AutomaticReactionDiscovery

Using quantum chemical computation to find important reactions without requiring human intuition.

Description

This repository contains Python code for automatically discovering chemical reactions using a freezing string method with a subsequent exact transition state search and reaction path verification by intrinsic reaction coordinate calculation.

There are two parts required in order to run the whole program. First, initial geometries and transition state jobs have to be generated by executing python ard.py input.txt from the command line. This will generate a reactions folder containing input files for each job. Each transition state job can then be run by python tssearch.py input.txt.

It is also possible to only run a freezing string method (without exact TS search and IRC calculation) by executing python sm.py input.txt A full transition state search (for only one reaction) can be run by executing python tssearch.py input.txt

Several arguments can be specified in the input file in the format arg value. The possible arguments are:

• reac_smi - Valid SMILES string describing the reactant structure
• nbreak - Maximum number of bonds that may be broken
• nform - Maximum number of bonds that may be formed
• dH_cutoff - Heat of reaction cutoff (kcal/mol)
• forcefield - Force field for 3D geometry generation (mmff94 or uff)
• distance - Initial distance between molecules
• geometry - Reactant and product geometry (see main.py for details)
• nsteps - Number or gradient calculations per optimization step
• nnode - Number of nodes for calculation of interpolation distance
• lsf - Line search factor for Newton-Raphson optimization
• tol - Perpendicular gradient tolerance
• nLSTnodes - Number of high density LST nodes
• qprog - Program for quantum calculations (currently only gau)
• theory - Level of theory (e.g., m062x/cc-pvtz)
• theory_low - Low level of theory for pre-optimizations
• nproc - Number of processors per job
• mem - Memory requirements for quantum software

Only reac_smi has to be specified for a full automatic discovery, all other arguments have default values or are set by running ard.py. Default values are:

• nbreak = 3
• nform = 3
• dH_cutoff = 20
• forcefield = mmff94
• distance = 3.5
• nsteps = 4
• nnode = 15
• lsf = 0.7
• tol = 0.1
• nLSTnodes = 100
• qprog = gau
• theory = m062x/cc-pvtz
• theory_low = None
• nproc = 1
• mem = 2000mb

The input file arguments can be specified in any order and comments can be added. An example is given in input.txt. If a freezing string method or single transition state search is run, geometry has to be specified.

Gaussian 03 or 09 has to be available at the command line and the appropriate environment variables have to be set.