bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolving water management institutions in Mexico
Authors: Hearne Robert R.
Published: November 2004

Mexico's water management institutions are undergoing a gradual but dramatic change that corresponds to other changes in Mexican society. Implementing these changes has led to the creation of new institutions, including river basin councils, state water commissions, aquifer management committees, and water user associations. Established institutions such as the National Water Commission have accepted new roles. Some of these changes can be considered to be superficial, but this institutional change is impressive. Successful practices can be identified. These include the transfer of the management of large irrigation districts to the users, the periodic practice of establishing a national water plan, the cautious approach to private sector participation in water supply and sanitation, and the national registry of water use. Remaining challenges include weak river basin and aquifer management organizations, overexploitation of key aquifers, polluted surface water, and the inability of water markets to facilitate intersectoral water transfers.
Temporal variability of Δ14C, δ13C, and C/N in sinking particulate organic matter at a deep time series station in the northeast Pacific Ocean
Authors: Hwang Jeomshik , Druffel Ellen R. M. , Griffin Sheila , Smith Kenneth L. , Baldwin Roberta J. , Bauer James E.
Published: November 2004

A 6‐year time series of Δ14C, δ13C, and C/N measurements in deep sinking particulate organic matter (POM) is presented for an abyssal site, Station M in the northeast Pacific Ocean. The Δ14C values revealed that sinking POM at 3450 m depth (650 m above bottom) contained old carbon despite its presumed short transit time in the water column. The isotopic and chemical properties of the sinking POM varied with time and appear to be controlled by more than one major process. In 1993, 1994, and late 1996, isotopic signatures and C/N molar ratios indicate negligible or vertically homogeneous influence of resuspended particles from the bottom or particles laterally transported from the margin to the study site. However, during early 1995 and 1998, Δ14C values were lower than those during other periods and C/N values at three deep depths were not equal, indicating that the study site was influenced by resuspended sediments more severely than during other periods. During mid‐1995 to mid‐1996, δ13C values decreased abruptly while Δ14C values increased slightly, and C/N values were extremely high (up to ∼80) at 50 and 600 m above bottom; these results suggest input of degraded, modern, terrestrial organic matter. The periods of anomalous isotopic signatures, as well as vertically heterogeneous C/N values [Smith et al., 2001], were correlated with high discharge periods of California rivers with a time lag of 2 to 4 months. The correlation suggests that regional meteorological events are important in controlling the biogeochemical properties of particles at Station M by varying the intensity of resuspension and transport of organic matter from the continental margin.
Disturbance and net ecosystem production across three climatically distinct forest landscapes
Authors: Campbell John L. , Sun O. J. , Law B. E.
Published: November 2004

Biometric techniques were used to measure net ecosystem production (NEP) across three climatically distinct forest chronosequences in Oregon. NEP was highly negative immediately following stand‐replacing disturbance in all forests and recovered to positive values by 10, 20, and 30 years of age for the mild and mesic Coast Range, mesic West Cascades, and semi‐arid East Cascades, respectively. The response of stand‐level NEP to individual disturbance events is greater than that attributable to edaphoclimatic differences between forest type. However, regional age class distributions are such that the variability in landscape‐level NEP attributable to disturbance regimes is equivalent to that attributable to regional edaphoclimatic differences between forest types. Simulations of age class distribution under varying disturbance frequencies suggest that the sensitivity of landscape‐level NEP to changes in disturbance regime varies among forest types and is linked to both remnant detritus and photosynthetic recovery rate that are partly a function of edaphoclimatic differences.
Dynamics of carbon sequestration in a coastal wetland using radiocarbon measurements
Authors: Choi Yonghoon , Wang Yang
Published: November 2004

Coastal wetlands are sensitive to global climate change and may play an important role in the global carbon cycle. However, the dynamics of carbon (C) cycling in coastal wetlands and its response to sea level change associated with global warming is still poorly understood. In this study, we estimated the long‐term and short‐term rates of C accumulation, using C and C isotopic measurements of peat cores collected along a soil chronosequence, in a coastal wetland in north Florida. The long‐term C accumulation rates determined by examining the C inventory and the radioactive decay of radiocarbon as a function of depth in the peat cores decrease with time from ∼130 ± 9 g C/m2/yr over the last century to ∼13 ± 2 g C/m2/yr over the millennium timescale. The short‐term C accumulation rates estimated by examining the differences in the radiocarbon and C contents of the surfacial peat between archived (1985, 1988) and present (1996 and 1997) samples range from 42 to 193 g C/m2/yr in low marsh, from 18 to 184 g C/m2/yr in middle marsh, and from −50 to 181 g C/m2/yr in high marsh. The high end‐values of our estimated short‐term C accumulation rates are comparable to the estimated rates of C sequestration in coastal wetlands reported by Chmura et al. [2003], but are significantly higher than our estimated long‐term rates in the marshes and are also much higher than the published rates of C sequestration in northern peatlands. The higher recent rates of C accumulation in coastal marshes, in comparison with the longer‐term rates, are due to slow but continuous decomposition of organic matter in the peat over time. However, other factors such as increased primary production in the coastal wetland over the last decades or century, due to a rise in mean sea level and/or CO2 and nitrogen fertilization effect, could also have contributed to the large difference between the recent and longer‐term rates. Our data indicate that salt marshes in this area have been and continue to be a sink for atmospheric carbon dioxide. Because of higher rates of C sequestration and lower CH4 emissions, coastal wetlands could be more valuable C sinks per unit area than other ecosystems in a warmer world.
Frictional melting can terminate seismic slips: Experimental results of stick‐slips
Authors: Koizumi Yosuke , Otsuki Kenshiro , Takeuchi Akihiro , Nagahama Hiroyuki
Published: November 2004

The appropriate setting of sensors and the use of a high speed data acquisition system enabled us to detect the exact time of melting of the slip surfaces during a stick‐slip event (fault displacement of 0.32 mm, stress drop of 230 MPa, rise time of 23 μs and maximum slip velocity of 40 m/s) in triaxial apparatus at 150 MPa confining pressure. Once slip started, the friction coefficient decreased continuously from 0.55 to 0.3, after which the frictional resistance recovered promptly and remarkably. This strengthening can be attributed to the highly resistive initial melt, a potential mechanism for arresting seismic slips.
Ebullition of methane‐containing gas bubbles from near‐surface Sphagnum peat
Authors: Baird Andrew J. , Beckwith Clive W. , Waldron Susan , Waddington J. M.
Published: November 2004

To date, very little information has been available on the build‐up and release of biogenic gas bubbles in poorly‐decomposed bog peats near the peatland surface (upper 1 m). We investigated the importance of ebullition of biogenic gas bubbles as a mechanism for the transport of CH4 to the atmosphere in eight cores (24 cm diameter, 22 cm depth) of poorly‐decomposed, near‐surface bog peat. Ebullition was recorded in all but one sample but varied greatly between samples. Maximum rates of CH4 efflux via ebullition were also highly variable, ranging from 2.2 to 83.0 mg CH4 m−2 day−1. These rates are similar to rates of diffusive CH4 efflux. Our results also show that wetland methane models are likely to need revision because they assume that unrealistically high CH4 pore‐water concentrations are required before bubbles can be produced and because, in part, they do not account for gas bubble build‐up prior to ebullition.
Protonation study of peroxynitric acid and peroxynitrous acid
Authors: Santiano Randy L. , Francisco Joseph S.
Published: November 2004

The equilibrium structures and harmonic vibrational frequencies of peroxynitric acid (HOONO2) and seven structures of protonated peroxynitric acid, along with peroxynitrous acid (HOONO) and its 12 protonated peroxynitrous acid structures, have been investigated using several ab initio and density functional methods. The ab initio methods include second-order Møller-Plesset perturbation theory, quadratic configuration interaction, including single and double excitations theory (QCISD), and the QCISD(T) methods, which incorporate a perturbational estimate of the effects of connected triple excitation. The Becke three-parameter hybrid functional combined with Lee, Yang, and Parr correlation function is the density functional method used. The lowest energy form of protonated peroxynitric acid is a complex between H2O2 and NO+ rather than between H2O and NO2+. For peroxynitrous acid, a complex between H2O2 and NO2+ is found to be the lowest energy structure. The ab initio proton affinity (PA) of HOONO and HOONO2 is predicted to be 182.1 and 175.1 kcal mol−1, respectively, at the QCISD(T)/6-311++G(3df,3pd) level of theory. The results are contrasted with an earlier study on nitrous acid, and is shown that peroxynitric acid and peroxynitrous acid have a smaller PA than nitrous acid.
Application of direct potential fitting to line position data for the X 1Σ+ and A 1Σ+ states of LiH
Authors: Coxon John A. , Dickinson Cameron S.
Published: November 2004

A collection of 9089 spectroscopic LiH line positions, of widely varying precision, which sample 84.9% and 98.6% of the A and X state well depths, respectively, have been employed in a direct least-squares fit of the effective potential energy and Born-Oppenheimer breakdown functions for the two states. For the four isotopomers LiH6, LiH7, LiD6, and LiD7, the data comprise both pure rotational and vibration-rotational transitions within the ground state, as well as rotationally resolved transitions in the A-X system. Despite the unusual shape and associated anomalous properties of the A state potential, no special features or considerations were required in the direct potential fitting approach. The reduced standard deviation of the fit was close to unity, indicating that the quantum mechanical eigenvalues calculated from the fully analytical functions of the Hamiltonians of the two states, which are characterized by a total of only 53 fitted parameters, represent the line positions, on average, to within the estimated uncertainties. A quantum mechanical calculation of the molecular constants Gν, Bν, Dν, Hν, Lν, Mν, Nν, and Oν from the fitted potential for the A state of LiH7 confirms that the usual polynomial expansion in J(J+1) is an unsatisfactory representation for the rotational terms of the lowest vibrational levels.
Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes
Authors: Wan Shunzhou , Stote Roland H. , Karplus Martin
Published: November 2004

With the advent of more powerful computers, the question of calculating thermodynamic quantities, such as the energy and the entropy, in solute-solvent systems is revisited. The calculation of these thermodynamic quantitites was limited in the past by their slow convergence relative to the free energy. Using molecular dynamics simulations, the energy, entropy, and free energy of solvation of NMA and CH3NH2, as well as their relative values, have been determined. Three different methods (the thermodynamic perturbation method, the thermodynamic integration method, and a finite-difference method) are compared. The finite difference method gives the best results and accurate values for the entropy and energy were obtained using a reasonable amount to computer time. The results suggest that a meaningful thermodynamic description of biomolecular processes can be realized with present methods and the available computer time.
An efficient method for calculating maxima of homogeneous functions of orthogonal matrices: Applications to localized occupied orbitals
Authors: Subotnik Joseph E. , Shao Yihan , Liang WanZhen , Head-Gordon Martin
Published: November 2004

We present here three new algorithms (one purely iterative and two DIIS-like [Direct Inversion in the Iteractive Subspace]) to compute maxima of homogeneous functions of orthogonal matrices. These algorithms revolve around the mathematical lemma that, given an invertible matrix A, the function f(U)=Tr(AU) has exactly one local (and global) maximum for U special orthogonal [i.e., UUT=1 and det(U)=1]. This is proved in the Appendix. One application of these algorithms is the computation of localized orbitals, including, for example, Boys and Edmiston-Ruedenberg (ER) orbitals. The Boys orbitals are defined as the set of orthonormal orbitals which, for a given vector space of orbitals, maximize the sum of the distances between orbital centers. The ER orbitals maximize total self-interaction energy. The algorithm presented here computes Boys orbitals roughly as fast as the traditional method (Jacobi sweeps), while, for large systems, it finds ER orbitals potentially much more quickly than traditional Jacobi sweeps. In fact, the required time for convergence of our algorithm scales quadratically in the region of a few hundred basis functions (though cubicly asymptotically), while Jacobi sweeps for the ER orbitals traditionally scale as the number of occupied orbitals to the fifth power. As an example of the utility of the method, we provide below the ER orbitals of nitrated and nitrosated benzene, and we discuss the chemical implications.
Ordered microstructures by assembly of ABC 3-miktoarm star terpolymers and linear homopolymers
Authors: Lu Teng , He Xuehao , Liang Haojun
Published: November 2004

Ordered microstructures assembled from the mixture of the ABC 3-miktoarm star terpolymers and the linear homopolymers have been investigated by using dynamic density functional theory. The simulations reveal that completely different ordered microphase pattern is found with addition of a few percent homopolymers that is identical in component to one of the arms on the ABC 3-miktoarm star terpolymer. For example, the original density pattern of ABC 3-miktoarm star terpolymers with parameters of NA=NB=NC=10 and χAB=0.90, χBC=χCA=0.45 is in a perfectly ordered knitting feature. However, with gradual addition of the linear polymer same as block C on ABC 3-miktoarm star terpolymer into the system, the density patterns evolve with the volume fraction of the linear polymer from the ordered knitting patterns into the hexagonal patterns. Furthermore, with addition of linear polymers same as block A, lamellar microstructure has finally resulted. The simulation points out a way for designing and manufacturing nanomaterials with totally different microstructures.
On the ultraviolet photodissociation of H2Te
Authors: Alekseyev Aleksey B. , Liebermann Heinz-Peter , Wittig Curt
Published: November 2004

The photodissociation of H2Te through excitation in the first absorption band is investigated by means of multireference spin-orbit configuration interaction (CI) calculations. Bending potentials for low-lying electronic states of H2Te are obtained in C2v symmetry for Te-H distances fixed at the ground state equilibrium value of 3.14a0, as well as for the minimum energy path constrained to R1=R2. Asymmetric cuts of potential energy surfaces for excited states (at R1=3.14a0 and θ=90.3°) are obtained for the first time. It is shown that vibrational structure in the 380–400 nm region of the long wavelength absorption tail is due to transitions to 3A′, which has a shallow minimum at large HTe-H separations. Transitions to this state are polarized in the molecular plane, and this state converges to the excited TeH(2Π1/2)+H(2S) limit. These theoretical data are in accord with the selectivity toward TeH(2Π1/2) relative to TeH(2Π3/2) that has been found experimentally for 355 nm H2Te photodissociation. The calculated 3A′←X̃A′ transition dipole moment increases rapidly with HTe-H distance; this explains the observation of 3A′ vibrational structure for low vibrational levels, despite unfavorable Franck–Condon factors. According to the calculated vertical energies and transition moment data, the maximum in the first absorption band at ≈245 nm is caused by excitation to 4A″, which has predominantly 21A″ (1B1 in C2v symmetry) character.
Coping with the node problem in quantum hydrodynamics: The covering function method
Authors: Babyuk Dmytro , Wyatt Robert E.
Published: November 2004

A conceptually simple approach, the covering function method (CFM), is developed to cope with the node problem in the hydrodynamic formulation of quantum mechanics. As nodes begin to form in a scattering wave packet (detected by a monitor function), a nodeless covering wave function is added to it yielding a total function that is also nodeless. Both local and global choices for the covering function are described. The total and covering functions are then propagated separately in the hydrodynamic picture. At a later time, the actual wave function is recovered from the two propagated functions. The results obtained for Eckart barrier scattering in one dimension are in excellent agreement with exact results, even for very long propagation times t=1.2 ps. The capability of the CFM is also demonstrated for multidimensional propagation of a vibrationally excited wave packet.
Interfacial stability of electrodeposition of cuprous oxide films
Authors: Neogi P.
Published: November 2004

Experiments on deposition of Cu2O films from basic cupper sulfate solution show that copper also deposits. At low, but basic values of pH only copper deposits and at high pH only cuprous oxide deposits. In the intermediate range where both compete the system shows oscillations at “constant current.” Linear stability analysis has been conducted for such an electrochemical cell to show that oscillations can take place in the parameter space identified in the experiments. The results are keeping with most of the experimental observations, which are many, but not with all. The physical mechanisms behind the oscillations are explained in terms of competing reactions.
Theoretical strategy to provide atomistic models of comblike polymers: A generation algorithm combined with configurational bias Monte Carlo
Authors: Curco David , Alemán Carlos
Published: November 2004

A computational strategy to model the amorphous phase of comblike polymers is presented. The strategy, denoted SuSi/CB (CB—configurational bias), combines the strength of an algorithm recently developed to generate reliable microstructures of dense amorphous polymers, which is based on a random search of energy minima, and configurational bias Monte Carlo method. The influence of different parameters used to define the characteristics of SuSi/CB on both the reliability of the generated structures and the computational effort has been examined in detail. Finally, we have modeled and characterized the supramolecular organization of poly(octadecyl acrylate) in the amorphous state.
Vapor-liquid transitions of dipolar fluids in disordered porous media: Performance of angle-averaged potentials
Authors: Spöler C. , Klapp S. H. L.
Published: November 2004

Using replica integral equations in the reference hypernetted-chain (RHNC) approximation we calculate vapor-liquid spinodals, chemical potentials, and compressibilities of fluids with angle-averaged dipolar interactions adsorbed to various disordered porous media. Comparison with previous RHNC results for systems with true angle-dependent Stockmayer (dipolar plus Lennard-Jones) interactions [C. Spöler and S. H. L. Klapp, J. Chem. Phys. 118, 3628 (2003); ibid.120, 6734 (2004)] indicate that, for a dilute hard sphere matrix, the angle-averaged fluid-fluid (ff) potential is a reasonable alternative for reduced fluid dipole moments m*2=μ2/(ε0σ3)⩽2.0. This range is comparable to that estimated in bulk fluids, for which RHNC results are presented as well. Finally, results for weakly polar matrices suggest that angle-averaged fluid-matrix (fm) interactions can reproduce main features observed for true dipolar (fm) interactions such as the shift of the vapor-liquid spinodals towards lower temperatures and higher densities. However, the effective attraction induced by dipolar (fm) interaction is underestimated rather than overestimated as in the case of angle-averaged ff interactions.
Bimodal proton transfer in acid-base reactions in water
Authors: Rini Matteo , Pines Dina , Magnes Ben-Zion , Pines Ehud , Nibbering Erik T. J.
Published: November 2004

We investigate one of the fundamental reactions in solutions, the neutralization of an acid by a base. We use a photoacid, 8-hydroxy-1,3,6-trisulfonate-pyrene (HPTS; pyranine), which upon photoexcitation reacts with acetate under transfer of a deuteron (solvent: deuterated water). We analyze in detail the resulting bimodal reaction dynamics between the photoacid and the base, the first report on which was recently published [M. Rini, B.-Z. Magnes, E. Pines, and E. T. J. Nibbering, Science 301, 349 (2003)]. We have ascribed the bimodal proton-transfer dynamics to contributions from preformed hydrogen bonding complexes and from initially uncomplexed acid and base. We report on the observation of an additional (6 ps)−1 contribution to the reaction rate constant. As before, we analyze the slower part of the reaction within the framework of the diffusion model and the fastest part by a static, sub-150 fs reaction rate. Adding the second static term considerably improves the overall modeling of the experimental results. It also allows to connect experimentally the diffusion controlled bimolecular reaction models as defined by Eigen-Weller and by Collins-Kimball [D. Shoup and A. Szabo, Biophys. J. 40, 33 (1982)]. Our findings are in agreement with a three-stage mechanism for liquid phase intermolecular proton transfer: mutual diffusion of acid and base to form a “loose” encounter complex, followed by reorganization of the solvent shells and by “tightening” of the acid-base encounter complex. These rearrangements last a few picoseconds and enable a prompt proton transfer along the reaction coordinate, which occurs faster than our time resolution of 150 fs. Alternative models for the explanation of the slower “on-contact” reaction time of the loose encounter complex in terms of proton transmission through a von Grotthuss mechanism are also discussed.
Collision energy transfer in collision of NH4+(NH3)n−1 (n=3–9) with ND3
Authors: Orii Takaaki , Okada Yoshiki , Takeuchi Kazuo , Ichihashi Masahiko , Kondow Tamotsu
Published: November 2004

An incorporation of ND3 into protonated ammonia cluster ions NH4+(NH3)n−1 (n=3–9), together with a dissociation of the cluster ions, was observed in the collision of the cluster with ND3 at collision energies ranging from 0.04 to 1.4 eV in the center-of-mass frame. The branching fractions of the cluster ion species produced in the reactions were obtained as a function of the collision energy. The branching fractions of the incorporation products were successfully explained in terms of the Rice–Ramsperger–Kassel (RRK) theory at collision energies lower than the binding energy of the cluster ion. In addition, the internal energy distributions of the parent cluster ions were determined, and found to be in good agreement with those predicted using the evaporative ensemble model. In incorporations at collision energies lower than the binding energy of the cluster ion, all of the collision energy was transferred to the internal energy of the cluster ions; subsequently, an evaporation of ammonia molecules occurred in an equilibrium process after a complete energy redistribution in the clusters. In contrast, at collision energies higher than the binding energy of the cluster ion, a release of an ammonia molecule from the incorporation products occurred in a nonequilibrium process. The transition from the complex mode to the direct mode in the incorporation was observed at collision energies approximately equal to the binding energy. On the other hand, the collision energy dependence of the cross sections for the dissociation and for a nonreactive collision were estimated by a RRK simulation in which the collision energy transfer was interpreted by using the classical hard-sphere collision model. A relationship between reactivity and reaction modes in the collision of NH4+(NH3)4 with ND3 is discussed via a comparison of the experimental results with the RRK simulation.
Effect of ionization on the temperature- and pressure-induced phase transitions of poly(N-isopropylacrylamide) gels
Authors: Nasimova Irina , Karino Takeshi , Okabe Satoshi , Nagao Michihiro , Shibayama Mitsuhiro
Published: November 2004

The ionization effects on the pressure-induced phase transition of weakly charged poly(N-isopropylacrylamide-co-acrylic acid) (PNIPA-AAc) gels have been investigated by small-angle neutron scattering. At low temperature, T, and pressure, P, the structure factor of PNIPA-AAc gels was well represented by a Lorentzian (L) function, which was similar to noncharged PNIPA gels. However, at high Ps, the contribution of inhomogeneities became large and a squared-Lorentzian term had to be added in addition to the L term. At high Ts, on the other hand, a scattering maximum appeared, indicating microphase separation. This scattering maximum was suppressed by increasing P up to P≈100 MPa and then reincreased at higher Ps. The following facts were disclosed: (1) The peak position and height were very sensitive to P, which is mainly ascribed to strong pressure dependence of hydrophobic interaction, (2) ionization leads to microphase separation at elevated temperatures, (3) the re-entrant phase behavior is commonly observed in the P-T plane due to the parabolic variation of the polymer-solvent interaction with P, and (4) the pressure and temperature dependence of the structure factor was reproduced with the Rabin–Panyukov theory and was interpreted with a convexity of hydrophobic interaction with respect to pressure.
Texture formation under phase ordering and phase separation in polymer-liquid crystal mixtures
Authors: Das Susanta K. , Rey Alejandro D.
Published: November 2004

Computational modeling of texture formation in coupled phase separation-phase ordering processes in polymer/liquid crystal mixtures is performed using a unified model based on the nematic tensor order parameter and gradient orientation elasticity. The computational methods are able to resolve defect nucleation, defect-defect interactions, and defect-particle interactions, as well as global and local morphological features in the concentration and order parameter spatiotemporal behavior. Biphasic structures corresponding to polymer dispersed liquid crystals (PDLCs), crystalline filled nematic (CFNs), and random filled nematics (RFNs) are captured and analyzed using liquid crystal defect physics and structure factors. Under spinodal decomposition due to concentration fluctuations, the PDLC structure emerges, and the nucleation and repulsive interaction of defects within nematic droplets leads to bipolar nematic droplets. Under spinodal decomposition due to ordering fluctuations, the CFNs structure emerges, and the stable polymer droplet crystal is pinned by a lattice of topological defects. For intermediate cases, where the mixture is unstable to both concentration and nematic order fluctuations, the RFN structure emerges, and polymer droplets and fibrils are pinned by a defect network, whose density increases with the curvature of the polymer-liquid crystal interface. The simulations provide an information of the role of topological defects on phase separation-phase ordering processes in polymer-liquid crystal mixtures.
Quantum statistical mechanics with Gaussians: Equilibrium properties of van der Waals clusters
Authors: Frantsuzov Pavel A. , Mandelshtam Vladimir A.
Published: November 2004

The variational Gaussian wave-packet method for computation of equilibrium density matrices of quantum many-body systems is further developed. The density matrix is expressed in terms of Gaussian resolution, in which each Gaussian is propagated independently in imaginary time β=(kBT)−1 starting at the classical limit β=0. For an N-particle system a Gaussian exp[(r−q)TG(r−q)+γ] is represented by its center q∈R3N, the width matrix G∈R3N×3N, and the scale γ∈R, all treated as dynamical variables. Evaluation of observables is done by Monte Carlo sampling of the initial Gaussian positions. As demonstrated previously at not-very-low temperatures the method is surprisingly accurate for a range of model systems including the case of double-well potential. Ideally, a single Gaussian propagation requires numerical effort comparable to the propagation of a single classical trajectory for a system with 9(N2+N)/2 degrees of freedom. Furthermore, an approximation based on a direct product of single-particle Gaussians, rather than a fully coupled Gaussian, reduces the number of dynamical variables to 9N. The success of the methodology depends on whether various Gaussian integrals needed for calculation of, e.g., the potential matrix elements or pair correlation functions could be evaluated efficiently. We present techniques to accomplish these goals and apply the method to compute the heat capacity and radial pair correlation function of Ne13 Lennard-Jones cluster. Our results agree very well with the available path-integral Monte Carlo calculations.
Full configuration interaction potential energy curves for the X 1Σg+, B 1Δg, and B′ 1Σg+ states of C2: A challenge for approximate methods
Authors: Abrams Micah L. , Sherrill C. David
Published: November 2004

The C2 molecule exhibits unusual bonding and several low-lying excited electronic states, making the prediction of its potential energy curves a challenging test for quantum chemical methods. We report full configuration interaction results for the X 1Σg+, B 1Δg, and B′ 1Σg+ states of C2, which exactly solve the electronic Schrödinger equation within the space spanned by a 6-31G* basis set. Within the D2h subgroup used by most electronic structure programs, these states all have the same symmetry (1Ag), and all three states become energetically close for interatomic distances beyond 1.5 Å. The quality of several single-reference ab initio methods is assessed by comparison to the benchmark results. Unfortunately, even coupled-cluster theory through perturbative triples using an unrestricted Hartree–Fock reference exhibits large nonparallelity errors (>20 kcal mol−1) for the ground state. The excited states are not accurately modeled by any commonly used single-reference method, nor by configuration interaction including full quadruple substitutions. The present benchmarks will be helpful in assessing theoretical methods designed to break bonds in ground and excited electronic states.
Fine structure of the (S1←S) band origins of phthalocyanine molecules in helium droplets
Authors: Lehnig Rudolf , Slipchenko Mikhail , Kuma Susumu , Momose Takamasa , Sartakov Boris , Vilesov Andrey
Published: November 2004

The laser-induced fluorescence (LIF) excitation spectra of free base phthalocyanine (Pc), Mg-Pc, and Zn-Pc molecules in superfluid helium droplets at T=0.38 K have been studied. The spectra reveal the rich vibronic structure of the S1←S0 electronic transitions. The band origins of the transitions consist of zero phonon lines accompanied by phonon wings, which originate from simultaneous electronic excitation of the molecule and excitation of the collective modes of the helium surrounding it. The phonon wings have discrete structures suggesting localization of some helium atoms in the neighborhood of the molecules. Zero phonon lines of Mg-Pc and Zn-Pc molecules are split into three components, which are separated by 0.2–0.4 cm−1. Possible mechanism of splitting involves static or dynamic Jahn–Teller interaction of metal-phthalocyanine molecules in the twofold degenerate S1(1Eu) state with the helium shell.
The Cotton-Mouton effect of neon and argon: A benchmark study using highly correlated coupled cluster wave functions
Authors: Rizzo Antonio , Kállay Mihály , Gauss Jürgen , Pawłowski Filip , Jørgensen Poul , Hättig Christof
Published: November 2004

The Cotton-Mouton effect (magnetic field induced linear birefringence) has been studied for neon and argon using state-of-the-art coupled cluster techniques. The coupled cluster singles, doubles and triples (CCSDT) approach has been used to obtain static benchmark results and the CC3 model with an approximate treatment of triple excitations to obtain frequency-dependent results. In the case of neon the effect of excitations beyond triples has also been estimated via coupled cluster calculations including quadruple excitations (CCSDTQ), pentuple excitations (CCSDTQP), etc. up to the full configuration-interaction level. The results obtained for the anisotropy of the hypermagnetizability Δη(ω), the molecular property that determines the magnetic field induced birefringence of spherically symmetric systems, are Δη=2.89 a.u. for neon and Δη=24.7 a.u. for argon, with a negligible effect of frequency dispersion. For neon we could estimate an absolute error on Δη of 0.1 a.u. The accuracy of these results surpasses that of recently reported experimental data.
Calculation of excited-state properties using general coupled-cluster and configuration-interaction models
Authors: Kállay Mihály , Gauss Jürgen
Published: November 2004

Using string-based algorithms excitation energies and analytic first derivatives for excited states have been implemented for general coupled-cluster (CC) models within CC linear-response (LR) theory which is equivalent to the equation-of-motion (EOM) CC approach for these quantities. Transition moments between the ground and excited states are also considered in the framework of linear-response theory. The presented procedures are applicable to both single-reference-type and multireference-type CC wave functions independently of the excitation manifold constituting the cluster operator and the space in which the effective Hamiltonian is diagonalized. The performance of different LR-CC/EOM-CC and configuration-interaction approaches for excited states is compared. The effect of higher excitations on excited-state properties is demonstrated in benchmark calculations for NH2 and NH3. As a first application, the stationary points of the S1 surface of acetylene are characterized by high-accuracy calculations.
Synthesis of silver molybdate clusters driven by laser-annealing
Authors: Bréchignac C. , Cahuzac Ph. , Kebaili N. , Lando A. , Masson A. , Schmidt M.
Published: November 2004

The synthesis of silver rich molybdate clusters is achieved by laser induced chemical reaction of coadsorbed MoO3 and O2 molecules on free silver clusters. The reactants MoO3 and/or O2 molecules condensed at low temperature (77 K–175 K) on free silver clusters. Then, the silver clusters together with their adsorbed molecules are flashed either ionized with a discharge or ionized and heated by a laser. Then they are cooled down by evaporation. The synthesized chemical compounds are analyzed by a high-resolution time-of-flight mass spectrometer. If only one type of reactant is adsorbed on the cluster, only one oxide molecule is stabilized on the metallic core after the heating and cooling cycle. On the contrary, the coadsorption of the two types of molecules MoO3 and O2 on Agn+, at 77 K, leads to complex aggregates that transform, after laser heating, into a molybdate rich metal clusters. These synthesized species cool down by evaporating silver atoms showing evidence of a binary oxide that is more stable than the metallic core. Moreover we demonstrate that for small size molybdate clusters, a stoichiometric composition may differ from the bulk one.
Differential and total (e,2e) cross sections of simple polyatomic molecules
Authors: Champion Christophe , Hanssen Jocelyn , Hervieux Paul-Antoine
Published: November 2004

In this paper, we present a theoretical approach to calculate differential and total ionization cross sections of polyatomic molecules by fast electron impact. More exactly, we have studied the ionization of ammonia (NH3) and methane (CH4) molecules, and previous results concerning the H2O molecule ionization are reported for comparison. The calculations are performed in the distorted wave Born approximation without exchange by employing the independent electron model. The molecular target wave functions are described by linear combinations of atomic orbitals. To describe the interaction between the inactive target electrons and the slow ejected electron, we have introduced a distortion via an effective potential calculated for each molecular orbital. The present theoretical calculations agree well with a large set of existing experimental data in terms of multiple differential and total cross sections.
Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice
Authors: Yu Haibo , van Gunsteren Wilfred F.
Published: November 2004

The properties of two improved versions of charge-on-spring (COS) polarizable water models (COS/G2 and COS/G3) that explicitly include nonadditive polarization effects are reported. In COS models, the polarization is represented via a self-consistently induced dipole moment consisting of a pair of separated charges. A previous polarizable water model (COS/B2), upon which the improved versions are based, was developed by Yu, Hansson, and van Gunsteren [J. Chem. Phys. 118, 221 (2003)]. To improve the COS/B2 model, which overestimated the dielectric permittivity, one additional virtual atomic site was used to reproduce the water monomer quadrupole moments besides the water monomer dipole moment in the gas phase. The molecular polarizability, residing on the virtual atomic site, and Lennard-Jones parameters for oxygen-oxygen interactions were varied to reproduce the experimental values for the heat of vaporization and the density of liquid water at room temperature and pressure. The improved models were used to study the properties of liquid water at various thermodynamic states as well as gaseous water clusters and ice. Overall, good agreement is obtained between simulated properties and those derived from experiments and ab initio calculations. The COS/G2 and COS/G3 models may serve as simple, classical, rigid, polarizable water models for the study of organic solutes and biopolymers. Due to its simplicity, COS type of polarization can straightforwardly be used to introduce explicit polarization into (bio)molecular force fields.
Nucleation rates of water and heavy water using equations of state
Authors: Obeidat Abdalla , Li Jin-Song , Wilemski Gerald
Published: November 2004

