bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurements and Analysis of Photochemical Oxidants and Trace Gases in the Rural Troposphere of the Southeast United States
Authors: Aneja Viney P. , Das Mita , Kim Deug‐Soo , Hartsell Benjamin E. 
Published: November 2013

AbstractAmbient concentrations of photochemical oxidants (O3, PAN, HNO3, H2O2) and various trace species including reactive nitrogen compounds as well as total NOy were measured during June and early July 1992 at a rural site, SONIA, in the central Piedmont region of North Carolina, as a part of the Southern Oxidants Study. The measurements were made in an effort to provide a comprehensive understanding of tropospheric photochemistry in the rural Southeastern United States. NOy, NO2, and NO showed diurnal variations with maxima in the morning between 0600 and 0900 EST. The maximum NOy, NO, and NO2 concentrations reached were 14.5, 5.4, and 7.8 ppbv, respectively. The mean NOy concentration was found to be 2.63 ± 1.72 ppbv (n = 819) with an average daily maximum of 3.6 ppbv. The mean concentrations of NO and NO2 for the entire period of measurement were found to be 0.18 ± 0.37 ppbv (n = 794) and 1.31 ± 0.99 ppbv/(n = 769). H2O2, HNO3, and PAN showed diurnal variation with maxima in the afternoon and minima at night. Mean concentrations were found to be 0.52 ± 0.36 ppbv (n = 312), 0.67 ± 0.33 ppbv (n = 250), and 0.41 ± 0.24 ppbv (n = 578). The NOx/NOy ratio was used as an indicator of the chemical age of airmasses and the ratio showed strong positive correlations with the photochemical oxidants HNO3 (r = 0.76), PAN (r= 0.68), and O3 (r = 0.79) measured at the site. The relationship between the accumulation rate of O3 and the deviation from the photostationary state was examined based on the measured PSS constant obtained from the values of [O3], [NO], and [NO2] measured at the site.
Grafting Kinetics of End‐Functional Polymers at Melt Interfaces
Authors: Kramer Edward J. 
Published: November 2013

AbstractExpressions for the kinetics of grafting chains from a pure end‐functional polymer melt to a reactive interface are derived under the assumption that the free energy of reaction is very large and negative. Two cases are considered: a case where the grafting is controlled by diffusion of free end‐functional chains through the “brush” of previously grafted chains and a case where the grafting is controlled by the kinetics of the interface reaction itself. Both cases lead to the same form of the grafting kinetics, but with different characteristic times τD = Rga/D, where Rg is radius of gyration, a is the statistical segment length, and D is the diffusion coefficient of the end‐functional polymer; and τR = Rg/(akf[B]) where kf is a forward rate constant and [B] is the concentration of groups at the interface that react with the end‐function of the polymer chains. The grafting density Σ approaches a practical limit after long times for each value of the degree of polymerization N, and this limit decreases strongly with N. These predictions are compared with the results of recent experiments in which deuterated polystyrene chains with carboxylic acid end groups were grafted to either epoxy‐ or amine‐rich cross‐linked epoxy networks. The reaction‐controlled grafting model fits the data best and permits us to extract forward rate constants of ˜0.18 kg s−1 mol−1 for the epoxy‐rich networks and ˜5 × 10−3 kg s−1 mol−1 for the amine‐rich ones.
Irreversibility, Energy Dissipation, and Time Effects in Intermolecular and Surface Interactions
Authors: Israelachvili Jacob , Berman Alan 
Published: November 2013

AbstractThe use of thermodynamic functions such as surface energy (y) or the reversible work of adhesion (W) implicitly assumes that two surfaces are interacting under conditions of thermodynamic equilibrium. Likewise, the concept of the adhesion force or pressure between two surfaces, molecules, or colloidal particles also suggests the existence of well‐defined time‐independent values for these quantities. Yet most interactions involving molecules, surfaces, and complex fluid systems are irreversible, involving the transfer of energy from one system to another; that is, they involve “energy dissipation”. We review the molecular origins nonequilibrium (irreversible) interactions of surfaces that give rise to adhesion hysteresis, contact angle hysteresis, friction, and other thin‐film properties, and discuss the important role of “time” in such processes which can have a significant effect on what we measure. We also consider the possible central role of nonequilibrium interactions in biological systems, where nature often makes use of the finite time of molecular processes for regulating the interactions of proteins, membranes, and cells.
High‐Performance Liquid Chromatographic Analysis of an Ancient Tyrian Purple Dyeing Vat from Israel
Authors: Koren Zvi C. 
Published: November 2013

AbstractThe high‐performance liquid chromatographic technique is utilized to analyze the dye components of crude “Tyrian Purple” residues obtained from modern Murex (Trunculariopsis) trunculus sea snails and from an archaeological source. This is the first time that this technique has been used to analyze these raw pigments. Previously, chromatographic analyses of cloth stains and textile vat dyeings produced from contemporary snails were published. The modern purple pigment analyzed in this study was produced from excised hypobranchial glands of trunculus snails, and the archaeological purple residue investigated was found on the interior of a potsherd from Tel Kabri, Israel. The two pigments studied showed nearly identical chromatographic fingerprints: The pigments consisted of the same four indigoid components and with matching compositions. The dyes found were indigotin, monobromoindigotin, dibromoindigotin, and a fourth colorant that may be dibromoindirubin. The following conclusions can be made regarding the archaeological sample: (1) the ancient potsherd bearing the purple pigment was from an ancient dyeing vat; (2) the biological provenance of the archaeological dyestuff was most probably Murex trunculus mollusks; and (3) the Mediterranean snails used for the vat were likely collected at or near the Akhziv beach area in Israel. This study indicates that a biological and geographical chromatographic mapping of the dye components of porphyra snails can be developed to assist in provenance determinations of archaeological purple pigments.
Ultrafast Spectroscopy of Rhodopsins — Photochemistry at Its Best!
Authors: Kochendoerfer Gerd G. , Mathies Richard A. 
Published: November 2013

AbstractRecent advances in laser technology now allow us to study the ultrafast primary photochemical events in rhodopsin, bacteriorhodopsin, and halorhodopsin in real time. The results of various ultrafast studies of rhodopsins are reviewed with an emphasis on (1) the relationship between the reaction rate and reaction efficiency and its implications for the mechanism of isomerization, (2) the homogeneity of the reaction pathways, and (3) the role of the protein in the reaction dynamics. The results mandate the introduction of a new paradigm to describe these ultrafast reactions that specifically considers the importance of the timescale of vibrational dephasing and relaxation relative to the reactive motion and the contribution of vibrational coherence to the reaction mechanism.
Application of Raman Spectroscopy to Retinal Proteins
Authors: Althaus T. , Eisfeld W. , Lohrmann R. , Stockburger M. 
Published: November 2013

AbstractRaman spectroscopic studies on photoreactive retinal proteins are comprehensively described, including the basic physics of Raman scattering and illustrative examples of the types of information on the structure and function of the retinal chromophore and its environment which can be obtained from the vibrational Raman spectra. In addition, practical advice and recipes are given which should enable the reader to plan and eventually perform a Raman experiment in a photolabile retinal protein. A dominant role is played by the resonance Raman (RR) experiment with visible laser excitation which selectively probes the retinal chromophore. Much discussion is devoted to bacteriorhodopsin (bR) and its photocycle as a paradigm for a light‐induced reaction of a retinal protein. Various time‐resolved techniques are described to study the temporal evolution of the bR chromophore by probing RR spectra of intermediate states. Vibrational Raman spectra are interpreted in terms of structure and structural changes of the chromophore. RR spectroscopic studies on halorhodopsin, sensory rhodopsin, and visual pigments are reported, as well as on modified proteins in which retinal analogues are incorporated, and on site‐specific mutants. Results of ultraviolet RR experiments which selectively probe the aromatic side chains in the protein backbone are reported. In addition, a promising new technique of near‐infrared Raman excitation is discussed. Finally, application of coherent anti‐Stokes Raman spectroscopy (CARS) to retinal proteins is reported.
Spectral and Kinetic Characterization of Visual Pigment Photointermediates
Authors: Kliger David S. , Lewis James W. 
Published: November 2013

