Composing a Molecular Symphony

This dataset contains the supplementary data belonging to the PhD thesis of Matthijs ter Harmsel titled ‘Composing a Molecular Symphony’. It consists of data related to two projects. The first project is an investigation of the mechanism of Fmoc deprotection through Density Functional Theory (DFT). The data available here are the coordinates of optimized stationary points, Gaussian output files of geometry optimizations and output files of Internal Reaction Coordinate (IRC) calculations. The second project is the development of a catalytically active small molecule oscillator based on autocatalytic Fmoc deprotection and acetylation reactions. In order to determine at what conditions sustained oscillations could be obtained kinetic rate laws were determined for all individual reactions and a model based on Ordinary Differential Equations (ODE) was built using these rate laws. The data included here are the scripts used to explore the conditions where oscillations take place, consisting of the model and a parallelized loop running simulations varying the concentrations of all components and the flow rate, as well as the outputs of these scripts.