bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular evolution of plant haemoglobin: two haemoglobin genes in nymphaeaceae Euryale ferox
Authors: Guldner E , Desmarais E , Galtier N , Godelle B
Published: January 2004

We isolated and sequenced two haemoglobin genes from the early-branching angiosperm Euryale ferox (Nymphaeaceae). The two genes belong to the two known classes of plant haemoglobin. Their existence in Nymphaeaceae supports the theory that class 1 haemoglobin was ancestrally present in all angiosperms, and is evidence for class 2 haemoglobin being widely distributed. These sequences allowed us to unambiguously root the angiosperm haemoglobin phylogeny, and to corroborate the hypothesis that the class 1/class 2 duplication event occurred before the divergence between monocots and eudicots. We addressed the molecular evolution of plant haemoglobin by comparing the synonymous and nonsynonymous substitution rates in various groups of genes. Class 2 haemoglobin genes of legumes (functionally involved in a symbiosis with nitrogen-fixing bacteria) show a higher nonsynonymous substitution rate than class 1 (nonsymbiotic) haemoglobin genes. This suggests that a change in the selective forces applying to plant haemoglobins has occurred during the evolutionary history of this gene family, potentially in relation with the evolution of symbiosis.
Phonons in conductors with magnetoimpurity electron states
Authors: Ermolaev A. M. , Rashba G. I.
Published: December 2003

A study is made of the changes in on the phonon spectrum and damping in a conductor in a quantizing magnetic field under the joint influence of quasilocal vibrations of impurity atoms in the lattice and magnetoimpurity electron states at those atoms. A system of equations for the electron and ion Green’s function is obtained on the basis an electron–ion model of a nonideal conductor in a magnetic field with the quasilocal vibrations and the magnetoimpurity states taken into account. At a low concentration of impurity atoms the magnetoimpurity states give resonance contributions to the polarization operator. They have a substantial influence on the phonon spectrum and damping. The magnetoimpurity states cause a crossover splitting of the phonon dispersion curves and give rise to new branches in the spectrum of elastic vibrations.
Superconductivity in quasi-two-dimensional nonadiabatic systems with arbitrary charge-carrier density at T=0
Authors: Palistrant M. E.
Published: December 2003

The basic system of equations of the theory of superconductivity at T=0 is obtained in an approximation linear in the nonadiabaticity, and analytic solutions for the order parameter Δ and the chemical potential μ are found in two limiting cases: μ≫Δ, and μ∼Δ. The dependence of these quantities on the density of charge carriers is investigated. It is found that the order parameter Δ can be increased by a factor of four to five in comparison with ordinary superconductors owing to the effects of nonadiabaticity and strong electronic correlations. The influence of the nonadiabaticity on the BCS–Bose crossover in the region of low charge-carrier densities is also investigated.
Inhomogeneity of the pseudogap state of a doped layered cuprate antiferromagnet
Authors: Sergeeva G. G.
Published: December 2003

The features of the pseudogap state in doped layered cuprate antiferromagnets and underdoped high-Tc superconductors (HTSCs) are investigated. It is shown that the transition to the pseudogap state is a dimensional crossover from three-dimensional motion to two-dimensional motion of charges in the copper–oxygen planes, which leads to the coexistence of light charge carriers and Jahn–Teller polarons and to the development of strong local correlations, as are characteristic for two-dimensional doped Mott–Hubbard insulators. In a doped antiferromagnet the d-wave pairing of light charge carriers and Jahn–Teller polarons leads to the formation of magnetic and bosonic clusters, i.e., substantial inhomogeneity of the copper–oxygen planes arises. It is found that the change in the properties of a doped layered cuprate antiferromagnetic insulator and in the metallic and superconducting states of an underdoped HTSC with decreasing temperature is due to a repeated dynamic reduction of their dimensionality. A model phase diagram in terms of the temperature and dopant concentration is proposed.
Superconductivity, negative magnetoresistance, and anisotropy of the conductivity of YFe4Al8 and ScFe4Al8 single crystals in the frequency range 0–108 Hz
Authors: Dmitriev V. M. , Prentslau N. N. , Zolochevskiı̆ I. V. , Ishchenko L. A. , Terekhov A. V. , Kotur B. Ya. , Suski W. , Talik E.
Published: December 2003

The anisotropy of the electrical resistivity of YFe4Al8 and ScFe4Al8 single crystals is investigated for the first time in the frequency range 0–108 Hz and temperature range 300–4.2 K. It is found that the conductivity is higher along the growth axis of the crystals than in the perpendicular direction, while the parameters governing the antiferromagnetic ordering, negative magnetoresistance, and superconductivity effects observed in these single crystals are isotropic. Some effects known previously for polycrystalline high-Tc superconductors containing magnetic impurities are observed in the single crystals investigated and are found to be anisotropic in them.
Structural and magnetic inhomogeneity and the NMR of Mn55 and La139 in the magnetoresistive ceramics La0.7Ba0.3−xSnxMnO3→La0.7−xBa0.3−xMnO3+0.5xLa2Sn2O7
Authors: Pashchenko V. P. , Shemyakov A. A. , Savosta M. M. , Khartsev S. I. , Derkachenko V. N. , Prokopenko V. K. , Turchenko V. A. , Pashchenko A. V. , Dyakonov V. P. , Buhanzev Yu. , Szymczak H.
Published: December 2003

