Reference no: EM133098539

Problem Set - Completing and Refining the Structure

In this problem set you will start with the Iodine position you determined in Problem Set 2 as your initial phasing model. Starting from that point you will run a series of difference maps to find the missing atoms. After all the atoms are found, you will then refine the structure to convergence.

In order to complete this problem set, you will need to download some crystallographic software. SHELXL will be used to do crystallographic calculations. A program called Mercury will be used to examine the structure graphically. You can also use a graphical user interface (GUI) front end to SHELXL called ShelXle or another GUI based program called Olex2. All software is free of charge and available on the web.

SHELXL requires registration

ShelXle (a GUI program for SHELXL) can be downloaded

Olex2 is a popular GUI program for structure solution and refinement and can be downloaded

All software is available for Linux, Mac OS X, and Windows. If you run Linux, I can help with your software installation. If you use another operating system, please ask for help from your departmental IT person.

SHELXL is a command line program. It has no graphical interface. You must use a text editor (not a word processor) or one of the graphical user interface programs (i.e. ShelXle or Olex2) to modify the input files and examine the output files. Mercury can read either SHELX .res files or CIF files.

Hints about this structure:

• There are a total of 21 non-hydrogen atomic positions in this structure.
• There is no disorder.
• Molecule contains two nitrogenous heterocycles
• The Sulfur atom is bound only to carbon atoms
• There is an N-CH3 group and a N-phenyl group.

Tasks and Questions

1. You are provided with a SHELX .ins and .hkl file. Rename the files to identity yourself using the following as an example for a student name "John Doe":

rename chem9541_problem_set_3.ins j_doe.ins rename chem9541_problem_set_3.hkl j_doe.hkl

2. Edit the SHELX..ins file to incorporate the Iodine atom position which you determined using the following format as a guide:
I1 5 0.xxxxx 0.yyyyyy 0.zzzzz 11.00000 0.04

(a) As a comment in the SHELX .ins file, explain what each of the fields are in the atom record lines. Each line of comments starts with a REM and should not exceed 80 characters in length total. If your comment would extend for more than 80 characters, start a second line beginning with REM.

(b) After the line containing SIZE and before the line containing FVAR, add the following SHELX commands to the SHELX .ins files and using comments, in your own words explain what each of the lines mean. In particular explain what any values after the keyword mean:
L.S. 0
FMAP 2
PEAK 50 BOND $H CONF HTAB

After making these edits, make a copy of the SHELX .ins file calling it, following from our example above, j_doe_initial.ins_save.

3. Run the SHELXL program from the command line. Disregard any messages regarding EXTI or SWAT. Note what the value of R1 is.

(a) Make a copy pof the SHELX .res and SHELX .lst file which were output. Naming the copies, as above, j_doe_initial.res_save and j_doe_initial.lst_save.

(b) Open the SHELX .res file in a text editor and copy an appropriate number of Q peaks into the atom list (i.e. after the Iodine position and before the HKLF 4 statement). Save this file, and open it in Mercury. Examine the results. Pick out which peaks make sense as possible atomic positions and delete the peaks which do not make chemical sense. You can look up the distances between peaks in the SHELX .lst file and/or use Mercury to calculate distances. At this point rename change the 'Q' to 'A' for your "good" atom peaks and incorporate them into the model.

Your first time through, you won't be able to differentiate C, and N peaks, but you should be able to pick out and assign the Sulfur atom position. If you don't know which element a peak represents, keep it as a carbon. Rename the SHELX .res file to the .ins file.

4. Execute the SHELXL program again, and repeat the process of interpreting peaks as possible atomic positions as outlined above.

4. After 21 atoms peaks with good molecule geometries have been found. Change the number on the line containing the L.S. command from 0 to 12. Rename the SHELX .res file to the .ins file and execute SHELXL. After the least-squares calculation has run, make note of the new value of R1. Carefully examine the isotropic displacement parameters (Uiso) values to try to assign the correct nitrogen positions, editing the .res file as appropriate. Make note of the Uiso values of the atoms you think are nitrogen atoms.

5. Rename the SHELX .res file to be the .ins file and rerun the SHELXL program. Does the R1 improve with the updated atom assignments? What are the new values of Uiso for nitrogen atoms and are they more consistent with the other atoms in the molecule, especially those atoms to which they are bonded? What is the significance of bonded atoms having similar Uiso values?

6. Assign the various atoms names and number the peaks in a sensible way (e.g. atoms in a phenyl group would be numbered and ordered sequentially starting at the ipso position). Order the peaks sequentially. You may either sort the atoms by atomic number and then sequence number or order the atoms in a "bonding order". In any case, the list of atom names and numbers should not be done haphazardly.

7. Edit the SHELX .res file changing the argument for L.S. command from "12 "to "12 4". Add the ANIS command and several HFIX commands as appropriate. Rename the SHELX .res file to be the new .ins file. As comments (REM statements) in the .res file. Explain the purpose of the ANIS and HFIX commands.

8. Converge the weights.

Attachment:- Completing and Refining the Structure.rar