EDHB

EDHB identifies and classifies inter- and intramolecular hydrogen bonds and hydrogen-bond networks within molecular structures to assess their electrostatic or covalent character and compute local-mode hydrogen bond force constants.

Key Features:

• Nearest neighbors algorithm: Uses a nearest neighbors algorithm to detect inter- and intramolecular hydrogen bonds and complex hydrogen-bond networks.
• Quantum-chemical analysis: Integrates natural bond orbital (NBO) analysis and second energy derivative information to assess electrostatic versus covalent character of hydrogen bonds.
• Local-mode force constants: Calculates local-mode hydrogen bond force constants as quantitative measures of intrinsic hydrogen bond strength.
• Versatility: Applicable to proteins, protein-ligand interactions, water clusters, and molecular dynamics simulations.
• Speed and efficiency: Offers rapid execution times compared with traditional hydrogen bond detection methods.

Scientific Applications:

• Protein structural analysis: Applied to a set of 163 proteins, revealing that intramolecular hydrogen bond networks often form rings of varying sizes that are integral to α-helices and turns but do not significantly influence hydrogen bond strength.
• Determinants of bond strength: Local-mode analysis identified hydrogen bond angle as a critical determinant of hydrogen bond strength within proteins.
• Protein-ligand interactions: Analyzes hydrogen-bonding patterns in protein-ligand complexes to characterize interaction networks.
• Water clusters and MD simulations: Evaluates hydrogen bonding in water clusters and along trajectories from molecular dynamics simulations.

Methodology:

EDHB employs a nearest neighbors algorithm to detect hydrogen bonds and integrates quantum chemical data (natural bond orbital analysis and second energy derivative information) to assess bond character and compute local-mode hydrogen bond force constants.