bluuebunny/crossref_metadata_2025 huggingface dataset:
Fine Structure in NMR Correlation Spectroscopy
Authors: Freeman Ray , Mcintyre Lisa
Published: November 2013

A simplified treatment of two‐dimensional homonuclear correlation spectroscopy (COSY) is proposed, based on a vector model and a consideration of the disturbance of energy level populations caused by the pulse sequence. It predicts the properties of diagonal and crosspeaks in the same manner as the more rigorous product operator treatment. Methods of studying the fine structure of COSY crosspeaks are discussed with a particular emphasis on the extraction of coupling constants when the splittings are poorly resolved. Three new schemes are described for the accurate measurement of couplings; they are called “J‐extension”, “J‐deconvolution”, and “J‐doubling”. All three rely on processing the experimental time‐domain signals with simple trigonometrical functions, followed by Fourier transformation. The J‐deconvolution and J‐doubling methods lend themselves to automated analysis by computer. These procedures can be applied to either active or passive couplings and yield an accuracy of ±0.04 Hz in the cases studied. J‐deconvolution may be implemented repetitively in order to reduce a COSY crosspeak to a single absorption peak at the chemical shift coordinates.
Multi‐band Adiabatic Inversion Pulses for Use with the 8th‐order Hadamard Spectroscopic Imaging Technique
Authors: Goelman Gadi , Leigh John S.
Published: November 2013

Rf pulses with frequency responses which correspond to the rows of the 8th‐order Hadamard matrix are developed. These pulses can be used in the B1 insensitive Hadamard Spectroscopic Imaging multi‐volume localization technique. It is shown how any adiabatic rf pulse, which inverts spin population at a well defined frequency band, can be modified to invert populations at several frequency bands simultaneously. Conditions on the frequency and amplitude functions which allow such modifications are defined. For increasing amplitude the interaction between the bands produces nonlinear irradiation at several frequencies. By using an integrated form of the Floquet formalism and perturbation theory, the interaction between the bands is described analytically by an effective Hamiltonian. From this description the conditions which guarantee minimization of the unwanted irradiation are defined. The experimental results agree very well with the theoretical predications.
Multiple Quantum Nuclear Coherences in Pulsed ENDOR Spectroscopy
Authors: Thomann Hans , Bernardo Marcelino
Published: November 2013

Experimental and theoretical aspects of multiple quantum (MQ) NMR coherence phenomena for paramagnetically coupled nuclei are presented. The spin interactions responsible for MQ NMR coherences observed in pulsed EPR and pulsed ENDOR (Electron Nuclear Double Resonance) are contrasted with those responsible for MQ coherences in pulsed NMR spectroscopy. MQ NMR coherences in pulsed ENDOR spectroscopy are demonstrated experimentally and described using an operator formalism approach. Detailed discussions of the phase incrementation technique for detecting MQ NMR coherences in ENDOR spectroscopy, different microwave excitation schemes for the preparation of nuclear spin order, off‐resonance excitation, and the evolution of MQ coherences under free precession are presented. Experimental results on a single crystal of irradiated malonic acid and on the conjugated polyene polymer poly acetylene are presented.
Surface Modification of CdS Colloids with Mercaptoethylamine
Authors: Kamat Prashant V. , de Lind van Wijngaarden Michael , Hotchandani Surat
Published: November 2013

Surface modification as well as size control of CdS colloids in acetonitrile has been achieved with mercaptoethylamine (MEA). The CdS emission yield increases as it interacts with the surface modifier. A decrease in the hole‐trapping yield was observed in optically excited CdS colloids which were modified with MEA. Use of such surface modifiers in bridging a semiconductor colloid with a gold colloid has also been demonstrated.
Comparative Semiconductor Photophysics of II‐VI (CdS) and I‐VII (AgBr) Quantum Dots
Authors: Johansson Katy , Cowdery Robin , O'Neil Michael , Rehm Julie , Mclendon George , Marchetti Alfred , Whitten David G.
Published: November 2013

