Water dimer simulation

Calculations of the properties of liquid water can be compared to calculations of the energy and structure the gas phase water dimer. The energy of dissociation and the angle between two water molecules in the gas phase (shown below) are known experimentally. Previous simulations of water have discussed the calculation of the water dimer (see for example Jorgensen et al. J. Chem. Phys. 1983, 79, page 927). In this problem you will build a model water dimer, perform a simple minimization and then determine interaction energy and the angle between the water bisector of one of the waters with respect to the hydrogen bonding axis.

 

Objectives

1. Determine the energy of hydrogen bond formation from the output of the DISCOVER minimization.

2. The general structure of the water dimer is shown below

calculate the angle between the vectors A and B where A points along the hydrogen bond axis and B is bisector of water 2.

 

3. Compare these numbers to those available in the literature.

 

Method

Go to the Builder pull-down menu. Use the Fragment/Get command and select hydroxy from the FRAGMENT_WINDOW to create the water molecule. The FRAGMENT_WINDOW will contain a number of groups. These groups can be used individually or can be bonded together. Once a water molecule has appeared on the screen the menu will be altered to allow you select a second fragment. For this module just select Cancel to exit the Fragment pull-down menu. Now you should see a single water molecule in the center of the monitor. To create a second water molecule perform these operations a second time. There will now be two separate water molecules on the screen. They may not appear separate. One way to move them independently is to click on the Connect Object button on the bottom menu bar. After you click on this button, the next object you select will be the only one attached to the mouse. You may move it independently.

To associate these molecules use the Assembly/Associate command.

Object 1 [water 1] (your molecules may have different names)

Object 2 [water 2] (you may click on the objects in parmeters window under Objects)

New Assembly Name [DIMER] (type this in to give your assembly a name)

Select Execute

 

Select Optimize in the builder. This function will automatically choose the forcefield and perform an energy minimization on the two water molecules.

 

If you get a strange orientation that does not in any way resemble the picture above you probably trapped in a local minimum. Simply displace one water several Å from the other and the retry the calculation.

 

To determine the angle you will need to use the Measure/Angle command in the INSIGHT menu bar. Once you have selected this function type on the three atoms whose angle you wish to determine. The angle will appear on the screen with dots outlining the atoms you have selected. To eliminate a selection select clear in the menu and then select Execute. This is often necessary to make more than one measurement since it is hard to read the overlapping values.

 

Once you have completed this exercise determine the average binding energy from the output file. Use trigonometry to determine the angle shown in the diagram above. Compare these to literature values.