This short presentation addresses the most common question posed at EXAFS training sessions: How do I use Feff with non-crystalline materials? While there is no single answer to that deep question, this presentation gives a few hints.
samples Bruce Ravel Synchrotron Science Group National Institute of Standards and Technology & Beamline for Materials Measurements National Synchrotron Light Source II New Challenges and Solutions for XAS Data Analysis Institute of Physics, Polish Academy of Sciences 14-17 April, 2015 1 / 18 Modeling non-crystalline samples
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I demonstrated by showing FeS2, which is a crystal. This allowed me to start with and crystal data. Atoms is just a tool It is useful when it’s useful. In this short talk, I will suggest various ways to get started on samples that are not crystalline. 3 / 18 Modeling non-crystalline samples
amorphous germanium Ge crystalizes into an orderly, hexagonal close pack arrangement. Given EXAFS data on the crystalline material, it is fairly obvious how to begin: Run starting from the known crystal data. space = f d 3 m a = 5.658 rmax = 6.00 atoms Ge 1/8 1/8 1/8 Amorphous Ge is a random continuous network. 4 / 18 Modeling non-crystalline samples aGe figure from V. Hugouvieux et al PRB 75, 104208 (2007) DOI: 10.1103/PhysRevB.75.104208
amorphous germanium Ge crystalizes into an orderly, hexagonal close pack arrangement. Given EXAFS data on the crystalline material, it is fairly obvious how to begin: Run starting from the known crystal data. space = f d 3 m a = 5.658 rmax = 6.00 atoms Ge 1/8 1/8 1/8 Amorphous Ge is a random continuous network. Do we have to run a molecular dynamics simu- lation just to then run ? 4 / 18 Modeling non-crystalline samples aGe figure from V. Hugouvieux et al PRB 75, 104208 (2007) DOI: 10.1103/PhysRevB.75.104208
amorphous germanium Ge crystalizes into an orderly, hexagonal close pack arrangement. Given EXAFS data on the crystalline material, it is fairly obvious how to begin: Run starting from the known crystal data. space = f d 3 m a = 5.658 rmax = 6.00 atoms Ge 1/8 1/8 1/8 Amorphous Ge is a random continuous network. Do we have to run a molecular dynamics simu- lation just to then run ? Happily, no. 4 / 18 Modeling non-crystalline samples aGe figure from V. Hugouvieux et al PRB 75, 104208 (2007) DOI: 10.1103/PhysRevB.75.104208
amorphous germanium As always, let’s start by looking at the data. A random continuous network has a near-neighbor pair correlation nearly identical to its ordered counterpart. We see this behavior in our Ge data. 5 / 18 Modeling non-crystalline samples Amorphous data is courtesy of Joe Woicik and was measured at NSLS X23A2. Crystalline data taken from the NSLS X18A website.
aGe We import the data and the first path from the calculation on crystalline Ge. We make a simple, first shell fitting model with terms for S2 0 , ∆E0, ∆R, and σ2 . guess parameters: amp = 1.10 +/- 0.07 enot = 3.94 +/- 0.75 delr = 0.006 +/- 0.004 ss = 0.00596 +/- 0.00040 We find that the bond length and coordination number for aGe is much the same as for cGe, while the disorder is a bit higher. 6 / 18 Modeling non-crystalline samples See the germanium example available at http://bruceravel.github.io/XAS-Education/.
formats Just because a material is not a crystal does not mean that its structure is not known. Atomic structures of molecules from coordination complexes up to biological macromolecules are known from theory and experiment and are available in a variety of file formats. needs a list of cartesian coordinates. Sadly, the current version of cannot help you convert a molecule file into a ‘feff.inp’ file, but it is not hard. 7 / 18 Modeling non-crystalline samples
chloride One of my standard teaching examples involves Sn K edge data on methyl tin chloride dissolved in an organic solvent. Dimethyl tin dichloride Monomethyl tin trichloride 8 / 18 Modeling non-crystalline samples
Bank file format A bit of googling turned up a structure for dimethyl tin dichloride in the form of a PDB file. It looks like this: COMPND 5261536 HETATM 1 C1 LIG 1 -0.027 2.146 0.014 1.00 0.00 HETATM 2 SN2 LIG 1 0.002 -0.004 0.002 1.00 0.00 HETATM 3 C3 LIG 1 1.042 -0.716 1.744 1.00 0.00 HETATM 4 CL4 LIG 1 -2.212 -0.821 0.019 1.00 0.00 HETATM 5 CL5 LIG 1 1.107 -0.765 -1.940 1.00 0.00 HETATM 6 1H1 LIG 1 0.996 2.523 0.006 1.00 0.00 HETATM 7 2H1 LIG 1 -0.554 2.507 -0.869 1.00 0.00 HETATM 8 3H1 LIG 1 -0.537 2.497 0.911 1.00 0.00 HETATM 9 1H3 LIG 1 0.532 -0.365 2.641 1.00 0.00 HETATM 10 2H3 LIG 1 1.057 -1.806 1.738 1.00 0.00 HETATM 11 3H3 LIG 1 2.065 -0.339 1.736 1.00 0.00 END The red bits are atomic species and cartesian coordinates — just what we need! 9 / 18 Modeling non-crystalline samples
file TITLE dimethyltin dichloride HOLE 1 1.0 * Sn K edge (29200 eV), S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 6.0 POTENTIALS * ipot Z element 0 50 Sn 1 17 Cl 2 6 C 3 1 H ATOMS * x y z ipot -0.027 2.146 0.014 2 0.002 -0.004 0.002 0 1.042 -0.716 1.744 2 -2.212 -0.821 0.019 1 1.107 -0.765 -1.940 1 0.996 2.523 0.006 3 -0.554 2.507 -0.869 3 -0.537 2.497 0.911 3 0.532 -0.365 2.641 3 1.057 -1.806 1.738 3 2.065 -0.339 1.736 3 1 Prepare ‘feff.inp’ boilerplate 2 Cut-n-paste the cartesian coordinates in the ATOMS list 3 Make a POTENTIALS list out the atomic species 4 The absorber must be potential #0, but it need neither be first in the ATOMS list nor be at (0,0,0) 5 The ATOMS list need not be in order of radial distance (or any other order) 6 This ‘feff.inp’ file can be imported directly into 10 / 18 Modeling non-crystalline samples
a fit Import each data set and one calculation into . Use the relevant paths with each data set. 11 / 18 Modeling non-crystalline samples See the methyltin example and presentation available at http://bruceravel.github.io/XAS-Education/.
