Pb compound determination fitting issue
Hi everyone, I recently acquired an EXAFS data set (albeit somewhat noisy) on the Pb-L3 edge. I have normalized it using Athena, and tried to fit the first shell using Artemis. I attached the Athena project file as well as the Artemis project file of what I obtained thus far. We have reason to believe the unknown compound is PbO or PbS (or a mixture). However, when I look at the R space curve, the first coordination shell is at rather low path distance (1.7 A), whereas one would expect larger bond distances for PbO and PbS. I found that a similar bond distance as to what the experimental spectrum shows can be found in PbCO3, but a fit using the mineral data of PbCO3 also doesn't do the trick. In any case, no matter what I try to fit in Artemis, nothing seems decent. Is the EXAFS fitting simply impossible due to the noisy data, did I extract my Chi(k) wrong or am I encountering some other issue? I realize it's probably not much to go on, but I'm rather new to EXAFS analysis so any help/advice is appreciated. Thanks a lot in advance! Best regards, Pieter Tack -- X-Ray Micro-Spectroscopy and Imaging Group Department of Analytical Chemistry Ghent University Krijgslaan 281 S12 B-9000 Ghent Belgium Phone: +32 (0)9 264 4723 Fax: +32 (0)9 264 49 60
On 02/25/2015 05:20 AM, Pieter Tack wrote:
I recently acquired an EXAFS data set (albeit somewhat noisy) on the Pb-L3 edge. I have normalized it using Athena, and tried to fit the first shell using Artemis. I attached the Athena project file as well as the Artemis project file of what I obtained thus far.
We have reason to believe the unknown compound is PbO or PbS (or a mixture). However, when I look at the R space curve, the first coordination shell is at rather low path distance (1.7 A), whereas one would expect larger bond distances for PbO and PbS. I found that a similar bond distance as to what the experimental spectrum shows can be found in PbCO3, but a fit using the mineral data of PbCO3 also doesn't do the trick.
Hi Pieter, I am willing to believe that the sample might contain a mixture of O and S. The first big peak reasonably looks like it has scatterers at two different lengths -- a big peak at about 1.5 and a shoulder at about 1.9, plausible distances for those scatterers. That said, your data isn't all that great. As Fred points out, Pb is never a spectroscopist's favorite absorber. Your data are quite noisy, both in terms of statistical noise and systematic error. The level of shot noise is rather high, as you can see from the "fuzziness" of the data beyond about 6 A^-1 and in the rather high level of the high-R portion of chi(R). The feature at about 10 A^-1 does not look at all like EXAFS to my eye. In fact, I suspect that you have a bit of bismuth contaminating your sample. The feature at 10^-1 A looks kind of like a small edge step. Translated into energy, that feature is at about 13420 eV, which is the Bi L3 edge energy. Your Athena project file had kmax for the Fourier transform set to 10.5. That is certainly a mistake. If I am correct about the Bi contamination (if we were discussing this at my beamline, I wouldn't be so circumspect, but circumspection is appropriate for the mailing list!), you certainly must stop the FT before 10 A^-1. I am also troubled that you had the kmin for the FT in the Athena project file set to 0.1 A^-1. That is a poor idea. By its nature, the background removal is most uncertain near the edge, where the data are changing most dramatically. The background function is a piecewise polynomial -- it simply does not have the freedom to follow the swiftly changing data in that energy range. Changing the FT range to [2.5:9.5] yields the chi(R) spectrum in the attached image. This does not leave much information content -- a bit more than 5 independent points, given the R range of [1:2.2] that you selected. You will be hard pressed to do substantive analysis on these data. A sensible fitting model for a situation with two kinds of scatterers would include a S02, an E0, and deltaR and sigma^2 for each scatterer. That's 6 parameters, which exceeds the information content of these data. Without better data, reliable over a longer range (or some kind of multiple data set analysis, or some kind of constraint on the model), you are not going to be able to meet your needs. This one data set simply does not support the amount of information you need to extract.
In any case, no matter what I try to fit in Artemis, nothing seems decent. Is the EXAFS fitting simply impossible due to the noisy data, did I extract my Chi(k) wrong or am I encountering some other issue?
My executive summary is that you likely have a Bi contaminant in your sample (probably not your fault, it was probably in whatever you used to prepare the sample). This limits your usable data range, which severely limits the information content of the data. Other than a few technical issues (mostly choice of FT range) you seem to be thinking about the problem correctly. Your best bet is to figure out how to make a better measurement at you next visit to the beamline. HTH, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Thanks Fred and Bruce for your fast responses!
