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At least 1,297 records · Page 72Linked to original sources
PubMed2000

Chromophore reorientation during the photocycle of bacteriorhodopsin: experimental methods and functional significance.

Light-induced isomerization leads to orientational changes of the retinylidene chromophore of bacteriorhodopsin in its binding pocket. The chromophore reorientation has been characterized by the following methods: polarized absorption spectroscopy in the visible, UV and IR; polarized resonance Raman scattering; solid-state deuterium nuclear magnetic resonance; neutron and X-ray diffraction. Most of these experiments were performed at low temperatures with bacteriorhodopsin trapped in one or a mixture of intermediates. Time-resolved measurements at room temperature with bacteriorhodopsin in aqueous suspension can currently only be carried out with transient polarized absorption spectroscopy in the visible. The results obtained to date for the initial state and the K, L and M intermediates are presented and discussed. The most extensive data are available for the M intermediate, which plays an essential role in the function of bacteriorhodopsin. For this intermediate the various methods lead to a consistent picture: the curved all-trans polyene chain in the initial state straightens out in the M intermediate (13-cis) and the chain segment between C(5) and C(13) tilts upwards in the direction of the cytoplasmic surface. The kink at C(13) allows the positions of beta-ionone ring and Schiff base nitrogen to remain approximately fixed.

Bacteriorhodopsins↗
PubMed1999

Orientational order and dynamics of hydration water in a single crystal of bovine pancreatic trypsin inhibitor.

The orientational order and dynamics of the water molecules in form II crystals of bovine pancreatic trypsin inhibitor (BPTI) are studied by (2)H NMR in the temperature range 6-50 degrees C. From the orientation dependence of the single crystal quadrupole splitting and linewidth, the principal components of the motionally averaged quadrupole interaction tensor and the irreducible linewidth components for the orthorhombic crystal are determined. With the aid of water orientations derived from neutron and x-ray diffraction, it is shown that the NMR data can be accounted for by a small number of highly ordered crystal waters, some of which have residence times in the microsecond range. Most of these specific hydration sites must be located at intermolecular contacts. The surface hydration layer that is also present in dilute solution is likely to be only weakly ordered and would then not contribute significantly to the splitting and linewidth from the protein crystal. To probe water dynamics on shorter time scales, the (2)H longitudinal relaxation dispersion is measured for a polycrystalline BPTI sample. The observed dispersion is dominated by rapidly exchanging deuterons in protein side chains, undergoing restricted rotational motions on a time scale of 10 ns.

Animals↗
PubMed2004

Structure and bonding of the vanadium(III) hexa-aqua cation. 1. Experimental characterization and ligand-field analysis.

Spectroscopic and crystallographic data are presented for salts containing the [V(OH(2))(6)](3+) cation, providing a rigorous test of the ability of the angular overlap model (AOM) to inter-relate the electronic and molecular structure of integer-spin complexes. High-field multifrequency EPR provides a very precise definition of the ground-state spin-Hamiltonian parameters, while single-crystal absorption measurements enable the energies of excited ligand-field states to be identified. The EPR study of vanadium(III) as an impurity in guanidinium gallium sulfate is particularly instructive, with fine-structure observed attributable to crystallographically distinct [V(OH(2))(6)](3+) cations, hyperfine coupling, and ferroelectric domains. The electronic structure of the complex depends strongly on the mode of coordination of the water molecules to the vanadium(III) cation, as revealed by single-crystal neutron and X-ray diffraction measurements, and is also sensitive to the isotopic abundance. It is shown that the AOM gives a very good account of the change in the electronic structure, as a function of geometric coordinates of the [V(OH(2))(6)](3+) cation. However, the ligand-field analysis is inconsistent with the profiles of electronic transitions between ligand-field terms.

Journal Article↗
PubMed2004

Magnetic phase control by an electric field.

The quest for higher data density in information storage is motivating investigations into approaches for manipulating magnetization by means other than magnetic fields. This is evidenced by the recent boom in magnetoelectronics and 'spintronics', where phenomena such as carrier effects in magnetic semiconductors and high-correlation effects in colossal magnetoresistive compounds are studied for their device potential. The linear magnetoelectric effect-the induction of polarization by a magnetic field and of magnetization by an electric field-provides another route for linking magnetic and electric properties. It was recently discovered that composite materials and magnetic ferroelectrics exhibit magnetoelectric effects that exceed previously known effects by orders of magnitude, with the potential to trigger magnetic or electric phase transitions. Here we report a system whose magnetic phase can be controlled by an external electric field: ferromagnetic ordering in hexagonal HoMnO3 is reversibly switched on and off by the applied field via magnetoelectric interactions. We monitor this process using magneto-optical techniques and reveal its microscopic origin by neutron and X-ray diffraction. From our results, we identify basic requirements for other candidate materials to exhibit magnetoelectric phase control.

Journal Article↗
PubMed2004

Raman spectra of ionic liquids: a simulation study of LaCl3 and its mixtures with alkali chlorides.

Theoretical Raman spectra of the elpasolite-structured crystal Cs2NaLaCl6 and of molten mixtures of LaCl6 with NaCl and CsCl have been obtained from computer simulations in order to examine how the Raman spectra reflect the coordination structure around the La3+ ions. This system is a model for many other trivalent metal halides and for examining how the network structure of the pure melts is broken down by the addition of alkali halides with different structure-breaking powers. The results suggest a way of reconciling the conclusions of Raman studies about the structures of the melts with those of neutron and x-ray-diffraction studies, which have already been examined with the same simulation methods. The Raman spectra, both polarized and depolarized, are calculated from a model for the dependence of the polarizability of the system on the ionic coordinates which was inspired by electronic structure calculations of the polarizabilities of ions in a condensed phase environment. Some results on the lifetimes of the coordination complexes responsible for the appearance of the discrete Raman bands are discussed.

Journal Article↗
PubMed2005

On the structure of aqueous LiCl solutions.

The structure of highly concentrated aqueous lithium chloride solutions was investigated by the Reverse Monte Carlo method. Two total structure factors, obtained from neutron and x-ray diffraction experiments, were applied as input information. From the resulting particle configurations, partial pair correlation functions, coordination numbers and cosine distributions of bond angles have been determined. It was found that, in accordance with common-sense expectations, the hydrogen bonded network of water molecules is breaking up continuously as the concentration of the electrolyte increases. The hydration shell of the cations becomes more and more distorted as concentration grows whereas the hydration structure of the anions appears to be nearly invariant. Ion-pairing was not detected even at the highest salt concentration.

Journal Article↗
PubMed2005

Spectroscopic characterization of microscopic hydrogen-bonding disparities in supercritical water.

The local hydrogen-bonding environment in supercritical water (380 degrees C, 300 bars, density 0.54 gcm3) was studied by x-ray Raman scattering at the oxygen K edge. The spectra are compared to those of the gas phase, liquid surface, bulk liquid, and bulk ice, as well as to calculated spectra. The experimental model systems are used to assign spectral features and to quantify specific local hydrogen-bonding situations in supercritical water. The first coordination shell of the molecules is characterized in more detail with the aid of the calculations. Our analysis suggests that approximately 65% of the molecules in supercritical water are hydrogen bonded in configurations that are distinctly different from those in liquid water and ice. In contrast to liquid water the bonded molecules in supercritical water have four intact hydrogen bonds and in contrast to ice large variations of bond angles and distances are observed. The remaining approximately 35% of the molecules exhibit two free O-H bonds and are thus either not involved in hydrogen bonding at all or have one or two hydrogen bonds on the oxygen side. We determine an average O-O distance of 3.1+/-0.1 A in supercritical water for the H bonded molecules at the conditions studied here. This and the corresponding hydrogen bond lengths are shown to agree with neutron- and x-ray-diffraction data at similar conditions. Our results on the local hydrogen-bonding environment with mainly two disparate hydrogen-bonding configurations are consistent with an extended structural model of supercritical water as a heterogeneous system with small patches of bonded molecules in various tetrahedral configurations and surrounding nonbonded gas-phase-like molecules.

Hydrogen↗
PubMed2007

Study of water dynamics and distances in paramagnetic solids by variable-temperature two-dimensional 2H NMR spectroscopy.

A recently proposed two-dimensional (2)H NMR experiment is used to measure the (2)H (spin I=1) quadrupolar and paramagnetic shift anisotropy interactions in powdered CuCl(2).2D(2)O as a function of temperature. The principal components of the quadrupolar and paramagnetic shift anisotropy tensors and the Euler angles describing the orientations of the tensors in the molecular frame are determined at each temperature. For this purpose an analytical approach is introduced to extract desired parameters from motionally averaged two-dimensional line shapes where the averaging is introduced by rapid 180 degrees flips around C(2) axes of D(2)O molecules. This approach can be readily applied to study various materials containing water of crystallization. It is also clearly shown that the rapid continuous rotation of D(2)O molecules around their C(2) axes is not taking place in the studied solid in the range of temperatures between 209 and 344 K. Once the paramagnetic shift anisotropy of a deuterium atom is measured accurately it is used to estimate the distance between deuterium and the nearest copper atom bearing an unpaired electron. Excellent agreement is found between structural parameters obtained in this study and those provided by neutron and x-ray diffraction, showing that the paramagnetic shift anisotropy is a sensitive probe of distances in paramagnetic solids.

Journal Article↗
PubMed2000

Anharmonicity in anisotropic displacement parameters

A quasi-harmonic molecular-mean-field model for analyzing anharmonic temperature evolution of anisotropic displacement parameters is described. Anharmonic effects are taken into account through a Gruneisen-type temperature dependence of effective vibrational frequencies. The method is applied to neutron and X-ray diffraction data of hexamethylenetetramine measured between 15 and 298 K. The resulting Gruneisen parameters and other characteristics of molecular motion in the solid state agree well with those obtained from independent vibrational data. The analysis also suggests errors in the ADP's due to insufficient extinction corrections in the diffraction data.

Journal Article↗
PubMed2004

The structure of the first coordination shell in liquid water.

X-ray absorption spectroscopy and x-ray Raman scattering were used to probe the molecular arrangement in the first coordination shell of liquid water. The local structure is characterized by comparison with bulk and surface of ordinary hexagonal ice Ih and with calculated spectra. Most molecules in liquid water are in two hydrogen-bonded configurations with one strong donor and one strong acceptor hydrogen bond in contrast to the four hydrogen-bonded tetrahedral structure in ice. Upon heating from 25 degrees C to 90 degrees C, 5 to 10% of the molecules change from tetrahedral environments to two hydrogen-bonded configurations. Our findings are consistent with neutron and x-ray diffraction data, and combining the results sets a strong limit for possible local structure distributions in liquid water. Serious discrepancies with structures based on current molecular dynamics simulations are observed.

Chemical Phenomena↗
PubMed1999

Chemical applications of neutron scattering.

Neutron scattering represents a versatile technique for chemists, as it explores the structure and dynamics of materials at the atomic scale. This review gives an outline of the neutron scattering formalism and describes diffraction and inelastic and quasielastic scattering techniques. Applications to chemistry are illustrated by examples from recent work on crystalline and liquid organic materials, including heterogeneous systems, bulk polymers and polymer solutions. There is particular emphasis on systems where hydrogen bonding plays a significant role. With more powerful sources and improved instrumentation in prospect, there is considerable potential for future extension of these methods to increasingly complex materials.

Journal Article↗
PubMed1987

The nature of the mineral component of bone and the mechanism of calcification.

From the physical chemical standpoint, the formation of a solid phase of Ca-P in bone represents a phase transformation, a process exemplified by the formation of ice from water. Considering the structural complexity and abundance of highly organized macromolecules in the cells and extracellular tissue spaces of mineralized tissues generally and in bone particularly, it is inconceivable that this phase transformation occurs by homogeneous nucleation, i.e., without the active participation of an organic component acting as a nucleator. This is almost surely true in biologic mineralization in general. Electron micrographs and low-angle neutron and X-ray diffraction studies clearly show that calcification of collagen fibrils occurs in an extremely intimate and highly organized fashion: initiation of crystal formation within the collagen fibrils in the hole zone region, with the long axes (c-axis) of the crystals aligned roughly parallel to the long axis of the fibril within which they are located. Crystals are initially formed in hole zone regions within individual fibrils separated by unmineralized regions. Calcification is initiated in spatially distinct nucleation sites. This indicates that such regions within a single, undirectional fibril represents independent sites for heterogeneous nucleation. Clearly, sites where mineralization is initiated in adjacent collagen fibrils are even further separated, emphasizing even more clearly that the process of progressive calcification of the collagen fibrils and therefore of the tissue is characterized principally by the presence of increasing numbers of independent nucleation sites within additional hole zone regions of the collagen fibrils. The increase in the mass of Ca-P apatite accrues principally by multiplication of more crystals, mostly by secondary nucleation from the crystals initially deposited in the hole zone region. Very little additional growth of the crystals occurs with time, the additional increase in mineral mass being principally the result of increase in the number of crystals (multiplication), not size of the crystals (crystal growth). The crystals within the collagen fibers grow in number and possibly in size to extend into the overlap zone of the collagen fibrils ("pores") so that all of the available space within the fibrils, which has possibly expanded in volume from its uncalcified level, is eventually occupied by the mineral crystals. It must be recognized that the calcification of separate tissue components and compartments (collagen, mitochondria, matrix vesicles) must be an independent physical chemical event.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2005

