2 research outputs found
Effect of Charge State on the Equilibrium and Kinetic Properties of Mechanically Interlocked [5]Rotaxane: A Molecular Dynamics Study
Rotaxanes can exhibit stimuli-responsive behavior by
allowing positional
fluctuations of their rota groups in response to physiochemical conditions
such as the changes in solution pH. However, ionic strength of the
solution also affects the molecular conformation by altering the charge
state of the entire molecule, coupling the stimuli-responsiveness
of rotaxanes with their conformation. A molecular-scale investigation
on a model system can allow the decoupling and identification of various
effects and can greatly benefit applications of such molecular switches.
By using atomistic molecular dynamics simulations, we study equilibrium
and kinetics properties of various charge states of the [5]rotaxane,
which is a supramolecular moiety with four rotaxanes bonded to a porphyrin
core. We model various physiochemical charge states, each of which
can be realized at various solution pH levels as well as several exotic
charge distributions. By analyzing molecular configurations, hydrogen
bonding, and energetics of single molecules in salt-free water and
its polyrotaxanated network at the interface of water and chloroform,
we demonstrate that charge-neutral and negatively charged molecules
often tend to collapse in a way that they can expose their porphyrin
core. Contrarily, positively charged moieties tend to take more extended
molecular configurations blocking the core. Further, sudden changes
in the charge states emulating the pH alterations in solution conditions
lead to rapid, sub-10 ns level, changes in the molecular conformation
of [5]rotaxane via shuttling motion of CB6 rings along axles. Finally,
simulations of 2D [5]rotaxane network structures support our previous
findings on a few nanometer-thick film formation at oil–water
interfaces. Overall, our results suggest that rotaxane-based structures
can exhibit a rich spectrum of molecular configurations and kinetics
depending on the ionic strength of the solution
Viscous Friction of Hydrogen-Bonded Matter
Amontons’ law successfully describes friction
between macroscopic
solid bodies for a wide range of velocities and normal forces. For
the diffusion and forced sliding of adhering or entangled macromolecules,
proteins, and biological complexes, temperature effects are invariably
important, and a similarly successful friction law at biological length
and velocity scales is missing. Hydrogen bonds (HBs) are key to the
specific binding of biomatter. Here we show that friction between
hydrogen-bonded matter obeys in the biologically relevant low-velocity
viscous regime a simple law: the friction force is proportional to
the number of HBs, the sliding velocity, and a friction coefficient
γ<sub>HB</sub>. This law is deduced from atomistic molecular
dynamics simulations for short peptide chains that are laterally pulled
over planar hydroxylated substrates in the presence of water and holds
for widely different peptides, surface polarities, and applied normal
forces. The value of γ<sub>HB</sub> is extrapolated from simulations
at sliding velocities in the range from <i>V</i> = 10<sup>–2</sup> to 100 m/s by mapping on a simple stochastic model
and turns out to be of the order of γ<sub>HB</sub> ≃
10<sup>–8</sup> kg/s. The friction of a single HB thus amounts
to the Stokes friction of a sphere with an equivalent radius of roughly
1 μm moving in water. Cooperativity is pronounced: roughly three
HBs act collectively