X-ray Diffraction Experiments (x-ray + diffraction_experiment)

Distribution by Scientific Domains
Distribution within Chemistry

Selected Abstracts

New Eremophilane Sesquiterpenes from the Roots of Ligularia fischeri

Meicai Deng
Abstract New eremophilane sesquiterpenes, (3,,6,,8,,10,)-3-acetyl-6,8,10-trihydroxyeremophil-7(11)-eno-12,8-lactone (1), (3,,6,,8,,10,)-3-acetyl-8,10-dihydroxy-6-(2-methyl-1-oxobutoxy) eremophil-7(11)-eno-12,8-lactone (2), (3,,6,,10,)- and (3,,6,,10,)-3-acetyl-6,10-dihydroxyeremophila-7(11),8-dieno-12,8-lactone (3 and 4, resp.), and a dinoreremophilane derivative, (3aR,4R,5S,7aS)-2-acetyl-3a,4,5,6,7,7a-hexahydro-7a-hydroxy-1H -inden-5-yl acetate (5), were isolated from the roots of Ligularia fischeri. Their structures were elucidated by spectroscopic methods including 1D and 2D NMR spectra, and the structure of 1 was further confirmed by a single-crystal X-ray diffraction experiment. Among the isolated compounds, lactone 1 exhibited inhibitory activity towards PTP1B with an IC50 value of 1.34,,Min vivo. The other compounds were inactive. [source]

Waveguide-enhanced scattering from thin biomolecular films

F. Pfeiffer
An X-ray diffraction experiment on multilamellar membranes incorporated into an X-ray waveguide structure is reported. In the device, the lipid bilayers are confined to one side by the silicon substrate and to the other side by an evaporated thin metal cap layer. Shining a highly brilliant X-ray beam onto the system, resonantly enhanced, precisely defined and clearly distinguishable standing-wavefield distributions (modes) are excited. The in-plane structure of the acyl chain ordering is then studied by grazing incidence diffraction under simultaneously excited modes. A significant gain in signal-to-noise ratio as well as enhanced spatial resolution can be obtained with such a setup. [source]

Intensified spin-dependent-transport and localized-spin freezing in magnetite sinter made from low size-dispersion hematite nanoparticles with low temperature calcination

H. Kobori
Abstract The spin-dependent-transport (SDT) has been studied for magnetite (Fe3O4) nano-particle sinter (MNPS) made from low size-dispersion hematite (,-Fe2O3) nanoparticles (LSDHN's) with low temperature calcination. Two kinds of LSDHN's are grown by the hydrothermal synthesis. The average sizes of them are 30 nm and 60 nm. The MNPS is produced by calcining the LSDHN's at 500 C for 5 hours in the atmosphere of Ar(90%)/H2(10%) mixed gases. As compared with a bulk single crystal, the considerable intensification of negative-differential-magnetoresistance (ND-MR) has been observed for the MNPS. We have not observed abrupt change of the electrical resistivity in the vicinity of the temperature of the Verwey transition (which is the metal-insulator transition) appeared for a bulk single crystal. The ND-MR for 30 nm shows larger values than that of 60 nm on the temperature dependence. From the X-ray diffraction experiment, the MNPS is found to include crystalline magnetite regions. We consider that the MNPS is composed of large amorphous-like grain-boundaries and small crystalline grains. The electrical current is inferred to flow in grain-boundary regions. In grain-boundary regions, since the localized spins are relatively random distributed, the spin-polarized conduction electrons show the SDT. Below the Verwey temperature, we have observed the magnetization difference between zero-field cooling (ZFC) and field-cooling (FC). This phenomenon indicates that the localized spins in the amorphous-like grain-boundaries are frozen in some degree. Above the Verwey temperature, the magnetoresistance is well fitted by the square of the Langevin function. We consider that the localized spins in the amorphous-like grain-boundaries do not form perfectly random configuration and are somewhat ordered in a short range region. ( 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Reversal magnetoresistance and unusual localized-spin freezing in magnetite sinter made from low size-dispersion hematite nano-particles with high temperature calcination

