BondMatcher: H-Bond Stability Analysis in Molecular Systems

Area of Science:

• Computational Chemistry
• Quantum Chemistry
• Molecular Modeling

Background:

• Hydrogen bonds (H-bonds) are crucial in molecular systems, but their stability, especially in dynamic environments, requires robust characterization.
• Existing methods may not fully capture the transient nature of H-bonds during molecular fluctuations.
• Water hexamers exhibit diverse isomeric structures (Ring, Book, Cage, Prism) with varying H-bond network dynamics.

Purpose of the Study:

• To investigate the stability of hydrogen bonds in various water hexamer isomers under structural perturbations.
• To develop and validate a novel, automated method for quantifying H-bond stability based on electron density analysis.
• To provide refined criteria for characterizing H-bond disappearance in molecular systems.

Main Methods:

• Generation of a database of 4544 electron densities for four water hexamer isomers, simulating dynamic behavior through geometric distortions.
• Application of the Quantum Theory of Atoms in Molecules (QTAIM) for topological analysis of electron densities.
• Development of a new stability metric, the 'bond occurrence rate', and an automated algorithm (BondMatcher) for its computation using geometry-aware partial isomorphism estimation.

Main Results:

• A comprehensive database of perturbed water hexamer electron densities was created.
• The bond occurrence rate successfully quantifies H-bond stability and identifies electron densities lacking H-bond paths.
• The topological analysis framework corroborates experimental findings and refines geometrical criteria for H-bond disappearance.

Conclusions:

• The developed bond occurrence rate and BondMatcher algorithm offer an effective, automated approach to assess H-bond stability.
• This method aids in identifying transient H-bonds and provides insights into molecular dynamics.
• The findings contribute to a better understanding of H-bond behavior in molecular systems, complementing experimental observations.