An Easy Structure - Sucrose

6/6) The Crystallographic Information File - CIF

We pick up from the end of part 4 or part 5 of this tutorial.

The CIF written by SHELXL must be edited before it can accompany a manuscript, or be deposited in a database. This is because some information is missing, and some is incorrect. This final part of the sucrose tutorial shows how to edit the CIF made by SHELXL so that it passes the IUCr structure checking program checkCIF. The IUCr (International Union of Crystallography) has another excellent tool, publCIF, for editing and checking CIFs, but in this tutorial we will not use it. If you intend to publish in an IUCr journal, it really pays to use publCIF as it is used by the Acta Crystallographica journals to typeset structure-related papers.

You should have your CIF from the last SHELXL job (part 4 of this tutorial). If you don't have it, you can download this copy: sucrose.cif. There is also a fully edited version of this CIF, sucrose-edited.cif, for you to inspect. Without getting into the arcana of the CIF format, the easiest way to get started is to compare a newly generated CIF with a fully edited version.

Warning: The CIF format is finicky. Misplaced semi-colons are a particular source of grief, as is the legacy 80 character per line limit.

Note: This tutorial does not show you how to construct a full report on your crystal structure, it merely shows you how to correct the problems with a SHELXL-generated CIF.

Start by opening the CIF in your text editor. As with editing SHELX files, do not use a word processor. In this tutorial you'll see successive portions of the CIF. If you roll over the image with your mouse it will highlight the lines that need to be edited in red. Each of these images will be followed by a brief description of the changes needed, followed by an image of the corresponding section of the CIF after it has been edited.

<i>CIF</i> tutorial

Some crystal structures have multiple fragments in the asymmetric unit, such as ions, solvent molecules, high Z' etc., and the _chemical_formula_moiety records the formulae of the various pieces (moieties). For sucrose it is just the same as the _chemical_formula_sum, so just duplicate the _chemical_formula_sum line. If you don't know what the proper moiety formula is, don't enter it yet. Later, the output from checkCIF will tell you what it is. If you happen to know the answer to any of the other items here, you should replace the ? with the correct response.

Scrolling down the CIF we come to this:

<i>CIF</i> tutorial

_symmetry_cell_setting is where you enter the crystal system, for sucrose this is monoclinic.
_symmetry_space_group_name_H-M is where you enter the Hermann-Mauguin space group symbol, here it is 'P 21', which is CIF-ese for P21.

There are other _symmetry_space_group_ CIF data names. For some strange reason it seems to have become common practice to enter Hall's otherwise little-used space-group notation, which for this space group is P2yb. Hall's nomenclature is not so well known, so if you don't know the Hall symbol for your space group, don't enter it yet. Later, the output from checkCIF will tell you what it should be. For sucrose it is:

_symmetry_space_group_name_Hall     'P 2yb'

Further down in the CIF we have this:

<i>CIF</i> tutorial

The number of reflections, theta_min and theta_max used for the cell determination are given in the nreport file. The _exptl_crystal_description just describes the crystal shape (e.g. block, plate, needle etc.), and its colour should be obvious. If you have forgotten these details, let this be a reminder to keep good notes.

On to the next section ...

<i>CIF</i> tutorial

The most common type of absorption correction nowadays is the multi-scan method. This is typically done with SADABS (by George Sheldrick), SORTAV (by Bob Blessing) or Scalepack (by Zbyszek Otwinowski). Unfortunately, although Scalepack is an excellent program, it does not give you the proper information to edit this section of the CIF, so it is probably better to use SADABS or SORTAV.

Notice that the T_min and T_max values are rounded to three decimal places, and that T_min is a little different from the value in the unedited file. The problem is that the unedited value is not derived from the absorption correction, it comes from a simple calculation based on crystal size (SIZE command in SHELXL) and chemical composition. If Scalepack was used for merging, that is the best estimate you have. For SADABS data though, the proper value requires you to look in the SADABS log (the default name of this file is sad.abs). Near the end of sad.abs you will find a line like this:

Ratio of minimum to maximum apparent transmission:    0.960326

The value for _exptl_absorpt_correction_T_min is found by multiplying this number (i.e. 0.960326 for this dataset) by the CIF value of T_max (0.9828 in this case), to give 0.944. If that seems a bit contrived, well that's because it is a bit contrived. Nevertheless, it's the best estimate we have, so that's what we use. Note that for analytical absorption corrections, the T_min and T_max values should be output by the program used, and you'll need to edit both of these values in the CIF.

Further down the CIF we find this:

<i>CIF</i> tutorial

There's a bunch of stuff to change. The next image shows what the right entries should be in this case, but other diffractometers require different information.

With area detector data, it is unusual for standard reflections to be collected, but you should change these entries anyway. In CIF-ese, the full stop, or period '.' and the question mark '?' mean different things. The former means "not applicable" while the latter means "not known". The difference is subtle, but you might as well get it right.

