5 research outputs found
Characterization of the Local Structure in Liquid Water by Various Order Parameters
A wide
range of geometric order parameters have been suggested
to characterize the local structure of liquid water and its tetrahedral
arrangement, but their respective merits have remained elusive. Here,
we consider a series of popular order parameters and analyze molecular
dynamics simulations of water, in the bulk and in the hydration shell
of a hydrophobic solute, at 298 and 260 K. We show that these parameters
are weakly correlated and probe different distortions, for example
the angular versus radial disorders. We first combine these complementary
descriptions to analyze the structural rearrangements leading to the
density maximum in liquid water. Our results reveal no sign of a heterogeneous
mixture and show that the density maximum arises from the depletion
in interstitial water molecules upon cooling. In the hydration shell
of the hydrophobic moiety of propanol, the order parameters suggest
that the water local structure is similar to that in the bulk, with
only a very weak depletion in ordered configurations, thus confirming
the absence of any iceberg-type structure. Finally, we show that the
main structural fluctuations that affect water reorientation dynamics
in the bulk are angular distortions, which we explain by the jump
hydrogen-bond exchange mechanism
Magnitude and Molecular Origin of Water Slowdown Next to a Protein
Hydration shell dynamics plays a critical role in protein
folding
and biochemical activity and has thus been actively studied through
a broad range of techniques. While all observations concur with a
slowdown of water dynamics relative to the bulk, the magnitude and
molecular origin of this retardation remain unclear. Via numerical
simulations and theoretical modeling, we establish a molecular description
of protein hydration dynamics and identify the key protein features
that govern it. Through detailed microscopic mapping of the water
reorientation and hydrogen-bond (HB) dynamics around lysozyme, we
first determine that 80% of the hydration layer waters experience
a moderate slowdown factor of ∼2–3, while the slower
residual population is distributed along a power-law tail, in quantitative
agreement with recent NMR results. We then establish that the water
reorientation mechanism at the protein interface is dominated by large
angular jumps similar to the bulk situation. A theoretical extended
jump model is shown to provide the first rigorous determination of
the two key contributions to the observed slowdown: a topological
excluded-volume factor resulting from the local protein geometry,
which governs the dynamics of the fastest 80% of the waters, and a
free energetic factor arising from the water–protein HB strength,
which is especially important for the remaining waters in confined
sites at the protein interface. These simple local factors are shown
to provide a nearly quantitative description of the hydration shell
dynamics
Vibrational Quantum Decoherence in Liquid Water
Traditional descriptions of vibrational
energy transfer consider
a quantum oscillator interacting with a classical environment. However,
a major limitation of this simplified description is the neglect of
quantum decoherence induced by the different interactions between
two distinct quantum states and their environment, which can strongly
affect the predicted energy-transfer rate and vibrational spectra.
Here, we use quantum–classical molecular dynamics simulations
to determine the vibrational quantum decoherence time for an OH stretch
vibration in liquid heavy water. We show that coherence is lost on
a sub-100 fs time scale due to the different responses of the first
shell neighbors to the ground and excited OH vibrational states. This
ultrafast decoherence induces a strong homogeneous contribution to
the linear infrared spectrum and suggests that resonant vibrational
energy transfer in H<sub>2</sub>O may be more incoherent than previously
thought
Dynamical Disorder in the DNA Hydration Shell
The reorientation
and hydrogen-bond dynamics of water molecules
within the hydration shell of a B-DNA dodecamer, which are of interest
for many of its biochemical functions, are investigated via molecular
dynamics simulations and an analytic jump model, which provide valuable
new molecular level insights into these dynamics. Different sources
of heterogeneity in the hydration shell dynamics are determined. First,
a pronounced spatial heterogeneity is found at the DNA interface and
explained via the jump model by the diversity in local DNA interfacial
topographies and DNA–water H-bond interactions. While most
of the hydration shell is moderately retarded with respect to the
bulk, some water molecules confined in the narrow minor groove exhibit
very slow dynamics. An additional source of heterogeneity is found
to be caused by the DNA conformational fluctuations, which modulate
the water dynamics. The groove widening aids the approach of, and
the jump to, a new water H-bond partner. This temporal heterogeneity
is especially strong in the minor groove, where groove width fluctuations
occur on the same time scale as the water H-bond rearrangements, leading
to a strong dynamical disorder. The usual simplifying assumption that
hydration shell dynamics is much faster than DNA dynamics is thus
not valid; our results show that biomolecular conformational fluctuations
are essential to facilitate the water motions and accelerate the hydration
dynamics in confined groove sites
Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent
Enzymes are widely
used in nonaqueous solvents to catalyze non-natural
reactions. While experimental measurements showed that the solvent
nature has a strong effect on the reaction kinetics, the molecular
details of the catalytic mechanism in nonaqueous solvents have remained
largely elusive. Here we study the transesterification reaction catalyzed
by the paradigm subtilisin Carlsberg serine protease in an organic
apolar solvent. The rate-limiting acylation step involves a proton
transfer between active-site residues and the nucleophilic attack
of the substrate to form a tetrahedral intermediate. We design the
first coupled valence-bond state model that simultaneously describes
both reactions in the enzymatic active site. We develop a new systematic
procedure to parametrize this model on high-level <i>ab initio</i> QM/MM free energy calculations that account for the molecular details
of the active site and for both substrate and protein conformational
fluctuations. Our calculations show that the reaction energy barrier
changes dramatically with the solvent and protein conformational fluctuations.
We find that the mechanism of the tetrahedral intermediate formation
during the acylation step is similar to that determined under aqueous
conditions, and that the proton transfer and nucleophilic attack reactions
occur concertedly. We identify the reaction coordinate to be mostly
due to the rearrangement of some residual water molecules close to
the active site