Diamond Version 5 User Manual: Exploring bonding and contact spheres

Exploring H-bonds and contact spheres

- About H-bonds and contact spheres and how they are defined (connectivity)
- Example: H-bonds in a spirocyclic keto-lactam (COD:7106313)

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Next article: Using Explore view with an individidually designed structure picture

About H-bonds and contact spheres and how they are defined (connectivity)

H-bonds and (non-bonding) contacts can be defined between atom group pairs (atom type pairs) or even more specifically atom site pairs or for 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.

You have access to the contact definition groups and H-bond definition groups via the command Build -> Connectivity, which is accessible from the regular Picture Edit view. More details about the organization of H-bond and contact definitions is shown in the article "Connectivity, part 2: H-bonds and non-bonding contacts".

Here in the Exploration view Diamond directly accesses these H-bond and contact definitions and shows non-bonding contacts between two atoms each or H-bonds between three atoms each (donor, acceptor, H) in the distances table of the Exploration controller.

If you add contacts and/or H-bonds in the Exploration view, Diamond creates a new contact/H-bond definition group, which is later accessible from the Connectivity dialog's Contacts or H-bonds page, rsp., with the title "Explored".

Example: H-bonds in a spirocyclic keto-lactam (COD:7106313)

In this example we use the same sample file "cod-7106313.cif" as in the previous article "Exploring bonding spheres", let the "File Import Assistant" create a blank (empty) picture, and enter the "Exploration view" with this blank picture. From the context menu of the graphics view we choose the command Get Molecules.

But in this case, we must ensure that "What to explore" is set to "Contact spheres" in the Exploration controller (rather than "Bonding spheres", which is the default setting) and "Apply to" is set to "Atom".

Moving the mouse cursor to the atom "O2" shows the info tip window as shown in the screenshot of the Exploration view's graphics view: The atom label, followed by the fractional coordinates (x/a, y/b, z/c), the fragment or molecule it belongs to, and finally informations about the contact sphere, here:
- the contact between the "O2" atom (as acceptor atom) and a hydrogen atom (not yet visible here),
- the contact between the acceptor atom "O2" and a donor atom (not yet visible here),
- no general non-bonding contact here.

Choosing the command Check Contact Sphere Around Atom "O2"creates the atoms in the contact sphere of atom "O2" alongside with two purple dashed lines. The summary of the atoms currently connected with the central atom is given in the bottom line of the info window, here: one O and one H atom:

The Exploration controller shows a next neighbour histogram for "O2". Like for the histogram for the bonding spheres, the sphere for strong (bonding) interactions is yellow. Additionally the sphere(s) for H-bonds and non-bonding contacts are given in purple. (You may shift the splitter between Exploration controller and graphics view to the right to see all columns.)

The distance table shows two more columns than the table for bonding spheres:
- d-vdW: The distance between Atom 1 and Atom 2 minus the sum of the two atoms' van der Waals radii, in Angstroem.
- Type: The type of connection between atom 1 and atom 2:
-- 'Bond' describes a strong interacting connections. This is grayed here, i.e. cannot be changed.
-- 'A..H' describes the connection between acceptor atom and H of an H-bond, where atom 1 is the acceptor and atom 2 the hydrogen atom.
-- 'H..A' describes the connection between acceptor atom and H of an H-bond, but here with atom 2 as acceptor and atom 1.
-- 'A..D' describes the connection between acceptor atom and donor atom of an H-bond, where atom 1 is the acceptor and atom 2 the donor atom.
-- 'D..A' describes the connection between acceptor atom and donor atom of an H-bond, but here with atom 2 as acceptor and atom 1 as donor.
-- 'D/A' describes the connection between acceptor atom and donor atom of an H-bond, where the role of donor and acceptor is ambiguous.
-- 'Cnt.' describes a non-bonding contact, not part of an H-bond.
-- 'inter' describes an intermolecular connection between atom 1 and atom 2.
-- 'intra' describes an intramolecular connection along with the number of bonds between atom 1 and atom 2.

[Note: The "Flags" column is not yet in use in preview version.]

To see the missing next bonded neighbours of the contacted atoms "H3" and "O3", click with the right mouse button on e.g. the atom "H3" and choose the command Grow (Pump up) Sphere At .... This also creates the missing covalent bond between donor atom "O3" and "H3".

To see distances between two atoms each, move the mouse cursor over the connection (bond or contact). This also informs about the type of connection:

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