bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isomerization Dynamics of Dicyanine A in n‐Alcoholic Solution
Authors: Pines Dina , Goldberg Sinay Y. , Huppert Dan 
Published: November 2013

AbstractThe radiationless relaxation of dicyanine A molecules in n‐alcohols methanol to butanol has been studied by picosecond fluorescence spectroscopy and time‐resolved nonlinear spectroscopy. The fluorescence decay rates have been measured as a function of viscosity, temperature, and fluorescence wavelength. It is shown that the wavelength dependence can be explained by coexistence of two ground‐state conformers. The intrinsic activation barrier for the nonradiative decay from the excited surface is very small, much less than 1 kcal/mol. In a particular solvent the time constants of the nonradiative relaxation show a linear dependence on the variation of viscosity. The experimental data are discussed in relation to the BFO theory (Bagchi, B.; Fleming, G.R.; Oxtoby, D.W. J. Chem. Phys. 1983, 78: 7375).
Polyatomic Molecules without Electron‐Pair Bonds: High‐Spin Trigonal, Tetrahedral, and Octahedral Lithium Clusters
Authors: Glukhovtsev Mikhail N. , Schleyer Paul Von Ragué 
Published: November 2013

AbstractBound polyatomic molecules without any spin‐paired valence electrons are exemplified by lithium clusters in high‐spin states. Three unpaired valence electrons are able to bind the (4A1) quartet states of Li3and of Li4+in trigonal (D3h) geometries. The tetrahedral Li4and Li5+(5A1) quintet state structures illustrate bound molecules with four unpaired valence electrons. Five, six, and seven spin‐uncoupled valence electrons bind the square pyramidal Li5(6B1) structure, the Li6(7A2u) distorted octahedral structure, and the Li6−(8A1g) octahedral (Oh) octuplet, respectively. However, these high‐multiplicity structures are only local minima; forms with lower spin states are more favorable energetically. Other high symmetry, high multiplicity clusters, e.g., triangular Be3+(6A1′), also have positive atomization energies. The results demonstrate that chemical bonding in multiatom species does not require spin‐coupling.
Overtone State‐Selective Isomerization by a Series of Picosecond Infrared Laser Pulses: Model Simulations for Be2H3D‐(C2v) → C3v)
Authors: Manz J. , Paramonov G.K. , Polášek M. , Schütte C. 
Published: November 2013

AbstractThe vibrational state‐selective isomerization of Be2H3D− in the electronic ground state by a series of picosecond infrared laser pulses is simulated, using a one‐dimensional model in the framework of the Born‐Oppenheimer and semiclassical dipole approximations. Three pulses pumping the sequential overtone transitions serve to excite the anion from its vibrational ground state, representing the stable C2v configuration, to a delocalized vibrational state with energy close to the potential energy barrier. These three pump‐pulses are followed by a dump‐pulse which induces the overtone transition from the delocalized state to a vibrationally‐excited state of the slightly less stable isomer of Be2H3D− with C2v symmetry. The overall reaction probability for optimal laser pulses with sin2‐shapes is about 95%.The model is based on ab initio calculations of the potential energy surface and the dipole function for the electronic ground state of Be2H3D− at the MP4/6–31 ++G* level, with corresponding vibrational energies and dipole transition matrix elements. The laser‐stimulated dynamics of the ultrafast state‐selective isomerization is described by a representative, time‐dependent wave packet which is driven by the laser pulses, according to the time‐dependent Schrödinger equation, equivalent to a set of linear differential equations for the time‐dependent amplitudes of vibrational eigenstates which constitute the wave packet. This set ofdifferential equations is solved by using both standard numerical techniques and an efficient quasiresonant smoothing algorithm.
Acetylcholinesterase: Effects of Ionic Strength and Dimerization on the Rate Constants
Authors: Antosiewicz Jan , Gilson Michael K. , Mccammon J. Andrew 
Published: November 2013

