Analysis of chemical shielding

TheoDORE provides functionalities to analyse chemical shielding tensors and, in particular their use to analyze aromaticity.

Visualisation of chemical shielding tensors (VIST)

The VIST method [Eur. J. Org. Chem., (2021)] allows to visualise chemical shielding tensors in the context of the molecular structure showing local variations of the shielding along with its anisotropy. The method proceeds in the following order

  • Computation of shielding tensors (at the moment only Gaussian is interfaced)

  • Creation of VIST input via theodore plot_vist

  • Rendering of VIST plot in VMD

The tools have only been recently developed and still might require a bit of manual tuning of script files by the user. Any feedback on the user-friendliness of the tools is appreciated.

Command line options

Run theodore plot_vist -h to see all command line options

plot_VIST.py [options] <logfile1> <logfile2>
Command line options:
 -h, -H, --help: print this help
 -v, --vist    : VIST for only these dummy atoms, e.g. -v '0 3 5'
 -o            : Name of output file (for VMD)
 -s, --scale   : Scale factor VIST dumb-bells
 -c, --coor    : Create coordinate files (using cclib)
 -p            : Render and plot all tensors separately

Simple example

Create a Gaussian input file for an NMR calculation with the positions of the shielding tensors indicated as dummy (Bq) atoms and run Gaussian.

# PBE1PBE/Def2SVP scf=tight nmr

Shielding tensors

0 1
C          0.00000        1.20802        0.69749
C          0.00000        1.20802       -0.69749
C          0.00000       -0.00000       -1.39501
C         -0.00000       -1.20802       -0.69749
C         -0.00000       -1.20802        0.69749
C         -0.00000       -0.00000        1.39501
H          0.00000        2.15464       -1.24395
H         -0.00000        2.15464        1.24395
H         -0.00000       -2.15464       -1.24395
H          0.00000       -0.00000       -2.48803
H         -0.00000       -0.00000        2.48803
H         -0.00000       -2.15464        1.24395
Bq         0.0            0.0            0.0
Bq         1.0            0.0            0.0
Bq         2.0            0.0            0.0

After the job finishes simply run (assuming you named the output file gaussian.log)

plot_VIST.py gaussian.log

Open a molecular coordinate file in VMD. Then from inside VMD click: File - Load Visualization State - VIST.vmd

In the first instance, this will plot the shielding tensors of all Bq positions on top of each other.

_images/VIST-all.png

Use, the -p option to plot them all individually or use the -v option to select individual tensors.

Processing several output files

In many cases, it is desirable to process several output files at the same time to produce a consistent representation of several output files, for example to represent the shielding in different electronic states. The following figures represent the shielding in the dication, neutral state, and dianion of a macrocycle.

_images/2P.png _images/neut.png _images/2M.png

This figure was created with the command

theodore plot_vist -c -v '0 4' */gaussian.log

The -c option specifies that the molecular coordinates are directly parsed from the log-file. -v 0 4 indicates that only the Bq atoms with index 0 and 4 are included in the representation. */gaussian.log indicates that the gaussian.log files in all subdirectories are processed.

The files are loaded into VMD via

vmd -e VIST.vmd

Initially all geometries are superposed on top of each other. To hide some of the molecules use the D option (part of T A D F Molecule) in the VMD Main menu.