Tutorial 3: How to Construct a Dimer Manually From Monomer Z‐Matrices?

In this tutorial, we will demonstrate how to go from a pair of monomers to a dimer interaction with coordinates using the rules file. Our selections will be bromobenzene bromine as our monomer A and the hydrogen of propane as our monomer B.

Marking a Site Point on Z-matrix Monomer A

For the first monomer bromobenzene, our goal is to mark the bromine with a virtual atom to mark the site point of interaction.

We modify the z-matrix by having the first atom be the site and a virtual atom that is placed at the end of the z-matrix. The virtual atom has a distance of 1.0 Angstroms and placed out of plane of the molecule. To make it visually easier you can replace X11 with SE11 temporarily to see the placement of the virtual atom.

Bromobenzene

BR11
C11  BR11  1.8000
C12  C11  1.3986   BR11  120.0000
C13  C12  1.3774   C11  120.0000   BR11  -180.0000
C14  C13  1.3774   C12  120.0000   C11     0.0000
C15  C14  1.3774   C13  120.0000   C12     0.0000
C16  C11  1.3774   C12  120.0000   C13    -0.0000
H11  C13  1.0756   C12  120.0000   C11   180.0000
H12  C14  1.0756   C13  120.0000   C12  -180.0000
H13  C15  1.0756   C14  120.0000   C13   180.0000
H14  C16  1.0756   C11  120.0000   BR11    -0.0000
H15  C12  1.0756   C11  120.0000   BR11     0.0000
X11  BR11  1.0000   C11   90.0000   C12     0.0000
0 1

Marking a Site Point on Z-matrix Monomer B

To create a monomer B z-matrix we of propane we will have to modify the Monomer A.

H11
C12 H11 1.1026
C11 C12 1.5332 H11 110.7849
H12 C12 1.1026 C11  110.7849   H11  119.4559
H13 C12 1.1026 C11  110.7849   H11 -119.4559
C13 C11 1.5332 C12  112.0949   H11   59.7279
H14 C13 1.1026 C11  111.6593   C12   59.7279
H15 C13 1.1026 C11  111.6593   C12  -59.7279
H16 C13 1.1014 C11  111.6593   C12  178.5023
H17 C11 1.1034 C12  109.5193   H11 -178.5023
H18 C11 1.1034 C12  109.5193   H11  -62.0416
X11 H11 1.0000 C12   90.0000   C11  180.0000
0 1

Replace all the atom names with with the index of 2 instead of 1 like so:

H21 
X21 H21 1.0000 
C22 H21 1.1026 X21  90.0000  
C21 C22 1.5332 H21 110.7849  
H22 C22 1.1026 C21  110.7849   H21  119.4559
H23 C22 1.1026 C21  110.7849   H21 -119.4559
C23 C21 1.5332 C22  112.0949   H21   59.7279
H24 C23 1.1026 C21  111.6593   C22   59.7279
H25 C23 1.1026 C21  111.6593   C22  -59.7279
H26 C23 1.1014 C21  111.6593   C22  178.5023
H27 C21 1.1034 C22  109.5193   H21 -178.5023
H28 C21 1.1034 C22  109.5193   H21  -62.0416
X21 H21 1.0000 C22   90.0000   C21  180.0000
0 1

Combining Z-Matrices Together

Next step is to follow a Rule 3 from as listed in the paper between a hetereoatom and a hydrogen. Where the :# atoms are numbered based on the 3-atoms of the Monomer A.

BR11
C11  BR11  1.8000
C12  C11  1.3986   BR11  120.0000
C13  C12  1.3774   C11  120.0000   BR11  -180.0000
C14  C13  1.3774   C12  120.0000   C11     0.0000
C15  C14  1.3774   C13  120.0000   C12     0.0000
C16  C11  1.3774   C12  120.0000   C13    -0.0000
H11  C13  1.0756   C12  120.0000   C11   180.0000
H12  C14  1.0756   C13  120.0000   C12  -180.0000
H13  C15  1.0756   C14  120.0000   C13   180.0000
H14  C16  1.0756   C11  120.0000   BR11    -0.0000
H15  C12  1.0756   C11  120.0000   BR11     0.0000
X11  BR11  1.0000   C11   90.0000   C12   180.0000
0 1
--
H21  :1 DISTANCE  :2 ANGLE      :3  DIHEDRAL
X21 H21 1.0000    :1  90.0000   :2   0.0000
C22 H21 1.1026 X21  90.0000     :1  180.0000
C21 C22 1.5332 H21 110.7849     :1  180.0000
H22 C22 1.1026 C21  110.7849   H21  119.4559
H23 C22 1.1026 C21  110.7849   H21 -119.4559
C23 C21 1.5332 C22  112.0949   H21   59.7279
H24 C23 1.1026 C21  111.6593   C22   59.7279
H25 C23 1.1026 C21  111.6593   C22  -59.7279
H26 C23 1.1014 C21  111.6593   C22  178.5023
H27 C21 1.1034 C22  109.5193   H21 -178.5023
H28 C21 1.1034 C22  109.5193   H21  -62.0416
X21 H21 1.0000 C22   90.0000   C21  180.0000
0 1

And voila you have successfully made a dimer z-matrix by manipulating the coordinates which you can use to perform various PES.