AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems.

ABSTRACT: A semiempirical method based on the AM1/d Hamiltonian is introduced to model chemical glycobiological systems. We included in the parameter training set glycans and the chemical environment often found about them in glycoenzymes. Starting with RM1 and AM1/d-PhoT models we optimized H, C, N, O, and P atomic parameters targeting the best performing molecular properties that contribute to enzyme catalyzed glycan reaction mechanisms. The training set comprising glycans, amino acids, phosphates and small organic model systems was used to derive parameters that reproduce experimental data or high-level density functional results for carbohydrate, phosphate and amino acid heats of formation, amino acid proton affinities, amino acid and monosaccharide dipole moments, amino acid ionization potentia

SUBMITTER: Govender K 

PROVIDER: S-EPMC4478602 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature