Diamond Version 5 User Manual: Building up structural parts

Inserting (dummy) atoms and bonds

How to use dummy atoms (and bonds) as centroids or as centers of coordination polyhedra

In this article:
- About dummy atoms and bonds
- Inserting an atom
- Dummy atoms as centers for coordination polyhedra
- About centroids
- Creating big bulbs in MOF frameworks

Previous article: Packing
Next article: Connectivity, part 2: H-bonds and non-bonding contacts

About dummy atoms and bonds

A dummy atom is an atom in the parameter list or its symmetry equivalent created atom, which has coordinates but no chemical meaning. It is normally used as a geometric auxiliary point, for example in the center of a cyclopentadienyl ring or the center of a polyhedron. See also the article "Atomic parameters".

In this context, we call a bond that is not based upon connectivity settings, typically used to connect a dummy atom with real atoms or even between two dummy atoms "dummy bond". To insert bonds between two (dummy) atoms each, you can use the chapter "Inserting a bond between two atoms" in the article "Generating bonds directly".

Inserting an Atom

You can define a new atom in the center of two or more selected atoms. Therefore a new atom will be added to the atomic parameter list as "Dummy" atom.

The most common uses of inserting an atom is to use a dummy atom for example in the center of a cyclopentadienyl ring, like in the following picture:

Reference:

Author(s)
van der Zeijden, Adolphus A. H., Mattheis, Chris, Fröhlich, Roland
Title
[1,2-Di(methoxyethyl)-h5-cyclopentadienyl]trichlorozirconium(IV)
Journal
Acta Cryst. (1998). C54, 458 - 460

To define a dummy atom - for example in the center of a cyclopentadienyl ring -, follow these steps:

1. Build up the structure as described in the previous articles. (For the above example, make use of the molecule function.)

2. Select the five C atoms of the cyclopentadienyl ring, and then choose the Insert Atom command from the Structure menu. This will open the Insert Atom dialog, like in the following example:

3. Change the atom symbol, which is "Dummy" by default (or "Dummy2" for the second dummy atom, etc.), if you want, and then confirm with OK.

4. Choose the Atom Designs command from the Display menu, which opens the Atom Groups and Sites dialog, if you want to change the shape of the dummy atom. (See the article "Designing atoms" how to edit the colors and other styles of atoms.)

How to connect the dummy atom with the praseodym atom like in the picture, see the chapter "Inserting a Bond Between Two Atoms" in the article "Generating bonds directly". To make the bond "fragmentated", read the chapter "Fragmentated Bonds" in the article "Designing bonds and contacts".

Dummy atoms as centers for coordination polyhedra

Another important application of dummy atoms is in the centers of coordination polyhedra, when there is no atom in the parameter list suitable as center. In Diamond a central atom is mandatory for a coordination polyhedra. If there is no chemically reasonable center, you have to define a dummy atom.

This is treated in the article "Polyhedra with no central atom".

About centroids

There are different situations in Diamond where centroids, defind in the center of a set of selected atoms and represented as a dummy atom in the atomic parameter list, are used:

Defining a polygon from a centroid
You can define a polygon by defining a dummy atom as centroid, e.g. in phenyl rings. This is described in the article "Creating polygons".

Defining a centroid as center of a spheroid
The example below shows how to define a centroid to illustrate a void in a metal-organic framework (MOF).

Defining a centroid to measure or calculate distances
Centroids can be used to calculate or measure the distances between e.g. phenyl rings. This is shown in the article "Measuring and reporting distances, angles, and torsion angles" as well as on the Diamond web site in the article "How To Measure Distances Between Centroids".

Creating big bulbs in MOF frameworks

A demonstration how to define a dummy atom with a big radius as spheroid (or "big bulb"), using the Build -> Insert Atom command is shown in the article "How to create big bulbs in MOF frameworks" on the Diamond web site. The spheroid illustrates a void in a metal-organic framework (MOF). We use a rather simple MOF compound, MOF-5 (Zn₄O[C₈H₄O₄]₃) and will create the picture below. The picture in the Wikipedia article about MOF-5 serves as a model for this.

Previous article: Packing
Next article: Connectivity, part 2: H-bonds and non-bonding contacts

[1] COD: 1004001. Jin, Song.; Zhou, Ran.; Scheuer, Ellen. M.; Adamchuk, Jennifer.; Rayburn, Lori. L.; DiSalvo, Francis. J.; "Synthesis, Characterization, and Ligand Exchange Studies of W₆S₈L₆ Cluster Compounds"; Inorganic Chemistry, 40, 2666-2674 (2001)

[2] COD: 1516287. Lock, Nina; Wu, Yue; Christensen, Mogens; Cameron, Lisa J.; Peterson, Vanessa K.; Bridgeman, Adam J.; Kepert, Cameron J.; Iversen, Bo B.; "Elucidating Negative Thermal Expansion in MOF-5"; The Journal of Physical Chemistry C, 114, 16181 (2010)