Practical Guide to Stucture Solution,

Refinement and Publication.

SHELXTL

Instructor : J. Reibenspies, Ph. D.

Nattamai Bhuvanesh, Ph.D.

Version 1.0.0

Practicals for X-ray Diffraction Series 1

Practicals for X-ray Diffraction Series 2
Practicals for X-ray Diffraction Series 3
Flow Chart
Raw Information XSHELL
.hkl and .p4p or notes SHELXTL, WINGX, XSEED

File preparation
XPREP, initialize

Structure Solution
XS, SIR, DIRDIF, XD

Structure Refinement Graphical Validation

XL, Crystals (model building) XP,
XSHELL, XSEED ,
SXGRAPH

Crystallographic Information Graphical Presentation

File (CIF) POVRAY, RASMOL, HG
Fo/Fc information file (FCF)

Plots

Write-up, Tables etc

Practicals for X-ray Diffraction Series 4

Shell Programs

SHELXTL – BRUKER
a) license stipulates that program can be loaded only on computers
owned by the university.

XSEED – L. Barbour
a) license stipulates that program must be used by university
employees. If you leave the university then your license is no
longer valid.

WINGX – L. Farrugia
a) Freeware, must register with Farrugia.

Other programs
SHELXS, SHELXL - Free must register with G. Sheldrick
SIR88,SIR97,SIR2002 – Free must sign license with C. Giacovazzo
RASMOL, POVRAY, MERCURY

Practicals for X-ray Diffraction Series 5

Data Input: 3I4, 2F8.2 h,k,l, I, σ(I) [*.hkl]
Parameter file from SMART [*.p4p]
Information required :
a) Molecular Formula (unit cell contents)
b) Anticipated structure

Output crystallographic information file CIF

Crystal Data
Coordinates
Bond lengths and angles
Thermal parameters
Hydrogen atoms

Fo/Fc information FCF

Practicals for X-ray Diffraction Series 6

Getting Started. SHELXTL

Move the *.hkl and *.p4p file to a new directory

Start SHELXTL
o Point to PROJECT and then NEW.

Find your files and name the project to begin

o Point to XPREP and start program

o A new widow will appear

Practicals for X-ray Diffraction Series 7

 in this case choose the primitive cell (based on the statistics)
Mean Intensity >> mean I/sigma(I) for A,B,C,I, F etc.
Number of I > 3 sigma(I) is large for A,B,C,I,F, etc.

Search for Higher Symmetry.

In this case the Monoclinic Cell is chosen (notice an Rsym > .1 may indicate that the
choice of the cell is wrong)

Practicals for X-ray Diffraction Series 8

Select Determine or Select Space Group from main menu.

Now set up the automatic space group determination

Practicals for X-ray Diffraction Series 9

notes :
The E2-1 statistics predict a non-centrosymmetric space group
I > I/sigma(I) for the a,c and n glides
I < I/sigma(I) for 21 screw axis
N (I>3 sigma(I)) is 0 for 21

Space group can be P 21 and P 21/m

P21/m is a centrosymmetric space group and not consistent with the E2-1 statistics.
The structure has a known chrial carbon center (i.e. the space group cannot contain a
mirror plane or an inversion center)

Space P 21 is chosen.

(see the attached handout for help in choosing space groups)

Practicals for X-ray Diffraction Series 10

Skip D (for now) and define unit-cell contents

Enter the formula C12H22O11 for sugar. Check the Tentative Z value (should be near 2 for
this space group) and the density (see density handout for more information)
If ok choose E and return to main menu.

Practicals for X-ray Diffraction Series 11

Choose F from the main menu and write the SHELXTL files.

You may need to write a new file/project name if the program has transformed the unit
cell. If you have a backup copy of the HKL file then overwrite the old file here.

