Bond detectors for molecular dynamics simulations, Part I: Hydrogen bonds
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Updated: May 9, 2026

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
Published on: November 29, 2013
Anna Stachowicz1, Jacek Korchowiec
1K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Krakow, Poland.
Abstract:
Charge sensitivity analysis in AMBER force-field resolution has been used in quest for detectors of hydrogen bonds (HBs). The process of HB formation was investigated on ab initio classical trajectories (B3LYP/6-31G*) of different nucleobase pairs. Several charge sensitivities, namely: electronegativity, hardness, Fukui function (FF), and polarization matrix, were analyzed. The global and constrained equilibria were considered. It was demonstrated that FF indices and polarization matrix elements are good detectors of HB formation.
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