bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Short Turn Motifs in Proteins Using Sequence and Structure Fingerprints
Authors: Wintjens René T. , Rooman Marianne J. , Wodak Shoshana J.
Published: November 2013

Families of 20‐residue turn motifs are identified in a dataset of known protein structures using a fully automatic classification procedure that relies on dihedral angle values and atomic root mean square deviations of the polypeptide backbone. Four of the identified motifs, a novel αα connection, and three well‐known αα, βα, and ββ motifs, are used to investigate the possibility of identifying sequences that adopt these motifs in a library of 20‐residue sequence segments from the protein dataset. To this end, several types of fingerprints are derived for individual members of each turn motif family, and for each family as a whole. These fingerprints represent the sequence conservation among family members, or different reduced descriptions of the protein 3D structure that consider the backbone conformation or the tertiary interactions in the context of the parent proteins. All sequence segments in the library are successively mounted onto the fingerprints, without allowing gaps, and the energy of each mount is evaluated using effective potentials derived from known protein structures. The results show that the ability to recognize native sequences associated with a turn motif is improved when different types of fingerprints are combined, and that it fluctuates significantly according to the specific turn family considered. Overall, however, this ability remains rather limited to a level which is much below the native recognition performance generally achieved for full proteins. The fingerprints and their associated potentials are nevertheless found to be quite effective in generating subsets of solutions that are significantly enriched for the correct sequence‐structure combinations. This may have very useful applications in protein folding simulations and in homology modeling.
The Chemistry of Precipitation in Israel
Authors: Singer Arieh
Published: November 2013

Recent concerns about the rapid deterioration in the quality of water resources in Israel, in addition to the widely documented anthropogenic acidification of precipitation in many parts of the world, have put a “state of the art” review of our knowledge of the chemistry of precipitation in Israel on the order of the day. Electrolyte content in precipitation in Israel is inversely related to average annual precipitation, and thus is 3–6 times higher in southern than in central Israel. The major reason for these differences is the differential enrichment in components of continental origin, such as Ca2+ and HCO3−. The chemical composition of precipitation is determined by the balance between components of marine and continental origin. Na+ and Cl− are the major ions contributed by sea spray, and therefore most of the precipitation exhibits Na/Cl (molar) ratios close to that of seawater. Precipitation in the southern parts of the country is an exception. Other ions of partly marine origin are Mg2+, SO42−, K+, and, to a limited extent, Ca2+. Marine contribution to precipitation decreases with distance from the sea. The most important component of continental origin in precipitation in Israel is Ca2+, similar to precipitation in other semiarid areas surrounding the Mediterranean. Calcium in precipitation is often associated with dryfall (dust) originating in North African desert areas. NH4+ concentration levels are relatively low, and thus, the importance of this ion as an acidity‐neutralizing agent is small compared to central/northern Europe. Precipitation in Israel is neutral to mildly alkaline, with an average pH of 6.5 ± 0.8. Mildly alkaline rain is the rule in central and southern Israel. In the Golan Heights, Galilee, and the northern coastal region, most of the precipitation events are acidic. On Mt. Carmel, 40% of the rain events examined during three rainy seasons were strongly acid, and in more than 65% of the events, pH was ≤5.6. Acidity in precipitation in Israel is determined primarily by excess SO42−. Nitrates have only a subordinate role. Synoptic analysis as well as sulfur isotopic data suggest that the excess sulfate is a long‐range import from over the Mediterranean Sea, either of anthropogenic European or of biogenic/marine dimethyl sulfide (DMS) origin. In southern Israel, an isotopic amount effect was observed, whereby rain in rainier years was isotopically lighter δ18O than precipitation in the less rainy years. δ34S values of precipitation were found to be in the range of 0–15‰, thus indicating that precipitation sulfate consisted of a mixture of marine and nonmarine sulfate. Cl and Sr isotope ratios in precipitation were determined as well.
Atmospheric Wet Depositions in Tropical America
Authors: Sanhueza Eugenio , Santana Magaly
Published: November 2013

The chemical composition of wet depositions at a “natural” regional scale and in local polluted areas in tropical America is reviewed. The available data indicate that at large regional scales, atmospheric wet depositions in tropical America are little affected by anthropogenic emissions, and that rain concentrations of non‐sea‐salt sulfate (SO4*), NO3−, and NH4* are much lower than the ones observed at midlatitudes in the northern hemisphere. The regional acidity of rainwater (pH −5) is mainly due to formic and acetic acids; however, the sources of these acids (probably natural) are not well identified as yet. Some “local‐regional” problems are observed in Brazil and Venezuela, and it is likely that other tropical urban‐industrial areas also present anthropogenic acidification of rain, but no measurements have been made. Since most soils in tropical America are sensitive to acid deposition, the evaluation in areas affected by local urban‐industrial emissions should be emphasized.
Acetone in the Urban Atmosphere: A Study in Denver, Colorado
Authors: Anderson Larry G. , Lanning John A. , Wolfe Pamela
Published: November 2013