The effects of substitution of barium by tin on the phase composition, structural imperfection, and properties of lanthanum manganite perovskites La0.7Ba0.3−xSnxMnO3 (x=0, 0.1, 0.15, 0.2, 0.3) are established by comprehensive studies done by x-ray diffraction, resistive, and magnetic (including NMR on Mn55 and La139) methods. It is shown that the introduction of Sn leads to the formation of a pyrochloric phase La2Sn2O7, to an increase in the density of lattice defects of the manganese-enriched main lanthanum manganite phase, and to a substantial decrease of the magnetoresistive effect. The smearing of the metal–semiconductor phase transition temperature is explained by an increase in the inhomogeneity and imperfection of the perovskite structure. The low activation energy is confirmed by a high degree of inhomogeneity and imperfection of the crystal lattice of the samples studied. The broad, asymmetric NMR spectra of Mn55 and La139 attest to high-frequency electron exchange between Mn3+ and Mn4+ and nonequivalence of the environment of those ions and La3+ due both to heterovalent ions and to vacancies and clusters.
Properties of low-temperature ytterbium condensates grown in a medium of gaseous helium
Authors: Kuz’menko V. M. , Vladychkin A. N.
Published: December 2003

The features of the electronic properties and mechanisms of crystallization of amorphous ytterbium films obtained by low-temperature condensation in a medium of gaseous helium (at a partial pressure of 2.3×10−3–7 Pa) are investigated. The changes of the conductivity, magnetoresistance, and Hall effect upon annealing of the films are investigated. The corresponding changes in the density and mobility of charge carriers are calculated in a two-band model. A model of the structural transformation of low-temperature condensates of gas-saturated ytterbium in the annealing process is proposed.
“High-temperature” oscillations of the magnetoresistance of bismuth: a possible alternative explanation
Authors: Komnik Yu. F.
Published: December 2003

It is shown that the known experimental results on the properties of the “high-temperature” oscillations of the magnetoresistance of bismuth—in particular, the angular dependence of the oscillation periods on the direction of the magnetic field—can be described by the Polyanovskiı̆ theory with the use of the condition that the cyclotron frequencies are equal or multiples.
High-frequency characteristics of contactless electromagnetic excitation of transverse sound in quasi-two-dimensional conductors
Authors: Galbova O. , Ivanovski G. , Krstovska D.
Published: December 2003

The contactless electromagnetic excitation of transverse sound with frequency ω in the semi-infinite space (z⩾0) of a quasi-two-dimensional conducting medium is considered. The distribution of the displacement field u(z), the electronic damping of sound, and the asymptotic behavior of the displacement field of an anomalous sound wave under conditions of the anomalous skin effect are calculated.
Anomalous charge transport in a quasi-one-dimensional electron system over liquid helium
Authors: Gladchenko S. P. , Kovdrya Yu. Z. , Nikolaenko V. A.
Published: December 2003

The conductivity σ in a quasi-one-dimensional electron system over liquid helium is measured in the temperature interval 0.5–1.7 K over a wide range of electron densities n. It is shown that the quantity σ/ne (e is the charge of the electron) initially increases with decreasing temperature and then, after passing through a maximum, begins to decline for T≈1 K. In this temperature region the value of σ/ne, above a certain value of the drift potential Vd, decreases with increasing Vd. It is conjectured that the anomalous charge transport observed in this study is due either to spatial ordering of the electrons in the quasi-one-dimensional channels or to the formation of many-electron polarons in the nonuniform potential along the channels.
Erratum: Thermal conductivity of solid parahydrogen with methane admixtures [Low Temp. Phys. 29, 527–529 (June 2003)]
Authors: Krivchikov A. I. , Korolyuk O. A. , Sumarokov V. V. , Mucha J. , Stachowiak P. , Jeżowski A.
Published: December 2003

The thermal conductivity of a solid parahydrogen crystal with methane admixtures was measured in the temperature range 1.5 to 8 K. Solid samples were grown from the gas mixtures at 13 K. The concentration of CH4 admixture molecules in the gas varied from 5 to 570 ppm. A very broad thermal conductivity peak with an absolute value of about 110 W/(m⋅K) was observed at 2.6 K. The data were interpreted using Callaway’s model with resonance scattering of phonons by quasilocal vibrations of CH4 molecules and phonon–grain boundary and phonon–phonon scattering. As grain boundary scattering increases, the broadening of the peak decreases. The analysis shows that a solid mixture of p-H2 and CH4 is a heterogeneous solution for CH4 concentration higher than 0.1 ppm.
Biaxial disclinated states in nematic elastomers
Authors: Fried Eliot , Korchagin Vladimir , Todres Russell E.
Published: December 2003

We use a continuum model to investigate the isochoric axial contraction and expansion of a right circular cylindrical specimen composed of a nematic elastomer that is cross-linked in a uniaxial state and then annealed. We build on previous work by relaxing the constraint that the molecular conformation be spherical or uniaxial, allowing instead for biaxiality. The material exhibits an energetic preference for states involving a disclination of strength +1 along the cylinder axis surrounded by a region in which the conformation of the polymer chains is indeed biaxial. We show that such states represent minimizers of the total free-energy. Also, the reactive pressure necessary to enforce the constraint of material incompressibility within the disclination core is found to be reduced by an order of magnitude when the conformation is biaxial rather than uniaxial. A bifurcation analysis is used to analytically determine the thresholds of axial expansion and contraction at which the material prefers a disclinated state. These thresholds are found to be consistent with numerical predictions. Finally, the stability of the solutions for the studied parameters is also investigated.
Elastic incoherent neutron scattering from homologous disaccharides/H2O mixtures
Authors: Magazù S. , Migliardo F. , Mondelli C.
Published: December 2003

An analysis in terms of elastic scans of the neutron intensity of homologous disaccharide (trehalose, maltose, sucrose)/H2O mixtures as a function of temperature and exchanged wave vector has been carried out. The experimental findings, showing a crossover in molecular fluctuations between harmonic and anharmonic dynamical regimes, allow us to characterize the system “flexibility.” A new operative definition for the “fragility” degree, by using elastic incoherent neutron scattering, is furnished. In this frame the lower flexibility and fragility character of trehalose/H2O mixture with respect to maltose and sucrose/H2O mixtures indicate a better attitude to encapsulate biostructures in more rigid and temperature insensitive structures in approaching the glass transition.
The permanent electric dipole moments and magnetic hyperfine interactions of ruthenium mononitride, RuN
Authors: Steimle Timothy C. , Virgo Wilton
Published: December 2003

The low rotational features of the (0,0) F 2Σ+←X 2Σ+ band system of a supersonic molecular beam of RuN have been recorded at high spectral resolution via laser induced fluorescence spectroscopy. The electric field induced dependence of the P11(1) and Q21R(0) branch features of the RuN104 isotopomer were analyzed to produce permanent electric dipole moments, μ, of 1.89(5) and 1.07(5) D for the X 2Σ+ and F 2Σ+ states, respectively. The splitting in the field free spectrum of the RuN101 isotopomer was analyzed to produce a Fermi contact, bF(X 2Σ+), parameter of −0.0349(4) cm−1. The results are interpreted using the electronic structure predictions for the F 2Σ+ and X 2Σ+ states given by Ram et al. [J. Chem. Phys. 109, 6329 (1998)] and compared with RuC and FeC.
Absorption, resonance, the preresonance Raman study of the 1,3-dicyanomethylene croconate dianion using complete active space self-consistent field and density functional theory methods
Authors: Makowski M. , Pawlikowski M. T.
Published: December 2003

The electronic structures of the 11B2 and 21A1 excited electronic states of the 1,3-dicyanomethylene croconate dianion are studied in the framework of complete active space self-consistent field (CASSCF) and Becke’s three-parameter hybrid method with a Lee–Yang–Parr correlation functional methods applied on the level aug-cc-pVDZ basis set. The CASSCF/aug-cc-pVDZ treatment provides the ground (11A1) and the excited 11B2 and 21A1 states geometries, which are then used to evaluate the Franck–Condon parameters in the 11B2 and 21A1 states. The quality of the numerical results is verified on the bases of experimental near-resonance and resonance Raman data available in the vis-UV excitation region. The analysis is done in terms of the vibronic model, which treats the totally symmetric vibrations as displaced harmonic oscillators. Under the resonance with the 11A1→11B2 electronic transition, that somewhat simplified vibronic model leads to excellent agreement between the theoretical and empirical excitation profiles for the ν2=2234 cm−1, ν9=911 cm−1, ν13=376 cm−1, and ν14=318 cm−1 fundamentals. At preresonance with the 11A1→11B2 electronic excitation the agreement with the experimental Raman spectrum is reasonable but some discrepancies are noticed for the ν4=1620 cm−1 and ν5=1546 cm−1 fundamental lines. We argue that the observed discrepancies can be removed when mode-mixing (Duszynski) effects between ν4 and ν5 vibrations in the 11B2 state are taken into account.
Experimental and theoretical studies of the optical and electronic properties of a zinc complex encapsulated in the nanocavities
Authors: Zhang Lei Z. , Cheng Peng
Published: December 2003

Optical and electronic properties of a novel zinc complex bis[bis(N-octylsalicylideneamineto) zinc(II)] (1) encapsulated in the nanocavities of Mobile Catalytic Material 41 (MCM-41) have been investigated by both experimental measurement and theoretical analysis. Ultraviolet-visible absorption and emission spectra and excited-state lifetimes of 1 in ethanol solution and nanoporous MCM-41 have been recorded. The bathochromic shift of the 0–0 transitions and the shortening of the excited-state lifetimes have been correlated with the reduction of the band gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital accompanying by the increased energies of the frontier molecular orbitals. The variations of the electronic states and band gaps are correlated with the increase of Coulomb integral α and the resonance integral β, which has been confirmed by the theoretical calculations.
Ab initio study of the electronic structures and conduction properties of some donor-acceptor polymers and their copolymers
Authors: Bakhshi A. K. , Bhargava Parul
Published: December 2003