Experimental evidence for internal structure in aqueous-organic nanodroplets.

The spatial distribution of species within an aerosol droplet influences how it interacts with its environment. Despite the ubiquity of multicomponent nanodroplets in natural and technological aerosols, there are no published measurements of their internal structure. Here, we report the first experimental results for structure in aqueous organic nanodroplets based on small angle neutron scattering by high number density aerosols. For H(2)O-n-butanol droplets, fitting of the diffraction patterns confirms the picture of an aqueous core containing approximately 3 mol% alcohol covered by a shell of densely packed alcohol molecules.

Aerosols↗
PubMed2005

The algebraic approach to the phase problem.

A rather detailed report is presented on the present status of the algebraic approach to the phase problem in the case of an ideal crystal in order to make clear that some points must still be proven for it to apply to neutron scattering. To make this extension, the most important results that were previously obtained in the case of X-ray scattering are derived again by a different procedure. By so doing, the three-dimensional case is treated explicitly, the polynomial equations in a single variable whose roots determine the positions of the scattering centres are explicitly reported and the procedure is shown to generalize to neutron scattering, overcoming the difficulty related to the non-positivity of the scattering density. In this way, it is fully proven that the atomicity assumption removes the phase ambiguity in the sense that the full diffraction pattern of an ideal crystal can uniquely be reconstructed from a suitable finite portion of it in both X-ray and neutron scattering. The procedures able to isolate these portions that contain the pattern's full information are also given.

Algorithms↗
PubMed2004

Analysis of myoglobin adsorption to Cu(II)-IDA and Ni(II)-IDA functionalized Langmuir monolayers by grazing incidence neutron and X-ray techniques.

The adsorption of myoglobin to Langmuir monolayers of a metal-chelating lipid in crystalline phase was studied using neutron and X-ray reflectivity (NR and XR) and grazing incidence X-ray diffraction (GIXD). In this system, adsorption is due to the interaction between chelated divalent copper or nickel ions and the histidine moieties at the outer surface of the protein. The binding interaction of histidine with the Ni-IDA complex is known to be much weaker than that with Cu-IDA. Adsorption was examined under conditions of constant surface area with an initial pressure of 40 mN/m. After approximately 12 h little further change in reflectivity was detected, although the surface pressure continued to slowly increase. For chelated Cu2+ ions, the adsorbed layer structure in the final state was examined for bulk myoglobin concentrations of 0.10 and 10 microM. For the case of 10 microM, the final layer thickness was approximately 43 A. This corresponds well to the two thicker dimensions of myoglobin in the native state (44 A x 44 A x 25 A) and so is consistent with an end-on orientation for this disk-shaped protein at high packing density. However, the final average volume fraction of amino acid segments in the layer was 0.55, which is substantially greater than the value of 0.44 calculated for a completed monolayer from the crystal structure. This suggests an alternative interpretation based on denaturation. GIXD was used to follow the effect of protein binding on the crystalline packing of the lipids and to check for crystallinity within the layer of adsorbed myoglobin. Despite the strong adsorption of myoglobin, very little change was observed in the structure of the DSIDA film. There was no direct evidence in the XR or GIXD for peptide insertion into the lipid tail region. Also, no evidence for in-plane crystallinity within the adsorbed layer of myoglobin was observed. For 0.1 microM bulk myoglobin concentration, the average segment volume fraction was only 0.13 and the layer thickness was < or = 25 A. Adsorption of myoglobin to DSIDA-loaded with Ni2+ was examined at bulk concentrations of 10 and 50 microM. At 10 microM myoglobin, the adsorbed amount was comparable to that obtained for adsorption to Cu2+-loaded DSIDA monolayers at 0.1 M. But interestingly, the adsorbed layer thickness was 38 A, substantially greater than that obtained at low coverage with Cu-IDA. This indicates that either there are different preferred orientations for isolated myoglobin molecules adsorbed to Cu-IDA and Ni-IDA monolayer films or else myoglobin denatures to a different extent in the two cases. Either interpretation can be explained by the very different binding energies for individual interactions in the two cases. At 50 microM myoglobin, the thickness and segement volume fraction in the adsorbed layer for Ni-IDA were comparable to the values obtained with Cu-IDA at 10 microM myoglobin.

