Sorbed complex in Atoms
Dear All, I am relatively new to Ifeffit and Artemis. I am trying to find a way to create four-shell model of an outer-sphere complex in Atoms or some other way readable by Atoms. I have no idea about the geometry, space group but some rough guess of bond-distances. The model to test against the EXAFS data is: Ni is the central atom Ni-O first shell Ni-Ni second shell Ni-Ti third shell Ni-Si fourth shell The model aims to test the adsorption of Ni on the surface of Ti-containing silicate mineral. Could you please help. Thanks.
This is an very vague and open-ended question. Have you read any of the very extensive literature applying EXAFS to outer-sphere complexation? Have you tried anything ... anything at all ... to solve your problem? If you ask specific questions, you will get good answers. If you ask folks on the list to do your work for you, that won't go so well. B On 06/09/2016 10:25 AM, Gnu script wrote:
Dear All,
I am relatively new to Ifeffit and Artemis. I am trying to find a way to create four-shell model of an outer-sphere complex in Atoms or some other way readable by Atoms. I have no idea about the geometry, space group but some rough guess of bond-distances. The model to test against the EXAFS data is: Ni is the central atom Ni-O first shell Ni-Ni second shell Ni-Ti third shell Ni-Si fourth shell
The model aims to test the adsorption of Ni on the surface of Ti-containing silicate mineral.
Could you please help.
Thanks.
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-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Hi Bruce,
Thanks for your reply. I am familiar with outer-sphere complexation and how
it works but I am much less familiar with Artemis and how such question can
be approached. In the past we used Excurve and DL-Excurve where you can
simply name the backscatter with initial estimates of N and R but without
any need for STRUCTURE. Now, having moved away from these tools into
Demeter and Artemis I am trying to learn rather than asking people to do
work for me!
So, what I have done so far was to replace Ti in the Atoms file by Ni but
it is not clear to me what I need to change in order to test outer-sphere
vs inner-sphere complexes of Ni.
space = P b c n
a = 8.71280 b = 5.23270 c = 14.48700
alpha = 90.00000 beta = 90.00000 gamma = 90.00000
rmax = 7.84905 core = Ti
# polarization = 0.0 0.0 0.0
shift = 0.00000 0.00000 0.00000
atoms
# el. x y z tag
Na 0.06430 0.64500 0.15370 Na
Ti 0.15130 0.13220 0.33090 Ti
Si 0.34210 0.29610 0.52670 Si
O 0.00000 0.00600 0.25000 O1
O 0.18170 0.44070 0.27580 O2
O 0.33360 0.29670 0.41520 O3
O 0.00890 0.24280 0.42800 O4
O 0.23570 0.05980 0.56700 O5
Thanks,
G
On Thu, Jun 9, 2016 at 3:58 PM, Bruce Ravel
This is an very vague and open-ended question.
Have you read any of the very extensive literature applying EXAFS to outer-sphere complexation? Have you tried anything ... anything at all ... to solve your problem?
If you ask specific questions, you will get good answers. If you ask folks on the list to do your work for you, that won't go so well.
B
On 06/09/2016 10:25 AM, Gnu script wrote:
Dear All,
I am relatively new to Ifeffit and Artemis. I am trying to find a way to create four-shell model of an outer-sphere complex in Atoms or some other way readable by Atoms. I have no idea about the geometry, space group but some rough guess of bond-distances. The model to test against the EXAFS data is: Ni is the central atom Ni-O first shell Ni-Ni second shell Ni-Ti third shell Ni-Si fourth shell
The model aims to test the adsorption of Ni on the surface of Ti-containing silicate mineral.
Could you please help.
Thanks.
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973
Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Gnu,
First, we prefer people to use their real names here, because we are all
adults discussing science.
On Thu, Jun 9, 2016 at 11:12 AM, Gnu script
Hi Bruce, Thanks for your reply. I am familiar with outer-sphere complexation and how it works but I am much less familiar with Artemis and how such question can be approached. In the past we used Excurve and DL-Excurve where you can simply name the backscatter with initial estimates of N and R but without any need for STRUCTURE. Now, having moved away from these tools into Demeter and Artemis I am trying to learn rather than asking people to do work for me!
So, what I have done so far was to replace Ti in the Atoms file by Ni but it is not clear to me what I need to change in order to test outer-sphere vs inner-sphere complexes of Ni.
space = P b c n a = 8.71280 b = 5.23270 c = 14.48700 alpha = 90.00000 beta = 90.00000 gamma = 90.00000 rmax = 7.84905 core = Ti # polarization = 0.0 0.0 0.0 shift = 0.00000 0.00000 0.00000 atoms # el. x y z tag Na 0.06430 0.64500 0.15370 Na Ti 0.15130 0.13220 0.33090 Ti Si 0.34210 0.29610 0.52670 Si O 0.00000 0.00600 0.25000 O1 O 0.18170 0.44070 0.27580 O2 O 0.33360 0.29670 0.41520 O3 O 0.00890 0.24280 0.42800 O4 O 0.23570 0.05980 0.56700 O5
Thanks, G
Atoms represents a crystallographic structure. That's not exactly what is need to simulate EXAFS - for that you want a cluster of atoms, as represented in the feff.inp file. The Atoms program (or Atoms step of Artemis) conveniently converts a crystallographic representation into a cluster of atoms. Atoms (rightly) refuses to do partial occupancy because for EXAFS it matters greatly how random any substitution would be, whereas for simple analysis of diffraction data, it often doesn't. For what you want to do (and for many other needs), you want to **edit the cluster of atoms in feff.inp**. To do this, you would probably start with your NaTi silicate. If you want to represent a surface, you could (for example) remove all atoms with Z > 0. You can move atoms around by changing their X,Y,Z coordinates. If you want to substitute a Ti atom with Ni, you could do this in two steps: 1. add a Ni "potential". If Ni is the absorbing atom, Make "IPOT=0" Ni by changing the atomic number for ipot 0. 2. change the central atom and any scatterers as desired. Again, the crystallographic data for Atoms is a convenient starting place, but actually as very little to do with the simulation of EXAFS. Hope that helps, --Matt
participants (3)
-
Bruce Ravel -
Gnu script -
Matt Newville