The electronic structures and conduction properties of four donor-acceptor polymers containing alternating electron-donating group SiF2 and electron-accepting group Y [Y=>C=CH2 in PSIFCH, >C=O in PSIFCO, >C=CF2 in PSIFCF, and >C=C(CN)2 in PSIFCN] along the conjugated trans-cisoid polyacetylene backbone, obtained on the basis of the ab initio Hartree-Fock crystal orbital method are compared. All the polymers are predicted to have band gap values ranging between 1 and 2 eV. The calculated band gap values are found to decrease in the order PSIFCO>PSIFCH>PSIFCF>PSIFCN. PSIFCO is predicted to be the strongest candidate for oxidative (p) doping while PSIFCN is found to have the greatest capacity for reductive (n) doping. The π-bond order data as well as the geometric structures of these polymers show them to have aromaticlike electronic structures. Using the ab initio band structure results of PSIFCO (A)x and PSIFCN (B)x, the electronic density of states of various quasi-one-dimensional compositional superlattices (copolymers) (AmBn)x, belonging to the type-II-staggered class have been determined using the negative-factor counting method, taking multineighbor interactions (up to six neighbors) into account. The trends in the electronic structures and conduction properties of these copolymers as a function of (i) block sizes m and n, (ii) composition (m/n), and (iii) arrangement of blocks (periodic or aperiodic) in the copolymer chain are discussed. The results are important guidelines for molecular designing of copolymers with tailor-made conduction properties.
Isomerization of the interstellar molecule silicon cyanide to silicon isocyanide through two transition states
Authors: Richardson Nancy A. , Yamaguchi Yukio , Schaefer Henry F.
Published: December 2003

A range of highly correlated ab initio methods is used to predict the geometrical parameters of silicon cyanide (SiCN), silicon isocyanide (SiNC), and two transition states (2A′ and A″)2 for the isomerization reaction transforming one to the other. Also predicted are dipole moments, rotational constants, and harmonic vibrational frequencies. At all levels of theory, the SiCN and SiNC molecules are predicted to have linear equilibrium structures. The SiNC isomer is found to lie 1.5 kcal/mol above the SiCN species at the coupled cluster (CC) with single, double, and full triple excitations (CCSDT) level of theory with the correlation-consistent polarized valence quadruple zeta (cc-pVQZ) basis set. These theoretical predictions complement the recent laboratory production of SiCN and SiNC and subsequent astronomical detection of SiCN in the envelope of the C Star IRC+10216/CW Leo. The theoretical Be values of 5481 MHz (SiCN) and 6316 MHz (SiNC) at the CC with single, double, and iterative partial triple excitations (CCSDT-3) level of theory with the cc-pVQZ basis set are consistent with the experimental B0 values of 5543 MHz (SiCN) and 6397 MHz (SiNC). The transition states for the isomerization reaction SiCN→SiCN are found to proceed through the A′2 and A″2 surfaces, which lie 20.9 and 21.8 kcal/mol above the SiCN minimum at the cc-pVQZ CCSDT-3 level of theory. The ground states of SiCN and SiNC radicals are subject to Renner–Teller interactions. At the CC with single, double, and perturbative triple excitations [CCSD(T)] level of theory, the Renner parameters and the averaged harmonic bending vibrational frequencies are determined to be 0.318 and 249 cm−1 for SiCN and 0.412 and 195 cm−1 for SiNC.
The effect of grid quality and weight derivatives in density functional calculations of harmonic vibrational frequencies
Authors: Malagoli Massimo , Baker Jon
Published: December 2003

We investigate the accuracy of harmonic vibrational frequencies computed with and without the inclusion of quadrature weight derivatives in our recently completed initial implementation of density functional theory (DFT) analytical second derivatives. Unlike the situation with analytical DFT gradients, second derivatives are much more sensitive to the inclusion of weight derivatives, and omitting them can produce nonsensical results unless the numerical grid is of sufficiently high quality. Results are presented for the homonuclear diatomics F2, Cl2, Br2, and I2 and for a number of larger molecules. Errors introduced by excluding weight derivatives increase with increasing atomic number and increasing basis set size. The origin of the error is the difficulty of accurately integrating high-order derivatives of basis functions with large exponents around their own atomic center, and it is not the weight derivatives themselves that eliminate this error but the fact that proper allowance for atom-centered grids that “move” with the atom means that basis functions no longer directly contribute to derivative quantities evaluated on their own grid.
Rational classification of a series of aromatic donor–acceptor systems within the twisting intramolecular charge transfer model, a time-dependent density-functional theory investigation
Authors: Jamorski Christine Jödicke , Lüthi Hans-Peter
Published: December 2003

The goal of this paper is to rationalize the fluorescence activity, experimentally observed for 21 molecules of the same family as the 4-(N,N-dimethyl)anilines, based on their potential energy surfaces calculated within the twisting intramolecular charge transfer model. A classification in four groups is proposed according to the sign of two parameters, ΔEgap, characterizing the energy difference between the vertical locally and charge transfer excited states, and ΔE1S (or ΔẼ1S for pretwisted systems), representing the energy gain of the charge transfer excited state with a perpendicular conformation compared to the first vertical excited state. In this study, the time-dependent density-functional theory has been used to calculate the potential energy surfaces of the ground and excited states along the twisting angle. Computed excitation energies and optimized ground state geometries have been obtained with both B3LYP and MPW1PW91 functionals using a 6-311+G(2d,p), and a 6-31G(d) basis set, respectively. From this study, it follows that ΔEgap and ΔE1S are the main parameters necessary to understand the fluorescence activity of these molecules. The fact that the same fluorescence activity is observed for the members of each group (or subcategory for the particular case of group II), reveals the underlying twisting mechanism as a common process for all the investigated molecules, which explains their experimental dual and nondual emission.
Gaussian basis sets of quadruple zeta valence quality for atoms H–Kr
Authors: Weigend Florian , Furche Filipp , Ahlrichs Reinhart
Published: December 2003

