- Ifeffit - millenia.cars.aps.anl.gov

Crystallographic data for V(CO)6
by Ismael Graff 08 Mar '12

08 Mar '12

Dear XAS fellows: I have to fit EXAFS data of a nanoparticle colloidal suspension. TEM and NMR data indicate that I have nanoparticles of V(CO)_6 (vanadium hexacarbonyl). The system is orthorhombic, space group Pnma (Nr. 62), and I know the nominal values for the lattice parameters. However, I need the different atomic positions/coordinates to enter in ATOMS. Usually I get such information from a CIF (Crystallographic Information File) card. But in this case, I didn´t find it in the open data banks. Is anyone out there that could help me? Cheers, Ismael. PS: A similar structure/material would also help (like Mo(CO)_6)! -- ************************************ * Ismael Leandro Graff * * * * Universidade Federal do Paraná * * Departamento de Física, CP 19044 * * 81531-990, Curitiba, Brazil. * * Tel (office): +55 41 3361 3278 * * Tel (Lab): +55 41 3361 3427 * * Fax: +55 41 3361 3418 * * http://fisica.ufpr.br/graff * ************************************

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Re: [Ifeffit] inquire for the EXAFS of the mixture of species
by fred.mosselmans＠diamond.ac.uk 08 Mar '12

08 Mar '12

Hi Winejia, I think your problem may well be harder than an LC approach as suggest by Darius will solve, as it is possible (probable) that the reaction intermediates are not known structurally so you don't have model spectrum of them. Complex solution equilibrium mixtures are about as tough as it gets for soluble EXAFS problems. The methods that tend to work are Principal component analysis (which is available in sixpack and Athena) This will probably tell you how many species you have in your reactant spectra, and will also tell you by target transformation if a spectrum of a model you have is one of those species. However to identify the unknowns you may need to use a more advanced approach like iterative transformation factor analysis (ITFA) . there is an itfa package available from the RoBL esrf beamline http://www.esrf.eu/UsersAndScience/Experiments/CRG/BM20/Software/ This should be able to give you the spectra of the separate solution spectra which then you can analyse with Artemis. The key things you need to have is more spectra representing in different ratios of the solution species than the total no of solution species, otherwise your problem is underdetermined, preferably quite a lot more. Regards Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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what is the reasonable arc-tan for edge jump
by Takahide Yamaguchi 08 Mar '12

08 Mar '12

Dear all, I was so glad that Bruce and Zajac gave me advice about MS path treatment in last time. Thank you very much. Now, I am working on analysis of Cu K edge by using EDG_FIT, following previous papers. I am wondering if someone gave me comment about current problem for me. And my question about XANES analysis is "what the reasonable arc-tan is as a back ground of XANES." In previous some papers, Cu K edge were deconvoluted by assuming arc-tan edge jump function. But I couldn't found the reasonable mention for the shape of arc-tan. For example of Cu(II), one paper (1), which has interest in the metalloproteins active site, the arc-tan were positioned around 8992 eV with 5 eV hwhm approximatly. 　 But in another paper (2), which reported about high valence Cu(III), the arc-tan for Cu(II) complex looks having narrow hwhm at higher positons (around at 8984 eV). (1) /J. Phys. Chem./ B 2000, 104,10814-10819 (2) /JACS/ 2000, 122, 5775-5787 Are there any reason which can explain these difference? I hope any comment and advice. Takahide

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what is the reasonable arc-tan for edge jump
by Takahide Yamaguchi 08 Mar '12

08 Mar '12

Dear all, I was so glad that Bruce and Zajac gave me advice about MS path treatment in last time. Thank you very much. Now, I am working on analysis of Cu K edge by using EDG_FIT, following previous papers. I am wondering if someone gave me comment about current problem for me. And my question about XANES analysis is "what the reasonable arc-tan is as a back ground of XANES." In previous some papers, Cu K edge were deconvoluted by assuming arc-tan edge jump function. But I couldn't found the reasonable mention for the shape of arc-tan. For example of Cu(II), one paper (1), which has interest in the metalloproteins active site, the arc-tan were positioned around 8992 eV with 5 eV hwhm approximatly. 　 But in another paper (2), which reported about high valence Cu(III), the arc-tan for Cu(II) complex looks having narrow hwhm at higher positons (around at 8984 eV). (1) /J. Phys. Chem./ B 2000, 104,10814-10819 (2) /JACS/ 2000, 122, 5775-5787 Are there any reason which can explain these difference? I hope any comment and advice. Takahide

