191 research outputs found
How the Liquid-Liquid Transition Affects Hydrophobic Hydration in Deeply Supercooled Water
We determine the phase diagram of liquid supercooled water by extensive
computer simulations using the TIP5P-E model [J. Chem. Phys. {\bf 120}, 6085
(2004)]. We find that the transformation of water into a low density liquid in
the supercooled range strongly enhances the solubility of hydrophobic
particles. The transformation of water into a tetrahedrally structured liquid
is accompanied by a minimum in the hydration entropy and enthalpy. The
corresponding change in sign of the solvation heat capacity indicates a loss of
one characteristic signature of hydrophobic hydration. The observed behavior is
found to be qualitatively in accordance with the predictions of the information
theory model of Garde et al. [Phys. Rev. Lett. {\bf 77}, 4966 (1996)].Comment: 4 pages, 4 figures, twocolumn Revtex, modified text applied changes
to figure 1, 2d, 3,
Adding Salt to an Aqueous Solution of t-Butanol: Is Hydrophobic Association Enhanced or Reduced?
Recent neutron scattering experiments on aqueous salt solutions of
amphiphilic t-butanol by Bowron and Finney [Phys. Rev. Lett. {\bf 89}, 215508
(2002); J. Chem. Phys. {\bf 118}, 8357 (2003)] suggest the formation of
t-butanol pairs, bridged by a chloride ion via
hydrogen-bonds, and leading to a reduced number of intermolecular hydrophobic
butanol-butanol contacts. Here we present a joint experimental/theoretical
study on the same system, using a combination of molecular dynamics simulations
and nuclear magnetic relaxation measurements. Both theory and experiment
clearly support the more intuitive scenario of an enhanced number of
hydrophobic contacts in the presence of the salt, as it would be expected for
purely hydrophobic solutes [J. Phys. Chem. B {\bf 107}, 612 (2003)]. Although
our conclusions arrive at a structurally completely distinct scenario, the
molecular dynamics simulation results are within the experimental errorbars of
the Bowron and Finney work.Comment: 15 pages twocolumn revtex, 11 figure
Steady-State Properties of Single-File Systems with Conversion
We have used Monte-Carlo methods and analytical techniques to investigate the
influence of the characteristic parameters, such as pipe length, diffusion,
adsorption, desorption and reaction rate constants on the steady-state
properties of Single-File Systems with a reaction. We looked at cases when all
the sites are reactive and when only some of them are reactive. Comparisons
between Mean-Field predictions and Monte-Carlo simulations for the occupancy
profiles and reactivity are made. Substantial differences between Mean-Field
and the simulations are found when rates of diffusion are high. Mean-Field
results only include Single-File behavior by changing the diffusion rate
constant, but it effectively allows passing of particles. Reactivity converges
to a limit value if more reactive sites are added: sites in the middle of the
system have little or no effect on the kinetics. Occupancy profiles show
approximately exponential behavior from the ends to the middle of the system.Comment: 15 pages, 20 figure
Meteorites and the RNA World: Synthesis of Nucleobases in Carbonaceous Planetesimals and the Role of Initial Volatile Content
Prebiotic molecules, fundamental building blocks for the origin of life, have
been found in carbonaceous chondrites. The exogenous delivery of these organic
molecules onto the Hadean Earth could have sparked the polymerization of the
first RNA molecules in Darwinian ponds during wet-dry cycles. Here, we
investigate the formation of the RNA and DNA nucleobases adenine, uracil,
cytosine, guanine, and thymine inside parent body planetesimals of carbonaceous
chondrites. An up-to-date thermochemical equilibrium model coupled with a 1D
thermodynamic planetesimal model is used to calculate the nucleobase
concentrations. Different from the previous study (Pearce & Pudritz 2016), we
assume initial volatile concentrations more appropriate for the formation zone
of carbonaceous chondrite parent bodies. This represents more accurately
cosmochemical findings that these bodies have formed inside the inner, , warm region of the solar system. Due to these
improvements, our model represents the concentrations of adenine and guanine
measured in carbonaceous chondrites. Our model did not reproduce per se the
measurements of uracil, cytosine, and thymine in these meteorites. This can be
explained by transformation reactions between nucleobases and potential
decomposition of thymine. The synthesis of prebiotic organic matter in
carbonaceous asteroids could be well explained by a combination of i)
radiogenic heating, ii) aqueous chemistry involving a few key processes at a
specific range of radii inside planetesimals where water can exist in the
liquid phase, and iii) a reduced initial volatile content (H, CO, HCN,
CHO) of the protoplanetary disk material in the parent body region compared
to the outer region of comets.Comment: Accepted for publication in The Astrophysical Journal. 30 pages, 9
figures (all colored). Supporting figure sets are available at
https://doi.org/10.6084/m9.figshare.2154514
X-ray Diffraction and Molecular Dynamics Study of Medium-range Order in Ambient and Hot Water
We have developed x-ray diffraction measurements with high energy-resolution
and accuracy to study water structure at three different temperatures (7, 25
and 66 C) under normal pressure. Using a spherically curved Ge crystal an
energy resolution better than 15 eV has been achieved which eliminates
influence from Compton scattering. The high quality of the data allows a
precise oxygen-oxygen pair correlation function (PCF) to be directly derived
from the Fourier transform of the experimental data resolving shell structure
out to ~12 {\AA}, i.e. 5 hydration shells. Large-scale molecular dynamics (MD)
simulations using the TIP4P/2005 force-field reproduce excellently the
experimental shell-structure in the range 4-12 {\AA} although less agreement is
seen for the first peak in the PCF. The Local Structure Index [J. Chem. Phys.
