3 Visualising the results with VMD

The molecular visualisation tool VMD can be used to visualise the data created by Waveplot. Also, any other tool being able to parse the Gaussian cube file format is appropriate. (The pictures presented here were generated using VMD 1.8.6.)

3.1 Total charge distribution

The cube file containing the total charge distribution wp-abs2.cube can be read by using the File/New Molecule menu. VMD should automatically recognise, that the file has the Gaussian cube format. After successful loading, the VMD screen shows the sceleton of the molecule.

In order to visualise the charge distribution, the graphical representation of the molecule has to be changed. This can be achieved by using the Graphics/Representations... submenu. The sceleton representation can be turned to a CPK represenation (using balls and stick) by selecting CPK for the Drawing method in the Graphical Representations dialog box. Then one should create an additional representation (Create Rep) and change the drawing method for it to be Isosurface. The type of isosurface (Draw) should be changed from Points to Solid Surface and instead of Box+Isosurface only Isosurface should be selected. Then, by tuning the Isovalue one can select the isosurface to be plotted. Figure 1 was created using 0.100. (Display background color had been set to white using the Graphics/Colors menu.)

Figure 1: Total charge density for the H2O molecule, created by Waveplot, visualised by VMD.

3.2 Charge distribution difference

The charge distribution difference can be plotted in a similar way as the total charge. One has to load the file wp-abs2diff.cube. One should then, however, make not one, but two additional graphical representations of the type Isosurface. One of them should have positive isovalue, the other one a negative one. The different isosurfaces can be colored in a different way by using ColorID as coloring method and choosing different color values for the different representations.

Figure 2 demonstrates this for the water molecule. Negative net charges were colored red, positive net charges blue. One can clearly see, that there is a significant charge transfer from the hydrogens to the oxygen (lone pair on the oxygen).

Figure 2: Charge density difference (total density minus sum of atomic densities) for the H2O molecule, as created by Waveplot and visualised by VMD.

3.3 Molecular orbitals

The plotting of molecular orbitals can be, depending which property is plotted, done in the same way as the total charge distribution or the total charge difference. If the charge density (probability distribution) of an orbital is plotted, the data contains only positive values, therefore only one isosurface representation is necessary (like for the charge distribution). If the real (or for periodic systems also the imaginary part) of the wavefunction is to be plotted, two isosurface representations are needed, one for the positive and one for the negative values (like for the charge difference).

Figure 3 shows the distribution of the electron (wavefunction squared) for the HOMO, while 4 shows the HOMO wavefunction itself (blue - positive, red - negative). You can easily recognise the p-type of the HOMO, positive on one side, negative on the other side, a node plane in the middle.

Figure 3: Highest occupied molecular orbital of a water molecule (wavefunction square).

Figure 4: Highest occupied molecular orbital of a water molecule (real part of the wavefunction).