Crystal-Structures SHELX 97 BOOK

A Practical Guide to Solving Single Crystal
Structures
Manuel A. Fernandes
15 Mar 2006
School of Chemistry
University of the Witwatersrand
Johannesburg, South Africa, 2006
Solving Crystal Structures 1
Frequently asked questions
What are the aims of this manual?
The aims of this document is to enable students and researchers to fully solve their
crystal structures such that they are able to submit their structures to Acta
Crystallographica C or E (from now on referred to as an ACTA paper; see
www.iucr.org) or insert it into their thesis documents without the help of a
crystallographer.
What is covered by this manual?
The following areas are covered:

[1] The use of WinGX, SHELX-97, ORTEP-3 and PLATON to solve crystal
structures.
[2] The use of CIFTAB (part of SHELX-97 and incorporated into WinGX) to finish
of crystal structures in association with PLATON. Included will be information
on what is needed to finish a crystal structure for insertion into a paper or
thesis.
[3] The use of PLATON, ORTEP-3 and PovRay to draw pictures.
[4] How to use all the above software to prepare your structure for an ACTA
paper.
[5] Some general guidelines on how to discuss your structure in a synthesis
journal, a more crystallographic journal and the ACTA journals. As part of
this section some discussion of crystal packing, classical hydrogen bonding
and weak interactions will be covered.
Required software
In order to solve and publish crystal structures the following software will need to be
downloaded and installed:
WinGX. The main software package required to solve and refine structures. It
includes SHELX, Sir-97 and PLATON. There are other packages that do
similar things to WinGX but in my opinion WinGX is one of the easiest to use
and to teach and hence is presented here. Download from
http://www.chem.gla.ac.uk/~louis/wingx.
PLATON. This software package allows one to pick up errors in a crystal
structure solution, do many crystallographic manipulations and draw
molecular and packaging diagrams of the structure. Download from
http://www.chem.gla.ac.uk/~louis/software/platon.
ORTEP-3. This software program allows to draw ORTEP, packing and povray
diagrams. Download from http://www.chem.gla.ac.uk/~louis/software/ortep3.
Mercury. This software program allows one to find and draw interesting
interactions in crystal structures. It is also possible to export some of these
pictures but they are often not of good quality. Download from
http://www.ccdc.cam.ac.uk/mercury/.
Encifer. An editor which is designed for editing CIF files. Though not a bad
program I tend to prefer simpler editors such as wordpad or SCINTILLA
(available at http://www.scintilla.org). Download ENCIFER from
http://www.ccdc.cam.ac.uk/free_services/encifer.
GhostScript and GhostView. These programs allow one to convert the
graphical output files from PLATON and ORTEP-3 to other formats or to paste
them directly into MS-word or MS-power point. Download from
http://www.cs.wisc.edu/~ghost/.
Povray. This is a scene rendering program that allows some very fancy
graphics to be rendered. It is not a crystallography program. All it does is
convert a set of instructions (contained in a POV file) into a picture. Some
people like it though I almost never use it. Download it from
http://www.povray.org.
It is assumed that MS-office is installed on your computer. If you cannot get
hold of MS-office then you can use OpenOffice (available from
www.openoffice.org) instead which is a very good and free alternative

allowing read and write access to all of the MS-office formats.
It is also assumed that you have access to the internet and know how to use
one of the following web browsers: Internet Explorer, Mozilla or Firefox (the
last two are available from www.mozilla.org).
In addition you will need to know how to extract data from ZIP files. You will
need Winzip (www.winzip.com) or unzip (www.unzip.org) to do this though
many other programs that are able to do this are available.
Chapter 2: Solving your first crystal structure
In this chapter you will be solving a simple crystal structure. In addition, you will
shown how to prepare it for publication and how it was eventually published. Before
getting started you will obviously have to install the recommended software packages.
2.1 Getting started
Before getting started you will need to download the data from
http://www.gh.wits.ac.za/manuel/solving-xtals/struct1/md1.zip. Extract the data to a
directory on your computer. In my case I installed the data to
D:\GH8\solving-xtal\data\struct1\ but it really does not matter.
Now you will need to start and point your WinGX program to your data directory. Do
this by doing the following:
[1] Either double click the WinGX icon on your desktop or click the Wingx32 link
on your windows start menu. It usually looks something like the Fig 2.1.
.
Fig 2.1
[2] Once you have done this you will see the WinGX toolbar which looks like
Fig. 2.2
Fig 2.2
If you look carefully you will see that the program is currently pointing to a
project called 5m_lc4_a which is in the d:\strcts\wits\carlton\5m_lc4 directory.
To work on our data you will need to select a new project by clicking on File >
CHANGE PROJECT > Select New Project. You will now see a menu that
looks like Fig. 2.3.
Fig 2.3
Click on Browse and work your way to the directory containing your data and
double click on the INS file. In this case it's called md1_s.ins. The above window
should now look like Fig 2.4.
Fig 2.4
[3] Now click OK and you should have the Model Summary information box
poping up (Fig 2.5).
Fig 2.5
[4] This provides you with some information about you structure. In this case the
crystallographer has determined that the space group is probably P-1 and that
the unit cell parameters are 6.85 etc. Click OK and have you will see that
the project name and directory have changed those you selected (Fig 2.6).
Fig 2.6
2.2 Solving the crystal structure
In this document only two structure solution programs will be shown. The first
involves using SHELXS-97 while an alternative is to use SIR-92 (or SIR-97 or SIR-
2002 if you have them). The SIR programs are very easy to use and often are able to
solve a structure to almost completion making the structure refinement a little easier
(saves you about 5-10 mins in time when you have a small but busy structure). SIR is
often very useful when you have a data set that stubbornly refuses to be solved using
SHELXS.
In this manual only the use of SHELXL will be shown. Using SIR is just as easy and
the results are often a little better. It is left to the reader to try to solve and refine his or
her data set using SIR.
To solve your structure using SHELXL clink on Solve > Shelxs-97. A window
looking like Fig 2.7 should pop up.
Fig 2.7
As you can see the DIRECT panel is selected which means that the structure is going
to be solved by direct methods (a brief explanation for this will be given in one of the
appendices).
Now click OK and a new window will appear (Fig 2.8).

Fig 2.8
Very briefly you can see that the program reports that you have an R(int) of 1.4 % and
a R(sigma) of 2.5 %. These are both excellent values (see appendix AX for details).
The contents of the end of this window are given in Fig 2.9.
Fig 2.9
Here you can see that the RE (a kind of R-factor) is about 19% for 12 atoms, i.e. the
structure has about 12 atoms. In general you can consider a structure solution with RE
less than 30% as solved though the higher the number the more difficult the
refinement phase. An RE of about 19% tells us that this structure should be
reasonably straight forward to refine from now on.
2.3 Refining the crystal structure
At this stage you can close the SHELXS-97 output window and click on the SHELX-
GRAPH icon on the WinGX toolbar (Fig 2.9).
Fig 2.9
A new window looking like Fig 2.10 will appear.
Fig 2.10
Moving the molecule around (simply click and hold the left mouse button on the cyan
area and move the molecule around) and activating Label atoms check box gives you
a picture that looks like Fig 2.11.
Fig 2.11
As you can see the SHELXS program has already marked the probable position of the
suphur atom (SIR could probably do better in this case). If you look carefully you will
see that there is a five membered ring (made up of the white spots) connected through
a bond to a six membered ring. As I'm sure you have noticed I have not shown you
what the structure should look like. All you are given is the space group and unit cell
parameters (provided by the crystallographer and mentioned earlier) as well as the
basic elemental composition of the molecule which is C H N S. This is all you need to
solve the structure and SHELXS has already told you where the sulphur probably is.
Now activate the Label Q-peaks check box. The SHELX-GRAPH screen should now
look like Fig 2.12.
Fig 2.12
You will see that the white peaks are numerically ordered from Q1 to Q20. The
important thing to realize is that this is really an ordered list that comes from the res
file outputted by SHELXS. If you open the md1_s.res (open with wordpad, notepad or
scintilla) you will see lines looking like the following:
Q1 1 0.5960 0.7081 0.6909 11.000000 0.05 343.61

Q2 1 0.6409 0.7441 0.4527 11.000000 0.05 316.70
Q3 1 0.5069 0.7420 0.5575 11.000000 0.05 298.34
Q4 1 0.2958 0.7671 0.5428 11.000000 0.05 266.91
Q5 1 0.5085 0.7446 0.8198 11.000000 0.05 263.80
Q6 1 0.8358 0.6442 0.6896 11.000000 0.05 221.84
Q7 1 0.2200 0.7996 0.4150 11.000000 0.05 208.50
Q8 1 0.5659 0.7825 0.3266 11.000000 0.05 205.85
Q9 1 0.6738 0.6844 0.9227 11.000000 0.05 203.74
Q10 1 0.3600 0.8077 0.3014 11.000000 0.05 195.51
Q11 1 0.8881 0.5630 0.8391 11.000000 0.05 174.45
Q12 1 0.2693 0.8959 0.6229 11.000000 0.05 93.24
Q13 1 0.5305 0.7950 1.0084 11.000000 0.05 89.43
Q14 1 0.6683 0.6953 0.5759 11.000000 0.05 85.54
Q15 1 0.3025 0.8361 0.9855 11.000000 0.05 79.45
Q16 1 0.4681 0.6770 0.7555 11.000000 0.05 74.12
Q17 1 0.0000 1.0000 0.5000 10.500000 0.05 72.59
Q19 1 0.5537 0.6623 0.2472 11.000000 0.05 66.55
Q20 1 1.1178 0.3572 0.8630 11.000000 0.05 63.60
These represent residual peaks (the intensity of which is given in the last column) in
the electron density map and give an indication of where the atoms of the molecule
are. The list is ordered from the most intense peak (Q1) to the least intense peak
(Q20). You can actually select how many residual peaks SHELXL will give you but
more on that latter. If you look at the residual peak list you will see that peaks Q1 to
Q11 are significantly more intense than the remainder and there is an obvious jump in
the peak height on going from Q11 and Q12. 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 positions of C and N atoms, is separated from the H
atoms at this point.
Looking at the last SHELX-GRAPH screen (Fig 2.12) you will see that details of the
Q1 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 an atom or peak you
are interested in. In this case I had the mouse cursor over the Q1 peak. If you look at
the Q1 in the list I gave above and compare it with this you will see that they are
identical, i.e. SHELX-GRAPH is telling you in a graphical manner the information
that available from the md1_s.res file directly.
As I mentioned peaks Q1 to Q11 seem to be the main peaks of this structure. Together
with the S atom you have the 12 atoms that were mentioned by SHELXS in its final
output. Fig 2.12 shows that peaks Q1 to Q11 make up the 5 membered and 6
membered rings which are from a geometric point of view chemically sensible.
At this point it is a good idea to delete the picks that do not make chemical sense. To
do this simply clicking on the peaks you don't want (Fig 2.13).
Fig 2.13
You will notice that these correspond to peaks Q12 to Q20, i.e. the weak peaks I
showed in the Q list earlier. Now click on Delete > Selected atoms. This will give
you a diagram that looks like Fig 2.14.
Fig 2.14
You know can see what the molecule will probably look like. At this stage you have a
choice or relabelling all the Q peaks to something that is chemically sensible such a C
atoms. In this particular structure we know that the back bone is made up mostly of C
atoms. So we can either change the labels by hand one by one or we can cheat
initially. Lets rather take the second approach and ask SHELX-GRAPH to convert all
the Q atoms to C atoms. To do this click on Model > Change Q >> C. You should
now have something that looks like Fig 2.14.
Fig 2.14
Though the labels are all wrong the residual peaks have all been labelled as carbons
and it is now time to pass our model as we have it now through SHELXL and see how
the structure refines. There are two ways to do this. The easy way is to run SHELXL
through SHELX-GRAPH itself though when things go wrong people get very
confused and don't know what to do. The other way is more difficult but is easier to
recover from if things go wrong. For novices I prefer to teach the slightly harder way
as it's hard to make mistakes this way. This is the method I will demonstrate here.
First of all save the changes you have made by clicking on Save INS file. This creates
a new ins file named md1_s.ins in the case of this structure. Now close SHELX-
GRAPH either by clicking on the "x" on the top right corner or by clicking on File >
Exit in SHELX-GRAPH. The WinGX toolbar should still be available.
We now are going to pass the md1_s.ins file which contains our current structural
model through SHELXL and ask it to both refine our current atom positions (the peaks
we chose) and give a new list of residual peaks (or from SHELX's point of view Q
peaks). To do this click on Refine > SHELXL-97.
A new window will appear with information similar to that shown in Fig 2.15.
Fig 2.15
As you can see the final Rfactor (R1) was 0.17 or 17%. The highest residual peak was
2.26 which means that the highest residual peak has an estimated height of 2.26
electrons. In this case this value does not really matter as its lies right next to the S
atom. Lets now look at SHELX-GRAPH again. Click the SHELX-GRAPH icon on the
WinGX toolbar. You should now have something that looks like Fig 2.16.
Fig 2.16
As you can see almost all the residual peaks surround the S and C atoms positions. In
this particular structure the reason for this is the fact that we still have isotropic atoms.
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 those
in the ORTEP1 diagram shown in Fig 2.17.
Fig 2.17
1
The meaning of an ORTEP will become clear later.
However, the reality is that in nature very few things behave isotropically. More often
than not atoms are arranged in a less random manner and atoms vibrate more in some
directions than in others. The residual peaks shown in Fig 2.16 reflect this as they tell
you that the spherical atom model (or isotropic) in insufficient to describe the electron
density surrounding each atom. In SHELX-GRAPH take a close look at the S atom.
You will see that it is surrounded by the two biggest residual peaks (Q1 and Q2).
If you open the md1_s.res file using a text editor you will see that the line for the S
atom looks like the following:
S1 4 0.238186 0.853746 0.874298 11.00000 0.06045
In this case the last number represents the magnitude of the displacement (or size of
the ellipsoid) around S1. When you have an isotropic atom, as in this case, all you
need is one number as this defines the radius of the sphere around the atom (see Fig
2.17).
Lets now change the description we are using for our atoms from isotropic to
anisotropic as this will better describe the electron density around the molecules
atoms. There are two ways to do this. If you have a complicated structure then it is
often a good idea to make a few atoms anisotropic at a time. In this particular case the
molecule is quite simple so its not a bad idea to make all the atoms anisotropic at the
same time.
To do this first uncheck the Display Q-peaks check box which will hide the Q peaks.
You now 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 in the
cyan area of SHELX-GRAPH and a new window will appear Fig 2.18.
Fig 2.18
Now click the Set Uij's anisotropic check box followed by OK. This will set the
thermal ellipsoids of all the atoms you selected to anisotropic. The meaning of this
will become clear in a moment.
Lets now save your changes and click on Save INS file and close SHELX-GRAPH as
before. This will have saved your changes to a new version of md1_s.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 the Rfactor (R1) to 0.088 or about 9%.
An ORTEP diagram after applying anisotropic ADP's is shown in Fig 2.19. If you
open the md1_s.res file now using a text editor you will see that the line for the S
atom now looks like the following:
S1 4 0.238089 0.853981 0.874423 11.00000 0.04365 0.08868 =

