Instructions for viewing NBO Orbitals

These instructions are based on using the following programs:

The procedure is as follows:

  1. Use Gaussian keywords of the type: 
    rwb97xd/6-311g(d,p) pop(nbo,SaveNBOs)
    (this presumes the geometry has already been properly optimised)
  2. Obtain the .fchk file (this is automatically available if the job has been run via the uportal)
  3. Using Gaussview, double click the .fchk file and invoke edit/MOs
  4. Visually identify the index numbers of the filled orbital/empty orbital combination you want to illustrate. Let us say that they are orbital 35 and orbital 41 for example.
  5. In Gaussview go to Results/Surfaces-contours, select an orbital and from cube actions, save it to disk.
  6. Or, instead of the previous step, locate a computer with the cubegen utility installed on it, and type the following command:
    ./cubegen 0 MO=41 dichloropyran.fchk dcp-41.cub 0
./cubegen 0 MO=35 dichloropyran.fchk dcp-35.cub 0

    where dichloropyran.fchk is the original name of the .fchk file.
  7. The cube files so generated (i.e. dcp-41.cub) are likely quite large. One can reduce the size of this vastly by processing it using Jmol. Run a (partially illustrated) .html file containing the following lines, in a directory also containing the Jmol signed applet:
    <body>
    <script type="text/javascript">
//<![CDATA[
jmolInitialize(".","JmolAppletSigned.jar")
//]]>
</script>
<script type="text/javascript">
//<![CDATA[
jmolApplet(800,'isosurface ch2 cutoff +0.02 color red sign "dcp-35.cub";color isosurface translucent;color background white;write isosurface @{"/Users/rzepa/documents/conformational-analysis/conf/dcp-35.jvxl"};')
//]]>
</script>
  8. This generates a .jvxl file, which is tiny in comparison to the original cube file. Call this file from a (partial) Web page as follows:
    <body>
  <script type="text/javascript">
//<![CDATA[
jmolInitialize(".","JmolAppletSigned0.jar")
//]]>
</script>
    <script type="text/javascript">
//<![CDATA[
jmolSetAppletColor("yellow"); 
jmolApplet([250,380],'load "dcp-35.jvxl";isosurface "" translucent;set fontscaling TRUE; font label 18;select atomno=11;color black;label %A O Lp orbital;','cs')
//]]>
</script>