bluuebunny/crossref_metadata_2025 huggingface dataset:
Heat capacity effects associated with the hydrophobic hydration and interaction of simple solutes: A detailed structural and energetical analysis based on molecular dynamics simulations
Authors: Paschek Dietmar
Published: May 2004

We examine the SPCE [H. J. C. Berendsen et al., J. Chem. Phys. 91, 6269 (1987)] and TIP5P [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys 112, 8910 (2000)] water models using a temperature series of molecular-dynamics simulations in order to study heat-capacity effects associated with the hydrophobic hydration and interaction of xenon particles. The temperature interval between 275 and 375 K along the 0.1-MPa isobar is studied. For all investigated models and state points we calculate the excess chemical potential for xenon employing the Widom particle insertion technique. The solvation enthalpy and excess heat capacity is obtained from the temperature dependence of the chemical potentials and, alternatively, directly by Ewald summation, as well as a reaction field based method. All three methods provide consistent results. In addition, the reaction field technique allows a separation of the solvation enthalpy into solute/solvent and solvent/solvent parts. We find that the solvent/solvent contribution to the excess heat capacity is dominating, being about one order of magnitude larger than the solute/solvent part. This observation is attributed to the enlarged heat capacity of the water molecules in the hydration shell. A detailed spatial analysis of the heat capacity of the water molecules around a pair of xenon particles at different separations reveals that even more enhanced heat capacity of the water located in the bisector plane between two adjacent xenon atoms is responsible for the maximum of the heat capacity found for the desolvation barrier distance, recently reported by Shimizu and Chan [J. Am. Chem. Soc. 123, 2083 (2001)]. The about 60% enlarged heat capacity of water in the concave part of the joint xenon–xenon hydration shell is the result of a counterplay of strengthened hydrogen bonds and an enhanced breaking of hydrogen bonds with increasing temperature. Differences between the two models with respect to the heat capacity in the xenon–xenon contact state are attributed to the different water model bulk heat capacities, and to the different spatial extension of the structure effect introduced by the hydrophobic particles. Similarities between the different states of water in the joint xenon–xenon hydration shell and the properties of stretched water are discussed.
Hamiltonian theory for vibrational line shapes of atoms adsorbed on surfaces
Authors: Guantes R. , Vega J. L. , Miret-Artés S. , Pollak Eli
Published: May 2004

The vibrational motions of atomic adsorbates on surfaces can be probed by helium atom scattering. The experimental observable is the dynamic structure factor, which shows an inelastic peak around the vibrational frequency of the isolated adsorbates known as the frustrated translational or T-mode peak. In this paper we develop a theory for the line shape of this peak, as well as for its temperature-dependent shift and broadening, based on a Hamiltonian equivalent of the generalized Langevin equation. The theory can be used to infer physical parameters of the adatom–surface interaction, such as the friction coefficient, the barrier height to diffusion, and the anharmonicity parameter. Numerical simulations are used to ascertain the range of validity of the theory, which is also generalized to describe multidimensional systems and to include quantum corrections. We compare the theoretical predictions for the shift and broadening with experimental results for the Na/Cu(001) system, showing quantitative agreement within experimental resolution.
New theory of equation of state for surface monolayer
Authors: Rusanov Anatoly I.
Published: May 2004

A novel statistical-thermodynamic approach to deriving an equation of state for a surface monolayer has been elaborated on the basis of excluded area. A master differential equation relating surface (two-dimensional) pressure to excluded area has been derived to generate equations of state for a surface monolayer. The crudest solution (the zero approximation) of the master equation reproduces the known van Laar and Frumkin equations of state. The first approximation yields the two-dimensional van der Waals equation. The second, third, and fourth approximations lead to new and more accurate equations of state. The particular result of the fourth approximation is a precise equation of state for hard disks with deviation not more than 0.46% from data obtained by Monte Carlo and molecular-dynamics simulations within the whole range of surface density. The role of the third dimension for surface equations of state is discussed. An orientation equation of state has been proposed for monolayers containing anisometric particles. It follows from the orientation equation obtained that the orientation effect creates possibility for a two-dimensional phase transition.
Dipole-induced structure in aromatic-terminated self-assembled monolayers—A study by near edge x-ray absorption fine structure spectroscopy
Authors: Luk Yan-Yeung , Abbott Nicholas L. , Crain J. N. , Himpsel F. J.
Published: May 2004

The structure of self-assembled monolayers presenting aromatic rings at a surface is studied by near edge x-ray absorption fine structure spectroscopy (NEXAFS). Fluorine substitution at asymmetric positions in the aromatic rings is used to generate a layer of dipoles at the surface of the monolayer. We find that fluorine substituted aromatic rings are more ordered than unsubstituted aromatic rings by a factor of two based on the polarization dependence of the lowest C 1s to π* transition, which is associated with transitions from phenyl carbons attached to hydrogens. This result is consistent with the influence of dipole–dipole interactions and quadrupolar interactions between the aromatic groups due to the substitution of fluorine atoms. The work also serves to illustrate how subtle variations in the orientation of an end group of a self-assembled monolayer can be determined by using NEXAFS.
Application of the exact exchange potential method for half metallic intermediate band alloy semiconductor
Authors: Fernández J. J. , Tablero C. , Wahnón P.
Published: May 2004

