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 * Interfaces exists for Gaussian, Q-Chem and Turbomole. * 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 .. code-block:: text plot_VIST.py [options] 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 -l/--lab_min : Add labels for eigenvalues above this value (in ppm), e.g. -l 10 -q/--qccode : Quantum chemistry code (g09, qchem, turbomole) 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. .. figure:: figures/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. .. image:: figures/2P.png .. image:: figures/neut.png .. image:: figures/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.