Saturday, November 21, 2009

Electron density

Figure 3.1.
(a) A contour plot of the density of H2O computed using RHF/6-31G(d). The maximum and minimum contour values are 0.05 and 0.002 aus. (b) The corresponding 0.002 au isodensity surface. (c) The surface corresponding defined by atomic spheres with van der Waals radii.
From Molecular Modeling Basics CRC Press, May 2010.

Here's a screencast about how I made the figure:

When making the contour plot (Figure 3.1.a) I pick 0.05 au as the maximum value (this will be the contour line closest to the nuclei) and 25 contour lines. This means that the spacing between the contour lines and thus the outer contour line will be 0.05/25 = 0.002 au.

Another, more common, representation of the density is a 3D version of one of the contour values: the isodensity surface (Figure 3.1.b). A common choice is 0.002 au, since that corresponds roughly to experimental estimates of molecular size, such as the van der Waals surface (Figure 3.1.c).

Unfortunately, MacMolPlt doesn't have a van der Waals display style, so I have to use Avogadro. This means I have to re-size (by eyeball) this part of the figure to make it the same size as the density plots. See this post about using screen capture to get a file with the graphic.

The interactive version of this figure is the subject of a future post.
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