bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mineral Assemblages in Kebara and Hayonim Caves, Israel: Excavation Strategies, Bone Preservation, and Wood Ash Remnants
Authors: Weiner Stephen , Schiegl Solveig , Goldberg Paul , Bar‐Yosef Ofer 
Published: November 2013

AbstractThe mineral assemblages in prehistoric sites can provide essential information on several important topics in archaeology. One of the key analytical tools used is Fourier‐transform infrared spectrometry, which is operated both on‐site during the excavation and in the laboratory. Three topics are reviewed here based on studies of Hayonim and Kebara caves in Israel. (1) Reaction rims form on calcitic and dolomitic rocks buried in the sediments. They are normally the result of interaction of the rock minerals with phosphate‐rich groundwater. The mineralogical nature of these reaction rims can be indicative of prevailing chemical conditions in the sediments, which in turn provide information on whether or not bones are preserved at the site, or are preserved at specific locales within the site. Thus, a survey of reaction rims can be helpful in determining the potential of a future excavation site, or areas within a site, and for optimizing excavation strategies during an ongoing project. (2) The preservational states of the bones themselves, together with information on the mineralogical nature of some of the more labile sediment components, can be used for ascertaining whether or not the bone distribution patterns as excavated represent the original burial locations, or have been affected by secondary dissolution of bones in some areas and not others. (3) The ashes from wood fires are a major component of the sediments in both caves studied. Understanding and monitoring the complex series of diagenetic changes that ashes undergo in these environments can provide invaluable information, not only on the manner in which fire was used by the cave occupants, but also on a series of important processes that affect the depositional history of the site itself. The study of mineral assemblages in prehistoric cave sites, as illustrated here with 3 examples, and possibly in open‐air sites as well, has the potential for contributing significantly to a better understanding of many archaeological problems.
A Multi‐Disciplinary Contribution to the Provenance Determination of Ancient Greek and Roman Marble Artifacts
Authors: Moens Luc , De Paepe Paul , Waelkens Marc 
Published: November 2013

AbstractThe problem of determining the provenance of the white marble used for antique artifacts has been tackled in different ways. During the past decade it became clear that a multimethod approach is required to solve the problem. In addition, reliable reference material, i.e., samples collected at the ancient quarry sites in an archaeologically and geologically justified manner, turned out to be a prerequisite for reliable provenance determination. A multimethod approach based on petrography, stable isotope analysis of O and C, and trace element analysis yields complementary information. These methods were applied to the same set of 225 quarry samples. When processed with powerful statistical methods, the data thus obtained allowed all major types of marble used in antiquity to be distinguished. Thus, most problems concerning the provenance of artifacts can be solved. This approach was successfully applied to the provenance determination of about 75 artifacts from different museums in Europe and the USA.
Sequences and Structures of Retinal Proteins
Authors: Tang Li , Ebrey Thomas G. , Subramaniam Shankar 
Published: November 2013

AbstractThe past few years have been an exciting period in the field of the structure of retinal proteins, especially the visual pigments. A significant achievement is the 9 Å projection map of bovine rhodopsin. This not only provides knowledge of the three‐dimensional structure of visual pigments, but also establishes a more reliable basis for the structural modeling of all the G‐protein‐coupled receptors. The modeling of such three‐dimensional structures will eventually lead to a better understanding of the function of visual pigments and other G‐protein‐coupled receptors. Our goal in this article is to draw attention to recent developments in the structure of retinal proteins, with special emphasis on visual pigments. By combining a wide range of existing experimental data with the results of theoretical calculations, a new three‐dimensional structure of visual pigments, which differs from the models which have so far been reported, is proposed.
Application of FTIR Spectroscopy to the Investigation of Dark Structures and Photoreactions of Visual Pigments
Authors: Siebert Friedrich 
Published: November 2013

AbstractExperiments are reviewed in which the photoreactions of the visual pigments rhodopsin and octopus rhodopsin have been investigated by FTIR spectroscopy. It is shown that from the spectra important characteristic structural elements can be derived for the dark state as well as for the intermediates. Since the spectra contain contributions from the chromophore as well as from the protein, methods are described which allow one to discriminate between them. In the case of rhodopsin, the influence of single amino acids on spectra and function is assessed by investigations of specific mutants. The role of the chromophore‐protein interaction for the photoreaction and the activation mechanism is addressed by studies of modified rhodopsins containing retinal analogues as chromophores. Characteristics of the active state, which is capable of transducin activation, are especially emphasized.
Structure and Function of Retinochrome
Authors: Tokunaga Fumio , Yoshihara Kazuo 
Published: November 2013

