CHARMM additive all-atom force field for aldopentofuranoside carbohydrates and fructofuranoside

COMP 216

Elizabeth R Hatcher,, Olgun Guvench,, and Alexander D. MacKerell Jr., Department of Pharmaceutical Sciences, University of Maryland, 20 Penn St., Baltimore, MD 21201
We present the parametrization of monosaccharide furanoses for the CHARMM force field. Furanoside carbohydrates are contained in many biological and natural products, including Mycobacterium Tuberculosis cell wall. Initially, parameters are transferred from hexopyranoses and cyclic ethers. The non-bonded parameters are optimized to reproduce monosaccharide-water pair interactions. The bonded parameters are optimized to reproduce crystallographic data and gas-phase quantum mechanical conformational energies at the MP2/cc-pVTZ//MP2/6-31g(d) level. Torsional parameters are optimized using a Monte-Carlo simulated annealing procedure. Optimized parameters are validated by comparing crystal simulations and aqueous-phase simulations data to experimental crystal lattice parameters, molecular densities, diffusion coefficients and NMR data. Moreover, we investigate the pseudorotation angle, characterized by the five-member ring pucker, as well as the exocyclic rotamer populations. The carbohydrate force field will be applied to bacteria cell walls, glycoproteins, glycolipids and lectins.

Poster Session
6:00 PM-8:00 PM, Tuesday, August 18, 2009 Walter E. Washington Convention Center -- Ballroom A, Poster

8:00 PM-10:00 PM, Monday, August 17, 2009 Walter E. Washington Convention Center -- Hall D, Sci-Mix

Division of Computers in Chemistry

The 238th ACS National Meeting, Washington, DC, August 16-20, 2009