[Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fit

Robert Gordon ragordon at alumni.sfu.ca
Sun Feb 9 11:51:47 CST 2014


Was there no attachment to my earlier response?
I printed out the ICSD page with the correct parameters
and attached it as a pdf. My outgoing message indicates
the attachment is there.

-R.

On 2/9/2014 7:40 AM, Sathish Mayanna wrote:
> Dear Dr. Robert
>
> Thanks a lot for your information that's very helpful.
>
> I checked the ICSD, but unfortunately we don't have access to the 
> crystal data. It would be great, if you or someone has the access to 
> the crystal data to provide me the coordinates, the *collection code: 
> 202727, Author: Post, Year: 1988. *
> *
> *
> *Please let me know, if someone has the access to the data.*
> *
> *
> Regards
> Sathish
> *
> *
> **
>
>
> On Thu, Feb 6, 2014 at 11:05 PM, 
> <ifeffit-request at millenia.cars.aps.anl.gov 
> <mailto:ifeffit-request at millenia.cars.aps.anl.gov>> wrote:
>
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>        1. Re: Correct Crystallographic parameters for Todorokite EXAFS
>           fitting in Artemis (Robert Gordon)
>
>
>     ----------------------------------------------------------------------
>
>     Message: 1
>     Date: Thu, 06 Feb 2014 16:05:30 -0600
>     From: Robert Gordon <ragordon at alumni.sfu.ca
>     <mailto:ragordon at alumni.sfu.ca>>
>     To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
>     <mailto:ifeffit at millenia.cars.aps.anl.gov>>
>     Subject: Re: [Ifeffit] Correct Crystallographic parameters for
>             Todorokite EXAFS fitting in Artemis
>     Message-ID: <52F4072A.1070008 at alumni.sfu.ca
>     <mailto:52F4072A.1070008 at alumni.sfu.ca>>
>     Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
>     Hi Satty,
>
>     The crystal data in your inp file came from the paper. I checked the
>     International
>     Crystal Structure Database (ICSD) - printout attached. The structure
>     data in the paper
>     are not in standard form - atoms might not give the correct results if
>     the input is bad- and there
>     are typos for two of the O5 coordinates according to the ICSD warning.
>     Does your institution have access to the ICSD - Online or on disc?
>     If you
>     are not familiar with it, try talking to one of your institution's
>     reference librarians.
>
>     I'm not certain what you mean by the corner-corner Mn. You were
>     choosing Mn1
>     as the core in your inp. When I look at the structure, Mn1 sits in the
>     middle of
>     the set of 3 octahedra that make up a side of the tunnel. Where would
>     the corner-corner
>     distance be relative to the middle of the chain? You have 4
>     different Mn
>     sites.
>
>     Fitting in R-space is common.
>
>     As for learning about crystal structures, try sitting in on a
>     coordination chemistry
>     or solid state chemistry course. For a basic learning book, I like
>     West's "Basic Solid
>     State Chemistry" or Muller's "Inorganic Structural Chemistry" (again,
>     try the library
>       if you don't want to buy a copy). More recent books may be
>     available.
>     A bit of
>     googling may reveal some online lessons, like:
>     http://www.seas.upenn.edu/~chem101/sschem/solidstatechem.html
>     <http://www.seas.upenn.edu/%7Echem101/sschem/solidstatechem.html>
>
>
>     regards,
>     Robert
>
>
>     On 2/6/2014 3:16 AM, Sathish Mayanna wrote:
>     > Hi
>     >
>     > I am having some problem to get the real crystallographic parameters
>     > for Todorokite (I know there are many literature available) I
>     used the
>     > parameters from Post et al 1988 (/Rietveld refinement of the
>     > Todorokite structure/) and others as well (*attached Todorokite.inp
>     > file*).
>     >
>     > I except the corner corner Mn in Todorokite, since its a tunnel
>     > structure, but the Feff calculations do not provide any corner
>     corner
>     > Mn, in addition I cannot fit exactly even Mn-O or Mn-Mn.
>     >
>     > But If I use Ramsdellite (*attached Ramsdellite.inp file*), which is
>     > also a tunnel structure, I could get the Corner-Corner Mn and
>     can fit
>     > perfectly the Mn-O, Mn-Mn, but cannot fit in K space.
>     >
>     > It would be really great, if anyone could provide me the model
>     Tunnel
>     > type-Mn oxide crystallographic parameters to fit the data *(attached
>     > Mn Spectra.prj)*
>     >
>     > p.s: I tried my best to learn and understand the crystallographic
>     > parameters and miller indices, but still I feel that I am very poor,
>     > it would be nice, if someone suggest some good and basic source to
>     > learn more about pure mineralogy (which is crucial to know the basic
>     > parameters for fitting in Artemis).
>     > --
>     > Satty
>     >
>     >
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>     --
>     Dr. Robert Gordon
>     Staff Scientist, PNCSRF
>     APS Sector 20 (PNC/XSD)
>     9700 S Cass Ave. 435E
>     Argonne, IL, USA  60439
>
>     630-252-0581 <tel:630-252-0581>
>     630-252-0580 <tel:630-252-0580> fax
>
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>     End of Ifeffit Digest, Vol 132, Issue 5
>     ***************************************
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>
>
>
> -- 
> Satty
>
>
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-- 
Dr. Robert Gordon
Staff Scientist, PNCSRF
APS Sector 20 (PNC/XSD)
9700 S Cass Ave. 435E
Argonne, IL, USA  60439

630-252-0581
630-252-0580 fax

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