natorbs 1.0.2

Quantum-chemical utility for computing natural orbitals

Natorbs computes natural orbitals and natural spin-density orbitals based on canonical unrestricted (UHF-type) orbitals resulting from HF or DFT calculations. It can also compute natural orbitals for chemical valence (NOCVs) based on the orbitals of a molecule and its constituing fragments.

The program was created in response to the demand in the course of our own studies on the electronic structure of open-shell systems, especially transition-metal complexes. By generating natural/spin orbitals one can immediately identify the orbitals carrying unpaired electrons among, possibly, hundreds of orbitals, most of which are empty or describe closed shells. Such a diagnosis tool is particularly valuable for complicated electronic structure (broken-symmetry solutions / antiferromagnetic coupling / biradicals and multiradicals). It could be useful, however, to facilitate interpretation of any open-shell UHF-type calculations.

Natorbs is designed as post-processing tool for the results of quantum-chemical (QC) calculations. It was with the aim of being independent on any particular QC package and indeed could be used with many of them. Natorbs reads the input data (geometry and MOs) either using the cclib (http://cclib.sourceforge.net) library or via Molden format (http://www.cmbi.ru.nl/molden). Natorbs saves the output orbitals (the desired flavour of natural orbitals) in Molden format, so that they can be visualized with programs like Molden or Gabedit.

Note that the distinguising feature of Natorbs, that makes it independent of any partcular QC package, is that it reconstructs the overlap integrals of the atomic basis functions from the provided molecular orbitals (LCAO coefficients). The obtained overlap integrals are exact if all the virtuals are provided as input data or approximate otherwise.

License

Program Natorbs is made available free of charge under the terms of the terms of the 3-clause BSD license. Copyright 2021 Uniwersytet Jagielloński, Dr hab. Mariusz Radoń. For details, see attached file LICENSE.txt .

Documentation

To get help and the list of options:

natorbs --help

There is also a man page. To use it, make sure that (prefix)/share/man is included in yout MANPATH. This README file and the LICENSE file are provided in (prefix)/share/doc.

Recommended Citation

• Mariusz Radoń, Natorbs v1.0.2, Jagiellonian University, Krakow, Poland, 2021; available from https://tungsten.ch.uj.edu.pl/~mradon/natorbs

Further Information

Definitions of natural/natural-spin orbitals can be found in quantum-chemistry literature. Basically, they are defined as eigenvectors of one-particle density or spin-density matrix, respectively.

The connection between spin-unrestricted orbitals and natural orbitals is explained in the seminal paper:

• A. Amos and G. Hall, Proc. Roy. Soc. A, 1961, 263, 483, doi: 10.1098/rspa.1961.0175

For description of the NOCV method see the following paper:

• M. Mitoraj and A. Michalak, J. Mol. Model., 2007, 13, 347, doi: 10.1007/s00894-006-0149-4

The pairing property of NOCVs:

• M. Radon Theor. Chem. Acc., 2008, 120, 337, doi: 10.1007/s00214-008-0428-5

Papers mentioning applications of programs Natorbs, mainly the NOCV stuff, can be found in the following papers:

• M. Radon, E. Broclawik, J. Chem. Theory Comput., 2007, 3, 728-734, doi 10.1021/ct600363a

• M. Radon, P. Kozyra, A. Stepniewski, J. Datka, E. Broclawik, Can. J. Chem., 2013, 91, 538-543, doi: 10.1139/cjc-2012-0536

• P. Kozyra, M. Radon, J. Datka E. Broclawik Struct. Chem., 2012, 23, 1349-1356, doi: 10.1007/s11224-012-0050-y

• K. Gora-Marek, A. Stepniewski, M. Radon, E. Broclawik, Phys. Chem. Chem. Phys., 2014, 16, 24089-24098, doi: 10.1039/C4CP03350G

• E. Broclawik, A. Stepniewski, M. Radon, J. Inorg. Biochem., 2014, 136, 147-153, doi 10.1016/j.jinorgbio.2014.01.010