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XAS Tutorials XAS Data Analysis | Model Construction (CSD) (This tutorial presumes that the user has access to CCDC software ConQuest, which provides a search tool for the Cambridge Structure Database, CSD. At UGA in 2007, this license is supported by the Research Computing Center and ConQuest can be locally installed on a Windows PC.) There are many uses for the CSD related to XAS; two common ones are (1) to obtain empirical evidence for chemical intuition about coordination environments, including coordination numbers, metal-ligand distances, etc., and (2) to create a structural model for feff to use in calculating scattering paths and parameters. In this tutorial, we will use an example in which both goals are considered in analyzing Hg L3 EXAFS data for which we hypothesize a Hg(S-Cys)3 environment. We will use ConQuest to search the CSD for appropriate model compounds. We can then survey an appropriate selection of crystal structures to determine typical Hg–S bond distances for such coordination environments. We can also choose a crystal structure to use in creating the model for feff. Refinement of the coordinates for feff is best handled in a molecular modeling application and it is common to transfer crystal structure coordinates into such an application using a standard coordinate file format defined by the Protein Data Bank (PDB). This is an ASCII text format that can be easily edited to provide coordinates for the feff.inp file, the input to feff. This tutorial also describes how to export .pdb files from the CSD to use in ChemBio3D Ultra, one example of a molecular modeling application. When ConQuest is started, the main window opens with the Build Queries tab open by default. The buttons along the left represent different ways to build search queries, but for our purposes, the Draw function is the best choice.
The Draw window provides a way to sketch the connectivity of a substructure to use in searching the CSD. We want to find all structures in which Hg is connected to three S atoms and nothing else. A row of buttons at the bottom of this window provide easy selection of common elements, but unusual elements (e.g., Hg) are available from the More … button; choose Other Elements … from the dropdown menu.
This brings up a periodic table, in which you click on the element of interest (Hg in our case), then click on OK.
Once you have selected an element, clicking anywhere on the drawing canvas creates an atom of that type. Once you have the Hg central atom, to continue building, you first select another element; this time we can use the list on the bottom to select S. Then, click and drag from the Hg to create a bonded S atom (below). Note the dropdown menu on the right side of the bottom bar labeled Bond:, where you can choose something other than a Single bond, which is the default.
Use the same technique to create two other Hg–S single bonds. Searching with this structure would find any Hg structures in which at least three S are bonded to the Hg (other ligands could also be bonded); we prefer to search for Hg structures in which only three S are bonded to the Hg. This can be done using the Number of Bonded Atoms selection from the Atoms menu; choose 3 from the dropdown menu …
… This brings up a Select Atoms window and clicking on the Hg atom (on the drawing canvas) enters the element symbol and atom number in this window; you should then click Done. A superscript T3 appears on the Hg atom to alert you to this constraint.
You may also wish to limit the search results to structures in which the bonded S atoms are part of organic ligands (e.g., aryl or alkyl thiols). One way to do this is to require each S to be also bonded to a C atom. Select C from the bottom list and click and drag from each S.
Satisfied with our substructure to use, we click the Search button near the bottom right of the Draw window (above). This opens a Search Setup window in which we can add other constraints to our search. In particular, you should check the checkbox labeled 3D coordinates determined in the right Filters tab to limit the search to only those entries that have 3d structures determined and coordinates available. You may also want to give your search a meaningful name (using the Search Name textbox at top left) so you can recognize it later. When you are satisfied with your constraints, click the Start Search button at the bottom of the window.
This puts you back in the ConQuest main window, but now with the View Results tab selected. As the search progresses, the six-character code for each hit is listed in the right window (under Analyse Hitlist) and the progress bar below advances to 100%. You can select any hit by clicking on its code. For the selected hit, you can examine many aspects using the menu on the left side; by default, the Diagram tab is selected. (You can also see the 3d structure by selecting the 3D Visualiser tab.) This is a good time to look through the hitlist (assuming it is not too long) and deselect structures that you do not wish to consider. For example, we decided that the structure below would not be representative of Hg–S distances of more normal thiol complexes, so we clicked the green checkmark in the hitlist to change it to a red X (this deselects the hit). A few others were also deselected.
Once you are satisfied with the (de)selections you have made, it is time to export the hits as PDB-formatted coordinate files. From the File menu, choose Export Entries as …
From the resulting Export Entries window, use the top dropdown menu to select PDB: Original PDB format …
… then in the same window, be sure the radio buttons All selected entries and One file per entry … are selected, then click the File Popup button to get a save dialog box that allows you to pick a name (e.g., Hg) and a folder for the PDB files. It is recommended that you create a separate folder to hold the PDB results from each search. This creates a set of files with names like KELVUS.Hg.pdb.
Now you have a .pdb file that you can manually edit using any simple text editor (e.g., NotePad, WordPad) to extract coordinates that will be used in the feff.inp file. Alternatively, you can use a structure modeling program, such as ChemBio3D Ultra (see tutorial), to trim unnecessary atoms and save a simpler .pdb file for use in feff.inp. It is recommended that you also save your search query so that you don't have to reconstruct the search substructure. This allows you to go back and rerun the same search on an updated database or to make different choices of which hits to retain. You can also use this query as a template to create new queries. From the File menu, choose Save Search As …. Choose a name you can recognize; installation usually creates a searches folder to use to collect these.
scott@chem.uga.edu |