In this paper we present an analysis of the convergence of the band structure properties, particularly the influence on the modification of the bandgap and bandwidth values in half metallic compounds by the use of the exact exchange formalism. This formalism for general solids has been implemented using a localized basis set of numerical functions to represent the exchange density. The implementation has been carried out using a code which uses a linear combination of confined numerical pseudoatomic functions to represent the Kohn–Sham orbitals. The application of this exact exchange scheme to a half-metallic semiconductor compound, in particular to Ga4P3Ti, a promising material in the field of high efficiency solar cells, confirms the existence of the isolated intermediate band in this compound.
The effect of spin–orbit coupling on fast neutral chemical reaction O(3P)+CH3→CH3O
Authors: Yagi Kiyoshi , Takayanagi Toshiyuki , Taketsugu Tetsuya , Hirao Kimihiko
Published: May 2004

The effect of nonadiabatic transitions through the spin–orbit couplings has been investigated on the fast neutral reaction, O(3P)+CH3→CH3O. Adiabatic potential energies and the spin–orbit coupling terms have been evaluated for the four electronic states of CH3O (2E, A22, E4, and A24) that correlate with the O(3P)+CH3 asymptote, as a function of CO distance and OCH angle under the C3v symmetry, by ab initio electronic structure calculations using multireference internally contracted single and double excitation configuration interaction method with the 6-311G(2df,2pd) basis sets. Multistate quantum reactive scattering calculations have been carried out with the use of thus obtained potential energies and spin–orbit coupling matrices, based on the generalized R-matrix propagation method. The calculated thermal rate constants show a slight positive dependence on temperature in a range between 50 and 2000 K, supporting the previous experimental results. It is shown that the spin–orbit coupled excited states give rise to reflections over the centrifugal barrier due to the quantum interference. Classical capture calculations yield larger rate constants due to the neglect of quantum reflections. It is concluded that the effect of nonadiabatic transitions is of minor importance on the overall reactivity in this reaction.
Wavelength dependence of the hyper Rayleigh scattering response from gold nanoparticles
Authors: Russier-Antoine Isabelle , Jonin Christian , Nappa Jérôme , Bénichou Emmanuel , Brevet Pierre-François
Published: May 2004

The wavelength dependence of the quadratic hyperpolarizability of 11 nm diam gold nanoparticles, is reported as measured by hyper Rayleigh scattering. An important photoluminescence background underlying the hyper Rayleigh signal is observed, a contribution attributed to radiative electron–hole recombinations following multiphoton excitation favored by adsorbed organic compound like citrate on the surface of the nanoparticles. The absolute value of the quadratic hyperpolarizability of gold spherical nanoparticles is determined and a strong enhancement is observed for harmonic frequencies in resonance with the dipolar surface plasmon excitation. No contribution of the interband transition is observed. The absolute values reported, βC=5.1×10−26 esu at the second harmonic energy 2.39 eV, have been measured with femtosecond long laser pulse, and are 1 order of magnitude weaker that the one previously reported with nanosecond long pulses. This difference can be related to similar measurements performed on the second order hyperpolarizability of gold nanoparticles and may be attributed to different electronic relaxation regimes. Finally, the spectrum of the quadratic hyperpolarizability is compared to the theoretically expected one.
Broadening and line mixing in the 20 0←01 10, 11 10←00  and 12 20←01 1 Q branches of carbon dioxide: Experimental results and energy-corrected sudden modeling
Authors: Predoi-Cross A. , May A. D. , Vitcu A. , Drummond J. R. , Hartmann J.-M. , Boulet C.
Published: May 2004

Using both a difference frequency spectrometer and a Fourier transform spectrometer, we have measured transitions in the 12 20←01 10 band of carbon dioxide at room temperature and pressures up to 19 atm. The low-pressure spectra were analyzed using a variety of standard spectral profiles, all with an asymmetric component to account for weak line mixing. For this band, we have been able to retrieve experimental line strengths and the broadening and weak mixing parameters. In this paper we also compare the suitability of the energy-corrected sudden model to predict mixing in the two previously measured Q branches 20 00←01 10, the 11 10←00 00, and the present Q branch of pure CO2, all at room temperature.
Relative vibrational overtone intensity of cis–cis and trans–perp peroxynitrous acid
Authors: Matthews Jamie , Sinha Amitabha , Francisco Joseph S.
Published: May 2004

The vibrational overtone spectrum of HOONO is examined in the region of the 2νOH and 3νOH bands using action spectroscopy in conjunction with ab initio intensity calculations. The present measurements indicate that the oscillator strength associated with the higher energy trans–perp conformer of HOONO is stronger relative to the lower energy cis–cis conformer for both these vibrational overtone levels. Ab initio intensity calculations carried out at the QCISD level of theory suggest that this disparity in oscillator strength apparently arises from differences in the second derivative of the transition dipole moment function of the two isomers. The calculations indicate that the oscillator strength for the trans–perp isomer is ∼5.4 times larger than that of the cis–cis isomer for the 2νOH band and ∼2 times larger for 3νOH band. The band positions and intensities predicted by the calculations are used to aid in the assignment of features in the experimental action spectra associated with the OH stretching overtones of HOONO. The observed relative intensities in the experimental action spectra when normalized to the calculated oscillator strengths appears to suggest that the concentration of the higher energy trans–perp isomer is comparable to the concentration of the cis–cis isomer in these room temperature experiments.
Postnucleation droplet growth in supersaturated gas with arbitrary vapor concentration
Authors: Pines V. , Zlatkowski M. , Chait A.
Published: May 2004

