bluuebunny/crossref_metadata_2025 huggingface dataset:
Hyperfine Interactions in the Lowest Triplet State of Pyridine
Authors: Groenen E.J.J. , Buma W.J. , Schmidt J.
Published: November 2013

Results are reported of nitrogen and deuterium hyperfine studies of the triplet state of pyridine‐d5 as a guest in a single crystal of benzene at 1.2 K. Through the use of electron spin echo (ESE) techniques complete hyperfine tensors have been obtained: for nitrogen from the ESE detected EPR spectra and for the para‐deuterium atom from the modulations of the ESE envelope. These tensors unambiguously show that the molecule is no longer planar in the lowest triplet state T0. Pyridine's structure considerably changes upon excitation, but the mirror plane perpendicular to the molecule is preserved. Experimental and theoretical evidence is presented for the fact that this deformation is an intrinsic property of T0 and is not induced by the crystal field. About fourty percent of the triplet electron spin density is found to be localised in the π‐orbital of nitrogen, about ten percent in the lone pair orbital of nitrogen and somewhat more than thirty percent in the π‐orbital of the para‐carbon atom.
Steric Modulation of the Porphycene System by Alkyl Substituents: 9,10,19,20‐Tetraalkylporphycenes
Authors: Vogel Emanuel , Köcher Matthias , Lex Johann , Ermer Otto
Published: November 2013

Porphycene (2), a planar structural isomer of porphyrin (1) recognized and synthesized only recently, exhibits short N … N distances allowing exceptionally strong N‐H … N hydrogen bonds to be formed. Although the N4‐coordination hole of 2 is smaller than that of 1, the new tetrapyrrolic macrocycle is capable of complexation with a broad spectrum of metal ions to give the respective metalloporphycenes. In accord with model considerations, both N‐H … N hydrogen bonding and complexation of 2 may be modulated by peripheral alkyl groups through changes in the geometry of the porphycene skeleton arising from non‐bonded repulsions between the substituents. In this publication are delineated some of the consequences of structural variation of 2 by introduction of alkyl groups at the 9,10,19,20‐positions.
Photodynamics of Small Aliphatic Ketones in a Supersonic Jet Expansion
Authors: Haas Yehuda , Zuckermann Hanna
Published: November 2013

The photodynamics of acetone and some other simple aliphatic ketones in the nπ* state are discussed in the light of recent results obtained in seeded supersonic beams. The Born‐Oppenheimer approximation is used to describe the sequence of events beginning with light absorption and ending in molecular fragmentation. Intersystem crossing is shown to be an important process even for the isolated molecule. Its rate increases with the internal energy and may be related to the density of states in the triplet state. For all molecules studied so far, the results can be rationalized by assuming that dissociation takes place on the triplet surface, the S1 surface being stable in the energy range pertinent to these experiments (up to 35,000 cm−1 above the ground state). Fluorescence spectroscopy may be used also to detect small clusters. In the case of acetone, their presence is indicated by the decrease in the intensity of some spectral lines as a function of cooling efficiency. The results are used to estimate an upper limit for the van der Waals binding energies.
Light Scattering Probes of the H + H2 Reaction
Authors: Krause Jeffrey L. , Shapiro Moshe
Published: November 2013

We present calculated Raman and CARS (coherent anti‐Stokes Raman scattering) spectra of the collinear H + H2 reaction. These spectra, obtained by detuning the laser frequencies from all H2 absorptions, show strong enhancements as the collision energy on the ground state potential energy surface is scanned through a reactive scattering resonance. We also demonstrate that the Rayleigh scattering and degenerate four‐wave mixing spectra show enhancements greater by orders of magnitude than the corresponding Raman and CARS peaks. The experiments suggested in this paper offer a unique, direct method for obtaining information about the vibrational dynamics of the transition state of chemical reactions.
Superexchange‐Assisted Through‐Bridge Electron Transfer: Electronic and Dynamical Aspects
Authors: Kosloff Ronnie , Ratner Mark A.
Published: November 2013

The effects of electronic structure on bridge‐assisted electron transfer are considered. Using static perturbation theory, time‐dependent perturbation theory, and direct time‐dependent dynamics within generalized tight binding models, we examine the role of energy gaps, relative energetics of donor and acceptor orbitals with hole‐type and electron‐type superexchange sites, damping and dephasing, and overall energetics in electron transfer. We find that a generalization of the simple McConnell relationship to nonresonant transfer can in fact be made, but that no simple formula describes all limits; this is important in applications to a number of systems, including photosynthetic reaction centers, in which such superexchange occurs. The dynamical studies indicate some important and unexpected phenomena: these include quantum interferences between different pathways, recurrences and oscillations, and competitive effects of hole‐type and electron‐type superexchange. We suggest that direct dynamical study, as has begun to appear from several laboratories, provides an excellent way to visualize the intermediate state contributions to intramolecular electron transfer processes.
Bixon‐Jortner Revisited
Authors: Kommandeur Jan , Meerts W. Leo
Published: November 2013

After twenty years, the theory of radiationless transitions in molecules is reviewed. Its qualities and its strengths are discussed. It is pointed out, however, that this theory does not explain properly the quantum yield for nonresonant excitation, which should approach unity for large values of detuning. Insertion of an intermediate state remedies this situation and leaves the theory largely unaffected. The requirement of an intermediate state may explain the rather arbitrary variation of quantum yields among organic molecules and it may also be responsible for the rather too large number of interacting states observed in a high‐resolution molecular eigenstate spectrum.
Kinetically Controlled Aggregation in Reactive Adsorbate Overlayers
Authors: Becker Oren M. , Silverberg Marvin , Ben‐Shaul Avinoam
Published: November 2013