We present Gaussian basis sets of quadruple zeta valence quality with a segmented contraction scheme for atoms H to Kr. This extends earlier work on segmented contracted split valence (SV) and triple zeta valence (TZV) basis sets. Contraction coefficients and orbital exponents are fully optimized in atomic Hartree–Fock (HF) calculations. As opposed to other quadruple zeta basis sets, the basis set errors in atomic ground-state HF energies are less than 1 mEh and increase smoothly across the Periodic Table, while the number of primitives is comparably small. Polarization functions are taken partly from previous work, partly optimized in atomic MP2 calculations, and for a few cases determined at the HF level for excited atomic states nearly degenerate with the ground state. This leads to basis sets denoted QZVP for HF and density functional theory (DFT) calculations, and for some atoms to a larger basis recommended for correlated treatments, QZVPP. We assess the performance of the basis sets in molecular HF, DFT, and MP2 calculations for a sample of diatomic and small polyatomic molecules by a comparison of energies, bond lengths, and dipole moments with results obtained numerically or using very large basis sets. It is shown that basis sets of quadruple zeta quality are necessary to achieve an accuracy of 1 kcal/mol per bond in HF and DFT atomization energies. For compounds containing third row as well as alkaline and earth alkaline metals it is demonstrated that the inclusion of high-lying core orbitals in the active space can be necessary for accurate correlated treatments. The QZVPP basis sets provide sufficient flexibility to polarize the core in those cases. All test calculations indicate that the new basis sets lead to consistent accuracies in HF, DFT, or correlated treatments even in critical cases where other basis sets may show deficiencies.
Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method
Authors: Rathinam Muruhan , Petzold Linda R. , Cao Yang , Gillespie Daniel T.
Published: December 2003

We show how stiffness manifests itself in the simulation of chemical reactions at both the continuous-deterministic level and the discrete-stochastic level. Existing discrete stochastic simulation methods, such as the stochastic simulation algorithm and the (explicit) tau-leaping method, are both exceedingly slow for such systems. We propose an implicit tau-leaping method that can take much larger time steps for many of these problems.
Paramagnetic susceptibility simulations from crystal field effects on Nd3+ in AgNd(WO4)2
Authors: Colón C. , Alonso-Medina A. , Montero J. , Fernandez F. , Cascales C.
Published: December 2003

Polycrystalline AgNd(WO4)2 has been prepared by a in solid-state reaction. X-ray diffraction measurements indicate that this compound crystallizes with a scheelite-type tetragonal structure. Absorption and emission spectra have been measured, using the technique of the crystal field parameters, to obtain the energy levels scheme for Nd3+ ions in the crystalline matrix. These data indicate the existence of a structural local disorder associated with a random distribution of the ions of Ag+ and Nd3+. The temperature variation of the paramagnetic susceptibility in the range from 2 to 300 K has been studied. The Van Vleck formula has been used to calculate the temperature variation of the paramagnetic susceptibility and it was compared with the experimental results. Particularly at low temperatures, satisfactory agreement has been obtained.
Liquid state theories for the structure of water
Authors: Reddy Govardhan , Lawrence C. P. , Skinner J. L. , Yethiraj Arun
Published: December 2003

Liquid state theories are investigated for the local structure of the simple point charge (SPC) and a modified SPC (MSPC) model of water. The latter model includes a van der Waals repulsion between the oxygen (O) and hydrogen (H) atoms, which is necessary for the implementation of some integral equation theories. Two integral equation theories, the reference interaction site model (RISM) and the diagrammatically proper Chandler–Silbey–Ladanyi (CSL) theory, are tested by comparison with simulations of the MSPC model (neither theory converges for the SPC model when the hypernetted chain closure is used). The RISM theory is in reasonable agreement with simulations, and is more accurate than the CSL theory. A density functional theory (DFT) is investigated, which treats the ideal gas functional exactly and uses a truncated expansion for the excess free energy functional. The DFT is in excellent agreement with simulations for the structure of the MSPC water model at all temperatures studied, and for the structure of the SPC water model at high temperatures. At room temperature, the DFT is in good agreement with simulations (of SPC water) for gHH(r) and gOH(r), but misses the location of the second peak in gOO(r). We attribute this deficiency to the importance of three-body correlations that are not properly incorporated in the theory.
Boundary slip as a result of a prewetting transition
Authors: Andrienko Denis , Dünweg Burkhard , Vinogradova Olga I.
Published: December 2003

Some fluids exhibit anomalously low friction when flowing against a certain solid wall. To recover the viscosity of a bulk fluid, slip at the wall is usually postulated. On a macroscopic level, a large slip length can be explained as a formation of a film of gas or phase-separated “lubricant” with lower viscosity between the fluid and the solid wall. Here we justify such an assumption in terms of a prewetting transition. In our model the thin-thick film transition together with the viscosity contrast gives rise to a large boundary slip. The calculated value of the slip length has a jump at the prewetting transition temperature which depends on the strength of the fluid-surface interaction (contact angle). Furthermore, the temperature dependence of the slip length is nonmonotonous.
Thermal effects on viscoelastic properties of silicate glass melts
Authors: Tordjeman Ph. , Felio J. M. , Gazagnes L.
Published: December 2003