AbstractBrownian dynamics simulations are used to calculate diffusion‐controlled rate constants for the binding of a positively‐charged ligand to acetylcholinesterase (AChE) at 300 K, pH 7, and several ionic strengths. Models of the enzyme were constructed on the basis of the crystal structure of Torpedo californica AChE, and the ligand was modeled as a 5‐Å sphere. Assignment of the charge distribution of the enzyme is based on calculation of the fractional charges of its ionizable groups as a function of pH and ionic strength, by the finite difference Poisson‐Boltzmann method. We find that the mean charge of the enzyme increases significantly with increasing ionic strength, with most of the increase occurring between 0 and 200 mM ionic strength. The charge distribution results in a very high dipole moment for the monomeric subunit of the protein: 1500 D relative to the Center of Diffusion. The magnitude and orientation of the dipole moment are relatively insensitive to the ionic strength. At physiological ionic strength, electrostatic steering of the ligand increases the rate constant of the enzyme‐ligand encounter by more than one order of magnitude. The increase in protein charge with rising ionic strength weakens the ionic strength dependence of the rate somewhat. The calculations reproduce the experimentally observed decrease of the rate constants with increasing ionic strength. We observe no intrinsic rate difference for dimeric AChE as compared to the monomer: the rate constant of the dimer is twice that of the monomer.
Thermal Motion and Conformational Disorder in Protein Crystal Structures: Comparison of Multi‐Conformer and Time‐Averaging Models
Authors: Burling F. Temple , Brünger Axel T. 
Published: November 2013

AbstractModels describing thermal motion and conformational variability in protein crystal structures were applied to the refinement of a 1.8 Å crystal structure of penicillopepsin. Three methods were tested: conventional refinement using restrained B factors, multiple‐conformer refinement, and time‐averaging refinement using molecular dynamics. The information content of the models was assessed by cross‐validation and by estimating the phase accuracy of the model using phases obtained by multiple isomorphous replacement. The R value always decreased when using multi‐conformer and time‐averaging methods, as compared to conventional refinement. In contrast, the cross‐validated (“free”) R value and the phase accuracy worsened for time‐averaging in vacuum. Inclusion of solvent produced a slight improvement of both measures compared to conventional refinement. Multi‐conformer refinements always improved both measures. An optimum was reached for simultaneous refinement of between four and eight conformers. At the resolution limit of the penicillopepsin data, multi‐conformer refinement is an efficient method to describe conformational variability and thermal motion.
Modeling the Combining Site of the Human Asialoglycoprotein Receptor
Authors: Khier Sharona , Tolchinsky Sandra , Lederkremer Gerardo Z. , Shaanan Boaz 
Published: November 2013

AbstractA model for the carbohydrate recognition domain (CRD) and combining site of the human asialoglycoprotein (ASGP) receptor has been computed on the basis of the close sequence homology with the mannose‐binding lectin (MBP), whose three‐dimensional structure in complex with a ligand has been determined by crystallographic methods (Weis, W.I.; Drickamer, K.; Hendrickson, W.A. Nature 1992, 360: 127). Within the limitations of modeling methods, the model is compatible with data on ligand binding of the family C‐type lectins, of which the MBP and the ASGP receptor are members. The model derived can serve as a guide for designing site‐directed mutagenesis experiments in order to further elucidate the origins of specificity of the ASGP receptor toward galactose. In particular, the model focuses attention on the possible role of position 207 (MBP sequence numbering) in promoting galactose binding.
Aspects of Modeling the Tropospheric Hydroxyl Radical Concentration
Authors: Thompson Anne M. 
Published: November 2013

AbstractThe global abundance of the hydroxyl radical, OH, is a principal determinant of the amount of acid deposition and the lifetime of literally hundreds of atmospheric trace gases. Local (“in situ” or point) measurements of OH have been made in a number of environments, and technical challenges in this area are being met over time. Typical concentrations near the surface range from (0.5 to 10) × 106 molecules cm−3. These measurements test photochemical theory. Discrepancies between models and measurements are sometimes larger than the apparent uncertainty in either one. There is no way to measure tropospheric OH directly on a global scale. Instead, measurement of species that react with OH are used with models to derive an estimate for the global burden. Through this route it appears that global OH has not significantly increased or decreased over the past decade. The complexities of OH interaction with O3, carbon monoxide, methane, nitrogen oxides, and nonmethane hydrocarbons and uncertainties in models make it difficult to interpret or predict global OH behavior.
The Conversion of SO2 to Sulfate in the Atmosphere
Authors: Eatough D.J. , Caka F.M. , Farber R.J. 
Published: November 2013

