Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.

Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2.1 Å. The NO geometry is compatible with those analyzed by XFEL-based cryo-crystallography and QM/MM calculations, indicating that we obtain an intact Fe3+-NO coordination structure that is free of X-ray radiation damage. The slightly bent NO geometry is appropriate to prevent immediate NO dissociation and thus accept H- from NADH. The combination of using XFEL and a caged-compound is a powerful tool for determining functional enzyme structures during catalytic reactions at the atomic level.

A nearly on-axis spectroscopic system for simultaneously measuring UV-visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline.

UV-visible absorption spectroscopy is useful for probing the electronic and structural changes of protein active sites, and thus the on-line combination of X-ray diffraction and spectroscopic analysis is increasingly being applied. Herein, a novel absorption spectrometer was developed at SPring-8 BL26B2 with a nearly on-axis geometry between the X-ray and optical axes. A small prism mirror was placed near the X-ray beamstop to pass the light only 2° off the X-ray beam, enabling spectroscopic analysis of the X-ray-exposed volume of a crystal during X-ray diffraction data collection. The spectrometer was applied to NO reductase, a heme enzyme that catalyzes NO reduction to N2O. Radiation damage to the heme was monitored in real time during X-ray irradiation by evaluating the absorption spectral changes. Moreover, NO binding to the heme was probed via caged NO photolysis with UV light, demonstrating the extended capability of the spectrometer for intermediate analysis.

Effect of functional group on the monolayer structures of biodegradable quaternary ammonium surfactants.

The monolayer structures and conformational ordering of cationic surfactants including the biodegradable quaternary ammonium molecules have been systematically characterized by π-A isotherm, surface potential, atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and sum frequency generation (SFG) vibrational spectroscopy. It was found that the monolayer of the typical dialkyl dimethylammonium on the water surface was less densely packed along with many conformational gauche defects. The packing density and ordering of these monolayers were improved as halide ions were added to the subphase. A similar condensation effect was also observed when amide or ester groups are present in the alkyl tails of the surfactant. These results are discussed on the basis of the repulsive electrostatic interactions between the terminal ammonium moieties, the hydrogen bonding between the functional groups in the alkyl chains, as well as the flexibility of the alkyl chains in these surfactants. The present study is crucial to understanding the relationship between the interfacial structures and the functionalities of the biodegradable quaternary ammonium surfactants.

Expression of genes responsible for biomineralization of Pinctada fucata during development.

This study compares the expression levels of nacrein, N16, MSI60, Prismalin-14, aspein and MSI31 genes during the ontogeny of Pinctada fucata. Several novel findings were obtained: 1) The early calcitic prismatic layer was distinguished as a thin membrane-like structure. 2) Initial formation of the nacreous layer started from the mantle pallial region at the age of 31days. 3) 18S rRNA of P. fucata was determined to be more suitable as a real-time PCR reference gene compared with GAPDH and beta-actin genes. 4) A relationship was recognized between the expression levels of the above six organic matrix genes and biomineralization of the larval shell. The lack of calcite in the shells of the veliger and pediveliger stages, when MSI31 and Prismalin-14 genes were expressed, makes a role of polymorph control by these genes less likely. The hypothetical involvement of N16 and MSI60 proteins in aragonitic nacreous layer formation was corroborated by the expression levels of N16 and MSI60 genes during ontogeny. Our results are important with respect to the control of CaCO(3) crystal polymorphism and shell microstructures in P. fucata.

Optical sum-frequency emission from langmuir-blodgett films of variable thickness: effects of the substrate and polar orientation of fatty acids in the films.

The nonlinear optical response arising from a model multilayer structure, i.e., Langmuir-Blodgett (LB) films comprised of different numbers of per-protonated (H) and per-deuterated (D) fatty acid layers on solid substrates, has been evaluated by sum-frequency generation (SFG) spectroscopy. The SFG signals depend significantly on the absolute polar orientation of the fatty acids in the individual layers and on the nonlinear optical response of the substrate. The SFG spectra on gold and fused quartz substrates demonstrate a totally different dependence on the number of the contributing H layers, which it is possible to analyze quantitatively. The results provide important information for understanding the origin of the nonlinear optical responses from ordered systems composed of multiple interfaces and therefore for extracting exact structural information about each interface from the observed SFG signals.

Oxidation states and CO ligand exchange kinetics in a self-assembled monolayer of a triruthenium cluster studied by in situ infrared spectroscopy.

Oxidation states and CO ligand exchange kinetics in a self-assembled monolayer (SAM) of an oxo-centered triruthenium cluster [Ru(3)(mu3-O)(mu-CH3COO)6(CO)(L1)(L2)] (L1 = [(NC5H4)CH2NHC(O)(CH2)10S-]2, L2 = 4-methylpyridine) have been extensively investigated on the surface of a gold electrode in aqueous and nonaqueous solutions. The SAM exhibits three consecutive one-electron transfers and four oxidation states, which have been characterized by electrochemistry, in situ infrared spectroscopy, and in situ sum frequency generation (SFG) vibrational spectroscopy measurements. The original electron-localized state of the Ru cluster center was changed to electron delocalization states by oxidation or reduction of the central Ru ions. These changes are revealed by the IR absorptions of the CO ligand and the bridging acetate ligands of the triruthenium cluster in the SAM. The IR absorptions of the two kinds of ligands are strongly dependent on the oxidation state of the Ru cluster center. One-electron oxidation of the central Ru ion in the SAM triggers a CO ligand liberation process. Solvent molecules may then occupy the CO site to result in a CO-free SAM. One-electron reduction of this CO-free SAM in a CO-saturated solution leads to re-coordination of the CO ligand into the SAM. Both processes can be precisely controlled by tuning the electrode potential. The kinetics of the CO exchange cycle in the SAM, including liberation and coordination, has been investigated by in situ IR and SFG measurements for the first time. The CO exchange cycle is significantly dependent on the temperature. The reaction rate greatly decreases with decreasing solution temperature, which is an important factor in the CO ligand exchange process. The activation energies of both CO liberation and coordination have been evaluated from the reaction rate constants obtained at various temperatures.

Sum frequency generation from Langmuir-Blodgett multilayer films on metal and dielectric substrates.

Sum frequency generation (SFG) vibrational spectra of cadmium arachidate multilayer films adsorbed on a substrate with high nonresonant susceptibility, i.e., gold, and on a low nonresonant susceptibility substrate, i.e., fused quartz, have been investigated in the C-H stretching region in air. The films were formed by Langmuir-Blodgett (LB) deposition and their spectra recorded using SFG spectrometers employing both 532-nm nanosecond and 800-nm femtosecond lasers, with counter-propagating and co-propagating beam geometries, respectively. Both kinds of substrate were rendered hydrophobic by coating them with per-deuterated octadecanethiol (gold) or per-deuterated cadmium arachidate (fused quartz) monolayers. Single per-protonated arachidate layers in otherwise per-deuterated 10-layer films were used to show that the SFG resonances arise only from the topmost and lowermost layers in a LB film comprised of an even number of per-protonated layers, although the SFG spectra from the two hydrophobic substrates are different from each other. The differences in the spectra from the same ten-layer per-protonated films deposited on the two types of hydrophobic substrate have been explained in terms of a simple model that accounts for resonant and nonresonant contributions.

Hydrogen bonding on the surface of poly(2-methoxyethyl acrylate).

Hydrogen bonding on the interface and in the bulk of a poly(2-methoxyethyl acrylate) (PMEA) thin film has been investigated by sum frequency generation, infrared reflection absorption, and Raman scattering measurements in different kinds of solutions containing hydrogen-bonding donators. These results indicate that the majority of the carbonyl groups on the PMEA surface are hydrogen-bonded with water or ethanol molecules, while the PMEA bulk is still dominated by the free carbonyl group.

Electrochemical control of CO/NO ligand exchange in a triruthenium cluster monolayer assembled on a gold electrode surface.

A highly selective ligand exchange reaction is realized in the self-assembled monolayer (SAM) of a triruthenium cluster on a gold electrode surface under precise electrochemical potential control. CO as well as NO molecules, which are known to play key roles in many chemical, biological, and environmental systems, can be efficiently introduced into the SAM by electrochemically tuning the electronic state of the Ru site. These unique surface reactions are more convenient and efficient than conventional ligand exchange reactions in solution and could be used for the elucidation of the electron-transfer mechanism in a biological system as well as in the development of molecular sensors and devices.

Cd2+-induced interfacial structural changes of Langmuir-Blodgett films of stearic acid on solid substrates: a sum frequency generation study.

The molecular structures and their stabilities at the outmost-layer of the Langmuir-Blodgett (LB) films of stearic acid on solid substrates have been investigated by a highly surface-sensitive spectroscopic technique, sum frequency generation (SFG), in air and in aqueous solution, using the combination of both normal and deuterated stearic acid. Peaks observed in the SFG spectra are mainly attributed to the terminal methyl group at the outmost layer of the LB films. The SFG spectra in air are virtually identical and are independent of the odd-even property and thickness (1-12) of the LB films, indicating that the even-numbered LB film changes its surface structure after passing through the interface between the water subphase and air, especially when the Cd2+ cation was included in the water subphase. Furthermore, we have demonstrated for the first time using in situ SFG measurement that the interfacial molecular structure at the LB bilayer of stearic acid on the hydrophilic substrates significantly change with immersion in the water subphase containing Cd2+ cation while such a structural change has not been observed in the water subphase without Cd2+. These results clearly indicate that a reorganization process takes place on the surface of the stearic acid bilayer induced by the Cd2+ cation. The electrostatic interaction between the carboxylate headgroup of stearic acid via the Cd2+ cation seems to play an important role in the surface reorganization process both in air and in solution.

Reaction of carbonyl compounds with trialkylsilyl phenylselenide and tributylstannyl hydride under radical conditions.

A novel method for the hydrosilylation of carbonyl compounds has been developed. When carbonyl compounds were allowed to react with trimethylsilyl phenylselenide and tributylstannyl hydride in the presence of a catalytic amount of AIBN as the radical initiator, hydrosilylation of the carbonyl compounds efficiently proceeded to give the corresponding silyl ethers in moderate to good yields. In the absence of carbonyl compounds, the triethylsilyl hydride was obtained by the reaction of PhSeSiEt(3) with Bu(3)SnH. Although the tributylgermyl phenylselenide instead of PhSeSiMe(3) was treated with tributylstannyl hydride in the presence of a benzaldehyde under radical conditions, hydrogermylated product was not obtained and tributylgermyl hydride was mainly formed.