Computer Aided Recipe Design: Optimization of Polydisperse Chemical Mixtures using Molecular Descriptors

26 October 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

A workflow has been developed allowing for the computer aided design and optimization of reactive systems using the concept of molecular descriptor-based similarity. Unlike single-molecule models most often used in polymer informatics, an important feature of this approach is to allow for a more realistic description of reaction mixtures by accounting for polydispersity and individual chain topology. Starting from a specific set of ingredients, i.e., a chemical recipe or formulation, simulations based on Gillespie’s kinetic Monte Carlo scheme are used to generate oligo- and polymeric reaction mixtures. By using the distance / similarity in molecular and topological descriptor space as a metric, the initial recipe is then modified iteratively using a Bayesian optimizer. Target of the optimization procedure is either another chemical recipe with different ingredients or alternatively, a set of desirable descriptors and properties. A key step of the process is the transformation of the graph representing individual polymer species as obtained by the kinetic simulation into atomistic species described as SMILES strings, which enables the computation of a rich set of additional descriptors. This rather general mapping is achieved exploiting similarities between the BNGL and the SMILES notation. The workflow is demonstrated on common polyether and polyester oligomeric systems as typically used in polymer industry, but is generally applicable to other polymer chemistries.

Keywords

Optimization
RDKit
kinetic Monte Carlo
Chemical Descriptors
Computer Aided Molecular Design
Polymers
Molecular Graphs

Supplementary materials

Title
Description
Actions
Title
Supplemental Material
Description
Supplemental Material containing NFsim inputs and additional analysis concerning descriptors and optimizers.
Actions
Title
Calculations Results
Description
Graphs, BNGL species, SMILES and descriptors for the examples shown in CSV format.
Actions

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.