Synthesis, crystal structure and herbicidal activity of mimics of intermediates of the KARI reaction

Two mimics of the intermediate in the reaction catalyzed by ketol-acid reductoisomerase (KARI) were synthesized. Their structures were established on the basis of elemental analyses, IR, H-1 NMR and GC/mass detector. The crystal structure of compound 2 was found to be a substituted dioxane, formed by the condensation of two molecules. The two compounds showed some herbicidal activity on the basis of tests using rape root and barnyard grass growth inhibition. However, the herbicidal effect was weaker in greenhouse tests. (c) 2004 Society of Chemical Industry.

Temperature dependence of the crystal structure and g-values of [(HC(Ph2PO)(3))(2)Cu] (ClO4)(2)center dot 2H(2)O: Influence of dynamic Jahn-Teller coupling and lattice strain interactions

The temperature dependence of the X-ray crystal structure and powder EPR spectrum of [(HC(Ph2PO)(3))(2)CU]-(ClO4)(2)center dot 2H(2)O is reported, and the structure at room temperature confirms that reported previously. Below similar to 100 K, the data imply a geometry with near elongated tetragonal symmetry for the [(HC(Ph2PO)(3))(2)Cu](2+) complex, but on warming the two higher Cu-O bond lengths and g-values progressively converge, and by 340 K the bond lengths correspond to a compressed tetragonal geometry. The data may be interpreted satisfactorily assuming an equilibrium among the energy levels of a Cu-O-6 polyhedron subjected to Jahn-Teller vibronic coupling and a lattice strain. However, agreement with the experiment is obtained only if the orthorhombic component of the lattice strain decreases to a negligible value as the temperature approaches 340 K.

Influence of lattice interactions on the jahn-teller distortion of the [Cu(H2O)(6)](2+) ion: Dependence of the crystal structure of K-2[Cu(H2O)(6)](SO4)(2x)(SeO4)(2-2x) upon the sulfate/selenate ratio

The temperature dependence of the structure of the mixed-anion Tutton salt K-2[Cu(H2O)(6)](SO4)(2x)(SeO4)(2-2x) has been determined for crystals with 0, 17, 25, 68, 78, and 100% sulfate over the temperature range of 85-320 K. In every case, the [Cu(H2O)(6)](2+) ion adopts a tetragonally elongated coordination geometry with an orthorhombic distortion. However, for the compounds with 0, 17, and 25% sulfate, the long and intermediate bonds occur on a different pair of water molecules from those with 68, 78, and 100% sulfate. A thermal equilibrium between the two forms is observed for each crystal, with this developing more readily as the proportions of the two counterions become more similar. Attempts to prepare a crystal with approximately equal amounts of sulfate and selenate were unsuccessful. The temperature dependence of the bond lengths has been analyzed using a model in which the Jahn-Teller potential surface of the [Cu(H2O)(6)](2+) ion is perturbed by a lattice-strain interaction. The magnitude and sign of the orthorhombic component of this strain interaction depends on the proportion of sulfate to selenate. Significant deviations from Boltzmann statistics are observed for those crystals exhibiting a large temperature dependence of the average bond lengths, and this may be explained by cooperative interactions between neighboring complexes.

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results Sur port the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

Synthesis and characterization of Pd(II) and Pt(II) complexes with triazolopyrimidine derivatives: The crystal structure of [Pd2L2Cl4] where L=5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine

The Pd(II) and Pt(II) complexes with triazolopyrimidine C-nucleosides L-1 (5,7-dimethyl-3-(2',3',5'-tri-O-benzoyl-beta-D-ribofuranosyl-s-triazolo)[4,3-a]pyrimidine), L-2 (5,7-dimethyl-3-beta-D-ribofuranosyl-s-triazolo [4,3-a]pyrimidine) and L-3 (5,7-dimethyl[1,5-a]-s-triazolopyrimidine), [Pd(en)(L-1)](NO3)(2), (Pd(bpy)(L-1)](NO3)(2), cis-Pd(L-3)(2)Cl-2, [Pd-2(L-3)(2)Cl-4]center dot H2O, cis-Pd(L-2)(2)Cl-2 and [Pt-3(L-1)(2)Cl-6] were synthesized and characterized by elemental analysis and NMR spectroscopy. The structure of the [Pd-2(L-3)(2)Cl-4]center dot H2O complex was established by Xray crystallography. The two L-3 ligands are found in a head to tail orientation, with a (PdPd)-Pd-... distance of 3.1254(17) angstrom.L-1 coordinates to Pd(II) through N8 and N1 forming polymeric structures. L-2 coordinates to Pd(II) through N8 in acidic solutions (0.1 M HCl) forming complexes of cis-geometry. The Pd(II) coordination to L-2 does not affect the sugar conformation probably due to the high stability of the C-C glycoside bond. (c) 2006 Elsevier B.V. All rights reserved.

Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation:are A′-RNA and A-RNA distinct conformational structures?

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA namely major groove width, inclination and the number of base pairs in a helical twist over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors). © CSIRO 2009.

Sensing properties of femtosecond laser-inscribed long period gratings in photonic crystal fiber

The use of near infrared, high intensity femtosecond laser pulses for the inscription of long period fiber gratings in photonic crystal fiber is reported. The formation of grating structures in photonic crystal fiber is complicated by the fiber structure that allows wave-guidance but that impairs and scatters the femtosecond inscription beam. The effects of symmetric and asymmetric femtosecond laser inscriptions are compared and the polarization characteristics of long period gratings and their responses to external perturbations are reported.

Characterisation of femtosecond laser inscribed long period gratings in photonic crystal fibre

The use of high intensity femtosecond laser sources for inscribing fibre gratings has attained significant interest. The principal advantage of high-energy pulses is their ability for grating inscription in any material type without preprocessing or special core doping - the inscription process is controlled multi-photon absorption, void generation and subsequent local refractive index changes. The formation of grating structures in photonics crystal fibre has proven difficult, as the presence of holes within the fibre that allow wave-guidance impair and scatter the femtosecond inscription beam. Here we report on the consistent manufacture of long period gratings in endlessly single mode microstructure fibre and on their characterisation to external perturbations. Long period gratings are currently the subject of considerable research interest due to their potential applications as filters and as sensing devices, responsive to strain, temperature, bending and refractive index. Compared to the more mature fibre Bragg grating sensors, LPGs have more complex spectra, usually with broader spectral features. On the other hand they are intrinsically sensitive to bending and refractive index. Perhaps more importantly, the fibre design and choice of grating period can have a considerable influence over the sensitivity to the various parameters, for example allowing the creation of a bend sensor with minimal temperature cross-sensitivity. This control is not possible with FBG sensors. Here we compare the effects of symmetric and asymmetric femtosecond laser inscription.

Sensing properties of femtosecond laser-inscribed long period gratings in photonic crystal fiber

The use of near infrared, high intensity femtosecond laser pulses for the inscription of long period fiber gratings in photonic crystal fiber is reported. The formation of grating structures in photonic crystal fiber is complicated by the fiber structure that allows wave-guidance but that impairs and scatters the femtosecond inscription beam. The effects of symmetric and asymmetric femtosecond laser inscriptions are compared and the polarization characteristics of long period gratings and their responses to external perturbations are reported.

Impedance analysis of Al2O3/H-terminated diamond metal-oxide-semiconductor structures

Impedance spectroscopy (IS) analysis is carried out to investigate the electrical properties of the metal-oxide-semiconductor (MOS) structure fabricated on hydrogen-terminated single crystal diamond. The low-temperature atomic layer deposition Al2O3 is employed as the insulator in the MOS structure. By numerically analysing the impedance of the MOS structure at various biases, the equivalent circuit of the diamond MOS structure is derived, which is composed of two parallel capacitive and resistance pairs, in series connection with both resistance and inductance. The two capacitive components are resulted from the insulator, the hydrogenated-diamond surface, and their interface. The physical parameters such as the insulator capacitance are obtained, circumventing the series resistance and inductance effect. By comparing the IS and capacitance-voltage measurements, the frequency dispersion of the capacitance-voltage characteristic is discussed.

Femtosecond and UV inscribed grating characterization in photonic crystal fibres:optimization for sensing applications

Photonic crystal fibres (PCF) and more commonly microstructure fibres, remain interesting and novel fibre types and when suitably designed can prove to be "ideal" for sensing applications, as the different geometrical arrangement of the air holes alters their optical wave-guiding properties, whilst also providing tailored dispersion characteristics. This impacts the performance of grating structures, which offer wavelength encoded sensing information. We undertake a study on different air hole geometries and proceed with characterization of fibre Bragg and long period gratings, FBG and LPG, respectively that have been inscribed (using either a femtosecond or ultraviolet laser system) within different designs of microstructured fibre that are of interest for sensing applications. © 2012 SPIE.

Periodic polymer photonic bandgap structures for on-chip optical cavities

Integrated on-chip optical platforms enable high performance in applications of high-speed all-optical or electro-optical switching, wide-range multi-wavelength on-chip lasing for communication, and lab-on-chip optical sensing. Integrated optical resonators with high quality factor are a fundamental component in these applications. Periodic photonic structures (photonic crystals) exhibit a photonic band gap, which can be used to manipulate photons in a way similar to the control of electrons in semiconductor circuits. This makes it possible to create structures with radically improved optical properties. Compared to silicon, polymers offer a potentially inexpensive material platform with ease of fabrication at low temperatures and a wide range of material properties when doped with nanocrystals and other molecules. In this research work, several polymer periodic photonic structures are proposed and investigated to improve optical confinement and optical sensing. We developed a fast numerical method for calculating the quality factor of a photonic crystal slab (PhCS) cavity. The calculation is implemented via a 2D-FDTD method followed by a post-process for cavity surface energy radiation loss. Computational time is saved and good accuracy is demonstrated compared to other published methods. Also, we proposed a novel concept of slot-PhCS which enhanced the energy density 20 times compared to traditional PhCS. It combines both advantages of the slot waveguide and photonic crystal to localize the high energy density in the low index material. This property could increase the interaction between light and material embedded with nanoparticles like quantum dots for active device development. We also demonstrated a wide range bandgap based on a one dimensional waveguide distributed Bragg reflector with high coupling to optical waveguides enabling it to be easily integrated with other optical components on the chip. A flexible polymer (SU8) grating waveguide is proposed as a force sensor. The proposed sensor can monitor nN range forces through its spectral shift. Finally, quantum dot - doped SU8 polymer structures are demonstrated by optimizing spin coating and UV exposure. Clear patterns with high emission spectra proved the compatibility of the fabrication process for applications in optical amplification and lasing.

High pressure and low temperature study of ammonia borane and lithium amidoborane

Hydrogen has been considered as a potentially efficient and environmentally friendly alternative energy solution. However, one of the most important scientific and technical challenges that the "hydrogen economy" faces is the development of safe and economically viable on-board hydrogen storage for fuel cell applications, especially to the transportation sector. Ammonia borane (BH3NH 3), a solid state hydrogen storage material, possesses exceptionally high hydrogen content (19.6 wt%).However, a fairly high temperature is required to release all the hydrogen atoms, along with the emission of toxic borazine. Recently research interests are focusing on the improvement of H2 discharge from ammonia borane (AB) including lowering the dehydrogenation temperature and enhancing hydrogen release rate using different techniques. Till now the detailed information about the bonding characteristics of AB is not sufficient to understand details about its phases and structures. ^ Elemental substitution of ammonia borane produces metal amidoboranes. Introduction of metal atoms to the ammonia borane structure may alter the bonding characteristics. Lithium amidoborane is synthesized by ball milling of ammonia borane and lithium hydride. High pressure study of molecular crystal provides unique insight into the intermolecular bonding forces and phase stability. During this dissertation, Raman spectroscopic study of lithium amidoborane has been carried out at high pressure in a diamond anvil cell. It has been identified that there is no dihydrogen bond in the lithium amidoborane structure, whereas dihydrogen bond is the characteristic bond of the parent compound ammonia borane. It has also been identified that the B-H bond becomes weaker, whereas B-N and N-H bonds become stronger than those in the parent compound ammonia borane. At high pressure up to 15 GPa, Raman spectroscopic study indicates two phase transformations of lithium amidoborane, whereas synchrotron X-ray diffraction data indicates only one phase transformation of this material. ^ Pressure and temperature has a significant effect on the structural stability of ammonia borane. This dissertation explored the phase transformation behavior of ammonia borane at high pressure and low temperature using in situ Raman spectroscopy. The P-T phase boundary between the tetragonal (I4mm) and orthorhombic (Pmn21) phases of ammonia borane has been determined. The transition has a positive Clapeyron slope which indicates the transition is of exothermic in nature. Influence of nanoconfinemment on the I4mm to Pmn2 1 phase transition of ammonia borane was also investigated. Mesoporus silica scaffolds SBA-15 with pore size of ~8 nm and MCM-41 with pore size of 2.1-2.7 nm, were used to nanoconfine ammonia borane. During cooling down, the I4mm to Pmn21 phase transition was not observed in MCM-41 nanoconfined ammonia borane, whereas the SBA-15 nanocondfined ammonia borane shows the phase transition at ~195 K. Four new phases of ammonia borane were also identified at high pressure up to 15 GPa and low temperature down to 90 K.^

Application of GPCR Structures for Modelling of Free Fatty Acid Receptors

Five G protein-coupled receptors (GPCRs) have been identified to be activated by free fatty acids (FFA). Among them, FFA1 (GPR40) and FFA4 (GPR120) bind long-chain fatty acids, FFA2 (GPR43) and FFA3 (GPR41) bind short-chain fatty acids and GPR84 binds medium-chain fatty acids. Free fatty acid receptors have now emerged as potential targets for the treatment of diabetes, obesity and immune diseases. The recent progress in crystallography of GPCRs has now enabled the elucidation of the structure of FFA1 and provided reliable templates for homology modelling of other FFA receptors. Analysis of the crystal structure and improved homology models, along with mutagenesis data and structure activity, highlighted an unusual arginine charge pairing interaction in FFA1-3 for receptor modulation, distinct structural features for ligand binding to FFA1 and FFA4 and an arginine of the second extracellular loop as a possible anchoring point for FFA at GPR84. Structural data will be helpful for searching novel small molecule modulators at the FFA receptors.

Direct Observation of Tetragonal Distortion in Epitaxial Structures through Secondary Peak Split in a Synchrotron Radiation Renninger Scan

This paper reports a direct observation of an interesting split of the (022)(022) four-beam secondary peak into two (022) and (022) three-beam peaks, in a synchrotron radiation Renninger scan (phi-scan), as an evidence of the layer tetragonal distortion in two InGaP/GaAs (001) epitaxial structures with different thicknesses. The thickness, composition, (a perpendicular to) perpendicular lattice parameter, and (01) in-plane lattice parameter of the two epitaxial ternary layers were obtained from rocking curves (omega-scan) as well as from the simulation of the (022)(022) split, and then, it allowed for the determination of the perpendicular and parallel (in-plane) strains. Furthermore, (022)(022) omega:phi mappings were measured in order to exhibit the multiple diffraction condition of this four-beam case with their split measurement.