SoftwareX (Sep 2024)
AutoChem: A comprehensive tool for reaction prediction, network generation, and free energy calculation in chemistry
Abstract
AutoChem is a software package consisting of two modules. The first module is a virtual chemical reactor that can generate reaction products starting from inserted reactants and reactions. The process can be iterated, calculating reactions of the products obtained from the previous steps. To avoid a combinatorial explosion of products, constraints can be inserted. AutoChem module can generate 3D structures of the products obtained as well as a list of all the reactions occurred (chemical network).This can be useful for the calculation of reaction free energies by using computational chemistry programs like Gaussian and ORCA. Usually, the computational step involves the geometry optimization of all products followed by the calculation of vibrational frequencies of the optimized structures, to assess if a local minimum is reached. Finally, when products free energies are obtained, the calculation of the reactions free energies can be done.The second module of Autochem, called check, helps to perform the latter step, launching the jobs, collecting products free energies, restarting false minima and calculating the reactions free energies. This module is intended as a general use even outside AutoChem and might be used to perform a large number of free energy calculations with a little effort from the user. This permits to have results at the level of theory needed. AutoChem might also be used for teaching organic chemistry and basic cheminformatics dealing with SMILES and SMARTS by inserting reactants and reactions and analyzing the products obtained.