The kinetics of surface chemical reactions depend critically on the lateral distribution of the adsorbed reactants. In some cases, the adsorbates are aggregated into islands and the rate of reaction is strongly influenced by the structural (sizes and shapes) and energetic (lateral interaction potentials) characteristics of the aggregated overlayer. Adsorbate aggregation or segregation on surfaces may be induced by a variety of mechanisms, three important types of which are briefly discussed here. The first process is driven by strong lateral interactions between the adsorbed particles, which favor their organization in an ordered two‐dimensional phase, but because of kinetic constraints the system only reaches a long‐lived metastable state characterized by finite islands with highly ramified edges. A somewhat more complex aggregation‐segregation process, in a system comprised of two interacting adsorbate species, is also described, and the consequences with respect to surface reaction kinetics are demonstrated. The second aggregation process reflects (Eden‐type) island formation during adsorption of molecules from the gas phase. More specifically, these islands result from the so‐called (extrinsic) precursor‐mediated chemisorption mechanism. Finally, we discuss the segregation of adsorbed reactants induced by the bimolecular annihilation reaction A + B → 0, under steady‐state conditions. Unlike in the first example, this segregation process takes place even in the absence of adsorbate interactions (except for the reactive A‐B interaction) and is most pronounced in the absence of particle diffusion.
Coherent Vibrational Wave Packet Dynamics in Femtosecond Laser Excitation of Diatomic Molecules
Authors: Letokhov V.S. , Tyakht V.V.
Published: November 2013

A scheme is discussed for real‐time observation of a finite vibrational motion of diatomic molecules. Observation schemes based on the Franck‐Condon principle, i.e., the “persistence” of a coordinate wave packet in an ultrashort excitation, are proposed.
Dynamic Behavior of Individual Rovibronic States in S1 Benzene
Authors: Schubert Ulrich , Riedle Eberhard , Neusser Hans J. , Schlag Edward W.
Published: November 2013

Pulsed Doppler‐free two‐photon excitation of single rotational states of the 141 vibronic state of benzene with a resolution of 70 MHz is employed to investigate the influence of molecular rotation on the decay behavior of these states. The analysis of the completely resolved (Δv = 15 MHz) spectrum of the 1410 band, measured with a CW laser, makes it possible to specify whether individual states are perturbed by other (“dark”) S1 states and allows the precise determination of the degree of admixture of these background states. The vibrational identity of the background states is known from emission spectra of single rovibronic states. Unperturbed rovibronic states were investigated up to J'K' = 6761, and a pure exponential decay was found which does not depend on molecular rotation in accord with a nonradiative decay of S1 benzene in the statistical limit. The decay of perturbed states, which was also found to be purely exponential, depends strongly on the degree of admixture of the background state and on its vibrational identity. Values of the decay time of two identified “dark” zero‐order S1 vibrational states, which cannot be directly excited by optical transitions, are determined by evaluation of the decay behavior of the perturbed states.
Homogeneous Desulfurization of Thiols and Sulfides by Yb[N(SiMe3)2]2.2 THF. Relevance to Heterogeneous and Biological Desulfurizations and the Synthesis of Lanthanide(II) Sulfides
Authors: Gretz Efi , Vetter William M. , Stecher Hilmar A. , Sen Ayusman
Published: November 2013

Yb[N(SiMe3)2]2·2THF was found to desulfurize thiols (RSH) and dibenzyl sulfide. With thiols, the extent of desulfurization was a function of the relative stability of the corresponding radical, R·. Radicals were also involved in the desulfurization of dibenzyl sulfide. A unified mechanism involving a series of one‐electron redox steps leading to the generation of organic radical intermediates has been proposed.
Molecular Adsorption on Porous Silica Gels from Binary Solutions
Authors: Drake J. M. , Levitz Pierre , Klafter Joseph
Published: November 2013

In this paper we present a detailed experimental study of molecular adsorption on interfaces of silica gels from binary solutions of alcohol/toluene. The adsorption measurements are corroborated with infrared spectra of the surface hydroxyl groups and with NMR results. The adsorption isotherms are analyzed within the framework of the Everett approach and possible scaling relations between alcohol monolayer capacities and adsorbate cross sections are discussed. We conclude that reliable morphological information on the interfaces cannot be obtained from these adsorption experiments.
Synthesis of (4S, 10R, 11S)‐4‐Methyl Juvenile Hormone I by Using Chiral Building Blocks of Biochemical Origin
Authors: Mori Kenji , Fujiwhara Mitsumko
Published: November 2013

The title compound 1 was synthesized starting from (2S, 3S)‐2‐ethyl‐3‐hydroxy‐2‐methylcyclohexanone (B) and (R)‐3‐methyl‐5‐pentanolide (3). The key step for the preparation of B was the reduction of the corresponding diketone with a yeast, Pichia terricola KI0117, and that for the preparation of 3 was pig liver esterase (PLE)‐catalyzed hydrolysis of C to give D.
Synthetic Receptors Possessing Non‐Covalent, Macrocyclic Rings
Authors: Libman J. , Tor Y. , Dayan I. , Shanzer A. , Lifson S.
Published: November 2013