The data was indeed measured at room temperature (cryo-cooling didn't
seem an option out of fear it might harm the sample; it's rather
delicate) and it also may be perfectly possible it was contaminated
with Bi (Earth literally spilled its guts all over it...).
So, to conclude, the noise is too bad to do decent EXAFS fitting. I
suspected/feared as much. The good news is that I was on the right
track concerning the thinking process, and indeed also had the
impression my k-range boundaries were a stretch. It's good to know for
sure they were too liberal ;)
I'll try to extract as much information from the EXAFS as possible
(e.g. the scatter distances do seem to agree with Pb-O and Pb-S) and
focus on the XANES part for more information on the speciation.
And, as Bruce suggest, think about how I can do better at the beamline
next time ;)
Thanks again for the help,
Best regards
Pieter Tack
Citeren Bruce Ravel
On 02/25/2015 05:20 AM, Pieter Tack wrote:
I recently acquired an EXAFS data set (albeit somewhat noisy) on the Pb-L3 edge. I have normalized it using Athena, and tried to fit the first shell using Artemis. I attached the Athena project file as well as the Artemis project file of what I obtained thus far.
We have reason to believe the unknown compound is PbO or PbS (or a mixture). However, when I look at the R space curve, the first coordination shell is at rather low path distance (1.7 A), whereas one would expect larger bond distances for PbO and PbS. I found that a similar bond distance as to what the experimental spectrum shows can be found in PbCO3, but a fit using the mineral data of PbCO3 also doesn't do the trick.
Hi Pieter,
I am willing to believe that the sample might contain a mixture of O and S. The first big peak reasonably looks like it has scatterers at two different lengths -- a big peak at about 1.5 and a shoulder at about 1.9, plausible distances for those scatterers.
That said, your data isn't all that great. As Fred points out, Pb is never a spectroscopist's favorite absorber. Your data are quite noisy, both in terms of statistical noise and systematic error. The level of shot noise is rather high, as you can see from the "fuzziness" of the data beyond about 6 A^-1 and in the rather high level of the high-R portion of chi(R).
The feature at about 10 A^-1 does not look at all like EXAFS to my eye. In fact, I suspect that you have a bit of bismuth contaminating your sample. The feature at 10^-1 A looks kind of like a small edge step. Translated into energy, that feature is at about 13420 eV, which is the Bi L3 edge energy. Your Athena project file had kmax for the Fourier transform set to 10.5. That is certainly a mistake. If I am correct about the Bi contamination (if we were discussing this at my beamline, I wouldn't be so circumspect, but circumspection is appropriate for the mailing list!), you certainly must stop the FT before 10 A^-1.
I am also troubled that you had the kmin for the FT in the Athena project file set to 0.1 A^-1. That is a poor idea. By its nature, the background removal is most uncertain near the edge, where the data are changing most dramatically. The background function is a piecewise polynomial -- it simply does not have the freedom to follow the swiftly changing data in that energy range.
Changing the FT range to [2.5:9.5] yields the chi(R) spectrum in the attached image. This does not leave much information content -- a bit more than 5 independent points, given the R range of [1:2.2] that you selected. You will be hard pressed to do substantive analysis on these data. A sensible fitting model for a situation with two kinds of scatterers would include a S02, an E0, and deltaR and sigma^2 for each scatterer. That's 6 parameters, which exceeds the information content of these data.
Without better data, reliable over a longer range (or some kind of multiple data set analysis, or some kind of constraint on the model), you are not going to be able to meet your needs. This one data set simply does not support the amount of information you need to extract.
In any case, no matter what I try to fit in Artemis, nothing seems decent. Is the EXAFS fitting simply impossible due to the noisy data, did I extract my Chi(k) wrong or am I encountering some other issue?
My executive summary is that you likely have a Bi contaminant in your sample (probably not your fault, it was probably in whatever you used to prepare the sample). This limits your usable data range, which severely limits the information content of the data.
Other than a few technical issues (mostly choice of FT range) you seem to be thinking about the problem correctly. Your best bet is to figure out how to make a better measurement at you next visit to the beamline.
HTH, B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973
Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
-- X-Ray Micro-Spectroscopy and Imaging Group Department of Analytical Chemistry Ghent University Krijgslaan 281 S12 B-9000 Ghent Belgium Phone: +32 (0)9 264 4723 Fax: +32 (0)9 264 49 60
participants (2)
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Bruce Ravel -
Pieter Tack