Diamond Version 5 User Manual: Polyhedra

Polyhedron construction from atoms and bonds

In this article:
- Construct Polyhedron dialog
- Construct one single polyhedron from selected atoms
- Choose a central atom or define a dummy atom
- Options if and how to consider bonds between the ligand atoms to be considered as polygon edges.

Previous article: Polyhedra with no central atom
Next article: Creating polygons

Construct Polyhedron dialog

You can build a single polyhedron from its coordinating atoms rather than starting from one or more central atoms as described in "Creating Coordination Polyhedra". To build ("construct") a polyhedron from its constituting atoms use the command Build -> Polyhedra -> Construct Polyhedron, which will open the Construct Polyhedron dialog, where you can select an atom from the parameter list or a new dummy atom to become the central atom of the polyhedron, the epsilon value (to combine triangular faces to higher polygons) as well as the design for the new polyhedron.

This polyhedron building mode is only available if at least three atoms or three bonds have been selected in the structure picture. A single polyhedron will be built after you confirm the dialog with OK.

All atoms which are currently selected in the active structure picture will be used as ligand atoms for the polyhedron. Alternatively the constituing atoms of the selected bonds will serve as ligand atoms. Selected bonds or bonds between selected atoms can be used to define the polygons' edges.

The dialog will either propose a suitable atom in the structure picture as central atom, or alternatively create a dummy atom (centroid), if there is no atom available in the center of the selected atoms.

Replacing existing polyhedra
If the Replace existing polyhedra checkbox is checked, an existing polyhedron will be deleted and renewed with the current settings. Otherwise a polyhedron will only be built around an atom which is not yet central atom of a previously created polyhedron.

Define polyhedron's design
The Design button opens the Polyhedron Design dialog, where you can define style, colors, material, hatching and surface properties of the polyhedron that is to be created with this dialog. More details about polyhedron design is available here: "Polyhedron design and hatching".

Construct a polyhedron from selected atoms

The option (radio button) Construct from selected atoms (and create polygons automatically) uses the currently selected atoms as corners of the polyhedron. Diamond uses an Angle epsilon to define the polygons, i.e. if a triangle can be extended to a polygon with four or more edges each. This is the same way of creating faces and edges as in the Add Polyhedra dialog.

Define the angle epsilon
The value behind Angle epsilon defines an angle used for the extension of triangular polyhedron faces to polygons with four or more edges. Its default value is one degree. Diamond tries to extend the initially built triangular faces to polygons with four or more edges. For that, additional points are checked whether they are positioned approximately in the plane formed by the points of the triangle. If such a point encloses an angle of less than Angle epsilon degrees with the plane, it will be added to the triangle leading to a square, pentagon, etc. This epsilon value applies only to this (i.e. the first mentioned) mode of operation.

Choosing a central atom

The list Choose central atom... contains all atoms, which can be created directly from the parameter list or by applying suitable symmetry operations to become central atom of the new polyhedron. For each atom, the atom symbol, the symmetry code and the distance of the atom from the center of the selected atoms (in Angstroems) is given. This value is usually zero for a "regular" polyhedron. If there is no suitable atom in the sphere (whose limits are given by the selected atom that is closest to the center), Diamond proposes the creation of a dummy atom (as centroid of the selected atoms). The option to choose a dummy atom instead of a real atom from the parameter list is available in any case. Diamond will add the selected atom automatically to the structure picture, if it has not yet been created.

The article "Inserting (dummy) atoms and bonds" describes in more details about using dummy atoms as centroids.

Considering bonds as polygon edges

The Construct Polyhedron dialog offers enhancements in the construction of coordination polyhedra from atoms and by additional options if and how to consider bonds between the ligand atoms to be considered as polygon edges.

Whereas the above mentioned option Construct from selected atoms [...] only considers the selected atoms and ignores bonds, there are three more options where you can choose how far selected bonds can be involved in the construction:.

Construct from selected atoms and use the bonds between as polygon edges:
Like the option above, this uses the current selection of atoms for building the polyhedron's corners. But rather than trying to extend triangles to higher polygons with the help of an angle, Diamond here uses the bonds between the selected atoms to delimit the polygons, i.e. to "convert" them to polyhedron edges.
Note: The bonds between the selected atoms are taken for edges, regardless if they are marked as selected or not.

Construct from selected bonds:
This option uses the currently selected bonds to delimit polygons and the constituing atoms of these bonds as polyhedron corners. It considers only bonds that are currently marked as selected. The atoms at the bonds' ends need not be selected, any atom selection is ignored with this option anway.

Construct from selected atoms _and_ selected bonds:
This option uses the selected atoms as corners and only the selected bonds to delimit the polygons. If there are bonds between the selected atoms that are not selected, these unselected bonds will not be considered as polygon edges.

Destroying the bonds
Since in most cases the bonds between the polyhedron's ligand atoms are just to become edges but not chemically meaningful, it is useful to delete these bonds after a successfull construction of the polyhedron, that means after they have been "converted" to polygon edges.
To destroy bonds that have been converted to edges - using the above mentioned three options - set the checkmark at Destroy bonds that have been converted to polyhedron edges.
Note: This checkbox is not available (grayed) when you use the first option Construct from selected atoms (and create polygons automatically).

How to get the bonds between the ligand atoms?
Since in most cases these "bonds" are not chemically meaningful, they most likely cannot be created with the default setting in connectivity or atomic environments.
There are two different approaches to create them yet:
(1) Use the command Build -> Insert Bonds to start a mode where you click on two atoms each to define a bond between each, regardless of any connectivity etc. settings. (See the article: Generating bonds directly).
(2) Use the command Build -> Connectivity and activate a checkmark in the list of bond groups (atom group pairs) and adjust the "bonding sphere" After that you have to call a suitable command that creates these bonds, e.g. Build -> Connect Atoms. In the Connect Atoms dialog you have the choice to apply your bond creation specifically to the atom group combinations used in the polyhedron's coordination sphere.
Method 1 is best, if you construct single or few polyhedra. If you have a lot of polyhedra to build you should use method 2 instead.

Previous article: Polyhedra with no central atom
Next article: Creating polygons