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

RE: [Ifeffit] weights data processing
by Kelly, Shelly D. 23 Jul '04

23 Jul '04

> -----Original Message----- > From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > Sent: Friday, July 23, 2004 6:31 AM > To: ravel(a)phys.washington.edu; XAFS Analysis using Ifeffit > Subject: [Ifeffit] weights data processing > > > Hi folks, > > 1) when removing background using athena, there is an option of using > a k-weight different than 1 (I am NOT talking about k-weight for FT). > I noticed that changing this parameter the resulting chi(k) does not > change significantly. Actually, going from 1 to 4 as a value for > k-weight for Bkgd removal, the only effect I see is a significant > reduction of the peak below the first coordination shell in chi(R) > while the other features of the spectrum are essentially the same in > terms of absolute and relative intensity. A drastic change in both > chi(k) and chi(R) is seen if I use k-weight = 5 and above. What is > the exact meaning of it? I know what the meaning is in the FT > process, but I do not see the reason why I should use a weight > different than 1 (let's say 3 for my noisy data) for background > removal. How should I behave? Should I take the largest value of > k-weight so that the essential features of the chi(k) and chi(R) do > not change? Hi Stefano, I have found a procedure for removing the background that "almost" always works well. It goes something like this and uses different k-weightings in the background removal process. 1) Check out the curvature of the XANES region and how quickly the data goes from zero to 1, call this DExanes. There are in my small opinion two categories for each of these different parameters. Curvature of Xanes can be step like or it can have a large peak. DExanes can be small ~10eV for k-edges of Cu or wide ~30eV for L3-edge of U. 2) Choosing Ezero for the first time: If you have a wide DExanes, then choose Ezero up near the top of the edge. If you have a small DExanes, then choose Ezero around the middle of the edge. 3)Set kweight equal to one or zero (and no theory) and remove the background. This will emphasize the low k-region around the edge, but often get the background for the higher k-region not as well...especially for noisy data. 4)Check out the shape of the background function, the chi(k) data and the FT. Make sure that rbkg=1.0 is a reasonable thing to do. Make sure that you look at the chik data with all three k-weights. Often people say that there is no change in the chik data by changing the kwieght but they are looking at the chik*k3. The change will be greatest at low k, which you don't really see with chik*k3. 5) If you have a large peak in the XANES region, Athena may need help getting the bkg to go through that peak. You have two options. A) increase rbkg so that the spline has more freedom to curve in this region. or B) increase kmin of the spline range, essentially removing the large peak from the data. 6) Fit the first shell of your data, use a well padded chik data range...don't include at least one full oscillation at the beginning. i.e. use kmin=3 or greater. Monitor the value for ezero. If it is greater than 10eV you need to start over. (I have some more details on how to create a theory to be used for bkg removal on my web site http://www.mesg.anl.gov/Skelly.html from the 2004 NSLS EXAFS workshop presentation) 7) Read the theory back into Athena. Now Athena knows what the low k-range should look like, and you can increase the k-weight of the background, use kw=2 or 3, to get the high k-range part of the data correct as well. 8) Fit the data again and use as much of the k-range as possible. > > 2) In artemis, is it a bug or a wanted feature to have the > possibility to activate more than one button for k-weight for the fit > and FT? I suppose it is a wanted feature, but then I wonder what is > the meaning of using more than one weight for the fit and FT. I am > sure some of you can unveil this enigma. > Another couple of reasons to use more than 1 k-weight in the FT of the data: I have found that the uncertainties in the fitted values are about half as big by using all three k-weights, as opposed to using just one k=weight. I have also found that using all three k-weights will force you to model the data much more correctly. When you look at the fits, you need to look at the FT and the chi(k) data using all three k-weights. HTH Shelly

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Re: [Ifeffit] Solution flow cells
by Scott Calvin 23 Jul '04

23 Jul '04

Thanks to all for the references, advice, etc.! This list really works wonders sometimes... --Scott Calvin Sarah Lawrence College

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using atoms and feff
by Barton, David (DG) 23 Jul '04

