10.3.1 Default Definition of Hydrogen Bonds

The default definition of a hydrogen bond (D-H...A) is a contact meeting the following criteria:

The donor (D) must be a nitrogen, oxygen or sulphur atom covalently bound to at least one hydrogen. It is not necessary for the 3D coordinates of the H atom to be known, i.e. H-bonds will be found even if H atoms have not been located in the crystal structure (see Hydrogen Atoms).

The acceptor (A) must be a nitrogen, oxygen, sulphur or halogen with at least one available lone pair (e.g. pyramidal trigonal nitrogen is regarded as a donor but planar trigonal nitrogen is not).

The D...A distance must be less than the sum of van der Waals Radii of the D and A atoms.

The contact may be (a) intermolecular, or (b) intramolecular involving donor and acceptor atoms separated by at least 3 covalent bonds within the molecule.

This pre-set default H-bond definition is always associated with an item (viz. H-Bond Default definition) in the list box underneath the display area in the main Mercury window:

The default definition can be edited by double-clicking on it and changing options as required in the resulting Define H-bonds dialogue box (see Section 10.4.3).

Hydrogen bonds satisfying the default definition can be displayed in the display area by switching on the tick box next to the words H-Bond Default definition: