Kj. Naidoo et M. Kuttel, Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations, J COMPUT CH, 22(4), 2001, pp. 445-456
We have analyzed a set of molecular dynamics (MD) trajectories of maltose i
n vacuum and water for solute imposed structuring on the solvent. To do thi
s, we used a novel technique to calculate water probability densities to lo
cate the areas in which the solvent is most populated in the maltose soluti
on. We found that only the layer of water within the first maltose hydratio
n shell has a probability density 50% and greater than that of bulk water.
On investigating this water layer using Voronoi polyhedra (VP) analysis it
was seen that only the waters adjacent to the hydrophobic (CH and CH2) grou
ps are more structured than bulk water. We found that in a maltose solution
of approximately 1.0 g/cm(3) the solute does not disrupt the structure of
the surrounding water beyond the first hydration shell. Next we performed a
700-ps MD simulation of a maltohexaose strand in a box of 4096 SPC/E water
s. The water probability density calculations and the VP analysis of the ma
ltohexaose solution show that the larger amylose repeat unit decreases the
solvent configurational entropy of the water beyond the first hydration she
ll. Analysis of this trajectory reveals that the helical conformation of th
e maltohexaose strand is preserved via bridging intermolecular water hydrog
en bonds, indicating that a single amylose helical turn in water is preserv
ed by hydrophilic and not hydrophobic interactions. Using VP analysis we pr
esent a method to accurately determine the number of water molecules in the
first hydration shell of dissolved solutes. In the case of maltose, there
are 40 water molecules in this shell, while for maltohexaose the number is
98. (C) 2001 John Wiley & Sons, Inc.