通过分析水六聚体氢键稳定性，提出可自动识别氢键消失的新型度量方法。
BondMatcher: H-Bond Stability Analysis in Molecular Systems
- 基于电子密度图构建氢键路径出现频率作为稳定性指标。
- 在4544组扰动结构中发现氢键断裂的临界几何条件。
- 适合研究分子动态行为与氢键网络的计算化学研究人员使用。
本文研究了氢键（H-bonds）的稳定性，采用原子在分子中的量子理论（QTAIM）进行分析。首先，我们构建了一个包含4544组电子密度的数据集，涵盖水六聚体四种异构体（环、书、笼、棱柱）在不同结构扰动下的非平衡构型，模拟分子系统的自然动态行为。其次，提出一种新稳定性度量——键路径出现率，将每个平衡态下的键路径与其在输入集合中的出现频率关联。我们还开发了名为BondMatcher的算法，通过针对极值图的几何感知部分同构估计，实现该度量的自动计算。新方法可自动识别缺失氢键路径的电子密度，支持进一步可视化分析。拓扑分析结果与实验观测一致，并提供了氢键路径消失的精细化几何判据。电子密度数据集和C++实现代码已公开于https://github.com/thom-dani/BondMatcher。
原文摘要 · Abstract (English)
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.
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