Step 1 - Create the Species

Draw the Molecule

The first thing we’ll do is draw a benzene molecule as best we can:

Species ⇨ Create… ⇨ Draw

A new editor window opens in which we can draw the rough geometry and connectivity for our molecule.

Draw a roughly hexagonal ring of six carbon atoms (carbon is the default drawing element) by left-click-dragging in the viewer

Change the drawing element from C to H by clicking on the button next to the draw mode icon

Connect a single hydrogen atom to each carbon by left-click-dragging from each carbon site

Click OK to close the editor and create the new species

Double-click on the new species’ tab and change its name to Benzene

Apply a Forcefield

Time to make it a little prettier! We’ll assign a standard forcefield to it, and optimise the geometry:

Species ⇨ Add Forcefield Terms

From the available forcefields choose OPLSAA2005/Aromatics and click Next

We will use the default Determine atom types for all atoms option to add atom types for every atom in the species, so click Next

There will be no conflicts with existing atom types as there are no atom types already defined, so click Next

For the intramolecular terms we want to assign them and reduce to master terms (the default settings) so click Next to proceed

There will be no conflicts with existing master terms, so click Finish to exit the wizard

We will also get ahead here and edit the master terms to reflect the geometry observed in the experimental data, since the forcefield we’ve applied here doesn’t get things quite right.

Forcefield tab, Master Terms section

Change the bond length (Parameter 2) of the CA-HA bond term from 1.08 to 1.09 Å

Change the bond length (Parameter 2) of the CA-CA bond term from 1.40 to 1.38 Å

Create Isotopologues

Since some of the experimental data was measured on deuterated benzene, we’ll need to create a suitable C₆D₆ isotopologue:

Benzene species tab, Isotopologues section

Click Add

Expand the entries for the ‘NewIsotopologue’ by clicking the [+] next to its name, or by clicking Expand All

Change the isotope for the HA atom type from Natural (bc = -3.739 fm) to 2 (bc = 6.671) by clicking on the isotopologue entry and chosing from the drop-down menu

Change the name of the isotopologue to ‘C6D6’ (click on the name to do so)

The other isotopologues we need are either generated automatically by Dissolve (i.e. the natural isotopologue for C₆H₆) or are created by mixing existing isotopologues (as will be the case for the 50:50 mix).

Add Analysis Sites

We’ll locate our analysis site at the centre of the benzene ring and give it some axes so that we may calculate orientational / spatial functions around it. The figure below shows the atoms we’ll select to define the origin (purple), x-axis (red) and y-axis (blue). Using these atoms as reference points for our coordinate system will set the XY plane to that of the ring, with the z axis perpendicular to the ring.

<img style='display: block; margin-left: auto; margin-right: auto;' src="site.png"></img>

Origin (purple), x-axis (red) and y-axis (blue) atoms defining the oriented benzene site

Benzene species tab, Analysis Sites section

Select all six carbon atoms by clicking on them in the viewer (you may need to click reset view first, to see the whole molecule)

Click Create in the viewer toolbar to create a new site with the origin at the center between these six atoms

Now select the single carbon atom and click X Axis in the toolbar to define the direction of the x axis

Finally, select the pair of adjacent carbon atoms and click Y Axis in the toolbar to define the direction of the y axis

Rename the site to COG by double-clicking C6

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Back to Overview

Next Step

Click the “medic” icon in the species viewer toolbar to optimise the geometry of the molecule

You can filter forcefields by keywords in name and description by using the filter box at the top-right of the forcefield selection controls.

Select draw mode from the toolbar above the species viewer