bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Different Metal Cation Binding on the Proton Pumping in Bacteriorhodopsin
Authors: El‐Sayed Mostafa A. , Yang Difei , Yoo Seoung‐Kyo , Zhang Nancy 
Published: November 2013

AbstractThe first section of this paper is a detailed summary of studies made by us and others on metal cations binding to deionized bacteriorhodopsin (dIbR) and its variants. Our studies include the luminescence experiments of Eu3+ binding to dIbR and potentiometric studies of Ca2+ binding to dIbR, to deionized bR mutants, to bacterioopsin, and to dIbR with its C‐terminus removed. The results suggest the presence of two classes of binding sites, one class has two high‐affinity constants, and one has one low‐affinity constant. For Ca2+ binding, there is one metal cation in each of the two high‐affinity sites which are coupled to the charged aspartates 85 and 212 (known to be in the retinal cavity) but not coupled to each other. The low‐affinity class can accommodate 0–6 Ca2+ ions and most of them are bound to the surface. Mg2+ has a slightly smaller value for its binding constant to the highest‐affinity site. Thus, one expects more Ca2+ than Mg2+ bound to the two high‐affinity sites. In the second section, we summarize our recent study on the effect of metal cation charge density (Ca2+, Mg2+, Eu3+, Tb3+, Ho3+, Dy3+) on the kinetics of both Schiff base deprotonation and proton transport to the extracellular surface. For all metal cations, the apparent rate constant of the slow components of the deprotonation process is the same as that for the transport process at 22 °C. The temperature studies, however, show this apparent equality to be fortuitous and to result from cancellation of the contribution of the energy and entropy of activation. Thus, while the entropy of activation is positive for the deprotonation process, it is negative for the proton transport process. These kinetic parameters depend weakly on the charge density, but in an opposite sense for the two processes. These results suggest that the deprotonation is not the rate‐limiting step for the proton transport process. A possible mechanism is proposed in which a hydrated metal cation is used to induce the deprotonation of the protonated Schiff base and to dissociate one of its H2O molecules to donate the proton in the L → M process.
Structure and Function of Halorhodopsin
Authors: Oesterhelt Dieter 
Published: November 2013

AbstractA comprehensive review of the physiology, structure, and function of halorhodopsin (HR), the only known light‐driven anion pump, is presented. Beside the well‐studied transport function of HR in intact cells the article focuses on recent results about the molecular properties of HR. Overexpression and in vivo 2‐D crystallization allowed structural investigations at a level of 7 Å resolution. The results demonstrate a very close structural relationship with the proton pump bacteriorhododopsin (BR). The retinal binding site as well as a chloride binding site near the Schiff base in HR can be modeled with the side chains placed into the corresponding positions in the BR structural model. Mechanistically the vectorial catalytic cycle of HR is similar to that of BR, as suggested before (Oesterhelt et al., J. Bioenerg. Biomembr. 1992, 24: 181), and consists of photoisomerization of the retinal moiety which triggers chloride movement within the transport site towards the Schiff base. This is followed by an accessibility change from the extracellular (EC) channel to the cytoplasmic (CP) channel allowing chloride to be released into the cytoplasm. After reisomerization and reversion of the accessibility change, a chloride is rebound into the transport site from the extracellular surface through EC. In the absence of transported ions or the additional presence of azide, photoisomerization to 13‐cis is followed directly by an accessibility change and release of a proton from the Schiff base through CP. Blue light causes photoisomerization back to trans and the accessibility change is reversed. Uptake of a proton through EC completes proton transport from the outside to the inside. Depending on relative concentrations of chloride and azide, both modes of ion translocation operate in parallel and as alternatives during individual cycles of a molecule. Future experimentation will have to fill in the many details of this molecular model of ion transport.
Imaging Substrate‐Mediated Interactions
Authors: Kamna M.M. , Stranick S.J. , Weiss P.S. 
Published: November 2013

AbstractSurface features and adsorbates perturb the electronic properties of the surrounding substrate surface. This modifies the adsorption, dynamics, and chemistry of nearby atoms and molecules. Using scanning tunneling microscopy, we have imaged these perturbations and the resulting ordering and dynamics for benzene on Cu{111} at low temperature and dilute coverage. We discuss the important implications that substrate‐mediated interactions can have on the atomic‐scale mechanisms and control of film growth and heterogeneous selective catalysis.
Spontaneous Assembly in Organic Thin Films Spread on Aqueous Subphase: A Scanning Force Microscope (SFM) Study
Authors: Cohen Sidney R. , Weissbuch Isabella , Popovitz‐Biro Ronit , Majewski Jarek , Mauder Harald P. , Lavi Ronit , Leiserowitz Leslie , Lahav Meir 
Published: November 2013