Quit the program now and go back to the SHELXTL program

Point to XS to get started (If you had to generate a new file in xprep then go back to
project and start a new project)

Practicals for X-ray Diffraction Series 12

The XS window will start

notes :
The Rint and Rmerge is low (structure is solvable!)
CFOM is low (below 0.1 structure is solved!)
RE is low (below 20%)

Practicals for X-ray Diffraction Series 13

Point to XSHELL

Here is the solution with a few false peaks (Q29, Q27, Q26 etc)

Move the cursor over a false peak (say Q29) and type K. Repeat for each false peak until
basic structure (or fragment) is seen. Not all of the atoms may be present in this run. For
example Q14 and Q26 in the example above may be misplaced. Let us delete both of
them and see if one of them returns in the next run.

When finished it should look like this.

Practicals for X-ray Diffraction Series 14

Now use the select command to choose atoms. Let us choose carbon atoms first. Move
cursor to Q11 and type S: Q11 will turn blue. Repeat for Q16, Q12, Q19, Q22, Q18,
Q15, Q13, Q17, Q20, Q21 and Q23 (in that order).
Now point to LABELS and GROUP LABEL… You will see

Select type C and initial number as 1 and OK. This will label the carbons(starting a Q11)

Practicals for X-ray Diffraction Series 15

Repeat for Oxygens starting at Q5 (Q5, Q9,Q8,Q19,Q2,Q3,Q4,Q6,Q1,Q7)

Point to LABELS and GROUP LABEL… and change type to O and type OK.

Now sort the atoms. Point to ATOMS and SORT… you will see

Practicals for X-ray Diffraction Series 16

Move all atoms to sort bin. Sort alpha numeric and insert all after <Top of List> (select
<Top of List> to proceed). Type OK.

Point to Refine

Practicals for X-ray Diffraction Series 17

point to OK and proceed.

Practicals for X-ray Diffraction Series 18

Notice the R1 is large (.1924) we are still missing an atom (the peak that is 1.43 A from
C12). Point to OK

Practicals for X-ray Diffraction Series 19

Select Q1 by moving the cursor over it and typing S. Use Group Label to Label it O11.
Kill the remaining Q peaks by pointing to EDIT this Kill all Q peaks. Point to atoms and
sort to resort atom list.

Point to refine again and repeat refinement.

The R1 should now be R1 = 0.0986. All non hydrogen atoms are now located. Find the
highest Q peak by moving the cursor over Q1 (find it near C11) and reading the Peak
height value in the upper left hand corner. If this is less than 2 than it is most likely a
Hydrogen or residual peak. If greater than 2 then you have missed a non hydrogen atom.

Kill and Q-peaks (point to edit/Kill Q-peaks) and add hydrogen atoms.

Point to ATOMS/Hybridize ALL and then ATOMS/Calculate Hydrogens. You will see
warning about HFIX 83 type OK.

Now point to refine again and repeat refinement. The R1 = 0.0775 now.

The final step will be the go anisotropic on all non-hydrogen atoms.

Practicals for X-ray Diffraction Series 20

 Select This
Button

Press OK. The R1 = 0.0613

Practicals for X-ray Diffraction Series 21

Draw the structure, kill all Q-peaks (EDIT/KILL ALL Q-PEAKS) . Point to
View/Rendition/Thermal Ellipsoid

Draw the thermal ellipsoid plot.

Practicals for X-ray Diffraction Series 22

The ellipsoids should be football shaped, not disks or saucers. Non Positive Definite
atoms will appear as regular shaped round gray spheres (like those seen for hydrogens
and isotropic atoms).

Run the final refinement. First edit the INS file. Point to EDIT/EDIT CURRENT FILE
and add

SIZE .2 .2 .2
TEMP –163
HTAB
CONF
WPDB -1

Save bye closing file and keep the changes. Point to refine and choose the ACTA button
and start the refinement.

Practicals for X-ray Diffraction Series 23

The final results can be examined in detail.
1) The R1 = 0.0597 (for Strong reflections) should be less than 0.10
2) The wR2 should be about 2 times R1 for all unique reflections, in this
case R1=0.0992. wR2 should be less than 2 * .099 or 0.198
3) The Goof (1.003) should be greater than 1.0 and less than 2.0
4) The Maximum = 0.011 is the max. shift and should be less than 0.2
5) The highest peak (unassigned) is 0.31 electrons and should be less than
1.00 and the absolute value should be about equal to the absolute value
of the deepest hole.
All parameters indicate that this refinement is finished.