0.04904 -0.00742 0.01031 -0.02388
As you can see the 0.06045 value of before has been replaced by six new numbers
(0.04365 0.08868 0.04904 -0.00742 0.01031 -0.02388). 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 (see Fig 2.19).
Fig 2.19
As you can see the ellipsoids around each atom are no longer perfectly spherical and
in fact many of them look slightly elongated. Notice that the ellipsoid belonging to
C001 is visually smaller than those of the rest of the molecule. There is a good reason
for this. Remember that we are expecting that the structure has one or more N atoms.
The way to look at ellipsoids is like this: N atoms have one more electron than C
atoms. That means that assigning a C atom where a N atom should be will give you a
small ellipsoid because the ellipsoid has to extend a smaller distance to account for
the electron density of a C atom. On the other hand if you place a N atom where a C
atom is actually present then the ellipsoid will appear much larger than those of the
rest of the molecule because the ellipsoid has to be drawn out much further to account
for the electron density associated with an N atom. The best way to see these effects is
to wrongly assign some atoms when we have completed the refinement of this
structure, i.e. change the N atom to a C and see what happens to the Rfactor and
ellipsoid once you refined the structure. Also, see what happens when you change a C
to an N atom. Finally change the S atom to a C atom.
So now we strongly suspect that C001 is actually a N atom what do we do to make

sure? That will become clear in a few minutes. Lets first see what residual peaks came
out of the SHELXL refinement. Start by opening SHELX-GRAPH again. You should
now have something that looks like Fig 2.20.
Fig 2.20
Notice that the H atoms are now visible, i.e. SHELXL has found them in the difference
map. If you open md1_s.res with a text editor you will see the following Q peaks:
Q1 1 0.8680 0.7424 0.6674 11.00000 0.05 0.64

Q2 1 0.9055 0.5200 0.6184 11.00000 0.05 0.60
Q3 1 0.2029 0.7619 0.6217 11.00000 0.05 0.59
Q4 1 0.0788 0.8186 0.3972 11.00000 0.05 0.54
Q5 1 1.0127 0.5830 0.8634 11.00000 0.05 0.50
Q6 1 0.3036 0.8384 0.2034 11.00000 0.05 0.49
Q7 1 0.9122 0.3998 0.8498 11.00000 0.05 0.49
Q8 1 0.6682 0.8210 0.9547 11.00000 0.05 0.46
Q9 1 0.6219 0.6403 1.0049 11.00000 0.05 0.46
Q10 1 0.6585 0.7943 0.2482 11.00000 0.05 0.45
Q11 1 0.2590 0.7847 0.5174 11.00000 0.05 0.33
Q12 1 0.3693 0.7750 0.8419 11.00000 0.05 0.31
Q13 1 0.4482 0.8423 0.3135 11.00000 0.05 0.29
Q14 1 0.2911 0.7434 0.8246 11.00000 0.05 0.25
Q15 1 0.3670 0.7720 0.5587 11.00000 0.05 0.17
Q16 1 0.2845 1.0359 0.1552 11.00000 0.05 0.17
Q17 1 0.8384 0.8485 0.4381 11.00000 0.05 0.10
Q18 1 0.2529 1.0240 0.9426 11.00000 0.05 0.09
Q19 1 0.8678 0.7299 0.4022 11.00000 0.05 0.09
Q20 1 0.8531 0.8046 0.4194 11.00000 0.05 0.08
As you can see there seems to be a jump in the height of the residual peak between
Q10 and Q11. Residual peaks Q1 to Q10 seem to there all be H atoms while the rest
do not seem to be important. Also notice the height of the residual peaks Q1 to Q10
are all less than 1 e3, i.e. less than 1 electron. This tells you that they are probably
hydrogen atoms. If the peak was higher e.g. 1.5 or 2.5 e3 then you should consider
wheter anything heavier is present instead of a H atom. Use bond length and angle
measurements to make sure. What I mean by this will become clear in a few minutes.
If you look at the H's around the C atoms using SHXG you will notice that atoms
C006, C009 and C011 all have two potential H's attached to them, i.e. these are all
probably CH2's. See if they are of sufficient height (account for significant electron
density) by checking the Q atoms against the list above or by holding the cursor over
them and reading the height of the peak one by one as before. As an alternative to
opening the md1_s.res file with a text editor you can also look at the Q atom list using
SHXG. Do this by clicking on Model > List Q-peaks which will bring a window up
looking like Fig 2.21.
Fig 2.21
Using this menu select those that are probably H atoms, i.e. Q1 to Q10 and click OK.
Notice that the molecule in SHXG is much clearer now (Fig 2.22).
Fig 2.22
Lets now insert the H atoms that we know into the structure or model. There are two
ways of doing this. One way is to change the Q labels to H labels directly. Never do
this unless you have a good reason2. Instead lets tell SHELXL to geometrically
calculate the positions for these H atoms. Lets do the CH2's first but before doing this
lets check that the C-C distances associated with these atoms are typical of single
bonds - about 1.45 to 1.55 . To check a distance in SHXG click on C009 followed by
C011. At the bottom of the SHXG window you will see the distance 1.533 (Fig
2.23). Doing the same for C005-C009, C011-C006 and C006-C001 will confirm that
these are all single bonds.
Lets now add the H atoms. Click on C009, C006 and C011 then click on Model >
Add Hydrogen > Methylene Group. Ignore the warning that WinGX (in this case as
we know supposedly know what we are doing) and click OK. A new window will
appear (Fig 2.24).
2
H atoms are weakly diffracting and as a consequence it is very difficult to determine their true
position from an electron density map unless you know what you are doing. Exceptions to this occur
for structures that have been done at low temperature (-100 C or lower) and generally only when you
are looking at H atoms involved in H bonding. If you do this make sure that the Uij associated with H
atom is reasonable - no details here because if you know what you are doing then you know what
reasonable is. In addition, all H atoms of a certain type in a structure, e.g. O-H should have O-H
distances within 0.05 of each other. Always use calculated H positions when you have a heavy atom,
e.g. second or third transition metal or an iodine atom etc., in the structure.
Fig 2.23
Fig 2.24
The default settings will do. Once you are quite familiar with SHELXL you will know
if need to change these but usually the default values are correct. Click OK. The
"HFIXED" atoms will now appear green.
Lets now add the H atoms to the aromatic C atoms but first lets check to make sure
that the distances correspond to aromatic bonds. A typical distance for an aromatic C-
C bond (or one involved in conjugation) is 1.35 to 1.45 . Now measure C003-C004,
C004-C007, C007-C010, C010-C008 and C008-C002. Notice that they are typical of
conjugated bonds. Now lets add H's to these atoms. Click on C004, C007, C010 and
C008 followed by Model > Add Hydrogen > Aromatic C-H. You will notice that
the HFIX code is 43. This is correct so just accept the defaults again.
Now that we have made these changes let run them through SHELXL. Click on Save
INS file and close SHXG. Open the new md1_s.ins file with a text editor.
You will notice that SHXG has added the following lines to the ins file:
HFIX 23 -1.20 C006 C009 C011