This work concerns the reexamination and extension of the current theory of phase transition dynamics for liquid droplets growing on soluble aerosols from a supersaturated gas mixture for the general case of arbitrary value of vapor concentration. We found that the inconsistency in the common treatment of the vapor diffusion, due to an implicit assumption of the constancy of gas density in the vicinity of a droplet by neglecting its dependency on temperature and vapor concentration, leads to the obvious discrepancy in the Maxwell expression for the growth rate regarding droplets of near critical size. Restoring the correct treatment of the vapor diffusion in terms of the mass concentration of water vapor and taking into the consideration variations of gas density in the vicinity of a droplet in compliance with the equation of state of moist air, we have obtained a new expression for the droplet growth rate valid for an arbitrary value of vapor concentration. The limitations imposed by the molecular kinetic fluxes to postnucleation diffusional growth of small droplets with a large Knudsen number are also reevaluated to include previously neglected physical effects. In particular, the essential contribution of the vapor molecular energy flux into the total kinetic molecular heat flux as well as the temperature variations of mean thermal velocities of air and vapor molecules in the vicinity of the droplet interface have been taken into consideration. Surprisingly significant differences have been found in new expressions derived for the droplet growth rate and droplet temperature, even in the limit of small vapor concentration, if comparing with commonly used results. These findings could help with better interpretation of experimental measurements to infer more reliable data for the mass and thermal accommodations coefficients.
A semiclassical generalized quantum master equation for an arbitrary system-bath coupling
Authors: Shi Qiang , Geva Eitan
Published: May 2004

The Nakajima–Zwanzig generalized quantum master equation (GQME) provides a general, and formally exact, prescription for simulating the reduced dynamics of a quantum system coupled to a, possibly anharmonic, quantum bath. In this equation, a memory kernel superoperator accounts for the influence of the bath on the dynamics of the system. In a previous paper [Q. Shi and E. Geva, J. Chem. Phys. 119, 12045 (2003)] we proposed a new approach to calculating the memory kernel, in the case of arbitrary system-bath coupling. Within this approach, the memory kernel is obtained by solving a set of two integral equations, which requires a new type of two-time system-dependent bath correlation functions as input. In the present paper, we consider the application of the linearized semiclassical (LSC) approximation for calculating those correlation functions, and subsequently the memory kernel. The new approach is tested on a benchmark spin-boson model. Application of the LSC approximation for calculating the relatively short-lived memory kernel, followed by a numerically exact solution of the GQME, is found to provide an accurate description of the relaxation dynamics. The success of the proposed LSC–GQME methodology is contrasted with the failure of both the direct application of the LSC approximation and the weak coupling treatment to provide an accurate description of the dynamics, for the same model, except at very short times. The feasibility of the new methodology to anharmonic systems is also demonstrated in the case of a two level system coupled to a chain of Lennard–Jones atoms.
Geminal model chemistry II. Perturbative corrections
Authors: Rassolov Vitaly A. , Xu Feng , Garashchuk Sophya
Published: May 2004

We introduce and investigate a chemical model based on perturbative corrections to the product of singlet-type strongly orthogonal geminals wave function. Two specific points are addressed (i) Overall chemical accuracy of such a model with perturbative corrections at a leading order; (ii) Quality of strong orthogonality approximation of geminals in diverse chemical systems. We use the Epstein–Nesbet form of perturbation theory and show that its known shortcomings disappear when it is used with the reference Hamiltonian based on strongly orthogonal geminals. Application of this model to various chemical systems reveals that strongly orthogonal geminals are well suited for chemical models, with dispersion interactions between the geminals being the dominant effect missing in the reference wave functions.
Spectroscopic properties of novel aromatic metal clusters: NaM4 (M=Al,Ga,In) and their cations and anions
Authors: Zhao Cunyuan , Balasubramanian K.
Published: May 2004

The ground- and several excited states of metal aromatic clusters, namely NaM4 and NaM4± (M=Al,Ga,In) clusters have been investigated by employing complete active-space self-consistent-field followed by multireference singles and doubles configuration interaction computations that included up to 10 million configurations and other methods. The ground states NaM4− of aromatic anions are found to be symmetric C4v (1A1) electronic states with ideal square pyramid geometries. While the ground state of NaIn4 is also predicted to be a symmetric C4v (2A1) square pyramid, the ground state of the NaAl4 cluster is found to have a C2v (2A1) pyramid with a rhombus base, and the ground state of NaGa4 possesses a C2v (2A1) pyramid with a rectangle base. In general, these structures exhibit two competing geometries, viz., an ideal C4v structure and a distorted rhomboidal or rectangular pyramid structure (C2v). All of the ground states of the NaM4+ (M=Al,Ga,In) cations are computed to be C2v (3A2) pyramids with rhombus bases. The equilibrium geometries, vibrational frequencies, dissociation energies, adiabatic ionization potentials, adiabatic electron affinities for the electronic states of NaM4 (M=Al,Ga,In), and their ions are computed and compared with experimental results and other theoretical calculations. On the basis of our computed excited states energy separations, we have tentatively suggested assignments to the observed X and A states in the anion photoelectron spectra of Al4Na− reported by Li et al. [X. Li, A. E. Kuznetov, H. F. Zheng, A. I. Boldyrev, and L. S. Wang, Science 291, 859 (2001)]. The X state can be assigned to a C2v (2A1) rhomboidal pyramid. The A state observed in the anion spectrum is assigned to the first excited state (2B1) of the neutral NaAl4 with the C4v symmetry. The assignments of the excited states are consistent with the experimental excitation energies and the previous Green’s function-based methods for the vertical transition energy separations between the X and A bands.
A systematic ab initio study of the equilibrium geometry and vibrational wave numbers of bismuthine
Authors: Breidung Jürgen , Thiel Walter , Figgen Detlev , Stoll Hermann
Published: May 2004

The equilibrium structure and the harmonic and anharmonic force fields of BiH3 are determined by high-level ab initio calculations using a variety of correlation treatments, basis sets, and pseudopotentials, partly in combination with core polarization potentials. Spin–orbit effects are included by a configuration interaction treatment. This systematic study serves to establish a reliable computational protocol for such calculations and, in particular, to minimize basis set superposition errors through an improved new basis set and/or counterpoise corrections. Using the recommended procedures, the best ab initio results for the equilibrium geometry and the fundamental vibrational wave numbers are in good agreement with the available experimental data, which further supports the recent spectroscopic identification of BiH3. The ground-state total atomization energy of BiH3 is predicted to be 153.1 kcal/mol.
Diffusion quantum Monte Carlo for equilibrium structures and harmonic frequencies of ethane and ozone molecules
Authors: Lu Shih-I
Published: May 2004

Application of the Ornstein–Uhlenbeck diffusion quantum Monte Carlo method in combination with a trial wave function constructed from the floating spherical Gaussian orbitals and spherical Gaussian geminals to studies on the equilibrium structures and harmonic frequencies of ethane and ozone is presented. These Monte Carlo computed results are compared with those of experiments as well as the coupled cluster methods with the correlation consistent basis sets for the two molecules. For ozone, we also compare the Monte Carlo results with the results from multireference calculations.
Size versus volume extensivity of a new class of density matrix functionals
Authors: Cioslowski Jerzy , Pernal Katarzyna
Published: May 2004

Despite being size-extensive, the “second-generation” 1-matrix functionals for the electron–electron repulsion energy Vee yield vanishing correlation energy for the homogeneous electron gas. This failure is directly related to the idempotency condition imposed upon an auxiliary matrix that enters the expression for Vee. In particular, the recently proposed Kollmar–Hess functional is not volume-extensive and thus is incapable of properly describing any delocalized system at its thermodynamic limit.
Atomic dipole moments calculated using analytical molecular second-moment gradients
Authors: Solheim Harald , Ruud Kenneth , Åstrand Per-Olof
Published: May 2004

We have implemented analytical second-moment gradients for Hartree–Fock and multiconfigurational self-consistent-field wave functions. The code is used to calculate atomic dipole moments based on the generalized atomic polar tensor (GAPT) formalism [Phys. Rev. Lett. 62, 1469 (1989)], and the proposal of Dinur and Hagler (DH) for the calculation of atomic multipoles [J. Chem. Phys. 91, 2949 (1989)]. Both approaches display smooth basis-set convergence toward a well-defined basis-set limit and give reasonable electron correlation effects on the calculated atomic properties. However, the atomic charges and atomic dipole moments obtained from the GAPT partitioning scheme are unable to provide even qualitatively meaningful molecular quadrupole moments for some molecules, and thus the atomic multipole moments calculated in this scheme cannot be considered well suited for analyzing the electron density in molecules and for calculating intermolecular interaction energies. In contrast, the DH approach gives atomic charges and dipole moments that by definition exactly reproduce the molecular quadrupole moments. The approach of DH is, however, restricted to planar molecules and thus suffers from not being applicable to molecules of arbitrary shape. Both the GAPT and DH approaches give rather poor results for octupole and hexadecapole moments, indicating that at least atomic quadrupole moments are required for an accurate representation of the molecular charge distribution in terms of atomic electric moments.
Geometry and electronic structure of Vn(Bz)m complexes
Authors: Kandalam Anil K. , Rao B. K. , Jena P. , Pandey Ravindra
Published: May 2004

First-principles calculations based on the generalized gradient approximation to the density functional theory are performed to explore the global geometries, ground-state spin multiplicities, relative stabilities, and energetics of neutral and anionic Vn(Bz)m (n=1–3, m=1–4, with n<m) complexes. The calculated results show that the Vn(benzene)m complexes clearly prefer sandwich structures to rice-ball structures. The ground-state spin multiplicities of the Vn(benzene)n+1 complexes increased linearly with the size of the system (i.e., n). In the anionic complexes, the V(benzene)2 complex is found to be unstable against the autodetachment of the extra electron. The energy difference between adiabatic and vertical electron affinities is found to be very less, indicating negligible ionization-induced structural changes in the ground-state geometries of Vn(benzene)n+1 complexes.
Optical properties of passivated silicon nanoclusters: The role of synthesis
Authors: Draeger Erik W. , Grossman Jeffrey C. , Williamson Andrew J. , Galli Giulia
Published: May 2004

