bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Dynamics Studies of Bacteriorhodopsin's Photocycles
Authors: Schulten Klaus , Humphrey William , Logunov Ilya , Sheves Mordechai , Xu Dong 
Published: November 2013

AbstractThe availability of the structure of bacteriorhodopsin from electron microscopy studies has opened up the possibility of exploring the proton pump mechanism of this protein by means of molecular dynamics simulations. In this review we summarize earlier theoretical investigations of the photocycle of bacteriorhodopsin including relevant quantum chemistry studies of retinal, structure refinement, molecular dynamics simulations, and evaluation of pKa values. We then review a series of recent modeling efforts which refined the structure of bacteriorhodopsin adding internal water, and which studied the nature of the J intermediate and the likely geometry of the K590 and L550 intermediates (strongly distorted 13‐cis) as well as the sequence of retinal geometry and protein conformational transitions which are conventionally summarized as the M412 intermediate. We also review simulations of the photocycle of light‐adapted bacteriorhodopsin at T=77 K and of the photocycle of dark‐adapted bacteriorhodopsin, both cycles differing from the conventional photocycle through a nonfunctional (pure 13‐cis) retinal geometry of the corresponding K590 and L550 states. The simulations demonstrate a potentially critical role of water and of minute reorientations of retinal's Schiff base nitrogen in controlling proton pumping in bR568; the simulations also indicate the existence of heterogeneous photocycles. The results exemplify the important role of molecular dynamics simulations in extending investigations on bacteriorhodopsin to a level of detail which is presently beyond experimental resolution, but which needs to be known to resolve the pump mechanism of bacteriorhodopsin. Finally, we outline the major existing challenges in the field of bacteriorhodopsin modeling.
Structural Studies of Catalytic Antibodies
Authors: Stevens Raymond C. , Hsieh‐Wilson Linda C. , Santarsiero Bernard D. , Wedemayer Gary J. , Spiller Ben , Wang Leo H. , Barnes Dwight , Ulrich Helle D. , Patten Phillip A. , Romesberg Floyd E. , Schultz Peter G. 
Published: November 2013

AbstractA panel of catalytic antibodies which catalyze ester hydrolysis, transesterification, porphyrin metallation, Diels‐Alder, and redox reactions has been selected for crystallographic study. While these examples are only a handful of the catalytic antibodies generated to date, they represent distinct and important aspects of antibody catalysis. Since the first reports of catalysis, a great deal of progress has been made with respect to the scope, selectivity, and efficiency of antibody catalysis and strategies for generating catalytic antibodies. However, it is clear that further progress in the field will benefit greatly from a detailed understanding of the molecular interactions occurring in the combining site. High‐resolution crystallographic data should allow the importance of general base catalysis, entropy effects, electrophilic catalysis, and transition‐state stabilization to be evaluated. Antibody and enzyme active sites have been shown to share considerable structural and mechanistic similarity, and ongoing structure‐function studies of catalytic antibodies may enhance our understanding of the mechanisms and evolution of enzymatic catalysis. Structural studies of antibodies which perform a biological or highly selective reactions should enhance our ability to generate catalysts for important synthetic applications. Finally, the combination of high‐resolution crystallographic analysis with rational mutagenesis should provide a basis for engineering antibodies with enhanced properties.
Hapten Design for Antibody‐Catalyzed Decarboxylation and Ring‐Opening Reactions of Benzisoxazoles
Authors: Sergeeva Masha V. , Yomtova Vihra , Parkinson Adrian , Overgaauw Marjolein , Pomp Rikus , Schots Arjen , Kirby Anthony J. , Hilhorst Riet 
Published: November 2013

AbstractThree benzisoxazole haptens designed to elicit antibody binding sites with widely differing polarity have been synthesized and used to induce antibodies in mice. Monoclonal antibodies were prepared using hybridoma technology, and screened for catalysis of the ring‐opening isomerization and/or decarboxylation of a series of related benzisoxazoles and their 3‐carboxy‐derivatives. No catalysis of decarboxylation was observed, but 4 of a total of 47 antibodies obtained against the three haptens catalyzed the isomerization process. Of 12 antibodies raised against the 3‐acetylbenzisoxazole structure 5 none was catalytically active; but one of 24 raised against a 3‐isopropenylbenzisoxazole 6 increased the rate of ring‐opening of 6‐nitrobenzisoxazole, and 5 of 11 antibodies raised against a benzisoxazole 7 with a 3‐amidinium group were moderately active against either 6‐nitro or 6‐acylaminobenzisoxazoles. Competitive binding studies suggest that at least some of the antibodies induced by the isopropenyl hapten do possess a recognizably hydrophobic binding site.
α‐Multistriatin: The First Total Synthesis of a Natural Product via Antibody Catalysis
Authors: Sinha Subhash C. , Keinan Ehud 
Published: November 2013

