Step 1 - Create the Species

Draw the Molecule

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

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

Select draw mode from the toolbar above the species viewer

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

You can create bonds by left-click-dragging between two existing atoms.

Your final species will look something like this:

A very badly drawn benzene molecule

Click OK to close the editor and create the new species

Double-click on the NewSpecies 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:

From the available forcefields choose OPLSAA2005/Aromatics and click Next

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

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

Click the Medic icon in the species viewer toolbar to optimise the geometry of the molecule using the forcefield we’ve just applied

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.

Go to the Forcefield tab, Master Terms section

In the Bonds table change the equilibrium bond length parameter (eq) of the ‘CA-HA’ bond term from 1.08 to 1.09 Å

Change the equilibrium bond length of the ‘CA-CA’ bond term from 1.40 to 1.38 Å

Create Deuterated Isotopologue

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

Go to the Benzene species tab, and click on the Isotopologues section

Click Add to create a new isotopologue for the species

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

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

The Natural isotopologue is always available and doesn’t need to be created, but doesn’t appear in the list of user-defined isotopologues. It is also not necessary to create “mixed” isotopologues (e.g. for 50:50 mixtures of H:D) as these are created by mixing individual isotopologues.

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, pointing out of its center.

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

Resulting axis definition in 3D

Go to the Benzene species tab

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

Right-click the selected atoms and click Create site from ⇨ Atoms This creates a new site with the Carbon atoms as the Origin Atoms

Now select the single carbon atom (as depicted in the image above) and right click it.

Click Modify current site ⇨ Set X-Axis Atoms to define the direction of the x axis

Finally, shift-click the pair of adjacent carbon atoms and right click on them

Click Modify current site ⇨ Set Y-Axis Atoms to define the direction of the y axis

Rename the site to COG by double-clicking its name

Back to Overview Next Step

Last modified November 27, 2024: docs: Updated for 1.6 release (#2000) (8cbaf4e5f)