In an attempt to provide access to biomimetic ion binders we aimed at molecules that would adopt conformationally restricted arrangements by virtue of non‐covalent, intramolecular interactions, and allow extension by suitable ion binding sites. This article introduces four Types of C3‐symmetric trispeptides, which satisfy both of these requirements. These trispeptides have been assembled from 1,3,5‐tris(aminomethyl)benzene (Type 1), tris(2‐aminoethyl)amine (Type 2), and two homologous triscarboxylates (Types 3 and 4) as anchors by symmetric extension with amino acid residues through peptide linkages. Spectral examination, supported by EFF calculations, demonstrates that all these compounds adopt chiral, propellerlike conformations which are stabilized by interstrand H‐bonds between amide linkages of different kinds. The stability of these conformations at equilibrium depends on the nature of the anchor, the amino acid residue and the solvent. Their H‐bond patterns share common features by consistently generating 15‐membered H‐bond rings. The differences between the four Types of trispeptides are interpreted in terms of a subtle balance between (i) stabilization through H‐bond formation, and (ii) imposed strain and entropy loss through the formation of non‐covalent, polycyclic arrangements. The success of this approach in providing biomimetic analogs of siderophores (iron carriers of microbial origin), by extension with catecholate or hydroxamate binding sites, is also indicated.
Activation of Glycerophosphocholine Phosphodiesterase in Friend Leukemia Cells Upon In‐Vitro Induced Erythroid Differentiation. 31P and 1H NMR Studies
Authors: Podo Franca , Carpinelli Giulia , Ferretti Amalia , Borghi Paola , Proietti Enrico , Belardelli Filippo
Published: November 2013

This paper reports the results of 31P and 1H NMR studies on alterations of glycerophosphocholine phosphodiesterase (EC 3.1.4.2) activity in Friend leukemia cells, upon in vitro induced erythroid differentiation, in which cells undergo a transition from a highly proliferative (proerythroblastic) to a more mature (normoblastic) state. Experiments on cell homogenates incubated in the presence of added glycerophosphocholine (GroPCho) demonstrated that in differentiated cells the activity of GroPCho phosphodiesterase was at least three times higher than in undifferentiated control cells. Activation of the same enzyme was also observed in previous studies on FLC tumors implanted in syngeneic mice and treated in vivo with antitumor cytokines. These results, together with the decrease of GroPCho reported also in other cell systems undergoing cell transitions to more mature forms, suggest the hypothesis that an activation of GroPCho phosphodiesterase might play a role in cell maturation and, perhaps, also in tumor cell proliferation. An interpretation is then proposed of the alterations observed in the levels of phospholipid precursors and/or catabolites in FLC in vitro and in vivo, in light of possible correlations between phospholipid turnover, cell stimulation, and signal transduction.
The Concept of FID‐detected Hole‐burning in Pulsed EPR Spectroscopy
Authors: Wacker Thomas , Sierra Gustavo A. , Schweiger Arthur
Published: November 2013

A new class of pulsed EPR experiments, based on FID‐detected hole‐burning, is introduced. A transient spectral hole burnt into an inhomogeneously broadened EPR line by means of a selective microwave pulse is shifted or broadened by different types of perturbations and is subsequently recorded in a single experiment via an FID following a nonselective microwave pulse. The proposed approach often exceeds corresponding electron spin‐echo experiments with respect to sensitivity and resolution. A number of applications of the FID‐detected hole‐burning technique are discussed and the predicted features of the new experiments are verified by model calculations and experiments.
Pulsed ESR at 140 GHz
Authors: Prisner T.F. , Un S. , Griffin R.G.
Published: November 2013

We report pulsed electron spin resonance (ESR) experiments at a static magnetic field (B0) of 5.0T, corresponding to a microwave frequency of ˜140 GHz for g = 2 electrons. The experiments were performed with a transmission spectrometer, utilizing a 300 watt extended interaction klystron (EIK) operating in pulsed mode, together with a crossed waveguide Fabry‐Perot resonator which provided 30–40 dB of receiver isolation. Signal averaging was accomplished by mixing the pulse from the EIK with a 139.95 GHz reference oscillator, which was subsequently mixed with a local oscillator to generate a trigger signal for a digital oscilloscope. Concurrently, the ESR signal was mixed to an intermediate frequency using a second low frequency oscillator which was phase‐locked to the same source as the trigger oscillator and detected with a transient digitizer. In this configuration we achieved π/2 pulses of −14 ns, and the isolation of the Fabry‐Perot provided short spectrometer dead times (20–50 ns, including the pulse) for subsequent detection of the free induction decays. The performance of the spectrometer is demonstrated with spectra obtained from crystals of fluoranthenyl hexafluorophosphate.
Quantum Chemistry of Semiconductor Clusters
Authors: Ramakrishna M.V. , Friesner R.A.
Published: November 2013

The effect of size on the electronic structure of semiconductor clusters is discussed and the evolution of the absorption spectrum with cluster size is quantitatively modeled using pseudopotentials.
Synthesis and Photochemistry of Quantum‐Size Semiconductor Particles in Solution and in Modified Layers
Authors: Weller H. , Eychmüller A. , Vogel R. , Katsikas L. , Hässelbarth A. , Giersig M.
Published: November 2013

