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XAS Tutorials XAS Data Analysis | Model Construction (ChemBio3D Ultra) (This tutorial presumes that the user has access to CCDC software ChemBio3D Ultra, a component of ChemBioOffice 2008, which provides a 3D modeling environment for molecular models. At UGA in late 2007, this license is supported by the Student Technology Fee and can be locally installed on a Windows PC. The Macintosh version of ChemBioOffice does NOT contain ChemBio3D at this time.) The purpose behind using ChemBio3D for XAS analysis is to generate coordinates (in PDB format) to use as input to feff (through feff.inp) for calculation of scattering paths used in modeling EXAFS data. There are two ways to generate these 3D models: (1) use the CSD (see tutorial) to find a crystal structure that contains the model fragment you wish (or something close enough to fine tune); (2) create a model fragment from scratch within ChemBio3D. Both of these procedures will be described in this tutorial. Refining structural model from CSD First we will look at using a CSD-generated PDB file as the starting point for creating our model fragment. Open the ChemBio3D Ultra application (it can be found in the Start menu All Programs list under ChemBioOffice 2008). Then, from the File menu, choose Open ... and locate the .pdb file you saved from your CSD session (our example will be the JEFVIZ.Hg.pdb file from the CSD tutorial).
(Note the ChemDraw panel on the right side of the display; by default, this always shows a two-dimensional sketch of the three-dimensional model in the main 3D display window. If this panel is not there, it can be turned on by selecting ChemDraw Panel under the View menu.) Often during the course of editing this structure, you may wish to summarize the metric parameters of the model. This can be done through the Measurements submenu of the Structure menu; for example, select the Generate All Bond Lengths command to create a table of bond lengths (you also have access to bond angles, dihedral angles, etc.). You can also do this one bond (or angle, etc.) at a time by selecting a bond or two or three adjacent bonds simultaneously and using the Display ... commands in the same submenu.
This opens a panel on the left with a table of measurements (in this case, bond lengths). This is just one of many panels you can use to look at details of your model. When you click back in the 3D display window, the panels should withdraw into the left margin as tabs; open them again by clicking on the tabs or names. You can also display selected parameters on the 3D display by checking the checkbox in the Display column of the Measurement panel. Note in the example below that the three Hg-S distances are not exactly the same. You may wish to change them (see next section).
Another useful tool in ChemBio3D is the ability to quickly delete extraneous molecules and/or atoms from the CSD structure to create a .pdb file with only the coordinates necessary for the EXAFS fit. In this case, we wish to delete the counterion (tetraethylammonium) as well as the tert-butyl groups attached to the sulfurs. Generally, you select (multiple) atoms and hit the Delete key. Selection can be by clicking on an atom then shift-clicking on other atoms. However, for large collections of atoms, you can use the selection tool to draw a marquis around atoms you wish to select. Note in the illustration below that the arrow tool at the far left of the lower toolbar is selected. You may need to rotate your molecule(s) by using the trackball rotation tool (two tools in from the far left on the lower toolbar). (It helps to become familiar with the first four tools on this toolbar: Select, Translate, Rotate, Zoom; note that Rotate also has a pulldown menu for fine control of rotation.)
After you have deleted the extraneous parts of your structure, note that ChemBio3D has "chemical intuition", eliminating any valence errors by adding hydrogens as necessary. In our case, this results in Hg(SH)3. If you wish to view the model without the hydrogens displayed, this can be done using the Show Hydrogen Atoms submenu of the Model Display submenu of the View menu. Choose Hide from this submenu.
(Note that hiding H atoms does not change the model, as you can see from the sketch in the ChemDraw panel.) Now that we have our model fragment trimmed to the essential pieces, we are almost ready to output a new .pdb file. However, it is useful to output coordinates that consider the metal atom (our absorbing atom) as the origin of our molecular coordinate system. ChemBio3D can do this for you. Click on the Hg atom in the 3D display window to select it. Then, select the Center Selection on Origin command from the Model Position submenu of the Structure menu. You can check that this has worked, but viewing the (x,y,z) coordinates of your model; use the XYZ (Cartesian coordinates) panel that is one of the tabs on the left window edge. If you don't see it there, choose Cartesian Table from the View menu.
Now you are ready to save this refined model fragment to a new .pdb file. Under the File menu, choose Save As ... and make sure the Save as type: dropdown has Protein Data Bank (*.pdb) selected. Below we chose to name this file the same CSD code, but without the .Hg suffix to distinguish it from the full CSD output.
