Diamond Version 5 User Manual: Building up structural parts

Generating Bonds Directly

This article is about generation of bonds on demand:
- Connecting all atoms of the structure picture or the selected atoms only
- Consideration of individual atom sites possible in "Connect Atoms" dialog.
- Inserting a bond between two atoms
- Creating bonds directly from the Table of bond parameters

Previous article: Cell edges
Next article: Filling spheres

While atomic positions are mandatory for Diamond to display a (crystal) structure, direct bonding information in the structural input parameters is not. Connection parameters (i. e. bonds, H-bonds and contacts) are just optional parameters. The articles "Connectivity, part 1: Bonding spheres" and "Atomic environments [...]" describe the choices to determine which atom types or sites can be connected and where the boundaries of the bonding spheres are.

There are three different ways to generate bonds between generated atoms:

1. Automatic generation when atoms are generated

Atoms are connected automatically when surrounding atoms in coordination spheres or molecules are created. For details, see the articles "Filling spheres" and "Generating molecules", rsp.

2. Connecting atoms on demand

All or selected atoms are connected with each other on command, e.g. after the atoms of the unit cell have been generated. This is described in "Connecting All or Selected Atoms".

Both methods work with the connectivity list by default or with atomic environments optionally.

3. Inserting bonds manually

Two selected atoms can be connected independent from the current settings in the connectivity list or atomic environments, that means even the strongest bonding geometry can be forced. "Inserting a Bond Between Two Atoms" describes how to insert bonds manually.

Connecting All or Selected Atoms

This part describes how some or all created atoms can be connected with each other basing on the bonding criteria, which are currently defined in the connectivity list or with the atomic environments. The default "sphere type" is "generic", that means derived from the connectivity. You can change this to "atomic environments" in the Connect Atoms dialog (see below).

To use several options how to connect atoms, choose the Connect Atoms command from the Build menu, which opens the Connect Atoms dialog. To directly connect atoms with each other push the (red marked) button in the Build toolbar, or use the accelerator key Shift+Ctrl+N.

Connecting all atoms of the structure picture

When run from the toolbar button or accelerator key, the connecting function applies to all created atoms, if no atom is currently selected. This means, all atoms of the structure picture will be connected with each other, provided that the atom type combinations (the bond types) are (a) enabled for bonding and (b) if the interatomic distances are within the bonding spheres.

Connecting selected atoms with each other

When run from the toolbar button or accelerator key, If two or more atoms are selected, only these selected atoms will be connected with each other, provided that the atom type combinations are (a) enabled for bonding and (b) if the interatomic distances are within the bonding spheres.

Creating bonds which are not enabled in the connectivity list

As stated above, the bonding criteria are derived from the connectivity list (or alternatively from atomic environments). If you must connect atoms, which are not presently enabled in the current connectivity list, you have two possibilities:

A. If there is only a few amount of atoms to be connected, you can insert the bonds manually, using the method that is described below: "Inserting a Bond Between Two Atoms".

B. If a rather large amount of atoms is to be connected, use the following way:

1. From the Build menu, choose the Connectivity command to open the Connectivity dialog.

2. In the Connectivity dialog go to the Bonds page and enable the atom group combination for bonding in the list Select atom group pair(s) to be connected.

3. Change the bonding sphere if necessary either by editing the values for DMin or DMax or by shifting the blue lines in the histogram.

4. Push the Connect Now button. This will connect all atoms with each other (or the selected atoms, rsp.) basing on the current setting of the connectivity list.

5. Close the Connectivity dialog using the Cancel button to leave the previous settings for the connectivity list unchanged.

Adjusting structure picture to current connectivity

Changes in the connectivity list do not reflect existing bonds. This means, a bond will not be destroyed automatically, if the corresponding atom type combination becomes disabled for bonding or if the bonding sphere becomes shorter or longer than the actual interatomic distance. (In similar way bonds will not automatically be created on changes of the connectivity list.)