We report 4‐h average concentration data for acetone, formaldehyde, acetaldehyde, and carbon monoxide measured in downtown Denver, Colorado, USA from January through December 1993. The correlations between these carbonyl compounds and CO measurements suggest that motor vehicles are a significant source for all three carbonyls, particularly during the winter. The diurnal character of the concentrations of formaldehyde and acetaldehyde suggests that there is at least a small net photochemical source for these compounds during the summer. The diurnal character of the acetone concentration suggests that there is a significant net photochemical source for acetone during the summer. An analysis of the initial photochemical production and loss processes for these carbonyls under typical atmospheric conditions suggests that the production and loss processes for formaldehyde nearly balance. This same analysis for the other carbonyls suggests that there should be a large net photochemical source for both acetaldehyde and acetone. Such a large photochemical source is not observed for acetaldehyde. Acetone is relatively unreactive in the atmosphere on a timescale of urban or regional interest. Thus, atmospheric measurements of acetone concentrations may serve as a useful indicator of the photochemical age or degree of photochemical processing of an air mass.
Ozone Levels in Central Israel
Authors: Peleg Mordechai , Luria Menachem , Setter Ilan , Perner Dieter , Russell Patricia
Published: November 2013

Measurements performed during the early summer months of 1988–1991 at a rural site in central Israel, some 50 km east of the highly urbanized coastal region, have shown that during the afternoon hours the area was often under the influence of ozone mixing ratios above the Israel ambient standard (117 ppbv) and occasionally even above 150 ppbv. Analysis of air mass back trajectories has shown that only those air masses passing over the Tel Aviv metropolitan area cause elevated ozone mixing ratios at the rural site. This highly urbanized region emits large amounts of precursors which are entrapped in the air parcels entering Israel under the predominantly westerly wind flows. As these air masses travel inland, sufficient time is available (3–5 h) to allow the photochemical reactions to generate ozone before reaching the rural site. The above hypothesis is further supported by the fact that parallel to the increase of ozone at the rural site, elevated carbon monoxide (up to 0.8 ppmv) and other trace gases were also observed. A significant correlation (R2 > 0.8) was found to exist between the ozone mixing ratio and the NOx concentrations in photochemically aged air masses. In several cases an excess of up to 12 ozone molecules was formed for each NOx molecule present.
Soft Matter in a Tight Spot: Nanorheology of Confined Liquids and Block Copolymers
Authors: Granick Steve , Demirel A. Levent , Cai Lenore L. , Peanasky John
Published: November 2013

The linear frequency‐dependent shear rheology and force–distance profiles of molecularly‐thin fluids of very different structure were contrasted: a globular molecule octamethylcyclotetrasiloxane (OMCTS), branched alkanes (3‐methylundecane and squalane), and a polymer brush in near‐theta solution (polystyrene‐polyvinylpyridine). In each case the data suggest a prolongation of the longest relaxation time (τ1) with increasing compression. At frequencies ω > 1/τ1 the shear response was “solid‐like”, but at ω < 1/τ1 it was “liquid‐like”. OMCTS under mild compression exhibited seeming power‐law viscoelastic behavior with G′(ω) = G″(ω) over a wide frequency range. Of the branched‐molecule fluids, 3‐methylundecane exhibited oscillatory force–distance profiles; this confirms prior computer simulations. But squalane (6 pendant methyl groups in an alkane chain 24 carbons long) showed one sole broad attractive minimum. Polymer brushes in a near‐theta solvent exhibited changes qualitatively similar to those OMCTS, in particular, a smooth progression of longest relaxation time, generating a transition from “liquid‐like” to “solid‐like” shear rheology with decreasing film thickness. The common trend of shear response in these systems, in spite of important differences in molecular structure and force–distance profiles, is emphasized.
Application of FTIR Spectroscopy to the Structural Study on the Function of Bacteriorhodopsin
Authors: Maeda Akio
Published: November 2013

Difference FTIR spectroscopy of the photointermediates of bacteriorhodopsin is informative for changes in H‐bonding, the protonation states, and the bond orientation of functional residues such as C=O, N‐H, and O‐H of the chromophore, protein residues, peptide bonds, and internal water molecules. The vibrational bands of the chromophore are found at frequencies similar to those observed by resonance Raman spectra. Moreover, FTIR gives clear results on the N— in‐plane bending vibration and C14–C15 stretching vibrational modes, both of which are useful for the analysis of the structure of the chromophore. The protonation states and H‐bonding changes of intramembrane protonated aspartic acid residues can be revealed only by FTIR spectroscopy, in combination with proper isotope labeling and site‐directed mutagenesis. The results with Asp‐96 and Asp‐85 in the L, M, and N photointermediates were especially useful for understanding the proton transfer mechanism. Besides amino acid groups in the protein, peptide C=O vibrations were assigned to a specific bond by the use of site‐directed isotope labeling. Water molecules which undergo structural changes upon photoreaction were attributed specifically to those interacting with particular protein residues by mutational studies. On the basis of these FTIR studies, the role of the L intermediate is emphasized as the key intermediate that creates the conditions for the proton transfer reaction from the Schiff base to Asp‐85 and subsequent proton uptake reactions in the cytoplasmic domain.
Atomically‐Resolved Investigations of Surface Reaction Chemistry by Scanning Tunneling Microscopy
Authors: Hamers Robert J. , Chen X. , Frank E.R. , Higgins S.R. , Shan J. , Wang Y.
Published: November 2013

Research by our group aimed at studying the chemistry of surfaces with atomic‐resolution scanning tunneling microscopy is reviewed. Three areas of application are discussed: semiconductor surface chemistry, adsorption processes at metals, and in situ studies of dissolution and oxidation‐reduction chemistry of minerals.
Thermally‐Induced Changes in Bonding Properties of C60 on Si(100)‐2×1 Surfaces
Authors: Yao Xiaowei , Chen Dong , Ruskell Todd G. , Workman Richard K. , Sarid Dror
Published: November 2013