The effect of preparation conditions on the structural and optical properties of silicon nanoparticles is investigated. Nanoscale reconstructions, unique to curved nanosurfaces, are presented for silicon nanocrystals and shown to have lower energy and larger optical gaps than bulk-derived structures. We find that high-temperature synthesis processes can produce metastable noncrystalline nanostructures with different core structures than bulk-derived crystalline clusters. The type of core structure that forms from a given synthesis process may depend on the passivation mechanism and time scale. The effect of oxygen on the optical of different types of silicon structures is calculated. In contrast to the behavior of bulklike nanostructures, for noncrystalline and reconstructed crystalline structures surface oxygen atoms do not decrease the gap. In some cases, the presence of oxygen atoms at the nanocluster surface can significantly increase the optical absorption gap, due to decreased angular distortion of the silicon bonds. The relationship between strain and the optical gap in silicon nanoclusters is discussed.
Coarse-grained nonequilibrium approach to the molecular modeling of permeation through microporous membranes
Authors: Tunca Canan , Ford David M.
Published: May 2004

We present a modeling technique that combines a statistical-mechanical coarse-graining scheme with a nonequilibrium molecular simulation algorithm to provide an efficient simulation of steady-state permeation across a microporous material. The coarse-graining scheme is based on the mapping of an atomistic model to a lattice using multidimensional free-energy and transition-state calculations. The nonequilibrium simulation algorithm is a stochastic, lattice version of the recently developed atomistic dual-control-volume grand canonical molecular dynamics. We demonstrate the approach on a model of methane permeating through a bulk portion of siliceous zeolite ZK4 at 300 K under imposed fugacity differences. We predict the coarse-grained (cage-level) density profiles and observe the development of nonlinearities as the magnitude of the fugacity difference is increased. From the net flux of methane we also predict a mean permeability coefficient under the various conditions. The simulation results are obtained over time scales on the order of microseconds and length scales on the order of dozens of nanometers.
Trends in the band structures of the group-I and -II oxides
Authors: Mikajlo Elisabeth A. , Dorsett Helen E. , Ford Michael J.
Published: May 2004

Measured and calculated band structures for the six lightest group-I and -II oxides are reported. Band structures have been measured using electron momentum spectroscopy, a technique that maps the ground-state occupied orbitals resolved both in energy and momentum. Measurements are compared with first-principles calculations carried out within the linear combination of atomic orbitals approximation using both Hartree–Fock (HF) and density functional (DFT) methods. Three DFT functionals are used representative of the local density approximation, the generalized gradient approximation, and a hybrid method incorporating exact exchange. The calculated O 2p bandwidths and O 2p–2s band gaps generally scale linearly with the inverse of the oxygen–oxygen separation squared, but consistently show an anomaly at Li2O. These trends, including the anomaly, are also observed in the experimental data. HF calculations consistently overestimate the oxygen 2p–2s band gap by almost a factor of two. Measured band gaps lie within the range of the three DFT functionals employed, with evidence that the description of exchange becomes more important as the cation size increases. Both HF and DFT calculations overestimate the oxygen valence bandwidths, with DFT giving more accurate predictions. Both observed and calculated bandwidths converge as the cation size increases, indicating that exchange-correlation effects become less important as the metallic ion becomes larger.
Mass-analyzed threshold ionization spectroscopy of p-methylphenol and p-ethylphenol cations and the alkyl substitution effect
Authors: Lin Jung Lee , Li Changyong , Tzeng Wen Bih
Published: May 2004

The mass-analyzed threshold ionization (MATI) spectra of p-methylphenol and p-ethylphenol have been recorded by ionizing via various vibronic levels. The adiabatic ionization energies (IEs) of p-methylphenol and p-ethylphenol are determined to be 65918±5 and 65628±5 cm−1, which are less than that of phenol by 2707 and 2997 cm−1, respectively. This redshift indicates that the interaction between the alkyl group and the ring of alkylphenols in the cationic D0 state is greater than that in the neutral S0 state. Moreover, a longer alkyl group gives rise to a greater redshift in the IE. Analysis of the MATI spectra shows that most of the active modes are related to the in-plane ring vibrations of these two cations. However, the length of the alkyl group has an insignificant effect on the frequency of the observed ring vibrations. No band with frequency less than 350 cm−1 is observed for the p-methylphenol cation. In contrast, many low-frequency bands resulting from the characteristic motions (e.g., the C–C2H5 torsion and C–C2H5 and C–OH bending vibrations) appear in the MATI spectra of p-ethylphenol. The present results show that the ethyl group enhances the substituent-sensitive and many large-amplitude vibrations of the cation.
Computer simulation study of the closure relations in hard sphere fluids
Authors: Fantoni R. , Pastore G.
Published: May 2004

