Drude polarizable force field parametrization of Carboxylate and N-acetyl Amine Carbohydrate derivatives

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dc.contributor.author Pandey, Poonam
dc.contributor.author Aytenfisu, Asaminew H.
dc.contributor.author MacKerell, Alexander D.
dc.contributor.author Mallajosyula, Sairam Swaroop
dc.date.accessioned 2019-08-21T14:15:37Z
dc.date.available 2019-08-21T14:15:37Z
dc.date.issued 2019-08
dc.identifier.citation Pandey, Poonam; Aytenfisu, Asaminew H.; MacKerell, Alexander D. and Mallajosyula, Sairam S., “Drude polarizable force field parametrization of Carboxylate and N-acetyl Amine Carbohydrate derivatives”, Journal of Chemical Theory and Computation, DOI: 10.1021/acs.jctc.9b00327, Aug. 2019. en_US
dc.identifier.issn 1549-9618
dc.identifier.issn 1549-9626
dc.identifier.uri https://repository.iitgn.ac.in/handle/123456789/4668
dc.identifier.uri https://doi.org/10.1021/acs.jctc.9b00327
dc.description.abstract 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 have been 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, including optimization of the electrostatic and bonded parameters. The optimized parameters were then used to generate the models for 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-glucuronate, 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 study were then applied to study the conformational properties of glycosaminoglycan polymer hyaluronan, composed of D-glucuronate and N-acetyl-D-glucosamine, in aqueous solution. Upon comparing the results from the additive and polarizable simulations it was found that the inclusion of polarization improved the description of the electrostatic interactions observed in hyaluronan resulting 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. en_US
dc.language.iso en_US en_US
dc.publisher American Chemical Society en_US
dc.subject Quantum mechanical en_US
dc.subject D-glucuronate en_US
dc.subject N-acetyl-D-glucosamine (GlcNAc) en_US
dc.subject N-acetyl-D-galactosamine (GalNAc) en_US
dc.title Drude polarizable force field parametrization of Carboxylate and N-acetyl Amine Carbohydrate derivatives en_US
dc.type Article en_US
dc.relation.journal Journal of Chemical Theory and Computation


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