Step 9b - Hydrogen Bond Geometry

Water is the archetypal hydrogen bonding fluid, and so it makes sense to analyse the hydrogen bonding contacts within the fluid. We will be principally interested in the geometry of O–H···O contacts occurring in the liquid in terms of the H···O distance and the O–H···O angle.

Define Atomic Sites

We’ll need simple atomic sites for the oxygen and each of the hydrogen atoms in our water molecule, so let’s create them now:

Open the Water and go to the Analysis Sites section

Click-drag with the left mouse button in the species viewer and draw a box around the oxygen atom to select it

Click the Create button in the viewer toolbar to create the new site (which will be called O)

Repeat this for each hydrogen atom individually, naming those sites H1 and H2

Create the Analysis Layer

Let’s now create a new layer and add the analysis module that we want:

Layer ⇨ Create ⇨ Empty

Rename the layer by double-clicking on the tab name, and change it to ‘Analyse HBond’

Show the module palette for the layer by clicking Show Available Modules at the very bottom of the module list

Drag a CalculateDAngle module over to the Current Modules list

As its name suggests, the CalculateDAngle module calculates distance and angle histograms, and their 2D map, from three target sites. Since the module is general-purpose, we’ll need to set up the module to give us information on our specific geometry of interest. CalculateDAngle assumes in the target interaction A–B···C that A–B occur on the same molecule, and gives us a choice as to whether we exclude C sites that are also on the same molecule.

Select the CalculateDAngle module to display its options

Open the Control settings group

Change the maximum value of the DistanceRange to 5.0 Å

Press the button for SiteA and choose the O site

For SiteB select both the H1 and H2 sites

For SiteC choose the O site

Enable the ExcludeSameMolecule to ignore interactions where site C is on the same molecule as A and B.

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