For Scalepack, the values for _diffrn_reflns_number and _diffrn_reflns_av_R_equivalents are in the
nreport file (see 'Total number of integrated reflections' and 'Overall R-merge (linear)' in the last table), while for SADABS look in the log file.

On to the next block ...

<i>CIF</i> tutorial

The Greek letter sigma (σ) is given as '\s' in CIF-ese. The _computing_ entries need to show the most current references for all the programs used. Note that if you use publCIF, this should be added on the _computing_publication_material line. For a CIF intended for an IUCr journal, you will also need to add a bunch of extra stuff, including _publ_section_references, but that is beyond the scope of this tutorial. If you are wondering what is meant by 'local procedures', it simply refers to tasks like manual editing of the CIF.

No matter what the intended purpose of the CIF, if there are hydrogen atoms in the structure there should be a description of how the hydrogen atoms were treated.

<i>CIF</i> tutorial

This description goes in the _publ_ section of the CIF, but SHELXL does not write any _publ_ lines at all. You can enter it by hand in the space indicated by the red line in the roll-over image. While you're at it, you may as well change the 'sigma' to '\s' in the _refine_special_details section. This ought to give you something like the following:

The last thing that needs editing in this first pass through the CIF is here:

<i>CIF</i> tutorial

By default, SHELXL writes 'mixed' on the _refine_ls_hydrogen_treatment line. This would only be appropriate if you used a combination of constrained and refined H atoms. In this sucrose example we used a riding model for all of them, so this should be changed to 'constr', which is short for constrained.

Notice that the CIF contains the lines _refine_ls_abs_structure_details and _refine_ls_abs_structure_Flack, even though you could not use Flack's parameter to establish the absolute structure (see part 4 of this tutorial). In a case like this, you may be asked to remove these lines. The argument made for removing them is that a Flack parameter with an SU (standard uncertainty) so large renders the parameter 'meaningless'. In point of fact, such a value is not 'meaningless' at all, it tells you in very definite terms that the x-ray data alone cannot establish the absolute configuration, particularly once Friedel pairs have been merged. As such, it confirms what we know from the physics of anomalous dispersion. This is a subtle point that is too often lost on journal editors and referees.

You should also add a line _chemical_absolute_configuration with the data value 'rm', which stands for 'reference molecule'. This states that the handedness of your model is fixed by a reference molecule, in this case obviously it is sucrose! If you prefer, you could put this extra line near the top of the CIF along with the other _chemical_ entries, but it doesn't really matter where it goes.

If you are lucky, your CIF may now be sufficiently complete to survive checkCIF. Since checkCIF gives lots of diagnostic comments, it can be helpful for correcting many CIF problems. It is also useful for detecting more general problems with your structure. So, open a browser and go to the checkCIF page:

For this sucrose example, checkCIF returned the following report:

A few things here are worth mentioning. The checkCIF report shows no syntax errors, and the table shows that calculated and reported data are very similar. The differences in Nref show that our dataset is missing three reflections out of about 1700. That's not so bad, and it's likely just because the program calculated hmax = 10 rather than the hmax = 9 present in the dataset, and that was likely due to a rounding error. It also shows that we merged the Friedel pairs (the number in square brackets for NRef is the expected unmerged number of reflections). This is also shown on the 'Data completeness' line, and again there's nothing to worry about.

Next comes the 'Alert' section of the report. There are four levels of alert: A, B, C, and G. Further down, the report tells you how serious these alert levels tend to be. Generally speaking, A-level alerts are serious and need to either be fixed or explained in a 'Validation Reply Form'. B-level alerts are potentially serious, and these too should either be fixed or you should have a well-reasoned explanation. Be aware, however, that checking programs are not infallible, so you may sometimes see A/B-level alerts when there is really no problem at all. That's ok so long as you have a cogent counter argument. C/G-level alerts usually just tell you things that you know already, but on occasion you may need to tweak the model (and re-refine!) to eliminate the alerts.

For this sucrose tutorial, there are no A/B-level alerts, but there are a bunch at C/G-level. None of them are serious. You already know about the 'meaningless Flack parameter' argument, and it's safe to dismiss it here. The data/parameter ratio is low simply because the Friedel pairs were merged, and again it's not serious for this structure. The link in the checkCIF report, reproduced here PLAT089_ALERT_3_C, shows the somewhat arbitrary cut-off point for generating this alert, and it is insignificant for this structure. A fairly close contact between H8a and H9a has been flagged, but a quick look at the structure shows that these hydrogen atoms are fine. The uncertainty in the Flack parameter is high, but that is to be expected; there was no discernible anomalous signal, so the Friedel pairs were merged. Again, no big deal. Lastly, the SUs of the cell parameters all happen to have the same value. These things happen sometimes, and it's not a problem. Further down, the G-level alerts give no reason for alarm.

Conclusion: The structure determination is now complete.

Part 1: Setting up instructions - XPREP
Part 2: Structure solution - SHELXS
Part 3: Molecule editing - XP
Part 4: Structure refinement - SHELXL
Part 5: Ellipsoid and packing plots - XP
Part 6: The Crystallographic Information File - CIF

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