23 Jul '04

I agree with Scott, the ICSD database of crystallographic structures has also been invaluable to my work on inorganic solids. However, the ICSD is truly an inorganic database in that it does not contain any compounds that contain carbon. For small molecule crystalline compounds that contain carbon the Cambridge Structural Database (http://www.ccdc.cam.ac.uk/ <http://www.ccdc.cam.ac.uk/> ) is quite useful. It contains ~300,000 crystal structures of organic and organometallic compounds. However, this database comes with a significant price tag, but if you can get access it is an amazing tool. Both of these crystallographic databases will write out the records in the CIF (Crystallographic Information File) format. I have written a command line Perl program which converts these CIF records to Atoms.inp files which can be used directly with Artemis. Shelly Kelly was kind enough to host the files: http://146.137.194.45/exafs.html <http://146.137.194.45/exafs.html> . Eventually, we may see a CIF import feature based on this code included in Artemis. Another Crystallographic File converter that I have found useful is CRYSCON (ShapeSoftware: http://www.shapesoftware.com/ <http://www.shapesoftware.com/> ). This shareware program will interconvert nearly all crystallographic file formats and, at my request, the author recently added support to export files with Ravel's ATOMS file format. Dave Barton The Dow Chemical Company, DND-CAT member at APS

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RE: Ifeffit Digest, Vol 17, Issue 18: RE: Solution flow cells
by Wojciech Gawelda 23 Jul '04

