SOLVING & REFINING THE FIRST CRYSTAL STRUCTURE

2.1. Creating instruction file In this part, you are going to solve a simple crystal structure. Before getting started, you need: Download the data from email and install to C:\Solving_Structure\Example1 Creating the file ex1.ins in the folder Example1 File *.ins is created by following general procedure: 1st step: Open *.crs file 2nd step: Delete all lines except the three following lines: TITL CELL ZERR rd 3 step: Add following lines: LATT 1 SFAC elements (element symbols which define the order of scattering factors to be employed by the program.) UNIT n1, n2 (number of atoms of each type in the unit-cell, in SFAC order ) HKLF 4 (read h, k, l, Fo2 , ( Fo2 ) from *.hkl; terminate *.ins file) END 4th step: Save as *.ins file 2.2. Getting started You need to start and point your WinGX program to your data folder. Do this by the following procedure: Double click the WinGX icon on your desktop. The icon usually looks like Fig.2.1.

Fig.2.1

When you have done this, you will see the WinGX toolbar which looks like Fig. 2.2.

Fig.2.2

To work on your data, you need to select a new project by clicking on File -----> CHANGE PROJECT -----> Select new project.

Fig.2.3

You will see a menu which looks like Fig. 2.4.

Fig.2.4

Click on Browse and point to the folder containing our data and double click on the file ex1.ins. After clicking on OK, you will see the Model Summary information box for ex1. This box provides you with some information about our structure.

Fig.2.5

Click OK and you will see that PROJECTNAME and DIRECTORY have changed into those you selected. 2.3. Assigning space group To assign space group, click on Model -----> PRELIM -----> Assign Space group

Fig.2.6

You will see Assign SpaceGroup Output Window and Assign SpaceGroup Control Panel like Fig.2.7 and Fig.2.8.

Fig.2.7

Fig.2.8

Click on OK. You will see Confirm SpaceGroup box.

Fig.2.9

Fill in Spacegroup box with particular space group. Notice: tick in Check box to update space group in INS file before clicking on OK. 2.4. Solving the crystal structure To solve the structure, we use SHELXL. Click on Solve -----> SHELXS-97.

Fig.2.10

A window looking like Fig.2.11 should appear.

Fig.2.11

As you can see the DIRECT panel is selected. This means that the structure is going to be solved by direct method. Click OK and a new window will appear (Fig. 2.12)

Fig.2.12

Briefly, you can see that the program reports that you have a R(int) of 10.41% and a R(sigma) of 24.66% (the meaning of these indices will be discussed latter) 2.5. Refining the crystal structure At this stage you can close the SHELXS-97 output window and click on the SHELXGRAPH icon on the WinGX toolbar (Fig.2.13)

Fig.2.13

A new window looking like Fig.2.14 will appear.

Fig.2.14

Moving the molecule around (simply click and hold the left mouse on the cyan area and move the molecule around) and activating Label atoms check box gives you a picture looking like Fig. 2.15

Fig.2.15

As you can see the SHELXS program has already marked the probable position of the S atom.

Now activate the Label Q-peaks check box. The SHELX-GRAPH screen should now look like Fig.2.16

Fig.2.16

You will see that the white peaks are numerically ordered from Q1 to Q37. Details of the particular peak are available to see on the side menu (look at the CURSOR atom area). This information is accessible by just holding the mouse cursor over atom or peak you are interested in. It is important to realize that this is really an ordered list that comes from the res file outputted by SHELXS. If you open the file ex1.res (Refine -----> Open RES file in WinGX toolbar), you will see lines looking like the following:

Fig.2.17

These represent residual peaks (the intensity of which is given in the last column) in the electron density map and given an indication of where the atoms of molecule are. This list is ordered from the most intense peak (Q1) to the least intense peak (Q37). If you look at the residual peak list, you will see that peaks Q1 to Q24 are more intense than the remainder. This feature is often very useful when solving crystal structures and you should remember this effect. In this case, it means that the heavy atoms, i.e. the position of O, N and C atoms, are separated from the H atoms. At this point, it is a good idea to delete peaks which do not make chemical sense. To do this simply clicking on the peaks you do not want (in this case: peaks Q25 to Q37).

Fig.2.18

Clicking on Delete -----> Selected atoms will give you a diagram that looks like Fig.2.19

Fig.2.19

Basing on intense of peaks Q1, Q2, Q3 and Q4, we can assign them to O1, N1, N2, N3 atoms, respectively. To do this, you select these peaks, then right click on cyan area of SHELX-GRAPH and a new window will appear Fig.2.

Fig.2.20

Fill in New names box with O1, N1, N2, N3. After clicking on OK, you can see a diagram that looks like Fig.2.21

Fig.2.21

Now, it is time to pass your current model through SHELXL and ask it to both refine your current atom positions (the peaks we chose) and give a new list of residual peaks (or Q peaks from SHELXs point of view). i. First of all save the changes you have made by clicking on Save INS file. This creates a new ins file named ex1.ins in the case of this structure. Close SHELXGRAPH by clicking on the x on the top right corner. The WinGX toolbar should still be available. ii. Click on Refine -----> SHELXL-97. A new window will appear with information which is similar to that shown in Fig. 2.22

Fig.2.22

As you can see the final R1 is 0.4878 or 48.78%. The highest residual peak is 4.24. This means that the highest residual peak has an estimated height of 4.24 electrons. Lets look at SHELX-GRAPH again. Click the SHELX-GRAPH icon on the WinGX toolbar. Isotropic & anisotropic refinement If you open the file ex1.res by using a text editor, you will see the line for the S atom looks like the following:
S1 4 0.441639 0.238006 0.418836 11.00000 0.03504

In this case, we have isotropic atom and the last number represents the magnitude of the displacement around S1. What does this mean? It means that you are assuming that the atoms vibrate symmetrically around a central position leading a molecule with atoms looking as in the ORTEP diagram shown in Fig.2.23.

Fig.2.23 ORTEP diagram of isotropic structure

When you have an isotropic atom, as in this case, you need only one number to define the radius of the sphere around the atom. Lets change the description from isotropic to anisotropic which will better describe the electron density around the atoms. To do this, you have two choices. Either you select all the atoms in the molecule one by one by clicking on them or you can click on Select -----> All atoms. Now right click on cyan area of SHELX-GRAPH and a new window will appear Fig.2.24

Fig.2.24

Now click the Set Uijs anisotropic check box followed by OK. This will be set the thermal ellipsoids of all the atoms you selected to anisotropic. Lets save your changes and click on Save INS file and close SHELX-GRAPH as before. This will save your changes to a new version of ex1.ins.

Rerun SHELXL-97 by clicking on Refine -----> SHELXL-97 which will create a new window with refinement information as before. At the end of the run, you will notice that making the atoms anisotropic has lowered R1. If you open the file ex1.res, you will see that the line for the S atom now looks like the following:

S1 =

0.441690

0.238050

0.418849

11.00000

0.03997

0.03386

0.03267 -0.00419 -0.00853 -0.00479

As you see, the value 0.03504 has been replaced by six new numbers ( 0.03997 0.03386 0.03267 -0.00419 -0.00853 -0.00479). The first three numbers represent the displacement of the ellipsoid along the three orthogonal directions defining its shape. The last three define the orientation of the ellipsoid relative to the unit cell axes.

Fig.2.25 ORTEP diagram for anisotropic structure

As you can see, the ellipsoids around each atom are no longer perfectly spherical and in fact many of them look slightly elongated.