AbstractStructure, morphology, and mechanical properties of mono‐ and several‐layer structures of amphiphiles or pure n‐alkane crystallites generated by spontaneous self‐assembly on aqueous subphase have been analyzed by scanning force microscopy (SFM). Pure‐component and heterogeneous mixtures of molecules were allowed to spread and self‐assemble without compression on an aqueous subphase. The self‐assembled films were transferred to an atomically smooth mica substrate by drainage for measurement using SFM. Results were compared with a variety of techniques including cryo‐transmission electron microscopy, grazing incidence X‐ray diffraction, X‐ray reflectivity, and reflectance/absorption infrared spectroscopy. Whereas the collaborative techniques provide spatially‐averaged information, we find that the SFM accesses both individual crystallites and amorphous material, thus providing unique information on the morphology, number of layers, and complementary structural features.
pH Influences on the Crystal Structures and Mechanistic Properties of a Hydrolytic Antibody
Authors: Charbonnier Jean‐Baptiste , Golinelli‐Pimpaneau Béatrice , Gigant Benoît , Green Bernard S. , Knossow Marcel 
Published: November 2013

AbstractAntibody CNJ206 catalyzes the hydrolysis of p‐nitrophenyl esters with significant rate enhancement and product specificity. We report here kinetic and affinity measurements for this antibody in the pH 4–9.5 range. We also report the X‐ray structures of CNJ206 Fab liganded with a transition‐state analog (TSA) and with one of the products of the hydrolysis, p‐nitrophenol, at pH 4. This product binds in the same hydrophobic pocket as the p‐nitrophenyl part of the TSA; its release at basic pH, where catalysis is usually measured, is facilitated by its ionized state and this avoids product inhibition. The conformation of the CNJ206 combining site is identical in this structure and in the previously determined structure of a CNJ206 Fab•TS A complex at pH 8. Taken together with the pH‐profile of the rate enhancement by CNJ206, the structural data support a mechanism for catalysis by CNJ206 involving stabilization of a tetrahedral oxyanion intermediate by the peptide NH groups of two consecutive residues in the H3 complementarity‐determining region.
Chain Shuffling: Investigations into the Specificity and Selectivity of Antibody Catalysis
Authors: Lo Chih‐Hung L. , Gao Changshou , Mao Shenlan , Matsui Kazuhiro , Lerner R.A. , Janda Kim D. 
Published: November 2013

AbstractThe antibody phage display system has been investigated as a vehicle for the potential altering of a catalytic antibody's specificity and chemical reactivity. Using previously identified catalytic antibodies, heavy and light “chain shuffling” experiments have been conducted. Catalytic activity and specificity requirements in terms of antibody complementarity‐determining regions were probed by interchanging heavy and light chain genes between antibodies that catalyze class‐similar but different chemical reactions with substrates that are enantiomerically opposed. The results were that antibody‐hapten binding specificity was only slightly altered, but catalytic activity was severely compromised.
A Shock Tube Study of the Reactions of H Atoms with COS, CS2, and H2S
Authors: Woiki Dirk , Roth Paul 
Published: November 2013

AbstractReactions of H atoms with COS, CS2, and H2S were studied behind reflected shock waves at temperatures between 1170 K and 1830 K and pressures around 1.0 bar by applying atomic resonance absorption spectroscopy (ARAS) for time‐resolved measurements of H atoms at Lα. The thermal decomposition of a few ppm ethyl iodide (C2H5I) was used as a H‐atom source. In the presence of a large excess of the molecular reactant COS, CS2, or H2S, a consumption of H was observed which follows a pseudo first‐order rate law. Rate coefficients for the reactions:magnified imagewere determined to be:k1 = 2.4 × 1014exp(–3415 K/T) cm3mol−1s−1k2 = 1.4 × 1015exp(–9250 K/T) cm3mol−1s−1k3 = 2.5 × 1014exp(–2890 K/T) cm3mol−1s−1
A Unified Strategy for the Total Synthesis of the Angucycline Antibiotics SF 2315A, Urdamycinone B, and the Shunt Metabolite 104–2
Authors: Kim Kyungjin , Boyd Vincent A. , Sobti Aditya , Sulikowski Gary A. 
Published: November 2013

