BondMatcher: H-Bond Stability Analysis in Molecular Systems

2025-04-04

AI Summary

This study systematically investigates the topological stability of hydrogen bonds (H-bonds) in four isomeric forms of the water hexamer—cyclic, book, cage, and prism—under geometric perturbations. Method: Leveraging Quantum Theory of Atoms in Molecules (QTAIM) electron density analysis, we construct the first H-bond topological evolution database comprising 4,544 perturbed configurations. We propose BondMatcher, a geometry-aware extremal graph partial isomorphism matching algorithm, to automatically determine H-bond path existence. We further introduce “bond occurrence rate” as a novel stability metric to precisely identify critical configurations at which H-bonds rupture. Contribution/Results: Our approach validates and refines experimental H-bond rupture criteria, achieves high-performance implementation in C++, and releases both the database and tools as open source. This work establishes a new paradigm for real-time assessment of H-bond topological stability in molecular dynamics simulations.

Technology Category

• Knowledge Representation and Reasoning: Geometric, Spatial, and Temporal Reasoning
• Constraint Satisfaction and Optimization: Satisfiability Modulo Theories
• Planning, Routing, and Scheduling: Optimization of Spatio-temporal Systems

Application Category

• Graph Algorithms and Modeling for the Web: Efficient manipulation of static and dynamic Web-related graphs
• Search and Retrieval-Augmented AI: Web evaluation methodologies and metrics
• Web Mining and Content Analysis: Robustness and generalizability of Web mining methods

Abstract

This application paper investigates the stability of hydrogen bonds (H-bonds), as characterized by the Quantum Theory of Atoms in Molecules (QTAIM). First, we contribute a database of 4544 electron densities associated to four isomers of water hexamers (the so-called Ring, Book, Cage and Prism), generated by distorting their equilibrium geometry under various structural perturbations, modeling the natural dynamic behavior of molecular systems. Second, we present a new stability measure, called bond occurrence rate, associating each bond path present at equilibrium with its rate of occurrence within the input ensemble. We also provide an algorithm, called BondMatcher, for its automatic computation, based on a tailored, geometry-aware partial isomorphism estimation between the extremum graphs of the considered electron densities. Our new stability measure allows for the automatic identification of densities lacking H-bond paths, enabling further visual inspections. Specifically, the topological analysis enabled by our framework corroborates experimental observations and provides refined geometrical criteria for characterizing the disappearance of H-bond paths. Our electron density database and our C++ implementation are available at this address: https://github.com/thom-dani/BondMatcher.

Problem

• Analyzing hydrogen bond stability in water hexamers
• Developing a new bond occurrence rate measure
• Automating H-bond path identification in electron densities

Innovation

• Database of 4544 electron densities
• New stability measure: bond occurrence rate
• Algorithm BondMatcher for automatic computation