Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Neutron Diffraction”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 883 records · Page 49Linked to original sources
PubMed2005

A new force field for atomistic simulations of aqueous tertiary butanol solutions.

We present a new tert-butanol force field parametrized to reproduce the mixture thermodynamics of tert-butanol/water over a wide range of solution compositions at room temperature and atmospheric pressure. The experimental Kirkwood-Buff integrals, which quantify preferential solvation of solution components by the same species or by the other components, were used as target values to be reproduced. Water was modeled using the simple point charge model. In the range of alcohol mole fractions between 0.02 and 0.98, our optimized model satisfactorily reproduces alcohol-alcohol, water-water, and alcohol-water aggregation behavior. As a consequence, the solution activity derivatives are reproduced as well. A comparison has been made with solution activities obtained by free energy calculations (i.e., thermodynamic integration). It clearly shows that the Kirkwood-Buff based approach performs superior in predicting solution activities of liquid mixtures. The new tert-butanol model has been used to examine the solution structure and hydrophobic interactions in aqueous tert-butanol at the various mixture compositions. A comparison is made with structural data obtained by neutron diffraction.

Journal Article↗
PubMed2005

Segregation in aqueous methanol enhanced by cooling and compression.

Molecular segregation in methanol-water mixtures is studied across a wide concentration range as a function of temperature and pressure. Cluster distributions obtained from both neutron diffraction and molecular dynamics simulations point to significantly enhanced segregation as the mixtures are cooled or compressed. This evolution toward greater molecular heterogenity in the mixture accounts for the observed changes in the water-water radial distribution function and there are indications also of a change in the topology of the water clusters. The observed behavior is consistent with an approach to an upper critical solution point. Such a point would appear to be "hidden" below the freezing line, thereby precluding observation of the two-fluid region.

Journal Article↗
PubMed2005

Ions in water: the microscopic structure of concentrated hydroxide solutions.

Neutron-diffraction data on aqueous solutions of hydroxides, at solute concentrations ranging from 1 solute per 12 water molecules to 1 solute per 3 water molecules, are analyzed by means of a Monte Carlo simulation (empirical potential structure refinement), in order to determine the hydration shell of the OH- in the presence of the smaller alkali metal ions. It is demonstrated that the symmetry argument between H+ and OH- cannot be used, at least in the liquid phase at such high concentrations, for determining the hydroxide hydration shell. Water molecules in the hydration shell of K+ orient their dipole moment at about 45 degrees from the K+-water oxygen director, instead of radially as in the case of the Li+ and Na+ hydration shells. The K+-water oxygen radial distribution function shows a shallower first minimum compared to the other cation-water oxygen functions. The influence of the solutes on the water-water radial distribution functions is shown to have an effect on the water structure equivalent to an increase in the pressure of the water, depending on both ion concentration and ionic radius. The changes of the water structure in the presence of charged solutes and the differences among the hydration shells of the different cations are used to present a qualitative explanation of the observed cation mobility.

Journal Article↗
PubMed2005

An optimized molecular potential for carbon dioxide.

An optimized molecular potential model for carbon dioxide is presented in this paper. Utilizing the established techniques of molecular-dynamics and histogram reweighting grand canonical Monte Carlo simulations, this model is demonstrated to show excellent predictability for thermodynamic, transport, and liquid structural properties in a wide temperature-pressure range with remarkable accuracies. The average deviations of this new model from experimental data for the saturated liquid densities, vapor densities, vapor pressures, and heats of vaporization are around 0.1%, 2.3%, 0.7%, and 1.9%, respectively. The calculated critical point is almost pinpointed by the new model. The experimental radial distribution functions ranging from 240.0 to 473.0 K are well reproduced as compared to neutron-diffraction measurements. The predicted self-diffusion coefficients are in good agreement with the nuclear-magnetic-resonance measurements. The previously published potential models for CO2 are also systematically evaluated, and our proposed new model is found to be superior to the previous models in general.

Journal Article↗
PubMed2005

High-resolution neutron-scattering study of slow dynamics of surface water molecules in zirconium oxide.

We have performed a quasielastic neutron-scattering experiment on backscattering spectrometer with sub-mueV resolution to investigate the slow dynamics of surface water in zirconium oxide using the sample studied previously with a time-of-flight neutron spectrometer [E. Mamontov, J. Chem. Phys. 121, 9087 (2004)]. The backscattering measurements in the temperature range of 240-300 K have revealed a translational dynamics slower by another order of magnitude compared to the translational dynamics of the outer hydration layer observed in the time-of-flight experiment. The relaxation function of this slow motion is described by a stretched exponential with the stretch factors between 0.8 and 0.9, indicating a distribution of the relaxation times. The temperature dependence of the average residence time is non-Arrhenius, suggesting that the translational motion studied in this work is more complex than surface jump diffusion previously observed for the molecules of the outer hydration layer. The observed slow dynamics is ascribed to the molecules of the inner hydration layer that form more hydrogen bonds compared to the molecules of the outer hydration layer. Despite being slower by two orders of magnitude, the translational motion of the molecules of the inner hydration layer may have more in common with bulk water compared to the outer hydration layer, the dynamics of which is slower than that of bulk water by just one order of magnitude.

Chemistry, Physical↗
PubMed2005

The effect of proton disorder on the structure of ice-Ih: a theoretical study.

A precise and accurate measurement of the crystal structure of ice-Ih is hindered by its disordered H-bond network. In this work, we carried out first-principle calculations to study the effects of H-bond topology on the structure of ice-Ih with emphasis on the molecular geometry of water and the distortion in oxygen lattice. An analytic algorithm based on group and graph theory is employed to enumerate all possible configurations in a given unit cell and to select a set of structures for detailed examinations. In total we have studied more than 60 ice-Ih structures in a hexagonal unit cell of 48 water molecules by quantum-chemical methods and found a significant amount of static distortion in the oxygen positions from their crystallographic positions which is in good agreements with highly significant higher-order terms obtained from both x-ray and neutron-diffraction data. Much debated structural information such as H-O-H angle and O-H bond length is found to be 106.34+/-0.36 degrees and 0.9997+/-0.0008 A, compared to experimental value of 106.6+/-1.5 degrees and 0.986+/-0.005 A. Detailed benchmarking calculations were carried out to gauge the influence of using different exchange and correlation functionals, pseudopotentials, and unit-cell sizes. Our results have proven that first-principle methods are useful complementary tools to experiments, especially for cases in which experimental accuracy is limited by intrinsic orientational disorder.

Journal Article↗
PubMed2006

Orientational correlations in liquid acetone and dimethyl sulfoxide: a comparative study.

The structure of acetone and dimethyl sulfoxide in the liquid state is investigated using a combination of neutron diffraction measurements and empirical potential structure refinement (EPSR) modeling. By extracting the orientational correlations from the EPSR model, the alignment of dipoles in both fluids is identified. At short distances the dipoles or neighboring molecules are found to be in antiparallel configurations, but further out the molecules tend to be aligned predominately as head to tail in the manner of dipolar ordering. The distribution of these orientations in space around a central molecule is strongly influenced by the underlying symmetry of the central molecule. In both liquids there is evidence for weak methyl hydrogen to oxygen intermolecular contacts, though these probably do not constitute hydrogen bonds as such.

Journal Article↗
PubMed2006

Infrared spectroscopy of Li(NH3)n clusters for n=4-7.

Infrared spectra of Li(NH3)(n) clusters as a function of size are reported for the first time. Spectra have been recorded in the N-H stretching region for n=4-->7 using a mass-selective photodissociation technique. For the n=4 cluster, three distinct IR absorption bands are seen over a relatively narrow region, whereas the larger clusters yield additional features at higher frequencies. Ab initio calculations have been carried out in support of these experiments for the specific cases of n=4 and 5 for various isomers of these clusters. The bands observed in the spectrum for Li(NH3)(4) can all be attributed to N-H stretching vibrations from solvent molecules in the first solvation shell. The appearance of higher frequency N-H stretching bands for n > or =5 is assigned to the presence of ammonia molecules located in a second solvent shell. These data provide strong support for previous suggestions, based on gas phase photoionization measurements, that the first solvation shell for Li(NH3)(n) is complete at n=4. They are also consistent with neutron diffraction studies of concentrated lithium/liquid ammonia solutions, where Li(NH3)(4) is found to be the basic structural motif.