The co‐adsorption of pre‐ and post‐annealed C60 molecules on Si(100)‐2×1 surfaces has been investigated using scanning tunneling microscopy in ultrahigh vacuum. The images reveal that the adsorption characteristics of the post‐annealed adsorbates are different from their pre‐annealed counterparts. The post‐annealed C60 molecules bond either to the top of the dimer rows or to the missing dimer defects, while the pre‐annealed molecules predominantly occupy the four‐dimer sites in the troughs. The apparent size and height of post‐annealed C60 molecules are smaller than those of the pre‐annealed ones. Our observations suggest that the post‐annealed C60 molecules are chemisorbed on the surface, because the molecules covalently bond to Si atoms during the sample annealing. In contrast, the adsorption of the pre‐annealed C60 molecules can be explained by a dipole‐induced‐dipole interaction between the molecules and the Si(100) surface, i.e., physisorption.
Chemically‐Specific Probes for the Atomic Force Microscope
Authors: Lee Gil U , Chrisey Linda A. , O'Ferrall C. Elizabeth , Pilloff Daniel E. , Turner Noel H. , Colton Richard J.
Published: November 2013

The atomic force microscope (AFM) measures force and displacement with high sensitivity and submillisecond temporal resolution. By functionalizing the AFM probe with specific chemical groups or macromolecules it is possible to characterize the chemical and physical properties of single molecules on the nanometer scale. In this paper we discuss the key issues that must be addressed when designing and characterizing a successful immobilization chemistry, and describe the chemistry we developed to covalently immobilize oligonucleotides in a specific orientation.
Catalytic Antibody Structures: An Early Assessment
Authors: Haynes Matthew R. , Heine Andreas , Wilson Ian A.
Published: November 2013

The three‐dimensional structures of four catalytic antibodies, three of which were complexed with transition‐state analogs, have been determined by X‐ray crystallographic methods. An additional catalytic antibody structure has been deduced using homology modeling methods, and the information derived from the resulting model has been the basis for site‐directed mutagenesis experiments. Analysis of these crystal structures suggests that the primary source of catalytic activity in three of the antibodies is primarily shape and charge complementarity between the combining sites and the transition‐state‐analog haptens. The fourth structure may contain a modified “catalytic triad,” with histidine, serine, and tyrosine side chains positioned so that they could participate in the chemical transformation. Otherwise, the abzyme structures are representative of antibody structures in general, and do not possess any particularly unusual features that would suggest a classification outside the normal range of variation expected within the immunoglobulin family. Rather, the catalytic activity of these antibodies can be explained entirely on the basis of the local arrangement of residues that line the binding sites for their haptenic antigens. In addition, the structures provide strong evidence that the conserved immunoglobulin framework can provide a highly suitable context to serve as the basis for a generalized, programmable catalyst.
Antibody‐Catalyzed Uni‐ and Multi‐Substrate Reactions Compared Using Transition‐State Binding (KTS)
Authors: Reymond Jean‐Louis , Chen Yuanwei
Published: November 2013

Catalytic antibody technology is based on the equivalence between catalysis, transition‐state binding, and transition‐state analog binding. This simple concept has attracted enormous creativity to the field. Unfortunately a similar degree of simplicity is usually not evident in kinetic analyses of antibody‐catalyzed reactions. In particular, the rate enhancement kcat/kuncat does not allow one to compare reactions of different orders. Here we propose a simple language based on expressing KTS, the dissociation constant of the antibody‐transition‐state complex, together with a drawing for the corresponding transition‐state. The constant KTS was introduced by Kurz in 1963 as a quantitative expression for Pauling's formulation of catalysis. A small value of KTS describes tight transition‐state binding, and thus efficient catalysis. We show that this analysis allows a unified and remarkably simple description of antibody‐catalyzed reactions with very different levels of complexity. It also enforces a proper formulation of the “uncatalyzed” reaction, which has a critical influence in assessing catalytic efficiency. Comparing KTS with Ki, the dissociation constant of the antibody‐hapten complex, shows how far binding to a designed hapten translates into catalysis.
The Unimolecular Decomposition of Cyclobutanol: Experimental and Theoretical Study
Authors: Tanaka Seiji , Tomariguchi Susumu , Saito Ko , Takahashi Osamu , Tabayashi Kiyohiko
Published: November 2013

The thermal decomposition of cyclobutanol has been investigated behind incident and reflected shock waves at temperatures between 950 K and 1450 K in the total density region (1.5 × 10−6 – 1.5 × 10−5) mol/cm3. A strong absorption by an intermediate was observed at the wavelength of 193 nm. By comparing the kinetics with that of pyruvic acid, this absorption was identified to be that of vinyl alcohol. The kinetic parameters of vinyl alcohol, both for the production and the decomposition, were determined. The production rate constant was in agreement with that obtained by Back (Can J. Chem. 1982, 60, 2357), who monitored the ethylene production. The total decomposition mechanism of cyclobutanol was discussed on the basis of MO calculations. It was shown that vinyl alcohol was produced through a biradical before it isomerized to acetaldehyde.
Reaction of Silane with Atomic Oxygen at High Temperatures
Authors: Iida Daisuke , Koshi Mitsuo , Matsui Hiroyuki
Published: November 2013