We study, using Monte Carlo simulations, the cavity and the bridge functions of various hard sphere fluids: one component system, equimolar additive, and nonadditive binary mixtures. In particular, we numerically check the assumption of local dependency of the bridge functions from the indirect correlation functions, on which most of the existing integral equation theories hinge. We find that this condition can be violated either in the region around the first and second neighbors shell, or inside the hard core, for the systems here considered. The violations manifest themselves clearly in the so-called Duh–Haymet plots of the bridge functions versus the indirect correlation functions and become amplified as the coupling of the system increases.
Nematic ordering in dilute solutions of rodlike polyelectrolytes
Authors: Potemkin Igor I. , Khokhlov Alexei R.
Published: May 2004

Quantitative theory of orientational behavior of rodlike polyelectrolytes in dilute solution is developed. We find that in salt-free solutions many-body Coulomb interactions between macro- and counterions favor nematic ordering. It is shown that the orientationally isotropic phase of the solution becomes unstable toward nematic ordering at polymer concentration smaller than the overlap concentration. Our predictions are consistent with experimental observations for synthetic polyelectrolytes poly(p-phenylene)sulfonates in aqueous solutions.
Density functional theory of fluids in the isothermal-isobaric ensemble
Authors: Gonżález A. , White J. A. , Román F. L. , Velasco S.
Published: May 2004

We present a density functional theory for inhomogeneous fluids at constant external pressure. The theory is formulated for a volume-dependent density, n(r,V), defined as the conjugate variable of a generalized external potential, ν(r,V), that conveys the information on the pressure. An exact expression for the isothermal-isobaric free-energy density functional is obtained in terms of the corresponding canonical ensemble functional. As an application we consider a hard-sphere system in a spherical pore with fluctuating radius. In general we obtain very good agreement with simulation. However, in some situations a peak develops in the center of the cavity and the agreement between theory and simulation becomes worse. This happens for systems where the number of particles is close to the magic numbers N=13, 55, and 147.
Spin–orbit coupling in O2(v)+O2 collisions: A new energy transfer mechanism
Authors: Dayou Fabrice , Campos-Martı́nez José , Hernández Marta I. , Hernández-Lamoneda Ramón
Published: May 2004

A reduced dimensionality model is used to study the relaxation of highly vibrationally excited O2(X 3Σg−,v⩾20) in collisions with O2(X 3Σg−,v=0). Spin–orbit coupled potential energy surfaces are employed to incorporate the vibrational-to-electronic energy transfer mechanism involving the O2(a 1Δg) and O2(b 1Σg+) excited states. The transition probabilities obtained show a sharp increase for v⩾26 providing the first direct evidence of the important role played by the electronic energy transfer processes in the depletion of O2(X 3Σg−,v⩾26).
Involvement of Per–Arnt–Sim (PAS) kinase in the stimulation of preproinsulin and pancreatic duodenum homeobox 1 gene expression by glucose
Authors: da Silva Xavier Gabriela , Rutter Jared , Rutter Guy A.
Published: May 2004

Per–Arnt–Sim (PAS) domain-containing kinases are common in prokaryotes, but a mammalian counterpart has only recently been described. Although the PAS domain of the mammalian PAS kinase (PASK) is closely related to the bacterial oxygen sensor
Fix
L, it is unclear whether PASK activity is changed in mammalian cells in response to nutrients and might therefore contribute to signal transduction by these or other stimuli. Here, we show that elevated glucose concentrations rapidly increase PASK activity in pancreatic islet β cells, an event followed by the accumulation of both PASK mRNA and protein. Demonstrating a physiological role for PASK activation, comicroinjection into clonal β cells of cDNA encoding wild-type PASK, or PASK protein itself, mimics the induction of preproinsulin promoter activity by high glucose concentrations. Conversely, anti-PASK antibodies block promoter activation by the sugar, and the silencing of PASK expression by RNA interference suppresses the up-regulation by glucose of preproinsulin and pancreatic duodenum homeobox 1 gene expression, without affecting glucose-induced changes in the levels of mRNAs encoding glucokinase or uncoupling protein 2. We conclude that PASK is an important metabolic sensor in nutrient-sensitive mammalian cells and plays an unexpected role in the regulation of key genes involved in maintaining the differentiated phenotype of pancreatic β cells.
The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1
Authors: Xie Kefang , Sowden Mark P. , Dance Geoffrey S. C. , Torelli Andrew T. , Smith Harold C. , Wedekind Joseph E.
Published: May 2004

Activation-induced deaminase (AID) uses base deamination for class-switch recombination and somatic hypermutation and is related to the mammalian RNA-editing enzyme apolipoprotein B editing catalytic subunit 1 (APOBEC-1). CDD1 is a yeast ortholog of APOBEC-1 that exhibits cytidine deaminase and RNA-editing activity. Here, we present the crystal structure of CDD1 at 2.0-Å resolution and its use in comparative modeling of APOBEC-1 and AID. The models explain dimerization and the need for trans-acting loops that contribute to active site formation. Substrate selectivity appears to be regulated by a central active site “flap” whose size and flexibility accommodate large substrates in contrast to deaminases of pyrimidine metabolism that bind only small nucleosides or free bases. Most importantly, the results suggested both AID and APOBEC-1 are equally likely to bind single-stranded DNA or RNA, which has implications for the identification of natural AID targets.
Functional photoreceptor loss revealed with adaptive optics: An alternate cause of color blindness
Authors: Carroll Joseph , Neitz Maureen , Hofer Heidi , Neitz Jay , Williams David R.
Published: May 2004

