Hi all, As I understand, the EXAFS fitting procedure using Artemis, for generating a theoretical model requires the crystal structure parameter like space group, cell parameters and *specially* *atom coordinates* etc. For this we have to perform XRD measurements of single crystals of the samples. I have some questions (1) In case we dont have the XRD data of a sample then how can the EXAFS analysis be done of that sample? (2) If we have already performed the XRD on the sample then by doing EXAFS what additional information are we getting ? (3) If the answer to the first question is that - *use the crystal structure of a * * similar sample,* then what are the conditions under which we can use the known crystal structure of one sample for other samples ? Thanks in advance Abhijeet Gaur
Hi Abhijeet, not in all cases you can get (or get full) crystal structure from database. Then, additional EXAFS experiments can be helpful. Of course, you can also imagine more situation, as doping, vacancies or substitutions, etc. You can also try to create crystal model without XRD data. Please, do not forget that EXAFS is the element selective method, and probes the structure locally. Answering the third question - if you have EXAFS data, and model of crystallographic structure you can compare both, and if it is needed adjust/model the structure to get better agreement. If you use know structure from another compound you should be sure that you have replaced elements according to elements, ocupancy and positions in your sample. regards kicaj W dniu 11-01-30 09:23, Abhijeet Gaur pisze:
Hi all, As I understand, the EXAFS fitting procedure using Artemis, for generating a theoretical model requires the crystal structure parameter like space group, cell parameters and _specially_ _atom coordinates_ etc. For this we have to perform XRD measurements of single crystals of the samples. I have some questions (1) In case we dont have the XRD data of a sample then how can the EXAFS analysis be done of that sample? (2) If we have already performed the XRD on the sample then by doing EXAFS what additional information are we getting ? (3) If the answer to the first question is that - *use the crystal structure of a * * similar sample,* then what are the conditions under which we can use the known crystal structure of one sample for other samples ? Thanks in advance Abhijeet Gaur
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Abhijeet,
On Sun, Jan 30, 2011 at 2:23 AM, Abhijeet Gaur
Hi all, As I understand, the EXAFS fitting procedure using Artemis, for generating a theoretical model requires the crystal structure parameter like space group, cell parameters and specially atom coordinates etc.
No, generating a theoretical model for EXAFS does not require information about a crystal structure. It does require a roughly realistic model for the atomic positions of a cluster of atoms. Here, "roughly realistic" means that it have inter-atomic distances for the near-neighbors to the element of interest that are within 0.1 Angstroms or so. Of course, the species of the neighboring atoms should be approximately correct too. It is often easy to start with a crystal structure to generate the appropriate cluster of atoms. It is not uncommon to have to modify the cluster (say, to model Mn in ZnO, you might start with the crystal structure of pure ZnO, then change the absorbing atom to Mn). For many organic and biological molecules, it is easy to find an entry from the Protein Data Bank that has a similar molecular structure. For some cases, non-crystalline structures predicted from DFT (or MD) calculations are most appropriate, and can certainly be used.
For this we have to perform XRD measurements of single crystals of the samples. I have some questions (1) In case we dont have the XRD data of a sample then how can the EXAFS analysis be done of that sample?
Make a guess of the local structure, model that local structure with x, y, z coordinates of the atoms in that structure, and run Feff. If you expect the sample is crystalline, starting with the expected crystal structure is an easy approach. If the sample is not crystalline, you could still start with a crystal structure close to the expected structure.
(2) If we have already performed the XRD on the sample then by doing EXAFS what additional information are we getting ?
That depends of the sample. Perhaps you're looking at an impurity in that crystal. Perhaps you're trying to refine the structure beyond what the bulk crystal structure gives. It is always a good idea to know when XRD or EXAFS or some other technique is most likely to answer the question you're asking.
(3) If the answer to the first question is that - use the crystal structure of a similar sample, then what are the conditions under which we can use the known crystal structure of one sample for other samples ?
To the extent that the refinement of the structure makes sense. --Matt
participants (3)
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"Dr. Dariusz A. Zając" -
Abhijeet Gaur -
Matt Newville