AbstractRetinochrome is a photo‐isomerase of all‐trans‐retinal to the 11‐cis‐isomer for rhodopsin synthesis. This protein is probably folded into seven α‐helices spanning the membranes. Upon irradiation, it is converted to metaretinochrome, via pre‐lumi‐ and lumiretinochrome, which are stable under 50 and 250 K, respectively. A series of analogue studies revealed that the cyclohexene ring and 6‐s‐cis‐twisted conformation are important for binding. Modification of the 14‐position suggests close location of the 14‐H to the counterion.
Microbial Sensory Rhodopsins: Photochemistry and Function
Authors: Spudich John L. , Zacks David N. , Bogomolni Roberto A. 
Published: November 2013

AbstractThe review covers recent progress on microbial sensory rhodopsins, visual pigment‐like retinylidene photoreceptors that function in phototaxis by archaeons, such as Halobacterium salinarium, and by unicellular eukaryotic algae, such as Chlamydomonas reinhardtii. Six demonstrably different sensory rhodopsins are known in halophilic archaea. The best characterized is sensory rhodopsin I (SR‐I), a color‐sensitive receptor that relays attractant and repellent photosignals to a tightly bound transducer protein HtrI (halobacterial transducer for sensory rhodopsin I). New advances in the mechanism of signal transduction by the SR‐I/HtrI complex from molecular‐biological and biophysical approaches are summarized. Effects of HtrI on light‐induced proton transfers in the receptor are discussed for their possible role in signaling. Current knowledge concerning the growing family of related archaeal sensory rhodopsins is presented.The evidence for a sensory rhodopsin in phototaxis by C. reinhardtii and other unicellular eukaryotic algae is reviewed. The molecular information is more limited than for the archaeal organisms, but the physiological information is rich and complex. Compelling data exist for a single retinal‐containing receptor mediating both phototaxis and photophobic responses in C. reinhardtii. From retinal analog studies, the isomeric configuration and ring/chain conformation of the retinal in the receptor appear to be identical to those of the archaeal sensory rhodopsins. Also, photoisomerization from all‐trans‐ to 13‐cis‐retinal appears to be the trigger for signaling, as in the archaeal pigments. Conflicting early studies suggesting an 11‐cis‐retinal chromophore and signaling without photoisomerization are analyzed and possible explanations for those reports are suggested.As a general conclusion, the microbial sensory rhodopsins provide an opportunity to explore photochemistry and protein/protein interaction in photosensory transduction in genetically tractable organisms.
Ultrahigh Vacuum Scanning Tunneling Microscope‐Based Nanolithography and Selective Chemistry on Silicon Surfaces
Authors: Lyding J.W. , Shen T.‐C. , Abeln G.C. , Wang C. , Scott P.A. , Tucker J.R. , Avouris PH. , Walkup R.E. 
Published: November 2013

AbstractNanofabrication on silicon surfaces has been achieved in a manner similar to e‐beam/resist technology, in which hydrogen serves as a monolayer resist for exposure by the electron beam from an ultrahigh vacuum (UHV) scanning tunneling microscope (STM). In this scheme, hydrogen is selectively desorbed from Si(100)2×1:H surfaces that have been prepared by atomic hydrogen dosing under UHV background conditions. To remove hydrogen, the tip bias is raised, under feedback control, and then the desired pattern is drawn. Two regimes of hydrogen desorption are observed: at higher energies, above ∼6.0 V, direct electron‐stimulated desorption occurs, whereas at lower biases, desorption occurs via a multiple excitation vibrational heating mechanism and exhibits a strong current dependence. Patterning linewidth down to a single dimer row has been achieved in the vibrational heating regime. The selective removal of hydrogen suggests many possibilities for subsequent chemical treatments in which the hydrogen‐terminated silicon remains inert. We have performed experiments which demonstrate selective oxidation of, and nitrogen incorporation into, the STM‐patterned regions.
Solid‐Phase Epitaxy of Thin Silicon Film on Si(111) Surface Studied by Scanning Tunneling Microscopy
Authors: Ter‐Ovanesyan Evgeny , Manassen Yishay , Shachal Dov 
Published: November 2013