When CdS and related II‐VI direct bandgap materials form semiconductor clusters in which the absorbance properties are dominated by quantum size effects, the emission properties are particularly sensitive to surface defects, which are associated with the unfilled valence of surface Cd2+ ions. These mid‐bandgap states result in large emission Stokes shifts. This shift can be overcome by binding ligand‐like amines to the surface. By contrast, the more ionic I‐VII materials (e.g., AgBr) show free exciton emission rather than surface defect emission. Since AgBr is an indirect bandgap material, the most obvious effect of size restriction is an increase in the free exciton probability which results from a breakdown in the momentum selection rules at small cluster size.
Size‐Quantized Nanocrystalline Semiconductor Films
Authors: Hodes Gary
Published: November 2013

This paper is a review of our work on nanocrystalline semiconductor films which exhibit pronounced size quantization effects in three dimensions, manifested by large blue‐shifts in their optical absorption spectra. The films are prepared by either chemical solution deposition (CdSe and PbSe) or by electrodeposition from nonaqueous electrolytes (CdSe and CdS). Except for PbSe, where the nanocrystals are surrounded by a matrix, the films are comprised of aggregated nanocrystals. Crystal size (typically from <4 nm to >6 nm), and therefore absorption spectra, can be controlled by deposition temperature, illumination during deposition (for chemically deposited films), solution composition, and post annealing. The crystal size dependence of chemically‐deposited films on experimental parameters (temperature, illumination, reactant concentrations) is discussed. CdSe nanocrystals were epitaxially electrodeposited on single‐crystal Au. The nanocrystal distribution (isolated or aggregated) could be controlled by deposition current and temperature. All these films exhibit photoelectrochemical behavior but no corresponding solid state photovoltaic behavior. A model is proposed based on electron/hole separation by kinetic differences in charge injection into an electrolyte rather than by a built‐in space charge layer in the semiconductor. The films can behave as both ‘n’ ‐ or ‘p’‐type, with respect to direction of photocurrent flow, by changes in the semiconductor surface properties and/or the electrolyte, in agreement with this model.
Charge Transfer at High Excitation Power of Solids
Authors: Mikhelashvili M.S. , Kapinus E.I.
Published: November 2013

Electron transfer between excited donor molecules followed by the back reaction is treated theoretically for a solid solution at high excitation power. An expression for the average donor cation probability P+(t) is derived. Calculations of the time dependence for P+(t) are presented. The results indicate that the maximum value of P+(t) in the nonlinear quenching process is less than the corresponding values of P+(t) for the linear quenching at a low excitation power due to the depletion of the acceptors with time t. The restriction of the reaction volume slows down the charge separation if the back charge transfer takes place.
Analytic Second Derivatives of the Potential Energy Surface
Authors: Handy Nicholas C. , Tozer David J. , Laming Gregory J. , Murray Christopher W. , Amos Roger D.
Published: November 2013

One of J. A. Pople's leading contributions in ab initio quantum chemistry was his 1979 paper in which he and his colleagues presented calculations for the analytic second derivatives of the Self Consistent Field Potential Energy surface. This led to the automatic characterization of stationary points as minima or transition states. Recently there has been an upsurge of interest in computational density functional theory (DFT). Here we describe our implementation of analytic gradients and second derivatives for the Kohn‐Sham potential energy surface. This parallels similar developments by Pople and his coworkers. We examine Pople's idea of differentiating the weights in the quadrature scheme to ensure that the energy gradient is exactly zero at the energy minimum. We present some calculations on small molecules which are as near ‘exact’ as possible for the LDA and BLYP functional which we use. In other words we use large basis sets and a large number of quadrature points to evaluate the extra (nonanalytical) integrals. We do not use any fitting procedures and no other approximations are introduced.
Scaling Factors for Obtaining Fundamental Vibrational Frequencies and Zero‐Point Energies from HF/6–31G* and MP2/6–31G* Harmonic Frequencies
Authors: Pople John A. , Scott Anthony P. , Wong Ming Wah , Radom Leo
Published: November 2013