23 Jul '04

Dear Scott, We have done some time-resolved XAFS measurements on aqueous solution of Ru(II)(bpy)3 complex using free-flowing jet. It forms a liquid sheet of approx. 100 microns thickness and thus you can avoid windows etc. However you might run into some trouble when using in vacuum. In principle you can find many manufacturers who provide these kinds of jets equipped with sapphire nozzles for dye lasers. I know that some of these jets are also used for cutting and polishing jewelry...if you need any more details you could look up our paper about the setup: M. Saes et al., Rev. Sci. Instrum., 75(2004), 24-30. I hope it helps, Wojciech Gawelda ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: wojciech.gawelda(a)epfl.ch WWW: http://lsu.epfl.ch ********************************************************************* -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: vendredi, 23. juillet 2004 08:47 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 17, Issue 18 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Solution flow cells (Scott Calvin) 2. RE: Solution flow cells (Kelly, Shelly D.) 3. Re: Solution flow cells (Tsu-Chien Weng) 4. RE: Solution flow cells (Matt Newville) 5. RE: Solution flow cells (Jensen, Mark P.) 6. RE: Solution flow cells (SCHLEGEL Michel 177447) ---------------------------------------------------------------------- Message: 1 Date: Thu, 22 Jul 2004 15:34:00 -0400 From: Scott Calvin <scalvin(a)slc.edu> Subject: [Ifeffit] Solution flow cells To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <3.0.1.32.20040722153400.00b14170(a)mail.slc.edu> Content-Type: text/plain; charset="us-ascii" Hi all, I've been doing a literature search for an article I'm writing up, and I can't seem to find any examples of an XAS flow cell desgined for liquids. Sealed cells for liquids, yes; flow cells for passing gases over solids, yes; but no solution-chemistry flow cell. I feel like someone must have published work in that area before, but I can't seem to find it. So, does anyone know of any work done using a liquid-phase XAS flow cell? --Scott Calvin Sarah Lawrence College ------------------------------ Message: 2 Date: Thu, 22 Jul 2004 14:55:29 -0500 From: "Kelly, Shelly D." <SKelly(a)anl.gov> Subject: RE: [Ifeffit] Solution flow cells To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <1C1577844A0BDF448E14E8CCB2F74424015A267F(a)ANLMAIL.anl.gov> Content-Type: text/plain; charset="us-ascii" Hi Scott, See below: > Hi all, > > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an XAS > flow cell desgined for liquids. Sealed cells for liquids, > yes; flow cells for passing gases over solids, yes; but no > solution-chemistry flow cell. I feel like someone must have > published work in that area before, but I can't seem to find it. > > So, does anyone know of any work done using a liquid-phase > XAS flow cell? Simon Bare uses a flow cell for passing liquids/gasses over a sample. This one is a glass container with kapton windows with ports for input and output. Also I have seen something like that at PNC cat. I think that Ed Stern et. al. was using it. The one at PNC cat circulated the liquid through a boron carbide section that is x-ray transparent. Shelly ------------------------------ Message: 3 Date: Thu, 22 Jul 2004 16:44:40 -0400 From: Tsu-Chien Weng <tsuchien(a)umich.edu> Subject: Re: [Ifeffit] Solution flow cells To: Scott Calvin <scalvin(a)slc.edu>, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <F452155A-DC1F-11D8-8255-000A959EB970(a)umich.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Scott, > I've been doing a literature search for an article I'm writing up, and > I > can't seem to find any examples of an XAS flow cell desgined for > liquids. > Sealed cells for liquids, yes; flow cells for passing gases over > solids, > yes; but no solution-chemistry flow cell. I feel like someone must have > published work in that area before, but I can't seem to find it. > > So, does anyone know of any work done using a liquid-phase XAS flow > cell? We (Penner-Hahn group) have done solution EXAFS measurement and time-resolved XAS at Bio-CAT at the APS. A Kapton tube is used for x-ray window and connected to PE tubes using epoxy glue. Tsu-Chien <Chien>001000</Chien> ------------------------------ Message: 4 Date: Thu, 22 Jul 2004 15:55:07 -0500 (CDT) From: Matt Newville <newville(a)cars.uchicago.edu> Subject: RE: [Ifeffit] Solution flow cells To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <Pine.LNX.4.44.0407221538340.2941-100000(a)millenia.cars.aps.anl.gov> Content-Type: TEXT/PLAIN; charset=US-ASCII Just to follow up on and add to Shelly's and Tsu-Chien's responses: There's a paper by M. Hoffmann, et al (J. Fulton, and others from PNNL) on a flow-cell, especially for high pressure fluids. I believe it's in J Phys Chem (1999), but don't have the exact citation. This might be the one Shelly saw at PNC CAT. Mark Antonio has a nice electrochemical cell in which he can change both potential, but can't remember if he can flow in a changed solution... is that "flow"? I believe the catalyst people who run at ESRF (esp. the DXAFS line) have some nice flow cells too, but don't know if or where it's published. --Matt ------------------------------ Message: 5 Date: Thu, 22 Jul 2004 16:06:41 -0500 From: "Jensen, Mark P." <mjensen(a)anl.gov> Subject: RE: [Ifeffit] Solution flow cells To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <0D4E53E4DC6CA449B9F71E5282984F8C2F0DE3(a)anchim2.chm.anl.gov> Content-Type: text/plain; charset="us-ascii" And just to add to Matt, Shelly, and Tsu-Chien's responses. Matt mentioned Mark Antonio's electrochemical cell. It is not a flow cell, though we did design a closely related, but unpublished, cell design for in the beam titrations. ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: Newville, Matthew G. > Sent: Thursday, July 22, 2004 2:55 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Solution flow cells > > Just to follow up on and add to Shelly's and Tsu-Chien's > responses: > > There's a paper by M. Hoffmann, et al (J. Fulton, and others > from PNNL) on a flow-cell, especially for high pressure fluids. > I believe it's in J Phys Chem (1999), but don't have the > exact citation. This might be the one Shelly saw at PNC CAT. > > Mark Antonio has a nice electrochemical cell in which he can > change both potential, but can't remember if he can flow in a > changed solution... is that "flow"? > > I believe the catalyst people who run at ESRF (esp. the DXAFS > line) have some nice flow cells too, but don't know if or > where it's published. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 6 Date: Fri, 23 Jul 2004 08:45:10 +0200 From: SCHLEGEL Michel 177447 <schlegel(a)azurite.cea.fr> Subject: RE: [Ifeffit] Solution flow cells To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <3808A7D2DCEAD6118B63009027287265078A27(a)azurite.saclay.cea.fr> Content-Type: text/plain; charset="iso-8859-1" Scott, > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an > XAS flow cell desgined for liquids. > Sealed cells for liquids, yes; flow cells for passing gases > over solids, yes; but no solution-chemistry flow cell. I > feel like someone must have published work in that area before, > but I can't seem to find it. Maybe not exactly a flow cell, but a rapid biblio research on "Web of Science" using the"stopped-flow" and "EXAFS or XAS or XANES" keywords has unearthed some 23 references over the last ten years, many of them probably utterly irrelevant. Nevertheless, I copied them in the attached text file. Best regards, Michel Schlegel