AbstractThe relevance of antibody catalysis to synthetic organic chemistry is demonstrated here by an efficient total synthesis of (–)‐α‐multistriatin, the aggregation pheromone of the European elm bark beetle, Scolytus multistriatus, which is the principal vector of the Dutch elm disease, responsible for the severe devastation of the elm population in Europe and North America. The key step in our synthesis of this natural product is an antibody‐catalyzed, enantioselective protonolysis of an enol ether to produce a branched ketone. The latter is obtained with an (S) configuration in greater than 99% enantiomeric excess. Catalysis follows Michaelis‐Menten kinetics (Km = 230 μM, kcat = 0.36 min−1) and useful rate enhancement (kcat/kun = 65,000 at pH 6.5). This abzymic step is followed by twelve chemical steps, with all four asymmetric centers originating from the chirality achieved in the antibody‐catalyzed reaction. That specific step is a unique example of a chemical transformation which is difficult to achieve either by an available synthetic methodology or via catalysis with a known enzyme. The synthetic pheromone has been checked in field experiments and found as active as the naturally occurring compound in attracting the European elm bark beetles.
Light‐Stimulated Formation and Dissociation of Supramolecular Donor–Acceptor Complexes between Eosin and Bipyridinium Azobenzenes: Design of Molecular Electronic Devices for the Piezoelectrical Transduction of Recorded Optical Signals
Authors: Ranjit Koodali T. , Marx‐Tibbon Sharon , Ben‐Dov Iddo , Willner Bilha , Willner Itamar 
Published: November 2013

AbstractThe photoisomerizable electron acceptors, trans‐4,4′‐bis(N‐methylpyridinium)azobenzene, (1t), and trans‐3,3′‐bis(N‐methylpyridinium)azobenzene, (2t), exhibit photoswitchable binding affinities to eosin. While the trans isomers, (1t) or (2t) exhibit high association affinities (Ka = 8.3 × 103 M−1 and 3.8 × 104 M−1, respectively), the cis isomers (1c) or (2c) reveal lower binding affinities (Ka = 3.4 × 103 M−1 and 1.4 × 104 M−1, respectively). The formation of the supramolecular donor–acceptor complexes between the eosin and the electron acceptors is associated with an absorbance change of the chromophore. This enables the cyclic spectroscopic transduction of the optically‐induced formation and dissociation of the complexes upon photoisomerization between the respective trans and cis states. An eosin monolayer was assembled onto the Au‐electrodes associated with a quartz piezoelectric crystal. The eosin‐functionalized crystal was employed for the microgravimetric, quartz‐crystal‐microbalance analyses of the association of (1t), (2t), (1c), or (2c) to the crystal interface. The microgravimetric analyses allowed the characterization of the kinetics of association of the electron acceptors to the monolayer and the association constants between the isomers (1t), (2t), (1c), and (2c) with the eosin monolayer. By cyclic photoisomerization of the electron‐acceptor between the trans and cis states, reversible piezoelectric transduction of the formation of the complexes with (1t) or (2t) at the monolayer interface, and their dissociation upon photoisomerization to (1c) or (2c) was accomplished.
Voltammetric and Scanning Electrochemical Microscopic Studies of the Adsorption Kinetics and Self‐Assembly of n‐Alkanethiol Monolayers on Gold
Authors: Forouzan Fardad , Bard Allen J. , Mirkin Michael V. 
Published: November 2013

AbstractThe adsorption kinetics and self‐assembly of hexadecyl mercaptan on gold have been investigated by scanning electrochemical microscopy (SECM), chronoamperometry, and cyclic voltammetry. The developed methodology allows one to evaluate the surface coverage and the average size of the defects in the monolayer film from the effective rate constant of electron transfer. Two kinetic regimes of self‐assembly were identified: a rapid initial adsorption of hexadecyl mercaptan onto a clean gold surface from 5 mM solution (more than 90% coverage obtained in 1 to 5 min), and a slower subsequent annealing of a thiol monolayer resulting in a more compact film. Typically, a long‐chain‐length thiol‐treated gold surface acts as an electronically insulating surface after about 1 h. The SECM images of partially covered gold surfaces were always featureless, suggesting that the defects in the film were smaller than 0.5 μm for any exposure time ≥ 1 min.
Photostimulated Interactions of Bipyridinium‐Azobenzene with a β‐Aminocyclodextrin Monolayer‐Functionalized Electrode: An Optoelectronic Assembly for the Amperometric Transduction of Recorded Optical Signals
Authors: Lahav Michal , Ranjit Koodali T. , Katz Eugenii , Willner Itamar 
Published: November 2013

AbstractAn amino‐functionalized β‐cyclodextrin is covalently linked to a thiopropionic acid‐active ester monolayer associated with a Au electrode to yield a cyclodextrin monolayer electrode. The photoisomerizable electron acceptor trans or cis N‐methylpyridinium‐4‐(4′‐N′‐methylenepyridinium)‐azobenzene, 1t or 1c, respectively, exhibit different binding affinities for the β‐cyclodextrin‐receptor‐monolayer. The photoisomer 1t has a high affinity for the cyclodextrin monolayer while 1c exhibits low binding interactions to the monolayer interface. The photostimulated binding and dissociation of 1t or 1c to and from the monolayer are transduced electrochemically. The association and dissociation of the photoisomerizable substrate to and from the monolayer are confirmed by microgravimetric, quartz‐crystal‐microbalance experiments.
Room‐Temperature Electrochemical Assembly of Copper/Cuprous Oxide Nanocomposites
Authors: Huang Ling‐Yuang , Bohannan Eric W. , Hung Chen‐Jen , Switzer Jay A. 
Published: November 2013

AbstractNanocomposite films of copper metal and cuprous oxide, Cu2O, are electrodeposited at room temperature from alkaline solutions of copper(II) lactate. The electrode potential oscillates spontaneously if the films are deposited galvanostatically. The oscillation period is a function of pH, varying from 69 seconds at pH 8.7 to 11 seconds at pH 9.7. No oscillations are observed if the pH is below 8.5 or above 10. The phase composition of films deposited at 0.5 mA/cm2 is a function of pH. The composition varies from nearly pure copper (93 mole%) at pH 8, to 42 mole% copper at pH 9.5, to pure cuprous oxide when the pH exceeds 10. The observation of quasi‐periodic potential oscillations suggests that the nanocomposites are layered. The calculated faradaic thickness of cuprous oxide is 5–8 nm, and the thickness of the copper layer is 1–11 nm. The thickness of each of the layers increases as the pH is lowered.
Single and Merged Beam Studies of the Reaction H2+ (v = 0,1; j = 0,4) + H2 → H3+ + H
Authors: Glenewinkel‐Meyer Thomas , Gerlich Dieter 
Published: November 2013

AbstractDifferent approaches for studying low‐energy (meV) reactive ion‐molecule collisions in molecular beams are presented. In particular, differences in the photoionization (REsonant Multi‐Photon Ionization / REMPI, Pulsed Field Ionization / PFI) experiments using single molecular beams vs. merged and crossed beams are discussed. We address the question of the proper determination of cross sections and rate constants in single beam experiments and the factors that influence the width of the collision energy distributions. We identify space charge effects as the dominant contribution under our experimental conditions. Problems pertinent to state‐selected primary ion preparation with narrow energy distributions are highlighted.In light of the detailed data analysis, the derived relations are applied to the four‐center reaction H2+ + H2 → H3+ + H, which was studied in single and merged molecular beam experiments. We present merged beam data for the absolute reaction cross section for primary ions created in a storage ion source in the energy range from 5 meV up to 5 eV and relative state‐selected cross sections for different vibrational and rotational ion states (v = 0,1; j = 0–4) generated by (3+1) REMPI for a mean collision energy of about 10 meV.
Tricky IR Monomer Spectroscopy in Planar Molecular Jets
Authors: Oomens Jos , Reuss Jörg 
Published: November 2013

AbstractAn experimental technique based on double resonance spectroscopy in the collisional environment of a seeded molecular jet expansion is described. Using this technique, hot band spectra of several small hydrocarbons have been investigated as well as the (related) collision‐induced relaxational behavior upon vibrational excitation. The collisional relaxation in the jet is of crucial importance to the experiments presented here as it distributes the population over many rovibrational states after initial excitation by a pump laser. A second IR laser then probes the transitions starting from the vibrationally excited state(s), as hot bands. In that way one enters an energy region around 4000 cm−1, beyond the highest fundamental bands. The possibility to label an individual rovibrational state with the pump laser enables us to obtain reliable initial spectroscopic assignments. In addition, the present technique allows one to distinguish the cold bands due to depletion of the vibrational ground state, which may reveal new and surprising spectral features as well.
The Relative Influences of Ring Modes and Methyl Internal Rotation on the Cold Beam IVR of p‐Fluorotoluene
Authors: Ju Quan , Parmenter Charles S. , Stone Todd A. , Zhao Zhong‐Quan 
Published: November 2013

AbstractRoom temperature (300 K) experiments have earlier established that the replacement of a fluorine atom in p‐difluorobenzene (pDFB) with a methyl group to make p‐fluorotoluene (pFT) generates a qualitative difference in intramolecular vibrational redistribution (IVR) characteristics as seen in the S1 states. Here we report S1–S0 fluorescence excitation and dispersed single vibronic level (SVL) fluorescence spectra that have been obtained for IVR comparisons in the cold (5 K) environment of supersonic expansions. As in the 300 K experiments, the cold beam S1 vibrational energy threshold for IVR is substantially lower in pFT. The vibrational congestion in dispersed fluorescence that reveals extensive S1 level interactions first appears after pumping an S1 pFT level near 800 cm−1. In contrast, congestion in pDFB spectra is still absent from levels with twice this energy. Attention is directed to the relative S1 ring level structures as a potential contributor to the distinctive IVR behaviors. Dispersed fluorescence from the S1 zero point levels and fluorescence excitation spectra are combined with published information about S1 fundamentals to show that the S1 vibrational level structures of the two molecules are as closely related as those of an isotopomer pair. It is argued that the small differences in S1 fundamentals cannot be a principal contribution to the qualitative IVR differences.
Binding Energies of Aromatic 1:1 Hetero‐Clusters in a Supersonic Jet
Authors: Haas Yehuda , Kendler Shai 
Published: November 2013

AbstractMethods used to experimentally estimate the binding energies of van der Waals clusters containing an aromatic molecule are surveyed. These include microwave and infrared absorption spectroscopies, single and two photon ionization, dispersed fluorescence, and stimulated emission pumping. The problems encountered in the application of these methods are briefly discussed, and prospects for the firm establishment of the binding energies are assessed. Although the present database is too small for firm conclusions, methods based on dispersed fluorescence (i.e., probing the excited state surface) tend to yield lower values for argon adducts than those based on ionization, probing the ground state, or ionic surfaces. A mechanism that may account for this tendency is proposed, and further experiments are proposed to test it.
Advances in Grating‐Based Photoacoustic Spectroscopy for the Study of Protein Dynamics
Authors: Dadusc Gami , Goodno Gregory D. , Chiu Hui‐Ling , Ogilvie Jennifer , Miller R.J. Dwayne 
Published: November 2013

AbstractRecent advances in transient grating spectroscopy are described in relation to extracting photoacoustic parameters. The time resolution for measurement of dynamically driven acoustics has been extended to the picosecond level. This improvement was achieved by adopting counter‐propagating beam geometries and resolving the acoustic phase shift in analogy to phase modulation spectroscopy. At the other extreme, the dynamic range of this technique has been extended to milliseconds in order to follow dynamical processes central to biological functions. In addition, diffractive optics were used for generating the necessary excitation and probe beam geometries. A novel optical setup was developed which permits both the rapid exploration of fringe spacing dependencies in separating thermal from nonthermal contributions to the observed signal as well as heterodyne detection without active feedback. The latter capability significantly increases the signal‐to‐noise ratio and permits separation of the real and imaginary components from the nonlinear four‐wave‐mixing signal. Applications of these new methods are demonstrated by following the functionally relevant structural relaxation processes of heme proteins over 10 decades in time.
Lateral Thermal Diffusion Effects on Photothermal Signals from Photovoltaic Cells
Authors: Büchner Bettine , Cella Norberto , Cahen David 
Published: November 2013

AbstractThermal diffusion, parallel to the photovoltaic junction and perpendicular to the direction of illumination, can be used to separate the contributions of injected and photogenerated carriers to the generation of heat in a photothermal experiment, and to demonstrate the influence of electronic carrier diffusion on the signal, already at relatively low modulation frequencies. We show this by using an experimental arrangement in which the distance is varied between the illuminated area of the photovoltaic cell and that over which the thermal signal is detected, and the two areas do not overlap. Our results agree with theoretical calculations used to simulate the photothermal responses of solar cells.
N2 Interaction with Fe Surfaces
Authors: Christoffersen Ebbe , Mortensen Jens‐Jørgen , Stoltze Per , Nørskov Jens Kehlet 
Published: November 2013

AbstractRecent density functional theory calculations of the energetics of N2 dissociation on Fe(111) and atomic N adsorption on all three low‐index Fe surfaces have given new detailed information about precursors for dissociation, new reaction channels, and new surface structures. We analyze the consequences of this insight for the surface structures on Fe catalysts during ammonia synthesis and for the kinetics and dynamics of the N2 dissociation process.
Palladium‐Catalyzed Acetylene Cyclotrimerization: From Ultrahigh Vacuum to High‐Pressure Catalysis
Authors: Tysoe Wilfred T. 
Published: November 2013

AbstractThe surface reactions involved in the palladium‐catalyzed formation of benzene from acetylene are discussed as an example of the way in which such strategies can be used to understand catalytic reaction pathways in detail. This provides an ideal system for surface science/catalysis studies since benzene is formed both in ultrahigh vacuum in temperature‐programmed desorption and under high‐pressure, catalytic conditions. It is found that benzene is synthesized on clean Pd(111) by an initial fast reaction between two adsorbed acetylene molecules to yield a tilted C4H4 metallocyclic intermediate. This reacts with a third acetylene to form benzene, and the hexagonal (111) surface of palladium acts as a template for the reaction. Under catalytic conditions, however, it is found that the surface is covered by a relatively unreactive vinylidene layer. Organometallic studies show that acetylene and vinylidene can react to form a C4H4 intermediate analogous to that found to form from acetylene on a palladium surface. This suggests an alternative possible reaction pathway under catalytic conditions in which acetylene and vinylidene react to eventually form benzene. This proposal is confirmed using NMR analysis of a 13C‐labeled vinylidene‐covered surface. This pathway also successfully rationalizes the observed change in activity as a function of reaction time found using supported palladium catalysts and the observed first‐order reaction kinetics.
Formation and Geometry of a High‐Coverage Oxygen Adlayer on Ru(001), the p(2 × 2)‐3O Phase
Authors: Gsell Marianne , Stichler Markus , Jakob Peter , Menzel Dietrich 
Published: November 2013

AbstractA detailed low‐energy electron diffraction (LEED)‐IV analysis, complemented by scanning tunneling microscopy (STM) observations, was carried out for the apparent (2 × 2) structure of the oxygen‐covered Ru(001) surface at a coverage of 0.75 ML. We present STM images of incomplete layers which allow one to define the symmetry of the ordered layer, in particular of the novel high density p(2 × 2)‐3O phase. In the LEED‐IV analysis we have tested 28 model structures; the results can be used for conclusions about the discrimination of this type of geometry determination. Our quantitative LEED analysis in connection with the STM results corroborates the model proposed before and shows that all of the oxygen atoms sit in the hcp sites with an averaged vertical distance to the outermost Ru layer of d⊥Ru–O = 1.22 Å. This value falls into the general trend of increasing d⊥Ru–O with oxygen coverage observed for the other ordered structures of adsorbed oxygen on Ru and is also predicted by recent total energy calculations. The O–Ru bonding distance of about 2.0 Å is essentially unchanged compared to the other structures. Considerable lateral and vertical displacements of both the O and the Ru atoms are found, with the O atoms being slightly displaced towards the fcc hollow site located in the center of three oxygen atoms. The two uppermost substrate layers are buckled; in the first layer three out of four Ru atoms of the (2 × 2) unit cell are shifted away laterally from their bulk positions. These shifts, globally as well as locally, can be understood in terms of local electron density changes induced by the adsorbed oxygen atoms.