Diamond Version 5 User Manual: Building up structural parts

Connectivity, part 2: H-bonds and non-bonding contacts

The Connectivity dialog has additional pages to define non-bonding contacts and for improved handling of H-bonds

This article is about:
- Consideration of connection parameters for bonds as well as for H-bonds and contacts.
- Support for multiple sets of H-bond and contact definitions: Contact and H-bond definition groups -- as there are "Standard contacts" and "Standard H-bonds", rsp., defined between the atom group pairs (like bonds are) and using van der Waals radii sum plus an offset as default.
- User-defined, special contact definition groups and H-bond definition groups, rsp. These may be defined on atom site level.
- Reported contacts/H-bonds (from connection parameters) are compiled in "Reported contacts" and "Reported H-bonds" definition groups, rsp., each.

Previous article: Inserting (dummy) atoms and bonds
Next article: Creating H-bonds and contacts directly from connection parameters

Connectivity dialog with three pages (tabs)

Since Diamond version 4 the Connectivity dialog uses three pages, one for "Bonds" (i.e. strong connections), a second for H-bonds and a third one for non-bonding contacts. The "Bonds" page is in principle what you already know from previous Diamond versions, whereas the other two pages serve to define H-bonds and contacts definitions between atom group pairs or atom site pairs or special element combinations.

While there is one set of N*(N+1)/2 bond groups (= atom group pairs) for N atom groups to define the bonding spheres, there may be multiple sets of pairs to define connection spheres for contacts and H-bonds. These pairs may be on atom group or even atom site level and are compiled in a so-called "definition group". This is because it enables to easily define a standard definition sphere "for all", usually relative to van der Waals radii sums, on one hand -- or to define special complicated contacts (for whatever reason) between several atom groups and/or atom sites.

The first screenshot shows the "Bonds" page with bonding spheres for all atom group pairs in the compound COD:1501635. The small green ticks below the zero line show bonding parameters, which are usually imported from CIF "_geom_bond_xxx" loops. (For details, see the article "Connectivity, part 1: Bonding spheres".)

The second screen shot shows the standard (non-bonding) contacts, which are compiled on atom group level -- as the bond groups on the "Bonds" page do. The pair C--Br is highlighted, the histogram shows the distances between all C and Br atoms in the current compound. The light blue rectangle describes the contact sphere and begins on the upper boundary of the strong bonding sphere and ends at the sum of van der Waals radii plus 0.1 Angstroem. Boundaries can be defined in absolute (Angstroem) values or relative to van der Waals radii sums.

You can define multiple contact definition groups, the "Standard contacts" are created automatically by the program - independent if there are contact parameters in the input file or not. The second contact definition group "Reported" has been derived from the contact parameters (i.e. typically from _geom_contact_xxx loops), and the atom pairs are given on atom site level -- e.g. as highlighted here -- contacts between "Br2" and "C5".

A group of contacts, the "contact definition group" can be defined on atom group or atom site level or defined for selected elements and be stored in the Registry for later access in other compounds. The boundaries can be defined with absolute boundaries or relative to van der Waals radii sums, and intermolecular contacts (between atoms of different molecules) and/or intramolecular contacts (between atoms of the same molecule) can be enabled or disabled:

The third page for the H-bonds show the (in sample COD:1501635 one and only) reported H-bond definition in the H-bond connection parameters:

Note: In Diamond version 4 and 5, the bonding sphere for H-bonds is defined like for (non-bonding) contacts via the distance (typically relative to van der Waals radii sums) between donor and acceptor -- not as the distance between H and acceptor, although the H..A bridge is usually drawn in the structure picture. This advantage enables the usage of H-bonds even if the H-atom's position has not been determined. That is different to the kind of definition of H-bonds used in Diamond version 3.x, where you define H-bonds directly by a H..A boundary range and an D-H..A angle range. The "Build"/"Create H-bonds" command and dialog is still available and works the way as Diamond 3 does.

Previous article: Inserting (dummy) atoms and bonds
Next article: Creating H-bonds and contacts directly from connection parameters

Reference for COD:1501635:
Ulrich Darbost, Janie Cabana, Eric Demers, Thierry Maris, James D. Wuest; Molecular Tectonics. "Use of Br...aryl Supramolecular Interactions for the construction of Organized Networks from 9,9'-spirobifluorene in the Crystalline State"; CheM, 1 (2011), 52-12369.