Pathfinder -- Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-based Approach

TL;DR

This paper introduces Pathfinder, a graph-based algorithm and software tool for analyzing chemical reaction networks (CRNs), enabling efficient exploration of reaction pathways and compound accessibility based on kinetic modeling and compound costs.

Contribution

We developed Pathfinder, a novel graph-optimization algorithm and software for analyzing CRNs, integrating compound costs and reaction probabilities to facilitate reaction pathway exploration.

Findings

Pathfinder effectively ranks compounds by formation probability.

The method successfully analyzes iodine disproportionation and comproportionation reactions.

Pathfinder integrates with Chemoton for autonomous CRN exploration.

Abstract

While the field of first-principles explorations into chemical reaction space has been continuously growing, the development of strategies for analyzing resulting chemical reaction networks (CRNs) is lagging behind. A CRN consists of compounds linked by reactions. Analyzing how these compounds are transformed into one another based on kinetic modeling is a nontrivial task. Here, we present the graph-optimization-driven algorithm and program Pathfinder to allow for such an analysis of a CRN. The CRN for this work has been obtained with our open-source Chemoton reaction network exploration software. Chemoton probes reactive combinations of compounds for elementary steps and sorts them into reactions. By encoding these reactions of the CRN as a graph consisting of compound and reaction vertices and adding information about activation barriers as well as required reagents to the edges of the graph yields a complete graph-theoretical representation of the CRN. Since the probabilities of the formation of compounds depend on the starting conditions, the consumption of any compound during a reaction must be accounted for to reflect the availability of reagents. To account for this, we introduce compound costs to reflect compound availability. Simultaneously, the determined compound costs rank the compounds in the CRN in terms of their probability to be formed. This ranking then allows us to probe easily accessible compounds in the CRN first for further explorations into yet unexplored terrain. We first illustrate the working principle on an abstract small CRN. Afterward, Pathfinder is demonstrated in the example of the disproportionation of iodine with water and the comproportionation of iodic acid and hydrogen iodide. Both processes are analyzed within the same CRN which we construct with our autonomous first-principles CRN exploration software Chemoton guided by Pathfinder.