this be made better? Open Babel (http://openbabel.org/) is a chemical toolbox that, among other things, translates between 98 different atomic structure file formats. Integrating Open Babel with and 1 Open Babel is written in C++ 2 File format I/O is handled by small extension modules, also written in C++ 3 Need a ‘feff.inp’ I/O module written and donated to the Open Babel project 4 Integrate Open Babel into 12 / 18 Modeling non-crystalline samples
this be made better? Open Babel (http://openbabel.org/) is a chemical toolbox that, among other things, translates between 98 different atomic structure file formats. Integrating Open Babel with and 1 Open Babel is written in C++ 2 File format I/O is handled by small extension modules, also written in C++ 3 Need a ‘feff.inp’ I/O module written and donated to the Open Babel project 4 Integrate Open Babel into This has long been on my to do list. This is a substantive, yet tractable, way that someone could make a contribution to the project. Any volunteers? 12 / 18 Modeling non-crystalline samples
Here’s a paper you should read X-ray absorption fine structure determination of pH-dependent U-bacterial cell wall interactions, S.D. Kelly, et al. Geochimica et Cosmochimica Acta 66:22 (2002) 3855-3871 DOI: 10.1016/S0016-7037(02)00947-X In it, the authors measure the pH dependence of the cell wall functional groups responsible for the absorption of aqueous UO2+ 2 to B. subtilis from pH 1.67 to 4.80. 13 / 18 Modeling non-crystalline samples
selectively from crystal analogs The monodentate U-P from the crystal resembles the phoshporyl coordination structure we are looking for: The bidentate U-C from the crystal resembles the carboxyl coordination structure we are looking for: 15 / 18 Modeling non-crystalline samples
of this story The practical version The structure used in the calculation doesn’t need to be “perfect”. Close is usually good enough to get started. 16 / 18 Modeling non-crystalline samples
of this story The practical version The structure used in the calculation doesn’t need to be “perfect”. Close is usually good enough to get started. The technical version Small changes in local coordination do not result in large changes to the complex scattering factor (F(k) and Φ(k) in the EXAFS equation). EXAFS is sensitive to small changes in local coordination, but this is due to the sin(2kR) term. A high quality EXAFS analysis can suffer an approximation to the local coordination environment in the calculation of the thoeretical fitting standards so long as the fitting model is parameterized in a way to capture the details of that local coordination. 16 / 18 Modeling non-crystalline samples
analogs in Artemis Here’s the outline: 1 Import each crystal structure into 2 Run , run 3 Examine the path list, select those SS and MS paths you need to describe your structure 4 Parameterize, fit 17 / 18 Modeling non-crystalline samples
Close is probably good enough Running on a structure that resembles the actual data is usually adequate. More technically — the computation of the scattering factor is not acutely sensitive to atomic positions. 18 / 18 Modeling non-crystalline samples
Close is probably good enough Running on a structure that resembles the actual data is usually adequate. More technically — the computation of the scattering factor is not acutely sensitive to atomic positions. Be creative What makes an expert practitioner is the ability to conceive of and implement an analytical strategy. There is no rule book (sadly) – new problems bring new challenges. An expert is just someone who sees an interesting idea through to completion. 18 / 18 Modeling non-crystalline samples
Close is probably good enough Running on a structure that resembles the actual data is usually adequate. More technically — the computation of the scattering factor is not acutely sensitive to atomic positions. Be creative What makes an expert practitioner is the ability to conceive of and implement an analytical strategy. There is no rule book (sadly) – new problems bring new challenges. An expert is just someone who sees an interesting idea through to completion. You never know nothing Use your prior knowledge of your sample. If you have a hunch (even a weak suspicion) about the local configuration, you have enough to get started with . 18 / 18 Modeling non-crystalline samples
Close is probably good enough Running on a structure that resembles the actual data is usually adequate. More technically — the computation of the scattering factor is not acutely sensitive to atomic positions. Be creative What makes an expert practitioner is the ability to conceive of and implement an analytical strategy. There is no rule book (sadly) – new problems bring new challenges. An expert is just someone who sees an interesting idea through to completion. You never know nothing Use your prior knowledge of your sample. If you have a hunch (even a weak suspicion) about the local configuration, you have enough to get started with . Some information is better than no information At the end of the day, you may only be able to extract a little bit of information about the local configuration. Scientific progress is made in tiny steps. 18 / 18 Modeling non-crystalline samples