AbstractSolid‐phase epitaxy (SPE) of thin silicon film with a thickness of 0.2–2 bilayers (BL) on Si(111)‐(7 × 7) surface was studied by scanning tunneling microscopy. At small coverage, the SPE growth proceeds via coarsening of islands. As the coverage exceeds the percolation threshold, a ‘mirror’ process consisting of coarsening of voids in the continuous layer takes place. The SPE growth of a thicker continuous layer results in a partly disordered flat surface, displaying a mixture of different reconstructions. Quantitative characterization of this surface by the formalism of pair distribution functions reveals an anisotropy in the orientational order that may indicate that SPE occurs preferably in the step direction. A possibility to use an SPE‐grown layer as a two‐dimensional model for bulk processes in solids is discussed.
Imaging Molecules with the Scanning Tunneling Microscope: A Theoretical Interpretation of Benzene on Platinum
Authors: Sautet P. , Bocquet M.‐L. 
Published: November 2013

AbstractThe images of benzene on Pt(111), as obtained by the scanning tunneling microscope, have been calculated theoretically. The simulations show that the shape of the molecule pattern in the image is strongly dependent on the chemisorption site on the surface, in agreement with the experimental data. For a given site, the variations of the images with the geometric parameters of the adsorption are discussed. The internal structure of the pattern is enhanced when the molecule is more distorted or adsorbed closer to the surface. By a decomposition of the calculated image on different subsets of molecular orbitals, the shape of the hollow site image is analyzed in detail. It is shown that is is not possible to restrict the calculation to the π orbitals of benzene and that the s orbitals built from the 2s atomic orbitals of carbon play an important role.
Microelectrochemistry on Surfaces with the Scanning Electrochemical Microscope (SECM)
Authors: Mandler Daniel , Meltzer Sheffer , Shohat Ilan 
Published: November 2013

AbstractThe scanning electrochemical microscope (SECM) is one of the scanning probe techniques that have been developed following the introduction of the scanning tunneling microscope. The approaches that have been used to modify surfaces with lateral resolution using the SECM are presented and discussed. These approaches made it possible to drive a variety of microelectrochemical reactions on surfaces, as well as to study the mechanism of these processes due to the unique advantages that the SECM offers.
Evolution of Catalytic Activity throughout a Polyclonal Immune Response Elicited by a Transition‐State‐Analog Hapten
Authors: Shreder Kevin , Thomas Richard , Wallace Michael , Helms Eric , Iverson Brent 
Published: November 2013

AbstractWe have carried out a comprehensive study that analyzes the evolution of catalytic activity in the polyclonal antibodies elicited by a phosphate hapten over the course of an immunization regimen. We have found that catalytic activity elicited by the phosphate hapten 1, measured as apparent kcat for the hapten‐specific fraction of polyclonal antibodies, increased through the first four or five immunizations, then decreased to differing extents in both of the rabbits studied. The initial increase in catalytic activity was correlated with increasing hapten affinity, but then hapten affinity remained high while catalytic activity decreased later in the response. These results indicate that consideration must be given to the temporal aspects of the catalytic immune response before any global conclusions are reached, e.g., a simple correlation of catalytic activity with hapten affinity. In addition, it is clear that the number of immunizations is an important parameter that must be considered when attempting to optimize antibody catalytic activity, and that more immunizations are not necessarily better.
Thermal Isomerization of Azulene. Single‐Pulse Shock Tube Investigation
Authors: Laskin Alexander , Lifshitz Assa 
Published: November 2013

AbstractThe thermal isomerization of azulene was studied behind reflected shocks in a pressurized driver single‐pulse shock tube. The temperature range covered was 1050–1400 K at overall densities of ∼2.5 × 10−5 mol/cm3. The main reaction of azulene under these conditions is a unimolecular isomerization to naphthalene, but it also isomerizes, although at a much lower rate, to another isomer. The suggested “tetracyclic triene” intermediate structure for the azulene‐naphthalene isomerization can lead also to transition states that can describe isomerizations to 1‐methylene‐1H‐indene and 1, 2,3‐metheno‐1H‐indene,2,3‐dihydro. Small quantities of C2H2, C4H2, C6H6, and C6H5‐C≡CH were also found in the post‐shock samples, particularly at high temperatures. The Arrhenius parameters of the two high pressure limit rate constants for the isomerization processes are:azulene → naphthalene, k1 = 1012.93 exp(–62.8 × 103/RT) s−1azulene → second isomer, k2 = 1012.42 exp(–69.5 × 103/RT) s−1A discussion of the mechanism for these isomerization processes is presented.
Hydrogen Atom Attack on Fluorotoluenes: Rates of Fluorine Displacement
Authors: Manion Jeffrey A. , Tsang Wing 
Published: November 2013