H. Kobori
Abstract The magneto-resistance and magnetization have been studied for magnetite (Fe3O4) sinter made from low size-dispersion hematite (,-Fe2O3) nanoparticles (LSDHN's) with high temperature calcination. Two kinds of LSDHN's were grown by the hydrothermal synthesis. The average particle sizes of them are 30 nm and 60 nm. The magnetite sinter was produced by calcining the LSDHN's at 800 C for 5 hours in the atmosphere of Ar(90%)/H2(10%) mixed gases. We have observed an abrupt change of the electrical resistivity by one order of magnitude in the vicinity of the Verwey temperature (123 K) of a bulk single crystal. From the X-ray diffraction experiment, we have found that the magnetite sinter includes crystalline region. The magnetite sinter is considered to be composed of relatively narrow grain-boundary regions of amorphous-like magnetite and large grain regions of crystalline magnetite. It is regarded that the grain-boundary-conduction is dominant below the Verwey temperature and the inter-grain-conduction is dominant above the Verwey temperature. We have observed the positive differential magnetoresistance (PD-MR) in low temperature regions and the negative differential magnetoresistance (ND-MR) in high temperature regions. The ND-MR is an ordinary phenomenon for magnetite, but the PD-MR is a peculiar one. In addition, an unusual localized-spin-freezing phenomenon has been also observed. Below the Verwey temperature, the magnetization difference between zero-field-cooling and field-cooling has been observed. The magnetization difference shows a sudden change in the vicinity of the Verwey temperature. ( 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

GABAergic phthalide dimers from Angelica sinensis (Oliv.) Diels

Shixin Deng
Abstract The methanol extract of Angelica sinensis (Oliv.) Diels roots (Dang Gui) has been shown to exhibit competitive binding to the GABAa receptor, suggesting the presence of GABAergic ligands. Chromatographic fractionation of the methanol extract led to the isolation of two GABAergic dimeric phthalides 1 and 2. Gelispirolide (1) was elucidated as a new phthalide dimer composed of a Z -ligustilide and a Z -butylidenephthalide unit on the basis of spectroscopic approaches including one- and two-dimensional NMR, HRESIMS and HRESIMS-MS. Compound 2 was identified as the known dimeric phthalide, riligustilide, by comparison of its spectroscopic data with literature values. Its dimeric linkage and stereochemistry were ascertained by a single crystal X-ray diffraction experiment. Both dimers 1 and 2 were found to be active in an in vitro GABAa receptor-binding assay with IC50 values of 29 and 24 m, respectively. Copyright 2006 John Wiley & Sons, Ltd. [source]

X-ray diffraction by a crystal in a permanent external electric field: general considerations

Semen V. Gorfman
The variations of X-ray diffraction intensities from a crystal in the presence of a permanent external electric field is modeled analytically using a first-order stationary perturbation theory. The change in a crystal, induced by an external electric field, is separated into two contributions. The first one is related to a pure polarization of an electron subsystem, while the second contribution can be reduced to the displacements of the rigid pseudoatoms from their equilibrium positions. It is shown that a change of the X-ray diffraction intensities mainly originates from the second contribution, while the influence of the pure polarization of a crystal electron subsystem is negligibly small. The quantities restored from an X-ray diffraction experiment in the presence of an external electric field were analyzed in detail in terms of a rigid pseudoatomic model of electron density and harmonic approximation for the atomic thermal motion. Explicit relationships are derived that link the properties of phonon spectra with E -field-induced variations of a structure factor, pseudoatomic displacements and piezoelectric strains. The displacements can be numerically estimated using a model of independent atomic motion if the Debye,Waller factors and pseudoatomic charges are known either from a previous single-crystal X-ray diffraction study or from density functional theory calculations. The above estimations can be used to develop an optimum strategy for a data collection that avoids the measurements of reflections insensitive to the electric-field-induced variations. [source]

How to easily replace the independent atom model , the example of bergenin, a potential anti-HIV agent of traditional Asian medicine