The reaction of silane with atomic oxygen (3P) was investigated by the shock‐tube–laser‐photolysis method over the temperature range of 900–1170 K. Oxygen atoms were produced by the ArF laser photolysis of SO2 behind reflected shock waves and monitored with atomic resonance absorption spectroscopy. The rate constant for the SiH4 + O reaction was evaluated by taking the possible contribution of the consecutive reaction into consideration. The Arrhenius temperature coefficient was determined to be Ea= 26.6 kJ mol−1, which is much higher than the experimental activation energies obtained at lower temperatures. Rate constants calculated by a transition state theory with the reaction barrier height of E0= 10.2 kJ mol−1 agreed well with both the present and the previous experimental results for a wide temperature range.
Real Gas Corrections in Shock Tube Studies at High Pressures
Authors: Davidson David F. , Hanson Ronald K.
Published: November 2013

Reaction kinetics studies at high pressure in shock tubes can be significantly affected by the influence of real gas effects on state variables. The effect on the temperature, pressure, and density can be calculated by solving the shock wave equations using real gas equations of state (EOS). We present a method to solve the shock wave equations in a straightforward way by taking advantage of the recently‐developed real gas properties package by Schmitt et al. (U. of Iowa Rep. UIME PPB 93–006, 1994). The solutions of these equations for shock waves in pure argon are presented. We find that the reflected shock temperatures and densities can be significantly different from those predicted by using an ideal gas EOS. Using the Peng‐Robinson EOS, for example, the calculated real gas reflected shock temperature is less than the ideal gas temperature by 83 K per 1000 atm. An illustrative example of the effect of real gas corrections on a rate coefficient determination is also presented.
Functionalized [2]Rotaxanes
Authors: Asakawa Masumi , Ashton Peter R. , Iqbal Sayeedha , Quick Andrew , Stoddart J. Fraser , Tinker Nigel D. , White Andrew J.P. , Williams David J.
Published: November 2013

The synthesis of a series of dumbbell‐shaped compounds, which can act as a host (e.g., toward alkali metal cations) and as a guest (e.g., toward cyclobis(paraquat‐p‐phenylene)) in a supramolecular context is described. The self‐assembly of [2]pseudorotaxanes and [2]rotaxanes, in which cyclobis(paraquat‐p‐phenylene) encircles polyether chains intercepted in their middles by a hydroquinone ring and terminated at each end by 12‐crown‐4, 15‐crown‐5, monoaza‐18‐crown‐6, 18‐crown‐6, or adamantyl groups, is achieved using either threading, clipping, or slipping procedures. All the [2]pseudorotaxanes and [2]rotaxanes are characterized in solution by spectroscopic means and, in the case of two of the [2]rotaxanes, by X‐ray crystal structures in the solid state. In the presence of metal ions, [2]pseudorotaxanes carrying 12‐crown‐4 or 15‐crown‐5 stoppers can be disassembled in solution. The research shows how one kind of complexation can affect another kind of complexation—manifesting itself in a physical change in the system and so acting as a prototype of a potential molecular device.
Alignment Photoregulation of a Nematic Liquid Crystal by Surface Adsorption of Aminoalkylated Azobenzenes
Authors: Ueda Masahide , Kudo Kazuaki , Ichimura Kunihiro
Published: November 2013

Adsorption behavior of azobenzenes having an aminoalkyl residue onto a silica surface is described. Immersion of a silica plate in a benzene solution of an aminoalkylated azobenzene resulted in efficient adsorption to form face‐to‐face aggregates which are converted into monomeric states by partial desorption. Silica plates adsorbing the azobenzene bearing an aminoalkyl residue were employed to achieve the surface‐assisted photoregulation of alignment of a nematic liquid crystal between homeotropic and planar modes. Based on these observations, a convenient method to prepare command surfaces for the orientational photoregulation of liquid crystals was presented by filling a liquid crystal containing an aminoalkylated azobenzene into an empty cell composed of clear silica plates.
Sugar‐Induced Chiral Orientation of Boronic‐Acid‐Appended Amphiphile Clusters Formed in the Dipalmitoylphosphatidylcholine (DPPC) Membrane
Authors: Kimura Taro , Takeuchi Masayuki , Hamachi Itaru , Shinkai Seiji
Published: November 2013

A boronic‐acid‐appended amphiphile bearing an azobenzene chromophore in the chain center (3) was synthesized. Although 3 could not form the membrane‐like, ordered aggregate by itself, it formed a phase‐separated aggregate in a dipalmitoylphosphatidylcholine (DPPC) matrix membrane. When saccharides were added, the boronic acid group reversibly formed the saccharide complexes, and 3 in the DPPC matrix membrane became CD‐active with the appearance of exciton‐coupling bands. Comparison of the saccharide absolute configuration with the CD intensity established that the saccharide possessing the OH group (as 3‐OH, 4‐OH, and 5‐CH2OH) in the same side as the cis‐1,2‐diol gives the strong CD band. Judging from the structure of 3–saccharide complexes, these “same‐side” OH groups can enjoy intermolecular hydrogen‐bonding interactions, which eventually induce the chiral orientation of azobenzene chromophores. This is a novel membrane system useful to read out the information stored in the saccharide structure and to create novel membrane structures by added saccharides.
Triplet EPR Dynamics of Randomly Oriented Dications and Dianions of Tetraoxaporphyrinoids
Authors: Berman Assia , Levanon Haim , Vogel Emanuel
Published: November 2013

