10.4.3 Defining a New Type of Hydrogen Bond; The Define H-bonds Dialogue Box

Hit the Contacts... button (located near to the bottom-centre of the main Mercury window), or select the top-level Calculate option followed by Contacts.... in the resulting pull-down menu, to bring up the Contacts dialogue box. Then hit Add in the Contacts dialogue box and pick H-bond... to bring up the Define H-bonds dialogue box.

Alternatively, you can get straight to the Define H-bonds dialogue by right-clicking anywhere in the white list box under the main Mercury display area and selecting Add H-bond... from the resulting menu.

Specify whether it is necessary for the position of the hydrogen atom involved in the H-bond to be known (i.e. for the H atom to have been located in the crystal-structure analysis).

If the Require hydrogen atom to be present button is set on, then a minimum value for the D-H...A angle must be specified (in degrees).

Select the required combination of donor and acceptor atoms via the tick-boxes provided in the scrolling windows labelled Donor atom types and Acceptor atom types. It is difficult to guarantee correct classification of donors and acceptors if one or more H atoms are missing from the structure (see Hydrogen Atoms). C-H is not available as a donor group; define a specific contact to find H-bonds involving C-H (see Section 10.4.5).

Set the required upper and lower distance limits (see Section 10.4.1). These may be specified as absolute distances in Angstroms, or as distances relative to the sum of vdW radii of the atoms involved in the H-bond. If the Require hydrogen atom to be present button is on, the distance constraint refers to the H...A distance; otherwise it refers to the D...A distance.

Specify whether the contacts are to be intermolecular only, intramolecular only, or whether both are allowed.

If intramolecular bonds are allowed, specify the minimum number of covalent bonds between the contact atoms (see Section 10.4.2). If the Require hydrogen atom to be present button is on, the bond count refers to the number of bonds between the H and A atoms; otherwise it refers to the number of bonds between D and A.

The following settings will find intermolecular and intramolecular H-bonds between all types of donors and 6-membered ring aromatic nitrogen acceptors, subject to the constraints that (a) the H atom must have been located in the crystal structure analysis, (b) the donor-H...nitrogen angle must exceed 150 degrees, (c) the hydrogen...nitrogen distance must be at least 0.1Å shorter than the sum of vdW radii of H and N, and (d) if the contact is intramolecular, the donor and N atoms must be separated by more than 4 covalent bonds:

Hit Default followed by Apply if you want to return all the settings to their default values.