Journal Article↗
PubMed2006

Eigen versus Zundel complexes in HCl-water mixtures.

There is an ongoing debate on the nature of hydration of the hydrogen ion, H+ in solution, and the extent to which Eigen or Zundel complexes occur. Here, our previous neutron diffraction data on a solution of 1:9 HCl in water are reanalyzed using a new starting hypothesis for the Monte Carlo simulation of the data. Either bare H+ ions, all H3O+ ions, or all H5O2 + ions are allowed in the simulation box together with the water and chlorine ions. All three simulations give a satisfactory fit to the experimental data. From the simulation with simple H+ ions, it is found that all H+ ions form one strong and very short hydrogen bond with water molecules and that on average 75% of them also engage in a second, slightly longer hydrogen bond. This result can be interpreted alternatively either in terms of the formation of a high percentage of asymmetric Zundel complexes or in terms of the formation of distorted H3O+ ions, which in turn form two or three hydrogen bonds, respectively, with neighboring molecules opposite their unbonded hydrogen sites (thus forming Eigen complexes). Therefore the new analysis is not inconsistent with our previous conclusion that the solution consists primarily of Eigen complexes, but does highlight the difficulty of making a clear distinction between Eigen and Zundel complexes due to the continuous random network of hydrogen bonds formed between water and hydrated protons. The role of hydrogen ion to chloride counterion contacts is also discussed in these solutions.

Journal Article↗
PubMed2006

Moving solvated electrons with light: nonadiabatic mixed quantum/classical molecular dynamics simulations of the relocalization of photoexcited solvated electrons in tetrahydrofuran (THF).

Motivated by recent ultrafast spectroscopic experiments [Martini et al., Science 293, 462 (2001)], which suggest that photoexcited solvated electrons in tetrahydrofuran (THF) can relocalize (that is, return to equilibrium in solvent cavities far from where they started), we performed a series of nonequilibrium, nonadiabatic, mixed quantum/classical molecular dynamics simulations that mimic one-photon excitation of the THF-solvated electron. We find that as photoexcited THF-solvated electrons relax to their ground states either by continuous mixing from the excited state or via nonadiabatic transitions, approximately 30% of them relocalize into cavities that can be over 1 nm away from where they originated, in close agreement with the experiments. A detailed investigation shows that the ability of excited THF-solvated electrons to undergo photoinduced relocalization stems from the existence of preexisting cavity traps that are an intrinsic part of the structure of liquid THF. This explains why solvated electrons can undergo photoinduced relocalization in solvents like THF but not in solvents like water, which lack the preexisting traps necessary to stabilize the excited electron in other places in the fluid. We also find that even when they do not ultimately relocalize, photoexcited solvated electrons in THF temporarily visit other sites in the fluid, explaining why the photoexcitation of THF-solvated electrons is so efficient at promoting recombination with nearby scavengers. Overall, our study shows that the defining characteristic of a liquid that permits the photoassisted relocalization of solvated electrons is the existence of nascent cavities that are attractive to an excess electron; we propose that other such liquids can be found from classical computer simulations or neutron diffraction experiments.

Computer Simulation↗
PubMed2007

A polarizable ion model for the structure of molten AgI.

The results are reported of the molecular dynamics simulations of the coherent static structure factor of molten AgI at 923 K using a polarizable ion model. This model is based on a rigid ion potential, to which the many body interactions due to the anions induced polarization are added. The calculated structure factor is in better agreement with recent neutron diffraction data than that obtained by using simple rigid ion pair potentials. The Voronoi-Delaunay method has been applied to study the relationship between voids in the spatial distribution of cations and the prepeak of the structure factor.

Journal Article↗
PubMed2007

Neutron scattering reveals extremely slow cell water in a Dead Sea organism.

