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NameMr. Aravinda Munasinghe Munasinghe
OrganizationUniversity Of Florida
TopicComputational Chemistry

CHARMM force field parameters for oxime bonds: linkers for bio-conjugates


Aravinda Munasinghe1, Ping Lin1 and Coray M. Colina1,2


Author Location(s)

1 - Department of Chemistry, University of Florida, Gainesville, FL 32611
2 - Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611


The CHARMM force field has been applied to molecules with a wide variety of functional groups to obtain information at the atomistic scale. In this work, a set of CHARMM parameters for molecules containing oxime functional groups (e.g., oxime ester, oxime ether, and oximes) is presented. The new set of parameters will enable investigations of protein-polymer conjugates with an oxime functional group as a linker. A set of small model compounds (e.g., Formaldehyde O- methyloxime) containing oxime functional groups was used as the training set for the parameterization. Target data for the parameterization was obtained from quantum mechanic (QM) calculations. During the parameterization process, force field parameters were optimized to get a good agreement with targeted data sets (i.e., equilibrium geometry, vibrational frequency, dipole moment, interaction energy with water and dihedral potential energy scan). Applicability of the developed parameters in larger molecules, not included in the training set,  was evaluated by comparing dihedral potential energy scans. Additionally, these parameters were evaluated by reproducing available experimental data such as enthalpy of vaporization and density of model compounds. The derived parameters are being used for studying the dynamics of bio-conjugates.