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Electrostatic potential maps

Figure 3.4. (a) Contour plot of the electrostatic potential of H₂O. The maximum and minimum contour value is 0.5 Hartrees/electronic charge (au). (b) The corresponding 0.05 au isopotential surface. (c) The electrostatic potential displayed on the 0.002 au isodensity surface of water. The maximum (darkest blue) value corresponds to 0.05 au.
From Molecular Modeling Basics CRC Press, May 2010.

Here is a screencast of how I made the figure:

The files I used were created in a previous post. The various values specified above are determined using trial and error, i.e. I kept fiddling with it until it looked good to me. When using plots like this it is important to specify these values, because using different values can lead to very different looking plots.

Also, different programs use different color scales and color intensity to indicate positive and negative charge, so it is rarely possible to directly compare electrostatic potential maps from different programs.

See this post about using screen capture to get a file with the graphic. This was done for each plot, and the combined in a word processor.

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

Electron density doesn't always tell the whole story

Figure 3.3. (a) RHF/6-31G(d) 0.002 au isodensity surface and (b) van der Waals surface of cis-HO(H)C=C(H)OH (click on the picture for a bigger version).
From Molecular Modeling Basics CRC Press, May 2010.

Looking at the electron density or the van der Waals surfaces one would expect steric strain in cis-HO(H)C=C(H)OH. (See this post on how to make such pictures and this post on how to make an interactive version such as the one shown below.)

However, contrary to CH₃(H)C=C(H)CH₃, the cis isomer is more stable than the trans isomer. This is of course due to the electrostatic attraction of the O and H atom in the hydrogen bond. Here the electron density tells only part of the story because this attraction involves the nuclei as well. Here an electrostatic potential map is more useful. How to make such plots will be the subject of future posts.

Figure 3.3. The RHF/6-31G(d) electron density of cis-HO(H)C=C(H)OH.
Click on the picture for an interactive version

Common error messages in GAMESS: charge and multiplicity

  *** CHECK YOUR INPUT CHARGE AND MULTIPLICITY ***
THERE ARE    33 ELECTRONS, WITH CHARGE ICHARG=  0
BUT YOU SELECTED MULTIPLICITY MULT=  1

This error message was produced by the following input file. Can you see what's wrong?

 $contrl runtyp=optimize $end
 $basis gbasis=pm3 $end
 $data
Title
C1
N     7.0    -0.39094     1.95659     0.14008
H     1.0     0.38874     1.60529    -0.40413
H     1.0    -0.08386     2.76975     0.70945
H     1.0    -0.72485     1.22934     0.80007
H     1.0    -1.14035     2.30329    -0.48754
O     8.0    -0.64579     0.16732     2.03360
H     1.0    -0.26212    -0.73042     2.10569
H     1.0    -1.00756     0.26750     2.93979
O     8.0    -1.80535     3.31298    -1.59619
H     1.0    -1.39440     3.81065    -2.33214
H     1.0    -2.74148     3.57968    -1.71559
O     8.0     0.26578     4.05264     1.54485
H     1.0     1.03270     4.27032     2.11226
H     1.0    -0.26135     4.87344     1.64760
 $end

As GAMESS tells you, it is not possible to have singlet state (i.e. a multiplicity of 1) if you have an odd number of electrons. You need to tell GAMESS whether you want to change the multiplicity (for example, $contrl mult=2 scftyp=rohf $end) or add ($contrl icharg=-1 $end) or remove ($contrl icharg=1 $end).

When looking at the molecule it is pretty clear that you want to remove an electron, since ammonium has a positive charge. So the first line in the input should be changed to

 $contrl runtyp=optimize icharg=1 $end

Click on the picture for an interactive version

Notice that you don't have to specify that the positive charge is on ammonium. The quantum mechanics will take care of that.

Electron density and steric strain

Figure 3.2. (a) RHF/6-31G(d) 0.002 au isodensity surface and (b) van der Waals surface of cis-CH₃(H)C=C(H)CH₃ (click on the picture for a bigger version).
From Molecular Modeling Basics CRC Press, May 2010.

This figure shows how the electron density and van der Waals surfaces can be used to visualize steric strain. See this post on how to make such pictures and this post on how to make an interactive version such as the one shown below.

Figure 3.2. The RHF/6-31G(d) electron density of cis-CH₃(H)C=C(H)CH₃.
Click on the picture for an interactive version

Common error messages in GAMESS: error reading IDUM

 **** ERROR READING VARIABLE IDUM     CHECK COLUMN  1
H     1.0    -0.08386     2.76975     0.70945                                
....V....1....V....2....V....3....V....4....V....5....V....6....V....7....V....8

This error message was produced by the following input file. Can you see what's wrong?

 $contrl runtyp=optimize $end
$basis gbasis=pm3 $end
 $data
Title
C1
N     7.0    -0.39094     1.95659     0.14008
H     1.0     0.38874     1.60529    -0.40413
H     1.0    -0.08386     2.76975     0.70945
H     1.0    -0.72485     1.22934     0.80007
H     1.0    -1.14035     2.30329    -0.48754
O     8.0    -0.64579     0.16732     2.03360
H     1.0    -0.26212    -0.73042     2.10569
H     1.0    -1.00756     0.26750     2.93979
O     8.0    -1.80535     3.31298    -1.59619
H     1.0    -1.39440     3.81065    -2.33214
H     1.0    -2.74148     3.57968    -1.71559
O     8.0     0.26578     4.05264     1.54485
H     1.0     1.03270     4.27032     2.11226
H     1.0    -0.26135     4.87344     1.64760
 $end

The answer is the missing space in front of the $basis, and the solution is to add a space in front of it, just like for $contrl and $basis.

Why does GAMESS complain about a line in $data when the problem is with $basis? The reason is that it is possible to specify a basis set for each atom in $data, so GAMESS tries to read this information if no $basis group is found.

The error message would clearly benefit from the line: "Did you mean to specify a $basis group?"

The future of scientific publishing is here today

I recently came across this paper on embedding interactive 3D graphics in pdf files. Unfortunately, I couldn't animate the 3D figures, and I wrote the author (Vlad Vasilyev) who kindly wrote back that:

(1) the publisher (Springer) is a bit behind the times so the interactive figures are found in the supplemental material, but

(2) the ACS is more on the ball, as can be seen in this paper (this is the one I use in the screencast), and

(3) he has made a bunch of tutorials on how to create such diagrams on this page.

This page also contains some pdf files with 3D graphics you can play around with if you don't have access to the papers. Be sure to use Adobe Acrobat Reader 9.

Note that it is also possible to include animations such as vibrational motion (NB: 16 MB file)

Very cool! I haven't tried this myself, but you can be sure I will. Unfortunately, it seems that you need a piece of commercial software (Adobe Acrobat 9 Pro Extended) to do this.

On a related note, check you the interactive figure of interactive figures created by fellow blogger Henry Rzepa (please give the page some time to load).