Dear Max and Scott, First of all sorry for late reply and thank you very much for you kind help. That explains a lot in this aspect. So just to summarize, technically, I am/was not doing anything wrong. and also, the amplitude value that I was considering (by plotting the graph in R space, and taking the peak values) were correct. however, since I do not have 'calibration curve' for nanoparticles for Pd synthesized under control conditions, I cannot really find out the diameter of the nanoparticles, in short? Secondly, could you please guide me with the publications or methods by which I can find out the diameter of nano particles more accurately? Anatoly mentioned about some recent paper in the thread, does anybody knows which one he is talking about? Max, do you happen to remember how did you modified the atoms program in order to get better/accurate results? as to what did you modify etc. I am not really a programmer, so if it is fairly technical, I probably would skip that part and instead focus on another method of particle size. But if it is technically simple method and only few USER FRIENDLY things are needed and I can get better insight, I would not mind applying them and I can cite your work as well in the paper I am writing. Thanks again to all for their prompt response and sorry again for my late response. Sincerely Pushkar On Fri, Jan 22, 2016 at 2:52 AM, Maxim Boyanov wrote:

Hi Pushkar,

We recently discussed a bit measuring particle size by interpreting coordination numbers obtained from fitting EXAFS data, also referring to the paper you mention:

http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-August/thread.html#s...

The basic idea is that surface atoms are not coordinated to other atoms on the outside (i.e., for your Pd foil the surface Pd atoms would have say 6-8 neighbors instead of 12 for the atoms on the inside) so when the particle size becomes less than a few nm the number of surface atoms become a significant proportion of the total number of atoms and you can now observe this undercoordination as a smaller amplitude (assumed to be due to average coordination number) of some coordination peaks in the FT. How you relate this average coordination decrease to particle size depends a bit on your system. Some approaches have been laid out in the literature, including the paper you mention. See the thread above for other. Some time back I used a “brute force” approach to calculate the average coordination vs size for a small particle of a certain crystal structure (see fig EA-7 in the supplementary material of Geochimica et Cosmochimica Acta 71 (2007) 1898–1912). I took the crystallographic structure and created the list of atom coordinates for a 10 nm spherical particle using the ATOMS program. I then wrote a simple program (which I can’t find now :-) to go through the list and calculate the average coordination for a certain shell by going to all atoms within a particle radius and counting the neighbors in each coordination shell of interest. The result is a graph of average coordination for that coordination shell vs radius, which you can then compare to the coordination numbers obtained in your fits of the EXAFS data to “read off” a particle size. This brute force approach takes into account the crystal structure of your material of interest and the slightly different surface density of atoms when you cut along different planes to create the particle. However, the improved accuracy from that will probably give you a difference in coordination number that is within the uncertainty of the coordination numbers in an EXAFS fit. You can use a spherical particle which is probably OK for your case with Pd, but you can also create say rod-shaped particles that emphasize certain crystallographic planes, depending on your case.

Be aware of some of the issues raised by Scott in his email and in the thread in the link above when comparing EXAFS and TEM determined sizes. Another source of discrepancy may be the assumption that the EXAFS peak amplitude reduction is due only to a coordination number decrease. It is also conceivable that the strain in a 2nm particle gives a contribution to the Debye-Waller factor, potentially affecting the determination of the average coordination number by EXAFS.

Overall, use particle size determinations as an estimate, regardless of the experimental or interpretation method used :-). More importantly, be aware of the pitfalls and their effect on the certainty of the conclusions you present. Unfortunately there doesn’t seem to be a recipe-like approach to the problem yet…

Best,

Max.

*From:* Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] *On Behalf Of *pushkar shejwalkar *Sent:* Thursday, January 21, 2016 3:02 AM *To:* XAFS Analysis using Ifeffit *Subject:* [Ifeffit] Regarding calculations for scattering amplitude

Dear All,

I sent a related question in the month of Dec but it seems that the question did not appeared on list because of mailbox being full, as we all have received an email. Since mailing list is started again I am sending this question once more.

My question is actually regarding finding out the nanoparticle size. In this respect, I am referring to Harris's work in which by using a simple equation we can roughly estimate the nanoparticle size

J. Appl. Phys., Vol. 94, No. 1, 1 July 2003

Now the question is that in this paper and another paper I found online as well, it refers to Nnano and Nbulk. I am guessing that this is basically coordination number of nanoparticle and bulk. But my first question is how do I calculate it?? e.g. I am working on Pd K-edge. So should I fit Pd foil with Pd crystal data and get the CN? but that would be 12 anyways. So would Nbulk be 12 in that case? and what will be Nnano then?

