bluuebunny/crossref_metadata_2025 huggingface dataset:
Stable Isotopes of Carbon and Oxygen as a Possible New Tool for Estimating Firing Temperatures of Ancient Pottery
Authors: Nissenbaum Arie , Killebrew Ann
Published: November 2013

The ratios of the stable isotopes of carbon (13C/12C) and oxygen (18O/16O) in calcite in clays that contain carbonate and that were fired at temperatures between 500 and 700 °C displayed a good correlation with the firing temperature for both isotopes. The isotopic composition indicated that the original carbonate was either completely decomposed or that it exchanged with environmental CO2 to obliterate the original isotopic signature. The isotopic effects seem to be kinetically controlled. The isotope thermometer is used to compare refiring temperatures of pottery which was fired under controlled conditions. The differences between calculated and actual temperatures did not exceed 132 °C and in most cases was about 50 °C or less. Isotopic analysis of pottery from Tel Miqne‐Ekron and Deir el Balah, dated to the 13th–12th centuries BC, gave an average ancient firing temperature of about 600 °C. If shown to be of general validity, then perhaps this technique can be used also for estimating preparation temperatures of ancient mortar, especially when preserved in dry climates where later changes would be minimized.
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

The 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

The 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

The 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

Experiments 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

Retinochrome 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

The 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

Nanofabrication 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

Solid‐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

The 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

The 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

We 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

The 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−1

azulene → second isomer, k2 = 1012.42 exp(–69.5 × 103/RT) s−1

A 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

Rates 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

An 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

Photobistable 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

This 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

The 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

A 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.
Hydroxyl Replacement in Calix[n]arenes
Authors: Biali Silvio E.
Published: November 2013

The synthetic methods by which the hydroxyl groups of calix[n]arenes have been formally dehydrated to afford xanthene derivatives, or have been replaced totally or partially by hydrogen, amino, halogen, alkyl, or mercapto groups are reviewed.
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

Supersonic 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

Three 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

By 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.
Surface Scattering of Hyperthermal (10–50 eV) C60 Molecules: Kinetic Energy Transfer, Vibrational Excitation, and Initial Vibrational Energy Effects
Authors: Bekkerman Anatoly , Tsipinyuk Boris , Budrevich Andrei , Kolodney Eli
Published: November 2013

Scattering of neutral C60 molecules from surfaces at hyperthermal impact energies of 10–50 eV was studied as a function of impact energy, scattering angle, surface temperature, and incident vibrational energy. Scattered kinetic energy scaled linearly with impact energy, and kinetic energy losses varied with scattering angle from ∼85% to ∼40% (peak values). Analyzing the results, we found nearly complete decoupling between normal and tangential energy losses. Tangential losses are described in terms of various models of rotational excitation and it is concluded that translational slip is involved during the scattering process. The C60 surface interaction well‐depth was determined from the scattering results and compared with the measured desorption energy. Using a newly developed vibrational thermometry method for C60 we measured kinetic energy losses and collisional vibrational excitation as a function of the average vibrational energy of the incident C60 ( = 7–15 eV). Kinetic energy loss was independent of initial vibrational energy for both near‐grazing and near‐normal scattering angles, while collisional vibrational excitation showed a weak inverse dependence on initial vibrational energy for both scattering angles. For the lowest incident C60 vibrational energy ( = 9.8 eV) and near‐normal scattering (30.7 eV in the normal impact energy component), vibrational excitation was 5% of the impact kinetic energy. Our detailed results describe the first real “bouncing” regime for C60 scattering off surfaces.
Lasers and Molecular Beams Applied to the Study of Clusters of Chiral Molecules
Authors: Giardini‐Guidoni Anna , Piccirillo Susanna
Published: November 2013

Resonance‐enhanced two‐photon ionization time‐of‐flight spectroscopy has been applied in a supersonic beam to study R‐(+)‐1‐phenyl‐1‐propanol (PR) and its diastereomeric clusters with R(–) and S(+) 2‐butanol (BR; BS) and with R(–) and S(+) 2‐butylamine (AR, AS). This mass resolved spectroscopy allowed us to assign a few vibronic frequencies of PR and measure the spectral shift of the diastereomeric clusters PRBR, PRBS, PRAR, and PRAS. The different bathocromic shifts observed in the two pairs indicates the possibility for spectroscopically differentiating the aggregates. Moreover, very reproducible differences in the fragmentation patterns provide an additional tool for their discrimination.
Intramolecular Electronic Energy Transfer in the Naphthalene—Anthracene Bichromophoric Molecular Complex in a Supersonic Jet Expansion
Authors: Rosenblum Gershon , Karni Yoram , Speiser Shammai
Published: November 2013

Intramolecular electronic energy transfer (intra‐EET) was investigated in an isolated bichromophoric naphthalene (N) and anthracene (A) 1:1 molecular cluster. Investigation of the spectroscopic properties of these chromophores, separately and loosely bound in a van der Waals complex, helps to understand the dependence of the EET rate on the initially excited vibronic level and on the cluster's interchromophoric orientation.

Measurement of fluorescence excitation spectra of anthracene at different anthracene pressures shows bands that can be assigned to dimers of anthracene. From measurement of the anthracene excitation spectrum at increasing naphthalene pressures one can identify other spectral features, characterized by different spectral shifts from excitations of the bare molecule. Some transitions are probably due to a 13.5‐cnr−1 progression associated with an interchromophore cluster bond. Pressure dependence of fluorescence intensity gives evidence for 1:1 cluster composition, and for a slow intra‐EET rate that is associated with an unfavored orientation of the two chromophores in one of the two possible conformers of the A‐N cluster, as supported by a calculation of the cluster geometry and by comparison with a recent study of intra‐EET in the A–(CH2)n‐N bichromophoric molecules.
Mass Spectrometric Studies of Fullerene Ion Beams
Authors: Laskin Julia , Lifshitz Chava
Published: November 2013

The energetics and dynamics of C2 evaporations from carbon cluster ions Cn+ were studied using time‐resolved mass spectrometric techniques. Time‐resolved appearance energies (AEs) were determined for C58+ and C56+ on a double‐focusing mass spectrometer using electron‐space‐charge trapping. The AEs were found to be nearly independent of time for times longer than 80 μs. A large intrinsic kinetic shift, IS=30.5 eV, was observed. This intrinsic shift is due to radiative decay in the visible, which is unusually efficient for fullerenes. Time‐resolved kinetic energy releases (KERs) and metastable fractions (MFs) for Cn+ (n = 48 −62) were measured on an ion trap/reflectron mass spectrometer for trapping times up to 100 μs. The average KER for C2 evaporation from fullerenes was observed to decrease with increasing precursor ion lifetime. This constitutes proof that the KER is due to the non‐fixed energy in the transition state rather than to a reverse activation energy, and the reaction takes place via a loose transition state. The metastable fractions decrease with increasing trapping time, as expected. The results obtained for C58+ → C56+ + C2 are successfully modeled taking into account radiative cooling. The shape of the plot of MFs versus ln(t2/t1) (where t1 and t2 are the times corresponding to the beginning and the end of a metastable time window, respectively) is mainly defined by the relation between dissociative and radiative rate constants.
Nucleation and Initial Growth Stages of Chemical Vapor Deposition (CVD) Diamond
Authors: Shima‐Edelstein Ruth , Gouzman Irina , Hoffman Alon
Published: November 2013

Nucleation of diamond on non‐diamond virgin substrates is characterized by low nucleation densities and long incubation times. Various methods have been developed to enhance nucleation densities and reduce the duration of incubation. This report describes a number of different but related studies of diamond nucleation on silicon and chemically modified silicon surfaces. The effect on the initial stages of deposition of mechanical abrasion with slurries and in‐situ sample biasing are especially discussed.

Substrate abrasion with diamond results in the embeddying of diamond debris into its surface. Destructive ion implantation into this diamond debris is found to prevent subsequent diamond growth, therefore leading to the conclusion that the diamond debris serves as growth centers. Abrasion of the substrate with mixed metal/diamond slurries is reported to further enhance nucleation relative solely to diamond abrasion. It is suggested that during the chemical vapor deposition (CVD) process some metals alter the composition of the gas phase above the growing surface. Also, the role of surface reactions is emphasized.

