  Studying the changed water dynamics in the hydration layers of biomolecules
is an important step towards fuller understanding of their function and
mechanisms, but has shown to be quite difficult. The measurement of the
time-dependent Stokes shift of a chromophore attached to the biomolecule is a
promising method to achieve this goal, as published in J. Phys. Chem. Lett. 5
(2014), 1845, where trehalose was used as biomolecule,
1-methyl-6-oxyquinolinium betaine as chromophore and water as solvent. An
overall retardation of solvent molecules is then obtained by comparison of the
linked system to the same system without trehalose, but contributions from
different subgroups of solvent molecules, for example molecules close to or far
from trehalose, are unknown. The difficulty arising from these unknown
contributions of retarded and possibly unretarded solvent molecules is overcome
in this work by conducting computer simulations on this system and decomposing
the overall signal into contributions from various molecules at different
locations. We performed non-equilibrium molecular dynamics simulation using a
polarizable water model and a non-polarizable solute model and could reproduce
the experimental time-dependent Stokes shift accurately for the linked
trehalose-oxyquinolinium and the pure oxyquinolinium over a wide temperature
range, indicating the correctness of our employed models. Decomposition of the
shift into contributions from different solvent subgroups showed that the
amplitude of the measured shift is made up only half by the desired retarded
solvent molecules in the hydration layer, but to another half by unretarded
bulk water, so that measured relaxation times of the overall Stokes shift are
only a lower boundary for the true relaxation times in the hydration layer of
trehalose.
