Capturing Carbohydrate Conformations and Hydration Interactions with a Polarizable Bond Dipole Potential

Area of Science:

• Computational Chemistry
• Molecular Modeling
• Carbohydrate Chemistry

Background:

• Accurate carbohydrate modeling faces challenges due to flexibility, hydration, and electrostatics.
• Existing force fields like GLYCAM06, CHARMM36, and AMOEBA have limitations in representing these properties.

Purpose of the Study:

• To develop and validate a novel polarizable bond dipole potential for carbohydrates (PBDPC25).
• To improve the accuracy of modeling carbohydrate conformations, electrostatic interactions, and hydration energies.

Main Methods:

• Developed PBDPC25 using intrinsically polarizable dipoles for C-O, O-H, and C-H bonds.
• Incorporated bond dipole coupling and an orbital overlap term for hydrogen bonding.
• Evaluated PBDPC25 against benchmark data for monomers and carbohydrate-water clusters.

Main Results:

• PBDPC25 achieved a 2.13 kcal/mol RMSE for conformational energies, outperforming GLYCAM06, CHARMM36, and AMOEBA.
• Optimized geometries were within 0.15 Å of reference structures.
• Hydration energies for clusters were predicted with a 3.50 kcal/mol RMSE, showing significant improvement.

Conclusions:

• PBDPC25 offers a reliable and accurate framework for computational carbohydrate chemistry.
• The new potential enhances the modeling of carbohydrate conformations and local hydration effects.
• PBDPC25 represents a significant advancement over current force fields for carbohydrate systems.