Results: Tables of Geometric Parameters

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Results: Tables of Geometric Parameters

In addition to tables of instrument parameters, fractional atomic coordinates and temperature factors, it is important to provide tables of the geometric parameters that are derived from the final refined atomic coordinates of the structure. Most commonly, these tables contain calculated bond lengths and bond angles. Typically, two versions of these tables are produced; a list of selected parameters only is published, but a fuller listing is provided for refereeing and deposition.

The tables should include the value and esd for each parameter included, unless the parameter has been constrained during refinement, as would be typical for a C-H bond, say. The selection of parameters for the shorter, published table depends on the chemical nature of the compound and the structural features which need to be emphasised. For example, in a coordination compound you might only want to include bonds involving a central metal atom and the angles subtended at it, or for an organic molecule it might only be worth publishing a selected list of torsion angles, since the bond lengths and angles in organic molecules have been characterised in numerous studies. Non-bonding distances and short contacts, such as hydrogen bonds may be included; again this depends on the particular structural points under discussion.

Examples of table styles for the bond lengths and angles in an AlO₆ octahedra are given below. Note how the bond lengths are repeated (two for O(1), O(2) and O(3)) so as to provide the reader with an understanding of how the full coordination sphere of the AlO₆ unit is built up.

(a) -x+1, -y+2, -z; (b) -x+1, y+0.5, z; (c) x, -y+1.5, -z: these symmetry transformations are applied to O(1), O(2) and O(3) (the values given in an accompanying table of atomic coordinates in the article) to generate the actual coordinates of the O(1), O(2) and O(3) sites bound to Al(1) in the tables of geometrical parameters.

Interpretation

Both the values and the esd's of the geometrical parameters should be examined, just as with the primary structure parameters. See if the values presented are consistent with those found in other structures with similar features. For example, compare the Al-O bond lengths given in the above table to those found for other AlO₆ octahedra which are generally found in the range 1.85 - 2.00 Å. If any reported values fall outside of the expected ranges look for an explanation of this in the discussion of the structure. If short contact distances occur, for example, if the oxygen atoms of two water molecules are 0.5 Å apart, then this clearly is not physically reasonable unless the total occupancy of the two sites is less than or equal to 50 %, and so the atomic occupancies of the atoms involved in the short contact should be carefully scrutinised in the table of atomic parameters and reference to the short contact distance should be sort in the discussion section of the article.
If any geometrical parameters are given without esd's then it is assumed that at least one of the atoms involved has not been refined freely. This should be stated in the experimental section of the article. If any geometrical parameters are constrained or restrained then they might have an associated esd. However, the value of the geometrical parameter, as it is not freely refined, should not be referred to as an absolute value in other work and should only be compared "loosely" to other similar values.

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