In this work, we report the development of Drude polarizable force-field parameters for the carboxylate and N-acetyl amine derivatives, extending the functionality of existing Drude polarizable carbohydrate force field. The force field parameters were developed in a hierarchical manner, reproducing the quantum mechanical (QM) gas-phase properties of small model compounds representing the key functional group in the carbohydrate derivatives. The optimized parameters were then used to model the carboxylate and N-acetyl amine carbohydrate derivatives. The transferred parameters were further tested and optimized to reproduce crystal geometries and J-coupling data from NMR experiments. The parameter development resulted in the incorporation of D-glucoronate, L-iduronate, N-acetyl-D-glucosamine (GlcNAc), and N-acetyl-D-galactosamine (GalNAc) sugars into the Drude polarizable force field. The parameters developed in this work were than used to probe the conformational properties of hyaluronan polymer, which consists of D-glucoronate and N-acetyl-D-glucosamine. Comparative analysis of additive and polarizable simulations reveals that the inclusion of polarization improved the description of the electrostatic interactions observed in hyaluronan system, which results in enhanced conformational flexibility. The developed Drude polarizable force field parameters in conjunction with the remainder of the Drude polarizable force field parameters can be used for the future studies involving carbohydrates and their conjugates in complex, heterogeneous systems.

Drude polarizable force field for molecular dynamics simulations of carboxylate and N-Acetyl amine carbohydrate derivatives

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

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