There is enormous variation in the X-linked L/M (long/middle wavelength sensitive) gene array underlying “normal” color vision in humans. This variability has been shown to underlie individual variation in color matching behavior. Recently, red–green color blindness has also been shown to be associated with distinctly different genotypes. This has opened the possibility that there may be important phenotypic differences within classically defined groups of color blind individuals. Here, adaptive optics retinal imaging has revealed a mechanism for producing dichromatic color vision in which the expression of a mutant cone photopigment gene leads to the loss of the entire corresponding class of cone photoreceptor cells. Previously, the theory that common forms of inherited color blindness could be caused by the loss of photoreceptor cells had been discounted. We confirm that remarkably, this loss of one-third of the cones does not impair any aspect of vision other than color.
Inhibition of acute graft-versus-host disease with retention of graft-versus-tumor effects by the proteasome inhibitor bortezomib
Authors: Sun Kai , Welniak Lisbeth A. , Panoskaltsis-Mortari Angela , O'Shaughnessy Matthew J. , Liu Haiyan , Barao Isabel , Riordan William , Sitcheran Raquel , Wysocki Christian , Serody Jonathan S. , Blazar Bruce R. , Sayers Thomas J. , Murphy William J.
Published: May 2004

Graft-versus-host disease (GVHD) represents a major hurdle impeding the efficacy of allogeneic bone marrow transplantation (BMT). Bortezomib is a proteasome inhibitor that was recently approved for treatment of myeloma. We found that bortezomib potently inhibitedin vitromixed lymphocyte responses and promoted the apoptosis of alloreactive T cells. Bortezomib given at the time of allogeneic BMT in mice resulted in significant protection from acute GVHD. Reductions in GVHD-associated parameters and biological evidence of proteasome inhibition were observed with this regimen but with no adverse effects on long-term donor reconstitution. Assessment of graft-versus-tumor responses in advanced leukemia-bearing mice demonstrated that only the combination of allogeneic BMT and T cells with bortezomib promoted significant increases in survival. Increased cytotoxic T cell killing of the tumor was also observed. Thus, the combination of proteasome inhibition with selective immune attack can markedly increase the efficacy of BMT in cancer.
Scanning electrochemical microscopy of menadione-glutathione conjugate export from yeast cells
Authors: Mauzeroll Janine , Bard Allen J.
Published: May 2004

The uptake of menadione (2-methyl-1,4-naphthoquinone), which is toxic to yeast cells, and its expulsion as a glutathione complex were studied by scanning electrochemical microscopy. The progression of the
in vitro
reaction between menadione and glutathione was monitored electrochemically by cyclic voltammetry and correlated with the spectroscopic (UV–visible) behavior. By observing the scanning electrochemical microscope tip current of yeast cells suspended in a menadione-containing solution, the export of the conjugate from the cells with time could be measured. Similar experiments were performed on immobilized yeast cell aggregates stressed by a menadione solution. From the export of the menadione-glutathione conjugate detected at a 1-μm-diameter electrode situated 10 μm from the cells, a flux of about 30,000 thiodione molecules per second per cell was extracted. Numerical simulations based on an explicit finite difference method further revealed that the observation of a constant efflux of thiodione from the cells suggested the rate was limited by the uptake of menadione and that the efflux through the glutathione-conjugate pump was at least an order of magnitude faster.
Dynamic mapping of human cortical development during childhood through early adulthood
Authors: Gogtay Nitin , Giedd Jay N. , Lusk Leslie , Hayashi Kiralee M. , Greenstein Deanna , Vaituzis A. Catherine , Nugent Tom F. , Herman David H. , Clasen Liv S. , Toga Arthur W. , Rapoport Judith L. , Thompson Paul M.
Published: May 2004

We report the dynamic anatomical sequence of human cortical gray matter development between the age of 4–21 years using quantitative four-dimensional maps and time-lapse sequences. Thirteen healthy children for whom anatomic brain MRI scans were obtained every 2 years, for 8–10 years, were studied. By using models of the cortical surface and sulcal landmarks and a statistical model for gray matter density, human cortical development could be visualized across the age range in a spatiotemporally detailed time-lapse sequence. The resulting time-lapse “movies” reveal that (i) higher-order association cortices mature only after lower-order somatosensory and visual cortices, the functions of which they integrate, are developed, and (ii) phylogenetically older brain areas mature earlier than newer ones. Direct comparison with normal cortical development may help understanding of some neurodevelopmental disorders such as childhood-onset schizophrenia or autism.
Genetic deletion of ghrelin does not decrease food intake but influences metabolic fuel preference
Authors: Wortley Katherine E. , Anderson Keith D. , Garcia Karen , Murray Jane D. , Malinova Lubomira , Liu Rong , Moncrieffe Marshena , Thabet Karen , Cox Hilary J. , Yancopoulos George D. , Wiegand Stanley J. , Sleeman Mark W.
Published: May 2004

