bluuebunny/crossref_metadata_2025 huggingface dataset:
The Photocycles of Bacteriorhodopsin
Authors: Lanyi Janos K. , Váró György
Published: November 2013

The photoisomerization of all‐trans‐retinal of bacteriorhodopsin to 13‐cis gives rise to a series of unstable states that thermally interconvert on the picosecond to millisecond timescale, and ultimately decay back to the initial state. Since this “photocycle” drives the translocation of a proton from the cytoplasmic to the extracellular side of the membrane, its detailed description is essential to understand the mechanism of the ion transport. The interconversions of the intermediates of the cycle, K610, L550, M410, N560, and O640, proceed with complex multiphasic kinetics, and there is much disagreement over the interpretation of this. However, many groups have described the photocycle as a single reaction sequence with several reversible reactions, some pH‐dependent. Through the use of time‐resolved spectroscopy and site‐specific mutations, such a scheme provides a reasonable model for how the retinal Schiff base first transfers its proton to Asp‐85, followed by release of a proton to the extracellular side; then the Schiff base is reprotonated from Asp‐96, and proton uptake from the cytoplasmic surface restores the initial protonation state of Asp‐96, while the retinal reisomerizes to all‐trans.
Molecular Dynamics Studies of Bacteriorhodopsin's Photocycles
Authors: Schulten Klaus , Humphrey William , Logunov Ilya , Sheves Mordechai , Xu Dong
Published: November 2013

The availability of the structure of bacteriorhodopsin from electron microscopy studies has opened up the possibility of exploring the proton pump mechanism of this protein by means of molecular dynamics simulations. In this review we summarize earlier theoretical investigations of the photocycle of bacteriorhodopsin including relevant quantum chemistry studies of retinal, structure refinement, molecular dynamics simulations, and evaluation of pKa values. We then review a series of recent modeling efforts which refined the structure of bacteriorhodopsin adding internal water, and which studied the nature of the J intermediate and the likely geometry of the K590 and L550 intermediates (strongly distorted 13‐cis) as well as the sequence of retinal geometry and protein conformational transitions which are conventionally summarized as the M412 intermediate. We also review simulations of the photocycle of light‐adapted bacteriorhodopsin at T=77 K and of the photocycle of dark‐adapted bacteriorhodopsin, both cycles differing from the conventional photocycle through a nonfunctional (pure 13‐cis) retinal geometry of the corresponding K590 and L550 states. The simulations demonstrate a potentially critical role of water and of minute reorientations of retinal's Schiff base nitrogen in controlling proton pumping in bR568; the simulations also indicate the existence of heterogeneous photocycles. The results exemplify the important role of molecular dynamics simulations in extending investigations on bacteriorhodopsin to a level of detail which is presently beyond experimental resolution, but which needs to be known to resolve the pump mechanism of bacteriorhodopsin. Finally, we outline the major existing challenges in the field of bacteriorhodopsin modeling.
Structural Studies of Catalytic Antibodies
Authors: Stevens Raymond C. , Hsieh‐Wilson Linda C. , Santarsiero Bernard D. , Wedemayer Gary J. , Spiller Ben , Wang Leo H. , Barnes Dwight , Ulrich Helle D. , Patten Phillip A. , Romesberg Floyd E. , Schultz Peter G.
Published: November 2013

A panel of catalytic antibodies which catalyze ester hydrolysis, transesterification, porphyrin metallation, Diels‐Alder, and redox reactions has been selected for crystallographic study. While these examples are only a handful of the catalytic antibodies generated to date, they represent distinct and important aspects of antibody catalysis. Since the first reports of catalysis, a great deal of progress has been made with respect to the scope, selectivity, and efficiency of antibody catalysis and strategies for generating catalytic antibodies. However, it is clear that further progress in the field will benefit greatly from a detailed understanding of the molecular interactions occurring in the combining site. High‐resolution crystallographic data should allow the importance of general base catalysis, entropy effects, electrophilic catalysis, and transition‐state stabilization to be evaluated. Antibody and enzyme active sites have been shown to share considerable structural and mechanistic similarity, and ongoing structure‐function studies of catalytic antibodies may enhance our understanding of the mechanisms and evolution of enzymatic catalysis. Structural studies of antibodies which perform a biological or highly selective reactions should enhance our ability to generate catalysts for important synthetic applications. Finally, the combination of high‐resolution crystallographic analysis with rational mutagenesis should provide a basis for engineering antibodies with enhanced properties.
Hapten Design for Antibody‐Catalyzed Decarboxylation and Ring‐Opening Reactions of Benzisoxazoles
Authors: Sergeeva Masha V. , Yomtova Vihra , Parkinson Adrian , Overgaauw Marjolein , Pomp Rikus , Schots Arjen , Kirby Anthony J. , Hilhorst Riet
Published: November 2013

Three benzisoxazole haptens designed to elicit antibody binding sites with widely differing polarity have been synthesized and used to induce antibodies in mice. Monoclonal antibodies were prepared using hybridoma technology, and screened for catalysis of the ring‐opening isomerization and/or decarboxylation of a series of related benzisoxazoles and their 3‐carboxy‐derivatives. No catalysis of decarboxylation was observed, but 4 of a total of 47 antibodies obtained against the three haptens catalyzed the isomerization process. Of 12 antibodies raised against the 3‐acetylbenzisoxazole structure 5 none was catalytically active; but one of 24 raised against a 3‐isopropenylbenzisoxazole 6 increased the rate of ring‐opening of 6‐nitrobenzisoxazole, and 5 of 11 antibodies raised against a benzisoxazole 7 with a 3‐amidinium group were moderately active against either 6‐nitro or 6‐acylaminobenzisoxazoles. Competitive binding studies suggest that at least some of the antibodies induced by the isopropenyl hapten do possess a recognizably hydrophobic binding site.
α‐Multistriatin: The First Total Synthesis of a Natural Product via Antibody Catalysis
Authors: Sinha Subhash C. , Keinan Ehud
Published: November 2013

The relevance of antibody catalysis to synthetic organic chemistry is demonstrated here by an efficient total synthesis of (–)‐α‐multistriatin, the aggregation pheromone of the European elm bark beetle, Scolytus multistriatus, which is the principal vector of the Dutch elm disease, responsible for the severe devastation of the elm population in Europe and North America. The key step in our synthesis of this natural product is an antibody‐catalyzed, enantioselective protonolysis of an enol ether to produce a branched ketone. The latter is obtained with an (S) configuration in greater than 99% enantiomeric excess. Catalysis follows Michaelis‐Menten kinetics (Km = 230 μM, kcat = 0.36 min−1) and useful rate enhancement (kcat/kun = 65,000 at pH 6.5). This abzymic step is followed by twelve chemical steps, with all four asymmetric centers originating from the chirality achieved in the antibody‐catalyzed reaction. That specific step is a unique example of a chemical transformation which is difficult to achieve either by an available synthetic methodology or via catalysis with a known enzyme. The synthetic pheromone has been checked in field experiments and found as active as the naturally occurring compound in attracting the European elm bark beetles.
Light‐Stimulated Formation and Dissociation of Supramolecular Donor–Acceptor Complexes between Eosin and Bipyridinium Azobenzenes: Design of Molecular Electronic Devices for the Piezoelectrical Transduction of Recorded Optical Signals
Authors: Ranjit Koodali T. , Marx‐Tibbon Sharon , Ben‐Dov Iddo , Willner Bilha , Willner Itamar
Published: November 2013

The photoisomerizable electron acceptors, trans‐4,4′‐bis(N‐methylpyridinium)azobenzene, (1t), and trans‐3,3′‐bis(N‐methylpyridinium)azobenzene, (2t), exhibit photoswitchable binding affinities to eosin. While the trans isomers, (1t) or (2t) exhibit high association affinities (Ka = 8.3 × 103 M−1 and 3.8 × 104 M−1, respectively), the cis isomers (1c) or (2c) reveal lower binding affinities (Ka = 3.4 × 103 M−1 and 1.4 × 104 M−1, respectively). The formation of the supramolecular donor–acceptor complexes between the eosin and the electron acceptors is associated with an absorbance change of the chromophore. This enables the cyclic spectroscopic transduction of the optically‐induced formation and dissociation of the complexes upon photoisomerization between the respective trans and cis states. An eosin monolayer was assembled onto the Au‐electrodes associated with a quartz piezoelectric crystal. The eosin‐functionalized crystal was employed for the microgravimetric, quartz‐crystal‐microbalance analyses of the association of (1t), (2t), (1c), or (2c) to the crystal interface. The microgravimetric analyses allowed the characterization of the kinetics of association of the electron acceptors to the monolayer and the association constants between the isomers (1t), (2t), (1c), and (2c) with the eosin monolayer. By cyclic photoisomerization of the electron‐acceptor between the trans and cis states, reversible piezoelectric transduction of the formation of the complexes with (1t) or (2t) at the monolayer interface, and their dissociation upon photoisomerization to (1c) or (2c) was accomplished.
Voltammetric and Scanning Electrochemical Microscopic Studies of the Adsorption Kinetics and Self‐Assembly of n‐Alkanethiol Monolayers on Gold
Authors: Forouzan Fardad , Bard Allen J. , Mirkin Michael V.
Published: November 2013

The adsorption kinetics and self‐assembly of hexadecyl mercaptan on gold have been investigated by scanning electrochemical microscopy (SECM), chronoamperometry, and cyclic voltammetry. The developed methodology allows one to evaluate the surface coverage and the average size of the defects in the monolayer film from the effective rate constant of electron transfer. Two kinetic regimes of self‐assembly were identified: a rapid initial adsorption of hexadecyl mercaptan onto a clean gold surface from 5 mM solution (more than 90% coverage obtained in 1 to 5 min), and a slower subsequent annealing of a thiol monolayer resulting in a more compact film. Typically, a long‐chain‐length thiol‐treated gold surface acts as an electronically insulating surface after about 1 h. The SECM images of partially covered gold surfaces were always featureless, suggesting that the defects in the film were smaller than 0.5 μm for any exposure time ≥ 1 min.
Photostimulated Interactions of Bipyridinium‐Azobenzene with a β‐Aminocyclodextrin Monolayer‐Functionalized Electrode: An Optoelectronic Assembly for the Amperometric Transduction of Recorded Optical Signals
Authors: Lahav Michal , Ranjit Koodali T. , Katz Eugenii , Willner Itamar
Published: November 2013

An amino‐functionalized β‐cyclodextrin is covalently linked to a thiopropionic acid‐active ester monolayer associated with a Au electrode to yield a cyclodextrin monolayer electrode. The photoisomerizable electron acceptor trans or cis N‐methylpyridinium‐4‐(4′‐N′‐methylenepyridinium)‐azobenzene, 1t or 1c, respectively, exhibit different binding affinities for the β‐cyclodextrin‐receptor‐monolayer. The photoisomer 1t has a high affinity for the cyclodextrin monolayer while 1c exhibits low binding interactions to the monolayer interface. The photostimulated binding and dissociation of 1t or 1c to and from the monolayer are transduced electrochemically. The association and dissociation of the photoisomerizable substrate to and from the monolayer are confirmed by microgravimetric, quartz‐crystal‐microbalance experiments.
Room‐Temperature Electrochemical Assembly of Copper/Cuprous Oxide Nanocomposites
Authors: Huang Ling‐Yuang , Bohannan Eric W. , Hung Chen‐Jen , Switzer Jay A.
Published: November 2013

Nanocomposite films of copper metal and cuprous oxide, Cu2O, are electrodeposited at room temperature from alkaline solutions of copper(II) lactate. The electrode potential oscillates spontaneously if the films are deposited galvanostatically. The oscillation period is a function of pH, varying from 69 seconds at pH 8.7 to 11 seconds at pH 9.7. No oscillations are observed if the pH is below 8.5 or above 10. The phase composition of films deposited at 0.5 mA/cm2 is a function of pH. The composition varies from nearly pure copper (93 mole%) at pH 8, to 42 mole% copper at pH 9.5, to pure cuprous oxide when the pH exceeds 10. The observation of quasi‐periodic potential oscillations suggests that the nanocomposites are layered. The calculated faradaic thickness of cuprous oxide is 5–8 nm, and the thickness of the copper layer is 1–11 nm. The thickness of each of the layers increases as the pH is lowered.
Single and Merged Beam Studies of the Reaction H2+ (v = 0,1; j = 0,4) + H2 → H3+ + H
Authors: Glenewinkel‐Meyer Thomas , Gerlich Dieter
Published: November 2013

Different approaches for studying low‐energy (meV) reactive ion‐molecule collisions in molecular beams are presented. In particular, differences in the photoionization (REsonant Multi‐Photon Ionization / REMPI, Pulsed Field Ionization / PFI) experiments using single molecular beams vs. merged and crossed beams are discussed. We address the question of the proper determination of cross sections and rate constants in single beam experiments and the factors that influence the width of the collision energy distributions. We identify space charge effects as the dominant contribution under our experimental conditions. Problems pertinent to state‐selected primary ion preparation with narrow energy distributions are highlighted.

In light of the detailed data analysis, the derived relations are applied to the four‐center reaction H2+ + H2 → H3+ + H, which was studied in single and merged molecular beam experiments. We present merged beam data for the absolute reaction cross section for primary ions created in a storage ion source in the energy range from 5 meV up to 5 eV and relative state‐selected cross sections for different vibrational and rotational ion states (v = 0,1; j = 0–4) generated by (3+1) REMPI for a mean collision energy of about 10 meV.
Tricky IR Monomer Spectroscopy in Planar Molecular Jets
Authors: Oomens Jos , Reuss Jörg
Published: November 2013

An experimental technique based on double resonance spectroscopy in the collisional environment of a seeded molecular jet expansion is described. Using this technique, hot band spectra of several small hydrocarbons have been investigated as well as the (related) collision‐induced relaxational behavior upon vibrational excitation. The collisional relaxation in the jet is of crucial importance to the experiments presented here as it distributes the population over many rovibrational states after initial excitation by a pump laser. A second IR laser then probes the transitions starting from the vibrationally excited state(s), as hot bands. In that way one enters an energy region around 4000 cm−1, beyond the highest fundamental bands. The possibility to label an individual rovibrational state with the pump laser enables us to obtain reliable initial spectroscopic assignments. In addition, the present technique allows one to distinguish the cold bands due to depletion of the vibrational ground state, which may reveal new and surprising spectral features as well.
The Relative Influences of Ring Modes and Methyl Internal Rotation on the Cold Beam IVR of p‐Fluorotoluene
Authors: Ju Quan , Parmenter Charles S. , Stone Todd A. , Zhao Zhong‐Quan
Published: November 2013

Room temperature (300 K) experiments have earlier established that the replacement of a fluorine atom in p‐difluorobenzene (pDFB) with a methyl group to make p‐fluorotoluene (pFT) generates a qualitative difference in intramolecular vibrational redistribution (IVR) characteristics as seen in the S1 states. Here we report S1–S0 fluorescence excitation and dispersed single vibronic level (SVL) fluorescence spectra that have been obtained for IVR comparisons in the cold (5 K) environment of supersonic expansions. As in the 300 K experiments, the cold beam S1 vibrational energy threshold for IVR is substantially lower in pFT. The vibrational congestion in dispersed fluorescence that reveals extensive S1 level interactions first appears after pumping an S1 pFT level near 800 cm−1. In contrast, congestion in pDFB spectra is still absent from levels with twice this energy. Attention is directed to the relative S1 ring level structures as a potential contributor to the distinctive IVR behaviors. Dispersed fluorescence from the S1 zero point levels and fluorescence excitation spectra are combined with published information about S1 fundamentals to show that the S1 vibrational level structures of the two molecules are as closely related as those of an isotopomer pair. It is argued that the small differences in S1 fundamentals cannot be a principal contribution to the qualitative IVR differences.
Binding Energies of Aromatic 1:1 Hetero‐Clusters in a Supersonic Jet
Authors: Haas Yehuda , Kendler Shai
Published: November 2013

Methods used to experimentally estimate the binding energies of van der Waals clusters containing an aromatic molecule are surveyed. These include microwave and infrared absorption spectroscopies, single and two photon ionization, dispersed fluorescence, and stimulated emission pumping. The problems encountered in the application of these methods are briefly discussed, and prospects for the firm establishment of the binding energies are assessed. Although the present database is too small for firm conclusions, methods based on dispersed fluorescence (i.e., probing the excited state surface) tend to yield lower values for argon adducts than those based on ionization, probing the ground state, or ionic surfaces. A mechanism that may account for this tendency is proposed, and further experiments are proposed to test it.
Advances in Grating‐Based Photoacoustic Spectroscopy for the Study of Protein Dynamics
Authors: Dadusc Gami , Goodno Gregory D. , Chiu Hui‐Ling , Ogilvie Jennifer , Miller R.J. Dwayne
Published: November 2013

Recent advances in transient grating spectroscopy are described in relation to extracting photoacoustic parameters. The time resolution for measurement of dynamically driven acoustics has been extended to the picosecond level. This improvement was achieved by adopting counter‐propagating beam geometries and resolving the acoustic phase shift in analogy to phase modulation spectroscopy. At the other extreme, the dynamic range of this technique has been extended to milliseconds in order to follow dynamical processes central to biological functions. In addition, diffractive optics were used for generating the necessary excitation and probe beam geometries. A novel optical setup was developed which permits both the rapid exploration of fringe spacing dependencies in separating thermal from nonthermal contributions to the observed signal as well as heterodyne detection without active feedback. The latter capability significantly increases the signal‐to‐noise ratio and permits separation of the real and imaginary components from the nonlinear four‐wave‐mixing signal. Applications of these new methods are demonstrated by following the functionally relevant structural relaxation processes of heme proteins over 10 decades in time.
Lateral Thermal Diffusion Effects on Photothermal Signals from Photovoltaic Cells
Authors: Büchner Bettine , Cella Norberto , Cahen David
Published: November 2013

Thermal diffusion, parallel to the photovoltaic junction and perpendicular to the direction of illumination, can be used to separate the contributions of injected and photogenerated carriers to the generation of heat in a photothermal experiment, and to demonstrate the influence of electronic carrier diffusion on the signal, already at relatively low modulation frequencies. We show this by using an experimental arrangement in which the distance is varied between the illuminated area of the photovoltaic cell and that over which the thermal signal is detected, and the two areas do not overlap. Our results agree with theoretical calculations used to simulate the photothermal responses of solar cells.
N2 Interaction with Fe Surfaces
Authors: Christoffersen Ebbe , Mortensen Jens‐Jørgen , Stoltze Per , Nørskov Jens Kehlet
Published: November 2013

Recent density functional theory calculations of the energetics of N2 dissociation on Fe(111) and atomic N adsorption on all three low‐index Fe surfaces have given new detailed information about precursors for dissociation, new reaction channels, and new surface structures. We analyze the consequences of this insight for the surface structures on Fe catalysts during ammonia synthesis and for the kinetics and dynamics of the N2 dissociation process.
Palladium‐Catalyzed Acetylene Cyclotrimerization: From Ultrahigh Vacuum to High‐Pressure Catalysis
Authors: Tysoe Wilfred T.
Published: November 2013

The surface reactions involved in the palladium‐catalyzed formation of benzene from acetylene are discussed as an example of the way in which such strategies can be used to understand catalytic reaction pathways in detail. This provides an ideal system for surface science/catalysis studies since benzene is formed both in ultrahigh vacuum in temperature‐programmed desorption and under high‐pressure, catalytic conditions. It is found that benzene is synthesized on clean Pd(111) by an initial fast reaction between two adsorbed acetylene molecules to yield a tilted C4H4 metallocyclic intermediate. This reacts with a third acetylene to form benzene, and the hexagonal (111) surface of palladium acts as a template for the reaction. Under catalytic conditions, however, it is found that the surface is covered by a relatively unreactive vinylidene layer. Organometallic studies show that acetylene and vinylidene can react to form a C4H4 intermediate analogous to that found to form from acetylene on a palladium surface. This suggests an alternative possible reaction pathway under catalytic conditions in which acetylene and vinylidene react to eventually form benzene. This proposal is confirmed using NMR analysis of a 13C‐labeled vinylidene‐covered surface. This pathway also successfully rationalizes the observed change in activity as a function of reaction time found using supported palladium catalysts and the observed first‐order reaction kinetics.
Formation and Geometry of a High‐Coverage Oxygen Adlayer on Ru(001), the p(2 × 2)‐3O Phase
Authors: Gsell Marianne , Stichler Markus , Jakob Peter , Menzel Dietrich
Published: November 2013

A detailed low‐energy electron diffraction (LEED)‐IV analysis, complemented by scanning tunneling microscopy (STM) observations, was carried out for the apparent (2 × 2) structure of the oxygen‐covered Ru(001) surface at a coverage of 0.75 ML. We present STM images of incomplete layers which allow one to define the symmetry of the ordered layer, in particular of the novel high density p(2 × 2)‐3O phase. In the LEED‐IV analysis we have tested 28 model structures; the results can be used for conclusions about the discrimination of this type of geometry determination. Our quantitative LEED analysis in connection with the STM results corroborates the model proposed before and shows that all of the oxygen atoms sit in the hcp sites with an averaged vertical distance to the outermost Ru layer of d⊥Ru–O = 1.22 Å. This value falls into the general trend of increasing d⊥Ru–O with oxygen coverage observed for the other ordered structures of adsorbed oxygen on Ru and is also predicted by recent total energy calculations. The O–Ru bonding distance of about 2.0 Å is essentially unchanged compared to the other structures. Considerable lateral and vertical displacements of both the O and the Ru atoms are found, with the O atoms being slightly displaced towards the fcc hollow site located in the center of three oxygen atoms. The two uppermost substrate layers are buckled; in the first layer three out of four Ru atoms of the (2 × 2) unit cell are shifted away laterally from their bulk positions. These shifts, globally as well as locally, can be understood in terms of local electron density changes induced by the adsorbed oxygen atoms.
The Surface Chemistry of 1‐Iodopropane Adsorbed on Pt(111)
Authors: Scoggins Troy B. , Ihm Hyeran , White John M.
Published: November 2013

On Pt(111) at 110 K, 1‐iodopropane, C3H7I, adsorbs molecularly, but for doses below 1.7 × 1014 molecules cm−2, only H2 and I appear in thermal desorption. C–I bond cleavage occurs between 160 and 220 K, forming adsorbed n‐propyl, C(a)H2CH2CH3, and atomic iodine, based on temperature‐programmed desorption (TPD), high‐resolution electron energy loss spectroscopy (HREELS), and X‐ray photoelectron spectroscopy (XPS). n‐Propyl undergoes β‐hydride elimination forming propylene, with desorption peaks at 185 and 240 K. At 240 K, hydrogenation to propane also occurs. Some di‐σ bonded propylene, C(a)H2C(a)HCH3, remains at 240 K and it rearranges to propylidyne near 300 K. Atomic H, bound to Pt, recombines and desorbs at ca. 260 K. Further desorption of H2 is limited by C–H bond breaking and occurs over a broad temperature range with local maxima at ca. 280, 320, and 420 K, typical of propylidyne fragments on Pt. Atomic iodine desorbs in a broad feature at 825 K.
A Compact UHV Tandem Quadrupole Mass Spectrometer for Surface‐Induced Dissociation Studies Using Well‐Characterized Surfaces
Authors: Bernasek Steven L. , Park Frederick D.S. , Phelan Lynn M. , Hayward Mark J.
Published: November 2013

Collision of low‐energy polyatomic ions with surfaces can be an effective method for ion activation and fragmentation for ion structural analysis. In order for this method to be more widely used, a better understanding of low‐energy ion‐surface reactions must be obtained. The design and construction of a compact tandem quadrupole mass spectrometer which can be used to investigate low‐energy ion‐surface reactions on well‐characterized surfaces is described. This UHV‐compatible instrument is designed to fit entirely on a standard eight‐inch UHV flange, and so can be easily mounted on a typical UHV electron spectroscopy system for preparing and characterizing the scattering surface. The operation of this instrument is illustrated by the discussion of two examples: the first, the associative reaction between benzene ions and a hydrocarbon surface to form C7H7+ via a sputtered‐ion mechanism; the second, an examination of the effect of organic monolayer structure on the reactivity of the monolayer for protonation of incident benzene ions.
Adsorption and Reactivity of CO2 on Potassium‐Covered Re(001)
Authors: Zhao Wei , Chacham Ilan , Vackart Yahel , Asscher Micha
Published: November 2013

The interaction of CO2 with potassium‐covered Re(001) has been investigated. This system has been studied by means of work function (Δϕ), optical second harmonic generation (SHG), and temperature‐programmed desorption (TPD) measurements. Strong electronic interaction between carbon dioxide and potassium is observed upon adsorption at 90 K. This is indicated by a rapid quenching of the SHG signal of K following postadsorption of CO2, with a quenching cross section of 70 Å2. Work function change measurements are consistent with such interaction, evidenced by an undepolarization effect, namely, further decrease of the work function upon CO2 adsorption, below the minimum obtained by pure potassium. In the presence of potassium, the dissociation probability of 0.5 ML adsorbed carbon dioxide increases from 0.5 on the clean metal surface to 0.85 on 1 ML potassium‐covered Re(001), information obtained from TPD measurements following heating to 1250 K. It is concluded that a K–CO2 surface compound is formed upon adsorption at 95 K on the potassium‐covered surface.
Absolute Concentration Measurements of Chemically‐Important Flame Radicals
Authors: Crosley David R. , Jeffries Jay B. , Smith Gregory P.
Published: November 2013

A fundamental understanding of flame chemistry is a necessary part of designing and optimizing combustors to meet environmental regulations while maintaining system efficiency. We have performed quantitative, absolute concentration measurements for several free radicals to test various aspects of the predictive capabilities of the natural gas combustion chemistry mechanism, GRI‐Mech 2.11, the chemical mechanism for methane combustion. The CH, NO, OH, and HCO radicals were studied in a series of low‐pressure methane/O2/N2 flames using the technique of laser‐induced fluorescence. The results show that GRI‐Mech 2.11 predicts well the hydrocarbon oxidation chemistry in lean and near stoichiometric flames, but appears to possess some inadequacies for rich flames. Of special importance is the finding that the rate coefficient for the important CH + N2 reaction in the current version of GRI‐Mech appears to be too low. Also, reburn of NO is correctly predicted in a lean flame but not a rich one.
Oxidation of Dimethyl Ether and its Interaction with Nitrogen Oxides
Authors: Alzueta Maria U. , Muro Julio , Bilbao Rafael , Glarborg Peter
Published: November 2013

The oxidation of dimethyl ether (DME) under flow reactor conditions has been studied experimentally and in terms of a detailed chemical kinetic model. The experiments were performed at atmospheric pressure in the temperature range 600–1500 K and at different air/fuel ratios. Of particular interest was the interaction of DME with nitrogen oxides. The results show that the oxidation of DME occurs readily at temperatures above 1000 K, largely independent of the stoichiometry. Addition of NO under stoichiometric and fuel‐rich conditions does not affect the oxidation chemistry for DME, but above 1100 K a minor amount of the NO is reduced to HCN and N2 in reburn‐type reactions. Addition of NO or NO2 under oxidizing conditions significantly enhances the oxidation rate of DME and shifts the temperature for onset of oxidation to lower values, a phenomenon similar to that of NOx‐sensitized oxidation of hydrocarbons.

The proposed chemical kinetic model provides a good description of DME oxidation in the absence of nitrogen oxides. Under the conditions of the present study, the conversion of DME proceeds mainly through the high‐temperature mechanism, with little importance of the intermediate peroxy species. In the presence of NO or NO2, the reaction CH3 + NO2 ⇌ CH3O + NO, followed by dissociation of CH3O, readily provides H atoms and thereby promotes the oxidation. At lower temperatures the mechanism involves CH3OCH2O2 and CH3O2 radicals. While the effect of NOx generally is described satisfactorily by the model, deviations at lower temperatures may indicate inadequacies in the reaction subset for these peroxy species.
Kinetics of Hexafluoropropylene Oxide Pyrolysis Studied by Gas‐Phase NMR. Kinetic Measurements Made Easy
Authors: Krusic Paul J. , Roe D. Christopher , Smart Bruce E.
Published: November 2013

Gas‐phase NMR complemented with a high‐temperature probe makes possible quantitative kinetic studies of homogeneous vapor‐phase reactions with unprecedented ease, as demonstrated with a study of the thermal fragmentation of hexafluoropropylene oxide. The reaction follows strictly first‐order kinetics, is unaffected by surface chemistry, and the resulting Arrhenius activation parameters compare well with those obtained by more laborious classical methods of gas‐phase reaction kinetics. The fragmentation kinetics is also unaffected by the presence of oxygen. The profiles for the evolution of the final products in this case show very graphically that singlet difluorocarbene, one of the initial products of the fragmentation of hexafluoropropylene oxide, does not react with oxygen, a ground‐state triplet, at chemically significant rates.
Free Radical Chemistry. Part 9.1 Approaches to Fluorinated Polyethers—Model Compound Studies
Authors: Chambers Richard D. , Hutchinson John , Kelly Noel M. , Joel Andrew K. , Rees Anthony J. , Telford Peter T.
Published: November 2013

Using peroxide, γ‐, and UV‐irradiation, free radical addition reactions of hexafluoropropene to diethers and to 18‐crown‐6 have been investigated and mono‐, di‐, and poly‐adducts have been obtained. Factors influencing these additions, especially polar characteristics of intermediate radicals, have been elucidated. Adducts of 18‐crown‐6 retain a capacity to complex to alkali‐metal ions.
1,8H‐Perfluorocyclooctatetraene and its Congeners. Dynamic Equilibrium among Four Valence Isomers
Authors: Takenaka Natalie E. , Hamlin Robert , Spector Tami , Junk Christopher P. , Lemal David M.
Published: November 2013

Synthesized from hexafluorobenzene, the title compound was found to interconvert readily via bond–shift isomerization and electrocyclization with significant amounts of three other valence isomers. The mobile equilibria were revealed by 19F NMR spectroscopy, and spin–saturation transfer experiments played a key role in identifying the isomers, tracing their interconversions, and assigning their spectra. The influence of fluorine substitution on the stability of carbon–carbon double bonds and of 4‐membered rings is discussed in the light of these results.
Fluorinated Isopentenyladenines: Synthesis and Cytokinin Activity
Authors: Marival‐Hodebar Laurence , Tordeux Marc , Wakselman Claude , Dias Marylène , Mornet René , Laloue Michel
Published: November 2013

Analogs of N6‐isopentenyladenine bearing one or two fluorine atoms at the allylic position were synthesized from simple fluorinated ketones. The monofluoro analog was found to be more active than N6‐isopentenyladenine and equivalent to the more potent zeatin, another natural plant growth hormone. The difluoro analog was even more powerful than zeatin.
Lewis Acid Mediated Peterson Fluoroolefination
Authors: Welch John T. , Gregor Tamas , Kornilov Andrei
Published: November 2013

Peterson olefination of the alkyl and aryl aldehydes with C,O‐bis(triethylsilyl)fluoroketene acetal 1 promoted by titanium tetrachloride and dimethylaluminum chloride was investigated. Desired fluoroolefins were formed with high stereoselectivity and moderate to high yields.
Single Electron Transfer Reactions of Perfluoroalkyl Iodides
Authors: Chen Qing‐Yun
Published: November 2013

Perfluoroalkyl iodides react with alkenes, alkynes, and nucleophiles in the presence of metals, transition metal complexes, oxidants, or under UV irradiation. A single electron transfer mechanism is proposed and discussed.
Photoinduced Double Proton Transfer: Inter‐ and Intramolecular Cases
Authors: Kyrychenko Alexander , Herbich Jerzy , Izydorzak Marcin , Gil Michał , Dobkowski Jacek , Wu Feiyue , Thummel Randolph P. , Waluk Jacek
Published: November 2013

Photoinduced two‐proton tautomerization has been studied in two types of chromophores: (i) alcohol complexes of azaaromatic molecules possessing both proton donor and acceptor groups; (ii) constitutional isomers of porphyrin. The reaction path for the intermolecular process may involve solvent reorientation around the excited chromophore. In this case, rapid internal conversion is activated, efficiently competing with proton transfer. Another possibility arises if cyclic, doubly‐hydrogen‐bonded complexes exist already in the ground state. Excitation of such species leads to a fast tautomerization, which is not stopped even at low temperatures. Excited‐state double proton transfer also has been observed in cyclic dimers in the crystal phase. In porphyrin isomers, the rate of the process is a function of the strength of the intramolecular hydrogen bond. Dependence of the phototautomerization rate on temperature and on the nature of the surrounding matrix has also been studied.
Evidence for 1La, 1Lb Dual State Emission in 1‐naphthol and 1‐methoxynaphthalene Fluorescence in Liquid Solutions
Authors: Magnes Ben‐Zion , Strashnikova Natalya V. , Pines Ehud
Published: November 2013

The steady‐state fluorescence spectra of 1‐methoxynaphthalene and 1‐naphthol were measured in pure organic solvents and in binary mixtures of water and several organic solvents. The 1‐isomers exhibited a much larger fluorescence Stokes‐shift than the corresponding 2‐isomers. The emission spectra of 1‐methoxynaphthalene and 1‐naphthol in pure nonpolar organic solvents exhibited roughly the same structured spectral features, while the fluorescence spectra in water and formamide exhibited much broader red‐shifted and less structured spectral features. In accord with previous observations, we attribute these spectral changes to two emitting states, 1Lb and 1La, whose relative fluorescence intensities are sensitive to solvent polarity. Our analysis of the fluorescence spectra of 1‐naphthol and 1‐methoxynaphthalene by Pekarian functions have demonstrated that the 1La state becomes the dominant emitting state in polar solvents. In addition, the 1La state was found to be further stabilized in hydrogen‐bond‐donating solvents. In contrast to previous suggestions, the onset of the excited‐state proton transfer reaction from 1‐naphthol occurred at higher solvent polarities than those required for the establishment of a dominantly 1La emitting state.
Gauging of Cytochrome c Structural Fluctuation by Time‐Resolved Proton Pulse
Authors: Marantz Yael , Nachliel Esther
Published: November 2013

A brief proton pulse technique, based on photo‐excitation of pyranine, was employed for measuring the protonation dynamics of cytochrome c in aqueous solutions. Time‐resolved monitoring of the protonation state of the pyranine anion yielded detailed information from which the temporal state protonation of the surface carboxylates and histidine residues were deduced.

The surface groups were found to be coupled by electrostatic interaction where the state of protonation of one affects the pK of the others. In the same sense, altering the charge distribution of a protein by a redox reaction affects the reactivity of the surface groups with protons in the bulk.

The surface groups can exchange protons among themselves at a very high rate. The velocities of these reactions are functions of the connectivity between the proton binding sites. A single proton exchange reaction between the surface groups could be identified as the proton exchange between H26 and E44. The reaction is fast and affected by the redox state of the protein. It is proposed that the enhanced rate of this reaction is coupled with transient conformational changes that are not noticeable in time‐averaging measurements such as X‐ray diffraction or NMR.
Evaluation of the potential anti‐adhesion effect of the PVA/Gelatin membrane
Authors: Bae Sang‐Ho , Son So‐Ra , Kumar Sakar Swapan , Nguyen Thi‐Hiep , Kim Shin‐Woo , Min Young‐Ki , Lee Byong‐Taek
Published: November 2013

A common and prevailing complication for patients with abdominal surgery is the peritoneal adhesion that follows during the post‐operative recovery period. Biodegradable polymers have been suggested as a barrier to prevent the peritoneal adhesion. In this work, as a preventive method, PVA/Gelatin hydrogel‐based membrane was investigated with various combinations of PVA and gelatin (50/50, 30/70/, and 10/90). Membranes were made by casting method using hot PVA–gelatin solution and the gelatin was cross‐linked by exposing UV irradiation for 5 days to render stability of the produced sheathed form in the physiological environment. Physical crosslinking was chosen to avoid the problems of potential cytotoxic effect of chemical crosslinking. Their materials characterization and mechanical properties were evaluated by SEM surface characterization, hydrophilicity, biodegradation rate, and so forth. Cytocompatibility was observed by in vitro experiments with cell proliferation using confocal laser scanning microscopy and the MTT assay by L‐929 mouse fibroblast cells. The fabricated PVA/Gel membranes were implanted between artificially defected cecum and peritoneal wall in rats and were sacrificed after 1 and 2 weeks post‐operative to compare their tissue adhesion extents with that of control group where the defected surface was not separated by PVA/Gel membrane. The PVA/Gel membrane (10/90) significantly reduced the adhesion extent and showed to be a potential candidate for the anti‐adhesion application. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 102B: 840–849, 2014.
Segmental mandibular bone reconstruction with a carbonate‐substituted hydroxyapatite‐coated modular endoprosthetic poly(ɛ‐caprolactone) scaffold in Macaca fascicularis
Authors: Chanchareonsook Nattharee , Tideman Henk , Feinberg Stephen E. , Jongpaiboonkit Leenaporn , Lee Shermin , Flanagan Colleen , Krishnaswamy Gita , Jansen John
Published: November 2013

A bio‐degradable scaffold incorporating osteoinductive factors is one of the alternative methods for achieving the regeneration of a mandibular bone defect. The current pilot study addressed such a bone reconstruction in a non‐human primate model, Macaca fascicularis monkeys, with an engineered poly(ɛ‐caprolactone) (PCL) scaffold, provided with a carbonate‐substituted hydroxyapatite coating. The scaffolds were implanted into unilaterally created mandibular segmental defects in 24 monkeys. Three experimental groups were formed: (1) scaffolds with rhBMP‐2 (n = 8), (2) scaffolds with autologous mixed bone marrow cells (n = 8), and (3) empty scaffolds as a control group (n = 8). Evaluation was based on clinical observation as well as micro‐CT, mechanical, and histological analyses. Despite a high infection rate, the overall results showed that the currently designed PCL scaffolds had insufficient load‐bearing capability, and complete bone union was not achieved after 6 months of implantation. Nevertheless, the group of PCL scaffolds loaded with rhBMP‐2 showed evidence of bone‐regenerative potential, in contrast to PCL with autologous mixed bone marrow cells and the control group. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 102B: 962–976, 2014.
Morphology, drug release, antibacterial, cell proliferation, and histology studies of chamomile‐loaded wound dressing mats based on electrospun nanofibrous poly(ɛ‐caprolactone)/polystyrene blends
Authors: Motealleh Behrooz , Zahedi Payam , Rezaeian Iraj , Moghimi Morvarid , Abdolghaffari Amir Hossein , Zarandi Mohammad Amin
Published: November 2013

For the first time, it has been tried to achieve optimum conditions for electrospun poly(ε‐caprolactone)/polystyrene (PCL/PS) nanofibrous samples as active wound dressings containing chamomile via D‐optimal design approach. In this work, systematic in vitro and in vivo studies were carried out by drug release rate, antibacterial and antifungal evaluations, cell culture, and rat wound model along with histology observation. The optimized samples were prepared under the following electrospinning conditions: PCL/PS ratio (65/35), PCL concentration 9%(w/v), PS concentration 14%(w/v), distance between the syringe needle tip and the collector 15.5 cm, applied voltage 18 kV, and solution flow rate 0.46 mL h−1. The FE‐SEM micrographs showed electrospun PCL/PS (65/35) nanofibrous sample containing 15% chamomile had a minimum average diameter (∼175 nm) compared to the neat samples (∼268 nm). The drug released resulted in a gradual and high amount of chamomile from the optimized PCL/PS nanofibrous sample (∼70%) in respect to PCL and PS nanofibers after 48 h. This claim was also confirmed by antibacterial and antifungal evaluations in which an inhibitory zone with a diameter of about 7.6 mm was formed. The rat wound model results also indicated that the samples loaded with 15% chamomile extract were remarkably capable to heal the wounds up to 99 ± 0.5% after 14 days post‐treatment periods. The adhesion of mesenchymal stem cells and their viability on the optimized samples were confirmed by MTT analysis. Also, the electrospun nanofibrous mats based on PCL/PS (65/35) showed a high efficiency in the wound closure and healing process compared to the reference sample, PCL/PS nanofibers without chamomile. Finally, the histology analysis revealed that the formation of epithelial tissues, the lack of necrosis and collagen fibers accumulation in the dermis tissues for the above optimized samples. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 102B: 977–987, 2014.
Phenacyl Bromides Revisited: Facile Synthesis of Some New Pyrazoles, Pyridazines, and Their Fused Derivatives
Authors: Abdelrazek Fathy M. , Hassaneen Hamdi M. , Nassar Ekhlass M. , Jager Anna
Published: November 2013

Phenacylmalononitriles 8a, 8b react with hydrazines under dry conditions to afford the pyrazole derivatives 9a, 9b, 9c, 9d and in refluxing dioxane to afford the pyrazolo[3,4‐c]pyridazine derivatives 11a, 11b, 11c, 11d and the pyridazine‐6‐imine derivatives 12a, 12b, 12c, 12d. Compounds 12a, 12b were transformed into their oxo analogs 13a, 13b upon reflux in ethanolic HCl, whereas 12c, 12d were transformed into the furan derivatives 14a, 14b under the same reaction conditions (reflux in ethanolic HCl). Compounds 8a, 8b could be transformed directly into the benzoyl‐pyrazole derivatives 16a, 16b, 16c, 16d upon coupling with diazotized aromatic amines in pyridine. The structures of the new compounds were substantiated by elemental analyses and spectral data as well as x‐ray crystallographic analysis. Plausible mechanisms for the unexpected transformations are suggested.
Effects of neural stem cells on synaptic proteins and memory in a mouse model of Alzheimer's disease
Authors: Zhang W. , Wang G.M. , Wang P.J. , Zhang Q. , Sha S.H.
Published: November 2013

Transplanting neural stem cells (NSC) to the damaged brain has been regarded as a potential treatment for neurodegenerative diseases such as Alzheimer's disease (AD), a condition characterized by memory loss. We hypothesized that transplantation of NSC into the hippocampal regions of APP + PS1 transgenic (Tg) mice, a well‐established model of AD, would enhance the expression of synaptic proteins, which may be helpful for improving cognitive function. Our results showed that NSC transplantation significantly improved spatial learning and memory function in Tg mice. The results obtained by real‐time RT‐PCR, immunofluorescence, and Western blot analyses demonstrated that the expression of synaptophysin (SYN) and that of growth‐associated protein‐43 (GAP‐43) in Tg‐NSC mice, 8 weeks after transplantation, were significantly improved compared with what was observed in Tg‐Veh (control) mice. This finding was confirmed by the increase in the number of synapses in Tg‐NSC mice as observed via electron microscopy. Our results suggest that NSC‐induced changes can recover memory loss in APP + PS1 transgenic mice, possibly by establishing new neural circuits resulting from the engrafted NSC. © 2013 Wiley Periodicals, Inc.
Applications of Stable Isotope Analysis in Zooarchaeology: An Introduction
Authors: Zangrando A. F. , Tessone A. , Ugan A. , Gutiérrez M. A.
Published: November 2013

This special volume brings together works that present cases of studies that combine analysis of stable isotopes and zooarchaeology in different areas of Chile and Argentina, with special emphasis on the latter. These analyses were conducted in order to examine paleoecological conditions and interactions between humans and animal resources in different spatial and temporal contexts. In this introduction, we examine three ways in which stable isotopes have been applied in zooarcheology: (i) past animal‐human relations, (ii) stable isotopes and zooarchaeology in conservation biology, and (iii) species biogeography, climate, and environment. The implications of the results of each of the papers in this volume stress that this type of study is a fruitful and promising line of research as it expands the thematic spectrum investigated, tests archaeological hypothesis, explores new lines of analysis, and enriches the interpretations about the past. Copyright © 2014 John Wiley & Sons, Ltd.