AbstractThe literature describing intermediates formed after photolysis of visual pigments is reviewed. Results obtained near physiological temperatures using time‐resolved optical density measurements in the UV/Vis region are emphasized. The general character of intermediates which appear in the course of protein function, and the role of methods with different time resolutions in their study, are discussed. Specific results for intermediates from bathorhodopsin to metarhodopsin II are treated in detail, with limited discussion of the earlier and later species. The discussion centers on the best‐understood pigment, bovine rhodopsin, but results for cone‐type and invertebrate pigments are also discussed. Comparison is made between the picture of the intermediates obtained using low‐temperature trapping methods and that obtained using kinetic measurements. The thermodynamic parameters of the intermediates are discussed, and their significance for the structure/function of heptahelical protein intermediates in general is considered.
Kinetics of Light‐Induced Intramolecular Charge Transfer and Proton Release in Bacteriorhodopsin
Authors: Moltke Stephan , Alexiev Ulrike , Heyn Maarten P. 
Published: November 2013

AbstractRecent advances in understanding the intramolecular charge transfer and proton release by the light‐driven proton pump bacteriorhodopsin (bR) are critically reviewed. The focus is on the time‐resolved electrical methods, i.e., photocurrent and photovoltage measurements, and on transient absorption experiments with pH‐sensitive dyes. Particular attention is paid to the following topics: charge translocation in the low‐pH forms of bR (acid‐blue and acid‐purple); electrogenicity of the 13‐cis cycle; results with bR mutants; surface‐bound dyes to detect the proton release at specific sites on either side of the protein; the question of kinetic coupling between the deprotonation of the Schiff base and proton release; and rapid long‐range migration of protons along the surface of the purple membrane.
Photoreactions of the Photointermediates of Bacteriorhodopsin
Authors: Balashov Sergei P. 
Published: November 2013

AbstractThe photochemical reactions of the intermediates of the photochemical cycle of bacteriorhodopsin (bR) are reviewed. These reactions constitute photochemical control of the cycle and provide an independent approach for the investigation of the mechanism of light energy transduction in the purple membrane. The absorption of a light quantum by the K, L, or M intermediates converts them back to bR. These transformations interrupt the photocycle so that no proton transfer occurs after absorption of the second quantum. The action of blue light on the M intermediate causes structural changes of the chromophore, as a result of which the Schiff base is reprotonated from Asp‐85, not from Asp‐96 as in the usual thermal transition of M. The photoreactions of the L, M, N, and O intermediates lead to the formation of new photoproducts. Studies of the photoconversion of the intermediates can serve as an additional source of information on the nature of photoprocesses in bR: they reveal several conformers of K and bR at 90 K, different M states, two N intermediates, and provide direct evidence for the existence of a thermal back reaction from N to M. The study of the photoreactions of the J, K, L, M, N, and O intermediates is a promising method for elucidating the structures and roles of these states. Reversible photoconversions of bR and its photointermediates provide a basis for potential applications of bR in optical registration of information.
Acid‐Base Equilibria and the Proton Pump in Bacteriorhodopsin
Authors: Honig B. , Ottolenghi M. , Sheves M. 
Published: November 2013

AbstractThe light‐induced proton pump in bacteriorhodopsin is reviewed with emphasis on acid‐base equilibria of protein residues and of the retinal Schiff base moiety. Pump mechanisms in bR and in some of its mutants are classified in terms of light‐induced pKa changes (class I) or light‐induced exposure changes, in which the proton accessibility of the protein changes from the outside to the inside of the membrane (class II). A discussion of the theoretical basis of the factors which determine the pKa of ionizable protein groups is followed by a review of the experimental phenomena associated with the titration of residues in both unphotolyzed bR and during its photocycle. The time‐resolved titrations of the Schiff base and of the Asp‐85 residue are discussed in terms of the accessibility of the two groups to external protons. Finally, the molecular aspects of the pH‐dependent proton pump in native bR and in various mutants are analyzed, focusing on the mechanism of the initial proton release reaction and on the subsequent molecular switch which allows reprotonation from the inside of the cell. Special attention is devoted to the question of coupling between the photocycle intermediates (primary M formation and decay) and the transmembrane proton translocation. Recent work with bR mutants raise the question as to whether proton transfer from the Schiff base to Asp‐85 at the M stage is directly responsible for proton translocation, as well as for the reprotonation switch.
Near‐Field Optical Microscopy in Jerusalem
Authors: Lewis Aaron , Lieberman Klony , Ben‐Ami Nily Kuck , Fish Galina , Khachatryan Edward , Strinkovski Alina , Shalom Shmuel , Druckmann Shula , Ottolenghi Michael , Ben‐Ami Udi 
Published: November 2013