AbstractRates of hydrogen atom attack on o‐fluorotoluene (o‐FTOL) and m‐fluorotoluene (m‐FTOL) at temperatures of 988–1144 K and pressures of 2–2.5 bar have been determined in a single‐pulse shock tube study. Hydrogen atoms, generated from the decomposition of hexamethylethane, were allowed to react with the substrates and the characteristic products observed. Rate constants for two reaction channels, displacement of fluorine or methyl, were determined relative to displacement of methyl from 1, 3,5‐trimethylbenzene (135TMB). Evidence is presented that abstraction of F is unimportant over the studied temperature range. With k(H + 135TMB → m‐xylene + CH3) = 6.7 × 1013 exp(–3255/T) cm3 mol−1s−1, the following rate expressions have been derived:k(H + o‐FTOL → C6H5CH3 + F) = 8.38 × 1013 exp(–6041/T) cm3 mol−1s−1; (1012–1142 K)k(H + o‐FTOL → C6H5F + CH3) = 2.37 × 1013 exp(–2938/T) cm3 mol−1s−1; (988–1142 K)k(H + m‐FTOL → C6H5CH3 + F) = 1.33 × 1014 exp(–6810/T) cm3 mol−1s−1; (1046–1144 K)k(H + m‐FTOL → C6H5F + CH3) = 2.04 × 1013 exp(–3104/T) cm3 mol−1s−1; (1008–1144 K)Uncertainties in the relative rate constants are estimated to be factors of about 1.1, while the above absolute values have estimated expanded uncertainties of about a factor of 1.4 in rate, 10 kJ mol−1 in the activation energy, and a factor of 3 in the A‐factor. The present data are compared with relevant literature data. From our data and the thermochemistry, a model of the elementary steps comprising displacement of F is developed. On the basis of the model fit to our data, rate constants for the addition of atomic fluorine to toluene at 1100 K are derived. Rate expressions for fluorination reactions of toluene are also determined. The significance of the present results is discussed in the context of the formation of fluorinated byproducts in high‐temperature systems.
Experimental and Modeling Study of the High‐Temperature Ignition of Methane and Methane Mixtures with Ethane and Propane
Authors: Yang Huixing , Qin Zhiwei , Lissianski Vitaly V. , Gardiner William C. 
Published: November 2013

AbstractAn important part of deepening our understanding of the reaction mechanism of natural gas oxidation is validating a detailed model against experimental flame and ignition data. Ignition delays in shock‐heated CH4–O2 mixtures, with and without ignition‐promoting additives, account for most of the available validation data. Most, but not all, ignition delays in such mixtures reported in the literature have been found to agree with calculations done using the GRI‐Mech 1.2 model. Additional reflected shock wave ignition experiments were done to explore possible reasons for the mismatches and to study the promotion of CH4 ignition by small amounts of C2H6 and C3H8 additives. Empirical correlations were derived that describe ignition delays in CH4–O2–C2H6 (C3H8).
Polymer‐Bound Chiroptical Molecular Switches; Photochemical Modification of the Chirality of Thin Films
Authors: Oosterling Michiel L.C.M. , Schoevaars Anne Marie , Haitjema Henk J. , Feringa Ben L. 
Published: November 2013

AbstractPhotobistable chiral polymers were obtained by covalent attachment of inherently dissymmetric 2‐hydroxy‐9‐(7′methyl‐1′,2′,3′,4′‐tetrahydrophenanthrene‐4′‐ylidene)‐9H‐thioxanthene to methacrylate copolymers with appropriate spacers. Upon irradiation at 300 nm the optical activity of thin films of these polymers could be altered.
Functionalized Self‐Assembled Monolayers Containing Preformed Binding Sites
Authors: Kaifer Angel E. 
Published: November 2013

AbstractThis is a review of recent work on the design, preparation, and characterization of thiolate‐on‐gold self‐assembled monolayers containing preformed binding sites. The use of these monolayer systems as molecular sensors in the vapor and solution phases is considered. General analytical properties of these systems are also covered. Recent reports by several groups are discussed, with particular emphasis on the author's own research work in the area.
An Approach to the Synthesis of the Manzamine Alkaloids Via the Vinylogous Amide PHotocycloAddition/Retro‐Mannich Fragmentation/Mannich Closure Cascade (pharM)
Authors: Winkler Jeffrey D. , Stelmach John E. , Siegel Miles G. , Haddad Nizar , Axten Jeffrey , Dailey William P. 
Published: November 2013

