fluorescence yield) on these and there is sort of a story here. Following up on Riti's comments, these spectra can definitely have over-absorption effects. In addition, these materials are apparently challenging to synthesize well, and keep as stable sulfides. We've been working with Stephen Parman at Brown and students on this, and have some spectra that we think are good. The MgS spectra has been published in a recent paper with Elizabet Head (Head et al GCA226, p149 2018 https://doi.org/10.1016/j.gca.2018.01.033). There are also MgS spectra from Mike Fleet, though we are unsure of how to explain the differences. Because some of this data is unpublished and still very new, I'm slightly reluctant to make it public, but will send some of the data we have privately.

...

2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling?

In my humble opinion,XANES calculations are useful for identifying features, but are less useful for Linear combination analysis with experimental spectra. Cheers, --Matt Newville

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Anatoly Frenkel
Carlo Segre
Don Baker
Matt Newville
Matthew Marcus
Ritimukta Sarangi

Interpreting old XANES data with missing standards

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