New scaling factors have been determined for obtaining fundamental vibrational frequencies and zero‐point vibrational energies from harmonic frequencies calculated at the HF/6–31G* and MP2/6–31G* levels. The scaling factors for the fundamental frequencies have been derived from a comparison of a total of 1066 calculated frequencies for 122 molecules with corresponding experimental values, while the zero‐point energy scaling factors were determined from a comparison of the computed values with the experimental zero‐point energies for a set of 24 molecules. The scaling factors recommended are, respectively, 0.8929 and 0.9427 for HF/6–31G* and MP2/6–31G* fundamental frequencies, and 0.9135 and 0.9646 for HF/6–31G* and MP2/6–31G* zero‐point energies. RMS errors were determined to be around 50 cm−1 for the HF and MP2 fundamental frequencies, and around 0.4 kJ mol−1 for the HF and MP2 zero‐point energies.
Combining Synchronous Transit and Quasi‐Newton Methods to Find Transition States
Authors: Peng Chunyang , Bernhard Schlegel H.
Published: November 2013

A linear synchronous transit or quadratic synchronous transit approach is used to get closer to the quadratic region of the transition state and then quasi‐newton or eigenvector following methods are used to complete the optimization. With an empirical estimate of the hessian, these methods converge efficiently for a variety of transition states from a range of starting structures.
Reaction of Sr with CH2Cl2, CHCl3, and CCl4; Laser‐Induced Fluorescence Studies on Relaxed and Unrelaxed SrCl
Authors: Keuzer Freek , Bulthuis Jaap , Stolte Steven
Published: November 2013

A combined spectroscopic and chemical study is performed on thermal and nonthermal SrCl. The Δv = 0 sequence of the B2Σ ← X2Σ electronic transition is used for absorption spectroscopy up to high vibrational quantum numbers v with the technique of laser‐induced fluorescence. Effective spectroscopic constants are derived that are valid up to high v. SrCl is investigated both as a product of oven reactions and of the reaction of Sr beam atoms with the chlorinated methane molecules in the observation region (henceforth referred to as the gas‐phase reaction), leading to thermal and nonthermal spectra, respectively. One of the possible oven reactions, the metal‐salt reaction Sr + SrCl2 → 2SrCl, yields a thermal spectrum with a vibrational temperature equal to the oven temperature. The reaction Sr + CH2Cl2 → SrCl + CH2Cl apparently has a small cross section for the gas phase, since only a thermal spectrum is observed. The reaction Sr + CHCl3 → SrCl + CHCl2 yields a combined thermal and nonthermal spectrum. The gas‐phase reaction leads to SrCl product molecules with a vibrational population distribution peaked around v = 17. The reaction Sr + CCl4 → SrCl + CCl3 has a large cross section for the gas phase with a distribution peaked around v = 27. In this reaction, nearly all available energy is disposed into internal energy of the SrCl product.
Raman Studies of Hydrogen Bonding in Polyamides
Authors: Triggs Nancy E. , Valentine James J.
Published: November 2013

We report Raman and pre‐resonant Raman spectra of the polyamides N,N‐ tetramethylene bisbutamide, N,N‐hexamethylene bishexamide, and 7,14‐diazacyclotetradecane‐1,6‐dione, as well as of a low molecular weight prepolymer of nylon 6,6 aimed at characterizing the nature of hydrogen bonding in these compounds. The relative intensities of the C=O stretch and C‐N stretch bands, the frequency width of the C=O band, the frequency of the N‐H stretch band, and the frequency width of the N‐H band indicate that these compounds do not show the Raman signatures of hydrogen bonding that we have established in our previous studies of many model amides. In this regard, these polyamides behave like the lactams 2‐azacyclononanone and 2‐azacyclotridecanone, for which all the Raman spectral indicators of hydrogen bonding are similarly negative. These results indicate that whatever the nature of the intermolecular interactions in these polyamides, they do not result in the changes in vibrational and electronic structure that we believe are associated with hydrogen bonding.
Derivation of Class II Force Fields. III. Characterization of a Quantum Force Field for Alkanes
Authors: Maple J.R. , Hwang M.‐J. , Stockfisch T.P. , Hagler A.T.
Published: November 2013