This paper deals with the photoexcited triplet state of several tetraoxaporphyrinoids studied by time‐resolved electron paramagnetic resonance (EPR). The porphyrinoids studied are tetraoxa[18]porphyrin (1a++), octaethyl‐tetraoxa[18]porphyrin (1b++), tetra‐n‐butyl tetraoxa[18]porphyrin (1c++), octaethyl‐tetraoxa[26]porphyrin (2++), and tetraoxa[18]porphycene (3++), all of them as per‐chlorate salts. To qualify as stable aromatic 18π‐ (or 26π‐) electron systems, they must exist as dications. Analysis of the triplet EPR spectra is characterized by unique features not found in their parent porphyrins and porphycenes. While in the case of the axially‐symmetric tetraphenylporphyrin, the triplet EPR spectra indicate deviation from axial symmetry, the tetraoxaporphyrin 1a++ exhibits, as expected, a vanishing E‐term of the zero‐field splitting (ZFS) tensor. A conspicuous difference is found between the triplet EPR spectra of the dications and the dianions of all tetraoxa compounds. The results are discussed in terms of the electronic structures of the porphyrinoids.
A Biomimetic Approach to Taxol: Stereoselective Synthesis of a 12‐Membered Ring Ene‐Epoxide
Authors: Takahashi Takashi , Okabe Tadashi , Iwamoto Hajime , Hirose Yoichiro , Yamada Haruo , Doi Takayuki , Usui Shuji , Fukazawa Yoshimasa
Published: November 2013

The stereoselective synthesis of a taxol intermediate via a biomimetic route is described. Aldol condensation of γ‐butyrolactone and citral derivatives generated three stereogenic centers at positions C1, C2, and C11 corresponding to taxol. Intramolecular alkylation of the cyanohydrin ether efficiently formed the 12‐membered ring system in which stereoselective reduction, followed by directed epoxidation, afforded the key intermediate epoxide.
Tremorgenic Indole Alkaloids. 10. An Improved Asymmetric Synthesis of a Tricyclic Common Intermediate
Authors: Smith Amos B. , Hartz Richard A. , Spoors P. Grant , Rainier Jon D.
Published: November 2013

An efficient third‐generation asymmetric synthesis of tricyclic lactone (+)‐1, designed to serve as the common intermediate for construction of the indole tremorgens, has been developed. The major challenge was stereocontrolled introduction of the vicinal quaternary methyl groups. Our initial approaches employed enolate chemistry to install the second methyl moiety; herein we exploit instead a hydroxyl‐directed Simmons‐Smith cyclopropanation followed by reductive opening of the three‐membered ring. The new 15‐step synthesis proceeds in 8.3% overall yield, nearly an eightfold increase over the second‐generation route, and is amenable to large‐scale production of (+)‐1.

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Asymmetric Sequential Michael Addition–N–Heterocyclization Reactions Involving Chiral Imines
Authors: D'angelo Jean , Cavé Christian , Desmaële Didier
Published: November 2013

The reaction of chiral imines ent‐14, 27, and 31 with α‐chloroacrylonitrile 6, maleic anhydride 9, and citraconic anhydride 35 has been investigated. Addition of imine 27 to 6 furnished, after NaBH3CN‐reduction of the crude product, the bicyclic derivative 28 as a single isomer. When the same protocol was applied to imine ent‐14, a mixture of adducts 29 and 30 was obtained. Addition of imine 31 to 6 gave the annulated pyrrole 32. Condensation of imine 27 with maleic anhydride 9 afforded compound 33 as a single isomer. Addition of imine ent‐14 to citraconic anhydride 35 led, after esterification of the crude product with CH2N2, to a mixture of adducts 36 and 37. The mechanism of these aza‐annulations was discussed on the basis of the regio‐ and stereoselectivities observed.
A Convenient Method for the Preparation of Disaccharides by Transglycosylation of Methyl Glycosides
Authors: Uchiro Hiromi , Kurusu Nobuyuki , Mukaiyama Teruaki
Published: November 2013

Transglycosylation of methyl glycosides with various glycosyl acceptors using a Sn(OTf)2–Me3SiCl promoter system in the presence of molecular sieves 5A afforded the corresponding glycosides. Several useful disaccharides are effectively prepared in good yields with moderate to good stereoselectivities.
Recent Developments in the Synthesis of Annonaceous Acetogenins
Authors: Marshall James A. , Hinkle Kevin W. , Hagedorn Chad E.
Published: November 2013

Synthetic routes to various bis‐THF annonaceous acetogenins and prototypes thereof are reviewed. These C35–C37 long‐chain diethers exhibit a remarkable range of biological activities. The core unit, with six oxygenated stereogenic centers, provides a challenging target for asymmetric synthesis.
Electrochemical Deposition of Hydrosulfide and Ethanethiolate Adlayers on Silver(111). Voltammetric Measurement of Structural Phase Transitions During Adlayer Formation
Authors: Stevenson Keith J. , Hatchett David W. , White Henry S.
Published: November 2013

