Example: Identification

Transcription

1 Example: Identification In this structure we will explore Atom identification Working with maps Working with projections Eliminating diffusely diffracting solvent Disorder modeling Restrain application The proposed structure of a Pd(II) complex is shown below. It was crystallized from acetone and hexanes. 1. We start with files identification.res and identification.hkl. The structure has been solved and all atoms we are sure about are shown. 2. Run a refinement (CTRL-R). Label the highest peak of 7.3 e/å 3 as follows: Under Work Toolbox Work click on the button. The cursor goes into the labeling mode, and the name of the next atom to be labeled is displayed. In this case it is O4. 1

2 Click on the highest Q peak to rename it and run an anisotropic refinement by clicking on the button. 3. The new O4 atom looks a little large. O4 To examine the Fourier difference map go to Tools Maps Electron Denisty and click on the button. Pull the Level slider all the way to the left and start pulling it to the right. The dark-colored meshwork around O4 indicates a hole; clearly too much electron density was assigned at this location: Click on the Map button again to hide the map. Moreover, if you type grow to examine the structure, the coordination from O4 to the Pd atom is inconsistent with the typical bridging coordination geometry of the acetate. We conclude that O4 is in fact a carbon, and the ligand is acetonate. Type fuse to reduce the molecule to the asymmetric unit, relabel O4 to be C5 and re-refine the structure. Then position the H atoms on C5 and refine the structure again this is done by clicking on under Work Toolbox Work: The meaning to the checkbox to the left of the Add H button is to ensure that a refinement is launched immediately after H atoms are assigned. If you wish to check the correctness of H atoms placement prior to the refinement uncheck the box. 2

3 4. There are some peaks of electron density that belong to the solvent molecules. They reside in the solvent accessible voids. To visualize their positions: a) make sure the Q peaks are displayed (press CTRL-Q if necessary). b) to make sure that each Pd atom forms no more than four bonds select Pd1 and type conn 4 c) type pack to generate a packing diagram. d) type cell to display the unit cell boundaries. e) to orient the unit cell along the a axis type matr 1 or matr a. In this case the best view is along the c axis (matr 3 or matr c): View along the c axis 5. Modeling the solvent in this case is left as an exercise for the reader. We ll mask the solvent out in a procedure alternative to SQUEEZE. More info on how OLEX2 masking compares to SQUEEZE and some literature references is available in Ilia Guzei s Notes on OLEX2 at xray.chem.wisc.edu/lab.html. Reduce the view to the asymmetric unit by typing run fuse>>cell>>compaq The run command allows command concatenation (useful if you plan to repeat a succession of commands in the future by pressing the key). Under Tools Maps Masks click on the Mask button. 3

4 Type cell to display the cell. Under the Maps menu check the Extended checkbox channels in the lattice: to see the solvent accessible voids as The numerical output is also generated in the console part of the GUI. It can also be examined in the output.txt file that is opened by clicking on the atop the GUI panel. The masking procedure computed a total of electrons for the diffusely diffracted species in the voids of 755 Å 3 : Void Vol/Ang^3 #Electrons For comparison, SQUEEZE computed a volume of Å 3 and 156 electrons. Click on the MASK button to hide the mask, and hide the cell either by typing cell or by View Symmetry Generation Symmetry Tools Show Cell. To refine the structure with the solvent masked out go to Work Refine and check the Run a refinement with CTRL-R. use solvent mask box. 6. The extended nature of the structure can be examined in a number of ways with View Symmetry Generation Symmetry Tools. We are not going to do that due to the self-explanatory nature of these tools. Instead, type mode grow 4

5 to enable manual generation of symmetry-related atoms. The dashed lines show where symmetry related atoms are located (diagram on the left). Extend the structure by clicking on the dashes: Press ESC to exit the grow mode. The text in the GUI can be toggled with CTRL-T. The H atoms can be toggled with CTRL- H. To determine the direction of the propagation of this polymeric structure select two Pd atoms in the direction of the propagation by clicking on them and type line n The line command draws lines, but when used with the n switch no line is generated and the structure is oriented so that this line is perpendicular to the screen: The drawing is oriented along the Pd Pd lines on the right. Type direction to numerically express the lattice direction perpendicular to the screen (in our case it is the direction defined by the two Pd atoms, thanks to the line n command). In this case the following output is generated: Direction: (-0.033*A, *B, 0.999*C) View along (normalised deviation: 0.022A) View along (normalised deviation: 0.022A) 5

6 View along (normalised deviation: 0.022A) View along (normalised deviation: 0.022A) Thus, the direction of propagation is along the c axis. OLEX2 also prints major directions if they are close to the direction of the current projection. 7. Reduce the structure to the asymmetric unit (fuse) and let us model the disorder of the CF 3 group. This is seriously cool. The idea is to split atoms F1, F2, F3 into two sets by rotating the CF 3 group about the C1-C2 axis. Select atoms C2 F1 F2 F3 by clicking on them in this order. In general, a selection can be made by drawing a box around the atoms of interest (by holding down the SHIFT key and dragging the mouse with the left button depressed), but in this case the order in which the atoms are selected is important. In the GUI type mode fit -s=1 to indicate that we will be fitting the whole group to a new location, but one atom (the first atom of the selection) will not be split. The colors change somewhat, but importantly, the C1 C2 bond is highlighted: Right click on the C1 C2 bond once. Press the left mouse button and drag on the C1 C2 bond to rotate the F atoms about the C1 C2 axis. When you find good positions for the new F atoms, press ESC. The anisotropic F atoms have been split into two sets of isotropic atoms: FVAR PART 1 F F F PART 2 F2a F3a F1a

7 Note that the F atoms are assigned to two parts with occupancies 21 and -21 and that the second free variable with a value of 0.75 has been added to the FVAR line. Run a refinement. The C F distances seem to vary between 1.26 and 1.43 Å, and the use of restraints is warranted. OLEX2 has a neat utility of restraining 1-2 distances and 1 3 distances with a couple of clicks. Select atom C2. Then select Tools SHELX compatible restraints SADI (from the drop-down menu). When you click on the GO button in this option, all C2-F and C2-C1 distances will be restrained to be similar and all F F separations will get a similarity restraint as follows: SADI 0.04 F1 F2 F1 F3 F2 F3 F2A F3A F2A F1A F3A F1A SADI C2 C1 C2 F1 C2 F2 C2 F3 C2 F2A C2 F3A C2 F1A These commands are automatically inserted in the INS file. Of course the C2 C1 bond on the second line does not belong and one may elect to assign different esd s on the SADI cards. To edit this command open the INS file by typing edit. In my case these two commands are modified to eliminate the C2 C1 bond and to assign tighter esd s: SADI 0.02 F1 F2 F1 F3 F2 F3 F2A F3A F2A F1A F3A F1A SADI 0.01 C2 F1 C2 F2 C2 F3 C2 F2A C2 F3A C2 F1A Another refinement does even out the C F distances and CF 3 group geometries. It also suggests that the CF 3 group may be split over three positions (see the ball-n-stick diagram on the left), a preprogrammed feature for splitting a group into three or more is being considered. 7