104, 7671 (1996)] identifies a tetrahedral minority giving the
intermediate-range oscillations in the PCF and a disordered majority providing
a more featureless background in this range. The current study supports the
proposal that the structure of liquid water, even at high temperatures, can be
described in terms of a two-state fluctuation model involving local structures
related to the high-density and low-density forms of liquid water postulated in
the liquid-liquid phase transition hypothesis.Comment: Submitted to Phys. Chem. Chem. Phy
Ab initio van der Waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like
The structure of liquid water at ambient conditions is studied in ab initio
molecular dynamics simulations using van der Waals (vdW) density-functional
theory, i.e. using the new exchange-correlation functionals optPBE-vdW and
vdW-DF2. Inclusion of the more isotropic vdW interactions counteracts highly
directional hydrogen-bonds, which are enhanced by standard functionals. This
brings about a softening of the microscopic structure of water, as seen from
the broadening of angular distribution functions and, in particular, from the
much lower and broader first peak in the oxygen-oxygen pair-correlation
function (PCF), indicating loss of structure in the outer solvation shells. In
combination with softer non-local correlation terms, as in the new
parameterization of vdW-DF, inclusion of vdW interactions is shown to shift the
balance of resulting structures from open tetrahedral to more close-packed. The
resulting O-O PCF shows some resemblance with experiment for high-density water
(A. K. Soper and M. A. Ricci, Phys. Rev. Lett., 84:2881, 2000), but not
directly with experiment for ambient water. However, an O-O PCF consisting of a
linear combination of 70% from vdW-DF2 and 30% from experiment on low-density
liquid water reproduces near-quantitatively the experimental O-O PCF for
ambient water, indicating consistency with a two-liquid model with fluctuations
between high- and low-density regions
Nanoscale Dynamics of Phase Flipping in Water near its Hypothesized Liquid-Liquid Critical Point
Achieving a coherent understanding of the many thermodynamic and dynamic
anomalies of water is among the most important unsolved puzzles in physics,
chemistry, and biology. One hypothesized explanation imagines the existence of
a line of first order phase transitions separating two liquid phases and
terminating at a novel "liquid-liquid" critical point in a region of low
temperature () and high pressure (). Here we analyze a common model of water, the ST2 model, and find
that the entire system flips between liquid states of high and low density.
Further, we find that in the critical region crystallites melt on a time scale
of nanoseconds. We perform a finite-size scaling analysis that accurately
locates both the liquid-liquid coexistence line and its associated
liquid-liquid critical point.Comment: 22 pages, 5 figure
Water in CavityâLigand Recognition
We use explicit solvent molecular dynamics simulations to estimate free energy, enthalpy, and entropy changes along the cavity-ligand association coordinate for a set of seven model systems with varying physicochemical properties. Owing to the simplicity of the considered systems we can directly investigate the role of water thermodynamics in molecular recognition. A broad range of thermodynamic signatures is found in which water (rather than cavity or ligand) enthalpic or entropic contributions appear to drive cavity-ligand binding or rejection. The unprecedented, nanoscale picture of hydration thermodynamics can help the interpretation and design of protein-ligand binding experiments. Our study opens appealing perspectives to tackle the challenge of solvent entropy estimation in complex systems and for improving molecular simulation models
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