Re: [Ifeffit] inquire for the EXAFS of the mixture of species
Hi Here an another routine for itfa (PCA_GUI executable). http://code.google.com/p/prestopronto/ You can use athena to create the input file (a file with one energy column and the rest of column are spectra). All the best Carmelo > > Message: 1 > Date: Thu, 08 Mar 2012 17:00:15 +0900 > From: Takahide Yamaguchi <11nm0...@mcs.ibaraki.ac.jp> > To: ifeffit@millenia.cars.aps.anl.gov > Subject: [Ifeffit] what is the reasonable arc-tan for edge jump > Message-ID: <4f58670f.5020...@mcs.ibaraki.ac.jp> > Content-Type: text/plain; charset="iso-2022-jp" > Message: 2 > Date: Thu, 8 Mar 2012 08:13:08 +0000 > From: > To: > Subject: Re: [Ifeffit] inquire for the EXAFS of the mixture of species > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > > 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 > > > > > > > > > > -- next part -- > An HTML attachment was scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120308/662b68ae/attachment-0001.htm> > > -- > -- Carmelo Prestipino Sciences Chimiques de Rennes UMR 6226 Solid State and Materials Chemistry group (CSM) Campus de Beaulieu, Bât 10B, bureau 122 F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] inquire for the EXAFS of the mixture of species
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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] inquire for the EXAFS of the mixture of species
Hi winejia, it is trivial but at the same time hard problem to solve. There are 2 ways: using Athena and using Artemis Using Athena you have measured your sample and all possible references. The result comes from the fit of the linear combination of your references. Using Artemis is similar but instead of measured references you create models (FEFF cards) from known structures and than fit to your experimental data. For sure you will find some more tricks in the archive of this mailing group. good luck kicaj W dniu 12-03-08 05:47, winejar8324 pisze: 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