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Re: [Ifeffit] inquire for the EXAFS of the mixture of species
by winejar8324 08 Mar '12

08 Mar '12

Hello everyone, I have a puzzle during analyzing of my EXAFS data. can someone please help me: I have a set of EXAFS data on solution sample at different pH. I wish to extract the structure information from the EXAFS region to accont for the reaction machanism. However, there are several configurations(as indicated by XANES) and species(as indicated by thermodynamics caculation) in solution due to the metal-Ligand complex balance. How can i obtain the structure information about this complex system from the EXAFS data? Thanks, winejia

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appropriatness of feff model when central atom is not "embedded" (or only 1 layer embedded)
by Andrea L Foster 07 Mar '12

07 Mar '12

Hello All, can someone please help with this: (1) feff requires that the adsorbing atom be "embedded" (that is, surrounded by) other atoms in order to calculate potentials correctly, but how deeply does the atom need to be embedded? For example, if I construct a model of an adsorbate on a mineral surface, where that adsorbate has a full complement of 1st shell coordinating OH, O, and H2O groups as appropriate, but if I do not include all the uncoordinated f water atoms that would be nearby (so that I essentially have a surface in vacuum), will the potentials for my central atom be calculated correctly (or correctly enough for use in IFEFFIT)? a more specific example: the AsO4 tetrahedron bonded to the goethite surface, which is made of octahedrally-coordinated iron. The arsenate bonds to the goethite by sharing 1 edge of the tetrahedron with the apices of 2 adjacent Fe octahedra. a related question that comes to mind: if I just wanted to see the signal from the 2 adjacent Fe atoms, could I create a perfectly "useable" FEFF model (for IFEFFIT) by limiting my calculations to the small cluster of 1 arsenate tetrahedron and 2 Fe octahedra? thanks, andrea ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andrea L. Foster, Ph.D. U.S.G.S. WMESC 345 Middlfield Rd., MS 901 Menlo Park, CA 94025 T: 650-329-5437 F: 650-329-5491

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running ifeffit-1.2.11 under 64-bit Windows 7
by sameh 07 Mar '12

07 Mar '12

Hi, I have a new computer with 64-bit windows7. I have noticed that Artemis is running in a strange manner, it never produces the same results when the same data is fitted twice. I have uninstalled and then reinstalled the whole (ifeffit-1.2.11) package with the compatibility wizard which suggested to run the package in compatible mode to windows XP. After doing so, any of the programs is not running at all. My old laptop was 32-bit which runs 32-bit windows 7 and the ifeffit-1.2.11 package was running normally with this computer. Thank you very much and best regards Sameh Ibrahim Ahmed

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Coordination numbers using Artemis and sixpack
by Nicolae L. Aldea 05 Mar '12

05 Mar '12

Dear users, I ealized some XAS measurements regarding to supported gold catalysts as well as a standard sample on Au foil. 1. I like to a comparative analysis using Artemis and sispack. I have obtained some results using Artemis code. Unfortunately, for me is not so clear how to determine coordination numbers associated with each shells. I set dgen =1, I obtained S**2 values then I introduced S**2 in fist sample for fit step but I do not how to obtained values for different coordination shells. 2. Additionally, I like to use sixpack code. In this way I determined all steps up to |chi(r)| I tried to continue with make FEFF SS paths and FEFF exafs fitting. Unfortunately I could start the last steps. Are you so kind to indicate me how to do. Can you indicate me any tutorials or some examples to understand how to create SS paths and exafs fitting. Tanking you in advance Nick Aldea ******************************************************* * Dr. Nicolae L. Aldea * * National Institute for Research and Development * * for Isotopic and Molecular Technologies * * Donath Street 65-103, P. O. Box 700 * * 400293 Cluj-Napoca, Romania * * E-mail: naldea(a)itim-cj.ro * * Details: http://L30.itim-cj.ro/~naldea/index.htm * *******************************************************

