Visualisation of Aromaticity and Antiaromaticity

Dylan has finished his MChem project entitled “Visualisation of Aromaticity and Antiaromaticity via the Computation of the Chemical Shielding on Multi-Dimensional Grids.” You can find his report here. The purpose of his project was to develop a convenient method for computing shielding tensors on a grid around a molecule. The developed code is available via github.

Below, an analysis of biphenylene is shown in the singlet (a) and triplet (b) state. For the singlet this representation highlights the aromaticity (red) of the benzene rings whereas the central 4-membered ring is found to be antiaromatic (blue). In the triplet (b), the whole molecule is found to be aromatic (red) according to Baird’s rule.

An analysis of norcorrole using either its doubly protonated form (a) or a nickel complex (b) highlights the antiaromaticity at the centre of this molecule whereas an aromatic pathway is found at the perimeter (see also [P. B. Karadakov, Org. Lett. 2020, 22, 8676]).

For more examples of how this type of analysis is used in the literature, see e.g., [Angew. Chemie – Int. Ed. 2020, 59, 19275] and [ChemPhysChem 2021, 22, 741].

Release of TheoDORE 2.4

Version 2.4 of the TheoDORE wavefunction analysis package is available. Download the current version below.

New features of TheoDORE 2.4:

TheoDORE – Download

Download the newest release of the TheoDORE wavefunction analysis program – TheoDORE 2.4 (22 April 2021)

Size: 12 MB
Version: 2.4

Full release notes:

Continue reading

3D visualisation of chemical shielding tensors

Aromaticity is a ubiquitous yet elusive concept in chemistry and chemists have spent a great deal of effort on developing methods to quantify and visualise aromaticity. One particularly popular method is the nucleus independent shift (NICS), which can be seen as a virtual NMR experiment carried out within a conjugated ring to evaluate the enhanced chemical shielding induced by aromatic ring-currents. Strikingly NICS also allows to quantify antiaromaticity, as this induces a net deshielding effect within the ring. NICS provides a powerful quantitative aromaticity criterion but the main challenge for its graphical representation is that the chemical shielding is a 3×3 tensor, which is difficult to visualise with the existing methods.

Therefore, we have developed a new method for the visualisation of chemical shielding tensors (VIST), which provides a local representation of the shielding tensor along with the molecular structure. The method, thus, allows to probe local aromaticity along with the underlying anisotropy of the shielding. The method is described in the preprint “3D Visualisation of chemical shielding tensors to elucidate aromaticity and antiaromaticity” available on ChemRxiv.

Within the preprent we exemplify the main concepts in the benzene and phenanthrene molecules and continue by studying

The underlying code is scheduled to be released within the next version of the TheoDORE wavefunction analysis package.

Release of TheoDORE 2.3.

Version 2.3 of the TheoDORE wavefunction analysis package is available. Download the current version below.

New features of TheoDORE 2.3:

  • Compute (unpaired) densities using orbkit
  • Fix for theo_test.bash
  • Fix for ORCA osc. strengths
  • Old RASSI interface removed (was not working properly)
TheoDORE – Download

Download the newest release of the TheoDORE wavefunction analysis program – TheoDORE 2.4 (22 April 2021)

Size: 12 MB
Version: 2.4

Full release notes:

Continue reading

Release of Columbus 7.0.1

A new release of Columbus (version 7.0.1) is available. The main improvement compared to previous releases is that the binary distribution now contains a pre-compiled parallel CI executable as well as an interface to Molcas.

  • The parallel CI executable is linked against the Intel MPI libraries, which should be available on most computing centres and can otherwise be downloaded freely from Intel.
  • The Molcas interface proceeds via the free Molcas@UU distribution.
    Note: At the moment, there is no interface to OpenMolcas available in the distribution.

Source and binaries as well as more detailed instructions are available via the usual download page (register here). Let me know about any successes or problems regarding these features.