Molecular dynamics of putrescine

Molecular dynamics simulations of the cationic polyamine putrescine have been performed at T = 300 K. Partial charges of putrescine were calculated with both the HF/STO-3G and HF/6-31G* methods. Solvent was represented either explicitly or via a distance-dependent dielectric of the form epsilon = r. Simulations were performed either with no counterions or with two chloride counterions present. In the case of the distance-dependent dielectric, two different sets of ionic parameters were used to model either hydrated or unhydrated ions. All possible combinations of partial charge set, ionic strength and type and solvent representation were simulated, giving ten different simulations. In general the putrescine molecule was found to adopt a number of different conformations that could be broadly characterised by the ranges in which the backbone torsion angles fell. The conformational behaviour of putrescine was found to be not strongly affected by the partial charges used or the hydration of the ions, however, it was significantly dependent on the representation of the solvent. With the distance-dependent dielectric, the putrescine favoured the ttt state at low ionic strength and the g(+)tt and g(+)tg(+/-) states at high ionic strength. When water molecules were explicitly included the ttt state was rarely adopted and the g(+)tg(+) state was the most favoured, however, the g(+)tt state was also represented.