AbstractThe application of the vinylogous amide [2+2] photocycloaddition/retro‐Mannich fragmentation/Mannich closure cascade (pharM) to the synthesis of the pentacyclic ring system of the anti‐leukemic marine alkaloid manzamine A is presented. Two approaches to the synthesis of the requisite pentacycle are described: (a) the transannular photocycloaddition of an 18‐membered vinylogous amide; and (b) photocycloaddition of an acyclic vinylogous amide, followed by macrolactamization of the derived pharM closure product to generate the pentacyclic ring system.
Applications of Free Radicals in Organic Synthesis
Authors: Boger Dale L. 
Published: November 2013

AbstractA summary of studies on the generation of acyl radicals and their subsequent use in intermolecular, intramolecular, macrocyclization, and tandem alkene addition reactions is provided. Similarly, the use of intramolecular free radical cyclization reactions in the total synthesis of (+)‐CC‐1065 and a series of structurally related analogs is summarized.
Magnetic Analysis of Supersonic Beams of Atomic Oxygen, Nitrogen, and Chlorine Generated from a Radio‐Frequency Discharge
Authors: Alagia Michele , Aquilanti Vincenzo , Ascenzi Daniela , Balucani Nadia , Cappelletti David , Cartechini Laura , Casavecchia Piergiorgio , Pirani Fernando , Sanchini Giampaolo , Volpi Gian G. 
Published: November 2013

AbstractSupersonic beams of oxygen, nitrogen, and chlorine atoms and of metastable oxygen and nitrogen molecules produced from a high‐pressure radio‐frequency discharge beam source have been characterized by coupling velocity selection with magnetic analysis in the transmission mode. The present work leads to the determination of the relative populations of the electronic states of the species in the produced beams, showing that estimates of the populations from plasma temperatures or final translational temperatures could bring on incorrect conclusions.
Three Dimensional Wavepacket Simulation on the H Atom Scattering for the Full Reaction of CF3H + Ar (3P) → CF3* + H + Ar
Authors: Takahashi Hideaki , Kasai Toshio , Yamaguchi Kizashi , Loesch Hansjuergen H. 
Published: November 2013

AbstractThree dimensional (3D) wavepacket simulation on the H atom scattering is carried out for a full reaction of CF3H + Ar(3P) → CF3* + H + Ar for the H‐end orientation since our previous study on the 2D wavepacket simulation showed a quantum interference effect only for collisions at the H‐end of CF3H. We treat the present 3D wavepacket simulation in a time‐dependent SCF (TDSCF) scheme, which enables us to reduce 3D to a coupled two and one dimensional (2D+1D) problem. The initial wavepacket of CF3H is prepared in the lowest rotational state, i.e., |JKM > = |111>. The calculated snapshots of the scattered wavepacket for the Fiend orientation show a clear quantum interference effect again in the angular distribution of the product H atom due to the so‐called one‐atom cage effect on the heavy‐light‐heavy collision configuration. Thus the present simulation suggests that a continuous wave character of the wavepacket would be responsible for such a relatively clear interference effect in the full reaction, unlike a blurred interference effect with a pulse‐type of wavepacket excitation in the half reaction.
High Resolution Electronic Spectroscopy of Molecular Conformers. Methyl‐3‐methoxybenzoic Acid Ester
Authors: Ribblett Jason W. , Sinclair Wayne E. , Pratt David W. 
Published: November 2013

AbstractBy combining the techniques of rotationally resolved fluorescence excitation spectroscopy in molecular beams and ab initio quantum mechanics, we have determined the identity of the four conformers that contribute to the S1←S0 electronic spectrum of methyl‐3‐methoxybenzoic acid ester in the gas phase. Each conformer exhibits a unique spectrum. Each conformer also exhibits a differently oriented electronic transition moment (TM) in the molecular frame, for which the distinguishable inertial and electronic contributions also have been determined. The results suggest that the S1←S0 TM vectors of all conformers are rotated by relatively large (counterclockwise) angles with respect to the a inertial axes, placing them close to the b axis of a —OCH3 substituted benzene, and that the exact values of these angles depend upon the mutual conformations of both attached groups with respect to each other.