If you must get rid of bonds, which are not more enabled by the connectivity list, you have to delete them manually. The most appopriate way to adjust the structure picture to the current connectivity list, is to delete all bonds first, then to call the Connect function:

1. If the data sheet or a list is active in the secondary pane, click into the structure picture with the mouse. (This is necessary to set the input focus to the main pane.)

2. From the Edit menu, choose the Select All command. This will mark all objects as selected.

3. With the right mouse button click into one of the selection markers, and choose the Bonds command from the Destroy submenu of the context menu. This will selectively destroy only the bonds, but leave all other selected objects, such as atoms or labels, unchanged.

4. Click into the structure picture. This will reset all selections.

5. Use the toolbar button or the accelerator key Shift+Ctrl+N. This will connect all atoms with each other basing on the current connectivity list.

Using Connect Atoms dialog

While the above mentioned toolbar button or accelerator key Shift+Ctrl+N directly applied -- without showing up a dialog for additional options -- to all atoms of the current structure picture and connected the atoms depending on the current settings in "Build"/"Connectivity". (When atoms were selected, only these atoms were considered in the command.)

The command Connect Atoms... -- when run from the Build menu -- shows the following dialog with several options:

Connection method
- "Between all atoms of structure picture": This connects all atoms of the structure picture. The result is the same as using the toolbar button or accelerator key, if no atoms are selected.
- "Between atoms currently selected in structure picture": This also connects atoms but considers only the currently selected atoms. The result is the same as using toolbar button or accelerator key when atoms are selected.
- "Between atom groups or sites selected below": Rather than considering the current atom selection, you can choose which atom types and/or individual sites to be considered when connecting atoms.
- A special option and in some way closer to the "coordination sphere" function is the fourth choice "Around atoms currently selected in structure picture". This considers the currently selected atoms as centers of spheres (type see below) and connects them with neighbouring atoms in that sphere regarding the atom types or sites selected in the "To atom groups/sites" list. Unlike the "Coordination Spheres" command, this does not create atoms that are (for whatever reason) missing in a sphere -- it just adds bonds between atoms "as is".

Type of bonding sphere
Here you can choose, if to use the connectivity or the atom sites' individual atomic environments to decide, if two atoms in question are to be connected or not. Besides this, you can also define a fixed-size connection sphere with Rmin and Rmax that is independent from the atom types or sites each.
Note: When you switch from "Generic [...] connectivity" to "Atomic environments" or back, the toolbar button or accelerator key Shift+Ctrl+N will use that sphere type in the next call. Toolbar button and accelerator key never use the "Fixed size" option, so it is only available from the dialog.

Inserting a Bond Between Two Atoms

A bond can be inserted between two selected atoms, independent from the connectivity list or atomic environments. This enables to create bonds that may have no chemical meaning.

Diamond supports two different modes to insert one or more bonds between two selected atoms each. The first mentioned mode is to select the two atoms, and then executing the command to insert the bond. The second mode enables you to select two atoms each, which will then automatically be connected. This mode is continued unless you end it.

Follow these steps to insert a bond between two atoms:

1. Click on the two atoms, which are to be connected, one after the other.

2. Push the (red marked) button in the Build toolbar.

Follow these steps to create multiple bonds:

1. From the Build menu, choose the Insert Bonds command. The mouse cursor will change its symbol.

2. Click on two atoms, which are to be connected, one after the other.

3. Repeat these two steps, if you want to connect other atom pairs.

4. To end this mode, choose the Insert Bonds command again or simply press the Esc key.

The design of the new bonds is copied from the design of the corresponding bond group (which is normally identical with the standard bond design), and can be changed after bond creation (like every bond may be edited individually). See the article "Designing bonds and contacts".

Creating bonds from the table of bond parameters

You can use the table of bond parameters (available through the corresponding command in the Table submenu of the View menu) to create the bonds that are selected in table directly or to add bonds at symmetry-equivalent positions.

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

Previous article: Cell edges
Next article: Filling spheres