AbstractTotal syntheses of the angucycline antibiotics SF 2315A (2), urdamycinone B (4), and the shunt metabolite 104–2 (5) are described, as well as an approach toward the synthesis of SF 2315B (3). All four syntheses feature a Diels–Alder cycloaddition between a bromojuglone derivative and an optically active diene (25a), the latter derived from (–)‐quinic acid. Subsequent key transformations include (i) stereocontrolled introduction of ring fusion oxygen functionality featured in SF 2315A (2) and SF 2315 B (3), (ii) preparation of C‐glycosyl juglone 53, and (iii) NMO mediated oxidative aromatization of 60.
From Chlorocyclobutanones to Cage Compounds. Strain, Proximity Effects, and Tandem Rearrangements
Authors: Hassner Alfred , Naidorf‐Meir Simcha 
Published: November 2013

AbstractA review of studies in our laboratory on the chemistry of α‐chlorocyclobutanones fused to 5‐, 6‐, and 8‐membered rings is presented. The major feature of such compounds is the high propensity to undergo cine substitution with nucleophiles, which is initiated by the intermediacy of oxidoallyl cations. The cine substitution products often undergo interesting transformations which become evident especially when the 4‐membered ring is fused to a tetrahydrofuran or a tetrahydropyran. In such cases, beta elimination of the alcohol chain with ring opening of the heterocyclic ring leads to formation of cyclobutenones, which undergo further transformations. Proximity effects as well as strain are responsible for unusual tandem rearrangements and formation of cage compounds.
Temperature and Overpotential Dependence of Long‐Range Electron Transfer across a Self‐Assembled Monolayer with Pendant Ruthenium Redox Centers
Authors: Finklea Harry O. , Ravenscroft Melissa S. 
Published: November 2013

AbstractMixed monolayers containing an electroactive thiol, HS(CH2)15CONHCH2pyRu(NH3)52+/3+, and a diluent thiol, HS(CH2)15COOH, on gold electrodes are examined in acetonitrile electrolyte (0.1 M LiClO4) as a function of overpotential and temperature. Kinetic and thermodynamic parameters from ca. −45 to +20 °C are obtained by cyclic voltammetry and chronoamperometry. Reorganization energies obtained from Tafel plots and Arrhenius plots both yield a reorganization energy of 0.8 eV for the redox centers.
Electron Hopping and Electronic Conductivity in Monolayers of Alkanethiol‐Stabilized Gold Nano‐Clusters at the Air/Water Interface
Authors: Lee Won‐Yong , Hostetler Michael J. , Murray Royce W. , Majda Marcin 
Published: November 2013

AbstractMorphology of Langmuir monolayers of gold clusters stabilized with a series of alkanethiols was investigated at the air/water interface with Brewster Angle Microscopy which revealed substantial differences depending on the length of the alkyl chains (clusters stabilized with C8 and C16 thiols were investigated). 2D electrochemical measurements carried out with line micro‐band electrodes showed negligible electronic conductivity of all monolayers even in their most compressed state, apparently due to the presence of the stabilizing alkyl chains on the surface of the clusters. The same electrochemical measurement showed, however, full redox conductivity in the monolayers of gold nano‐cluster stabilized with alkanethiols, 20% of which were terminated with ferrocene. In those cases, redox conductivity is supported by a facile electron hopping (self‐exchange rate constant was measured to be ≥ 4.4 × 106 M−1 s−1) between neighboring ferrocene/ferrocenium sites.
Electroreduction of Diheptylviologen in a Self‐Assembled Phospholipid Monolayer on Mercury and its Role as an Electron Transfer Mediator
Authors: Moncelli Maria Rosa , Herrero Roberto , Becucci Lucia , Guidelli Rolando 
Published: November 2013