Reversible, oxidative adsorption of hydrosulfide (HS−) and ethanethiolate (CH3CH2S−) on highly‐ordered, Ag(111) electrodes in aqueous 0.5 M NaOH solutions is reported. Oxidation of HS− and CH3CH2S− results in adlayer formation, as determined by voltammetry, coulometry, and in‐situ electrochemical quartz‐crystal measurements. The voltammetric response of Ag(111) in HS− solutions displays three characteristic waves. Two waves correspond to the reversible 1‐e− oxidative adsorption of HS”, resulting in the formation of a Ag‐SH adlayer. The third wave corresponds to the kinetically‐slow 1‐e− oxidation of the Ag‐SH adlayer, yielding an underpotential deposited monolayer of Ag2S. The voltammetric response observed in CH3CH2S− solutions is qualitatively similar to that of HS−, displaying two well‐resolved waves corresponding to oxidative adsorption. The observation of two voltammetric waves is suggestive of a mechanism of CH3CH2S− adlayer formation involving at least two distinct structural phases. However, unlike the situation for HS”, the resulting Ag‐SCH2CH3 adlayer is unable to undergo a second oxidative transition. The free energies of adsorption of HS” and CH3CH2S− on Ag(111) are measured to be ca. −23 kcal/mol.
Spectroelectrochemical Investigations of the Spreading of 4‐Pentadecyl Pyridine onto the Au(111) Electrode
Authors: Sagara Takamasa , Zamlynny Vlad , Bizzotto Dan , Mcalees Alan , Mccrindle Robert , Lipkowski Jacek
Published: November 2013

The adsorption of 4‐pentadecyl‐pyridine (C15‐4‐Py) onto the Au(111) electrode was investigated with the help of electrochemical and spectroscopic techniques. Electrochemical studies demonstrated that a film of C15‐4‐Py spreads onto the metal surface at potentials close to the potential of zero charge (pzc) and desorbs from the electrode surface at potentials which are sufficiently negative. The character of C15–4‐Py adsorption resembles adsorption of pyridine molecules at the Au(111) electrode, indicating that the film properties are to a large extent determined by the interaction between the pyridine moiety and the metal surface. Addition of 25 mol%) of 10‐decyl‐9‐[2‐(4‐pyridyl)ethyl]anthracene(DPEA), a dye molecule, to the C15–4‐Py film only slightly modified its properties but allowed the use of spectroscopic methods to study the film properties. Fluorescence spectroscopy and light scattering experiments were employed to study the potential‐induced desorption and adsorption of the surfactant molecules. Using spectroelectrochemical techniques we have demonstrated that the desorption of the film and its readsorption involves the formation of micelles in the subsurface region and spreading of the micelles onto the electrode surface. A general mechanism of spreading of insoluble surfactants onto electrode surfaces has been proposed.
Characterization and Electroanalytical Application of ω‐Mercaptoalkanesulfonic Acid Monolayers on Gold
Authors: Turyan Iva , Mandler Daniel
Published: November 2013

Self‐assembled monolayers (SAMs) of ω‐mercaptoalkanesulfonic acid on gold surfaces have been studied by electrochemistry and other surface techniques. In spite of the fact that these monolayers are disorganized, i.e., of “brush” type, they are impermeable to inorganic anions due to their high negative charge. Moreover, we find that an ω‐mercaptodecanesulfonic acid (MDS) monolayer is also impermeable to organic species, regardless of their charge, because of its high hydrophilicity. The combination of these properties made it possible to apply gold electrodes modified with MDS for the determination of iron(III) ions in the presence of organic species that are either electroactive throughout the same potential window or form strong complexes with iron(III).
Preparation of Self‐Assembled Monolayers from Micellar Solutions
Authors: Liu Jian , Kaifer Angel E.
Published: November 2013

The self‐assembly of alkanethiols on gold surfaces from micellar aqueous solutions was investigated using Triton X‐100, sodium dodecylsulfate, and cetyltrimethylammonium bromide as representative nonionic, anionic, and cationic surfactants, respectively. The surfactant solutions solubilized the otherwise water‐insoluble alkanethiols, which self‐assembled on gold to form organized assemblies very similar to those prepared using the conventional procedures, i.e., exposure of the gold surface to a nonaqueous solution of the alkanethiol. The resulting derivatized gold electrodes exhibited typical electrochemical properties, such as low capacitance values and substantial blocking of the voltammetric reduction of Ru(NH3)63+. The concentration of surfactant was found to have a profound effect on the rate of alkanethiol chemisorption.
Electrochemical Formation of CdSe Monolayers on the Low Index Planes of Au
Authors: Lister Tedd E. , Colletti Lisa P. , Stickney John L.
Published: November 2013

