# Plotting of natural bond orbitals (NBOs)

Which quantum chemistry programs can compute natural bond orbitals (NBOs)? Which visualisation tools can I use subsequently to plot pictures of the NBOs?

• Well, my experimental colleagues are as impatient as ever ;) Jun 17, 2020 at 19:13
• I can put a bounty on this question to draw more attention to it, if needed. It will only let me put a bounty after 2 days though. Jun 17, 2020 at 19:15
• I'm not sure if my answer helps you (you might have already known about that software). I googled it since your experimental colleagues are impatient and I wanted to help solve that, and this is just what I've found (I don't have experience with the program). Your question is posted on twitter: twitter.com/StackMatter/status/1273342612867514369 to get more attention, and you can re-tweet it to help raise more awareness. Jun 17, 2020 at 19:53
• is this question about computing NBOs or plotting them? The two are very different. Jun 17, 2020 at 22:12
• I was thinking about the whole workflow from computing to plotting. Actually in the meantime I found one possible solution with Q-Chem+Jmol. It took me a while to figures this out since the filenames are a bit cryptic. So, I think it is worth sharing (which I will do now) Jun 18, 2020 at 15:26

# NBO 7.0

The program NBO 7.0 seems to be quite well maintained, with version 7.0.9 released fewer than 30 days ago.

• Has interfaces to ADF, DEMON2K, FIREFLY/PC-GAMESS, GAMESS(US), GAUSSIAN, JAGUAR/SCHROEDINGER, MOLCAS, MOLPRO, NWChem, ORCA, PQS, Psi4, QChem, SPARTAN, TeraChem, TURBOMOLE.

• At least 2 new releases were issued already in 2020, and at least 2 new releases issued in 2019, so it seems the developers are still active and constantly maintaining the code.

• It has existed since 2001, so it is well established (probably not too many bugs).

• They have NBOView for plotting and visualizing. There is also a plug-in for visualization with JMol

• They have a detailed manual available online.

• It doesn't seem to have a presence on GitHub
• It is not free. The latest version seems to cost 100 USD or 30 USD as a plut-in to FIREFLY/PC-GAMESS.
• The interfaces to the software above, don't seem to be very up-to-date. For example the website says the MOLCAS interface is only to NBO3.0, not NBO7.0.
• The website seems old-fashioned.

With the Amsterdam Modeling Suite you can calculate (ADF, DFTB) and plot NBOs in the graphical user interface within the same package.

You are welcome to have a Free Trial!

# Q-Chem + Jmol

The combination of Q-Chem and Jmol seems to work well (but is not yet well documented).

## Q-Chem

In the Q-Chem input file one has to put

$$rem ... nbo = 1$$end

$$nbo PLOT$$end


This calls the NBO program and writes out the information of interest to the files \$QCSCRATCH/FILE.[31-39]

## NBO

The content of the files written is

• FILE.31 Basis set information
• FILE.32 PNAOs in the AO basis
• FILE.33 NAOs in the AO basis
• FILE.34 PNHOs in the AO basis
• FILE.35 NHOs in the AO basis
• FILE.36 PNBOs in the AO basis
• FILE.37 NBOs in the AO basis
• FILE.38 PNLMOs in the AO basis
• FILE.39 NLMOs in the AO basis

Here, the letter P corresponds to the pre-orthogonal orbitals, which are suggested for visualisation (WIREs, 2012, 2, 1).

## Jmol

In Jmol, one can just open the file of interest. In the first instance this may be the pre-NBOs as contained in FILE.36.

To automate the plotting of orbitals, one may use the jmol_MOs.py wrapper supplied with TheoDORE.

• Are you the developer of TheoDORE, fffelix? I was surprised to see that it works with TeraChem. Jun 21, 2020 at 22:53
• Yes, these TDDFT interfaces are quick :) We wrote the interface for this paper: dx.doi.org/10.1039/c7sc01600j Jun 23, 2020 at 12:18

# Jmol

Jmol is a free, open source viewer of molecular structures useful for students, educators and researchers in chemistry, biochemistry and other fields dealing with molecular structure. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

• The Jmol application is a standalone Java application that runs on the desktop.
• The JSmol is an object that can be integrated into web pages. It does not require Java, since it runs using just the browser's HTML5 and JavaScript engines..
• The JmolViewer is a development tool kit that can be integrated into other Java applications.