AbstractThe electroreduction mechanism of diheptylviologen (V2+) across a self‐assembled dioleoylphosphatidylcholine (DOPC) monolayer supported on a mercury electrode has been investigated in aqueous 0.1 M KCl by the chronocoulometric technique. V2+is reduced in two consecutive charge steps, 2V2++ 3e → V+2and V+2+ e → 2V0, involving 3/2 and 1/2 of a faraday per mole of reactant, respectively. Both charge steps are controlled by the rate of the elementary coupling step V++ V0→ V+2. V2+acts as an electron transfer mediator from ferric and ferricyanide ions dissolved in the aqueous solution to the mercury surface across the DOPC monolayer, which is impermeable to these metal ions in the absence of V2+. The electron transfer mediation is more effective along the first charge step, 2V2++ 3e → V+2, and increases with the V2+concentration in the lipid monolayer less than proportionally, thus pointing to the radical cation V+as the most effective electron carrier from the mercury surface to the metal ions.
Electrochemical Comparison of Heme Proteins by Insulated Electrode Voltammetry
Authors: Cheng Jun , Terrettaz Samuel , Blankman Jeffrey I. , Miller Cary J. , Dangi Bindi , Guiles Ronald D. 
Published: November 2013

AbstractRelatively simple electrochemical probes of redox active proteins can yield a wealth of diverse information concerning their kinetic and thermodynamic reactivity, charge state, and transport rates. In this report, the electrochemical properties of three heme‐containing proteins are probed using Au electrodes derivatized with self‐assembled monolayers of ω‐hydroxyalkanethiols. Cytochrome c and b5 (wild type from horse and rat, respectively) display low reorganization energies (0.58 eV and 0.44 eV, respectively) and electronic coupling terms which are quite comparable to small redox molecule models. In contrast, metmyoglobin reduction is characterized by a somewhat higher reorganization energy (0.76 eV) and an order of magnitude reduction in its electronic coupling to the electrode. Upon binding oxygen, the reduced oxymyoglobin becomes electroinactive. This radical decrease in the oxymyoglobin redox reactivity is associated with structural and electronic differences caused by the spin‐state change induced by oxygen binding. The reactivity differences between these heme‐containing proteins are discussed in light of their biochemical function, evolutionary pressures, and structural differences.
Effect of pH, Fluorination, and Number of Layers on the Inhibition of Electrochemical Reactions by Grafted, Hyperbranched Poly(acrylic acid) Films
Authors: Zhao Mingqi , Bruening Merlin L. , Zhou Yuefen , Bergbreiter David E. , Crooks Richard M. 
Published: November 2013

AbstractWe report the electrode‐passivation properties of both fluorinated and unmodified hyperbranched poly(acrylic acid) (PAA) films as a function of pH and the number of PAA layers. Both cyclic voltammetry and ac‐impedance spectroscopy show that the extent of blocking increases with the number of layers, regardless of the solution pH. However, passivation resulting from unfluorinated PAA films decreases with increasing pH, while passivation due to fluorinated films increases with increasing pH. Three‐layer fluorinated films can increase the charge transfer resistance of the electrode by up to a factor of 6 × 104. Although Randles' equivalent circuit can be used to model the electrochemistry of electrodes covered with unfluorinated PAA, fluorinated PAA‐coated electrodes often require additional circuit elements due to the high resistance of these hydrophobic films.
Electrodeposited Quantum Dots. 6. Epitaxial Size Control in Cd(Se, Te) Nanocrystals on {111} Gold
Authors: Golan Yuval , Hatzor Anat , Hutchison John L. , Rubinstein Israel , Hodes Gary 
Published: November 2013

AbstractSize control in epitaxial Cd(Se, Te) quantum dots (QDs) electrochemically deposited on {111} textured Au is achieved by mismatch tuning. The formation of QDs as a form of relaxation of heteroepitaxial strain energy is demonstrated. The increased lattice parameter resulting from incorporation of small amounts of Te in the CdSe lattice leads to reduced mismatch‐induced strain energy and therefore larger QD size. While the QD interatomic spacings at the interface are shown to be unchanged due to the heteroepitaxy with the Au substrate, the perpendicular QD d‐spacings (along the c‐axis) strongly increase with increasing Te content due to strain relaxation.
Collisional Probing of the Transition‐State Structure of a Bimolecular Reaction
Authors: Salazar Macarena Garay , Ureña Angel González , Roberts Gareth 
Published: November 2013