Intracellular water dynamics in Haloarcula marismortui, an extremely halophilic organism originally isolated from the Dead Sea, was studied by neutron scattering. The water in centrifuged cell pellets was examined by means of two spectrometers, IN6 and IN16, sensitive to motions with time scales of 10 ps and 1 ns, respectively. From IN6 data, a translational diffusion constant of 1.3 x 10(-5) cm(2) s(-1) was determined at 285 K. This value is close to that found previously for other cells and close to that for bulk water, as well as that of the water in the 3.5 M NaCl solution bathing the cells. A very slow water component was discovered from the IN16 data. At 285 K the water-protons of this component displays a residence time of 411 ps (compared with a few ps in bulk water). At 300 K, the residence time dropped to 243 ps and was associated with a translational diffusion of 9.3 x 10(-8) cm(2) s(-1), or 250 times lower than that of bulk water. This slow water accounts for approximately 76% of cell water in H. marismortui. No such water was found in Escherichia coli measured on BSS, a neutron spectrometer with properties similar to those of IN16. It is hypothesized that the slow mobility of a large part of H. marismortui cell water indicates a specific water structure responsible for the large amounts of K(+) bound within these extremophile cells.

Escherichia coli↗
PubMed2003

Ba2LnSbO6 and Sr2LnSbO6 (Ln = Dy, Ho, Gd) double perovskites: lanthanides in the geometrically frustrating fcc lattice.

Magnetic ground states in solids often arise as a result of a delicate balance between competing factors. One currently active area of research in magnetic materials involves compounds in which long-range magnetic ordering at low temperatures is frustrated by the geometry of the crystalline lattice, a situation known as geometrical magnetic frustration. The number of systems known to display the effects of such frustration is growing, but those that are sufficiently simple from theoretical, chemical, and physical perspectives to allow for detailed understanding remain very few. A search for model compounds in this family has led us to the double perovskites Ba2LnSbO6 and Sr2LnSbO6 (Ln = Dy, Ho, and Gd) reported here. Ba2DySbO6,Ba2HoSbO6,Sr2DySbO6, and Sr2HoSbO6 are structurally characterized by powder neutron diffraction at ambient temperature. The trivalent lanthanides and pentavalent antimony are found to be fully ordered in the double-perovskite arrangement of alternating octahedra sharing corner oxygens. In such a structure, the lanthanide sublattice displays a classical fcc arrangement, an edge-shared network of tetrahedra known to result in geometric magnetic frustration. No magnetic ordering is observed in any of these compounds down to temperatures of 2 K, and in the case of the Dy-based compounds in particular, frustration of the magnetic ordering is clearly present. Lanthanide-based double perovskites are proposed to be excellent model systems for the detailed study of geometric magnetic frustration.

Journal Article↗
PubMed1973

Disulfide bond dihedral angles from Raman spectroscopy.

Raman spectra of several compounds containing the CS-SC moiety were obtained (in the solid phase) from 450-800 cm(-1) to investigate the S-S and C-S stretching behavior. The S-S stretching frequency varied linearly with the CS-SC dihedral angle (obtained from either x-ray or neutron diffraction or ultraviolet absorption) for compounds whose CC-SS dihedral angles were not very different. The ratio of the intensities of the S-S and C-S stretching bands exhibited no recognizable correlation with either the CS-SC dihedral angle or the CSS bond angle, probably because this ratio is sensitive to the crystalline environment. The linear dependence of the S-S stretching frequency on dihedral angle leads to a dihedral angle for the plant hormone, malformin A, that is in excellent agreement with that estimated from the longest wavelength CS-SC ultraviolet absorption band.

Journal Article↗
PubMed1979

Metal cluster chemistry: Structure and stereochemistry in the polynuclear rhodium hydrides H(n)Rh(n)[P(OR)(3)](2n).

