Diamond Version 5 User Manual: Building up structural parts

Expand or Reduce Clusters of Molecules

Use intramolecular contacts or H-bond definitions to find neighbouring molecules

Previous article: Creating H-bonds and contacts directly from connection parameters
Next article: Grow or cut molecular fragments or polymers

This article in brief:
- Dialog "Build/Expand" with several settings if to apply to all atoms or selected atoms or selected molecules, to enable intramolecular contacts, to regard H-bond definitions, too, and what to do with the contacted neighbouring atoms (broken-off bonds around or complete fragments).
- "Settings" page in that dialog, so you can choose the current connectivity settings or use different contact spheres, either relative to van der Waals radii or in absolute Angstroem boundaries.
- Push buttons to do expansion step-by-step: Add contacts now, Expand now. Push buttons to remove contacts or fragments, that means to step back.
- Dialog "Build/Reduce" to remove molecules step-by-step, either the farmost molecules or all neighbouring molecules. Several settings to apply to or to start from and if and how to consider H-bonds and contacts.
- Accelerator keys and toolbar icons to expand or to reduce: "Create atoms' neighbouring atoms", "Create molecules' neighbouring atoms", "Create neighbouring molecules", and "Reduce directly".

Definition of "Expand" and "Reduce"
In Diamond version 4 and 5, we call the finding and creation of atoms or molecules neighbouring to the existing atoms or molecules as "expanding". We use "reducing" for the reverse function. For both "expand" and "reduce" there are several options, if and how to use contact and H-bond definitions or just to involve (closest) distances to neighbouring molecules, cf. the descriptions of the dialogs "Expand" and "Reduce" below.

This article shows how to expand from a set of atoms or a molecule via neighbouring molecules to a cluster and to reduce that cluster back to a smaller ensemble of molecules again. You can do this with or without H-bond and/or contact definitions -- starting from a selected atom or a selected molecule or from the whole current ensemble in the structure picture.

Sample #1: Expand via neighbouring atoms

We use the sample compound "COD-1500005-molecules.diamdoc" to demonstrate that. This file comes up with a structure picture "Molecules" containing ten molecules created from the atomic parameter list. (This is done, as you already know from older Diamond versions, with Shift+Ctrl+M or the corresponding icon in the Picture toolbar, which is normally at the bottom of the Diamond application window.)

Note: The screenshots have been made with Diamond version 4 but all functions are available in current version 5, too.

Switching from data sheet in the right half of the Diamond application window to the table of created molecules ("View" menu, "Table" sub-menu) we get a list with molecule titles and formula sums and how far the molecules are complete or still fragmentated. Since we will put "Molecule 4" into the focus of our interest, the corresponding row is highlighted and the properties shown in the "Properties" pane below.

Clicking with the right mouse button on the "Molecule 4" row in the table of created molecules and choosing command "Select Reference Atom" marks the atom "Co1" (at x,y,z) in the lower left of the structure picture. Running command "Edit"/"Select Molecule" (or accelerator Ctrl+M), followed by "Edit"/"Invert Selection" (or Ctrl+I), followed by "Edit"/"Delete" (or "Del" key) leaves the "Molecule 4" alone in the picture, which will serve as starting point for our expansions and reductions. We also press accelerator key Ctrl+Alt+4 to switch the model from "ball and stick" to "ellipsoid".

Clicking the button (highlighted in the bottom center of the screen shot above) "Create Atoms' Neighbouring Atoms" or simply pressing Shift+Ctrl+X (for "eXpand") three times leads to the following sequence:

Contacts from the atoms of the molecule to neighbouring atoms (depicted as dotted lines

Next "Expand" command creates broken-off bonds to the next bonded atoms of the neighbouring molecules each

Running "Expand" again completes these fragmentated molecules

If you want to, you may start another round finding neighbouring molecules.

The example above applies to the whole molecule "Molecule 4", but you could have marked a special atom of the molecule, for instance one of the N atoms rather than the "Co1" in the center, to show selectively the neighbourhood of that N atom.

Sample #2: Create neighbouring molecules

Finding and creating neighbouring molecules goes quicker with the "Create Neighbouring Molecules" symbol in the toolbar (or Shift+Ctrl+Z). Go back to the picture with the one molecule "Molecule 4" (close and re-open document or make undo steps). Two runs of the command lead to the following screen shot. (Maybe you have to hit the F9 key to adjust the picture into its structure picture window.)

Sample #3: Reduce (a molecule cluster) directly

You can dismantle a molecule cluster step-by-step using the Reduce command (either from the Build menu, giving you several options, such as where to start from -- a selected atom/molecule or from the center of the picture) or simply clicking the button highlighted at the bottom of the next screen shot:

And repeating "Reduce" several times leads you finally back to a picture with the one and only "Molecule 4".

