Molecular dynamics simulations of aqueous solutions of varying concentrations NALMA (N-Acetyl-leucine-methylamide), an amphiphilic dipeptide, were performed.  One nanosecond simulations were performed at 298 K and ambient pressure. NALMA was modeled using the Amber force field [Kirschner, K.N., Yongye, A.B., Tschampel, S.M., Daniels, C.R., Foley, B.L., Woods, R.J. J. Comput. Chem. 29, 622-655 (2008)] while the SPC/E model was used for water [Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269]. Site-site radial pair distribution functions and orientational time correlation functions were analyzed for each system. Results showed significant changes in the solvation shell of NALMA as its concentration increased.  Additionally, possible aggregation of NALMA occurs at high concentration.  Orientational time correlation functions revealed slower relaxation times of water with higher NALMA concentration.

Molecular simulation study of aqueous solvation of a model peptide

247th National Meeting (2014)

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