Birger Dittrich
Bergenin, which has been isolated from a variety of tropical plants, has several pharmacological applications in traditional Asian medicine. Its electron-density distribution was obtained from a room-temperature low-resolution X-ray data set measured with point detection making use of multipole populations from the invariom library. Two refinement models were considered. In a first step, positional parameters and ADPs were refined with fixed library multipoles (model E1). This model was suitable to be input into a second refinement of multipoles (model E2), which converged smoothly although based on Cu,K, room-temperature data. Quantitative results of a topological analysis of the electron density from both models were compared with Hartree,Fock and density-functional calculations. With respect to the independent atom model (IAM) more information can be extracted from invariom modelling, including the electrostatic potential and hydrogen-bond energies, which are highly useful, especially for biologically active compounds. The reliability of the applied invariom formalism was assessed by a comparison of bond-topological properties of sucrose, for which high-resolution multipole and invariom densities were available. Since a conventional X-ray diffraction experiment using basic equipment was combined with the easy-to-use invariom formalism, the procedure described here for bergenin illustrates how it can be routinely applied in pharmacological research. [source]

Know your dose: RADDOSE

Karthik S. Paithankar
The program RADDOSE is widely used to compute the dose absorbed by a macromolecular crystal during an X-ray diffraction experiment. A number of factors affect the absorbed dose, including the incident X-ray flux density, the photon energy and the composition of the macromolecule and of the buffer in the crystal. An experimental dose limit for macromolecular crystallography (MX) of 30,MGy at 100,K has been reported, beyond which the biological information obtained may be compromised. Thus, for the planning of an optimized diffraction experiment the estimation of dose has become an additional tool. A number of approximations were made in the original version of RADDOSE. Recently, the code has been modified in order to take into account fluorescent X-ray escape from the crystal (version 2) and the inclusion of incoherent (Compton) scattering into the dose calculation is now reported (version 3). The Compton cross-section, although negligible at the energies currently commonly used in MX, should be considered in dose calculations for incident energies above 20,keV. Calculations using version 3 of RADDOSE reinforce previous studies that predict a reduction in the absorbed dose when data are collected at higher energies compared with data collected at 12.4,keV. Hence, a longer irradiation lifetime for the sample can be achieved at these higher energies but this is at the cost of lower diffraction intensities. The parameter `diffraction-dose efficiency', which is the diffracted intensity per absorbed dose, is revisited in an attempt to investigate the benefits and pitfalls of data collection using higher and lower energy radiation, particularly for thin crystals. [source]

Electronic Properties of 3,3,-Dimethyl-5,5,-bis(1,2,4-triazine): Towards Design of Supramolecular Arrangements of N-Heterocyclic CuI Complexes

Blandine Courcot Dr.
Abstract A new efficient and safe synthesis of 3,3,-dimethyl-5,5,-bis-(1,2,4-triazine) is presented. The electron-density distribution and electrostatic properties (charge, electrostatic potential) of this molecule were analyzed. These properties were derived from a high-resolution single-crystal X-ray diffraction experiment at 100,K and compared to the results obtained from ab initio DFT quantum-mechanical calculations. Comparisons of its electrostatic potential features and integrated atomic charges (quantum theory of atoms in molecules, QTAIM) have been made with those of related molecules such as bipyrimidine ligands. Two methods were used to derive integrated charges: one is based on the conventional analytical procedure and the second uses a steepest-ascent numerical algorithm. Excellent agreement was obtained between these two methods. Charges and electrostatic potential were used as predictive indices of metal chelation and discussed in the light of complexation abilities of the title compound and related molecules. The crystal structure of a CuI complex of 3,3,-dimethyl-5,5,-bis(1,2,4-triazine) is reported here. In the solid state, this complex forms a three-dimensional multibranch network with open channels in which counterions and solvent molecules are located. This architecture involves both cis and trans isomers of the title compound. [source]

A Novel Copper(I) Halide Framework Templated by Organic,Inorganic Hybrid Polyoxometalate Chains Formed In Situ: A New Route for the Design and Synthesis of Porous Frameworks

Hua Jin
Abstract A 1D organic,inorganic hybrid polyoxometalate chain has been used as a non-coordinating anionic template for the construction of a novel 3D copper halide 4,4,-bipy framework, namely [Cu3ICl(4,4,-bipy)4][CuII(1,10-phen)2Mo8O26]. X-ray diffraction experiments revealed that the title compound consists of chloride-bridged trinuclear CuI units linked by neutral organic 4,4,-bipy groups into a 3D framework with hexagon-like channels in which 1D organic,inorganic hybrid polyoxometalate chains reside. This is the first example of a 1D organic,inorganic hybrid polyoxometalate chain functioning as a novel anionic template for the construction of a 3D framework. ( Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

Consecutive Nucleation Events During Divetrification of Zr52.5Cu17.9Ni14.6Al10Ti5 Bulk Metallic Glass,

L. Yang
Differential scanning calorimetry revealed two exothermal peaks in Zr52.5Cu17.9Ni14.6 -Al10Ti5 bulk metallic glass during divetrification. Analysis of the calorimetry data as well as in-situ X-ray diffraction experiments show that the exothermal peaks correspond to two nucleation events, controlled by interface and long-range diffusion, respectively. [source]

Synthesis and structural studies of N -(p -toluenesulfonyl)-amino acid 3,5-di- tert -butyl-2-phenolamides

Margarita Tlahuextl
This paper describes the synthesis and structural studies of N -(p -toluenesulfonyl)-amino acid 3,5-di- tert -butyl-2-phenolamides by 1H, 13C, and 15N. The presence of intra - and intermolecular hydrogen bonds were studied by variable temperature NMR spectroscopy. The molecular structure of two amides in the solid state was determined by X-ray diffraction experiments. The results show that tert -butyl substituents in the phenolic ring have important effects in the nature of hydrogen bonds and conformation of these amides. 2004 Wiley Periodicals, Inc. Heteroatom Chem 15:114,120, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.10223 [source]

Local atomic structure in tetragonal pure ZrO2 nanopowders

Leandro M. Acua
The local atomic structures around the Zr atom of pure (undoped) ZrO2 nanopowders with different average crystallite sizes, ranging from 7 to 40,nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO2 nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr,O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye,Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to the z direction; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments. [source]

A heating stage up to 1173,K for X-ray diffraction studies in the whole orientation space

R. Resel
A multi-purpose heating attachment designed primarily for X-ray four-circle diffractometers but applicable also for classical powder diffraction is presented. When working in reflection geometry, the air-cooled heating stage allows diffraction studies to be performed on plate-like samples up to 1173,K in the whole orientation space. This paper gives a detailed description of the assembly and important technical specifications for the performance of experiments. The heating characteristics of the heating stage, the displacement of the sample from the goniometer centre as a result of thermal expansion and the influence of the protecting dome on the diffraction experiment are presented. The simple technical construction, the low weight, the small size and good heating performance make this equipment a general purpose heating attachment for X-ray diffraction experiments in reflection geometry. [source]

Synthesis, pharmacology, crystal properties, and quantitative solvation studies from a drug transport perspective for three new 1,2,4-thiadiazoles

German L. Perlovich
Abstract A novel 1,2,4-thiadiazoles were synthesized. Crystal structures of these compounds were solved by X-ray diffraction experiments and comparative analysis of molecular conformational states, packing architecture, and hydrogen bonds networks were carried out. Thermodynamic aspects of sublimation processes of studied compounds were determined using temperature dependencies of vapor pressure. Thermophysical characteristics of the molecular crystals were obtained and compared with the sublimation and structural parameters. Solubility and solvation processes of 1,2,4-thiadiazoles in buffer, n -hexane and n -octanol were studied within the wide range of temperature intervals and thermodynamic functions were calculated. Specific and nonspecific interactions of molecules resolved in crystals and solvents were estimated and compared. Distribution processes of compounds in buffer/n -octanol and buffer/n -hexane systems (describing different types of membranes) were investigated. Analysis of transfer processes of studied molecules from the buffer to n -octanol/n -hexane phases was carried out by the diagram method with evaluation of the enthalpic and entropic terms. This approach allows us to design drug molecules with optimal passive transport properties. Calcium-blocking properties of the substances were evaluated. 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:3754,3768, 2010 [source]

Energetic aspects of diclofenac acid in crystal modifications and in solutions,mechanism of solvation, partitioning and distribution

German L. Perlovich
Abstract Temperature dependency of saturated vapor pressure and heat capacity for the diclofenac acid (Form II) were measured and thermodynamic functions of sublimation calculated (,,=,49.3 kJ,,mol,1; ,,=,115.6,,1.3 kJ,,mol,1; ,,=,222,,4 J,,mol,1,,K,1). Crystal polymorphic Forms I (P21/c) and II (C2/c) of diclofenac acid have been prepared and characterized by X-ray diffraction experiments. The difference between crystal lattice energies of the two forms were obtained by solution calorimetry: ,,Hsol(I,,,II),=,1.6,,0.4 kJ,,mol,1. Temperature dependencies of the solubility in buffers with pH 2.0 and 7.4, n-octanol and n-hexane were measured. The thermodynamic functions of solubility, solvation, and transfer processes were deduced. Specific and non-specific solvation terms were distinguished using the transfer from the "inert" n-hexane to the other solvents. The transfer of diclofenac acid molecules from the buffers to n-octanol (partitioning and distribution) is an entropy driven process. 2007 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 96: 1031,1042, 2007 [source]

Linear polarization scans for resonant X-ray diffraction with a double-phase-plate configuration

Valerio Scagnoli
An in-vacuum double-phase-plate diffractometer for performing polarization scans combined with resonant X-ray diffraction experiments is presented. The use of two phase plates enables the correction of some of the aberration effects owing to the divergence of the beam and its energy spread. A higher rate of rotated polarization is thus obtained in comparison with a system with only a single retarder. Consequently, thinner phase plates can be used to obtain the required rotated polarization rate. These results are particularly interesting for applications at low energy (e.g. 4,keV) where the absorption owing to the phase plate(s) plays a key role in the feasibility of these experiments. Measurements by means of polarization scans at the uranium M4 edge on UO2 enable the contributions of the magnetic and quadrupole ordering in the material to be disentangled. [source]

Facilities for high-pressure research with the diamond anvil cell at GSECARS

Guoyin Shen
An overview of facilities for high-pressure research with the diamond anvil cell (DAC) at the GeoSoilEnviroCARS (GSECARS) sector at the Advanced Photon Source (Argonne, Illinois) is presented. There are three operational experimental stations (13-ID-C, 13-ID-D and 13-BM-D) where DAC instrumentation is installed for various types of experiments at high pressure and extreme temperature conditions. A fourth station (13-BM-C) is under construction and will be operational in 2006. While most X-ray diffraction experiments have been undertaken with powder samples so far, there is a growing demand for single-crystal diffraction (SCD) at high pressure. As one of the principal components at GSECARS, SCD is currently under rapid development. Other relevant techniques have also been developed for obtaining complementary information from powder or single-crystal samples at high pressure. For example, an on-line Brillouin system is installed and operational at 13-BM-D for acoustic velocity and single-crystal elasticity determinations. In addition, various X-ray spectroscopy techniques (e.g. X-ray emission and X-ray Raman) are employed for measuring electronic and magnetic properties. Future developments are discussed with the DAC program at GSECARS. [source]

Helium implantation into 4H-SiC

Jean Franois Barbot
Abstract The paper provides the properties of single crystalline 4H-SiC under helium implantation at temperatures of implantation up to 750,C and fluences in the range 5,,1015,1,,1017,cm,2. The microstructure evolution was studied by transmission electron microscopy cross-section and X-ray diffraction experiments. The mechanical property changes were investigated by using nanoindentation tests followed by atomic force microscopy observations and by using tribological tests. At elevated temperature of implantation and/or in the low fluence regime at room temperature where only the strained state of SiC is obtained, SiC becomes more resistant to crack formation but no significant change in mechanical properties is seen. At room temperature with increasing fluence the damage accumulation leads to the amorphous state for which a strong degradation of the mechanical properties is observed. At elevated temperature of implantation, amorphization is avoided and a thermally activated saturation of the strain is observed in the near surface region whereas defect accumulation occurs near the maximum of damage. Upon annealing subsequent to room temperature implantation, the near surface strain progressively relaxes while the helium ions agglomerate into platelets around the maximum of strain. These platelets evolve into bubble clusters at temperatures where the vacancies become mobile. Under particular conditions of implantation (high fluence and elevated temperature) the swelling of the surface increases during annealing due to the growth of bubbles and the formation of stacking faults resulting from the migration of interstitials towards the maximum of damage. [source]

Internal friction investigation of reverse martensitic transformation in oil-quenched Ni64Al36 alloy

Z. C. Zhou
Abstract Low-frequency internal friction investigation of reverse martensitic transformation in oil-quenched Ni64Al36 alloy has been carried out using a multifunctional internal friction apparatus from room temperature to 400 C and additionally differential scanning calorimetry and X-ray diffraction experiments were also completed. It has been shown that an internal friction peak presents at about 220 C in the internal friction,temperature curve during heating for the oil-quenched Ni64Al36 alloy but not for the furnace-cooled Ni64Al36 alloy. The peak still appears during cooling and the peak temperature shifts to lower temperature. The changes of the peak temperature positions cannot be visibly observed when the vibration frequency is changed. The peak heights increase with decreasing vibration frequency and increasing heating rate, being linearly directly proportional to It has been suggested that the internal friction peak results from reverse martensitic transformation of L10 , , during heating and originates from martensitic transformation of , , L10 during the subsequent cooling process. The influence of the thermal cycles on the transformation is not observed for the limited thermal cycles. ( 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Photoluminescence properties of erbium-doped amorphous gallium-germanium-selenium films fabricated by RF sputtering

Takahiko Imai
Abstract Chalcogenide glasses have various useful features for optical devices such as a high refractive index, low-loss transmission in the mid-IR, and low phonon energies. The fabrication of thin films is important for use in waveguide applications and integrated photonics. In this work, we report the properties of vacuum deposited films of gallium-germanium-selenium glasses onto fused silica substrates by an RF magnetron sputtering technique (RF electric power of 40-250 W and growth rate of 0.01-2.1 ,m/min). The concentration of Er3+ ions is controlled by the number of sintered Er2S3 small plates on a target. Samples are shown to be in an amorphous-like state as measured by X-ray diffraction experiments. Film thicknesses are proportional to the RF sputtering power and sputtering time. The compositions of films obtained from energy dispersive X-ray (EDX) analysis. There are much dependent on the condition of the sputtering target, for example whether the target is in the bulk or powder-state. Photoluminescence (PL) spectrum, intensity, and lifetime at 1550 nm band are measured by excitation from a 973 nm laser. The PL band of the films has a similar shape to those of bulk glasses. The PL intensity increased with the RF electric power. The PL lifetime at the 1550 nm band of the film is about 1.8-2.6 ms; the latter values are similar to those of bulk samples. The results show that the RF sputtering is a potential method of fabrication for Er-doped GeGaSe thin films. ( 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects

Jeongho Kim
In recent years, the time-resolved X-ray diffraction technique has been established as an excellent tool for studying reaction dynamics and protein structural transitions with the aid of 100,ps X-ray pulses generated from third-generation synchrotrons. The forthcoming advent of the X-ray free-electron laser (XFEL) will bring a substantial improvement in pulse duration, photon flux and coherence of X-ray pulses, making time-resolved X-ray diffraction even more powerful. This technical breakthrough is envisioned to revolutionize the field of reaction dynamics associated with time-resolved diffraction methods. Examples of candidates for the first femtosecond X-ray diffraction experiments using highly coherent sub-100,fs pulses generated from XFELs are presented in this paper. They include the chemical reactions of small molecules in the gas and solution phases, solvation dynamics and protein structural transitions. In these potential experiments, ultrafast reaction dynamics and motions of coherent rovibrational wave packets will be monitored in real time. In addition, high photon flux and coherence of XFEL-generated X-ray pulses give the prospect of single-molecule diffraction experiments. [source]

Structural changes of hexamethylenetetramine and undecanedioic acid co-crystal (HMT-C11) as a function of the temperature

Carlos Baslio Pinheiro
HMT-C11 belongs to the family of adducts formed by the co-crystallization of N4(CH2)6 molecules (hexamethylenetetramine or HMT) and aliphatic dicarboxylic acids HOOC(CH2)n, 2COOH with 5 ,n, 13 (Cn). The adducts exhibit a layered structure in which the packing between HMT and Cn is determined by strong hydrogen bonds. The compounds in this family studied so far present thermotropic structural phase transitions and, depending on the chain length, disordered, twinned and modulated phases. The structure refinement of HMT-C11 based on X-ray diffraction experiments indicates three distinct phases from the melting point down to liquid nitrogen temperature: phase I is not crystalline; phase II is disordered (stacking fault) and its average structure is described in space group Bmmb; phase III is partially disordered and its symmetry is P21/c. The systematic study of the structure evolution of phase III upon cooling revealed that the disorder has a dynamic character (anharmonicity). The main structural change observed from 293,K down to 93,K is the increase of the tilting angle of the C11 chains relative to the layer plane and the rotation of the HMT molecules. Both HMT and C11 behave like rigid bodies in the temperature range investigated. The quality of the refinements leads to a conclusive model for the O,H,N hydrogen bonds linking HMT and C11. [source]

X-ray diffraction study of the phase transition of K2Mn2(BeF4)3: a new type of low-temperature structure for langbeinites

A. Guelylah
The potassium manganese tetrafluoroberyllate langbeinite compound has been studied in the temperature range 100,300,K. Using DSC measurements, a phase transition has been detected at 213,K. The space group of the low-temperature phase was determined to be P1121 using X-ray diffraction experiments and optical observations of the domain structure. The b axis is doubled with respect to the prototypic P213 cubic phase. Lattice parameters were determined by powder diffraction data [a = 10.0690,(8), b = 20.136,(2), c = 10.0329,(4),, , = 90.01,(1)]. A precise analysis of the BeF4 tetrahedra in the low-temperature phase shows that two independent tetrahedra rotate in opposite directions along the doubled crystallographic axis. A symmetry mode analysis of the monoclinic distortion is also reported. This is the first report of the existence of such a phase transition in K2Mn2(BeF4)3 and also of a new type of low-temperature structure for langbeinite compounds. [source]

Influence of organotin compounds on phosphatidylserine membranes

Jos A. Teruel
Abstract Organotin compounds are widely distributed toxicants. They are membrane-active molecules with broad biological toxicity. We have studied the interaction of tributyltin and triphenyltin with phosphatidylserine model membranes using differential scanning calorimetry, infrared spectroscopy and X-ray diffraction techniques. Organotin compounds produced a broadening of the gel to the liquid-crystalline phase transition of the phospholipid and a shifting of the phase transition temperature to lower values. Infrared spectroscopy experiments showed that tributyltin exerted a fluidizing effect on the apolar part of the bilayer, and that both tributyl- and triphenyltin interact with the interfacial region of the bilayer, making the carbonyl groups less accessible to water. As seen by X-ray diffraction experiments, organotin compounds were unable to change the bilayer macroscopic organization of the phospholipid, but they were able to reduce the long-range order of the multibilayer system and to disorder the packing of the phospholipid molecules. The observed interaction between organotin compounds and phosphatidylserine membranes promotes physical perturbations that could affect membrane function and may mediate some of their toxic effects. Copyright 2004 John Wiley & Sons, Ltd. [source]

Expression, purification, crystallization and preliminary X-ray diffraction data of methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis

Hlne Dubourg
Methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis was cloned and overexpressed in Escherichia coli. Suitable crystals for X-ray diffraction experiments were obtained by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. The crystals belong to space group P212121, with unit-cell parameters a = 195.2, b = 192.5, c = 83.5,, and contain one tetramer per asymmetric unit. X-ray diffraction data were collected to 2.5, resolution using a synchrotron-radiation source. The crystal structure was solved by the molecular-replacement method. [source]

