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Development and Validation of CHARMM Force Field Parameters for Major Phytochemicals of Phyllanthus emblica
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DOI：10.1002/jcc.70391.png)
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Abstract
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Polyphenolic phytochemicals derived from Phyllanthus emblica (amla) exhibit diverse chemical functionalities that are poorly represented in existing biomolecular force fields, limiting reliable molecular simulations of their structure and interactions. Here, we report the systematic development and validation of an all-atom, additive CHARMM force-field parameter set for major Phyllanthus emblica phytochemicals, including gallic acid, ellagic acid, quinic acid, ascorbic acid, ethyl gallate, and their relevant ionized forms. Parameterization was performed following established CHARMM protocols using high-level quantum mechanical reference data, with targeted fragmentation and model-compound strategies employed to address challenging conjugated and polyphenolic motifs. The optimized parameters accurately reproduce quantum mechanical conformational energetics, hydrogen-bonding interactions, and vibrational characteristics, exhibiting low deviations in both energies and geometries. Further validation is demonstrated through molecular dynamics simulations of experimentally resolved crystal structures and long-timescale protein–ligand complexes, where the parameters preserve structural stability and native interaction patterns. This work expands the chemical space accessible to CHARMM-based simulations and provides a robust, transferable framework for realistic molecular modeling of structurally complex natural products relevant to biomolecular recognition and function.
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