Thermodynamic calculations for phosphorylation reactions

This dataset accompanies a manuscript in preparation. sugars.csv contains thermodynamic parameters formatted for the OBIGT database in CHNOSZ. The parameters for organic phosphates and related species were developed in the manuscript. plot.R is an R script for creating plots of the non-standard Gibbs energy of phosphorylation reactions as a function of temperature (T), pressure (P), and pH. It depends on the phospho.plot() and phosphorylate() functions in the development version of CHNOSZ. Installation and usage Install R and run these commands to install the development version of CHNOSZ (>= 2.2.0-61).Note: Version 2.2.0 (the current release version on CRAN) is insufficient to run the code. install.packages("remotes")remotes::install_github("jedick/CHNOSZ") Put plot.R and sugars.csv in the R working directory.Then, source the script and run the function to create the plots. source("plot.R")plotall() This saves the plots as PDF files in the working directory. The T-pH and P-pH plots are made for constant P and T, respectively (defaults: Psat and 25 °C).Modify the arguments to make the plots at different constant P and T (example: 5000 bar and 200 °C): plotall(const_T = 200, const_P = 5000)