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 Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