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Fe K-Edge in Zirconium alloys and flattening effect
by adrien couet 01 Mar '12

01 Mar '12

Dear all, I am currently a PhD student working on the corrosion of zirconium alloys used in nuclear reactors. A very commonly used alloy in the industry is called Zircaloy-4 and has the following chemical formula in wt%: Zr-1.2Sn-0.2Fe-0.1Cr. The iron and chromium solubility limit in zirconium is very low. A large portion of the iron precipitates out as Zr(Cr,Fe) precipitates with approximately 40wt% of Fe, approximately 0.02wt% of Fe is left in solid solution in the zirconium matrix. Sn is completely soluble in zirconium. I am working on XANES of the Fe K-Edge absorption line in this material. To do so, I use the microbeam (0.2x0.2 microns) at the 2IDD beamline at the APS in fluorescence mode. To quantify my results, I needed proper standards of metallic Fe. I quickly realized that metallic Fe powder mixed with Zr powder did not give me the same XANES signal as the Zircaloy-4 metal (in which metallic Fe is embedded). Indeed, if you compare the "Fe powder in Zr" group to both Zircaloy-4 groups after normalization and flattening they look different. My thinking is that the Fe in precipitates and the Fe in solid solution, even if they are both metallic, could have different XANES patterns. So I decided to create a thin sample where I could probe either a precipitate or the matrix to get standards of metallic Fe in my Zircaloy-4 metal. Both signals (from Fe in a precipitate and Fe in solid solution) look similar once they are normalized and flattened (see in the attached project file). However, the data before flattening look significantly different! The post-edge of Fe in precipitates abruptly decreases whereas the post-edge of Fe in solid solution increases. I also acquired spectra in between these two extreme cases. When I scan in between the matrix and the precipitate, I see an evolution of the post edge, which looks more and more similar to the precipitate post-edge as I get closer to it. But after flattening they all look identical and the XANES spectra does not look too bad. I have some questions regarding this: - Is the flattening process changing anything such as the edge energy in a way that I should not use it when the post-edge slopes are significant as is the case here (even though my XANES spectra in solid solution and in the precipitate match after flattening)? - Have you ever seen this kind of post edge behavior before flattening? Do you think it could be due to a concentration effect since I am going from 0.02wt% of Fe in solid solution to 40wt% of Fe in the precipitate? I should mention that I have checked that no other elements present in the metal have edges that could potentially disturb the Fe post-edge. Thanks a lot for your help!!! -- Adrien Couet Graduate Student Dept of Nuclear Engineering, Penn State University +1 814 865 9709 axc1019(a)psu.edu

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Problem with creation of feff paths for americium in artemis
by Froehlich, Daniel 01 Mar '12

01 Mar '12

Dear Sir or Madam, We are looking forward to a beamtime investigating americium complexes and I wanted to create feff-paths for americium sulfate by using crystallographic data of europium sulfate and replacing Eu by Am. Atoms runs well and creates the feff.inp but when I then try tu run Feff I just get the error message Feff 6L.02 ? Eu H4 N O8 S2 Ruiz-Valero, Caridad New catalytically active neodymium sulfate Calculating potentials and phases... free atom potential and density for atom type 0 cannot remove an electron from this level Fatal Error: at GETORB-1 Their seems to be a problem with the atomic number because if I change Z=95 to 94 it runs without any problem. Is it possible to run it anyway with Z=95 or must I go for 94 instead which is the atomic number of Pu? Furthermore, I wanted to calculate the potentials with SCF approach but I read a lot of "google search results" without finding any helpful information.Or isn't it needed at all...? Many thanks in advance and best regards Daniel Fröhlich ______________________________________________ Dr. Daniel Fröhlich Physikalisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 253 D-69120 Heidelberg, Germany Institut für Nukleare Entsorgung (INE) Karlsruher Institut für Technologie (KIT) Campus Nord P.O. Box 3640 D-76021 Karlsruhe, Germany

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