The electrochemical analog of atomic layer epitaxy (ALE) is being studied. ALE is a method for growing thin films of materials using a cycle of surface limited reactions. The surface limited reactions control the deposition by limiting the growth to an atomic layer at a time. In electrochemistry, a surface limited deposition is generally referred to as underpotential deposition (UPD), and UPD is used to form the atomic layers in electrochemical ALE (ECALE). The work presented here is an atomic level study of the deposition of the first few monolayers of CdSe via ECALE: by the alternated UPD of atomic layers of Se and Cd on the low index planes of Au. UPD of Se resulted in the formation of ordered structures on each of the low index planes of Au, as observed by low energy electron diffraction (LEED) and scanning tunneling microscopy (STM). The subsequent UPD of Cd resulted in CdSe deposits which exhibited 1:1 stoichiometry, as determined by coulometry and Auger electron spectroscopy (AES). The following LEED patterns were observed for the CdSe monolayers: Au(111)(√7×√7)R19.1°, Au(111)(3×3), Au(110)(2×3), and the Au(100)(√2×2√2)R45°. Similar LEED patterns were observed on each surface for deposits formed using up to three ECALE cycles. In situ STM studies of Cd deposition on Se‐covered Au(111) indicated the formation of a (3×3) structure, consistent with LEED results, and with previous TEM studies. The same LEED patterns were also observed for CdSe monolayers where Cd was deposited as the first atomic layer. AES indicated that the element deposited first remained on the bottom, and that deposited second remained on top.
Spectroscopic Characterization of Supersonic Molecular Beams
Authors: Vaida Veronica , Frost Gregory J. , Goss Lisa M.
Published: November 2013

A general spectroscopic method is described by which samples prepared in supersonic molecular beams can be characterized independently in their ground and excited electronic states. The centerpiece of this experiment is a Fourier transform spectrometer operating at high resolution in the infrared, visible, and ultraviolet. This method is illustrated with studies of the NO2 and OClO radicals prepared in supersonic molecular beams at temperatures and pressures characteristic of the Earth's atmosphere.

This general spectroscopic method is discussed by analogy with low‐ and high‐resolution studies of electronic states which in limited cases have been used to characterize sample conditions in supersonic molecular beam experiments.
Heteroepitaxy of Diamond on Cubic Boron Nitride
Authors: Koizumi Satoshi
Published: November 2013

The epitaxial growth process of diamond from the gas phase on a cubic boron nitride (c‐BN) {111} surface has been investigated. At the initial growth stage, carbon adsorption progressed on a boron‐terminated surface of c‐BN ({111}B). The coordination of the carbon atoms was found to be the same as that observed in diamond, as confirmed by electron energy loss spectroscopy (EELS). The epitaxial growth of diamond particles has been observed after formation of the carbon layer. On the other hand, on the nitrogen‐terminated surface ({111}N), neither stable adsorption of carbon nor nucleation of diamond has been observed. The stability of adsorbed carbon atoms in the chemical vapor deposition (CVD) ambient, in which large amounts of atomic hydrogen are supplied to the substrate heated at high temperature, is quite important for the nucleation of diamond. Using cross‐sectional transmission electron microscopy (TEM), numerous crystal defects were observed, both in c‐BN and diamond. Formation of the epitaxial diamond particles has been observed especially at defect sites on c‐BN. The misfit dislocation has been observed near the interface with the diamond particle. Even though there exist misfit dislocations that relieve the stress caused by the lattice mismatch between diamond and c‐BN, the epitaxial film involved retains a tensile strain of about 0.29% for a film thickness of about 200 nm.
Diamond Electrodes
Authors: Tenne Reshef , Lévy‐Clément Claude
Published: November 2013

With their unique chemical stability and high electron mobility, boron‐doped thin diamond films are likely to have favorable properties for a number of electrochemical applications. A review of the recent developments in this field is presented with critical evaluation of the experimental data. In particular, the relationship between the material's characteristics and the electrochemical behavior of the electrodes is discussed in detail. A number of potential applications for these electrodes are presented: for dimensionally stable electrodes in highly corrosive environments, for discharging toxic effluents, and for electrochemical sensors.
Applications of Conformal CVD Diamond Films
Authors: Rotter Shlomo
Published: November 2013

A method for enhanced nucleation of diamond growth on non‐diamond substrates is introduced via the results obtained in a wide variety of applications. The exact details of the method are still proprietary, but the outcome, as demonstrated in this paper, is unique and promises to be of great practical use. The main feature of the growth following the nucleation step is a very high density of nucleation sites which instantly started to grow over any structured surface in a perfectly conformal fashion.
Laser‐Excited Photothermal Lens Spectrometry in a Low‐Volume Cylindrical Sample Cell
Authors: Bialkowski Stephen E.
Published: November 2013

A new apparatus for performing laser‐excited photothermal lens spectroscopy is described. The apparatus uses a sub‐microliter cylindrical sample cell, chopped laser excitation, and a continuous probe laser to perform photothermal lens spectrometry. The sample is irradiated with a constant irradiance beam, and the photothermal lens forms due to thermal diffusion through the sample cell walls. Solutions for the thermal diffusion equations predict a parabolic temperature change under continuous irradiation. Experimental results are obtained for organic and inorganic complexes in ethanol solution and compared to those obtained using a standard sample cell. Results for dicyclopentadienyl iron solutions excited with 10mW 514.5 nm Ar+ laser radiation show that the cylindrical sample cell signal is 32% of that obtained using the standard sample cell. This ratio is in reasonable agreement with that expected based on thermal diffusion models. Results obtained for ruthenium tris‐bipyridyl chloride and perchlorate salts are not stable with respect to irradiation time. The latter results suggest that a significant amount of ruthenium tris‐bipyridyl complex is photolyzed with the mild irradiation conditions used in these experiments.
The Surface Chemistry of Hydrocarbons on Transition Metal Surfaces: A Critical Review
Authors: Zaera Francisco
Published: November 2013

