Conformational Study of Mannitol and Sorbitol in water.

BARRIOS, I.A.; MCCARTHY, A.N.; GRIGERA, J.R.

Universidad Nacional de Quilmes

Congreso; Primer Congreso Argentino de Bioinformática y Biología Computacional; 2010

Universidad Nacional de Quilmes

Conformational Study of Mannitol and Sorbitol in WaterBarrios, I.A.; McCarthy, A.; Grigera, J.R.IFLYSIB, University of La Plata, c.c. 565, 1900, La Plata, Argentina.BackgroundBoth Mannitol (MTL) and Sorbitol (SOR) are polyalcohols with the same chemical formula, butare different structural isomers, that differ only in the position of one of their six hydroxylgroups (Fig.1). They have quite different properties in water and it is generally assumed thatthe differences are due to specific interaction with this solvent.Mannitol SorbitolFig.1 Fisher projection of Mannitol and Sorbitol.SOR and MTL have been modeled previously using Molecular Dynamic (MD) simulation. Grigerareported from a relatively short simulation that the conformation of SOR in water is bent, as observed incrystalline forms of pure SOR; MTL in water adopt a planar zig-zag conformation.1 Recently aconformational analysis suggest that the SOR chain remains extended in solution, in contrast to the bentconformation found experimentally in the crystalline form.2We report here a series of 20 ns MDsimulations run of SOR and MTL in SPE/E3 water analyzing the influence of a change in molecularconformation on atomic partial charge and its consequences on the simulation. The results are analyzedin terms of conformation. Torsional angles and their flexibilities have been determined and compared tothose derived from an analysis of the 3J values and the Karplus equation. We also analyze the end to enddistance for both polyols. The hydratation structure was analyzed by determining the water oxygenradial distribution RDF of the water around each oxygen atom of the polyols and the distribution ofwater-water hydrogen bond.Materials and MethodsWe carried out the MD simulations using the GROMACS 3.2.1 package4. Two cases for partial charges ofboth oxygen and carbon-containing groups were considered: one in which the charge was taken fromliterature1 and another group were charges were calculated by quantum-mechanical semiempiricalmethod. For the last group charges were recalculated with the same level of theory for different step ofthe first simulation and a new simulation with the updated charge was performed.ConclusionsFrom the simulation data we can describe the behavior of SOR and MTL according with the assumptionmade on the charges and the procedure to manage them.Acknowledgements CONICET, UNLP,CIC.References1 Grigera, Raul J., Conformation of Polyols in water. J.Chem.Soc., Faraday Trans., 1, 1988, 84: 2603-2608.2 A. Lerbret, P. E. Mason, R. M. Venable, A. Cesàro, M.-L. Saboungi, R. W. Pastor, J. W. Brady. Molecular dynamics studies of the conformation of sorbitol. CarbohydrateResearch, 2009, 344: 2229–2235.3 H.J.C. Berendsen, J.R. Grigera, T.P. Straatsma, The missing term in effective pair potentials, J. Chem. Phys.,1987, 91: 6269-6271.4 a)Berendsen, H. J. C., van der Spoel, D., van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation. Comp. Phys. Comm. 1995, 91: 43–56. b)Lindahl, E., Hess, B., van der Spoel, D. Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 2001, 7:306–317. c) van Gunsteren, W. F.,Berendsen, H. J. C. Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry. Angew. Chem. Int. Ed. Engl. 1990, 29:992–1023.