The role of solvent transport in cryo-annealing of macromolecular crystals

Douglas H. Juers
Macromolecular crystals are usually cooled to ,100,K for X-ray diffraction experiments in order to diminish lattice damage arising from the ionizing radiation. Such cooling often produces lattice disorder, but this disorder can sometimes be substantially reduced by cycling the crystal between low and higher temperatures (called annealing). Here, two related aspects of cryocooling and annealing are investigated using crystals of ,-galactosidase and thermolysin. Firstly, as has been reported with other systems, there is an optimal cryoprotectant concentration above and below which diffraction is poor, with high mosaicity, diffuse scatter and low signal to noise. Measurements of the bulk density of the respective cryosolvents are consistent with the idea that at the optimal cryoprotectant concentration the contraction of the bulk solvent on cooling largely compensates for the contraction of the macromolecular lattice. Secondly, by controlling the relative humidity of the gas that contacts the crystal during the high (room) temperature phase, it is found that water is either imported into or exported out of the crystals during the melting phase of annealing. This water transport appears to change the concentration of the cryoprotectant solution and in so doing alters its thermal contraction. Thus, annealing appears to be involved, at least in part, in the tuning of the thermal contraction of the bulk solvent to best compensate for lattice contraction. Furthermore, it is found that if the cryoprotectant concentration is initially too high then annealing is more successful than if the concentration is initially too low. This result suggests that the search for optimal cryoprotectant conditions may be facilitated by equilibration of the crystal to relatively high cryoprotectant concentration followed by annealing. [source]

A distinct binding mode of a hydroxyethylamine isostere inhibitor of HIV-1 protease

Jan Dohnlek
Crystallization conditions for an HIV-1 protease,inhibitor complex were optimized to produce crystals suitable for X-ray diffraction experiments. The X-ray structure of the HIV-1 protease complex was solved and refined at 3.1, resolution. In contrast to Saquinavir, the mimetic hydroxy group of the inhibitor Boc-Phe-,[(S)-CH(OH)CH2NH]-Phe-Glu-Phe-NH2 is placed asymmetrically with respect to the non-crystallographic twofold axis of the protease dimer so that hydrogen bonds between the amino group of the inhibitor and the catalytic aspartates can be formed. The inhibitor binds in the centre of the active site by a compact network of hydrogen bonds to Gly27, Gly127, Asp25, Asp125 and via the buried water molecule W301 to Ile50 and Ile150. [source]

Crystallization and preliminary crystallographic analysis of N -acetylglucosamine 6-phosphate deacetylase from Escherichia coli

F. M. Ferreira
N -Acetylglucosamine 6-phosphate deacetylase (E.C., an enzyme from Escherichia coli involved in aminosugar catabolism, has been crystallized by the vapour-diffusion technique using phosphate as precipitant. X-ray diffraction experiments show the crystals to belong to the orthorhombic crystal system, with space group P21212. The unit-cell parameters are a = 82.09,(2), b = 114.50,(1), c = 80.17,(1),. The crystals diffract to a maximum resolution of 1.8, and an initial data set was collected to 2.0,. [source]

Purification, crystallization and preliminary X-ray diffraction experiments on the breakage-reunion domain of the DNA gyrase from Mycobacterium tuberculosis

Jrmie Piton
Mycobacterium tuberculosis DNA gyrase, a nanomachine that is involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and hence is the sole target for fluoroquinolone action. The breakage-reunion domain of the A subunit plays an essential role in DNA binding during the catalytic cycle. Two constructs of 53 and 57,kDa (termed GA53BK and GA57BK) corresponding to this domain have been overproduced, purified and crystallized. Diffraction data were collected from four crystal forms. The resolution limits ranged from 4.6 to 2.7, depending on the crystal form. The best diffracting crystals belonged to space group C2, with a biological dimer in the asymmetric unit. This is the first report of the crystallization and preliminary X-ray diffraction analysis of the breakage-reunion domain of DNA gyrase from a species containing one unique type II topoisomerase. [source]