The catalytic chemical conversion of hydrocarbons on transition metals is at the heart of a good number of processes of industrial importance, including oil and food processing, pharmacological synthesis, manufacturing of specialty chemicals, and polymer production, to name a few. This is an old field that has advanced in great measure by process development work based on trial and error. It has only been in the last few decades, with the advent of a battery of new surface‐sensitive techniques, that it has been possible to address the fundamental questions on the basic chemistry behind those hydrocarbon conversion reactions. In this review we highlight some of the main ideas advanced in this field by modern surface‐science studies. Particular emphasis is given here to the pioneering work of Professor Somorjai's group as well as our more recent contributions. A discussion is provided on the state of the art of the knowledge available in terms of the elementary steps involved in the transformations of hydrocarbons on metals, as obtained in experiments performed under well‐controlled vacuum conditions; on the connection between that knowledge and the reactions that may prevail under the atmospheric pressures encountered in real catalytic processes; and on the key questions that remain unanswered to date and the possible future directions in this area of research.
The Rotational State Distributions of Photodesorbed Ammonia as a Local Probe of Corrugation
Authors: Bornscheuer Karl‐Heinz , Binetti Marcello , Hasselbrink Eckart
Published: November 2013

Photodesorption of ammonia follows a curved reaction path. Electronic excitation of, or electron attachment to, the adsorbate molecule leads to a transition from the pyramidal ground state to an excited state with planar geometry. During the short residence time in the excited state, the hydrogen atoms are accelerated towards the surface, resulting in an inversion of the molecule and a strong repulsion from the surface which eventually leads to desorption. In this paper, we present evidence that in the inverted geometry the molecule feels the corrugation of the surface potential on rotation around its symmetry axis. This gives rise to a strong torque in cases where the 3‐fold symmetry of the molecule is not matched by the lattice symmetry, resulting in energy transfer to the rotational degrees of freedom. Secondly, it is demonstrated that when both ammonia and oxygen are coadsorbed on a Ru surface, in which case the rotation of adsorbed NH3 is frustrated, a large fraction of the zero point energy is released as rotational energy.
Realistic Surface Science Models of Supported Catalysts: The Chromium Oxide Ethylene Polymerization Catalyst
Authors: Thüne P.C. , Niemantsverdriet J.W.
Published: November 2013

Depositing catalytically active particles onto flat, thin oxide films which have electric conductivity forms an attractive way to make supported catalysts suitable for surface science investigations. Here we describe the development of a model system for the chromium oxide on silica catalyst used in industry for the polymerization of ethylene, the so‐called Phillips catalyst. The model system, consisting of molecularly dispersed chromium ions, deposited by wet chemical impregnation on a thin silica film and anchored to it by treating it in oxygen, displays a representative activity for polyethylene formation.
Laser Diagnostics of Combustion Processes: From Chemical Dynamics to Technical Devices
Authors: Ebert Volker , Schulz Christof , Volpp Hans‐Robert , Wolfrum Jürgen , Monkhouse Penelope
Published: November 2013

Laser‐based in situ diagnostic techniques with high temporal, spectral, and spatial resolution have become valuable tools to study the molecular dynamics of gas‐phase and heterogeneous reactions as well as complex technical combustion processes. Results of recent experiments will be presented in which laser‐induced fluorescence, sum‐frequency generation surface vibrational spectroscopy, Rayleigh scattering, excimer laser‐induced fragmentation fluorescence, and high‐resolution tunable diode laser absorption spectroscopy were applied to investigate elementary chemical gas‐phase and catalytic combustion reactions, internal combustion engine processes, as well as coal combustion and waste incineration.
The Sulfinatodehalogenation Reaction
Authors: Huang Wei‐Yuan , Wu Fan‐Hong
Published: November 2013

Sulfinatodehalogenation is a simple and efficient reaction for the synthesis of polyfluoroalkane‐sulfinates and sulfonates. The reaction can also be applied for the polyfluoroalkylation of organic compounds. A brief account is given of its development and scope, reaction mechanism, and applications in organic synthesis.
Influence of Electrostatic Interactions on Complexes with Short O···O Hydrogen Bonds in Basic Salts of Pyridine Betaines and Acid Salts of ω‐Phenyloalkanocarboxylic Acids
Authors: Szafran Mirosław , Kowalczyk Iwona , Barczyński Piotr
Published: November 2013

The isostructural complexes [C5H5N+(CH2)nCOO]2HX and [C6H5(CH2)nCOO]2HK (n = 1–4), which differ in their counterions and charge on the ring, were synthesized, and their powder FT‐IR spectra analyzed. All complexes containing a charged pyridine ring are of Hadži type iii, characterized by an intense broad (continuum) absorption below 1600 cm−1typical of a short‐strong hydrogen bond (SSHB) with a delocalized proton and a singlevC=O band. The positively charged nitrogen atoms interact electrostatically with the X−ion and, additionally, with one of the oxygen atoms of the carboxylic group, producing a more or less symmetric environment of the H‐bonded proton, and stabilizing the SSHB. The broad absorption of [C6H5CH2COO]2HK is very similar to that of other pyridine complexes. Upon addition of methylene groups the broad absorption moves to higher wavenumbers, the O···O distance is elongated, and the H‐bonded proton becomes more localized. In the spectrum of [C6H5(CH2)4COO]2HK thevC=O andvasCOO bands were found at 1704 and 1641 cm−1, respectively, which shows that the H‐bonded proton is asymmetrically located. The observed variation of absorption with the number of CH2groups reflects changes of contacts between the K+ion and COO−groups.