Diamond Version 5 User Manual: Building up structural parts

Grow or Cut Molecular Fragments or Polymers

Repeatedly add spheres to molecular fragments or to polymers or remove them

This article is about:
Growing means adding another sphere of bonded neighbouring atoms to the existing polymer or molecular fragment, whereas Cutting back is the opposite of growing. Here Diamond looks for the outmost atoms of a polymer or molecule (or molecular fragment) and destroys them.
- Command "Build/Grow or Cut": Apply to all or selected atoms (molecules or polymers), option to step over broken-off bonds.
- Also available from "Build" toolbar: "Grow directly" and "Cut directly".

Previous article: Expand or reduce clusters of molecules
Next article: Pump Up or Shrink Polymeric Frameworks

In this article we use the sample document "COD-4064373.diamdoc" to demonstrate the step-by-step growing and cutting of a 1,2-diphosphinoethanide complex. The document comes up with a picture of a polymer fragment that has been created with the function "Get molecules directly", followed by a "Create broken-off bonds". The molecule function tries to create one or more (closed) molecules from the atoms in the parameter list but stops when it grows into a neighbouring cell. The subsequent creation of broken-off bonds is to symbolize where the molecule generator has stopped and where the polymer continues to grow.

Initial structure picture of COD:4064373 as result of "Get molecules" and "Create broken-off bonds" functions. This and the following screenshots have been made with Diamond version 4.

In the first sequence of growing (and cutting), we directly access the toolbar buttons for "Grow directly" and "Cut directly", rsp.

Clicking multiple times on the "Grow directly" button (highlighted in the above screenshot) results in the following sequence:

The function "Grow directly" and "Cut directly" use broken-off bonds in every step only, if the starting picture has broken-off bonds. If you don't want the broken-off bonds (or explicitely want broken-off bonds, if the initial picture has none) or choose if to apply the growing (or cutting) function to all molecules/polymeric fragments in the picture or just tot the selected ones, use the "Grow or Cut" dialog, which is accessible through the "Grow or Cut..." command in the "Build" menu:

Please note, that the "Cut" command works independently from a (series of) previous "Grow" command(s). Instead it searches for the end of a polymeric fragment (or complete molecule) and removes the atoms beginning with the atoms of the outmost sphere. If you want to play a grow sequence back and forth, we recommend to use the Undo and Redo functionality. There is also the "Pump" and "Shrink" functionality that works somewhat more precise when you start from a certain selected atom; cf. the next article.

Previous article: Expand or reduce clusters of molecules
Next article: Pump Up or Shrink Polymeric Frameworks

Reference:
COD:4064373: Lithium[2-(1,3-bis-(2',6'-dimethylphenyl)[1,3,2]diazaphospholenyl-3- diphenylphosphino-1-cyanoethanide]dichloropalladium(II).
Förster, Daniela; Nieger, Martin; Gudat, Dietrich; "Synthesis and Characterization of an Unsymmetrical 1,2-Diphosphinoethanide Complex "; Organometallics, 30, 2628 (2011).