Diamond Version 5 User Manual: Building up structural parts

Creating and Modifying Broken-off Bonds

In this article:
Creating broken-off bonds
Using Broken-off Bonds dialog to convert or delete broken-off bonds
Using atom style "invisible" to simulate broken-off bonds

Previous article: Filling spheres
Next article: Generating molecules

Creating Broken-off Bonds

The so-called "broken-off" bonds are usually used to display an infinitesimal framework, that means especially for inorganic 3D frameworks or layer structures.

The most common way to create broken-off bonds is to choose the Coordination Spheres command from the Build menu. In the Coordination Spheres dialog, select the atom groups (or sites) for central atoms as well as the atoms to be generated, and check the Create broken-off bonds checkbox. Then press the OK or Apply Now button to start the generation of broken-off bonds.

There is a shortcut available from the Build toolbar by opening the dropdown menu right beneath the Fill Coordination Spheres Directly toolbar button or using the accelerator key Shift+Ctrl+K:

When Diamond generates broken-off bonds during filling of coordination spheres, the created atoms get the "broken-off" flag. Each time Diamond draws a bond (or contact) between a visible and a "broken-off" atom, this will be shortened to 0.7 of its normal length (distance between centerpoints of the two atoms each).

Example: Contents of the unit cell of alpha quartz (left) with Si in cyan and O in red color. The second picture shows the next Si neighbours of the O atoms, whereas the right picture shows broken-off bonds to these Si atoms instead.

If you use a Number of cycles greater than one, only those atoms become invisible that are generated in the last cycle.

The relative length of a broken-off bond can be changed from its default value 0.7. Use a value of 1, if you want the broken-off bond have the same length as the "normal" bond. The value is defined on the "Others" page of the "Bond [Group] and Contact Design" dialog. See the article "Designing bonds and contacts" for details. This explains also how to define the default design for broken-off bonds.

The option to use broken-off bonds is also available when you grow (inorganic) polymeric frameworks, i. e. complete build up coordination spheres step by step. See the article "Grow or cut molecular fragments or polymers" for details.

The attribute "broken-off" can also be used for (non-bonding) contacts or H-bonds. See the article "Expand or reduce clusters of molecules".

Using Broken-off Bonds dialog to convert or delete broken-off bonds

In this dialog you can:
- convert selected bonds or bonds around selected atoms into broken-off bonds,
- (re-)convert broken-off bonds into normal bonds,
- or destroy selected or all broken-off bonds (which also destroys the atoms at the invisible ends of the bonds each).

Unit cell of an Antimony (Sb+3/Sb+5) Fluoride (from PCD:1251073) where coordination spheres around "Sb 1" sites (Sb+3) have been completed with F atoms. The Sb--F bonds will be converted to broken-off bonds with the terminal F atoms made invisible (below).

Note: This function works also for non-bonding contacts and H-bonds (H....acceptor atom or donor....acceptor atom).

The dialog offers three modes of operation:
Make broken-off bonds [...] from normal bonds: This converts normal bonds (or contacts or H-bonds) into broken-off bonds. Not all application methods (see below) can convert bonds etc. in this operational mode, since a broken-off bond is not bi-directional as a normal bond.
Convert broken-off bonds [...] to normal bonds: This converts broken-off bonds (or contacts or H-bonds) (back) into normal bonds. The atoms at the invisible ends of the broken-off bonds then become visible.
Destroy broken-off bonds: This simply destroys the selected or all broken-off bonds, depending on the application method. This also destroys the atom at the invisible end of a broken-off bond each.

There are several ways of application from the Apply to dropdown box, not all are available for all above mentioned modes:
Selected bonds: This converts the bonds that are currently selected in the structure picture into normal bonds or destroys them.
Selected atoms indirectly: This converts the atom at the opposite end of the bond each when converting between normal and broken-off bond.
Selected atoms directly: This directly turns the selected atom(s) into invisible or visible - depending on the mode of operation.
All bonds: This can be used to convert all broken-off bonds (contacts, H-bonds) in the structure picture into normal bonds (contacts, H-bonds) or to destroy all broken-off bonds, contacts, or H-bonds, depending on mode of operation.
All atoms: The same as "All bonds".
Note: The operational mode that converts normal bonds into broken-off bonds only works for "Selected atoms directly" and "Selected atoms indirectly". 

Note: The functions in this dialog only convert broken-off bonds (or contacts, H-bonds) into normal bonds or vice versa - or simply destroy them. But they do not create new broken-off bonds by filling coordination spheres with the neighbouring ("ligand") atoms set to invisible and the bonds to "broken-off". For this use the command "Coordination Spheres" from the "Build" menu and check the "Create broken-off bonds" checkbox in the dialog.

Using atom style "invisible" to simulate broken-off bonds

Manual creation of broken-off bonds

Due to compatibility with older versions of Diamond there is another way to make bonds look broken-off and to make atoms at the broken-off end invisible: You can manually assign the attribute "invisible" to one or more atoms with the help of the Atom Design dialog. See the article "Designing atoms" how to edit the attributes (the design) of one or more selected atoms. Bonds to such invisible atoms will then automatically look as broken-off bonds.

Resetting broken-off bonds to normal bonds

You can reset broken-off bonds to normal bonds by resetting the "invisible" attribute of the corresponding atoms. Please note that the "invisible" attribute may be changed automatically, if you edit designs of atom groups or sites with the "Update created atoms" flag (in the "Atom Groups and Sites Design" dialog) switched on.

Previous article: Filling spheres
Next article: Generating molecules

Reference for PCD-1251073:
Sb₄F₁₆ in P12₁/c1 (14);
"The Crystal Structure of the 1:1 Adduct of Antimony Trifluoride and Antimony Pentafluoride", by: Gillespie R.J., Slim D.R., Vekris J.E.; J. Chem. Soc. (Dalton Trans.) 1977, p. 971.