AbstractDuring the past decade the area of near‐field optics has seen an exponential growth. This is a result of the resolution of the technical problems that had prevented the potential of this powerful optical methodology from being generally applied. As a result of committed and steady progress in resolving these technical problems the fundamental principles of near‐field optics are now generally accepted and the technology is widely used. The potential of these advances has important implications in a variety of areas, from chemistry to information storage to the characterization of structures with potential in fundamental mesoscopic physics, and in the characterization of practical devices in electronics and photonics which are rapidly reaching nanometer dimensionalities. In this paper, the progress that has been made in Jerusalem in developing a near‐field microscope fully integrated with conventional far‐field, confocal far‐field, and all forms of force and other scanned probe microscopies will be described. The potential of this unique imaging system in chemical applications is also discussed.
Approaches to Antibody‐Catalyzed Cationic Cyclizations: Chemical Studies of Leaving Groups and Cyclization Modes
Authors: Lawrence Christopher , Bell Ian M. , Abell Chris , Leeper Finian J. 
Published: November 2013

AbstractThe solvolysis of a range of esters of 2‐methylbenzyl alcohol 10 has been studied. It was found that sulphonate esters are solvolyzed very rapidly in aqueous solution (t1/2 ≈ 35 s), whereas sulphinates react slowly (t1/2 ≈ 35 h) and a phosphonate diester is stable. The fluorescent 5‐dimethylaminonaphthalene‐1‐sulphinate (dansinate) esters (e.g. 22) held the most promise as substrates for antibody‐catalyzed cationic cyclizations. It was shown by 18O‐labeling studies that ester 13 is hydrolyzed predominantly (but not exclusively) by SN1 reaction at the benzylic position.A number of conditions were tried to effect cationic cyclizations of an unsaturated benzylic alcohol 26, whose ester is intended as the substrate for the antibody‐catalyzed reaction. The products obtained were the result of attack of the non‐benzylic alcohol on either the benzylic cation, to give 31 and 32, or on the protonated alkene, to give 29. No cyclization of the alkene onto the benzylic cation, to give 4, was observed, suggesting that this is a disfavored reaction in solution.
Isomerization and Decomposition of Chloromethylacetylene
Authors: Kumaran Soundararajan S. , Lim Kee P. , Michael Joe V. , Tilson Jeffrey L. , Suslensky Aya , Lifshitz Assa 
Published: November 2013

AbstractThe isomerization and thermal decomposition of chloromethylacetylene (CMA) has been studied with two shock tube techniques. The first experiment (Jerusalem) utilizes single‐pulse shock tube methods to measure the isomerization rate of CMA to chloroallene. In addition, equilibrium constants can be estimated at ∼1200 K. The second experiment (Argonne) monitors Cl‐atom formation at temperatures above ∼1150 K. Absolute yield measurements have been performed over the 1200–1700 K range and indicate that two decomposition channels contribute to CMA destruction, namely, Cl fission and HCl elimination. The results show that the branching fraction between processes is temperature dependent. Therefore, direct Cl‐atom fission is accompanied by molecular elimination, undoubtedly giving HCl and one or more isomers of C3H2.MP2 6–31G(d,p) ab initio electronic structure calculations have been used to determine vibration frequencies and moments of inertia for three C3H3Cl isomers. Using these quantities, the experimental equilibrium constants required that ΔH00(CH2Cl–C≡CH ⇌ CHCl=C=CH2) = −;0.24 kcal mole−1. A potential energy surface pertinent to the present system has been constructed, and RRKM calculations have been carried out in order to explain the isomerization rates. The isomerization data can be explained with E0 = 52.3 kcal mole−1 and 〈ΔEdown〉 = 225 cm−1. Subsequent semi‐empirical Troe and RRKM‐Gorin modeling of the Cl atom rate data require E0 = (67.5 ± 0.5) kcal mole−1 with a 〈ΔEdown〉 = (365 ± 90) cm−1. This suggests a heat of formation for propargyl radicals of (79.0 ± 2.5) kcal mole−1.
Stereochemistry of the Thermal Conversion of 1‐Vinyl‐2,3‐cis‐dideuteriocyclobutane to Butadiene and 1,2‐Dideuterioethylenes
Authors: Lewis David K. , Hutchinson Avery , Lever Steven J. , Spaulding Eric L. , Bonacorsi Samuel J. , Baldwin John E. 
Published: November 2013

AbstractThis study has examined the stereochemistry of the decomposition at 900–1000 K in a single‐pulse shock tube of 1‐vinyl‐2,3‐cis‐dideuteriocyclobutane to ethylenes and buta‐1,3‐dienes. The deuterated ethylenes formed during the decomposition, CHDCH2, (E)‐CHDCHD, and (Z)‐CHDCHD, were quantified via two independent techniques, FTIR and IR absorption spectroscopy using a tunable diode laser spectrometer. The results of both analyses indicated that equal amounts of (E)‐CHDCHD and (Z)‐CHDCHD were formed from the cis‐labeled reactant. In an earlier shock tube study of the decomposition at 1000–1200 K of two deuterium‐labeled cyclohexenes to ethylenes plus buta‐1,3‐dienes, a pathway via a vinylcyclobutane intermediate was implicated in a significant fraction of the decomposition events; the measured ratios of (E)‐CHDCHD to (Z)‐CHDCHD in that study were consistent with a complex mechanistic model in which the stereochemistry of deuterium labels in the cyclohexene reactant was lost in ethylene products formed via vinylcyclobutane. The present results provide additional support for that model.
Silicon Particle Formation in Pyrolysis of Silane and Disilane
Authors: Frenklach Michael , Ting Larry , Wang Hai , Rabinowitz Martin J. 
Published: November 2013

AbstractSilane and disilane diluted in argon and hydrogen mixtures were pyrolyzed behind incident shock waves at temperatures ranging from 900 to 2000 K, pressures from 0.2 to 0.7 atm, and total concentration from 3 × 1016 to 1 × 1017 silicon atoms per cm3. Formation of silicon particles was monitored by the attenuation of laser beams of two different wavelengths, thereby determining particle size, number density, and fractional yield. The conversion of silane and disilane into silicon particles exhibited a pronounced maximum at about 1150 K, which was found to be affected by reaction pressure, initial reactant concentration, and addition of hydrogen. Selected silicon particle samples were examined by electron diffraction, transmission electron microscopy, and secondary ion mass spectrometry. The results indicated that the produced particles were spherical, ranging from 100 to 400 Å in diameter, loosely agglomerated, and contained about 15% hydrogen on an atomic basis. A detailed chemical kinetic model was developed that describes gas‐phase pyrolysis of the parent molecule and homogeneous nucleation of silicon particles by 117 elementary reactions of 42 chemical species, and coagulation of the forming particles and their growth by gas‐surface deposition reactions with a method of moments. The model predictions were found to be extremely sensitive to the values of optical constants assigned to the silicon particle material.
Reactions of Azides with Electrophiles: New Methods for the Generation of Cationic 2‐Azabutadienes. Synthesis of 1,2, 3,4‐Tetrahydroquinolines and 1,2‐Dihydroquinolines via a Hetero Diels–Alder Reaction
Authors: Pearson William H. , Fang Wen‐Kui 
Published: November 2013

AbstractTwo methods for the generation of iminium ions of the type ArN+(X)=CHR (X = H or alkyl, R = H or alkyl) are reported: (1) the Bronsted‐acid‐promoted rearrangement of benzylic azides and (2) the intermolecular Schmidt reactions of azides XN3 (X = aliphatic) with benzylic carbocations derived from benzylic alcohols ArCH(R)OH. The iminium ions ArN+(X)=CHR behave as cationic 2‐azabutadienes in the presence of alkenes and alkynes, producing 1,2, 3,4‐tetrahydroquinolines and 1,2‐dihydroquinolines by a hetero Diels–Alder reaction.
Desymmetrization of Prochiral Diesters Via Transition Metal Catalyzed Reactions
Authors: Trost Barry M. 
Published: November 2013

AbstractThe development of asymmetric induction in palladium catalyzed allylic alkylation has led to the notion of creating a chiral pocket. Two platforms for ligand design that may generate such “chiral space” evolve from derivatizing chiral diols or diamines with 2‐diphenylphosphinobenzoic acid or chiral diacids with 2‐diphenylphosphinoaniline. Palladium complexes derived from such ligands effect excellent enantiodiscrimination in the desymmetrization of esters of meso‐cycloalk‐2‐en‐1,4‐diols and gem dicarboxylates of α,β‐unsaturated aldehydes. These methods prove useful for asymmetric syntheses of carbanucleosides, nucleosides, and the antitumor alkaloid (+)‐pancratistatin.