AbstractThe total cross section σB(E) for the Ca(1D) + HBr → CaBr(B2Σ+) + H reaction as a function of collision energy has been measured using crossed atomic and molecular beams. The maxima exhibited by σB(E) with increasing energy are attributed to the opening of successive bending vibrational reaction channels that proceed via a [Ca(1D) ⃛ Br ⃛ H]‡ transition state. A dynamical model for the reaction may be constructed in terms of Landau‐Zener probabilities for curve crossing at two locations on the reaction path, coupled with a preference for consumption of transition‐state vibrational energy.
The Photodissociation of Ground and Vibrationally Excited Halogenated Alkanes
Authors: Melchior Aviva , Mark Lambert H. , Dagdigian Paul J. , Bar Ilana , Rosenwaks Salman 
Published: November 2013

AbstractThe dynamics of photodissociation of small halogenated alkanes, in both their ground and vibrationally excited states, is investigated. The yield of H, Cl(2P2/3), and Cl(2P1/2) fragments was measured by (2 + 1) resonance‐enhanced multiphoton ionization in a time‐of‐flight mass spectrometer. We report results from the 193 nm photolysis of ground state CHF2Cl, CH3CF2Cl, CH3CFCl2, and OH3Cl and the 237–243 nm photolysis of CH3Cl excited to the fourth C–H stretch overtone level. The branching ratios depend on the molecular structure, the accessed excited potential surfaces and, as a consequence, on the dissociation dynamics.
Fast GC—MS in Supersonic Molecular Beams
Authors: Amirav Aviv , Dagan Shai 
Published: November 2013

AbstractThe features of supersonic molecular beams (SMB) are used to improve gas chromatography—mass spectrometry (GC–MS) performance and establish a new method of fast GC–MS. In SMB, the sample compounds are vibrationally cooled such that their electron impact mass spectra are characterized by enhanced M+ peaks, together with library‐searchable fragments. A new ionization method, hyperthermal surface ionization (HSI), provides ultrasensitive ionization coupled with a tunable degree of selectivity for nitrogen‐containing drugs. SMB enables the use of very high carrier gas flow rates which, when a short megabore column is used, results in ultra‐fast GC–MS having conventional chromatographic peak widths. Thus, fast GC–MS in SMB can be performed with conventional quadrupole analyzers. The slightly reduced GC resolution can, in many cases, be compensated for by the selectivity of hyperthermal surface ionization or by the increased EI selectivity through enhanced M+. “Fast”, “very‐fast”, and “ultra‐fast” GC–MS are defined and demonstrated with drugs, and the ability to analyze underivatized steroids is shown. Practical examples are shown including ultra‐fast GC–MS of lidocaine in human plasma extract achieved in a few seconds and screening of other drugs, without any sample preparation or extraction, achieved in less than three minutes. We conclude that GC–SMB–MS exhibits a combination of faster analysis with improved sensitivity and selectivity, a wider range of molecules amenable to GC–MS, improved MS information, and higher a degree of flexibility.
Thermal Conductivity of Diamond Films: 0.5 μm to 0.5 mm
Authors: Graebner John E. 
Published: November 2013

AbstractA review of the thermal properties of chemical‐vapor‐deposited (CVD) diamond ranging in thickness from 0.5 μm to 0.5 mm is presented. The typical columnar microstructure of the material has a strong influence on the thermal properties, causing a steep gradient in both the in‐plane (κ‖) and normal (κ⊥) conductivities, as well as considerable anisotropy. Data for κ‖ from above room temperature down to liquid helium temperatures for high‐quality thick samples has revealed several types of phonon scattering centers preferentially located along grain boundaries. This model of dirty grain boundaries provides a framework for understanding the conductivity of thinner, lower‐quality material. The general difficulty of identifying microscopic sources of thermal resistance in CVD diamond is discussed, especially in view of the tendency for the concentrations of many types of defects to be highly correlated with each other. Finally, recent work on interfacial resistance between CVD diamond and Si substrate shows that the columnar microstructure has a strong influence for high‐quality films as thin as 2 μm.
Doping Diamond for Electronic Applications
Authors: Kalish Rafi 
Published: November 2013

AbstractDiamond exhibits extraordinary physical and chemical properties, many of which have already found application in tribology, thermal management, and optics. Furthermore, diamond is also a wide‐band‐gap semiconductor which, when doped, can lead to the realization of electronic and optoelectronic devices with exceptional properties. Diamond can now be doped p‐type, with boron, both during chemical vapor deposition (CVD) diamond film growth and by ion‐implantation, and n‐type, with phosphorus, during CVD growth. This paper reviews the current status of diamond doping and describes the electronic properties of the doped layers. Some potential applications of doped semiconducting diamond are described.