We describe the preparation of highly monodisperse, quantum‐size CdS particles. In these samples a band splitting into discrete exciton‐like states is observed. A mechanism for the excitonic fluorescence is presented involving shallow traps as a reservoir for electrons which finally recombine with free positive holes across the bandgap. Quantum‐size CdS and PbS particles prepared in situ on highly porous, polycrystalline TiO2 electrodes work as highly efficient sensitizers. Photocurrent yields of more than 70% are reported. In the case of PbS, it is shown that an efficient electron transfer is possible only with particles in the size of the quantization regime.
Ultrasmall Metal Oxide Particles: Preparation, Photophysical Characterization, and Photocatalytic Properties
Authors: Bahnemann Detlef W.
Published: November 2013

This paper gives an overview of the author's activities in the research of extremely small metal oxide particles in recent years. In particular, the synthesis of transparent colloidal solutions of extremely small zinc oxide, titanium dioxide, hematite, and titanium/iron mixed oxide particles (2 nm < d 20 nm) in water, ethanol, and 2‐propanol is described. Quantum (Q)‐size effects are observed during particle growth and at me final stages of synthesis. A simple molecular orbital (MO) picture is presented for the qualitative interpretation of these effects, while quantitative calculations have been carried out using a quantum mechanical model developed by Brus. The photophysical properties of the particles have also been investigated extensively. Fluorescence spectra of the ZnO sols suggest that adsorbed electron relays are necessary to shuttle electrons from the conduction band to lower‐lying traps. Excess negative charge on the particles, resulting from either deprotonated surface hydroxyl groups or from photogenerated or externally injected charge carriers, causes a blue‐shift in the electronic absorption spectrum, which is explained by electrostatic and MO models. The zero point of charge (pHzpc) of the aqueous colloidal suspensions has been determined by several independent methods. While zinc oxide, titanium dioxide, and titanium/iron mixed oxide particles exhibit considerable photocatalytic activity (as illustrated for the reduction of molecular oxygen and the oxidation of various halogenated carboxyl acids), hematite particles are only found to oxidize S(IV) under bandgap illumination to a reasonable extent (ϕ < 0.3). A mechanism involving surface‐bound molecules and free radical intermediates is presented to explain these differences in reactivity.
Modelling Photochemical Reactivity of Organic Systems — A New Challenge to Quantum Computational Chemistry
Authors: Bernardi Fernando , Olivucci Massimo , Robb Michael
Published: November 2013

The applicability of modern methods of quantum computational chemistry to the problem of modelling photochemical mechanisms is discussed. It is demonstrated that one of the central mechanistic features is the surface‐crossing region which takes the form of a conical intersection. It is shown that this mechanistic feature can yield a new rationalization of common experimental observations such as the simultaneous production of different photoproducts, the occurrence of rigid stereochemistry, and the occurrence of very low fluorescence quantum yields. In addition, a simple VB model can often lead to accurate predictions about the nature of the surface‐crossing region and the nature of the recoupling pathways on the ground‐state surface.
A GAUSSIAN‐1 Type Ab Initio MO Study of the [CH2NO]+ Potential Energy Surface. Theoretical Support for the Existence of Three Experimentally Distinguishable Isomers in the Gas Phase
Authors: Hrušák Jan , Holthausen Max C. , Goldberg Norman , Iraqi Muhammad , Koch Wolfram , Schwarz Helmut
Published: November 2013

The potential energy surface (PES) of [CH2NO]+ ions with an NCO connectivity has been explored by GAUSSIAN‐1 type calculations. Six isomers having an NCO backbone are found and characterized as minima on the PES; three of them are separated by isomerization barriers reasonably large enough to allow an experimental verification. The favored protonation site of neutral isocyanic acid (HNCO) is the nitrogen atom (proton affinity, calculated = 171.4 kcal/mol; experimental = 173 ± 1 kcal/mol) leading to the most stable isomer H2NCO+ (1). For the protonation of NCOH at the nitrogen atom we predict a proton affinity for the cyanic acid of 179.7 kcal/mol. The resulting ion HNCOH+ (2) is 15.9 kcal/mol higher in energy than 1. The third stable isomer 5 having the NCO connectivity can be formally viewed as a complex between CN and the water radical cation; 5 is 72.9 kcal/mol less stable than H2NCO+ (1). In addition, two high‐energy isomers HN‐C(H)O+(3) and HO‐C(H)N+ (4) have been found, but according to the shape of the PES, they are predicted not to be accessible experimentally. The calculated thermochemical data are in excelled agreement with experimentally available values. The calculations are extended to the unimolecular fragmentation channels, which should be observed in mass‐spectrometric experiments. The analysis of the results suggests that the hydrogen‐atom elimination process is favored over all other dissociation channels, followed by loss of NH2‐· and NH.
Electronic Spectral Shifts and Linebroadening of Heteroclusters
Authors: Heidenreich Andreas , Jortner Joshua
Published: November 2013

In this paper we report on molecular dynamics simulations of the lineshapes of the absorption spectra of perylene Arn heteroclusters (n = 2–22), which rest on the spectral density method in conjunction with the excited‐state potential modelling scheme. Inhomogeneous semiclassical absorption lineshapes were calculated by averaging of microcanonical spectra over the accessible phase space region. The size dependence and isomer specificity of the spectral shifts and spectral linewidths were elucidated, with the spectral shifts providing a powerful tool for the identification of structural isomers. Some information on isomerization dynamics was inferred from the temperature dependence of the linewidths, which mark the onset of correlated surface motion for (5|0) and (5|5) heteroclusters, as well as the onset of 2D ⇄ 3D isomerization and side crossing for (22|0) heteroclusters.
Photoinduced Charge‐Transfer Dissociation in van der Waals Complexes. III. Na···FCH3
Authors: Polanyi J.C. , Wang J.‐X. , Yang S.H.
Published: November 2013

