Biomedical subjects

R M Lynden-Bell

Publications and source records attributed to R M Lynden-Bell.

9 recordsLinked to original sources

PubMed2006

The surface structure of ionic liquids: comparing simulations with x-ray measurements.

The surface-normal electron density profile of an ionic liquid, [bmim][PF6], derived from x-ray reflectivity measurements, is compared with two independent molecular-dynamics simulations. It is shown that a meaningful comparison requires a detailed accounting for both thermal and nonthermal surface roughening effects. The former is due to thermally excited capillary waves, and the latter is due to the molecular zero-point motion and form. These quantities influence very significantly, but differently, the simulated and measured density profiles. Stripping off these effects from both types of profiles yields the intrinsic structure factor of the surface. The simulated intrinsic structure factors are found to deviate considerably from the measured one. The introduction of additional ad hoc surface roughness to the simulated profiles greatly reduces the deviation, however, no physical origin for this effect can be identified. The method employed in this study should prove useful for simulation-experiment comparisons of other liquid surfaces, provided they obey capillary-wave theory, as do almost all liquid surfaces studied to date by x-ray reflectivity.

Journal Article↗

PubMed2005

Simulation of the surface structure of butylmethylimidazolium ionic liquids.

Molecular dynamics simulations of the liquid/vacuum surfaces of the room temperature ionic liquids [bmim][PF(6)], [bmim][BF(4)] and [bmim][Cl] have been carried out at various temperatures. The surfaces are structured with a top monolayer containing oriented cations and anions. The butyl side chains tend to face the vacuum and the methyl side chains the liquid. However, as the butyl chains are not densely packed, both anions and rings are visible from the vacuum phase. The effects of temperature and the anion on the degree of cation orientation is small, but the potential drop from the vacuum to the interior of the liquid is greater for liquids with smaller anions. We compare the simulation results with a range of experimental observations and suggest that neutron reflection from samples with protiated butyl groups would be a sensitive probe of the structure.

Borates↗

PubMed2005

Size-dependent maximum in ion conductivity: the levitation effect provides an alternative explanation.

We propose an alternative explanation of the size-dependent maximum in ion mobility in water in terms of the levitation effect, which accounts for the observed size-dependent maximum in the mobility of guest diffusion in porous media. In this explanation, the size at which the maximum occurs is related to the structure of the void space of the water; at the mobility maximum, the diffusant passes smoothly through necks connecting voids, and its potential energy shows minimum fluctuations. Molecular dynamics simulations of charged spheres of varying sizes are used to support this hypothesis. As in the levitation effect, the friction coefficient, the potential energy fluctuations, and the activation energy are found to be minima for particles with maximum self diffusivities similar to the guest diffusion in zeolites. Wavelength-dependent self diffusivities indicate a monotonic and oscillatory dependence, respectively, on wavenumber k for anomalous (AR) and linear regimes (LR). These are associated with single and biexponential decay of the incoherent intermediate scattering function.

Journal Article↗

PubMed2005

Computational investigation of order, structure, and dynamics in modified water models.

Model liquids have been constructed to study the role of local structure in the anomalous properties of liquid water. The intermolecular potentials were modified by increasing the weight of the Lennard-Jones term relative to the electrostatic term in the SPC/E model for water. The resulting family of liquids varies from SPC/E water to a Lennard-Jones-like liquid. Properties were measured as a function of density and temperature. The local structure was described by two order parameters, one measuring the tetrahedral order and the other measuring the translational order. The translational order parameter was found to be large for both tetrahedral and Lennard-Jones liquids, but to go through a minimum as the potentials were modified, demonstrating that the two types of structure are incompatible. Just as in water several properties (e.g., the translational diffusion coefficient, entropy) exhibit anomalous density dependence as a result of the breakdown of local tetrahedrality, we observed nonmonotonic behavior of the translational diffusion constant and reorientational relaxation rate as the fluids were transformed from tetrahedral to Lennard-Jones-like. This is also an indication of the incompatibility between Lennard-Jones and water-like structure.

Journal Article↗

PubMed2005

Solvent-induced symmetry breaking: varying solvent strength.

The triiodide ion is an example of a system where symmetry breaking may be induced by a solvent. The Landau free energy is expected to have a similar form to that for the mean field Ising model, but with solvent strength rather than temperature as the control parameter determining whether there is symmetry breaking. In order to examine the extent of anomalous behavior near the critical point we have studied the properties of the ion in a solvent based on a model for water with charges scaled by a factor lambda . As lambda is increased from zero the solvent strength increases and the system changes from one with no symmetry breaking to one with strong symmetry breaking. The Shannon entropy as a function of lambda shows only a weak maximum near the critical value of lambda= lambda(c) , while the susceptibility has no anomalous behavior. We examine a simple model and show that anomalies near the critical point would increase as the temperature decreases, but divergences associated with a second order phase transition would only be seen in the limit of zero temperature.