AbstractThe atmospheric chemistry responsible for the conversion of SO2(g) to particulate sulfate in areas impacted by anthropogenic emission of SO2 is reviewed. The major reaction mechanism for the homogeneous conversion process in the absence of clouds or fog is the oxidation of SO2(g) by the hydroxyl radical. The rate of this conversion process increases with both increasing temperature and relative humidity. Correlations are described for the effects of these two variables on the conversion process, and equations given which correlate all of the available literature data for the homogeneous conversion process in ambient atmospheres. The conversion of S(IV) to sulfate via aqueous solution chemistry in clouds and fog is more complex and dependent on several variables, including concentrations of the principal oxidants (hydrogen peroxide and ozone), ammonia, droplet size and composition, and meteorology. The gas‐phase homogeneous conversion process can vary from less than 1% SO2(g) converted per hour to a maximum of about 10% converted per hour at high temperature and relative humidity. In contrast, the rate of conversion of S(IV) to sulfate in the aqueous‐phase homogeneous process is controlled by mixing and reactant limitations, rather than kinetic considerations. The process can involve 100% SO2 converted per hour under optimum conditions. Consequences of the various conversion processes on environmental quality are briefly illustrated with a discussion of the impact of sulfate‐containing aerosols on PM10 concentrations and visibility degradation.
Heterogeneous Reactions of Chlorine Nitrate and Dinitrogen Pentoxide on Sulfuric Acid Surfaces Representative of Global Stratospheric Aerosol Particles
Authors: Manion Jeffrey A. , Fittschen Christa M. , Golden David M. , Williams Leah R. , Tolbert Margaret A. 
Published: November 2013

AbstractIncreasing evidence from field measurements, modeling studies, and laboratory experiments suggests that heterogeneous reactions on stratospheric sulfate aerosol particles can change the partitioning in the nitrogen and chlorine families and thereby affect global ozone levels. In this study, a Knudsen cell flow reactor was used to measure the uptake of ClONO2 and N2O5 by sulfuric acid solutions representative of background and volcanic stratospheric aerosol particles. The uptake coefficient (γ) of chlorine nitrate on 50–75 wt% H2SO4 at 223 K was found to be markedly dependent on the acid concentration, with γ ranging from about 1 × 10−2 to 1 × 10−4. These results are in good agreement with literature reports and the data fit the expression log γ= 1.87 – 0.074 × (wt% H2SO4). This reaction will thus have its largest impact when stratospheric temperatures are low and sulfuric acid aerosols are most dilute. Uptake of N2O5 was studied on solutions with compositions in the range 58–96 wt% H2SO4 at temperatures from 193 to 303 K. N2O5 reacted readily on sulfuric acid surfaces with uptake coefficients of about 0.06. The uptake coefficient was found to be independent of the sulfuric acid concentration and the solution temperature over the ranges studied. These results suggest that the reaction of N2O5 with H2O will occur readily on sulfuric acid aerosol particles for most stratospheric conditions.
Long‐Range Interactions in Thin Smectic Films on Substrates: X‐Ray Reflectivity Studies
Authors: Davidov D. , Tarabia M. , Cohen G. , Keller P. 
Published: November 2013

AbstractLong‐range forces between interfaces of thin and ultrathin smectic films are responsible for their thickness and stability. We present here X‐ray reflectivity studies of the forces in spin‐coated thin films of three different commercial liquid crystal (LC) mixtures as well as in main‐chain LC polymers based on polysiloxane. All these LC materials possess a smectic C* phase at room temperature. We demonstrate spontaneous molecular self‐assembly after spin coating into a nearly perfect smectic layer structure on various substrates. However, annealing at room temperature is essential to achieve an equilibrium state. Measurements on ultrathin annealed films of the LC mixtures show dramatic variation of the smectic layer spacing, L, as a function of the number of smectic layers, n (or film thickness, d). The functional dependence of L(n) for all three different liquid crystal mixtures suggests a long‐range interaction between the interfaces that decays algebraically as 1/nκ where κ = 2 ± 0.3. This decay is consistent with a van der Waals type of interaction, although its magnitude cannot be explained by the existing mechanisms.X‐ray studies of thick and thin annealed polysiloxane films allow determination of the phases, the phase transition temperatures, and the temperature dependence of the tilt angle in the smectic C* phase. Thin (300 Å to 600 Å) polysiloxane films far above the bulk smectic–isotropic phase transition temperature show the formation of smectic film at the film–substrate interface due to surface freezing phenomena. Preliminary investigations of the temperature dependence of the smectic film thickness indicate that the interaction between the interfaces decays algebraically, with an exponent κ = 1.5 ± 0.5.
Thermal Expansion of Thin Diblock Copolymer Films
Authors: Bassereau P. , Russell T.P. 
Published: November 2013

AbstractThe thermal expansion of thin films of symmetric diblock copolymers of polystyrene (PS) and poly(methyl methácrylate) (PMMA) was investigated by X‐ray reflectivity. The confinement of the copolymer to the substrate, coupled with the multilayering of the copolymer where PS and PMMA layers are oriented parallel to the substrate, gives rise to unusual thermal expansion characteristics. The total thickness of the film increases as 3αL, where αL is the linear thermal expansion coefficient of the copolymer. Unlike homopolymer films, the thermal expansion of an ordered block copolymer film results in an excessive stretching of the copolymer chains at the interface between the PS and PMMA layers. This excess stretching is a result of the confinement of the junction points of the copolymer chains to the interfaces and the suppression of the lateral expansion of the copolymer. When the stretching of the chains becomes too high, relaxation occurs by transporting copolymer chains to the surface. This is evidenced by a reduction in the period of the multilayer. After the copolymer chains have relaxed, the change in the multilayer period with temperature closely follows αL.
Pattern Formation in the Evaporation of Thin Liquid Films
Authors: Elbaum M. , Lipson S.G. 
Published: November 2013

AbstractWe investigate the patterns formed by thin liquid films evaporating from clean substrates. The system in equilibrium is entirely homogeneous, yet a remarkably regular, symmetric pattern is generated by a change in an isotropic parameter: the vapor pressure. The hydrodynamic instabilities which come into play display strong nonlinearities, distinguishing them from the classical capillary instabilities described by Rayleigh.
“Chrysanthemums”: Weak Micellization
Authors: De Gennes P.G. 
Published: November 2013

AbstractA statistical copolymer (A/B, with 50%–50% composition) immersed in a B polymer matrix, should display a novel form of micellization: portions which are slightly B‐rich protruding outward, and portions which are slightly A‐rich concentrating in a core. The average length of one portion is Neff ≅ 16χ−2, where χ is the AB Flory parameter. The total length N of the copolymer may range between Neff and Neff3/2. The limit N ‐ Neff corresponds to weak association, while N ˜ Neff3/2 corresponds to very few chains/micelle. Systems of this type should micellize equally well in B or A polymer solvents.
Diffusion‐Limited Segregation of Diblock Copolymers to a Homopolymer Surface
Authors: Budkowski Andrzej , Losch Andreas , Klein Jacob 
Published: November 2013

AbstractUsing nuclear reaction analysis, we have measured the rate of surface segregation of an asymmetric diblock polyisoprene–polystyrene (PIPS) copolymer to the free surface of polystyrene (PS) homopolymers within which it is incorporated at low bulk concentrations. We have also measured the tracer diffusion coefficient of PIPS in PS under similar conditions, and shown it to equal, within error, the self‐diffusion coefficient of PS of a similar length. The equilibrium surface excess Γ of the diblock is low (<Rg, the radius of gyration of the PS block of the copolymer), so that the diffusion rate is not expected to be significantly reduced by energy barrier effects. The rate of segregation appears considerably slower than a diffusion‐limited picture based on a sink‐boundary condition for the PIPS molecules at the PS surface would suggest. A much better description of our data is provided by a simple kinetic model which assumes local equilibrium between unattached and tethered diblocks at the free PS surface.
Thermoluminescence Dating and the Problem of Geochemical Evolution of Sediments — A Case Study: The Mousterian Levels at Hayonim
Authors: Mercier N. , Valladas H. , Joron J.L. , Schiegl S. , Bar Yosef O. , Weiner S. 
Published: November 2013

AbstractThe thermoluminescence dating of burnt flints has become a major tool in the elaboration of the chronology of human settlements of the last half a million years. The reliability of an age estimate depends to a great extent on the accuracy with which the internal and external radiation dose rates prevailing during the duration of burial can be determined. While determining the internal dose rate is relatively straightforward, the same cannot be said of the external, particularly if the sediment surrounding the flints is mineralogically heterogeneous or has undergone diagenetic changes during prolonged burial. In this article we show some examples of the problems confronted when one attempts to determine the external dose rates experienced by flints buried in a relatively heterogeneous environment of sediments, such as those sampled at the Middle Paleolithic occupation levels at Hayonim (Israel) which show evidence of past mineralogical evolution. The impact of changes produced by leaching and chemical reactions between the components of hearth ashes on the radioisotopic composition of the sediment and consequently the environmental dose rates were examined by subjecting several distinct sediment layers to thorough mineralogical, radiochemical, and dosimetric analyses. The problems of external dose‐rate determinations in mineralogically heterogeneous sediments are examined, particularly in those consisting of variable amounts of siliceous aggregates, apatite, and other phosphorus‐rich minerals produced by diagenetic reactions with bone residues.
On Early Myths and Formative Technologies: A Study of Pre‐Pottery Neolithic B Sculptures and Modeled Skulls From Jericho
Authors: Goren Yuval , Segal Irena 
Published: November 2013

AbstractDuring the last two decades, considerable interest has been expressed in the development of lime and lime plaster products in the Near Eastern Pre‐Pottery Neolithic B. The occurrences of lime products in numerous Levantine sites have raised questions concerning their methods of production, their role in the development of craft specialization, and their social and economic implications. Lime plaster was the first product that entailed the intentional chemical alteration of materials and the complete control over their properties. This was probably the reason for the wide spectrum of uses to which it was put, amongst which “daily” architectural functions appear to coexist with the symbolic or spiritual applications of this material.Amongst the variety of plaster products which appeared in the PPNB, it seems that the practice of skull plastering and sculpture production was the most “socially oriented” one, lacking any apparent relation to daily, functional use. In the present study two modeled skulls and a collection of plaster sculptures from Jericho were examined by means of thin section petrographic analysis, inductively coupled plasma atomic emission spectrometry, scanning electron microscopy, X‐ray diffraction, and Fourier‐transform infrared spectrometry. The results of the mineralogical and chemical analyses, when compared to data obtained from similar artifacts from other sites, demonstrate pronounced intersite variability in the methods of production of the skull and sculpture modeling. The full implications of this issue are discussed in detail in the paper.
Structure and Function of Activated Rhodopsin
Authors: Hofmann Klaus P. , Jäger Stefan , Ernst Oliver P. 
Published: November 2013

AbstractAftercis/transisomerization of retinal and early photoproducts, activated rhodopsin (R*) develops signaling states for different proteins in a time‐ordered sequence. Rhodopsin kinase binds all Meta forms, including the early Meta I, while interaction with transducin (Gt) or arrestin requires the deprotonated Schiff base form, Meta II (MII). Gtrecognizes a specific conformation, termed MIIb, which arises from an additional, spectrally silent conversion, linked to proton uptake. Collisional coupling with the GDP‐bound Gtholoprotein induces the release of GDP and formation of a stable R*—Gtcomplex, in which the nucleotide binding site of Gtis empty. The empty site complex, once formed, remains stable, even if the retinal is re‐isomerized to thecisconfiguration. The cytoplasmic surface of rhodopsin appears to provide the majority of interaction sites for other proteins. Physical analyses and mutagenesis have emphasized the loops connecting helices C/D and E/F of the seven‐helix structure. Any interaction between R* and Gtdepends on a conserved charge pair at the interface between the helix C and the adjacent loop CD. Replacements or deletions in loops CD and EF were found to cause more specific functional defects, including slow release of GDP or failure of GTP‐induced complex dissociation. In the dark, signaling states with low activity can be generated by reversible binding of all‐trans‐retinal to opsin. These light‐independent signaling states are different from the Meta forms.