Complexes Na···FCH3)n, n = 1–6, in beams were identified by photoionization time‐of‐flight (TOF) mass spectrometry. Dissociation of Na···FCH3 was studied by photodepletion. The depletion spectrum (450–750 nm) suggested excitation of Na in the complex followed by charge‐transfer to yield Na+···FCH3− → NaF + CH3. The depletion cross section was substantial, peaking at 1.1 Å2.
The Reactions of O(1D) with Propane and Water Monomers and Clusters
Authors: Hurwitz Y. , Rudich Y. , Naaman R.
Published: November 2013

Reactions of O(1D) with water and propane monomers and clusters were investigated via a crossed molecular beam experiment and by dissociation of ozone in a water‐ozone complex, applying laser‐induced fluorescence for the detection of the OH product. The rotational and spin‐orbit state populations were analyzed. A strong preference for the 2Π3/2 spin‐orbit state of the OH product is observed. The new results presented here demonstrate the effect of the initial rotational temperature of propane on the spin‐orbit states distribution in the product OH. The preference for the low 2Π3/2 state is attributed to conservation of electronic angular momentum. It is conserved through the curve crossing which occurs in the entrance channel and during the lifetime of the long‐lived collision complexes. A quantitative model is presented which rationalizes all the experimental observations.
Preparing Reagents: Time Dependence of HCl(v =1, J) Alignment Following Pulsed Infrared Excitation
Authors: Orr‐Ewing A.J. , Simpson W.R. , Rakitzis T.P. , Zare R.N.
Published: November 2013

We discuss the use of photon absorption as a means of aligning reagents for studies of dynamical stereochemistry. A linearly polarized infrared beam from an optical parametric oscillator prepares HCl(v = 1, J = 1), and the alignment is monitored at subsequent times by (2+1) resonance‐enhanced multiphoton ionization. The degree of alignment oscillates in time caused by hyperfine quantum beats. Experimental observations are well matched by calculations that account for the presence of unresolved hyperfine structure. Following reagent preparation by optical pumping, a cumulative hyperfine‐depolarization coefficient can be used to describe the effective reagent alignment in a subsequent chemical reaction.
Relative Laser Phase in the Coherent Control and Interference Control of Photodissociation Branching Ratios
Authors: Brumer Paul , Chen Zhidang , Shapiro Moshe
Published: November 2013

Product properties in molecular photodissociation can be controlled by simultaneous excitation through a number of coherent excitation routes. Examples of simplified methods for maintaining laser phase coherence of the multiple routes, required for control, are described. Of particular interest is a new high field approach where multiple paths are generated in such a manner as to make relatively coherent lasers unnecessary.
Acetylcholine Recognition by an Aromatic Host: the Role of an All‐Hydrogen Topology in Simulations of the Cation‐π Interaction
Authors: Axelsen Paul H.
Published: November 2013

The contribution of cation‐π interactions to the affinity of a synthetic aromatic host for acetylcholine in a molecular mechanics simulation was estimated using a thermodynamic cycle‐free energy perturbation approach. Compared to a host in which aromatic dipole ring charges were set to zero, the affinity of the host for acetylcholine is greater by 1.8 kcal/mole when using a set of typical simulation parameters. The role of four ether oxygens in the host is probably negligible. Although acetylcholine binding may be driven in large part by hydrophobic effects, cation‐π interactions most likely make a significant contribution to the selectivity of this host for quaternary ammonium cations.
The Kinetic Inversion Problem in Ligand‐Binding Heme Proteins
Authors: Lerner Daniel M. , Agmon Noam
Published: November 2013

For a two‐dimensional potential of intersecting parabolic bowls, we obtain an analytical approximation for the survival probability in the limit that the reactive mode is diffusive and the perpendicular protein mode frozen. The approximation is used in an automated computer algorithm for determining the parameters of the potential. Using this program, we are able to obtain a reasonably good fit to the low‐ temperature data of CO binding to horse myoglobin. We find, however, that features of the potential such as the saddle‐point energy and the effective barrier, expected to dictate the high‐temperature kinetics, are not uniquely determined for this potential from fitting the low‐temperature data.
Conformational Sampling of Loop Structures Using Genetic Algorithms
Authors: Ring Christine S. , Cohen Fred E.
Published: November 2013

BLoop, a method for generating plausible loop conformations for protein models, is described. Conformations that are compatible with the local sequence are generated by using the search mechanisms of genetics algorithms to explore the possible combinations of tetrapeptide conformers. Because the amino acid propensities that are used to judge the quality of the structures are derived from a data set of known protein structures, BLoop reproduces many features of database loop searches. But unlike these strategies that are limited by their contents, BLoop is capable of generating novel conformations. The expected accuracy of the database and BLoop methods for loop generation are compared on a set of loops as a function of residue length.
Measurements and Analysis of Photochemical Oxidants and Trace Gases in the Rural Troposphere of the Southeast United States
Authors: Aneja Viney P. , Das Mita , Kim Deug‐Soo , Hartsell Benjamin E.
Published: November 2013