We also introduce the dc‐glow discharge process as a novel, in situ surface pretreatment method for the formation of a precursor for diamond nucleation. Our results show that the promotion of diamond growth by this method is primarily due to formation of nano‐size diamond particles during the pretreatment process. It is suggested that, to some extent, graphitic carbon with a high degree of defects may serve as a diamond nucleation center as well.
Diamond Electronic Devices—The End of a Dream?
Authors: Collins Alan T.
Published: November 2013

Because diamond has a high band gap, high‐thermal conductivity, high‐breakdown voltage, high‐saturated electron velocity, low permittivity, and is exceptionally hard and resistant to chemical attack, it has long been argued that it is the ultimate electronic material. In this article the early history of diamond electronic devices is briefly reviewed. The relevant properties of diamond are then compared with those of silicon, GaAs, SiC, and the group III nitrides, and selected recent research on diamond electronic devices is covered in detail. Although exceptional advances have been made, it is concluded that the prospects for commercially successful electronic devices are poor.
Transient Lens Spectroscopy in a Fast Timescale
Authors: Terazima Masahide
Published: November 2013

Using the thermal lens experimental configuration, many types of fast molecular dynamics besides the density variation (the normal thermal lens signal) are reflected by the lens signal. Various transient lens techniques in a fast timescale are reviewed. By using the population lens signal, excited state dynamics can be studied with a probe light which has less restricted wavelength range over a wide timescale from a few femotoseconds to seconds. From the optical Kerr lens signal, molecular reorientational dynamics in solution can be revealed. The temporal development of the temperature lens signal provides unique information such as the thermalization time after nonradiative transition from the excited state, which is usually very difficult to determine by other spectroscopies. Identification of the lens components and the advantages of the time‐resolved transient lens method are discussed.
Differential Thermal Lens Spectrometry in the Infrared
Authors: Franko Mladen , Bicanic Dane
Published: November 2013

The operational principle and the first application of a novel infrared differential thermal lens spectrometer for optical studies of liquid samples is described. Compared to a conventional double‐beam (pump/probe) configuration, the instrumental setup described here offers the possibility to substantially reduce (as much as 30 times) the background signal caused by the absorption of solvent, and hence to achieve improved limits of detection (LOD).

Differential thermal lens spectrometry (TLS) with a CO laser as the excitation source was applied to detect tuberculostearic acid and the insecticide Carbaryl, both extracted into CCl4; the corresponding LOD are 200 μg/L and 150 μg/L, respectively. Results of preliminary studies also suggest the potential use of differential TLS for detection of citric acid dissolved in water.
Copper(II) Mediated Homo‐Coupling of 1,2‐difluorovinylstannanes
Authors: Blumenthal Eric J. , Burton Donald J.
Published: November 2013

The reaction of substituted 1,2‐difluorovinylstannanes with anhydrous Cu(OAc)2 in dimethylformamide, under an oxygen atmosphere, at room temperature stereospecifically gives the corresponding symmetrical 1,3‐dienes in good to excellent yields. Moisture drastically reduces the yield of homo‐coupled product and produces significant amounts of RCF=CFH. The Cu(II) promoted homo‐coupling of the fluorinated vinylstannanes is superior to the Cu(I)Cl mediated homo‐coupling of the corresponding hydrocarbon vinylstannanes. When 1,2‐difluorovinylstannanes are treated with Cu(I)Cl, the reaction is sluggish and significant amounts of RCF=CFH are formed.
Palladium(0)‐Catalyzed Allylation Reaction with Dimethyl 2‐fluoromalonate
Authors: Kawasaki Tomoko , Kitazume Tomoya
Published: November 2013

The palladium(0)‐catalyzed allylation reaction of dimethyl 2‐fluoromalonate with allylic carbonates proceeds smoothly under neutral conditions to give the SN2 allylation product. However, using the nucleophile NaCF(CO2Et)2 under basic conditions increased the chemical yield. Moreover, the SN2′ allylation product was increased up to 75% yield.
Intermolecular Excited‐State Proton Transfer in Clusters of 1‐Naphthol with Water and with Ammonia
Authors: Knochenmuss Richard , Fischer Ingo , Lührs Daniel , Lin Qiong
Published: November 2013

The excited‐state proton transfer reactions of 1‐naphthol(H2O)n and 1‐naphthol(NH3)n clusters are compared. Both exisiting and new data suggest that the two systems may react in strikingly different fashions, roughly corresponding to non‐adiabatic and adiabatic limiting cases, respectively. In water clusters, the reaction is kinetically limited by solvent motion, and there is a strong dynamic interaction involving the water and two lowest electronic excited states, which thereby invert. In ammonia clusters, the excited states appear to be premixed by the the stronger base, and the reaction may proceed in a rapid manner, resembling intracluster vibrational relaxation, with relatively little solvent reorganization.
Hydrogen‐Bond Rearrangement and Intermolecular Proton Transfer in Protonated Methanol Clusters
Authors: Chang Huan‐Cheng , Jiang Jyh‐Chiang , Chang Hai‐Chou , Wang Lillian R. , Lee Yuan T.
Published: November 2013