Recently, a quantum mechanical Class II force field (QMFF) was derived from a fit of HF/6–31G* ab initio energy and energy derivative data for alkanes, and a comparison of this quantum force field and the ab initio energy and energy derivatives was presented. In this work, the quantum force field is further evaluated with regard to its accuracy, and, more importantly, transferability. A detailed comparison between structures, frequencies, and energies calculated from quantum mechanics and from the classical analytical form is given for a set of molecules selected from both those used in the original training set and molecules selected from outside the training set. None of these properties were used directly in the original derivation of the force field. In order to assess the importance of anharmonic and coupling interactions that occur in and contribute to molecular energy surfaces, the results are compared to a diagonal quadratic force field. It is demonstrated that the QMFF functional form is capable of calculating the ab initio bond lengths, bond angles, torsion angles, and conformational energy differences to an rms accuracy of 0.003 Å, 0.4°, 1.2°, and 1.0 kcal/mol, respectively. This compares quite well to corresponding deviations of 0.006 Å, 0.8 Å, 2.3°, and 3.3 kcal/mol for a harmonic diagonal force field. Excluding three‐ or four‐membered rings, the QMFF rms frequency deviations were 24 cm−1, which again is much better than the ˜100 cm−1 deviations for the harmonic diagonal force field. Larger average rms frequency deviations of 36 and 71 cm−1 were found with QMFF for molecules with three‐ and four‐membered rings. An in‐depth analysis of C‐H and C‐C bond length, H‐C‐H, H‐C‐C, and C‐C‐C bond angle, and C‐C‐C‐C torsion angle deviations is also presented, along with a similar characterization of frequency deviations in C‐H stretching, C‐C stretching, C‐C‐C bending, and torsion modes. It is concluded from these results that the use of quantum energy surfaces allows us to derive a (Class II) functional form which is not only more accurate, but also more transferable than previous generation force fields.
Dynamics of tRNA: Experimental Neutron Spectra Compared with a Normal Mode Analysis
Authors: Nardi F. , Doster W. , Tidor B. , Karplus M. , Cusack S. , Smith J.C.
Published: November 2013

A comparison is made of experimental inelastic neutron scattering spectra from tRNA with spectra calculated from a normal mode analysis of the molecule. The experimental data indicate that a dynamic transition occurs with temperature, as is seen in proteins. At low temperatures a broad peak is seen in the dynamic structure factor, due to the lowest frequency collective modes. This peak is centered at ˜40 cm−1, somewhat higher in frequency than that observed in small globular proteins. The vibrational frequency distribution calculated from the normal mode analysis rises to a broad maximum at 50 cm−1, in general accord with the experiment. However, the lowest frequency vibrations in the harmonic model (<40 cm−1) are not present in the experimental sample. Possible reasons for this are discussed.
Effect of Solvent Quality on Pure and Mixed Brushes
Authors: Chen C. , Dan N. , Dhoot S. , Tirrell M. , Mays J. , Watanabe H.
Published: November 2013