Ambient concentrations of photochemical oxidants (O3, PAN, HNO3, H2O2) and various trace species including reactive nitrogen compounds as well as total NOy were measured during June and early July 1992 at a rural site, SONIA, in the central Piedmont region of North Carolina, as a part of the Southern Oxidants Study. The measurements were made in an effort to provide a comprehensive understanding of tropospheric photochemistry in the rural Southeastern United States. NOy, NO2, and NO showed diurnal variations with maxima in the morning between 0600 and 0900 EST. The maximum NOy, NO, and NO2 concentrations reached were 14.5, 5.4, and 7.8 ppbv, respectively. The mean NOy concentration was found to be 2.63 ± 1.72 ppbv (n = 819) with an average daily maximum of 3.6 ppbv. The mean concentrations of NO and NO2 for the entire period of measurement were found to be 0.18 ± 0.37 ppbv (n = 794) and 1.31 ± 0.99 ppbv/(n = 769). H2O2, HNO3, and PAN showed diurnal variation with maxima in the afternoon and minima at night. Mean concentrations were found to be 0.52 ± 0.36 ppbv (n = 312), 0.67 ± 0.33 ppbv (n = 250), and 0.41 ± 0.24 ppbv (n = 578). The NOx/NOy ratio was used as an indicator of the chemical age of airmasses and the ratio showed strong positive correlations with the photochemical oxidants HNO3 (r = 0.76), PAN (r= 0.68), and O3 (r = 0.79) measured at the site. The relationship between the accumulation rate of O3 and the deviation from the photostationary state was examined based on the measured PSS constant obtained from the values of [O3], [NO], and [NO2] measured at the site.
Grafting Kinetics of End‐Functional Polymers at Melt Interfaces
Authors: Kramer Edward J.
Published: November 2013

Expressions for the kinetics of grafting chains from a pure end‐functional polymer melt to a reactive interface are derived under the assumption that the free energy of reaction is very large and negative. Two cases are considered: a case where the grafting is controlled by diffusion of free end‐functional chains through the “brush” of previously grafted chains and a case where the grafting is controlled by the kinetics of the interface reaction itself. Both cases lead to the same form of the grafting kinetics, but with different characteristic times τD = Rga/D, where Rg is radius of gyration, a is the statistical segment length, and D is the diffusion coefficient of the end‐functional polymer; and τR = Rg/(akf[B]) where kf is a forward rate constant and [B] is the concentration of groups at the interface that react with the end‐function of the polymer chains. The grafting density Σ approaches a practical limit after long times for each value of the degree of polymerization N, and this limit decreases strongly with N. These predictions are compared with the results of recent experiments in which deuterated polystyrene chains with carboxylic acid end groups were grafted to either epoxy‐ or amine‐rich cross‐linked epoxy networks. The reaction‐controlled grafting model fits the data best and permits us to extract forward rate constants of ˜0.18 kg s−1 mol−1 for the epoxy‐rich networks and ˜5 × 10−3 kg s−1 mol−1 for the amine‐rich ones.
Irreversibility, Energy Dissipation, and Time Effects in Intermolecular and Surface Interactions
Authors: Israelachvili Jacob , Berman Alan
Published: November 2013

The use of thermodynamic functions such as surface energy (y) or the reversible work of adhesion (W) implicitly assumes that two surfaces are interacting under conditions of thermodynamic equilibrium. Likewise, the concept of the adhesion force or pressure between two surfaces, molecules, or colloidal particles also suggests the existence of well‐defined time‐independent values for these quantities. Yet most interactions involving molecules, surfaces, and complex fluid systems are irreversible, involving the transfer of energy from one system to another; that is, they involve “energy dissipation”. We review the molecular origins nonequilibrium (irreversible) interactions of surfaces that give rise to adhesion hysteresis, contact angle hysteresis, friction, and other thin‐film properties, and discuss the important role of “time” in such processes which can have a significant effect on what we measure. We also consider the possible central role of nonequilibrium interactions in biological systems, where nature often makes use of the finite time of molecular processes for regulating the interactions of proteins, membranes, and cells.
High‐Performance Liquid Chromatographic Analysis of an Ancient Tyrian Purple Dyeing Vat from Israel
Authors: Koren Zvi C.
Published: November 2013

The high‐performance liquid chromatographic technique is utilized to analyze the dye components of crude “Tyrian Purple” residues obtained from modern Murex (Trunculariopsis) trunculus sea snails and from an archaeological source. This is the first time that this technique has been used to analyze these raw pigments. Previously, chromatographic analyses of cloth stains and textile vat dyeings produced from contemporary snails were published. The modern purple pigment analyzed in this study was produced from excised hypobranchial glands of trunculus snails, and the archaeological purple residue investigated was found on the interior of a potsherd from Tel Kabri, Israel. The two pigments studied showed nearly identical chromatographic fingerprints: The pigments consisted of the same four indigoid components and with matching compositions. The dyes found were indigotin, monobromoindigotin, dibromoindigotin, and a fourth colorant that may be dibromoindirubin. The following conclusions can be made regarding the archaeological sample: (1) the ancient potsherd bearing the purple pigment was from an ancient dyeing vat; (2) the biological provenance of the archaeological dyestuff was most probably Murex trunculus mollusks; and (3) the Mediterranean snails used for the vat were likely collected at or near the Akhziv beach area in Israel. This study indicates that a biological and geographical chromatographic mapping of the dye components of porphyra snails can be developed to assist in provenance determinations of archaeological purple pigments.
Ultrafast Spectroscopy of Rhodopsins — Photochemistry at Its Best!
Authors: Kochendoerfer Gerd G. , Mathies Richard A.
Published: November 2013

Recent advances in laser technology now allow us to study the ultrafast primary photochemical events in rhodopsin, bacteriorhodopsin, and halorhodopsin in real time. The results of various ultrafast studies of rhodopsins are reviewed with an emphasis on (1) the relationship between the reaction rate and reaction efficiency and its implications for the mechanism of isomerization, (2) the homogeneity of the reaction pathways, and (3) the role of the protein in the reaction dynamics. The results mandate the introduction of a new paradigm to describe these ultrafast reactions that specifically considers the importance of the timescale of vibrational dephasing and relaxation relative to the reactive motion and the contribution of vibrational coherence to the reaction mechanism.
Application of Raman Spectroscopy to Retinal Proteins
Authors: Althaus T. , Eisfeld W. , Lohrmann R. , Stockburger M.
Published: November 2013

Raman spectroscopic studies on photoreactive retinal proteins are comprehensively described, including the basic physics of Raman scattering and illustrative examples of the types of information on the structure and function of the retinal chromophore and its environment which can be obtained from the vibrational Raman spectra. In addition, practical advice and recipes are given which should enable the reader to plan and eventually perform a Raman experiment in a photolabile retinal protein. A dominant role is played by the resonance Raman (RR) experiment with visible laser excitation which selectively probes the retinal chromophore. Much discussion is devoted to bacteriorhodopsin (bR) and its photocycle as a paradigm for a light‐induced reaction of a retinal protein. Various time‐resolved techniques are described to study the temporal evolution of the bR chromophore by probing RR spectra of intermediate states. Vibrational Raman spectra are interpreted in terms of structure and structural changes of the chromophore. RR spectroscopic studies on halorhodopsin, sensory rhodopsin, and visual pigments are reported, as well as on modified proteins in which retinal analogues are incorporated, and on site‐specific mutants. Results of ultraviolet RR experiments which selectively probe the aromatic side chains in the protein backbone are reported. In addition, a promising new technique of near‐infrared Raman excitation is discussed. Finally, application of coherent anti‐Stokes Raman spectroscopy (CARS) to retinal proteins is reported.
Spectral and Kinetic Characterization of Visual Pigment Photointermediates
Authors: Kliger David S. , Lewis James W.
Published: November 2013

The literature describing intermediates formed after photolysis of visual pigments is reviewed. Results obtained near physiological temperatures using time‐resolved optical density measurements in the UV/Vis region are emphasized. The general character of intermediates which appear in the course of protein function, and the role of methods with different time resolutions in their study, are discussed. Specific results for intermediates from bathorhodopsin to metarhodopsin II are treated in detail, with limited discussion of the earlier and later species. The discussion centers on the best‐understood pigment, bovine rhodopsin, but results for cone‐type and invertebrate pigments are also discussed. Comparison is made between the picture of the intermediates obtained using low‐temperature trapping methods and that obtained using kinetic measurements. The thermodynamic parameters of the intermediates are discussed, and their significance for the structure/function of heptahelical protein intermediates in general is considered.
Kinetics of Light‐Induced Intramolecular Charge Transfer and Proton Release in Bacteriorhodopsin
Authors: Moltke Stephan , Alexiev Ulrike , Heyn Maarten P.
Published: November 2013

Recent advances in understanding the intramolecular charge transfer and proton release by the light‐driven proton pump bacteriorhodopsin (bR) are critically reviewed. The focus is on the time‐resolved electrical methods, i.e., photocurrent and photovoltage measurements, and on transient absorption experiments with pH‐sensitive dyes. Particular attention is paid to the following topics: charge translocation in the low‐pH forms of bR (acid‐blue and acid‐purple); electrogenicity of the 13‐cis cycle; results with bR mutants; surface‐bound dyes to detect the proton release at specific sites on either side of the protein; the question of kinetic coupling between the deprotonation of the Schiff base and proton release; and rapid long‐range migration of protons along the surface of the purple membrane.
Photoreactions of the Photointermediates of Bacteriorhodopsin
Authors: Balashov Sergei P.
Published: November 2013

The photochemical reactions of the intermediates of the photochemical cycle of bacteriorhodopsin (bR) are reviewed. These reactions constitute photochemical control of the cycle and provide an independent approach for the investigation of the mechanism of light energy transduction in the purple membrane. The absorption of a light quantum by the K, L, or M intermediates converts them back to bR. These transformations interrupt the photocycle so that no proton transfer occurs after absorption of the second quantum. The action of blue light on the M intermediate causes structural changes of the chromophore, as a result of which the Schiff base is reprotonated from Asp‐85, not from Asp‐96 as in the usual thermal transition of M. The photoreactions of the L, M, N, and O intermediates lead to the formation of new photoproducts. Studies of the photoconversion of the intermediates can serve as an additional source of information on the nature of photoprocesses in bR: they reveal several conformers of K and bR at 90 K, different M states, two N intermediates, and provide direct evidence for the existence of a thermal back reaction from N to M. The study of the photoreactions of the J, K, L, M, N, and O intermediates is a promising method for elucidating the structures and roles of these states. Reversible photoconversions of bR and its photointermediates provide a basis for potential applications of bR in optical registration of information.
Acid‐Base Equilibria and the Proton Pump in Bacteriorhodopsin
Authors: Honig B. , Ottolenghi M. , Sheves M.
Published: November 2013

The light‐induced proton pump in bacteriorhodopsin is reviewed with emphasis on acid‐base equilibria of protein residues and of the retinal Schiff base moiety. Pump mechanisms in bR and in some of its mutants are classified in terms of light‐induced pKa changes (class I) or light‐induced exposure changes, in which the proton accessibility of the protein changes from the outside to the inside of the membrane (class II). A discussion of the theoretical basis of the factors which determine the pKa of ionizable protein groups is followed by a review of the experimental phenomena associated with the titration of residues in both unphotolyzed bR and during its photocycle. The time‐resolved titrations of the Schiff base and of the Asp‐85 residue are discussed in terms of the accessibility of the two groups to external protons. Finally, the molecular aspects of the pH‐dependent proton pump in native bR and in various mutants are analyzed, focusing on the mechanism of the initial proton release reaction and on the subsequent molecular switch which allows reprotonation from the inside of the cell. Special attention is devoted to the question of coupling between the photocycle intermediates (primary M formation and decay) and the transmembrane proton translocation. Recent work with bR mutants raise the question as to whether proton transfer from the Schiff base to Asp‐85 at the M stage is directly responsible for proton translocation, as well as for the reprotonation switch.
Near‐Field Optical Microscopy in Jerusalem
Authors: Lewis Aaron , Lieberman Klony , Ben‐Ami Nily Kuck , Fish Galina , Khachatryan Edward , Strinkovski Alina , Shalom Shmuel , Druckmann Shula , Ottolenghi Michael , Ben‐Ami Udi
Published: November 2013

During the past decade the area of near‐field optics has seen an exponential growth. This is a result of the resolution of the technical problems that had prevented the potential of this powerful optical methodology from being generally applied. As a result of committed and steady progress in resolving these technical problems the fundamental principles of near‐field optics are now generally accepted and the technology is widely used. The potential of these advances has important implications in a variety of areas, from chemistry to information storage to the characterization of structures with potential in fundamental mesoscopic physics, and in the characterization of practical devices in electronics and photonics which are rapidly reaching nanometer dimensionalities. In this paper, the progress that has been made in Jerusalem in developing a near‐field microscope fully integrated with conventional far‐field, confocal far‐field, and all forms of force and other scanned probe microscopies will be described. The potential of this unique imaging system in chemical applications is also discussed.
Approaches to Antibody‐Catalyzed Cationic Cyclizations: Chemical Studies of Leaving Groups and Cyclization Modes
Authors: Lawrence Christopher , Bell Ian M. , Abell Chris , Leeper Finian J.
Published: November 2013

The solvolysis of a range of esters of 2‐methylbenzyl alcohol 10 has been studied. It was found that sulphonate esters are solvolyzed very rapidly in aqueous solution (t1/2 ≈ 35 s), whereas sulphinates react slowly (t1/2 ≈ 35 h) and a phosphonate diester is stable. The fluorescent 5‐dimethylaminonaphthalene‐1‐sulphinate (dansinate) esters (e.g. 22) held the most promise as substrates for antibody‐catalyzed cationic cyclizations. It was shown by 18O‐labeling studies that ester 13 is hydrolyzed predominantly (but not exclusively) by SN1 reaction at the benzylic position.

A number of conditions were tried to effect cationic cyclizations of an unsaturated benzylic alcohol 26, whose ester is intended as the substrate for the antibody‐catalyzed reaction. The products obtained were the result of attack of the non‐benzylic alcohol on either the benzylic cation, to give 31 and 32, or on the protonated alkene, to give 29. No cyclization of the alkene onto the benzylic cation, to give 4, was observed, suggesting that this is a disfavored reaction in solution.
Isomerization and Decomposition of Chloromethylacetylene
Authors: Kumaran Soundararajan S. , Lim Kee P. , Michael Joe V. , Tilson Jeffrey L. , Suslensky Aya , Lifshitz Assa
Published: November 2013

The isomerization and thermal decomposition of chloromethylacetylene (CMA) has been studied with two shock tube techniques. The first experiment (Jerusalem) utilizes single‐pulse shock tube methods to measure the isomerization rate of CMA to chloroallene. In addition, equilibrium constants can be estimated at ∼1200 K. The second experiment (Argonne) monitors Cl‐atom formation at temperatures above ∼1150 K. Absolute yield measurements have been performed over the 1200–1700 K range and indicate that two decomposition channels contribute to CMA destruction, namely, Cl fission and HCl elimination. The results show that the branching fraction between processes is temperature dependent. Therefore, direct Cl‐atom fission is accompanied by molecular elimination, undoubtedly giving HCl and one or more isomers of C3H2.

MP2 6–31G(d,p) ab initio electronic structure calculations have been used to determine vibration frequencies and moments of inertia for three C3H3Cl isomers. Using these quantities, the experimental equilibrium constants required that ΔH00(CH2Cl–C≡CH ⇌ CHCl=C=CH2) = −;0.24 kcal mole−1. A potential energy surface pertinent to the present system has been constructed, and RRKM calculations have been carried out in order to explain the isomerization rates. The isomerization data can be explained with E0 = 52.3 kcal mole−1 and 〈ΔEdown〉 = 225 cm−1. Subsequent semi‐empirical Troe and RRKM‐Gorin modeling of the Cl atom rate data require E0 = (67.5 ± 0.5) kcal mole−1 with a 〈ΔEdown〉 = (365 ± 90) cm−1. This suggests a heat of formation for propargyl radicals of (79.0 ± 2.5) kcal mole−1.