Visualizing NBOs in Jmol

In the previous post, concept and usage of NBO analysis were introduced. This post outlines steps for visualization of natural bond orbitals in open source viewer - Jmol. We will also assume the least practical scenario - running our calculations in Gaussian 09 for Windows (G09W). 

There are two prerequisite parts that we need for NBO analysis:

• Molecular system wavefunction and
• NBO program that perform the analysis

The former is usually generated by our electronic structure system (ESS), the latter one is either part of the ESS or has to be purchased separately (see NBO web site). Currently, the most recent version of the NBO program is at version 5.9 (aka NBO5). Unfortunately, users of Windows version of Gaussian have only access to the older version of NBO (3.1), which is incorporated in binaries G03W or G09W. To gain access to NBO5 options, Windows users have to use GENNBO 5.0W application, which performs analysis of wavefunction generated by the Gaussian ESS. 

The process of obtaining NBO5 output files and results of NBO analysis is following:

1. Specify POP=NBOREAD keyword in route card of Gaussian input file ($NBO keylist will be read and processed)
2. Include the ARCHIVE and FILE=name in the $NBO keylist that is specified after the "standard" Gaussian input (Fig. 1). Leave one blank line before and after the keylist.
3. File name.47 (in our case form.47) will be stored in "Scratch" directory of the G09W install path (typically C:\G09W).
4. Open this name.47 file in any text editor and enter keywords "file=form plot" between $NBO ... $END delimiters at the top of the file (Fig. 2).
5. Save the file and use it as input for GENNBO 5.0W analysis.

Fig. 1 Example of G09W input file for formamide

Fig. 2 Setting up $NBO keylist in name.47 file

After GENNBO analysis finishes, the corresponding .31-.46 plot files will be in the GENNBO5 main directory. I usually just move them into directory where all other output files reside. At this point, our directory should contain the following files (Fig. 3):

Fig. 3 List of created files

Having GaussView 5.0, but not GENNBO 5.0W? For direct output of NBOs from G09W/NBO3.1 binary, include command "POP=(nbo,savenbo)" in the input file route card. Only NBOs (not other orbitals) are then saved in .chk file for further analysis. Format the checkpoint .chk file with Gaussian utility to formatted .fch file and use GaussView 5.0 to visualize NBOs. Due to the slight differences in NBO3.1 and NBO5 calculations, NBOs may look a bit different.

With plot files .32-.46 in place, we are ready to inspect shapes and size of NBOs. Actually, not just yet. We need to install Jmol application that will run on our desktop. It is a free, open-source molecule viewer, running on Windows, Mac OS X, and Linux/Unix systems. Jmol can be downloaded from jmolsourceforge.net as .zip file. Unpack it in any place you wish and make shortcut to Jmol.jar file on your desktop. Then, just run it.

To make generation of the NBO imagery easier, we will use Jmol scripts that can be run as "macro". Save the following text between the dashed lined into file called, nbo12.macro
---------------------------------------------

Title=NBO12
Script=reset;background [0,0,150];load F:/your/path/to/plotfiles/form.37;mo 12;wireframe 30;spacefill 50;center {0.0 0.419936 0.0}; rotate z 145.3; rotate y 176.92; rotate z 13.53; translate x 3.92; translate y 5.95; set rotationRadius 3.27;isosurface color [247,255,71] [113,168,254] mo 12 opaque;mo nomesh;isosurface translucent 0.3;

---------------------------------------------

This file should have no line breaks after the first line (just a long line text). You will need to change the path to your set of .32-.40 plot files and orbital number after "mo" command. Currently, it will display mo 12 (NBO), which is the HOMO in our formamide example.

Now, save the above created file nbo12.macro in the "macro" folder located at:
C:\Users\username\.jmol\macros (Windows 7)

Launch the Jmol, click on "Macros" in the menu and click on "NBO12". You should see the following image.

Fig. 4  NBO 12 of formamide (HOMO)

In the next post, we will explore Jmol Applet and Visualiziation of NBOs in web browsers. Some other time, I'll take a look at the same visualization using Molekel 4.3.

• Weinhold, F.; Discovering Chemistry With Natural Bond Orbitals, Willey, 2012.
• Natural Bond Orbitals (NBO) visualization at Dr. Joaquin Barroso's blog.