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

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    $\begingroup$ Well, my experimental colleagues are as impatient as ever ;) $\endgroup$
    – Felix
    Jun 17 '20 at 19:13
  • $\begingroup$ 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. $\endgroup$ Jun 17 '20 at 19:15
  • $\begingroup$ 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. $\endgroup$ Jun 17 '20 at 19:53
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    $\begingroup$ is this question about computing NBOs or plotting them? The two are very different. $\endgroup$
    – Cody Aldaz
    Jun 17 '20 at 22:12
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    $\begingroup$ 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) $\endgroup$
    – Felix
    Jun 18 '20 at 15:26
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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.

Advantages:

  • 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.

Disadvantages:

  • 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.
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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.

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  • $\begingroup$ Are you the developer of TheoDORE, fffelix? I was surprised to see that it works with TeraChem. $\endgroup$
    – Cody Aldaz
    Jun 21 '20 at 22:53
  • $\begingroup$ Yes, these TDDFT interfaces are quick :) We wrote the interface for this paper: dx.doi.org/10.1039/c7sc01600j $\endgroup$
    – Felix
    Jun 23 '20 at 12:18
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ADF

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!

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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.

You can download it from here.

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    $\begingroup$ I guess one may add here that the files of interest are called FILE.3[1-9] and that Jmol can open these directly. $\endgroup$
    – Felix
    Jun 18 '20 at 16:03
  • $\begingroup$ @Felix, as you asked about software, these files you mention may not correspond to other ones likes MOPAC. $\endgroup$
    – Camps
    Jun 24 '20 at 18:10
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MOPAC

MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation.

If you qualify for Academic not-for-profit use, request your password here.

Using the keyword local, you can calculate the localized orbitals are also known as Natural Bond Orbitals or NBO.

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