Vibrational predissociation spectra (VPS) of hydrogen‐bonded and non‐hydrogen‐bonded (free) OH stretches within the frequency range of 2700–3800 cm−1 are closely analyzed to determine the isomeric structures and proton location in protonated methanol clusters, H+(CH3OH)n. The present report emphasizes protonated methanol tetramers and pentamers, which are predicted by ab initio calculations to exist in linear and cyclic forms. Only one isomer with linear structure was identified in the VPS of protonated methanol tetramers in a supersonic expansion. Both linear and cyclic configurations were found for protonated methanol pentamers, and an isomeric transition between these two structures due to hydrogen‐bond rearrangement was observed at a cluster temperature of 190 K. Ab initio calculations indicated that the excess proton in these clusters can be either localized on one methanol unit, as in cyclic H+(CH3OH)4 and linear H+(CH3OH)5 isomers, or delocalized between two methanol molecules, as in linear H+(CH3OH)4 and cyclic H+(CH3OH)5 isomers. Such unique proton delocalization behavior is revealed in the VPS of cyclic H+(CH3OH)5, which is recognized as a symmetric five‐membered pentamer by its characteristic free‐OH stretching absorption at 3647 cm−1 and hydrogen‐bonded OH stretches at 3448 and 3461 cm−1. Using protonated methanol pentamers as a model system, a proton transfer mechanism is suggested to involve intracluster proton transfer mediated by a sequence of hydrogen‐bond breaking and reforming processes. This appealing mechanism can be closely associated with the exceptionally high proton mobility in liquid methanol.
Effects of Model Protein Environments on the Dynamics of Proton Wires
Authors: Decornez Hélène , Hammes‐Schiffer Sharon
Published: November 2013

The multiconfigurational molecular dynamics with quantum transitions (MC‐MDQT) method is utilized to study the impact of model protein environments on the dynamics of proton wires. The MC‐MDQT method allows the realtime nonequilibrium quantum dynamical simulation of proton transport along water chains and provides a framework for analyzing the detailed dynamical mechanisms of these multiple proton transfer reactions. In this paper, the protein environment is modeled by applying structural restraints to the oxygen atoms of the chain, by applying external electric fields, and by including solvating water molecules hydrogen‐bonded to the ends of the water chain. Our simulations illustrate that the protein environment could strongly impact the dynamics of proton wires through a combination of structural restraints, fluctuating electric fields, solvation, and hydrogen bonding. Our simulations also indicate that quantum effects such as hydrogen tunneling and nonadiabatic transitions play a significant role under certain nonequilibrium conditions.
The Deuterium Isotope Effect as a Tool to Investigate Enzyme Catalysis: Proton‐Transfer Control Mechanisms in Cytochrome c Oxidase
Authors: Karpefors Martin , Ädelroth Pia , Aagaard Anna , Smirnova Irina A. , Brzezinski Peter
Published: November 2013

Cytochrome c oxidase is a membrane‐bound redox‐driven proton pump. The coupling of the exergonic electron‐transfer reactions from cytochrome c to oxygen to proton translocation across the membrane requires control of internal electron‐ and proton‐transfer reactions. In this work, we focus on the kinetics of electron and proton transfer during those reaction steps that are coupled to proton pumping in cytochrome c oxidase. The results show that during the first pumping step (peroxy → oxoferryl transition), proton transfer regulates intramolecular electron transfer. The proton transfer takes place in two steps: (1) Internal proton transfer from a protonatable group, proposed to be Glu(I‐286), in the so‐called D‐pathway, to an oxygen intermediate at the binuclear center (τ ≅ 100 μs); (2) Rapid re‐protonation of Glu(I‐286) from the bulk solution (τ < 100 μs). Only after proton uptake from solution the last (fourth) electron is transferred “one step closer” towards the binuclear center (from CuA to heme a). During the second proton‐pumping step (oxoferryl → oxidized), this electron is transferred to the binuclear center, linked to the uptake of a proton through the D‐pathway. The electron‐transfer rate displays a kinetic‐isotope effect (kH/kD) of 6 ± 1 (in a pH range in which the pH dependence of the rate is small), which indicates that the electron transfer is rate‐limited by the proton transfer. The entry into the D‐pathway (around Asp(I‐132)) is composed of a cluster of negatively‐charged amino acid residues together with a number of histidines, forming a so‐called proton‐collecting antenna designed to allow rapid protonation of groups within the proton‐transfer pathway.
Quantum–Classical Simulation of Proton Migration in Water
Authors: Zahn Dirk , Brickmann Jürgen
Published: November 2013

