[Jmol-developers] at long last: Jmol LCAO "cartoon" orbitals/lone pairs/hybrid orbitals

[Bob H. <ha...@st...>]

Jmol users/developers

Ever since I have been involved with Jmol there have been requests for 
lone pair or p orbital or hybrid "cartoon" orbitals -- i.e. the sort of 
thing you see in textbooks but bear little resemblence to the real 
thing; sort of a tear-drop "lobe" shape that isn't really based on any 
actual orbital picture (as far as I can tell).
Jmol 10.x.17 now provides extensive mechanisms for depicting pi systems 
in 3D, sp2 and sp3 hybrid orbitals, lone pairs, etc. This is done using 
a relatively simple miniature isosurface "template" lobe that can be 
positioned, oriented, scaled, and colored to suit. It comes with a set 
of "standard" configurations that are accessed using the "lcaoCartoon" 
keyword. For example:


  isosurface lcaoCartoon "pz" (atomno=3)

draws a p orbital in the generally appropriate orientation if, say, atom 
3 is part of an aromatic ring.

  isosurface lcaoCartoon "sp2" (atomno=5)

draws an sp2 orbital on, say, a pyridine nitrogen.

There are several keywords that work, including:

px py pz pxa pxb pya pyb pza pzb
sp2 sp2a sp2b sp2c
sp3 sp3a sp3b sp3c sp3d
lp1 lp2

The "a" "b" "c" "d" refer to the different lobes of an orbital cartoon set.
A minus sign in front of any of these swaps the colors for easy 
depiction of pi systems using the LCAO (linear combination of atom 
orbitals) approximation or Hueckel method.
 
These are demonstrated at

 http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm

I'm sure there will be suggestions for improvement as people start using 
these. For now at least we have something to work with. We could, for 
example, experiment with different lobe patterns. Mine is based on one 
half of a Schroedinger 2pz orbital squished in the x/y directions to 1/2 
its original width, then flipped 180 degrees about the center of the 
lobe and scaled to what I thought looked reasonably good. It's the 
closest I could come to what I saw in two textbooks.


Bob Hanson