R script for the automated generation of reaction coordinate diagrams (RCDs) of chemical reaction energies and transformation networks

R script for the automated generation of reaction coordinate diagrams (RCDs) of chemical reaction energies and transformation networks. This R script is part of the supplementary information for Torralba-Sanchez TL, Bylaska EJ, Salter-Blanc A, Meisenheimer DE, Lyon MA, Tratnyek PG. Reduction of 1,2,3-trichloropropane (TCP): Pathways and mechanisms from computational chemistry calculations. Environ Sci : Processes Impacts. 2020. DOI: 10.1039/C9EM00557A.

RCDs are 2D figures in which reaction thermodynamic values (e.g., change in reaction Gibbs free energy, ΔGrxn) are plotted (y axis) vs. reaction coordinates (e.g., stages/reactions in a transformation pathway). RCDs are useful for graphically comparing the energetics of reaction pathways and activation energies (if transition states are included), and provide insight into reaction barriers and therefore kinetics.

The script given here automates the plotting of RCDs using R (https://www.r-project.org). The script translates ΔGrxn data for large and complex networks of transformation pathways into RCD graphs. The script was originally written to generate RCDs for the transformation network of 1,2,3-trichloropropane (TCP, a halocarbon of environmental concern) presented in Figure 2 of Torralba-Sanchez et al. (citation above). The code was designed for easy adaptation to other chemical reactions and/or transformation networks.

Four files are provided as .zip or .rar archives. The contents of these archives include the same set of four files: (i) README.txt containing general instructions, (ii) ReactionCoordinateDiagram.r containing the R script, (iii) ReactionCoordinateDiagram_Input.csv as an example of the input data format, and (iv) ReactionCoordinateDiagram_Output.pdf as an example of the script output.