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Re: Ifeffit Digest, Vol 17, Issue 18
by m.bondin＠pgrad.unimelb.edu.au 23 Jul '04

23 Jul '04

Hi Scott, I have read a paper in a recent issue from Journal of Synchrotron Radiation which may be of interest: J. Synchrotron Rad. (2004). 11, 204-208 [ DOI 10.1107/S0909049503028474 ] A versatile rapid-mixing and flow device for X-ray absorption spectroscopy K. Zhang, R. Liu, T. Irving and D. S. Auld Synopsis: A low-temperature rapid-mixing and flow system has been designed and implemented to monitor catalysis involving metal ions by X-ray absorption spectroscopy at the ID-18 beamline of the Advanced Photon Source. The results of the initial testing of the system are presented. The reseach in our group (Stephen Best) in Australia involves EXAFS of short-lived electrochemically generated solution species prepared via an "ex situ" continuous flow electrosynthesis cell (Australian Journal of Chemistry, Volume 54, page 705, 2001) - from what I understand though you are more interested in an "in situ" method as mentioned above. Cheers, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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RE: [Ifeffit] Solution flow cells
by Irit Sagi 23 Jul '04

23 Jul '04

Dear Scott Enclosed is our NSB paper on rapid XAS of metalloenzyme + the news and views article written by J. Penner-Hahn on this article. Irit Prof. IRIT SAGI Department of Structural Biology The Weizmann Institute of Science ISRAEL Tel : 972-8-9342130 http://www.weizmann.ac.il/sb/faculty_pages/Sagi/home.html e-mail: irit.sagi(a)weizmann.ac.il >>> schlegel(a)azurite.cea.fr 23/07/04 09:45:10 >>> Scott, > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an > XAS flow cell desgined for liquids. > Sealed cells for liquids, yes; flow cells for passing gases > over solids, yes; but no solution-chemistry flow cell. I > feel like someone must have published work in that area before, > but I can't seem to find it. Maybe not exactly a flow cell, but a rapid biblio research on "Web of Science" using the"stopped-flow" and "EXAFS or XAS or XANES" keywords has unearthed some 23 references over the last ten years, many of them probably utterly irrelevant. Nevertheless, I copied them in the attached text file. Best regards, Michel Schlegel

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RE: [Ifeffit] Solution flow cells
by SCHLEGEL Michel 177447 23 Jul '04

23 Jul '04

Scott, > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an > XAS flow cell desgined for liquids. > Sealed cells for liquids, yes; flow cells for passing gases > over solids, yes; but no solution-chemistry flow cell. I > feel like someone must have published work in that area before, > but I can't seem to find it. Maybe not exactly a flow cell, but a rapid biblio research on "Web of Science" using the"stopped-flow" and "EXAFS or XAS or XANES" keywords has unearthed some 23 references over the last ten years, many of them probably utterly irrelevant. Nevertheless, I copied them in the attached text file. Best regards, Michel Schlegel

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RE: [Ifeffit] Solution flow cells
by Jensen, Mark P. 22 Jul '04