Adsorption↗
PubMed1999

Geometrical effects in diffraction analysis.

The use of X-ray and neutron scattering as a tool to study phase transitions is well established. As techniques improve and experiments are made under successively higher resolution, the need to consider the role of both the distribution of diffracting length scales and the incident-beam coherence volume is emphasized. The interplay of diffracting length scales and the beam coherence volume no longer permits calculation of diffraction profiles in terms of the sample intensity response convolved with an instrumental resolution function. Rather, the probe and sample now enter the calculation on an equal footing at the level of the scattering amplitudes. Under these conditions, it is found that the summation of coherent scattering amplitudes leads to characteristic profiles in wave-vector and, in the case of resonant X-ray scattering, energy space. In this latter case, in the vicinity of strong absorption edges, as used for example in resonant magnetic X-ray diffraction, the energy dependence of diffraction profiles may uniquely allow spatial localization of the scattering volume below the sample surface. This observation may considerably augment the range and power of resonant X-ray scattering.

Journal Article↗
PubMed2005

Neutron and X-ray scattering studies of cholera toxin interactions with lipid monolayers at the air-liquid interface.

Using neutron/X-ray reflectivity and X-ray grazing incidence diffraction (GID), we have characterized the structure of mixed DPPE:GM(1) lipid monolayers before and during the binding of cholera toxin (CTAB(5)) or its B subunit (CTB(5)). Structural parameters such as the density and thickness of the lipid layer, extension of the GM(1) oligosaccharide headgroup, and orientation and position of the protein upon binding are reported. Both CTAB(5) and CTB(5) were measured to have approximately 50% coverage when bound to the lipid monolayer. X-ray GID experiments show that both the lipid monolayer and the cholera toxin layer are crystalline. The effects of X-ray beam damage have been assessed and the monolayer/toxin structure does not change with time after protein binding has saturated.

Cholera Toxin↗
PubMed2000

137Cs distribution and geochemistry of Lena River (Siberia) drainage basin lake sediments.

The Lena River is the second largest river that discharges into the Arctic Ocean. It is therefore important to determine not only the direct impact its discharge has on the 137Cs concentration of the Arctic, but also the potential its drainage basin has as a 137Cs source. 137Cs surface sediment concentrations and inventory values, which range from 4.97 to 338 Bq kg(-1) and 357 to 1732 Bq m(-2), respectively, were determined for the Lena River drainage basin lake samples, via gamma analysis. The average geochemical and mineralogical composition of a subset of samples was also determined using neutron activation analysis, X-ray diffraction and X-ray fluorescence spectrometry techniques. Results of these geochemical analyses allowed for the identification of key geochemical factors that influence the distribution of 137Cs in the Lena River drainage basin. 137Cs profiles indicate that Lena River drainage basin lacustrine sediments serve as a record of 137Cs fallout. Based on the downcore 137Cs, %illite, %smectite, %Al and %Mn distribution patterns, it was concluded that a small fraction of non-selectively bound 137Cs was remobilized at depth in some cores. Inconsistencies between the actual 137Cs fallout record and the 137Cs profiles determined for the lake sediments were attributed to 137Cs remobilization in subsurface sediments. In addition to establishing the agreement between the global atmospheric fallout record and the downcore 137Cs distribution patterns determined for these sediments, results indicate that 137Cs deposited during periods of maximum atmospheric release was buried and is not susceptible to surface erosion processes. However, mean 137Cs concentrations of the lacustrine surface sediments (125 Bq kg(-1)) are still significantly higher than those of the nearby Lena River estuary (11.22 Bq kg(-1)) and Laptev Sea (6.00 Bq kg(-1)). Our study suggests that the Lena River drainage basin has the potential to serve as a source of 137Cs to the adjacent Arctic Ocean.

Cesium Radioisotopes↗