High-temperature viscoelastic properties of two different silicate glass melts have been measured with a new high-temperature rheometer between 700 °C and 900 °C. Our experiments demonstrate that the viscoelastic properties in the terminal zone, a low-frequency domain which has never been explored, are very sensitive to the chemical composition of the glass and to the thermal treatment applied during the preparation of the samples. The storage shear modulus G′ and the loss shear modulus G″ were measured at constant temperature between 10−3 and 102 rad/s. The two chosen silicate glass melts have different chemical compositions and, moreover, each of them was prepared with two thermal treatments during the sample molding. In the experimental range of temperature, the viscoelastic properties of the two glass melts are characteristic of the ultimate rheological behavior at low frequencies called the terminal zone. We tested the possibility of building the rheological master curve for the two liquids over a wide frequency domain. Experiments show that one quenched glass melt has a Maxwell viscoelastic behavior and obeys time–temperature superposition, while the same glass annealed below the glass transition temperature presents changes in the viscoelastic behavior and does not obey time–temperature superposition. The second glass is non-Maxwellian and does not obey time–temperature superposition for the two thermal conditions of molding showing a phase transition, or a structural change transition, between 700 °C and 900 °C. We observed a great influence of the thermal treatment on the viscoelastic properties in the melted state for the two silicates.
The kinetic energy dependence of association reactions. A new thermokinetic method for large systems
Authors: Koizumi Hideya , Armentrout P. B.
Published: December 2003

The reactions of bare alkali metal ions (M+=Li+, Na+, or K+) with dimethoxyethane (CH3OCH2CH2OCH3, DXE) are studied using guided ion beam tandem mass spectrometry. The bimolecular reaction forms an associative M+(DXE) complex that is long-lived and dissociates back to the reactants. The kinetic energy dependences of the cross sections for formation of the complexes are interpreted with several different models (including rigorous phase space theory) that assume that the complex lifetimes are limited by dissociation over a loose, orbiting transition state. After accounting for the effects of multiple ion–molecule collisions, internal energy of the reactant ions, Doppler broadening, and dissociation lifetimes, the analyses yield 0 K bond energies as the only adjustable parameter. These values are compared with bond energies obtained from previous collision-induced dissociation (CID) studies of the M+(DXE) complexes and found to be self-consistent for all models studied. Association and CID form the same energized M+(DXE) complex in two distinct ways, such that a comparison of these results allows an assessment of the models used to interpret CID thresholds and test the limits of statistical theories such as RRKM and phase space theory.
Hydrogen bond breaking probed with multidimensional stimulated vibrational echo correlation spectroscopy
Authors: Asbury John B. , Steinel Tobias , Stromberg C. , Gaffney K. J. , Piletic I. R. , Fayer M. D.
Published: December 2003

Hydrogen bond population dynamics are extricated with exceptional detail using ultrafast (<50 fs) infrared multidimensional stimulated vibrational echo correlation spectroscopy with full phase information and frequency resolved infrared pump–probe experiments performed on the hydroxyl stretch of methanol–OD oligomers in CCl4. Hydrogen bond breaking makes it possible to acquire data for times much greater than the hydroxyl stretch vibrational lifetime. The correlation spectra and detailed calculations demonstrate that vibrational relaxation leads to hydrogen bond breaking for oligomers that have hydroxyl stretch frequencies on the low energy (red) side of the hydroxyl stretch spectrum, the spectral region that is associated with the strongest hydrogen bonds. Frequency resolved pump–probe data support the conclusions drawn from the correlation spectra. Using a global fit to the pump–probe spectra, in conjunction with assignments made possible through the correlation spectra, it is demonstrated that the residual ground state and photoproduct of hydrogen bond breaking are prepared near their thermal equilibrium distribution. The spectrum of the hydrogen bond breaking photoproduct and the residual ground state approach the steady-state temperature difference spectrum on the tens of picoseconds time scale, indicating the system thermalizes on this time scale.
Influence of electronic transitions on the collision-induced multifragmentation dynamics of Na4+ cluster ions
Authors: Sizun Muriel , Aguillon François , Sidis Victor
Published: December 2003

The collision-induced multifragmentation of Na4+ alkali metal cluster ions by He impact in the 100 eV (center of mass) collision energy range is investigated theoretically using a DIM-based nonadiabatic molecular dynamics method. Compared to our earlier adiabatic molecular dynamics calculations new fragmentation channels are populated and new relaxation processes of excited electronic states to the ground state take place. The mechanisms of the different processes are analyzed. Comparisons with experiments are presented and discussed.
Stark maps and Rydberg transitions in the presence of an electric field for Li, Na, and K. A quantum defect orbital approach
Authors: Menéndez J. M. , Martı́n I. , Velasco A. M.
Published: December 2003

The Stark structure of the Rydberg states of the lighter alkali atoms, Li, Na, and K, and the Stark oscillator strength distribution for Li have been calculated by diagonalization of the quantum defect orbital (QDO) Hamiltonian matrix. The presently obtained Stark maps are in excellent agreement with those resulting from theory and experiment, as reported in the literature by other authors. Good accord is also found for the presently calculated oscillator strength distribution, within a Stark manifold, with that of other theoretical approach and experimental measurements. The adequacy of the QDO procedure for accurately dealing with properties related to the Stark effect in atoms is suggested.
Fast, scalable master equation solution algorithms. III. Direct time propagation accelerated by a diffusion approximation preconditioned iterative solver
Authors: Frankcombe Terry J. , Smith Sean C.
Published: December 2003