In another context, CN is proportional to amplitude, so in that case is it directly proportional? as in, can I simply replaced in formula, Nbulk/Nnano with Amplitudebluk/amplitudenano?

Third thing is that, if above is true then how should/can I calculated the amplitude? isnt that amplitude is always calculated by Feff? if so could someone help me with the procedure to do so? How will I know amplitude for nanoparticles, because I cannot have FEFF for nanoparticles, right?

I went through lot of material, however, so far my calculations give me a solution that is vaguely correlated to TEM images. The TEM value is about 2nm (rouhgly 20 angstrom). my current values I am getting by solving the equation by my current understanding is only 2Ao. about 10 times less. What I am doing is simply plotting the crude data in athena to get x(R) Vs radial distance graph, calculate A-3 for nanoparticles and bulk and using this as amplitudes. It is possible that I may be doing something totally irrelevant, so please help me in this aspect.

Thank you

Sincerely

Pushkar

--

Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,

Tokyo Engineering University,

Tokyo-to

Japan

_______________________________________________ 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

-- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

Dear Anatoly, Thank you very much for your kind response. My Pd particles size (as per TEM images) have narrow size distribution and are measured as 2 nm and are not exposed to Hydrogen so hydrides are not expected. Although, measurements were done at room temperatures and not at elevated temp. It is probably on the borderline for such methods to be employed. However, if it is ok with you, could you please send me the link to the software that we can use to generate the nanoclusters coordinates for FCC Pd-metal? is it fairly simpler to use such program? I do not have much information about software and programming so if there are technical terms it will be difficult for me to understand such things. I would be be happy to use such software and try to generate XYZ coordinates for nanoclusters of 2nm diameter. Thank you very much for your help Waiting for the references and software link. (is it mac compatible or Windows 10 compatible? or I should use specific version as such?) Sincerely Pushkar On Mon, Jan 25, 2016 at 1:02 PM, Anatoly I Frenkel wrote:

Hi Pushkar,

Modeling nanoparicle size, shape, structure and morphology reliably by EXAFS is possible only if you have evidence that your particles have narrow size distribution, especially if the average size is expected to be around 1-2nm.

Also, in the case of Pd, beware of formation of beta-hydride if you exposed your NPs to hydrogen and measured your samples below 400 C.

If it is a metal NP (not a hydride) and it has narrow size distribution, the next step depends crucially on the average size. For 1nm or so, you may try to take advantage of multiple scattering modeling methods we developed in 1997 and there are a few reviews. We have posted web-based software to generate cluster coordinates for regular polyhedral clusters of various symmetries and I can send you a link if you are interested. We also have a software to calculate CN in such clusters, or any clusters with xyz coordinates known, including bimetallics. It is the same idea as what Max described in his post earlier. For larger particles, Scott Calvin's method in his JAP paper works great.

For strained clusters, completely different approaches should be used but those are usually tried after regular cluster models do not work well or you expect strain to be large. If that is the case let me know and I will send a summary of recent works by us and others to show how to take into account strain.

For clusters with broad size distributions we developed approach which combines a correlated analysis of XAFS and TEM data. Let me know if that interests you and I will send references.

Anatoly

Sent from my iPhone

On Jan 24, 2016, at 10:28 PM, pushkar shejwalkar < pshejwalkar2004@gmail.com> wrote:

Dear Max and Scott, First of all sorry for late reply and thank you very much for you kind help. That explains a lot in this aspect. So just to summarize, technically, I am/was not doing anything wrong. and also, the amplitude value that I was considering (by plotting the graph in R space, and taking the peak values) were correct. however, since I do not have 'calibration curve' for nanoparticles for Pd synthesized under control conditions, I cannot really find out the diameter of the nanoparticles, in short? Secondly, could you please guide me with the publications or methods by which I can find out the diameter of nano particles more accurately? Anatoly mentioned about some recent paper in the thread, does anybody knows which one he is talking about? Max, do you happen to remember how did you modified the atoms program in order to get better/accurate results? as to what did you modify etc. I am not really a programmer, so if it is fairly technical, I probably would skip that part and instead focus on another method of particle size. But if it is technically simple method and only few USER FRIENDLY things are needed and I can get better insight, I would not mind applying them and I can cite your work as well in the paper I am writing. Thanks again to all for their prompt response and sorry again for my late response. Sincerely Pushkar

On Fri, Jan 22, 2016 at 2:52 AM, Maxim Boyanov wrote:

...