HFIX 43 -1.20 C004 C007 C008 C010
This is the actual instruction that SHELXL will be given to do what you requested
above. However, the addition of H atoms to a structure is temperature dependent. IN
other words the C-H distance that SHELXL uses is dependent on the temperature at
which the collection is done. To find out what this temperature was open the
md1_s.pcf file with a text editor. The following line tells you that the data collection
was done at 293 K:
_diffrn_ambient_temperature 293(2)
Lets now tell SHELXL what the data collection temperature was. To do this first
convert the above temperature to Celsius which in this case is 20 C. Now type the
following line as a new line into the ins file anywhere between the UNIT and FVAR
lines:
TEMP 20
Now save you changes and close the ins file. Now run this file through SHELXL -
click Refine > SHELXL-97. Notice that R1 has now dropped to about 7.3 %. Close
the SHELXL window and open SHXG again. Opening the res file using ORTEP-3
yields the ORTEP shown in Fig 2.25.
Fig 2.25
Notice that ellipsoid or ADP (atomic displacement parameter) around C001 is still
significantly smaller than most of the other C atoms. If you look at your SHXG
window you will notice that C002 is also suspicious as no residual peak
corresponding to a H atom is present. Is this perhaps also a N atom. Well lets place
the N atoms one by one.
Click on C001. Now right click on it. A new window will appear (Fig 2.26).
Fig 2.26
Change C001 to N1 and click OK followed by Save INS file. If we are correct R1
should drop when we run SHELXL. Run SHELXL. Note that R1 is now 6.2 % so our
guess has been correct. The ORTEP diagram at this stage is shown in Fig 2.27.
Fig 2.27
Notice that the size of the ADP around N1 is more like those around it. Lets see if
C002 is also an N atom. If you check SHXG you will see that there is still no residual
peak next to C002.
Measure the C002-C003 and C001-C008 distances. For convenience you can switch
off the Q-peaks (uncheck Display Q-peaks). You will see that the distances are about
the distance of a C=C bond (about 1.30 - 134 ). However, a C=C=C system will be
linear and not bent like C008-C002-C003. It is therefore very probable that you have
a C-N=C system here. Lets therefore relabel C002 to N2 and run SHELXL as we did
for N1. R1 will now be about 4.4 % so this too has been a good decision. The ORTEP
diagram for this molecule is shown in Fig 2.28.
Fig 2.28
As you can see everything in Fig 2.28 looks chemically sensible so the structure is
just about refined but we still have to make the structure suitable for publication. To
do this we need to apply a sensible labeling scheme. Do this by following steps:
1. Delete all the H atoms but remember what types were where - select all of
them and then click Delete > Selected Atoms, or click Delete > All Type... >
H atoms.
2. Relabel all the C atoms by selecting C005 C009 C011 C006 C003 C004 C007
C010 C008 in that order. Right click in the cyan area. A new window will
appear (Fig 2.29). In the New names text area type the replacement labels C1
C2 C3 C4 C5 C6 C7 C8 C9 and click OK (in you structure you can choose
you own labeling system but make sure that it looks systematic). The new
labels will now appear in SHXG. If you make a mistake in the labeling
sequence just left click then right click on those atoms one by one and change
their labels.
3. Now add the H atoms again, i.e. CH2 H's on C2, C3 and C4 and aromatic H's
on C6, C7, C8 and C9. Do this the way you were shown earlier.
4. Now close SHXG and refine the structure as you have seen before. Don't
forget to save the new ins file before exiting SHXG.
Fig 2.29
After refining the structure you will get a R1 of about 4.4 %, i.e. no real change. The
ORTEP diagram at this stage is shown in Fig 2.30.
Fig 2.30
2.4 Preparing the structure for publication
Very nice (or pretty) picture but will the structure be publishable as is? In other words
are there changes that we might need to make to the structure refinement or data to
make it publishable.
To test this we need to run a program which is designed to check for problems with
structure solutions. This program is called PLATON. However, before you use
PLATON you need to create a file summarizing your current results. The format
which is currently the standard is the CIF format (Crystallographic Information
Format). Though you have been refining your structure you will see that no file exists
with a cif extension in your current working directory. To get SHELXL to create it you
will need to do the following. Open SHXG and save the current res file as a ins file
(just click Save INS file). Now open md1_s.ins in a text editor and type in the
following lines:
OMIT -2.00 180.00

ACTA
CONF
HTAB
BOND $H
If the ins file contains an OMIT line then just replace it with the one above. Make sure
that only one OMIT line exists. OMIT as defined above tells SHELXL to omit any
reflections with a negative signal to noise ratio of less than minus two (yes you can
get these from the data reduction programs) from our next refinement, i.e. any peak
with a I/I ratio greater than -2 will be included in our next refinement. By the way
OMIT line in the beginning of a structure refinement process (e.g. at the beginning of
the refinement of this structure) is usually defined as:
OMIT 4 180
In other words we were telling SHELXL until now to ignore reflections that did not
have a I/I ratio higher than 4. One of the reasons this is done is that it speeds up the
structure solution process as SHELXL ends up working on much less than the full data
contained in the hkl file.
The second number in the OMIT line simply tells SHELXL that we want all the data
from a diffraction angle point of view - 180 (180) implying that the X-rays are being
diffracted back to the X-ray source. In reality this does not happen and a more
realistic value is anywhere from 50 (the minimum you should use as this is an ACTA
or structure refinement requirement) to about 70 depending on the quality of your
data. At WITS we tend to collect data so that it is 100% complete to 0.75 resolution
which is more than good enough for standard data collections. In our case the last
number is therefore anywhere between 50 (the minimum acceptable) and 56-57 (the
maximum complete data range of our data collection).
The next line (ACTA) tells SHELXL to generate a cif file. SHELXL will not generate a
cif if you have an OMIT line other than the above, i.e., OMIT must be written as
OMIT -2 or -4 or -1 even 0 might work but it cannot be greater than 0.
CONF tells SHELXL that you want bond lengths and angles.
HTAB tells SHELXL that you want a list of hydrogen bonds if they exist. These are
listed in the lst file (as in shelxl.lst in the case of WinGX).
BOND $H tells SHELXL that you want a list of bond lengths including those to H
atoms (hence the $H).
For more information on these commands take a look at the SHELXL manual.
Once you have added all this information into the ins file save it and refine the
structure again. You will see that R1 is still about 4.4 %. In addition you will notice
that there are two new file in your work directory: md1_s.cif and md1_s.fcf. For now
ignore the fcf file except that you should know that it contains you hkl data in CIF
format and is required by the PLATON program to fully determine the quality of your
data and structure refinement.
Let's now do the actual validation of our current structure. We are going to do this the
"hard" way by running a PLATON externally of WinGX3. The reason that we are
doing it this way is to make you realize that PLATON is actually a separate program
which WinGX can run for you. To run platon double click on your PWT icon (PWT is
a toolbar for PLATON; Fig 2.31)
3
To run the PLATON validation program from within WinGX click on Publish > Validate CIF >
Platon Validate in the WinGX toolbar. However, you will need to install PLATON as suggested by the
WinGX program just read the error message properly and follow its instructions.
Fig 2.31
At this point a new window should appear (Fig 2.32).
Fig 2.32
You now need to tell PWT which data it should work on. Click on the open folder
icon (Fig 2.33) or File > Select Data File and select the newly created CIF file
(md1_s.cif in this case).
Fig 2.33
Now click on the tick icon (Fig 2.34) or click on Publish > CIF VALIDATE which
will run the actual structure validation program.
Fig 2.34
A window containing the following output (for brevity I have omitted some of the
information below this) is obtained after running the PLATON validation command:
#==============================================================================#
# PLATON/CHECK-(220505) versus check.def version of 220305 for entry: md1_s
# Data From: md1_s.cif - Data Type: CIF Bond Precision C-C = 0.0031 A
# Refl Data: md1_s.fcf - Data Type: SHELXL
#
# Cell 6.8504(8) 7.3247(9) 9.5740(11) 87.965(2) 85.299(2) 64.705(2)
# WaveLength 0.71073 Volume Reported 432.87(9) Calculated 432.87(9)
# SpaceGroup from Symmetry P -1 Hall: -P 1
# Reported ? ?
# MoietyFormula C9 H10 N2 S
# Reported ?
# SumFormula C9 H10 N2 S
# Reported C9 H10 N2 S
# Mr = 178.26[Calc], 178.25[Rep]
# Dx,gcm-3 = 1.368[Calc], 1.368[Rep]
#Z = 2[Calc], 2[Rep]
# Mu (mm-1) = 0.315[Calc], 0.315[Rep]
# F000 = 188.0[Calc], 188.0[Rep] or F000' = 188.30[Calc]
# Calculated T limits: Tmin=0.000 Tmin'=0.000 Tmax=0.000
# Reported Hmax= 9, Kmax= 9, Lmax= 12, Nref= 2092 , Th(max)= 28.32
# Obs in FCF Hmax= 9, Kmax= 9, Lmax= 12, Nref= 2092 , Th(max)= 28.32
# Calculated Hmax= 9, Kmax= 9, Lmax= 12, Nref= 2149 , Ratio = 0.97
# rho(min) = -0.27, rho(max) = 0.29 e/Ang^3
# R= 0.0443( 1565), wR2= 0.1311( 2092), S = 1.008, Npar= 109
#===============================================================================
>>> The Following ALERTS were generated <<<

-------------------------------------------
Format: alert-number_ALERT_alert-type_alert-level text
052_ALERT_1_A (Proper) Absorption Correction Method Missing .. ?

053_ALERT_1_A Minimum Crystal Dimension Missing (or Error) ... ?
054_ALERT_1_A Medium Crystal Dimension Missing (or Error) ... ?
055_ALERT_1_A Maximum Crystal Dimension Missing (or Error) ... ?
093_ALERT_1_A No su's on H-atoms, but refinement reported as . mixed
122_ALERT_1_A No _symmetry_space_group_name_H-M Given ........ ?
#===============================================================================
029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.97
048_ALERT_1_C MoietyFormula Not Given ........................ ?
120_ALERT_1_C Reported SPGR ? Inconsistent with Explicit P-1
125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ?
199_ALERT_1_C Check the Reported _cell_measurement_temperature 293 K
200_ALERT_1_C Check the Reported _diffrn_ambient_temperature . 293 K
795_ALERT_4_C C-Atom in CIF Coordinate List out of Sequence .. C1
911_ALERT_3_C # Missing FCF Refl Between THmin & STh/l= 0.600 10
912_ALERT_3_C # Missing FCF Reflections Above STH/L=0.6 ...... 48
#===============================================================================
ALERT_Level and ALERT_Type Summary

==================================
6 ALERT_Level_A = In General: Serious Problem
9 ALERT_Level_C = Check & Explain
10 ALERT_Type_1 CIF Construction/Syntax Error, Inconsistent or Missing Data.

3 ALERT_Type_3 Indicator that the Structure Quality may be Low.
2 ALERT_Type_4 Improvement, Methodology, Query or Suggestion.
#===============================================================================
Explanation and Advice for the Reported ALERTS

================================================================================
As you can see by looking at the first line I ran a 22-05-05 version of PLATON with a
rule set (structure quality reference file check.def) dating back to 22-03-05. This is
important as the quality indicators for crystallographic analyses become stricter with
time so a newer version of either PLATON or check.def will probably yield more
alerts than the ones listed above. Looking at the validation output again you will see
that all sorts of structure information has been listed including R1 and GOOF. In
some places you will see the words Reported (or Rep) and Calculated (or Calc).
Reported indicates information that is obtained directly from your interpretation of the
structure, i.e., from the CIF file. Calculated indicates the equivalent information
determined from your atom coordinates, unit cell and space group information. With
some exceptions (usual when a structure is disordered) the Reported and Calculated
indicators should have identical information. If not you will have to fix these
discrepancies between your reported information and the calculated information.
The exact nature of the errors in md1 as we current have it is shown over the next few
lines. There are 6 level A and 9 level B alerts as defined in this version of check.def.
The format of each alert is as follows:
The reference number (052) leads you to a paragraph of information further down the
window (omitted in the above output but shown below) which gives you an indication
of how to solve this particular problem.
================================================================================
ALERT_052 Type_1 CIF Construction/Syntax Error, Inconsistent or Missing Data.
================================================================================
The treatment/method of absorption(correction) should be given explicitly.
This simply tells you that it very important to report (give explicitly) the type of
absorption correction carried out for this structure. I will describe the exact nature of
each of the alerts and how to solve them a little later. The next part of the alert
(ALERT_1_A) simply tells you that this is an A alert or as Platon has it In
General: Serious Problem. In this particular case it is not a serious problem but rather
a serious omission of experimental information. The final part of the alert gives you a
very short description of the problem: (Proper) Absorption Correction Method
Missing. Nothing new here.
Before going ahead and fixing all these alerts lets see if we can easily fix some of
them. You will find the following three alerts in every structure you solve and refine:
053_ALERT_1_A Minimum Crystal Dimension Missing (or Error) ... ?

054_ALERT_1_A Medium Crystal Dimension Missing (or Error) ... ?
055_ALERT_1_A Maximum Crystal Dimension Missing (or Error) ... ?
Obviously our cif file is missing its crystal size information. Looking at the extra
information associated with 053 yields the following:
================================================================================
ALERT_053 Type_1 CIF Construction/Syntax Error, Inconsistent or Missing Data.
================================================================================
The smallest crystal dimension should be supplied in the CIF.