Ghrelin is a recently identified growth hormone (GH) secretogogue whose administration not only induces GH release but also stimulates food intake, increases adiposity, and reduces fat utilization in mice. The effect on food intake appears to be independent of GH release and instead due to direct activation of orexigenic neurons in the arcuate nucleus of the hypothalamus. The effects of ghrelin administration on food intake have led to the suggestion that inhibitors of endogenous ghrelin could be useful in curbing appetite and combating obesity. To further study the role of endogenous ghrelin in appetite and body weight regulation, we generated ghrelin-deficient (
ghrl
–/–
) mice, in which the ghrelin gene was precisely replaced with a
lacZ
reporter gene.
ghrl
–/–
mice were viable and exhibited normal growth rates as well as normal spontaneous food intake patterns, normal basal levels of hypothalamic orexigenic and anorexigenic neuropeptides, and no impairment of reflexive hyperphagia after fasting. These results indicate that endogenous ghrelin is not an essential regulator of food intake and has, at most, a redundant role in the regulation of appetite. However, analyses of
ghrl
–/–
mice demonstrate that endogenous ghrelin plays a prominent role in determining the type of metabolic substrate (i.e., fat vs. carbohydrate) that is used for maintenance of energy balance, particularly under conditions of high fat intake.
Molecular changes in neurons in multiple sclerosis: Altered axonal expression of Na
v
1.2 and Na
v
1.6 sodium channels and Na
+
/Ca
2
+ exchanger
Authors: Craner Matthew J. , Newcombe Jia , Black Joel A. , Hartle Caroline , Cuzner M. Louise , Waxman Stephen G.
Published: May 2004

Although voltage-gated sodium channels are known to be deployed along experimentally demyelinated axons, the molecular identities of the sodium channels expressed along axons in human demyelinating diseases such as multiple sclerosis (MS) have not been determined. Here we demonstrate changes in the expression of sodium channels in demyelinated axons in MS, with Na
v
1.6 confined to nodes of Ranvier in controls but with diffuse distribution of Na
v
1.2 and Na
v
1.6 along extensive regions of demyelinated axons within acute MS plaques. Using triple-labeled fluorescent immunocytochemistry, we also show that Na
v
1.6, which is known to produce a persistent sodium current, and the Na
+
/Ca
2+
exchanger, which can be driven by persistent sodium current to import damaging levels of calcium into axons, are colocalized with β-amyloid precursor protein, a marker of axonal injury, in acute MS lesions. Our results demonstrate the molecular identities of the sodium channels expressed along demyelinated and degenerating axons in MS and suggest that coexpression of Na
v
1.6 and Na
+
/Ca
2+
exchanger is associated with axonal degeneration in MS.
How well do Australian women comply with dietary guidelines?
Authors: Ball Kylie , Mishra Gita D , Thane Christopher W , Hodge Allison
Published: May 2004

Objective:

To investigate the proportion of middle-aged Australian women meeting national dietary recommendations and its variation according to selected sociodemographic and behavioural characteristics.

Design:

This cross-sectional population-based study used a food-frequency questionnaire to investigate dietary patterns and compliance with 13 commonly promoted dietary guidelines among a cohort of middle-aged women participating in the Australian Longitudinal Study on Women's Health.

Setting:

Nation-wide community-based survey.

Subjects:

A total of 10 561 women aged 50–55 years at the time of the survey in 2001.

Results:

Only about one-third of women complied with more than half of the guidelines, and only two women in the entire sample met all 13 guidelines examined. While guidelines for meat/fish/poultry/eggs/nuts/legumes and ‘extra’ foods (e.g. ice cream, chocolate, cakes, potatoes, pizza, hamburgers and wine) were met well, large percentages of women (68–88%) did not meet guidelines relating to the consumption of breads, cereal-based foods and dairy products, and intakes of total and saturated fat and iron. Women working in lower socio-economic status occupations, and women living alone or with people other than a partner and/or children, were at significantly increased risk of not meeting guidelines.

Conclusions:

The present results indicate that a large proportion of middle-aged Australian women are not meeting dietary guidelines. Without substantial changes in their diets, and help in making these changes, current national guidelines appear unachievable for many women.
Homocysteine and cobalamin status in German vegans
Authors: Waldmann Annika , Koschizke Jochen W , Leitzmann Claus , Hahn Andreas
Published: May 2004

Objective:

The study aimed to evaluate the homocysteine and cobalamin status of German vegans and determine whether the intake of very small amounts of foods of animal origin can improve this status.

Design and setting:

Cross-sectional study, Germany.

Subjects:

The dietary and nutritional intakes of 131 vegans (73 women, 58 men; a range: 20.2–82.1 years) were evaluated using a general questionnaire and two food–frequency questionnaires.

Results:

The prevalence of inadequate cobalamin status in volunteers of the German Vegan Study was 28.2%, and that of hyperhomocysteinaemia, 38.1%. Moderate vegans were affected to a lesser extent than were strict vegans. Duration of veganism and cobalamin concentration were inversely correlated (Spearman'sr= -0.175,P= 0.047). Folate concentration and erythrocyte aspartic acid aminotransferase activity were not correlated with plasma homocysteine concentration, but duration of veganism correlated positively with homocysteine concentration (Spearman'sr= 0.319,P< 0.001). Cobalamin and homocysteine concentrations were inversely correlated (when controlling for duration of veganism;r= -0.602,P< 0.001).

Conclusion:

Cobalamin status needs to be improved in order to minimise the risk of hyperhomocysteinaemia.