Crystallographic analyses of x-ray and neutron diffraction data have provided a definitive structural representation of {HRh[P(O-i-C(3)H(7))(3)](2)}(2) and {HRh[P(OCH(3))(3)](2)}(3). These polynuclear hydrides are generated from square planar H(2)Rh[P(OR)(3)](2) units by edge (hydrogen atom) sharing and by vertex (hydrogen atom) sharing to form the dimeric and trimeric structures, respectively. The square-planar units are held together through four-center and three-center two-electron Rh-H-Rh bonds in the dimer and trimer, respectively. The dimer and trimer molecules each add one molecule of hydrogen to form H[(i-C(3)H(7)O)(3)P](2)RhH(3)Rh [P(O-i-C(3)H(7))(3)](2) and H(5)Rh(3)[P(OCH(3))(3)](6), respectively. NMR spectral information has served to define the stereochemical features of these polyhydrides. The significance of this chemistry in the metal cluster-metal surface analogy is described.

Journal Article↗
PubMed1988

Voltage gating of conductance in lipid bilayers induced by porin from outer membrane of Neisseria gonorrhoeae.

Porins, polypeptides of approximately 35 kDa, are present as integral membrane proteins in the outer membranes of a variety of Gram-negative bacteria. As reported previously for a purified porin from Escherichia coli, voltage gating of conductance was found to be induced in a lipid bilayer by the solubilized purified porin, protein I, from Neisseria gonorrhoeae. The unitary response to an applied potential showed a cascade of current from an initial level through at least three levels, more or less equal, to a persisting lower level. The initial level of current corresponded to 1.0-1.3 nS for 0.2 M NaCl on either side of the bilayer. Briefly reducing the potential to zero restored the current to its initial level. Interpretation of the unitary response is suggested by electron microscopic data obtained on negatively stained outer membranes of E. coli indicating the presence of "pores" appearing in triplets. Moreover, low-resolution x-ray and neutron diffraction studies on crystals obtained with an E. coli porin show that three polypeptides associate to form a unit. Combining such structural data with the present electrical data lends support for the hypothesis that the unitary response results from three pores acting as a unit in response to an applied potential. Evidence obtained with the patch-clamp technique is mounting for a similar mechanism of many channels operating as a unit in a variety of cell membranes. The porin channel holds promise as a concrete model for the analysis of voltage gating of ionic conductance.

Bacterial Outer Membrane Proteins↗
PubMed1991

Model for the structure of the lipid bilayer.

A detailed model for the structure and dynamics of the interior of the lipid bilayer in the liquid crystal phase is presented. The model includes two classes of motion: (i) the internal dynamics of the chains, determined from Brownian dynamics simulations with a continuous version of the Marcelja mean-field potential, and (ii) noncollective reorientation (axial rotation and wobble) of the entire molecule, introduced by a cone model. The basic unit of the model is a single lipid chain with field parameters adjusted to fit the 2H order parameters and the frequency-dependent 13C NMR T1 relaxation times of dipalmitoyl phosphatidylcholine bilayers. The chain configurations obtained from the trajectory are used to construct a representation of the bilayer. The resulting lipid assembly is consistent with NMR, neutron diffraction, surface area, and density data. It indicates that a high degree of chain disorder and entanglement exists in biological membranes.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1993

Protein hydration elucidated by molecular dynamics simulation.

Molecular dynamics (MD) simulation covering a wide range of hydration indicate that myoglobin is fully hydrated by 350 water molecules, in agreement with experiment. These waters, originally placed uniformly about the protein, form clusters that hydrate every charged group throughout the entire simulation. Some atoms in charged groups are hydrated by two water layers while 37% of the protein surface remains uncovered. The locations of the 350 waters are consistent with those of crystallographic waters resolved by x-ray and neutron diffraction. Hydration by 350 waters at 300 K stabilizes the conformation of carboxymyoglobin measured by x-ray diffraction throughout the entire protein, halves the rate of torsional transitions, and promotes alternative conformations for surface atoms. The glass transition observed experimentally in hydrated myoglobin near 220 K is also seen in the simulations and correlates with an increase in the number of dihedral angles undergoing transitions. The anharmonic protein motion above 220 K is enhanced by protein hydration.

Computer Simulation↗