Proton transport in water is treated within a mixed quantum–classical molecular dynamics scheme. Therein the migration of a positive charge is treated as a two‐step process: (i) the displacement of a hydronium ion, followed by (ii) proton transfer between a hydronium ion and an adjacent water molecule. Both the hydronium ion and the water molecules are treated as flexible molecules. In the H5O2+‐complex, the proton no longer belongs to a single water molecule, but is delocalized between the two oxygen atoms. The proton transfer is treated quantum mechanically as a function of a transfer coordinate within a single complex. The quantum description is changed to another pair of water molecules after strong proton localization to one of the water molecules in the complex and according to distance criteria with respect to adjacent water molecules. It is demonstrated that the proposed formalism is well suited for an effective simulation of the proton migration in water. In particular, the lifetimes of Eigen complexes and the proton diffusion coefficient (as obtained from simulations) are in very good agreement with corresponding experimental data.
Reproducible quantification of osteoclastic activity: Characterization of a biomimetic calcium phosphate assay
Authors: Maria Salwa M. , Prukner Christiane , Sheikh Zeeshan , Mueller Frank , Barralet Jake. E. , Komarova Svetlana V.
Published: November 2013

Osteoclasts are responsible for bone and joint destruction in rheumatoid arthritis, periodontitis, and osteoporosis. Animal tusk slice assays are standard for evaluating the effect of therapeutics on these cells. However, in addition to batch‐to‐batch variability inherent to animal tusks, their use is clearly not sustainable. Our objective was to develop and characterize a biomimetic calcium phosphate assay based on the use of phase pure hydroxyapatite coated as a thin film on the surface of culture plates, to facilitate the reproducible quantification of osteoclast resorptive activity. Osteoclasts were formed from RAW 264.7 mouse monocyte cell line using a pro‐resorptive cytokine RANKL (50 ng/mL). No change in substrate appearance was noted after culture with media without cells, or undifferentiated monocytes. Only in the presence of osteoclasts localized areas of calcium phosphate dissolution were observed. The total area resorbed positively correlated with the osteoclast numbers (R2 = 0.99). The resorbed area was significantly increased by the addition of RANKL, and decreased after application of known inhibitors of osteoclast resorptive activity, calcitonin (10 μM), or alendronate (100 μM). Thus, calcium phosphate coated substrates allow reliable monitoring of osteoclast resorptive activity and offer an alternative to animal tusk slice assays. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 102B: 903–912, 2014.
Augmentation of engineered cartilage to bone integration using hydroxyapatite
Authors: Dua Rupak , Centeno Jerry , Ramaswamy Sharan
Published: November 2013

Articular cartilage injuries occur frequently in the knee joint. Photopolymerizable cartilage tissue engineering approaches appear promising; however, fundamentally, forming a stable interface between the subchondral bone and tissue engineered cartilage components remains a major challenge. We investigated the utility of hydroxyapatite (HA) nanoparticles to promote controlled bone‐growth across the bone‐cartilage interface in an in vitro engineered tissue model system using bone marrow derived stem cells. Samples incorporated with HA demonstrated significantly higher interfacial shear strength (at the junction between engineered cartilage and engineered bone) compared with the constructs without HA (p < 0.05), after 28 days of culture. Interestingly, this increased interfacial shear strength due to the presence of HA was observed as early as 7 days and appeared to have sustained itself for an additional three weeks without interacting with strength increases attributable to subsequent secretion of engineered tissue matrix. Histological evidence showed that there was ∼7.5% bone in‐growth into the cartilage region from the bone side. The mechanism of enhanced engineered cartilage to bone integration with HA incorporation appeared to be facilitated by the deposition of calcium phosphate in the transition zone. These findings indicate that controlled bone in‐growth using HA incorporation permits more stable anchorage of the injectable hydrogel‐based engineered cartilage construct via augmented integration between bone and cartilage. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 102B: 922–932, 2014.