Aromaticity is a chemical concept that accounts for different molecular features such as reactivity, structural shapes, relative energetic stability, and spectroscopic properties of the so-called "aromatic molecules". Here, we introduce the NICSall software for evaluating aromaticity via NICS methods. It offers an automated building process of input files for different software (Gaussian, ADF, Orca) and analysis of their outputs files (the induced magnetic field, scan-NICS, FiPC-NICS, and symmetry properties of the shielding tensor).
• Inostroza, D.; García, V.; Yañez, O.; Torres-Vega, J. J.; Vásquez-Espinal, A.; Pino-Rios, R.; Báez-Grez, R.; Tiznado, W. On the NICS Limitations to Predict Local and Global Current Pathways in Polycyclic Systems. New J. Chem. 2021. DOI:10.1039/D1NJ01510A https://doi.org/10.1039/D1NJ01510A.
1) Prerequisites
NICSall is a Perl program. NICSall is optimized and tested for Linux, so it can’t be guaranteed to run on other operating systems.
Ensure to install the following Library and software before installing NICSall.
-Install Perl environment.
-Install CPAN modules (http://www.cpan.org/modules/INSTALL.html or https://egoleo.wordpress.com/2008/05/19/how-to-install-perl-modules-through-cpan-on-ubuntu-hardy-server/)
user$ sudo cpan install Array::Split
user$ sudo cpan install Parallel::ForkManager
-Install External softwares
• ADF (https://www.scm.com/)
• Gaussian (http://gaussian.com/)
• Orca (https://orcaforum.cec.mpg.de/)
• NBO for Gaussian to perform Sigma-Pi separation (http://nbo6.chem.wisc.edu/webnbo_css.htm)
2) Install & Running NICSall
The NICSall program works through the command-line interface using straightforward instructions. NICSall program read parameters from standard NMR shielding computations performed by various external quantum chemistry programs, including Gaussian, ADF (work in progress), and Orca (work in progress). Thus, the external program must be available.
To download the NICSall, you need Git installed on your computer. If Git is installed, use the following command to download the NICSall:
user$ git clone https://github.com/HumanOsv/NICSall.git
user$ cd ./NICSall
user$ chmod 777 NICSall.pl
user$ chmod 777 ./src/*
The following necessary files should appear in the working directory:
• FileName.xyz : XYZ cartesian coordinates format .xyz
• Config.in : The NICSall input file
• NICSall.pl : The executables files for NMR parameters
./src/
|_ GraphMaker.pl : Build the ValuesICSS.backup file with all NMR parameters
|_ CubeToVTK.pl : Change cube format to VTK formst
|_ ReadResults.pl : Read all the NMR parameters obtained by Gaussian software and extract them to be saved
Now use the following commands to execute this program:
user$ perl NICSall.pl Config.in > out.log
alternatively, the user can set NICSall to run in the background using:
user$ nohup perl NICSall.pl Config.in > out.log
or:
user$ setsid perl NICSall.pl Config.in > out.log
After a successful run the program will make several output files named as: ValuesICSS.backup,BOX.vmd, FileName.cube, FileName(Pos|Neg).vti, FileName.vtk, Filename_SCANS.txt, Filename_FiPC.txt and Filename_SPST.txt.
out.log : Output file from NICSall software
ValuesICSS.backup : File contains the main NMR parameters. If this file is present in the directory or Gaussian outputs,
it is not necessary to send the quantum calculation again
./Resources
|_ BOX.vmd : The size of the box (in Angstroms) length, width, and height.
|_ FileName.cube : The cube file describes volumetric data as well as atom positions.
|_ FileName_Pos.vti : The Induced Magnetic Field (VTI File Format, Positive Vectors)
|_ Filename_Neg.vti : The Induced Magnetic Field (VTI File Format, Negative Vectors)
|_ FileName.vtk : The Induced Magnetic Field (VTK File Format, Isolines)
|_ Filename_SCANS.txt : Scan-NICS values computed along the axis perpendicular to the molecular plane
|_ Filename_FiPC.txt : FiPC-NICS is computing NICS profiles along the axis perpendicular to the molecular plane
|_ Filename_SPST.txt : Symmetry Properties of the Shielding Tensor (SPST) profiles along the axis perpendicular to the
molecular plane
NOTE: Files Format
ValuesICSS.backup
Column Description
1 Type of Atom
2,3,4 Cartesian Coords XYZ
5 Isotropy
6 Anisotropy
7 Component XX
8 Component YY
9 Component ZZ
10 Component XZ
11 Component YZ
Filename_SCANS.txt
Column Description
1 Type of Atom
2 Z axis coord
3 Component ZZ
4 Isotropy
5 Anisotropy
Filename_FiPC.txt
Column Description
1 Type of Atom
2 Z axis coord
3 Component XX
4 Component YY
5 Component ZZ
6 In-Plane
7 Out-Plane
Filename_SPST.txt
Column Description
1 Type of Atom
2 Z axis coord
3 Component XX
4 Component YY
5 Component ZZ
6 Sigma(av)
7 Delta
8 Nu
3) Input File
NICSall needs an input file, Config.in, that contains all the necessary parameters for a correct calculation. Each variable is explained below.
a) The XMol file cartesian coordinates format (https://openbabel.org/docs/dev/FileFormats/XYZ_cartesian_coordinates_format.html).
coords = FileName.xyz
NOTE: For a better analysis it's recommended that all the molecular rings must be placed in the XY plane, in such a way that the external magnetic field is on the Z axis.
b) Quality grid of NICS parameters.
quality = 0.2
NOTE: For efficiency consideration, the default quality of grid data is 0.4
c) The size of the box (in Angstroms) length, width, and height. NICSall build an automatic box.
box_size =
NOTE: The value "0" in any parameter (length, width or height) will make a plane. Two "0" in the parameters will build a line
d) Choose NMR chemical shieldings (0) or Sigma-Pi separation (1)
option = 0
e) Orbitals to perform Sigma-Pi separation
orbitals = 20,21,22,23,-19,-18,-24,-25
NOTE: The Sigma and Pi orbitals correspond to Negative and Positive values.
f) Nucleus-independent chemical shifts (NICS)
type_graph = 1,2,5,8
NOTE: NICS and related properties.
1 = Isotropy
2 = Anisotropy
3 = Component XX
4 = Component YY
5 = Component ZZ
6 = FiPC-NICS
7 = Scan-NICS
8 = FiPC-NICS & Scan-NICS
9 = Symmetry Properties of the Shielding Tensor (SPST)
g) Software gaussian (gaussian)
software = gaussian
Configuring the program for chemistry packages
h) The number of processors to use in the run (the value may be used to create the input file) and memory to be used in GB.
core_mem = 8,8
i) The charge and multiplicity of the candidate.
charge_multi = 0,1
j) keywords for gaussian
Gaussian
header = B3lyp/6-31g*
k) A model potential be substituted for the core electrons (https://bse.pnl.gov/bse/portal).
pseudopotentials
... Inputa data ...
pseudopotentials
General Note: Respect the spaces of separation between the symbol "=".
Correct : software = gaussian
Wrong : software=gaussian