The .pdb file is text-only and can be viewed and edited using a simple text editor (be sure to always save any changes as text-only). For example, opening the JEFVIZ.pdb file with WordPad shows the contents below.
There is much more in this file than feff.inp needs, so you can clean it up by removing a lot of the lines that PDB needs but you don't need. All the highlighted lines above are unnecessary and can be deleted. Also, feff.inp doesn't use REMARK or SEQRES lines. More detail about feff.inp format is available in a separate tutorial. Creating structural model from scratch ChemBio3D Ultra also has excellent tools to create structural models from scratch for use in feff.inp. Generally speaking, you use the ChemDraw window (on the right below) to sketch the model you want. Let's take two examples. The first will consider creating a Hg-S fragment that we could use in place of the model covered in the previous section. A single Hg-S bond could be enough for an EXAFS fit if what you want is a homogeneous shell of n Hg-S interactions (i.e., no static Debye-Waller term), since you can just change the coordination number in the EXAFS fit to create additional Hg-S bonds. This will work as long as you are convinced that there are no significant multiple scattering paths among multiple ligands in the model. (You can always check this by starting with a single bond to create a shell of n atoms by setting the coordination number in the EXAFS fit, then creating a full structural model with n ligand atoms and using that to create a feff.inp file for an independent EXAFS fit, comparing the results of the two.) Starting with a new window, click in the ChemDraw panel to select it (this opens the ChemDraw tool palette, floating near the left side below). By default, the single bond tool is selected and all you need do is click once in the ChemDraw panel to create your first bond. By default, this is a C-C bond valence-completed to create ethane.
You don't want C-C; you want Hg-S. So you only need to change the labels to get ChemBio3D to recognize new atom types. In the ChemDraw panel, right-click on one of the atoms and select Edit Label from the popup menu. You will see a textbox attached to that atom into which you should type 'Hg' (case-sensitive). This changes the atom type in the 3D display window also.
Right-click on the other atom and change its Label to S. Note that ChemBio3D understands S valence, but is not clear about Hg valence, not a concern for us.
You may have an idea about the Hg-S bond length you want to start with in your EXAFS fits. It pays to get as close as possible to the expected result from EXAFS fitting before doing the feff calculation. Holding the cursor over the Hg-S bond in the 3D display window brings up the parameter (bond length).
A simple way to change this bond distance is to open the Internal Coordinates panel from the left window edge tabs (if it is not displayed, you can access it from the View menu; if the tab is not spelled out, look for the 'ZM' icon.) This displays a number of parameters, including bond lengths that are editable. Just type in a new distance and hit Return/Enter. You can check on your model that the bond distance has changed. Now you can repeat the steps above to move the Hg atom to (0,0,0) and save a PDB file as usual. Alternatively, you can add more to your model (two more S atoms for example), set their bond distances, regularize angles, and save that.
Let's do another example in which we want to create a Zn-imidazole fragment for a multiple scattering EXAFS fit. Also, let's say we know we want the Zn-N(imid) distance to be 2.00 Å. This more complex structure is made easy by the availability of ChemDraw templates. Back in a new window, clicking in the ChemDraw panel gives us the tool palette, from which you should click and hold on the Templates icon (below). In the Templates popup window, choose Amino Acids, then from the next popup window, choose the histidine structure (below).
This creates a structure of a histidine amino acid. We only want the imidazole ring, so we can select everything else (you may need to rotate the 3D structure to do this easily) and hit the Delete key.
Now we need to add a Zn bonded to one of the N atoms on the ring. Below I chose the unprotonated N, made sure that bond tool was selected on the ChemDraw tool palette, and just clicked on that N to generate a new bond. By default this bond goes to a C atom, but right-clicking and choosing Edit Label (as above) allows us to change it to Zn.
ChemBio3D has a default bond length for Zn-N, but you can change that using the Internal Coordinates panel as we did above for Hg-S.
Now we have our Zn-imidazole fragment, which can be saved as a PDB file as we have done for all the other models above. Alternatively, additional atoms can be added to Zn to represent other portions of the coordination sphere, including more imidazoles if appropriate. The ChemBio3D model-building tools allow fairly sophisticated structures to be created and saved as PDB coordinates.
scott@chem.uga.edu |