Hi Pushkar,

We recently discussed a bit measuring particle size by interpreting coordination numbers obtained from fitting EXAFS data, also referring to the paper you mention:

http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-August/thread.html#s...

The basic idea is that surface atoms are not coordinated to other atoms on the outside (i.e., for your Pd foil the surface Pd atoms would have say 6-8 neighbors instead of 12 for the atoms on the inside) so when the particle size becomes less than a few nm the number of surface atoms become a significant proportion of the total number of atoms and you can now observe this undercoordination as a smaller amplitude (assumed to be due to average coordination number) of some coordination peaks in the FT. How you relate this average coordination decrease to particle size depends a bit on your system. Some approaches have been laid out in the literature, including the paper you mention. See the thread above for other. Some time back I used a “brute force” approach to calculate the average coordination vs size for a small particle of a certain crystal structure (see fig EA-7 in the supplementary material of Geochimica et Cosmochimica Acta 71 (2007) 1898–1912). I took the crystallographic structure and created the list of atom coordinates for a 10 nm spherical particle using the ATOMS program. I then wrote a simple program (which I can’t find now :-) to go through the list and calculate the average coordination for a certain shell by going to all atoms within a particle radius and counting the neighbors in each coordination shell of interest. The result is a graph of average coordination for that coordination shell vs radius, which you can then compare to the coordination numbers obtained in your fits of the EXAFS data to “read off” a particle size. This brute force approach takes into account the crystal structure of your material of interest and the slightly different surface density of atoms when you cut along different planes to create the particle. However, the improved accuracy from that will probably give you a difference in coordination number that is within the uncertainty of the coordination numbers in an EXAFS fit. You can use a spherical particle which is probably OK for your case with Pd, but you can also create say rod-shaped particles that emphasize certain crystallographic planes, depending on your case.

Be aware of some of the issues raised by Scott in his email and in the thread in the link above when comparing EXAFS and TEM determined sizes. Another source of discrepancy may be the assumption that the EXAFS peak amplitude reduction is due only to a coordination number decrease. It is also conceivable that the strain in a 2nm particle gives a contribution to the Debye-Waller factor, potentially affecting the determination of the average coordination number by EXAFS.

Overall, use particle size determinations as an estimate, regardless of the experimental or interpretation method used :-). More importantly, be aware of the pitfalls and their effect on the certainty of the conclusions you present. Unfortunately there doesn’t seem to be a recipe-like approach to the problem yet…

Best,

Max.

*From:* Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] *On Behalf Of *pushkar shejwalkar *Sent:* Thursday, January 21, 2016 3:02 AM *To:* XAFS Analysis using Ifeffit *Subject:* [Ifeffit] Regarding calculations for scattering amplitude

Dear All,

I sent a related question in the month of Dec but it seems that the question did not appeared on list because of mailbox being full, as we all have received an email. Since mailing list is started again I am sending this question once more.

My question is actually regarding finding out the nanoparticle size. In this respect, I am referring to Harris's work in which by using a simple equation we can roughly estimate the nanoparticle size

J. Appl. Phys., Vol. 94, No. 1, 1 July 2003

Now the question is that in this paper and another paper I found online as well, it refers to Nnano and Nbulk. I am guessing that this is basically coordination number of nanoparticle and bulk. But my first question is how do I calculate it?? e.g. I am working on Pd K-edge. So should I fit Pd foil with Pd crystal data and get the CN? but that would be 12 anyways. So would Nbulk be 12 in that case? and what will be Nnano then?

In another context, CN is proportional to amplitude, so in that case is it directly proportional? as in, can I simply replaced in formula, Nbulk/Nnano with Amplitudebluk/amplitudenano?

Third thing is that, if above is true then how should/can I calculated the amplitude? isnt that amplitude is always calculated by Feff? if so could someone help me with the procedure to do so? How will I know amplitude for nanoparticles, because I cannot have FEFF for nanoparticles, right?

I went through lot of material, however, so far my calculations give me a solution that is vaguely correlated to TEM images. The TEM value is about 2nm (rouhgly 20 angstrom). my current values I am getting by solving the equation by my current understanding is only 2Ao. about 10 times less. What I am doing is simply plotting the crude data in athena to get x(R) Vs radial distance graph, calculate A-3 for nanoparticles and bulk and using this as amplitudes. It is possible that I may be doing something totally irrelevant, so please help me in this aspect.

Thank you

Sincerely

Pushkar

--

Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,

Tokyo Engineering University,

Tokyo-to

Japan

_______________________________________________ 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

-- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

_______________________________________________ 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

_______________________________________________ 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

-- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan