Gold Nanoparticle first shell fitting
Dear Ifeffit Community, I'm trying to fit a gold nanoparticle in the size of about 2 nm that is immobilized by polymers. For my research it's enought to fit the first shell only, becaues all I would like to analyze is the atomic distance in the nanoparticle. After the (hopefully) correct background substraction in Athena (athena file attached), there is a shoulder at approx. 2.1 Angström in the R-space. In Artemis, fitting this shoulder seems not to be possible, while the fit for the reference (gold foil) seems to be fine. (both artemis files are attached to the e-mail). If the k-range is decreased from 12.388 to a value between 9 an 10, the shoulder disappears and the fit works fine. But I think by this change I might modify the data too much. Would be really nice, if sombody has an idea how to deal with the problem, to get a hint how to solve this. Thanks a lot, Julian ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
Something is horribly wrong with the data here. I overplotted your reference Au foil against mine, and yours has distorted XANES and too high EXAFS intensity compared to my data. Your amplitude factor is 1.54 which also confirms that something was wrong in the experiment. Perhaps - a misalignment? The NP data also look strange... I would not focus on the NP analysis until you figure out why your foil data is so strange. Anatoly ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Kaiser, Julian [julian.kaiser@helmholtz-berlin.de] Sent: Tuesday, October 11, 2011 1:06 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Gold Nanoparticle first shell fitting Dear Ifeffit Community, I'm trying to fit a gold nanoparticle in the size of about 2 nm that is immobilized by polymers. For my research it's enought to fit the first shell only, becaues all I would like to analyze is the atomic distance in the nanoparticle. After the (hopefully) correct background substraction in Athena (athena file attached), there is a shoulder at approx. 2.1 Angström in the R-space. In Artemis, fitting this shoulder seems not to be possible, while the fit for the reference (gold foil) seems to be fine. (both artemis files are attached to the e-mail). If the k-range is decreased from 12.388 to a value between 9 an 10, the shoulder disappears and the fit works fine. But I think by this change I might modify the data too much. Would be really nice, if sombody has an idea how to deal with the problem, to get a hint how to solve this. Thanks a lot, Julian ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
Dear Anatoly, thanks a lot for your reply! I don't see the problem yet. In the attached file ("different_Au_foils.prj), there are two different gold reference foils measured at two different synchrotrons. There is some difference but not realy much. Could you please describe the regions that are worse comparing my gold foil-file to yours, or if possible, attache the file with both foils or at least a screenshot of the plot? Best regards, Julian ________________________________ Von: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov]" im Auftrag von "Anatoly I Frenkel [afrenke2@yu.edu] Gesendet: Dienstag, 11. Oktober 2011 20:29 Bis: XAFS Analysis using Ifeffit Betreff: Re: [Ifeffit] Gold Nanoparticle first shell fitting Something is horribly wrong with the data here. I overplotted your reference Au foil against mine, and yours has distorted XANES and too high EXAFS intensity compared to my data. Your amplitude factor is 1.54 which also confirms that something was wrong in the experiment. Perhaps - a misalignment? The NP data also look strange... I would not focus on the NP analysis until you figure out why your foil data is so strange. ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Kaiser, Julian [julian.kaiser@helmholtz-berlin.de] Sent: Tuesday, October 11, 2011 1:06 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Gold Nanoparticle first shell fitting Dear Ifeffit Community, I'm trying to fit a gold nanoparticle in the size of about 2 nm that is immobilized by polymers. For my research it's enought to fit the first shell only, becaues all I would like to analyze is the atomic distance in the nanoparticle. After the (hopefully) correct background substraction in Athena (athena file attached), there is a shoulder at approx. 2.1 Angström in the R-space. In Artemis, fitting this shoulder seems not to be possible, while the fit for the reference (gold foil) seems to be fine. (both artemis files are attached to the e-mail). If the k-range is decreased from 12.388 to a value between 9 an 10, the shoulder disappears and the fit works fine. But I think by this change I might modify the data too much. Would be really nice, if sombody has an idea how to deal with the problem, to get a hint how to solve this. Thanks a lot, Julian ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
Dear Julian, I should've guessed earlier, but now I see that the only reason is that you did not take natural log when you constructed your transmission EXAFS signal from detector data. I assume it is transmission since your group name says so. It explains all problems with your data in the foil, and the NP fit, weird looking XANES and wrong S02. And, by the way, the differences between the two synchrotrons is acctually huge, especially in the XANES, but it is hard to discuss differences in the signals that are exp(mu) instead of mu. Anatoly ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Kaiser, Julian [julian.kaiser@helmholtz-berlin.de] Sent: Friday, October 14, 2011 10:14 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Gold Nanoparticle first shell fitting Dear Anatoly, thanks a lot for your reply! I don't see the problem yet. In the attached file ("different_Au_foils.prj), there are two different gold reference foils measured at two different synchrotrons. There is some difference but not realy much. Could you please describe the regions that are worse comparing my gold foil-file to yours, or if possible, attache the file with both foils or at least a screenshot of the plot? Best regards, Julian ________________________________ Von: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov]" im Auftrag von "Anatoly I Frenkel [afrenke2@yu.edu] Gesendet: Dienstag, 11. Oktober 2011 20:29 Bis: XAFS Analysis using Ifeffit Betreff: Re: [Ifeffit] Gold Nanoparticle first shell fitting Something is horribly wrong with the data here. I overplotted your reference Au foil against mine, and yours has distorted XANES and too high EXAFS intensity compared to my data. Your amplitude factor is 1.54 which also confirms that something was wrong in the experiment. Perhaps - a misalignment? The NP data also look strange... I would not focus on the NP analysis until you figure out why your foil data is so strange. ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Kaiser, Julian [julian.kaiser@helmholtz-berlin.de] Sent: Tuesday, October 11, 2011 1:06 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Gold Nanoparticle first shell fitting Dear Ifeffit Community, I'm trying to fit a gold nanoparticle in the size of about 2 nm that is immobilized by polymers. For my research it's enought to fit the first shell only, becaues all I would like to analyze is the atomic distance in the nanoparticle. After the (hopefully) correct background substraction in Athena (athena file attached), there is a shoulder at approx. 2.1 Angström in the R-space. In Artemis, fitting this shoulder seems not to be possible, while the fit for the reference (gold foil) seems to be fine. (both artemis files are attached to the e-mail). If the k-range is decreased from 12.388 to a value between 9 an 10, the shoulder disappears and the fit works fine. But I think by this change I might modify the data too much. Would be really nice, if sombody has an idea how to deal with the problem, to get a hint how to solve this. Thanks a lot, Julian ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
Dear Anatoly, dear Dave, thanks a lot for your help! I've imported the data agin by using the natural log and fitted the Gold-Nanoparticle again. Unfortunately the problem with the shoulder that can be fitted in the reference gold foul but not in the nanoparticle still remains. (See attached Artemis and Athena files) Do you have an idea how to solve this problem? Thanks a lot in advance, regards, Julian ________________________________ Von: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov]" im Auftrag von "Anatoly I Frenkel [afrenke2@yu.edu] Gesendet: Freitag, 14. Oktober 2011 16:58 Bis: XAFS Analysis using Ifeffit Betreff: Re: [Ifeffit] Gold Nanoparticle first shell fitting Dear Julian, I should've guessed earlier, but now I see that the only reason is that you did not take natural log when you constructed your transmission EXAFS signal from detector data. I assume it is transmission since your group name says so. It explains all problems with your data in the foil, and the NP fit, weird looking XANES and wrong S02. And, by the way, the differences between the two synchrotrons is acctually huge, especially in the XANES, but it is hard to discuss differences in the signals that are exp(mu) instead of mu. Anatoly ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Kaiser, Julian [julian.kaiser@helmholtz-berlin.de] Sent: Friday, October 14, 2011 10:14 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Gold Nanoparticle first shell fitting Dear Anatoly, thanks a lot for your reply! I don't see the problem yet. In the attached file ("different_Au_foils.prj), there are two different gold reference foils measured at two different synchrotrons. There is some difference but not realy much. Could you please describe the regions that are worse comparing my gold foil-file to yours, or if possible, attache the file with both foils or at least a screenshot of the plot? Best regards, Julian ________________________________ Von: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov]" im Auftrag von "Anatoly I Frenkel [afrenke2@yu.edu] Gesendet: Dienstag, 11. Oktober 2011 20:29 Bis: XAFS Analysis using Ifeffit Betreff: Re: [Ifeffit] Gold Nanoparticle first shell fitting Something is horribly wrong with the data here. I overplotted your reference Au foil against mine, and yours has distorted XANES and too high EXAFS intensity compared to my data. Your amplitude factor is 1.54 which also confirms that something was wrong in the experiment. Perhaps - a misalignment? The NP data also look strange... I would not focus on the NP analysis until you figure out why your foil data is so strange. ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Kaiser, Julian [julian.kaiser@helmholtz-berlin.de] Sent: Tuesday, October 11, 2011 1:06 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Gold Nanoparticle first shell fitting Dear Ifeffit Community, I'm trying to fit a gold nanoparticle in the size of about 2 nm that is immobilized by polymers. For my research it's enought to fit the first shell only, becaues all I would like to analyze is the atomic distance in the nanoparticle. After the (hopefully) correct background substraction in Athena (athena file attached), there is a shoulder at approx. 2.1 Angström in the R-space. In Artemis, fitting this shoulder seems not to be possible, while the fit for the reference (gold foil) seems to be fine. (both artemis files are attached to the e-mail). If the k-range is decreased from 12.388 to a value between 9 an 10, the shoulder disappears and the fit works fine. But I think by this change I might modify the data too much. Would be really nice, if sombody has an idea how to deal with the problem, to get a hint how to solve this. Thanks a lot, Julian ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
participants (2)
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Anatoly I Frenkel -
Kaiser, Julian