We investigate, theoretically and experimentally, the effect of solvent quality on pure, one‐component, and two‐component brushes. Both mean‐field and self‐consistent field models are developed, and their predictions compared to surface forces experiments on polystyrene and mixed polystyrene–polybutadiene brushes. We find that in pure brushes the structure and interactions between surfaces are highly sensitive to solvent quality. In a good solvent, the brush is extended and the interactions are repulsive, while in a poor solvent the brush is “collapsed” and the interactions are strongly attractive. Mixing two incompatible chains significantly reduces the sensitivity of the brush to solvent properties. While one of the chains collapses in a selective solvent, the other chain remains solvated, thus providing long‐range repulsive interactions between surfaces. Our experiments show that the interactions between surfaces carrying a 1:1 mixed brush of styrene–butadiene are repulsive even in hexane, a poor solvent for polystyrene. Theoretically, we calculate that incorporating only 10% of an equi‐molecular‐weight chain into a collapsed brush can eliminate attractive interactions between surfaces.
Structure and Shear Response in Nanometer‐Thick Films
Authors: Thompson Peter A. , Robbins Mark O. , Grest Gary S.
Published: November 2013

Simulations of the structure and dynamics of fluid films confined to a thickness of a few molecular diameters are described. Confining walls introduce layering and in‐plane order in the adjacent fluid. The latter is essential to transfer of shear stress. As the film thickness is decreased, by increasing pressure or decreasing the number of molecular layers, the entire film may undergo a phase transition. Spherical molecules tend to crystallize, while short‐chain molecules enter a glassy state with strong local orientational and translational order. These phase transitions lead to dramatic changes in the response of the film to imposed shear velocities v. Spherical molecules show an abrupt transition from Newtonian response to a yield stress as they crystallize. Chain molecules exhibit a continuously growing regime of non‐Newtonian behavior where the shear viscosity drops as v−2/3 at constant normal load. The same power law is found for a wide range of parameters, and extends to lower and lower velocities as a glass transition is approached. Once in the glassy state, chain molecules exhibit a finite yield stress. Shear may occur either within the film or at the film/wall interface. Interfacial shear dominates when films become glassy and when the film viscosity is increased by increasing the chain length.
Metals in Ancient Israel: Archaeological Interperetation of Chemical Analysis
Authors: Shalev Sariel
Published: November 2013

Over a thousand metal finds are now known from Chalcolithic and Early Bronze habitation sites, burial caves, and hoards in Israel and Jordan. To answer the question as to how these artifacts were made, more than 200 objects were sampled for metallographic analysis and for chemical analysis by electron‐probe X‐ray microanalysis and by atomic absorption spectrophotometry.

In the Chalcolithic period (4th millennium BC), within a confined zone of southern Israel and Jordan, three entirely different groups of metal objects were found together. Various materials (Cu‐As‐Sb; Au; Cu) from totally separate sources were used in diverse production methods to produce specific classes of objects, of a specific shape and color, totally different from one another.

In contrast, the components of Early Bronze Age (3rd millennium BC) metal production indicate a fundamental change in the structure and level of craft specialization. This change may be recognized mainly by the unity of the repertory of objects and the use of the same source‐metal (Ag; Au; Cu) for a wider range of products, as well as by the total technological and geographical separation between extraction and production.

The transformation from proto‐urban to urban society documents an important stage of social, economic, and political development in Early Bronze Age Israel and Jordan. Many explanations have been offered for this transformation, most of them based on external intervention or stimulus. This paper adds to the existing arguments for the beginning of urbanization, the missing local socioeconomic factor, based on changes in social complexity as reflected in the first two thousand years of metallurgy.
Application of Artificial Pigments to Structure Determination and Study of Photoinduced Transformations of Retinal Proteins
Authors: Nakanishi Koji , Crouch Rosalie
Published: November 2013

The protonated Schiff bases of all‐trans‐retinal and its double bond isomers, 11‐cis‐ and 13‐cis‐retinals, comprise the chromophores of bacteriorhodopsin, sensory rhodopsin, rhodopsin, and the Chlamydomonas photoreceptor pigment. Absorption of photons by these chromophores is directly responsible for the functioning of the various photopigments. Clarification of their extremely complex structures and mechanisms requires multidisciplinary collaboration. The study of synthetic retinal analogs and pigments reconstituted from analogs provides a powerful and indispensable tool for such clarification. This article summarizes the application of retinal analogs in the bioorganic, biophysical, and biochemical investigations of the various retinal pigments.
Application of NMR‐Spectroscopy to Retinal Proteins
Authors: Engelhard Martin , Bechinger Burkhard
Published: November 2013

