Calculation Files

The following GAUSSIAN input, script, and spreadsheet files are provided to assist researchers in performing the steps dicussed in our Instructions page. We found these to be useful ourselves, but cannot guarantee that they will function exactly as intended on other systems.

Contents:

GAUSSIAN input files for generating custom scaling factors for computed chemical shifts

Click here to download a zipped archive folder containing the files listed below. Note that all coordinate files refer to either our Test Set or Probe Set of molecules as detailed on the molecule databases page. These files have been optimized to remove all imaginary frequencies from the structures with the given level of theory, and are designed to work with specific Linux script files to generate sets of linked G03G03a jobs to process all molecules in the set.

GenericInput_Test.txt: This file contains starting coordinates for all molecules in our test set and is designed to be used with the concatfilemodifier script (see below) to optimize the geometries with a new level of theory.

GenericInput_Probe.txt: This file contains starting coordinates for all molecules in our probe set and is designed to be used with the concatfilemodifier script (see below) to optimize the geometries with a new level of theory.

TestSetGeom_B3LYP631Gd.com: This file contains coordinates for our test set optimized with the B3LYP/6-31G(d) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.

TestSetGeom_B3LYP631plusGdp.com: This file contains coordinates for our test set optimized with the B3LYP/6-31+G(d,p) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.

TestSetGeom_B3LYP6311plusG2dp.com: This file contains coordinates for our test set optimized with the B3LYP/6-311+G(2d,p) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.

TestSetGeom_MP2631Gd.com: This file contains coordinates for our test set optimized with the MP2/6-31G(d) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.

TestSetGeom_MP2631plusGdp.com: This file contains coordinates for our test set optimized with the MP2/6-31+G(d,p) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.

ProbeSetGeom_B3LYP631Gd.com: This file contains coordinates for our probe set optimized with the B3LYP/6-31G(d) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.

ProbeSetGeom_B3LYP631plusGdp.com: This file contains coordinates for our probe set optimized with the B3LYP/6-31+G(d,p) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.

ProbeSetGeom_B3LYP6311plusG2dp.com: This file contains coordinates for our probe set optimized with the B3LYP/6-311+G(2d,p) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.

ProbeSetGeom_MP2631Gd.com: This file contains coordinates for our probe set optimized with the MP2/6-31G(d) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.

ProbeSetGeom_MP2631plusGdp.com: This file contains coordinates for our probe set optimized with the MP2/6-31+G(d,p) level of theory and is designed to be used with the catnmrgen script (see below) to generate an input for running NMR single point calculations.



Script files for generating custom scaling factors for computed chemical shifts

Click here to download a zipped archive folder containing the files listed below. These files are designed to work with the above G03G03a input files and the below spreadsheet file to generate and process NMR calculation jobs for the complete test and probe sets of molecules.

catnmrgen: This script is written to take the various optimized geometry sets above and generate a G03G03a input file for running linked NMR single point calculations for all molecules in the set, with a specified level of theory.

testnmrparse: This script is written to take the ouput file from a linked NMR single point test set job and parse out data that can be used to populate the spreadsheet below.

probenmrparse: This script is written to take the ouput file from a linked NMR single point probe set job and parse out data that can be used to populate the spreadsheet below.

concatfilemodifier: This script is written to take the generic test and probe set input files above and generate a G03G03a input file for optimizing the coordinates for all molecules in the set with a new level of theory.

geomextract: This script is written to take the output file from a linked geometry optimization job and generate a new input file for NMR single point calculations. In essence, this file creates new TestSetGeom_ and ProbeSetGeom_ files (see above) with coordinates optimized with the new desired level of theory.



Spreadsheet for processing data for computed chemical shifts

Click here to download the Excel spreadsheet file designed to work with data generated from the above calculation and script files.



Script files for creating complete simulated proton NMR spectra

Click here to download a zipped archive folder containing the files listed below.

get_geom: extracts the optimized geometry from a B3LYP/6-31 G(d) optimization; input is a Gaussian fff.out (or fff.log) file, the output is a fff.xyz file.

mk_input_file: generates a Gaussian input file (fff_nmr.inp), using the geometry in the “fff.xyz” file generated by get_geom.

extract_spectrum: extracts the 1H chemical shifts and the 1H-1H coupling constants from a Gaussian output file_nmr (fff_nmr.out/log), performs the empirical scaling, and tabulates chemical shifts and coupling constants in a file fff_nmr.txt.

average_spectrum: performs averaging between degenerate conformations; input is an fff_nmr.txt file, output an fff_nmr_avg.txt file.

average_molecules: performs averaging between non-degenerate conformations; input is a series of fff_nmr.txt (or fff_nmr_avg.txt) files. The output filename is specified by the user.