Constructing molecular Voronoi-Dirichlet polyhedra for benzene molecules and estimating their sizes 


Algorithm:

1. Go to the C6H6 record, compute the adjacency matrix and open an IsoCryst window. Grow molecules and select one of them. Click button to get the Voronoi-Dirichlet polyhedron for the molecule.
   
   
   
   Unselect the molecule, select all domain vertices (ZA nodes) and choose the Wire model for them.
   
   
   
   Unselect the nodes and select the molecule again.
   
   
2. Perform Calculate/Selected Atoms and pay attention to the total volume (107.66 ų) of the domain that estimates the volume of the molecule.
   
   



3. Close the IsoCryst window and open an ADS window. Clear all Topology options and specify the following Common and Molecular VDP options:
   
   
   
   Run ADS and choose the Whole Molecule mode. You will get the following output:
   
   

   ---

   Central atoms: none
   Structure consists of molecules (ZA1). The composition of molecule is C6H6  

   H		1		0.9080		0.2438		0.0067	( 0 0 0)
   H		1		1.0920		-0.2438		-0.0067	( 2 0 0)
   H		3		1.2329		-0.0880		0.2049	( 2 0 1)
   C		1		1.0565		-0.1450		-0.0049	( 2 0 0)
   H		2		0.8631		-0.1585		-0.2348	( 1 0 0)
   C		2		0.9165		-0.0960		-0.1399	( 1 0 0)
   H		3		0.7671		0.0880		-0.2049	( 0 0-1)
   C		3		1.1374		-0.0530		0.1230	( 2 0 1)
   H		2		1.1369		0.1585		0.2348	( 1 0 0)
   C		2		1.0835		0.0960		0.1399	( 1 0 0)
   C		3		0.8626		0.0530		-0.1230	( 0 0-1)
   C		1		0.9435		0.1450		0.0049	( 0 0 0)

   Mass=78.114;Vol=107.66;Rsd=2.951
   GravityC: 1.0000 0.0000 0.0000
   Centroid: 1.0000 0.0000 0.0000
   
   Crystal chemical formula: 0D
   Topology for ZD1

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   Pay attention to the value of the molecular domain volume.
   
   

Exercise: Estimate volumes for solvate benzene molecules in the three remaining structures (WAYFAT, ZIRJUF10, WUVVOY). How large are the differences in their volumes?

Answers: WAYFAT Vol = 124.33; ZIRJUF10 Vol = 127.02; WUVVOY Vol = 130.18.
The differences are not very large.

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