22 Jul '04

And just to add to Matt, Shelly, and Tsu-Chien's responses. Matt mentioned Mark Antonio's electrochemical cell. It is not a flow cell, though we did design a closely related, but unpublished, cell design for in the beam titrations. ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: Newville, Matthew G. > Sent: Thursday, July 22, 2004 2:55 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Solution flow cells > > Just to follow up on and add to Shelly's and Tsu-Chien's > responses: > > There's a paper by M. Hoffmann, et al (J. Fulton, and others > from PNNL) on a flow-cell, especially for high pressure fluids. > I believe it's in J Phys Chem (1999), but don't have the > exact citation. This might be the one Shelly saw at PNC CAT. > > Mark Antonio has a nice electrochemical cell in which he can > change both potential, but can't remember if he can flow in a > changed solution... is that "flow"? > > I believe the catalyst people who run at ESRF (esp. the DXAFS > line) have some nice flow cells too, but don't know if or > where it's published. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] Solution flow cells
by Kelly, Shelly D. 22 Jul '04

22 Jul '04

Hi Scott, See below: > Hi all, > > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an XAS > flow cell desgined for liquids. Sealed cells for liquids, > yes; flow cells for passing gases over solids, yes; but no > solution-chemistry flow cell. I feel like someone must have > published work in that area before, but I can't seem to find it. > > So, does anyone know of any work done using a liquid-phase > XAS flow cell? Simon Bare uses a flow cell for passing liquids/gasses over a sample. This one is a glass container with kapton windows with ports for input and output. Also I have seen something like that at PNC cat. I think that Ed Stern et. al. was using it. The one at PNC cat circulated the liquid through a boron carbide section that is x-ray transparent. Shelly

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using atoms and feff
by Bruce Ravel 21 Jul '04

21 Jul '04

Hi folks, I suppose I should preface this message by saying that I will not say anything new and profound. Indeed, this email is something of a rant -- so some of you may want to click ahead to the next email right now and avoid the whole darn thing! Today I was asked a Frequently Asked Question about using atoms and feff and getting started with some fits. This particular question is pretty common, but it's one that kind of bugs me. It's been rattling around in my brain for the remainder of the evening. To get it out of my brain, I figured I would write a message to the mailing list. A colleague showed me some data and explained a bit about the sample. This person had the lattice constants and space group for the oxide form of the absorbing element but expressed a confusion about how to proceed. I asked to see the rest of the crystallographic data -- specifically the atomic positions. I was shown a printout of some stuff from webelements.com or some similar web compilation of information about the elements. Sure enough, the lattice constants were given for the oxide form, but neither complete crystallographic data nor a crystallographic reference were listed. As everyone here should know, feff requires a list of atomic coordinates as its input data. To get a feff calculation, you must tell feff where the atoms are. Ifeffit and Artemis rely upon feff to provide theoretical fitting standards, thus to start fitting you need somehow to run feff. It is a syllogism, then, that you need some kind of list of atomic coordinates before you can begin fitting with Ifeffit and Artemis. With but a passing understanding of crystallography, it should be clear that you cannot generate a list of atomic coordinates given *only* the space group and lattice constants of a crystal. The space group and lattice constants tell you the shape and size of the unit cell, but, by themselves, do not tell you what is inside the unit cell. You see, a unit cell is just like a birthday present. The box might be big and pretty, but it's not a very good present until you open it up and find out what's inside. So........ if you intend to start your analysis by using Atoms, you have to find the COMPLETE crystallographic data. Often, this is one of the more difficult parts of the analysis problem. Sometimes crystallography data is hard to find. Matt keeps a big pile of atoms.inp files on one of his web sites and that helps a lot. Many libraries have copies of Wyckoff -- that also helps a lot. Google can be awfully handy -- indeed I ended up finding the missing crystallographic data earlier today with the help of Google. Often times you will be reduced to an exhausting search through the crystallography journals looking for the data you need. Other times you will never find what you are looking for and will just have to use something similar (but not the same) as your starting point. I presume it was already abundantly clear to everyone reading this message that the space group and lattice constants by themselves are not enough to use Atoms. But I needed to vent and so availed myself of this public forum. B P.S. The question of what to do when your sample is different from its crystalline form or when your sample is not a crystal at all has been discussed several times recently. If, after reading this little rant, that's your concern, you should read and respond to one of those threads rather than to this one. P.P.S. The next time you dig through the literature to find some obscure crystal structure, save someone else the effort. Be a hero, donate the atoms.inp file to Matt's database. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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