Hints for Nonbonded Contact Searching

•	Searches for intermolecular interactions take longer than those for purely covalent substructures. Searches for patterns involving two or more non-covalent interactions can be very time-consuming.

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A typical search consists of two (occasionally more) covalent substructures and the non-covalent interactions required between them. The non-covalent interactions must be defined geometrically. For example, if you are searching for O-H...O hydrogen bonds, you must specify the maximum permissible O...O or H...O distance.

•	The most common geometrical constraints are maximum and minimum distances, e.g. D...A or H...A distances for hydrogen bonds D-H...A (D = donor, A= acceptor).

•	In choosing non-covalent distance constraints, it can help to carry out a preliminary search using quite generous limits (e.g. sum of van der Waals radii plus 0.5Å). This establishes the range of values in the CSD.

•	It is only sensible to specify distance constraints with respect to van der Waals radii if you are searching for contacts between the common non-metallic elements unless you choose to set your own van der Waals radii.

•	H-atoms are not always present in CSD entries, particularly in older entries. You may need to use D....A distance constraints instead of H...A constraints in H-bonding studies.

•	H-atoms are poorly defined by X-ray diffraction: the direction of D-H bonds is usually satisfactory, but the D-H valence-bond distances are shortened. You can correct for this by normalising H-atom positions.

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Other geometric constraints can be used to further define the non-covalent interaction, especially if the interaction is directional. The angle D-H...A in a hydrogen bond prefers to be linear, so some constraints on this angle may be appropriate, particularly for stronger hydrogen bonds. It is wise to examine typical values in the CSD before setting such geometrical constraints.

•	Scattergrams from IsoStar, distributed as part of the CSD System, are valuable for assessing search constraints.

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Sometimes it is better to combine searches. For example, all H-bonds involving N or O acceptors and N-H or O-H donors can be found with a generic search for X-H...X, where X is assigned the variable element type N or O (see Setting Variable Element Types). The labels of the X atoms actually found in any interaction can be output by ConQuest, so that the different types of H-bonds can be separated out after searching, e.g. in Vista.

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Searches for common interactions, e.g. O-H....O(sp2) hydrogen bonds, can generate very large numbers of hits. The number of hits can be reduced by either (a) defining the chemical environment of the groups more exactly (keto-O, carboxylate-O, etc.), or (b) lowering the R-factor acceptance limit (e.g. R <= 0.05).