Press ok and redraw the structure. Again kill the q-peaks. Redraw the thermal
parameters. Point to label and turn off Hydrogen labels. Now move the cursor over an
atom and type P. The label now will move with the cursor. Move it to a free area and
click the mouse. Repeat for all atoms.

Practicals for X-ray Diffraction Series 24

Point to render/color/to high-quality JPEG file and name the file sucrose.jpg.

Use the anti-aliasing for best pictures

Practicals for X-ray Diffraction Series 25

Now exit xshell and point to XCIF

Follow the defaults and write a new Crystallographic Information File

Exit XCIF and return to SHELXTL. Point to EDIT/EDIT .CIF and edit the CIF file.

Practicals for X-ray Diffraction Series 26

 Add crystal information

Add multi-scan
And SADABS

Finally change fine-focus to normal-focus

The CIF is now ready for publication.

At this point your structure is finished. You should have three files

Sucrose.CIF, Sucrose.FCF and Sucrose.JPG.

To write a table for WORD return to XCIF. Follow the menu for crystal/atom tables.
For the filename type Sucrose.RTF. For filename extension type RTA. Choose the
crystal table, the atomic coordinate table, full bond lengths/angles, aniostropic table and
the hydrogen atom table. Say no (N) to all other questions.

The rich text file Sucrose.RTF can now be read into any word processing program.

Practicals for X-ray Diffraction Series 27

Example of SUCROSE

Sucrose

Practicals for X-ray Diffraction Series 28

 Table 1. Crystal data and structure refinement for sucrose.
Identification code sucrose
Empirical formula C12 H22 O11
Formula weight 342.30
Temperature 110(2) K
Wavelength 0.71073 Å
Crystal system Monoclinic
Space group P2(1)
Unit cell dimensions a = 7.7576(18) Å α= 90°.
b = 8.702(2) Å β= 102.946(4)°.
c = 10.861(3) Å γ = 90°.
Volume 714.6(3) Å3
Z 2
Density (calculated) 1.591 Mg/m3
Absorption coefficient 0.143 mm-1
F(000) 364
Crystal size 0.20 x 0.20 x 0.20 mm3
Theta range for data collection 1.92 to 28.37°.
Index ranges -10<=h<=10, -11<=k<=11, -14<=l<=14
Reflections collected 8208
Independent reflections 3297 [R(int) = 0.0535]
Completeness to theta = 28.37° 94.3 %
Absorption correction None
Max. and min. transmission 0.9721 and 0.9721
Refinement method Full-matrix least-squares on F2
Data / restraints / parameters 3297 / 1 / 216
Goodness-of-fit on F2 1.029
Final R indices [I>2sigma(I)] R1 = 0.0594, wR2 = 0.1278
R indices (all data) R1 = 0.1095, wR2 = 0.1543
Absolute structure parameter 0.8(16)
Largest diff. peak and hole 0.303 and -0.296 e.Å-3

Practicals for X-ray Diffraction Series 29

Table 2. Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (Å2x 103)
for sucrose. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor.
________________________________________________________________________________
x y z U(eq)
________________________________________________________________________________
C(1) 2046(5) 4721(5) 6407(4) 37(1)
C(2) 569(5) 3548(5) 6266(4) 39(1)
C(3) -632(5) 3899(5) 7141(4) 37(1)
C(4) -1357(5) 5506(4) 6877(4) 35(1)
C(5) 152(5) 6689(5) 6993(3) 33(1)
C(6) 3160(5) 4537(5) 5438(3) 42(1)
C(7) 1303(5) 8332(4) 8754(3) 32(1)
C(8) 2868(5) 8352(4) 9930(3) 33(1)
C(9) 4439(5) 8582(5) 9334(3) 35(1)
C(10) 3712(5) 9643(5) 8233(4) 36(1)
C(11) -427(5) 8942(5) 8975(4) 39(1)
C(12) 4528(5) 9434(5) 7115(4) 44(1)
O(1) 1315(3) 6272(3) 6227(2) 37(1)
O(2) 2138(4) 4789(4) 4190(3) 50(1)
O(3) 1445(4) 2120(4) 6519(3) 57(1)
O(4) -2027(4) 2773(4) 6914(3) 52(1)
O(5) -2479(4) 5893(4) 7705(3) 42(1)
O(6) 1088(3) 6783(3) 8289(2) 32(1)
O(7) 1837(3) 9310(3) 7875(2) 35(1)
O(8) -1210(4) 7903(4) 9701(2) 44(1)
O(9) 2958(4) 7074(3) 10737(2) 40(1)
O(10) 5891(3) 9280(4) 10216(2) 43(1)
O(11) 4601(4) 7885(4) 6732(3) 49(1)
________________________________________________________________________________

Practicals for X-ray Diffraction Series 30

Table 3. Bond lengths [Å] and angles [°] for sucrose.
_____________________________________________________
C(1)-O(1) 1.460(5)
C(1)-C(6) 1.512(5)
C(1)-C(2) 1.516(5)
C(2)-O(3) 1.414(5)
C(2)-C(3) 1.504(5)
C(3)-O(4) 1.440(5)
C(3)-C(4) 1.511(6)
C(4)-O(5) 1.425(5)
C(4)-C(5) 1.543(5)
C(5)-O(1) 1.405(4)
C(5)-O(6) 1.434(4)
C(6)-O(2) 1.426(4)
C(7)-O(7) 1.409(4)
C(7)-O(6) 1.436(4)
C(7)-C(11) 1.511(5)
C(7)-C(8) 1.553(5)
C(8)-O(9) 1.408(4)
C(8)-C(9) 1.515(5)
C(9)-O(10) 1.440(4)
C(9)-C(10) 1.516(5)
C(10)-O(7) 1.448(4)
C(10)-C(12) 1.501(5)
C(11)-O(8) 1.422(5)
C(12)-O(11) 1.416(6)

O(1)-C(1)-C(6) 105.7(3)
O(1)-C(1)-C(2) 110.3(3)
C(6)-C(1)-C(2) 113.3(3)
O(3)-C(2)-C(3) 113.3(3)
O(3)-C(2)-C(1) 104.6(3)
C(3)-C(2)-C(1) 111.1(3)
O(4)-C(3)-C(2) 107.6(3)
O(4)-C(3)-C(4) 111.3(3)
C(2)-C(3)-C(4) 109.0(3)

Practicals for X-ray Diffraction Series 31

O(5)-C(4)-C(3) 110.7(3)
O(5)-C(4)-C(5) 110.5(3)
C(3)-C(4)-C(5) 111.0(3)
O(1)-C(5)-O(6) 110.2(3)
O(1)-C(5)-C(4) 110.8(3)
O(6)-C(5)-C(4) 109.1(3)
O(2)-C(6)-C(1) 111.2(3)
O(7)-C(7)-O(6) 110.9(3)
O(7)-C(7)-C(11) 107.6(3)
O(6)-C(7)-C(11) 110.4(3)
O(7)-C(7)-C(8) 104.9(3)
O(6)-C(7)-C(8) 107.9(3)
C(11)-C(7)-C(8) 115.1(3)
O(9)-C(8)-C(9) 116.0(3)
O(9)-C(8)-C(7) 115.1(3)
C(9)-C(8)-C(7) 101.9(3)
O(10)-C(9)-C(8) 110.9(3)
O(10)-C(9)-C(10) 111.4(3)
C(8)-C(9)-C(10) 103.0(3)
O(7)-C(10)-C(12) 109.8(3)
O(7)-C(10)-C(9) 105.3(3)
C(12)-C(10)-C(9) 114.5(3)
O(8)-C(11)-C(7) 111.7(3)
O(11)-C(12)-C(10) 113.9(3)
C(5)-O(1)-C(1) 116.2(3)
C(5)-O(6)-C(7) 113.0(3)
C(7)-O(7)-C(10) 111.7(3)
_____________________________________________________________
Symmetry transformations used to generate equivalent atoms:

Practicals for X-ray Diffraction Series 32

Table 4. Anisotropic displacement parameters (Å2x 103) for sucrose. The anisotropic
displacement factor exponent takes the form: -2π2[ h2 a*2U11 + ... + 2 h k a* b* U12 ]
______________________________________________________________________________
U11 U22 U33 U23 U13 U12
______________________________________________________________________________
C(1) 38(2) 36(2) 35(2) -2(2) 4(2) 5(2)
C(2) 43(2) 34(2) 37(2) 5(2) 6(2) 0(2)
C(3) 44(2) 36(2) 31(2) 0(2) 7(2) -2(2)
C(4) 35(2) 36(2) 34(2) -2(2) 6(2) -5(2)
C(5) 33(2) 40(2) 26(2) 1(2) 4(2) -3(2)
C(6) 37(2) 48(3) 41(2) -8(2) 9(2) 2(2)
C(7) 31(2) 32(2) 30(2) 0(2) 2(2) 1(2)
C(8) 32(2) 32(2) 34(2) 0(2) 3(2) 1(2)
C(9) 30(2) 37(2) 35(2) -7(2) 4(2) -4(2)
C(10) 29(2) 37(2) 41(2) -2(2) 6(2) -6(2)
C(11) 26(2) 44(2) 45(2) -2(2) 6(2) 3(2)
C(12) 36(2) 52(3) 42(2) 8(2) 8(2) 2(2)
O(1) 41(2) 35(2) 35(1) -1(1) 9(1) -3(1)
O(2) 58(2) 54(2) 39(2) -7(1) 12(2) -8(2)
O(3) 60(2) 40(2) 74(2) 4(2) 23(2) 8(2)
O(4) 64(2) 45(2) 49(2) -6(2) 19(2) -18(2)
O(5) 36(2) 48(2) 44(2) 0(1) 11(1) -1(1)
O(6) 32(1) 31(2) 29(1) -2(1) -1(1) 1(1)
O(7) 25(1) 40(2) 39(1) 9(1) 3(1) -2(1)
O(8) 38(2) 52(2) 43(2) -5(2) 12(1) -4(1)
O(9) 41(2) 41(2) 36(2) 6(1) 3(1) 2(1)
O(10) 24(1) 56(2) 46(2) -9(1) 0(1) -4(1)
O(11) 40(2) 62(2) 47(2) -11(2) 9(2) -2(2)
______________________________________________________________________________

Practicals for X-ray Diffraction Series 33

Table 5. Hydrogen coordinates ( x 104) and isotropic displacement parameters (Å2x 10 3)
for sucrose.
________________________________________________________________________________
x y z U(eq)
________________________________________________________________________________

H(1) 2823 4636 7273 44

H(2) -135 3557 5374 46
H(3) 48 3826 8037 44
H(4) -2079 5537 5990 42
H(5) -369 7718 6718 40
H(6A) 4153 5278 5621 50
H(6B) 3665 3488 5498 50
H(8) 2748 9294 10431 40
H(9) 4812 7581 9024 42
H(10) 3879 10733 8528 43
H(11A) -215 9940 9422 46
H(11B) -1254 9121 8151 46
H(12A) 3839 10036 6398 52
H(12B) 5743 9856 7325 52
H(2A) 2312 5687 3961 75
H(3A) 694 1410 6435 85
H(4A) -2358 2606 7587 77
H(5A) -3153 6616 7391 63
H(8A) -1537 7107 9275 65
H(9A) 3082 6269 10338 60
H(10A) 6845 8874 10142 65
H(11) 3569 7534 6508 74
________________________________________________________________________________

Practicals for X-ray Diffraction Series 34