Journal Article↗

PubMed2005

Simulation of interfaces between room temperature ionic liquids and other liquids.

The structure and properties of the interfaces between the room temperature ionic liquid dimethylimidazolium chloride ([dmim]Cl) and different Lennard-Jones fluids and between ionic liquid and water have been studied by molecular dynamics simulations, and compared to the ionic liquid-vapour interface. Two contrasting types of interface were investigated, thermodynamically stable interfaces between ionic liquid and vapour and between ionic liquid and Lennard-Jones fluids, and diffusing interfaces between miscible phases of different compositions involving water. The density profiles of different species through the interface are presented. The cations and water molecules near the former type of interface are aligned relative to the surface, but no orientational preference was found near or in the broad diffusing interface. The ionic liquid has a negative electrostatic potential relative to vapour or Lennard-Jones fluid, but is more positive than pure water. This contrast is explained in terms of the relative importance of orientation and concentration differences in the two types of interface.

Journal Article↗

PubMed2003

Solvent-induced symmetry breaking.

Symmetry breaking can be induced in a number of ways including interactions with a solvent. An example is the triiodide ion which is centrosymmetric in the gas phase. Molecular dynamics simulations of the triiodide ion in solution have been used to investigate the extent of symmetry breaking in a variety of solvents. We find that the triiodide ion loses its symmetry in water, ethanol, and methanol which form hydrogen bonds with the ion. This results in a localization of charge at one end of the ion and breaking of the geometric symmetry. The extent of symmetry breaking increases as the temperature is lowered. Correlation times for interconversion are reported and the energetics of symmetry breaking are presented. Analogies are made with second-order phase transitions.

Journal Article↗

PubMed1993

What is the natural boundary of a protein in solution?

At what distance do proteins in solution interact? Molecular simulation of water around two helices is used to address this question. Calculations are done with two ideal, parallel, polyalanine alpha-helices separated by 9 A, 11 A, 13 A, and 15 A. The second peak in the oxygen density (or loosely the second shell of water molecules) is used to define a hydration surface around the protein, which separates bulk solvent from water molecules strongly influenced by the protein. The hydration surface is contrasted with the Richards-Connolly molecular surface. It indicates that the helices are not completely separate until 15 A, while the molecular surface shows complete separation at 13 A. Suggesting shape-dependent aspects of hydration, the hydration surface only loosely follows the van der Waals outline of the protein surface. In particular, at the 9 A separation, the van der Waals envelopes of the helices make contact; two narrow crevices are formed on either side of the contact; and the water within the crevices is strongly localized in arrangements bridging the helices. A comparison of these 'normal' water simulations with a simulation of a simple, uncharged solvent highlights the importance of hydrogen bonding in structuring liquid water and further contrasts the molecular surface and the hydration surface.

Calorimetry↗

PubMed1972

Spin-spin interaction between molybdenum and one of the iron-sulphur systems of xanthine oxidase and its relevance to the enzymic mechanism.

1. Electron-paramagnetic-resonance (e.p.r.) studies at 9 and 35GHz at helium temperatures have given new information relating to the structure and mechanism of action of xanthine oxidase. 2. As reported by others, the enzyme gives two types of e.p.r. signal attributed to iron-sulphur systems. The first has g(av.)=1.95. Parameters of the second are determined as g(1) 2.12, g(2) 2.007 and g(3) 1.91, with g(av.)=2.01. This species seems to have a slightly higher redox potential than the former one. 3. Temperature-dependent changes in the form of Mo(v) e.p.r. signals from the enzyme, observed under certain conditions, are shown to be due to weak spin-spin interaction between Mo(v) and g(av.)=1.95 Fe/S. The phenomenon has been studied most fully for the Slow Mo(v) signal. Here, the spectral change takes the form of an additional approximately isotropic 11G splitting, detected below about 45 degrees K only. Samples without Fe/S reduced showed no such changes of spectrum. 4. Similar spectral changes were observed in the Rapid Mo(v) signals, obtained in rapid-freezing experiments, but only in samples corresponding to relatively long reaction times with the substrate. It is suggested therefore that the phenomenon may provide a means of distinguishing enzyme centres with Mo only reduced from those in which both Mo and Fe/S are reduced. 5. Additional rapid-freezing data tending to support a two- rather than a one-electron transfer of reducing equivalents from substrates to xanthine oxidase are reported.

Deuterium↗