Molecular dynamics simulation of aqueous solutions of 26-unit segments of p(NIPAAm) and of p(NIPAAm) "doped" with amino acid based comonomers

We have performed 75-ns molecular dynamics (MD) simulations of aqueous solutions of a 26-unit NIPAAm
oligomer at two temperatures, 302 and 315 K, below and above the experimentally determined lower critical
solution temperature (LCST) of p(NIPAAm). We have been able to show that at 315 K the oligomer assumes
a compact form, while it keeps a more extended form at 302 K. A similar behavior has been demonstrated
for a similar NIPAAm oligomer, where two units had been substituted by methacryloyl-l-valine (MAVA)
comonomers, one of them being charged and one neutral. For another analogous oligomer, where the same
units had been substituted by methacryloyl-l-leucine (MALEU) comonomers, no transition from the extended
to the more compact conformation has been found within the same simulation time. Statistical analysis of the
trajectories indicates that this transition is related to the dynamics of the oligomer backbone, and to the formation
of intramolecular hydrogen bonds and water-bridges between distant units of the solute. In the MAVA case,
we have also evidenced an important role of the neutral MAVA comonomer in stabilizing the compact coiled
structure. In the MALEU case, the corresponding comonomer is not equally efficacious and, possibly, is
even hindering the readjustment of the oligomer backbone. Finally the self-diffusion coefficient of water
molecules surrounding the oligomers at the two temperatures for selected relevant times is observed to
characteristically depend on the distance from the solute molecules.