The expected value should be a real number (i.e. not 0.35mm)
If you open the md1_s.cif file in an editor and look for the following lines you will
understand the problem, i.e., instead of crystal size information you have ? symbols.
This means that cif file is incomplete and hence triggers an error.
_exptl_crystal_size_max ?
_exptl_crystal_size_mid ?
_exptl_crystal_size_min ?
Lets solve this easy problem. Close any validation related windows. Now open SHXG
and save the current res file as an ins file (by clicking the Save INS file button). Now
open md1_s.ins and md1_s.pcf (a file containing some experimental details
information that should have been given to you by your crystallographer). In the pcf
file you will find the following three lines as well as other experimental data including
collection temperature and crystal description:
_exptl_crystal_size_max 0.38
_exptl_crystal_size_mid 0.18
_exptl_crystal_size_min 0.09
Given this information there are three ways to get rid of the crystal size alert that we
are currently have. You could replace the equivalent lines in md1_s.cif with these, you
could use a program called ciftab (in WinGX you would click on Publish > CIF
TABLES) or you can use a SIZE card in the ins file. We will see how ciftab works in
a next few pages. In the meantime lets use what I consider to be the easiest method.
Insert the following line into your ins file near the top of the file but below the SFAC
line but above the atom lines:
SIZE 0.38 0.18 0.09
Now close the ins file (and the pcf file if you want) as well as SHXG and refine the
structure again. In terms of R1 and other statistics nothing much will change however
a brand new cif file will be created. Now run the new cif file through the Platon
validation command as explained earlier. The output from the program should look
like the following:
#==============================================================================#
#
# Cell 6.8504(8) 7.3247(9) 9.5740(11) 87.965(2) 85.299(2) 64.705(2)
# Reported ? ?
# Reported ?
# Mr = 178.26[Calc], 178.25[Rep]
# Dx,gcm-3 = 1.368[Calc], 1.368[Rep]
# Mu (mm-1) = 0.315[Calc], 0.315[Rep]
# Reported T limits: Tmin=0.890 Tmax=0.972 '?'
# R= 0.0444( 1565), wR2= 0.1329( 2092), S = 1.076, Npar= 109
#===============================================================================

-------------------------------------------

#===============================================================================
795_ALERT_4_C C-Atom in CIF Coordinate List out of Sequence .. C1
#===============================================================================
As you can see the alerts related to the crystal dimensions are now gone. There are
however two alerts that require the use of shelxl to sort them out - alerts 029 and 795.
Alert 029 simply tells us that the data that was collected is 97% complete up to an
angle of 28.32 (see the calculated and reported HMAX lines in the report above).
Ideally the data should be 100% complete up to the chosen collection angle though
this is often not possible, especially if the crystal was a bad diffractor (due to
insufficient size or crystal quality or due to extensive molecular disorder within the
crystal) or if the material crystallizes in a triclinic space group (really only a problem
on 3 circle diffractometers like we have especially if the crystal was mounted on a
unit cell axis). The minimum cut off angle is 25 below which you will have to
explain why the crystal was unable to diffract normally.
Alert 795 tells us that we have not sorted our atoms, i.e., we do not have a logical
sequence of atoms in our cif file (and ins and res files).
Lets now get rid of these two problems. Open SHXG and click on Model > Sort
Atom List. This simply organizes your atom list so that the atoms are arranged in
sequence, i.e. C1 C2 C3 C4 etc. You might want to look at your ins file before and
after doing this just to see the change. Now click on the Save Ins Button and close
SHXG. In some structures you might want to sort the atoms before adding your
hydrogen atoms as these sometimes confuse the sorting algorithm especially if the
structure contains disorder. Open the ins file in a text editor and alter the OMIT line to
the following:
OMIT -2 56
The 56 simply tells SHELXL that we want to limit the range of the data we use for our
refinement to 28 (or 56 2). If you were paying attention while in SHXG you
would have noticed that it was quite difficult to see your structure through all the Q
peaks (you might want to open SHXG to check this now but do not save anything or
you will change the ins file you are busy editing). Since the structure is refined we
really do not need so many extra peaks. There change the PLAN line to the following:
PLAN 5
This instructs SHELXL to only give us the 5 highest residual peaks from the
difference Fourier map. Now save the ins file and run SHELXL.
Now run the cif file through Platon validation algorithm as before. The output from
the program should look like the following:
#==============================================================================#
#
# Cell 6.8504(8) 7.3247(9) 9.5740(11) 87.965(2) 85.299(2) 64.705(2)
# Reported ? ?
# Reported ?
# Mr = 178.26[Calc], 178.25[Rep]
# Dx,gcm-3 = 1.368[Calc], 1.368[Rep]
# Mu (mm-1) = 0.315[Calc], 0.315[Rep]
# R= 0.0442( 1547), wR2= 0.1322( 2047), S = 1.078, Npar= 109
#===============================================================================

-------------------------------------------

#===============================================================================
#===============================================================================
As you can see alert 795 has now gone but alert 029 is still present. This shows that
we have to further limit the range of the data we use for the refinement. To do this
simply open SHXG (notice that there are now only 5 Q peaks) and save the res file as
an ins file (click on the Save Ins Button). Now close SHXG and change the OMIT
line in the ins file to the following using a text editor as before:
OMIT -2 54
We are now limiting the range of the data used in the refinement to 27 . Now save
the file and refine the structure as before. Running Platon Validation should give you
the following output:
#==============================================================================#
#
# Cell 6.8504(8) 7.3247(9) 9.5740(11) 87.965(2) 85.299(2) 64.705(2)
# Reported ? ?
# Reported ?
# Mr = 178.26[Calc], 178.25[Rep]
# Dx,gcm-3 = 1.368[Calc], 1.368[Rep]
# Mu (mm-1) = 0.315[Calc], 0.315[Rep]
# R= 0.0430( 1463), wR2= 0.1308( 1863), S = 1.111, Npar= 109
#===============================================================================

-------------------------------------------

#===============================================================================
#===============================================================================
As you can see the 029 alert has now disappeared. Also, the following alerts can be
ignored:
Alerts 199 and 200 these can be ignored in this case as the data collection was
carried out at 20C. You can even check by read the following line in the md1_s.pcf
file:
_cell_measurement_temperature 293(2)
Also, alerts 911 and 912 can be ignored as there is nothing that can be done about
them at this stage. These simply tell you that some reflections (data) are missing - 10
below theta min and 18 in our data collection range. This is quite common for low
symmetry systems such as triclinic unit cells (see unit cell parameters in the output).
The remaining alerts can be dealt with by simply editing the cif file. If you open the
cif and pcf files in an editor you will find that the following information (amongst
others) is absent in the cif file:
_symmetry_cell_setting ?
_symmetry_space_group_name_H-M ?
_exptl_crystal_description ?
_exptl_crystal_colour ?
_diffrn_measurement_device_type ?
_diffrn_measurement_method ?
but present in the pcf file:

_symmetry_cell_setting 'Triclinic'
_symmetry_space_group_name_H-M 'P-1 '
_exptl_crystal_description 'Flat plate'
_exptl_crystal_colour 'Colourless'
_diffrn_measurement_device_type 'CCD area detector'
_diffrn_measurement_method 'phi and omega scans'
Notice that the title in the cif file is data_md1_s while in the pcf file its data_md1_m.
Now close these two files. We are now going to use a program called ciftab to copy
the missing data from the pcf file into the cif file.
To do this click on Publish > Cif Tables. The following window will appear:
Fig 2.35
To use my method of completing a cif file click on No. The following window will
now appear:
Fig 2.36
As you can see the default procedure at this point is to use another CIF file to resolve
? items. This is what we want at the moment as it will do exactly what we want.
Now click on OK. This will open the following window:
Fig 2.37
Now delete archive.cif (just click on the back space button), type in md1_s.pcf (our
reference file) and click OK. The program now asks if we are sure that we want to use
this particular pcf (reference) file (Fig 2.38). Notice that the title comes from the pcf
file.
Fig 2.38
Clicking on Yes leads to a new window requesting the name of the cif file we want to
alter (Fig. 2.39).
Fig 2.39
Since the program has correctly selected the cif file we want to edit simply click OK
which will lead to the following window:
Fig 2.40
Clicking on the Yes button will now copy the missing information from the pcf file to
the cif file. This will now bring you back to the main ciftab menu (Fig 2.41).
Fig 2.41
At this point we are done with ciftab as we need to use the platon validation program
to make sure that our cif file is now as free of alerts as possible. Therefore select Quit
and click OK. If you want you can now check the cif file to see what lines were
edited.
NB: ciftab will only replace lines with ? marks with data (if available) but will
not touch any lines already containing data. This is sometimes a problem if the
information in the cif file is wrong and needs to be replaced by correct
information contained in the pcf or some other file.
Lets now use Platon validate to see how many alerts remain. Doing this will lead to
the following output:
#==============================================================================#
#
# Cell 6.8504(8) 7.3247(9) 9.5740(11) 87.965(2) 85.299(2) 64.705(2)
# Reported P-1 ?
# Reported ?
# Mr = 178.26[Calc], 178.25[Rep]
# Dx,gcm-3 = 1.368[Calc], 1.368[Rep]
# Mu (mm-1) = 0.315[Calc], 0.315[Rep]
# Reported T limits: Tmin=0.890 Tmax=0.972 'NONE'
# R= 0.0430( 1463), wR2= 0.1308( 1863), S = 1.111, Npar= 109
#===============================================================================

-------------------------------------------

#===============================================================================

#===============================================================================
Notice that only alerts 093, 048 and 125 remain. These require direct editing of the cif
file. Open the cif file using a text editor.
Alert 093 simply tells us that we have calculated all our H-atom positions and not
placed any from the Fourier difference map. Calculating all the H-atom positions is
the normal method of refining a structure with data collected using X-ray diffraction.
One might sometimes place H-atoms involved in H-bonding if the data is very good
and the resulting Uiso (no more than 1.5X that of the parent atom) and O-H (or N-H)
bond length values reasonable.
Therefore to get rid of this alert change the following line in the cif file:
_refine_ls_hydrogen_treatment mixed
to:
_refine_ls_hydrogen_treatment constr
Constr simply informs anybody reading the cif file that we constrained (calculated)
the H-atom positions in this structure rather than using a mixture of calculated and
located positions (mixed).
Alert 048 tells us that the moiety formula is missing in this structure, i.e., there is a
? at the end of the following line:
_chemical_formula_moiety ?
If you look at the validation output above you will see that a line containing the
following information is present:
This tells you what the molecular formula is. If the structure also had one solvent
molecule (such as benzene) per molecule then the molecular formula would be C9
H10 N2 S, C6 H6 while the sum formula would be C15 H16 N2 S. Now change
the moiety formula line as suggested by Platon to:
_chemical_formula_moiety C9 H10 N2 S
Alert 125 tells us the Hall symbol (a type of space group symbol) is missing from the
cif file. This has to be inserted in the cif file the long way. You will need to type in the
following line directly below the _symmetry_space_group_name_H-M P-1
line:
_symmetry_space_group_name_Hall -P -1
This information is obtainable directly from the validation output given above:
Also, notice that the Hall symbol contains a space within it: P 1. When putting a
piece of information containing a space within it use single quotes () to indicate the
boundries of the information, i.e., write it as -P 1 as give above. NB that the
following method using two semicolons (;) is also acceptable though not very
efficient unless you need to write a lot of information:
_symmetry_space_group_name_Hall
;
-P 1
;
You can now save your changes and close the cif file. Run the Platon validation
program again. This will lead to the following output:

-------------------------------------------

#===============================================================================
Notice that all the alerts that can be fixed have disappeared. The structure refinement
is now complete and is ready to be reported in a paper or thesis. Take note that
running SHELXL now will destroy your cif file making it necessary to reedit your cif
file all over again.
To publish the structure in a IUCr journal such as Acta-C or E you will also need to
add the appropriate information into the following lines:
_cell_measurement_reflns_used ?
_cell_measurement_theta_min ?
_cell_measurement_theta_max ?
This comes from the *._ls file but will only be explained in the next section. At this
point all the information related to the crystal structure and its refinement is given in
the cif file. Though it is possible to read things such as bond lengths directly from this
file it would be easier to convert this into human readable form.
To do this we will need to use ciftab again. In WinGX click on Publish > CIF
TABLES. This will bring up the following window:
Fig 2.42
As before click No. This will bring up the following window:

Fig 2.43
Since we now want a human readable file click on Crystal/atom tables from .CIF
followed by OK. This will lead to the following window:
Fig 2.44
Let us create a MS-WORD compatible file. Click on Rich Text Format for
MS-WORD/Angstrom units as well as anything in the list below that does not have
the word Selected in it as follows:
Fig 2.45
Clicking on OK leads to the following window:
Fig 2.46
This simply confirms that we want to tabulate the information from the cif file
containing the title data_md1_s. Clicking on Yes leads to the following window:
Fig 2.47
This obscure message occurs whenever the structure does not contain any H-bonding
tables as in this case. In the next structure (a sugar) I will show you what happens
when this information is present. Click OK as this is nothing more than a piece of
information. You will now get the following window back:
Fig 2.48
Click on Quit followed by OK as we have now finished. If you check your data
directory you will find a file called md1_s.tex. Rename (right click and select rename)
this file to md1_s.rtf. At this point interesting things happen depending on the
operating system you are using. If you are using windoze2000 or older you can
simply open the file using wordpad (right click and select Open With > Wordpad or
Choose program) and everything will work directly. You can now save the file in
MS-word format (.doc): File > Save As. Select Word for Windows 6.0 as the file type
and change the output extension to .doc as follows:
Fig 2.49
You can now open md1_s.doc in MS-word and edit as required. If you are using
windoze-XP as your operating system then you will probably have to use MS-office
directly as this seems to work (though it does not seem to work in windoze2000).
If you now look at the contents of the doc file you will see that it contains several
tables. Table 1 lists crytal data and refinement information. Table 2 lists the structure
atom coordinates. Tables 3 and 6 list the bond lengths, bond angles and torsion
angles.
At this point apart from pictures only one piece of information is missing and that is a
description of how the structure was solved and refined. Here is a description for the
current structure:
*******************************************************************
Crystal structure solution and refinement
Intensity data were collected on a Bruker SMART 1K CCD area detector

diffractometer with graphite monochromated Mo K radiation (50kV, 30mA). The
collection method involved -scans of width 0.3. Data reduction was carried out
using the program SAINT+ (Bruker, 1999a).
This simply explains how the crystallographer collected the data. You should get this
from your crystallographer. This is however a typical collection at WITS.
The crystal structure was solved by direct methods using SHELXS (Sheldrick, 1997).
Non-hydrogen atoms were first refined isotropically followed by anisotropic
refinement by full matrix least-squares calculations based on F2 using SHELXL
(Sheldrick, 1997). Hydrogen atoms were first located in the Fourier difference map
then positioned geometrically and allowed to ride on their respective parent atoms.
Diagrams and publication material were generated using CIFTAB (Sheldrick, 1997)
and PLATON (Spek, 2003).
You are responsible for this section. It simply explains how the structure was solved
and refined.
References
Bruker (1999). SAINT+. Version 6.02 (includes XPREP and SADABS). Bruker AXS Inc.,
Madison, Wisconsin, USA.
Sheldrick, G. M. (1997). SHELX97. Release 97-2 (includes SHELXS97, SHELXL97,

CIFTAB). University of Gttingen, Germany.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.
*******************************************************************
If you are interested to find out how one might write up this structure you might want
to download the paper in which this structure was published:
Datt, M.S., de Koning, C.B., Fernandes, M.A. & Michael, J.P. (2004). Acta Cryst.
E60, o2298-o2300.
The paper can be downloaded directly from the IUCr site:

http://www.iucr.org
Due to the lack of hydrogen bonding and other interesting weak interactions you will
see that the discussion of the structure was kept very simple. This is not necessarily
the only way to discuss this structure but is at least one way of doing so.
Chapter 3: Drawing simple diagram of your crystal structure
At this point you will probably want to generate some pictures. Here the use of
ORTEP-3 and Platon for this purpose will be shown. For now we will ignore Mercury
as its use is quite intuitive. Perhaps all you need to know is that it is possible to cut
and paste pictures directly from Mercury to MS-word if you need them for a quick
report. It is also possible to delete and add molecules to the diagram you are creating
and show some feature of interest.
3.1 Getting started
For this section it is assumed that you have installed ORTEP-3, Platon, Ghostview
and though not really required Povray. These programs can be downloaded from the
websites listed on Page 2 of this manual.
It is also assumed that you have completed the structure that was refined and solved in
the previous chapter md1_s. Though we are going to be using the completed cif file
of this structure for all our drawings it is often possible to do the exact same thing
using the final res and ins files. Just select these if you want to use them instead of the
cif file.
3.2 Using Platon to generate diagrams
Platon is an extremely easy program to use for diagrams. Though the diagrams are
not always the best looking you will take almost no time to generate most of them.
Though Platon can output diagrams in various formats my personal favourite is
postscript. Postscipt is a vector format (if you know what that means) which can be
loaded into programs such as CorelDraw and edited. You might want to use
CorelDraw to change the thickness or colour of the lines or perhaps add or remove
some labels. However, you should understand that you cannot change the orientation
of the molecule in a diagram once you save it in its parent program. This should be
obvious but I get asked this at least once a year usually by somebody thinking that
altering a picture will only take a second or two. Grumble Grumble. Keep in mind
that a diagram is a 2D object while a structure is a 3D object. It is therefore

impossible to manipulate a picture like a 3D structure.
To run Platon double click on your PWT icon (Fig 3.1) to get the Platon toolbar
going.
Fig 3.1
At this point a new window should appear (Fig 3.2).
Fig 3.2
You now need to tell PWT which data it should work on. Click on the open folder
icon (Fig 3.3) or File > Select Data File and select the CIF file (md1_s.cif) you
created in the previous chapter.
Fig 3.3
Though PWT offers several short cuts to drawing pictures we will be using the general
route to these routines. Click on the hammer and square icon (Fig 3.4).
Fig 3.4
This will bring up a window with most of the possible Platon routines (Fig 3.5
shown with colours reversed to save ink). In this chapter we will only be using the
PLUTONauto and ORTEP/ADP routines.
Fig 3.5
For now go and lets make a stick diagram of our molecule. Click on PLUTONauto.
The following window will appear:
Fig 3.6
As you can see the Fig 3.6 is composed of a plotting area containing the molecule, a
prompt (shown by >> which can be used if you know any commands) and a menu
bar of the right.
At the moment you can see that the picture is surrounded by information. If you were
to save the picture now this information would be saved too. To see the effect of this
lets save a picture. Click once on the EPS button in the right menu bar. This will save
the picture in a file called md1_s.ps.
To remove this information click on the Decoration button. Again click on the EPS
button. This will append this picture into the md1_s.ps file above.
At the moment the picture is shown in colour and will be saved in colour. If you want
to save a picture in black & white click on the Col button. If you click on the Eps
button then this picture will be saved. Change the plot area back to colour using the
Col button.
Now lets alter the size of the labels. Click on one of the small notches below the
LabelSize button. Clicking more towards the right produces larger labels.
To move the molecule around click on either the RotX, RotY or RotZ buttons.
There are other options that can be accessed to do display other types of diagrams. To
access these play around with the OptionMenus button by clicking one of the small
notches below.
As you can see most things are obvious in the menus and with some experimentation
you will become used to them.
Lets now return to the main Platon routines window (Fig 3.5) by clicking on the End
button.
We are now going to create an ORTEP diagram. Click on ORTEP/ADP button. The
following window will appear:
Fig 3.7
As the decoration shows the ellipsoids are currently drawn at the 50% probability
level (PROBA= 50). To change this simply choose the probability level you want by
clicking on one of the notches in the Probability button. You can also change the
label size by clicking on the LabelSize button. You might also want to move, delete
and reinsert some of these labels by using the MoveLabel, DeleteLabel and
IncludLabel buttons.
At some point save one or two of your pictures by clicking on the b&w-EPS or
EPS-col buttons. At this point you can exit from Platon by clicking on the Exit
button.
You should now see the newly created .ps file (md1_s.ps in this case) in the directory
containing your cif file. NB: unless you do intend to overwrite this file always
rename it to something else as Platon will simply destroy it if you restart it. If you
have installed ghostview correctly you should simply be able to double click on the
file which will automatically start ghostview (Fig 3.8).
Fig 3.8
If the diagram is not correctly orienated click on Orientation > Landscape. You will
sometimes also have to click on Swap Landscape. To insert the picture into a word
document simply cut and paste it as usual (use the Edit menu or Ctrl-c). An example
is shown in Fig 3.9.
Fig 3.9
Sometimes the resolution of these pictures are low. If this is the case in some of your
pictures simply click on the button containing a magnifying glass and + sign a few
times before copy and pasting the picture into word.
Sometimes you may need to convert the picture into a jpeg or gif format. To do this
click on File > Convert and select the options you need. If you need to convert the .ps
file into a .eps file click on File > PS to EPS. If you have saved more than one picture
then use the arrows to navigate through them. If you need to extra one of these
diagrams click on File > Extract.
There are also times when one needs to edit a picture internally. The easiest way to do
this is to use CorelDraw 8 or above (Fig 3.10).
Fig 3.10
3.3 Using ORTEP-3 to generate diagrams
Like Platon ORTEP-3 is easy to use. However, it too has some quirks that you will
have to get used to. To open a structure in this program either drag and drop a cif file
(md1_s.cif in this case) onto the ORTEP-3 icon on your desktop (Fig 3.11) or start
ORTEP-3 and use the usual File>File Open.
Fig 3.11
The following window should appear (Fig 3.12):

Fig 3.12
To rotate the molecule either click on the icons on the top of the window or use the
arrow keys ( ). The rate of rotation is can be changed by changing the value in
the Rotation text box (top right).
Like Platon the best way to save a picture is as a postscript file (File>
WritePostscriptFile> Colour or Monochrome) which can be altered in Ghostview
or CorelDraw as you see fit.
In general the program is quite intuitive and is best learned by use. There is however
one feature that is really great for those who love graphics (hence the reason I wrote
this section). If you click on File >Write POV-ray File the following window will
appear:
Fig 3.13
By changing parameters in the ATOMS, BONDS and GENERAL sections you can
alter the look of the final picture. Clicking on OK produces a file called
ORTEP001.POV in your data directory. If you installed PovRay correctly then simply
double clicking on the file will bring up the PovRay window (Fig 3.14).
Fig 3.14
Clicking on Run produces an output screen showing you the rendering process
(Fig 3.15) as well as a file in your work directory. To change the resolution of the
picture made alter the resolution in the text box in the top left (shown as [512x384,
No AA] in the Fig 3.14).
Fig 3.15
PovRay is really powerful if you learn to use it. Though I am able to use it reasonably
well I hate the program because good results often take some effort to obtain. Often it
is just not worth it. In addition, the occasional ORTEP-3 bug will produce a slightly
damaged .POV file which you then have to edit so that PovRay will display it
properly. This is really annoying. If however you have the time or need some fancy
pictures you will probably have to learn how to use the PovRay scripting language to
use it properly. Luckily it is not difficult to learn. In addition, PovRay is unable to add
labels to your diagram. As a consequence you will have to add them by editing the
created picture using another program such as CorelDraw.
Chapter 4: Solving the crystal structure of sucrose generating hydrogen

bonding tables
In this chapter you will be solving the crystal structure of sucrose as in the stuff you
put into your coffee (e.g. Huletts sugar actually this was the source of the crystal
for this example ). Since sucrose is capable of extensive hydrogen bonding this
chapter will really focus on the discovery and tabulation (in the CIF file) of these
hydrogen bonding networks. This is very important if you want to publish a paper in
Acta-C or E. In addition you will also learn how to use Mercury as a tool to find or
check various H-bonds in these networks.
4.1 Getting started
To carry out this exercise you will need to download the data from
http://www.gh.wits.ac.za/manuel/solving-xtals/struct2/sucrose.zip. Extract the data to
your computer. In this case I installed it to E:\GH8\solving-xtal\data\sucrose\soln\
but as before it does not really matter.
In this chapter I have assumed that you correctly and completely solved and refined
the example given in Chapter 2 (md1). As a consequence you will need to solve this
crystal structure yourself including making all the non-hydrogen atoms anisotropic
and adding hydrogen atoms (using calculated positions as before) to all atoms
requiring them. However, stop after you have relabeled the structure as given in
Figs 4.1 and 4.2. Since this is a light atom structure it is recommended that you solve
it using Direct Methods. Also, do not forget to check the data collection temperature
in the pcf file and include it in the refinement in Celsius before adding the H atoms -
check Chapter 2 if you have forgotten about this.
In short do the following:

1. Solve the structure using direct methods.
2. Refine all the atoms anisotropically.
3. Add H atoms in calculated positions. Use HFIX code 147 and not 83 when
adding the O-H hydrogen atoms. This code simply ensures that SHELXL will
rotate the H atom around the O atom unless the best fit to the electron density
map is found. If the data is good and the method reliable then this usually will
also be the correct H bonding orientation.
4. Relabel the structure as shown in Figs 4.1 and 4.2. Take especial care of the
O-H atom labels.
5. Sort the atom list.
Fig 4.1
Fig 4.2 Note the O-H labels

At this point your refinement should give you a summary window similar to Fig 4.3 -
note the 2.9% R-factor (R1). If your R-factor is more than 3.2% at this point then you
have probably done something wrong. If you have a Highest peak value greater than
0.5 e3 then you have probably mislabeled a O atom as a C atom or have missed and
H atom. Note the warning. If you remember how I solved it in Chapter 2 then do it
now if not dont worry.
Fig 4.3
4.2 Using the SHELXL HTAB command to generate H bond tables
At this point insert (or alter them if already present) the following lines into your ins
file:
OMIT -2.00 56.00
ACTA
CONF
HTAB
BOND $H
SIZE 0.30 0.30 0.19
TEMP 20.00
PLAN 5
You have seen most of these before (see Chapter 2). You should have already inserted
the TEMP instruction earlier. The PLAN 5 line simply tells SHELXL to give you the
positions of the five highest peaks. The default is 20. All the other instructions have
been previously described in Chapter 2.
The only instruction that is really interesting from an H bonding point of view is
HTAB. HTAB tells SHELXL that you want a list of hydrogen bonds if they exist.
These are listed in the lst file (as in shelxl.lst in the case of WinGX).
After you have inserted the instruction into your ins file save it and refine the
structure. Opening the shelxl.lst file with wordpad (or some other text editor) will
give you the following lines:
....
Hydrogen bonds with H..A < r(A) + 2.000 Angstroms and <DHA > 110 deg.
D-H d(D-H) d(H..A) <DHA d(D..A) A
O2-H2H 0.820 2.040 169.40 2.850 O11 [ x+1, y, z ]
O3-H3H 0.820 2.043 178.00 2.863 O9 [ -x, y-1/2, -z ]
O4-H4H 0.820 2.375 116.08 2.833 O8 [ x, y-1, z ]

O4-H4H 0.820 2.614 154.96 3.375 O6 [ -x, y-1/2, -z+1 ]
O6-H6H 0.820 2.044 164.31 2.842 O3 [ -x, y+1/2, -z+1 ]
O7-H7H 0.820 2.005 156.79 2.777 O2
O9-H9H 0.820 2.056 167.42 2.862 O10 [ -x-1, y-1/2, -z ]
O10-H10H 0.820 1.905 169.66 2.716 O7 [ x-1, y, z ]
O11-H11H 0.820 2.039 168.58 2.848 O5

....
Reading the first line of this table tells us that H atom H2H bonded to O2 is hydrogen
bonded to atom O11 which is at the symmetry position described by x+1, y, z, i.e. the
second molecule containing the O11 atom is related to the first by translation by one
unit cell along the a axis. The O2-H2H bond length is 0.82 , while the H atom to H
bond acceptor distance is 2.040 , and the H atom donor (O2 or D) and H atom
acceptor (O11 or A) is 2.85 . The D-H.A or O2-H2HO11 angle is 169.4. Note
that none of these have any error estimates. These will only be reported by SHELXL if
we instruct the program to list them for us specifically. Note also that all the D-H
distances are identical at 0.82 . This is a result of the H atom positions being
calculated rather than being determined from the difference Fourier map. By the way
2.6 to 3.0 are good DA distances for hydrogen bonding while 2.8 is a typical
DA distance for a O-HO hydrogen bond. If you look carefully you will see that
there is one very long DA distance 3.375 for O4O6.
Lets now use a program called Mercury to see if the H bond involving O2O11 and
O4O6 are real. To do this click on Graphics > Mercury on the main WinGX if you
set WinGX up correctly or drag and drop the cif (or res) file onto the Mercury icon on
your desktop. The following window should appear:
Fig 4.4
In this case I have replaced the original black of the drawing window with a lighter
color to save ink. To manipulate the molecule the following is useful to know:
1. Moving the mouse while pressing the left mouse button rotates the molecule.
2. Moving the mouse while pressing the middle mouse button translates the
molecule around.
3. Moving the mouse while pressing the right mouse button allows you to zoom
in or out of the structure.
Lets now check the hydrogen bonds of interest. Click on Label atoms (bottom of the
window), Style: Capped Sticks (top left) followed by H-bond (also bottom of the
window). After zooming in a little and manipulating the structure so that the
O2O11 H bond is easier to see leads to a picture similar to Fig 4.5.
Fig 4.5
Make sure that the Expand Contacts option is on in the Picking Mode section (top
right). Now click on O11 at the end of the O2O11 bond which will cause the rest of
the molecule connected to O11 expanded. Now select the Measure Distance option
in the Picking Mode section and click on the O2 and O11 atoms which will give you
a distance of 2.850 . You should now have a window resembling Fig 4.6.
Fig 4.6
From these quick checks it is obvious that the O2O11 hydrogen bond is real as the
following criteria are satisfied:
1. The H atom attached to the donor atom (O2) is correctly pointed at the lone
pair area of the acceptor atom (O11).
2. The O2O11 distance is reasonable at 2.850 .
3. The D-HA (O2-H2HO11) angle is above 120 (actually above 150 is
more ideal) which is also an important criteria.
At this point click on Reset followed by H-bond. After re-orientating the molecule,
expanding the O4O6 and O4O8 contacts as well as the and measuring the
distance between the Donor (O4) and acceptor (O6 and O8) atoms for each contact
followed by more reorientation and zooming in should give you a picture resembling
Fig 4.7.
Fig 4.7
The DA distances for the O4O6 and O4O8 contacts are 3.375 and 2.833 .
Usually 2.8 is a more typical DA distance for an H bond while 3.375 is much
too long for this kind of interaction. In this case H4H (the H atom attached to O4) has
the possibility of interacting with either O8 or O6. It is also possible to have a
situation where and H atom is involved in a bifurcated H-bond with two acceptor
atoms. However, in this case since the O4O8 distance is about 0.5 shorter than
the O4O6 distance I think that the O4O8 H-bond is real while the O4O6 bond
is not. It is unlikely that H4H is being shared by the two acceptor atoms (i.e. involved
in a bifurcated H-bond) as the DA distances differ too much. If the O4O6 and
O4O8 distances differed by less than 0.2 then I might have considered the
possibility of a bifurcated hydrogen bond.
As you can see H4H (attached to O4) appears to point more towards O6 than towards
O8. This sometimes happens (as in this case) if SHELXL is used to provide calculated
H atom positions. Quite simply it could not unambiguously determine the correct
orientation for this H atom. If we had perhaps had a data set collected at low
temperature (e.g. -100 C) then we might have been able to determine the position of
H4H directly from the difference Fourier map (the Q peaks in SHXG) and refined it
freely as we did for the non-H atoms. In this case though the D-HA angle is more
ideal for O4-H4HO6 (154.96 - see the shelxl.lst output shown a few pages back or
measure using Mercury) and much less ideal for O4-H4HO8 (116.08) I think that
this is simply due to the calculated position of H4H not being ideal. As a consequence
I still believe that the H bond involving O4O8 is real while the O4O6 is simply a
possibility.
In the same way you can check to see if all the other possible H bonds listed in
shelxl.lst are reasonable. With the exception of O4O8 and O4O6 which we
checked above I have simply assumed that if the DA distance is about 2.8 and
the angle above 150 the H bond is reasonable. In a real paper it is always a very good
idea to check before you report them.
Lets now get SHELXL to tabulate these H bonds in your cif file. At the moment if
you open your cif file in WordPad (or another editor) and scroll to the very bottom of
the file you will find the following information:
O1 C8 O8 C11 -102.14(10) . . . . ?
C7 C8 O8 C11 137.45(9) . . . . ?
C9 C8 O8 C11 14.55(11) . . . . ?
C12 C11 O8 C8 132.70(10) . . . . ?
C10 C11 O8 C8 8.24(12) . . . . ?
_diffrn_measured_fraction_theta_max 1.000
_diffrn_reflns_theta_full 28.00
_diffrn_measured_fraction_theta_full 1.000
_refine_diff_density_max 0.296
_refine_diff_density_min -0.287
_refine_diff_density_rms 0.060
As you can see there is no H bonding information. Lets correct this problem. Simply
save your current res file as an ins file using SHXG as before. Now open the ins file in
an editor and add the following lines below the UNIT line but above the FVAR line:
EQIV $1 x+1, y, z
EQIV $2 -x, y-1/2, -z
EQIV $3 x, y-1, z
EQIV $4 -x, y+1/2, -z+1
EQIV $5 -x-1, y-1/2, -z
EQIV $6 x-1, y, z
HTAB O2 O11_$1
HTAB O3 O9_$2
HTAB O4 O8_$3
HTAB O6 O3_$4
HTAB O7 O2
HTAB O9 O10_$5
HTAB O10 O7_$6
HTAB O11 O5
The EQIV lines simply assign a variable to each symmetry operator in our H bond
list. For example from now on if I type $1 at any point in the ins file SHELXL will
know that I want the x+1, y, z operator to be substituted there, i.e. O11_$1 is the
SHELXL and neater way of writing O11_x+1, y, z in this case. So to tabulate the H
bond given in the first line of the shelxl.lst:
O2-H2H 0.820 2.040 169.40 2.850 O11 [ x+1, y, z ]
You would write the following in the ins file:

EQIV $1 x+1, y, z
HTAB O2 O11_$1
The HTAB line reads as tabulate the H bond between O2 and O11 which lies at the
symmetry operator position defined by x+1, y, z. As you can see from the many
HTAB and EQIV lines above and on the previous page I instructed SHELXL to
tabulate all the H bonds in this structure with the exception of O4O6. It is also quite
obvious that since O7O2 and O11O5 do not have any symmetry operators that
there must be intramolecular H bonds - if you have more than one molecule in the
asymmetric unit then this may not always be the case. You can check using Mercury.
At this point save your ins file and run SHELXL. Your R-factor should not change at
all. However, if you have a look at the bottom of your cif file now you will find the
following:
O1 C8 O8 C11 -102.15(10) . . . . ?
C7 C8 O8 C11 137.46(10) . . . . ?
C9 C8 O8 C11 14.54(11) . . . . ?
C12 C11 O8 C8 132.70(10) . . . . ?
C10 C11 O8 C8 8.25(12) . . . . ?
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
O2 H2H O11 0.82 2.04 2.8497(19) 169.4 1_655
O3 H3H O9 0.82 2.04 2.8627(17) 178.1 2_545
O4 H4H O8 0.82 2.38 2.8327(19) 116.0 1_545
O6 H6H O3 0.82 2.04 2.842(2) 164.4 2_556
O7 H7H O2 0.82 2.00 2.7771(17) 156.7 .
O9 H9H O10 0.82 2.06 2.8620(19) 167.6 2_445
O10 H10H O7 0.82 1.91 2.7158(18) 169.7 1_455
O11 H11H O5 0.82 2.04 2.8477(19) 168.5 .
_diffrn_measured_fraction_theta_max 1.000
_diffrn_reflns_theta_full 28.00
_diffrn_measured_fraction_theta_full 1.000
_refine_diff_density_max 0.295
_refine_diff_density_min -0.287
_refine_diff_density_rms 0.060
As you can see a new table containing H bond information has been added. The
contents of the table are mostly self evident. However, there is one new feature and
that is the last field in most of the lines, e.g. what does 1_655 mean? To interpret
these you need to find the symmetry operators in the cif file (its about 50 lines from
the top):
loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-x, y+1/2, -z'
The first is referred to as symmetry operator 1 and the second as operator 2. In the
1_655 code the first number (1) refers to the first symmetry operator or x, y, z. To
understand the last three numbers you need to understand that the code is always
written as a deviation from 555 where the first 5 refers to the x operator, the second to
the y operator and the third to the y operator. Therefore 655 means that we add 1 to
the x operator while keeping the y and z operators constant. Looking at the following
should make this clear to you:
1_555 equals x, y, z
1_655 equals x+1, y, z
1_666 equals x+1, y+1, z+1
1_544 equals x, y-1, z-1
2_655 equals 1-x, y+1/2, -z