In this paper we propose a novel fast and linearly scalable method for solving master equations arising in the context of gas-phase reactive systems, based on an existent stiff ordinary differential equation integrator. The required solution of a linear system involving the Jacobian matrix is achieved using the GMRES iteration preconditioned using the diffusion approximation to the master equation. In this way we avoid the cubic scaling of traditional master equation solution methods and maintain the low temperature robustness of numerical integration. The method is tested using a master equation modelling the formation of propargyl from the reaction of singlet methylene with acetylene, proceeding through long lived isomerizing intermediates.
Fast, scalable master equation solution algorithms. IV. Lanczos iteration with diffusion approximation preconditioned iterative inversion
Authors: Frankcombe Terry J. , Smith Sean C.
Published: December 2003

In this paper we propose a second linearly scalable method for solving large master equations arising in the context of gas-phase reactive systems. The new method is based on the well-known shift-invert Lanczos iteration using the GMRES iteration preconditioned using the diffusion approximation to the master equation to provide the inverse of the master equation matrix. In this way we avoid the cubic scaling of traditional master equation solution methods while maintaining the speed of a partial spectral decomposition. The method is tested using a master equation modeling the formation of propargyl from the reaction of singlet methylene with acetylene, proceeding through long-lived isomerizing intermediates.
Dipole-bound negative ions: Collisional destruction and blackbody-radiation-induced photodetachment
Authors: Suess L. , Liu Y. , Parthasarathy R. , Dunning F. B.
Published: December 2003

The lifetimes and collisional destruction of dipole-bound negative ions formed by electron transfer in collisions between K(np) Rydberg atoms and acetonitrile, deuterated acetonitrile, acrylonitrile, dimethylsulfoxide, and pyridazine are studied using a Penning ion trap. The data show that the rate constants for destruction of these ions by rotational energy transfer in collisions with residual target gas present in the trap are large, ∼10−7 cm3 s−1, consistent with the behavior to be expected for weakly bound species. Ion decay in the trap is characterized by a single exponential. When corrected for collision-induced destruction, the observed decay rates correspond to ion lifetimes that lie in the range ∼60 to 100 μs. These relatively short lifetimes are attributed to photodetachment induced by background thermal blackbody radiation.
Computational and experimental investigation of intermolecular states and forces in the benzene–helium van der Waals complex
Authors: Lee Soohyun , Chung James S. , Felker Peter M. , López Cacheiro Javier , Fernández Berta , Bondo Pedersen Thomas , Koch Henrik
Published: December 2003

A study of the intermolecular potential-energy surface (IPS) and the intermolecular states of the perprotonated and perdeuterated benzene–He complex is reported. From a fit to ab initio data computed within the coupled cluster singles and doubles including connected triples model for 280 interaction geometries, an analytic IPS including two- to four-body atom–atom terms is obtained. This IPS, and two other Lennard-Jones atom–atom surfaces from the literature, are each employed in dynamically exact (within the rigid-monomer approximation) calculations of J=0 intermolecular states of the isotopomers. Rotational constants and Raman-scattering coefficients for intermolecular vibrational transitions are also calculated for each of the three surfaces. The calculated results are compared with experimental results reported herein pertaining to intermolecular Raman spectra of benzene–He. The calculated rotational constants are compared with experimental values from the literature. The fitted IPS of this work leads to calculated observables that match the experimental results very well. The IPSs from the literature are not as successful, specifically in regard to the intermolecular Raman spectra.
Adsorption processes and structure of water molecules on Pt(110) electrodes in perchloric solutions
Authors: Zheng Wanquan , Tadjeddine Abderrahmane
Published: December 2003

The different adsorption processes and conformational structure of water molecules at a 0.1 M HClO4/Pt(110) interface have been studied by using in-situ infrared-visible sum-frequency generation (SFG) spectroscopy. The O–H stretch resonance is found to be quite weak, while the Pt–H stretch mode arises rapidly in the hydrogen adsorption region and the total symmetric stretch mode ν1 of ClO4− anions dominates the resonant signal in the double layer region. In this work we provide the first spectroscopic evidence that hydrogens and ClO4− anions are more favored than water molecules, despite their significant dipole moment, in the competitive adsorption processes below the oxidation potential. Our SFG results suggest that, for a platinum in the 0.1 M HClO4 solution, most interfacial water molecules are not directly adsorbed but rather are present at the electrode surface as the constituents of hydration shells.
Competing interactions of noble metals and fullerenes with the Si(111)7×7 surface
Authors: O’Shea James N. , Phillips Mick A. , Taylor Michael D. R. , Beton Peter H. , Moriarty Philip , Kanai Mito , Dennis T. John S. , Dhanak Vin R. , Patel Sunil , Poolton Nigel
Published: December 2003

