Bond detectors for molecular dynamics simulations, Part I: Hydrogen bonds

Area of Science:

• Computational chemistry
• Quantum chemistry
• Molecular dynamics

Background:

• Hydrogen bonds (HBs) are crucial in molecular interactions.
• Accurate detection of HB formation is essential for understanding molecular behavior.
• Current methods for detecting HBs can be computationally intensive.

Purpose of the Study:

• To explore charge sensitivity analysis for detecting hydrogen bond formation.
• To investigate the process of hydrogen bond formation in nucleobase pairs.
• To identify reliable indicators of hydrogen bond formation.

Main Methods:

• Ab initio classical trajectories using B3LYP/6-31G*.
• Analysis of charge sensitivities: electronegativity, hardness, Fukui function (FF), and polarization matrix.
• Consideration of global and constrained equilibria.

Main Results:

• Fukui function (FF) indices were found to be effective detectors of hydrogen bond formation.
• Polarization matrix elements also demonstrated significant utility in identifying hydrogen bonds.
• Charge sensitivity analysis provides valuable insights into the dynamics of hydrogen bond formation.

Conclusions:

• FF indices and polarization matrix elements are reliable indicators for detecting hydrogen bonds.
• Charge sensitivity analysis offers a robust computational approach for studying hydrogen bonding.
• The findings contribute to a deeper understanding of molecular interactions in nucleobase systems.