The contact definitions in the example above come from "_geom_hbond_xxx" definitions in the 1500005.cif file. But there are several possibilities to change, add, or remove definitions for non-bonding contacts in the "Connectivity" dialog ("Build" menu).

Using dialog "Expand" from the command "Build/Expand..."

The Expand dialog from the "Build/Expand" command offers several settings if to apply to all atoms or selected atoms or selected molecules, to enable intramolecular contacts, to regard H-bond definitions, too, and what to do with the contacted neighbouring atoms (broken-off bonds around or complete fragments).

Apply to
- All atoms in structure picture: The search for contacts starts from all atoms in the structure picture.
- Atoms currently selected in structure picture: The search for contacts starts only from the currently selected atoms.
- Atoms belonging to selected molecule(s): The search for contacts starts from all atoms belonging to the molecule(s) where at least one atom is selected.

Create contacts checkboxes
Use these checkboxes, if you want to use the non-bonding contact definitions or the H-bond definitions or both.
- Create contacts (from non-bonding contact definitions): Use the non-bonding contact definitions (cf. "Build"/"Connectivity...", "Contacts" page).
- Create D...A contacts from H-bond definitions: Use H-bond definitions (cf. "Build"/"Connectivity...", "H-bonds" page) to create contacts between donor and acceptor atom each.
- Create H...A bonds: Use H-bond definitions but create contacts between H and acceptor instead.
- Create contacted neighbouring atoms: This is checked by default in order to get the contacted neighbouring atom created in the structure picture. Otherwise the function can only contact neighbouring atoms that already exist in the picture.

Continuing from the contacted atoms
- Fill coordination spheres around contacted atoms: This is to show if and how the contacted atom continues to a molecule (or polymer). Use "cycles" to define how many spheres around the contacted atom are to be created. Use the checkbox "Use broken-off styled bonds for incomplete fragments" to have broken-off bonds symbolizing that the neighbouring molecule is incomplete or is a polymer.
- Complete fragments around contacted atoms: This calls the complete fragment function for a contacted atom each in order to complete the (contacted) neighbouring molecule. If the neighbour is a polymer, that will have broken-off bonds where the fragment "completion" has stopped, provided the checkbox "Use broken-off styled bonds for incomplete fragments" is set.

Contact settings for expanding
The "Expand" dialog has a second page called "Settings" to define the contact sphere size. You can choose between the current connectivity settings (default) or use different contact spheres, either
- a generic contact sphere with boundaries relative to the van der Waals radii sums plus an offset in Angstroem
- or a fixed-size contact sphere in absolute Angstroem boundaries.

Push buttons to do expansion step-by-step
The "Expand" dialog allows you to do the selected expansion functions in one rush (as common with OK or Apply Now) -- or by choosing the push buttons "Add Contacts Now" or "Expand Now". The "Remove [...]" buttons help you to step back and undo a previous "Contact Now" or "Expand Now" and perhaps try again with other contact settings, without leaving the dialog.

Using dialog "Reduce"

The Reduce dialog, opened from the "Build/Reduce" command, can be used to remove molecules step-by-step, either the farmost molecules or all neighbouring molecules. There are several settings to apply to or to start from and if and how to consider H-bonds and contacts, see the following screenshot of the "Reduce" dialog with a picture of "Molecule 4" and its contacted neighbouring molecules.

Mode of operation
Choose, if you want to step from outside to inside, that means begin to remove the farmost molecule first, or directly remove the neighbouring molecules.

Apply to or start from...
Default is to start from the centermost molecule, but you can also start from the currently selected atom or the molecule belonging to currently selected atom.

Connection criterion
- If "Contact or H-bond objects between the molecules" is chosen, the reducing processes along the contacts or H-bonds, rsp. Reducing does not work, if there are no more contact or H-bond pseudo-bond objects in the structure picture.
- "Current contact and H-bond definitions (connectivity)" uses the contact and H-bond spheres defined there.
- "Distances" simply uses the distances between (centers of) molecules as criterion.

Using accelerator keys

Diamond offers accelerator keys and toolbar icons to expand or to reduce directly without using "Expand" or "Reduce" dialog:
(1) "Create atoms' neighbouring atoms" (Shift+Ctrl+X),,
(2) "Create molecules' neighbouring atoms" (Shift+Ctrl+Y),
(3) "Create neighbouring molecules" (Shift+Ctrl+Z),
(4) and "Reduce directly".

Previous article: Creating H-bonds and contacts directly from connection parameters
Next article: Grow or cut molecular fragments or polymers

Reference:
COD:1500005: hexaammine cobalt(III) hydrogenarseniate tetrahydrate; Ritu Bala, Raj Pal Sharma, Rajni Sharma, Juan M. Salas, Miguel Quiroos, William T.A. Harrison; J. Mol. Struct. 828 (2007), 174-180.