The application of NMR spectroscopy to the retinal proteins bacteriorhodopsin (BR) and rhodopsin is reviewed. 2H‐, 15N‐, and 13C‐solid‐state NMR spectroscopy have contributed considerably to understanding the conformation and chemical environment of the protonated retinylidene Schiff base in BR as well as in rhodospin. The data from both pigments clarified the mechanism of the opsin shift which is quite different for rhodopsin and BR. An analysis of the chemical shifts of isotopically labeled aspartic acid, tyrosine, and proline incorporated into BR‐provided evidence for the protonation state of Asp and Tyr, and the isomerization state of the Xaa—Pro peptide bond, respectively. Solid‐state NMR spectroscopy was also applied to the investigation of the photocycle intermediates of BR, as well as bathorhodopsin and metarhodopsin II, which are formed after light‐activation of rhodopsin. Solution NMR spectroscopy of BR solubilized in detergents or organic solvents, as well as of opsin‐derived peptide segments, was also applied to the investigation of the two‐ and three‐dimensional structure of BR.
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

The 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

A 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

Surface 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

Structure, 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

Antibody 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

The 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

Reactions 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 image

were determined to be:

k1 = 2.4 × 1014exp(–3415 K/T) cm3mol−1s−1

k2 = 1.4 × 1015exp(–9250 K/T) cm3mol−1s−1

k3 = 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

Total 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

A 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

Mixed 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

Morphology 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

The 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

Relatively 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

We 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

Size 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

The 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

The 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

The 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

A 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

Diamond 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.
Volume and Enthalpy Changes upon Photoexcitation of Bovine Rhodopsin Derived from Optoacoustic Studies by Using an Equilibrium between Bathorhodopsin and Blue‐Shifted Intermediate
Authors: Gensch Thomas , Strassburger Julia M. , Gärtner Wolfgang , Braslavsky Silvia E.
Published: November 2013

A complex multistep model including an equilibrium was used for the first time to analyze data obtained by laser‐induced optoacoustic spectroscopy (LIOAS) with bovine rhodopsin in washed membranes (T = 5–32°C). The thermal equilibrium was between bathorhodopsin, batho, and the blue‐shifted intermediate (BSI), i.e., batho ⇄ BSI. This analysis considers a 14‐ns intermediate detected by LIOAS at 25°C (with similar decay activation parameters as those reported for BSI in solubilized rhodopsin). The energy content of lumirhodopsin (lumi) and the structural volume difference between lumi and rhodopsin were essentially the same (Elumi. = 80 kJ/mol and ΔVlumi–rho = 40 mL/mol) for both a model based on a simple batho → BSI → lumi sequence and one including the batho ⇄; BSI equilibrium. However, the structural volume changes for the individual steps batho → BSI and BSI → lumi were markedly changed by the introduction of the equilibrium. With the rate constant for the forward reaction batho → BSI for solubilized rhodopsin determined by Hug et al. (Hug, S.J.; Lewis, W.J.; Einterz, C.M.; Thorgeirsson, T.E.; Kliger, D.S. Biochemistry, 1990, 29, 1475–1485) the structural volume changes obtained with the equilibrium model are ΔVBSI‐batho = 79 mL/mol and ΔVlumi‐BSI = −44 mL/mol. The resulting batho → BSI expansion is larger than with the sequential model, and ΔVlumi‐BSI is now a contraction instead of an expansion. A small expansion of 5 mL/mol is derived for the formation of batho with both models. The estimated energy content of BSI is clearly higher than the value of lumi. The structural volume changes between batho, BSI, and lumi derived from the equilibrium model correlate better than those from the simple sequential model with the chromophore transition dipole moment changes determined in the literature using linear dichroism measurements. The structural volume changes are discussed in terms of the variations upon transformation of the chromophore–protein interactions.