Synchrotron-based photoelectron spectroscopy (PES) has been used to investigate the interaction of atomic gold and silver with a covalently bound C60-monolayer adsorbed on Si(111)7×7. In contrast to the relatively benign interaction of silver with the C60/Si(111)7×7 surface, core-level photoemission data reveal a strong interaction of gold with the underlying silicon despite the presence of a chemisorbed fullerene monolayer. The Si 2p PES data exhibit dramatic changes consistent with the formation of a gold silicide, which is also evident from the corresponding Au 4f spectra. Valence band photoemission also reveals the absence of any density of states at the Fermi level following the adsorption of either metal, indicating a negligible transfer of electrons from the adsorbed metal to the C60 cage.
Efficient generation of low-energy folded states of a model protein. II. Automated histogram filtering
Authors: Larrass Stefan A. , Pegram Laurel M. , Gordon Heather L. , Rothstein Stuart M.
Published: December 2003

A number of short, Monte Carlo simulated annealing runs are performed on a highly frustrated 69-mer off-lattice model protein, consisting of a chain of 69 beads that are either hydrophobic, hydrophilic, or neutral in nature, and which demonstrably folds into a six-stranded β-barrel structure. We employ an iterative, consensus-based scheme to cluster the 725 nonbonded distances between the hydrophobic beads using, in tandem, Ward’s method for hierarchical clustering and k-means partitional clustering. We also independently analyze the same data using computer-automated histogram filtering, a technology designed to cluster high-dimensional data, without the tedium and subjectivity required by our iterative implementation of the two classical clustering methods. The memberships of low-energy clusters obtained from both classical clustering and automated histogram filtering approaches are remarkably similar. Nonbonded distance constraints are derived from these clusters and from small sets of the original unclustered conformations obtained by simulated annealing. Employing a distance geometry approach, we efficiently generate novel, low-energy conformations from each set of distance constraints, including the apparent native structure, up to 40 times faster than by doing additional simulated annealing runs. Over 33 000 unique locally optimized conformations are generated in total, substantially augmenting the number of low-energy states located by the original simulated annealing runs.
Experiments and simulations of Ar scattering from an ordered 1-decanethiol–Au(111) monolayer
Authors: Gibson K. D. , Isa N. , Sibener S. J.
Published: December 2003

A study of the scattering of Ar from a well-ordered standing-up phase of 1-decanethiol adsorbed on Au(111) at surface temperatures from 110 to 185 K is presented. The final energies and intensities were measured as a function of incident polar and azimuthal angles using incident energies from 65 to 600 meV. These experimental results are compared to classical trajectory calculations. Scattering shows two distinct exit channels. The higher energies are due to direct inelastic scattering and have the greatest intensities at glancing incident and final angles. The lower energy channel is due to trapping-desorption; it has a Maxwell–Boltzmann energy distribution at the surface temperature and a cosine angular intensity profile. The simulations show that the timescale for normal momentum accommodation is very fast. The parallel momentum accommodation takes slightly longer, dependent on the initial conditions, but is still complete within only a few picoseconds. The result is that much of the Ar undergoes trapping-desorption, and the promptly scattered direct inelastic component, which interacts with the surface for ∼1 picosecond, retains more of its parallel than perpendicular momentum, leaving the surface preferentially at glancing polar angles. Another interesting observation is that the energy exchange between the surface and the directly scattered Ar has a dependence on the incident azimuthal angle. This is, in a sense, another type of structure scattering, where it is the anisotropic elastic response of the surface rather than the corrugation that leads to the angular dependence of the atom scattering.
Grand canonical molecular dynamics
Authors: Boinepalli Sharada , Attard Phil
Published: December 2003

A hybrid molecular dynamics-Monte Carlo grand canonical simulation technique is developed for systems with constant chemical potential and temperature. The method ensures that the particle number and energy fluctuate according to the standard grand canonical probability distribution. Partial coupling and fractional particles are used to enhance the success of insertion and deletion attempts, and the method is shown to be feasible in dense liquids. The method is applied to a Lennard-Jones fluid and it gives the density as a function of chemical potential in agreement with known results. It is demonstrated that the transport coefficients can be obtained with the method by analyzing the influence of the stochastic perturbation on the diffusion constant for an isothermal system.
Spectral investigation for phosphorescent polymer light-emitting devices with doubly doped phosphorescent dyes
Authors: Shen Fangzhong , Xia Hong , Zhang Chengbo , Lin Dong , Liu Xiaodong , Ma Yuguang
Published: December 2003

The photoluminescence and electroluminescence (EL) spectral characteristics of two phosphorescent dyes, green fac-tris(2-phenylpyridine) iridium(III) [Ir(ppy)3] and red tris-(4,7-diphenyl-1,10-phenanthroline)rhenium dications [Ru(4,7-Ph2-phen)3]2+, doubly doped poly(N-vinylcarbazol) (PVK) films were investigated. The efficient energy transfers from PVK host to both Ir(ppy)3 and [Ru(4,7-Ph2-phen)3]2+ dopants were observed in photoexcitation and EL devices. The intensity ratio (Ri) of red emission versus green emission as function of doping ratio (Rc) of [Ru(4,7-Ph2-phen)3]2+ and Ir(ppy)3 in PVK host is found according to a power-law function with the slopes of 2.28±0.2 for PL which obey the power-law with Ri–Rc2 predicated by Förster energy transfer model. EL spectra show a driving voltage depentent power law of Ri–Rc1.53±0.14 at low voltage and Ri–Rc1.16±0.08 at high voltage, respectively. The shift in the power law of Förster energy transfer is likely due to additional emission mechanisms such as carrier trapping and triplet exciton saturation at high current density.