Diamond Version 5 User Manual: Building up structural parts

Creating H-bonds and contacts directly from connection parameters

In this article:
- The command "Build/Add All Atoms and Connections" also considers bonds, H-bonds, and contact parameters from "Structure/Connection Parameters". This is a quick-and-easy option to create all atoms mentioned in the connection parameters, usually derived from _geom_xxx input loops as well as the bonds, H-bonds, and contacts between, as far as defined. (Cf. Building scheme basics option "Add all atoms".)
- Commands to add bonds, contacts or H-bonds from the context menu of the corresponding connection parameters tables.
- Commands in contact parameter table to expand to next atom or molecule.

Previous article: Connectivity, part 2: H-bonds and non-bonding contacts
Next article: Expand or reduce clusters of molecules

"Add All Atoms (and Connections)" dialog

In some cases, the bond parameters are used to strike out several bonding spheres, spheres that may differ from those generated by effective radii, for instance. But in many other cases, the bond parameters, together with the atomic parameters, can serve as a simple starting point to create molecule(s) directly from the atomic parameter list. This is done in Diamond with the command Add All Atoms and Connections... from the Build menu. This also considers non-bonding contacts and H-bonds when mentioned in the structure input parameters.

The following pictures of COD:1501635 are results of the command "Build"/"Add All Atoms and Connections". The left picture involves only atoms and bonds, whereas the right picture additionally involves contact parameters. The bond parameters (and contact parameters) consider only a part of the spirobifluorene molecule. This is a case where the bond parameters do not automatically create complete molecule(s). (Here we have 25 bonds and 12 contacts. It is somewhat more than the "asymmetric" half of the spiro molecule.)

Adding atoms (and bonds) directly

There is an acceleration key to create solely atoms and bonds (but no H-bonds and contacts) via Shift+Ctrl+A or the corresponding button in the Picture toolbar, which is located by default at the bottom of the Diamond application window. Shift+Ctrl+A and the toolbar button behave like in Diamond version 3, where contact and H-bond parameters were not supported anyway and bond parameters did not appear as editable structure parameters.

Commands to add bonds, contacts or H-bonds from the table's context menu

The commands Add Atoms and Contacts and Add Contacts can be used from the context menu of the table of contact parameters to add contacts selectively just from the contact(s) that is or are highlighted in the table. (The "Add All Atoms and Connections" dialog applies either all or none of the contacts.)
- Use "Add Atoms and Contacts" to directly add the two atoms each and the contact between of the contact(s) currently selected in the table.
- Use "Add Contacts" instead, if you want to add contacts, when the two atoms of the selected contact are already available. This command will add contacts between all (symmetry-equivalent) pairs of these two atoms in the structure picture.

The table of bond parameters uses equivalent commands Add Atoms and Bonds and Add Bonds, rsp.

The table of H-bond parameters offers similar commands in its context menu: Add Atoms and (H-)Bonds and Add H..A-bonds to insert H..A bridges where (symmetry-equivalent) atoms of H and A are already in the picture.

Command "Expand" from table of contact parameters

The following shows how to expand from a molecule via one contact definition from the table of contact parameters, here the first mentioned: Br1 -- Br2. To create the molecule, first destroy the picture (Shift+Ctrl+D or "Build"/"Destroy"/"All"), then click "Create molecule directly" symbol in the bottom picture toolbar or use Shift+Ctrl+M, and change the viewing direction to b-axis ("Picture"/"Viewing Direction").

Applying the command Expand via Contacts (with the contact #1 Br1--Br2) to the molecule leads to the left of the following picture, whereas Expand to Molecules leads to the right picture with five molecules in total.

Note: You can find more about expansion (via contacts or H-bonds or another way) from atoms or molecules to neighbouring atoms or molecules in the article "Expand or Reduce Clusters of Molecules".

Previous article: Connectivity, part 2: H-bonds and non-bonding contacts
Next article: Expand or reduce clusters of molecules

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.