2_644 equals 1-x, y-1/2, -1-z
Though I have not mention it until now it is possible to do a lot of what we did with
Mercury using Platon use the PLUTONauto, CALC INTER and CALC HBOND
options.
Also, though I have not mentioned them until now Mercury has some very useful
tutorials that can be used to learn to use the program. These can be accessed
through the Mercury window by clicking on: Help > Tutorials. I highly
recommend doing Tutorial 1 and becoming familiar with the help section in
general.
We have now completed the refinement of this structure and now need to prepare the
cif file for publication. To do this simply run cif file through the Platon validation
program as was explained in Chapter 2. You get the following output similar to the
following:
#==============================================================================#
# PLATON/CHECK-(220505) versus check.def version of 220305 for entry: 6m_ma1_0s
# Data From: 6m_ma1_0s.cif - Data Type: CIF Bond Precision C-C = 0.0019 A
# Refl Data: 6m_ma1_0s.fcf - Data Type: SHELXL
#
# Cell 7.753(5) 8.696(5) 10.853(5) 90 102.948(5) 90
# SpaceGroup from Symmetry P 21 Hall: P 2yb
# Reported ? ?
# MoietyFormula C12 H22 O11
# Reported ?
# SumFormula C12 H22 O11
# Reported C13 H23 O12
# Mr = 342.30[Calc], 371.31[Rep]
# Dx,gcm-3 = 1.594[Calc], 1.729[Rep]
# Mu (mm-1) = 0.143[Calc], 0.155[Rep]
# Calculated Hmax= 10, Kmax= 11, Lmax= 14, Nref= 1841( 3455), Ratio= 1.88( 1.00)

# R= 0.0292( 3380), wR2= 0.0734( 3455), S = 1.042, Npar= 216, Flack= 0.3(5)
#===============================================================================

-------------------------------------------
035_ALERT_1_A No _chemical_absolute_configuration info given . ?

#===============================================================================
024_ALERT_4_B Merging of Friedel Pairs is STRONGLY Indicated . !
043_ALERT_1_B Check Reported Molecular Weight ................ 371.31
044_ALERT_1_B Calculated and Reported Dx Differ .............. ?
#===============================================================================
032_ALERT_4_C Std. Uncertainty in Flack Parameter too High ... 0.50
041_ALERT_1_C Calc. and Rep. SumFormula Strings Differ .... ?
066_ALERT_1_C Predicted and Reported Transmissions Identical . ?
068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)... ?
120_ALERT_1_C Reported SPGR ? Inconsistent with Explicit P21
147_ALERT_1_C su on Symmetry Constrained Cell Angle(s) ....... ?
222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.05 Ratio
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd. # 1
C12 H22 O11
#===============================================================================
The most annoying Alerts that have to be fixed are 024, 068 and 790.
O24 is self explanatory if you read the blurb further down in the validation output, i.e.
we need to insert the following line into our next ins file:
MERG 4
Alert 068 and 041 are related and simply tells us that I do not report the correct
number of atoms in the UNIT instruction of my ins file in other words the sum
formula as determined by the validation program does not agree with our current
formula. In general the program is correct but it does on occasion get it wrong. To fix
this simply click on Model > Cell Contents then click on Update UNIT card on the
right side of the window. Finish off by clicking on Apply changes followed by
Refinement > Run SHELXL. Click on yes when it asks if you want to save the ins
file. If you re-run Platon validate you will get something like the following:

#===============================================================================
024_ALERT_4_B Merging of Friedel Pairs is STRONGLY Indicated . !
#===============================================================================
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd. # 1
C12 H22 O11
#========================================================================
Note that the list is much shorter than before. However, Alerts 024 and 790 still have
to be sorted out. Alert 790 simply tells us that the molecule is not within the unit cell
of the structure. This is easy to see using Mercury. Start the Mercury as before and
click on Show cell axis. After some manipulation you should get something
resembling Fig 4.8. As you can see the sucrose molecule is not inside the unit cell but
instead translated backwards or in the negative a direction. Therefore to move the
molecule into the unit cell we will need to move it by one unit translation along the a
axis, i.e. add 1 to all the x coordinates. If you are bored and energetic do this now or
if you are lazy like me you can simply use the MOVE instruction. In SHELXL
MOVE is simply an instruction that allows one to add or subtract numbers from our
coordinates or invert the structure if required. To achieve the change we need simply
add the following line into our new ins file (after saving it as usual) just before the
first atom line, i.e. my the first coordinate line in my ins file looks as follows:
FVAR 0.46434
MOLE 1
C1 1 -0.014677 0.372376 0.299993 11.00000 0.01964 0.01699 =
0.01691 -0.00050 0.00444 0.00011
After adding the MOVE instruction as well as the MERG 4 instruction it now looks as
follows:
FVAR 0.46434
MERG 4
MOLE 1
MOVE 1 0 0 1
C1 1 -0.014677 0.372376 0.299993 11.00000 0.01964 0.01699 =
0.01691 -0.00050 0.00444 0.00011
Fig 4.8
MOVE 1 0 0 1 tells SHELXL that we want 1 to be added to the x coordinates while

nothing (0) will be added to the y and z coordinates. The last 1 tells SHELXL that we
dont want the structure to be inverted, i.e. we dont want our x y and z coordinates to
be multiplied by -1.
The top part of my new ins file now looks as follows:

TITL 6m_ma1_0s in P2(1)
CELL 0.71073 7.7530 8.6960 10.8530 90.000 102.948 90.000
ZERR 2.00 0.0050 0.0050 0.0050 0.005 0.005 0.005
LATT -1
SYMM - X, 1/2 + Y, - Z
SFAC C H O
UNIT 24 44 22
OMIT -2.00 56.00

EQIV $1 x+1, y, z
EQIV $2 -x, y-1/2, -z
EQIV $3 x, y-1, z
EQIV $4 -x, y+1/2, -z+1
EQIV $5 -x-1, y-1/2, -z
EQIV $6 x-1, y, z
HTAB O2 O11_$1
HTAB O3 O9_$2
HTAB O4 O8_$3
HTAB O6 O3_$4
HTAB O7 O2
HTAB O9 O10_$5
HTAB O10 O7_$6
HTAB O11 O5
FMAP 2
PLAN 5
SIZE 0.19 0.30 0.30
ACTA
BOND
BOND $H
CONF
WGHT 0.04940 0.06790
L.S. 4
TEMP 20.00
FVAR 0.46434
MERG 4
MOLE 1
MOVE 1 0 0 1
C1 1 -0.014677 0.372376 0.299993 11.00000 0.01964 0.01699 =
0.01691 -0.00050 0.00444 0.00011
AFIX 13
H1 2 0.036447 0.473243 0.327016 11.00000 -1.20000
AFIX 0
.. etc
If you now run a SHELXL refinement by clicking on Refine > SHELXL-97 in the
main WinGX window you will see the following error information in the output
screen:
By moving the molecule around in the structure we affected our H bond table
calculation since our molecule is no longer in its original position. The simplest way
to fix this is to reinsert an ordinary HTAB line into the ins file and refine the structure.
Simply add the following line into the ins file:
HTAB
After refining the structure you will find the following information in shelxl.lst file:
O2-H2H 0.820 2.041 169.08 2.850 O11 [ x+1, y, z ]
O3-H3H 0.820 2.043 178.32 2.863 O9 [ -x+2, y-1/2, -z ]
O4-H4H 0.820 2.379 115.66 2.832 O8 [ x, y-1, z ]

O4-H4H 0.820 2.610 155.81 3.375 O6 [ -x+2, y-1/2, -z+1 ]
O6-H6H 0.820 2.042 164.99 2.841 O3 [ -x+2, y+1/2, -z+1 ]
O7-H7H 0.820 2.005 156.77 2.777 O2
O9-H9H 0.820 2.055 167.78 2.862 O10 [ -x+1, y-1/2, -z ]
O10-H10H 0.820 1.906 169.50 2.716 O7 [ x-1, y, z ]
O11-H11H 0.820 2.042 167.28 2.847 O5
Based on the above information you will now need change the original EQIV lines
from:
EQIV $1 x+1, y, z
EQIV $2 -x, y-1/2, -z
EQIV $3 x, y-1, z
EQIV $4 -x, y+1/2, -z+1
EQIV $5 -x-1, y-1/2, -z
EQIV $6 x-1, y, z
To:
EQIV $1 x+1, y, z
EQIV $2 -x+2, y-1/2, -z
EQIV $3 x, y-1, z
EQIV $4 -x+2, y+1/2, -z+1
EQIV $5 -x+1, y-1/2, -z
EQIV $6 x-1, y, z
Now save the ins file as usual and refine the structure again. The errors should no
longer appear in the SHELXL refinement window. You can also check to see if the
molecule is now indeed in the unit cell as we intend (perhaps it would have been
smarter to do this if we had done this before we altered the EQIV lines). The molecule
in its new position is shown in Fig 4.9.
Fig 4.9
Running the Platon validation program on our new cif file leads to the following
output:
#===============================================================================
033_ALERT_2_C Flack Parameter Value Deviates from Zero ....... -10.00

#===============================================================================
As you can see Alerts 024 and 790 have now disappeared. The only Alert requiring
more changes to the structure is 147. This tells us that there is a problem with the
constrained unit cell parameters. If you open the res file in an editor you will find the
following lines:
CELL 0.71073 7.7530 8.6960 10.8530 90.000 102.948 90.000
ZERR 2.00 0.0050 0.0050 0.0050 0.005 0.005 0.005
Since this is a monoclinic unit cell there should be no error estimates below the angles
constrained to 90. The reason for this is that a monoclinic system is defined as a cell
in which only one of the cell parameters deviates from 90 by an experimentally
measurable amount (with associated error estimate) while the other two angles are
exactly 90. This CELL and ZERR lines should therefore look as follows:
CELL 0.71073 7.7530 8.6960 10.8530 90.000 102.948 90.000
ZERR 2.00 0.0050 0.0050 0.0050 0.000 0.005 0.000
To apply this correction save the res file as an ins file and make the change to the
ZERR line as shown above. Now refine the structure as before.
Running the Platon validation program on our new cif file leads to the following
output:
#===============================================================================
#===============================================================================
These remaining Alerts are similar to those you saw for md1 and do not require any
extra refinements none of the Alerts seem to need changes to the structure (033 and
222 can be ignored for reasons explained latter) and can be sorted out by editing the
cif file itself.
At this point the process of getting rid of the Alerts will be similar to that shown in
Chapter 2 and hence will be dealt with briefly.
Click on Publish > CIF TABLES on the WinGX window. This will bring up the
following window:
Fig 4.10
Clicking on No leads to the next window:
Fig 4.11
We want to use our pcf file to fill in missing information in the cif file. The Use
another CIF to resolve ? item option is what we want. Click OK:
Fig 4.12
Type the name of the pcf file (6m_ma1_0s.pcf) into the window and click OK:
Fig 4.13
If you check you will find that data_6m_ma1_0m is the title inside the pcf file.
Click Yes:
Fig 4.14
This is the cif file we want to modify. Click OK:
Fig 4.15
Data_6m_ma1_0s is the correct title. Click Yes:

Fig 4.16
We have now successfully inserted all the information in the pcf file into the cif file.
Click on Quit followed by OK to exit CIFTAB (the program you just ran). At this
point run the Platon validation program on your cif file. You should get the following
output:
#==============================================================================#
#
# Cell 7.753(5) 8.696(5) 10.853(5) 90 102.948(5) 90
# Reported P2(1) ?
# Reported ?
# Mr = 342.30[Calc], 342.30[Rep]
# Dx,gcm-3 = 1.594[Calc], 1.594[Rep]
# Mu (mm-1) = 0.143[Calc], 0.143[Rep]
# Reported T limits: Tmin=0.958 Tmax=0.973 'NONE'

# R= 0.0288( 1812), wR2= 0.0736( 1841), S = 1.059, Npar= 216, Flack= -10(10)
#===============================================================================

-------------------------------------------

#===============================================================================
#===============================================================================
Now open the cif file in an editor and change or add the following items.
For Alert 035: insert the following line above or below the
_chemical_formula_moiety line:
_chemical_absolute_configuration rm
This tells the person (or program) checking the structure that we know the absolute
configuration of the molecule based on the fact that the absolute configuration of
sucrose has been for a long time. It is effectively its own reference molecule (rm). For
details see the Alert 035 explanation further down the file.
For Alert 093: change the following line:

_refine_ls_hydrogen_treatment mixed
to
_refine_ls_hydrogen_treatment constr
This says that all our H atom positions were calculated and refined using some form
of constraint, i.e. non were refined freely.
For Alert 048: change the following line:

_chemical_formula_moiety ?
to
_chemical_formula_moiety C12 H22 O11

This is simply the moiety formula for sucrose. I obtained it from the Platon but you
could have worked it out yourself. It is always a good idea to check it anyway.
For Alert 066: no absorption corrections were needed for this structure as it is only
composed of light atoms. The fact that the absorption coefficient (Mu) is below
1 mm-1 confirms this. As a consequence we do not need minimum and maximum
transmission coefficients for this structure. Change the following lines:
_exptl_absorpt_correction_T_min 0.9584
_exptl_absorpt_correction_T_max 0.9734
to
_exptl_absorpt_correction_T_min ?
_exptl_absorpt_correction_T_max ?
For Alert 125: after these two lines:

_symmetry_cell_setting Monoclinic
_symmetry_space_group_name_H-M P2(1)
add the following line:
_symmetry_space_group_name_Hall P 2yb
I obtained the Hall symbol by checking the Platon validation output shown earlier.
This takes care of all the Alerts that can be sorted out. The remaining ones can be or
have to be explained away.
Alert 032 and O33: since this is a light atom structure (does not contain any atoms
heavier than phosphorus) and since the data collection was carried out using Mo
radiation (0.71073 ) it is not possible to unambiguously determine the absolute
configuration of this molecule. Luckily the absolute configuration of sucrose is known
and was refined in the correct configuration so this is not a problem. See the
explanation for Alert 035 above.
Alert 199 and 200: these are simply checks to make sure that the data collection was
really collected at 20C. Since this is correct in this case we can ignore these.
Alert 222: this simply tells us that the ratio of the largest thermal ellipsoids to the
smallest thermal ellipsoids attached to the H atoms is relatively high. Since this is a
C-Alert we dont have to worry about this. However, this is also normal for this
example as H atoms attached to the carbon atoms will not vibrate as much as those
attached to O-H groups.
At this point save the changes to the cif file and run it through Platon validation. You
should get the following output:
#==============================================================================#
#
# Cell 7.753(5) 8.696(5) 10.853(5) 90 102.948(5) 90
# Reported P2(1) P 2yb
# Mr = 342.30[Calc], 342.30[Rep]
# Dx,gcm-3 = 1.594[Calc], 1.594[Rep]
# Mu (mm-1) = 0.143[Calc], 0.143[Rep]
# R= 0.0288( 1812), wR2= 0.0736( 1841), S = 1.059, Npar= 216, Flack= -10(10)
#===============================================================================

-------------------------------------------

#===============================================================================
At this point we are done with fixing Alerts. However, if you intend to publish the
structure in Acta-C or E you will also need to make sure that the following
information is present in the cif file:
_cell_measurement_reflns_used 5752
_cell_measurement_theta_min 2.70
_cell_measurement_theta_max 28.34
If your cif file does not contain this information open the 6m_ma1_0m._ls file (one of
the original files in the sucrose.zip file) in an editor and scroll to the bottom of the
file. You should see the following information:
Reflection Summary:
'RLV.Excl' are reflections excluded after cycle 1 because RLV error exceeded 0.0250:
Component Input RLV.Excl Used WorstRes BestRes Min.2Th Max.2Th
1 5752 0 5752 7.5555 0.7486 5.392 56.683
Orientation ('UB') matrix:

0.1076045 -0.0420057 0.0590040
0.0694447 0.0140302 -0.0665162
0.0334082 0.1061210 0.0321453
A B C Alpha Beta Gamma Vol

7.7526 8.6963 10.8526 89.998 102.948 89.999 713.08
0.0001 0.0001 0.0002 0.001 0.001 0.001 0.03
Corrected for goodness of fit:
0.0002 0.0002 0.0003 0.001 0.001 0.001 0.04
Crystal system constraint: 1(Triclinic)

Parameter constraint mask: 0
Eulerian angles: -151.712 73.090 164.703

Goniometer zeros (deg): 0.0000 0.1690 0.0000 -0.0287
Crystal translations (pixels): 0.0027 0.0237 0.1604
Detector corrections: X-Cen Y-Cen Dist Pitch Roll Yaw

0.6562 0.9885 0.0364 -0.0571 0.2421 0.1592
Refinement statistics: StartingRes FinalRes GOF #Cycles Code

3.02509e+004 3.02509e+004 1.36 1 0
New orientation is in C:\frames\guest\manuel\6m_ma1\work\6m_ma1_0m.p4p

End global unit cell refinement ======================== 02/07/06 10:16:13
This output is from the Bruker APEX diffractometer. The output from the software
attached to the SMART diffractometer is slightly different but you should still be able
to recognize the three numbers we need. As you can see in determining the unit cell
parameters 5752 reflections were used to determine the unit cell (just below Used).
The range in 2 of these reflections was 5.392 to 56.683 (see the end of the line
below Min.2Th and Max.2Th). To convert these to values simply divide them to by
2. As a consequence you will have the following numbers next to the cell
measurement details lines:
_cell_measurement_reflns_used 5752
_cell_measurement_theta_min 2.70
_cell_measurement_theta_max 28.34
If you did have to edit these lines save the cif file. Lets now convert the cif file into
human readable format as previously explained in Chapter 2.
Click on Publish > CIF TABLES. Click No in the next dialog box. In the next
window click on Crystal/atom tables from .CIF (Fig 4.17).
Fig 4.17
Now click on OK and select the options shown below (effectively everything not
containing the word Selected):
Fig 4.18
Now click OK followed by Yes. Now click on Quit followed by OK.
At this point you will find a new file in your data directory called 6m_ma1_0s.tex.
Rename (use right click if you dont know another quick method) this to
6m_ma1_0s.rtf (where RTF stands for rich text format).
Open this file using in either an old version of Wordpad (from Windoze2000 or older)
or MS-Word. Save the file as a .doc file. You can now do whatever you need with this
file. When compared to the output for the structure solved in Chapter 2 (md1) you will
find that you have an extra table of information:
Table 7. Hydrogen bonds for 6m_ma1_0s [ and ].

____________________________________________________________________________
D-H...A d(D-H) d(H...A) d(D...A) <(DHA)
____________________________________________________________________________
O(2)-H(2H)...O(11)#1 0.82 2.04 2.850(2) 169.1
O(3)-H(3H)...O(9)#2 0.82 2.04 2.863(2) 178.3
O(4)-H(4H)...O(8)#3 0.82 2.38 2.832(2) 115.7
O(6)-H(6H)...O(3)#4 0.82 2.04 2.842(3) 165.0
O(7)-H(7H)...O(2) 0.82 2.00 2.777(2) 156.8
O(9)-H(9H)...O(10)#5 0.82 2.05 2.862(2) 167.8
O(10)-H(10H)...O(7)#6 0.82 1.91 2.716(2) 169.5
O(11)-H(11H)...O(5) 0.82 2.04 2.847(2) 167.3
____________________________________________________________________________
Symmetry transformations used to generate equivalent atoms:
#1 x+1,y,z #2 -x+2,y-1/2,-z #3 x,y-1,z #4 -x+2,y+1/2,-z+1
#5 -x+1,y-1/2,-z #6 x-1,y,z
As you can see you now have an H bond table all automatically created for you. At
this point you should be able to create your own figures as well as write up the
structure using information from earlier chapters. Downloading some example papers
from www.iucr.org and doing some searches using the Cambridge Structural
Database (CSD) will also guide you on how to write up such a structure.

Crystal-Structures SHELX 97 BOOK

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A Practical Guide to Solving Single Crystal

Frequently asked questions

What are the aims of this manual?

What is covered by this manual?

The following areas are covered:

www.openoffice.org) instead which is a very good and free alternative

Chapter 2: Solving your first crystal structure

2.1 Getting started

2.2 Solving the crystal structure

Now click OK and a new window will appear (Fig 2.8).

2.3 Refining the crystal structure

A new window looking like Fig 2.10 will appear.

Q1 1 0.5960 0.7081 0.6909 11.000000 0.05 343.61

S1 4 0.238186 0.853746 0.874298 11.00000 0.06045

S1 4 0.238089 0.853981 0.874423 11.00000 0.04365 0.08868 =

So now we strongly suspect that C001 is actually a N atom what do we do to make

Q1 1 0.8680 0.7424 0.6674 11.00000 0.05 0.64

HFIX 23 -1.20 C006 C009 C011

2.4 Preparing the structure for publication

OMIT -2.00 180.00

>>> The Following ALERTS were generated <<<

052_ALERT_1_A (Proper) Absorption Correction Method Missing .. ?

ALERT_Level and ALERT_Type Summary

10 ALERT_Type_1 CIF Construction/Syntax Error, Inconsistent or Missing Data.

Explanation and Advice for the Reported ALERTS

052_ALERT_1_A (Proper) Absorption Correction Method Missing .. ?

The treatment/method of absorption(correction) should be given explicitly.

053_ALERT_1_A Minimum Crystal Dimension Missing (or Error) ... ?

The smallest crystal dimension should be supplied in the CIF.

SIZE 0.38 0.18 0.09

>>> The Following ALERTS were generated <<<

052_ALERT_1_A (Proper) Absorption Correction Method Missing .. ?

>>> The Following ALERTS were generated <<<

052_ALERT_1_A (Proper) Absorption Correction Method Missing .. ?

>>> The Following ALERTS were generated <<<

052_ALERT_1_A (Proper) Absorption Correction Method Missing .. ?

but present in the pcf file:

>>> The Following ALERTS were generated <<<

093_ALERT_1_A No su's on H-atoms, but refinement reported as . mixed

048_ALERT_1_C MoietyFormula Not Given ........................ ?

>>> The Following ALERTS were generated <<<

199_ALERT_1_C Check the Reported _cell_measurement_temperature 293 K

As before click No. This will bring up the following window:

Clicking on OK leads to the following window:

Intensity data were collected on a Bruker SMART 1K CCD area detector

Sheldrick, G. M. (1997). SHELX97. Release 97-2 (includes SHELXS97, SHELXL97,

Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.

The paper can be downloaded directly from the IUCr site:

Chapter 3: Drawing simple diagram of your crystal structure

3.1 Getting started

3.2 Using Platon to generate diagrams

that a diagram is a 2D object while a structure is a 3D object. It is therefore

At this point a new window should appear (Fig 3.2).

3.3 Using ORTEP-3 to generate diagrams

The following window should appear (Fig 3.12):

Chapter 4: Solving the crystal structure of sucrose generating hydrogen

4.1 Getting started

In short do the following:

Fig 4.2 Note the O-H labels

4.2 Using the SHELXL HTAB command to generate H bond tables

D-H d(D-H) d(H..A) <DHA d(D..A) A

O2-H2H 0.820 2.040 169.40 2.850 O11 [ x+1, y, z ]

O3-H3H 0.820 2.043 178.00 2.863 O9 [ -x, y-1/2, -z ]