The original formula of Gibbs for the reversible work of critical nucleus formation is evaluated in three approximate ways for ordinary and heavy water. The least approximate way employs an equation of state to evaluate the pressure difference between the new and old phases. This form of the theory yields a temperature dependence for the nucleation rate close to that observed experimentally. This is a substantial improvement over the most commonly used (and most approximate) form of classical theory.
Near-infrared laser spectroscopy of NiI
Authors: Tam W. S. , Ye Jianjun , Cheung A. S.-C.
Published: November 2004

Laser-induced fluorescence spectrum of NiI in the near infrared region of 714–770 nm has been recorded. Seven bands belonging to three electronic transition systems were observed and analyzed: the (0,0), (1,0), and (2,0) bands of [13.3] 2Σ+-A 2Π3/2 system; the (1,1) and (0,1) bands of [13.9] 2Π3/2-X 2Δ5/2 system; and the (0,0) and (1,0) bands of [13.9] 2Π3/2-A 2Π3/2 system. Spectra of isotopic molecules confirmed the vibrational quantum number assignment of the observed bands. Least-squares fit of rotationally resolved transition lines yielded accurate molecular constants for the v=0–2 levels of the [13.3] 2Σ+ state, the v=0 level of the A 2Π3/2, and the v=1 level of the X 2Δ5/2 state. The vibrational separation, ΔG1/2, of the ground state was measured to be 276.674 cm−1. With the observation of the [13.9] 2Π3/2-A 2Π3/2 and [13.9] 2Π3/2-X 2Δ5/2 transitions, we accurately determined the energy separation between the A 2Π3/2 and the X 2Δ5/2 to be 163.847 cm−1. This confirms that the order of the A 2Π3/2 and X 2Δ5/2 states in NiI is reversed when compared with other nickel monohalides.
Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers
Authors: Shinoda Keiko , Shinoda Wataru , Baba Teruhiko , Mikami Masuhiro
Published: November 2004

The lipid membranes found in archaea have high bilayer stability and low permeability. The molecular structure of their constituent lipids is characterized by ether-linked, branched hydrophobic chains, whereas the conventional lipids obtained from eukaryotic or eubacterial sources have ester linked straight chains. In order to elucidate the influence of the ether linkage, instead of an ester one, on the physical properties of the lipid bilayers, we have carried out comparative 10 ns molecular dynamics simulations of diphytanyl phosphatidylcholine (ether-DPhPC) and diphytanoyl phosphatidylcholine (ester-DPhPC) bilayers in water, respectively. We analyze bilayer structures, hydration of the lipids, membrane dipole potentials, and free energy profiles of water and oxygen across the bilayers. We observe that the membrane dipole potential for the ether-DPhPC bilayer, which arises mainly from the ether linkage, is about half of that of the ester-DPhPC. The calculated free energy barrier for a water molecule in the ether-DPhPC bilayer system is slightly higher than that in the ester-DPhPC counterpart, which is in accord with experimental data.
A molecular dynamics simulation of the melting points and glass transition temperatures of myo- and neo-inositol
Authors: Watt Stephen W. , Chisholm James A. , Jones William , Motherwell Sam
Published: November 2004

The heat of sublimation, density, melting point, and glass transition temperature are calculated for myo- and neo-inositol, using the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) [H. Sun, J. Phys. Chem. B 102, 7338 (1998)] force field and molecular dynamics techniques. Our results show that the calculated heats of sublimation and density are very close to the experimental values for both compounds. Furthermore, our simulated melting temperatures for myo- and neo-inositol also compare very well to the experimentally obtained data. The glass transition temperatures for myo- and neo-inositol have been calculated to be ca. 494 K and ca. 518 K, respectively, and the shape of the volume versus temperature plots produced are typical for a glass transition. As a result, it is our view that the COMPASS force field suitably describes these two compounds in molecular simulations and that molecular dynamics techniques, combined with this force field, can be used to simulate the melt and glass transitions for such molecules.
An extension of the quasicontinuum treatment of multiscale solid systems to nonzero temperature
Authors: Diestler D. J. , Wu Z.-B. , Zeng X. C.
Published: November 2004

Covering the solid lattice with a finite-element mesh produces a coarse-grained system of mesh nodes as pseudoatoms interacting through an effective potential energy that depends implicitly on the thermodynamic state. Use of the pseudoatomic Hamiltonian in a Monte Carlo simulation of the two-dimensional Lennard-Jones crystal yields equilibrium thermomechanical properties (e.g., isotropic stress) in excellent agreement with “exact” fully atomistic results.
Time-dependent electron localization functions for coupled nuclear-electronic motion
Authors: Erdmann M. , Gross E. K. U. , Engel V.
Published: November 2004

We study the quantum dynamics in a model system consisting of two electrons and a nucleus which move between two fixed ions in one dimension. The numerically determined wave functions allow for the calculation of time-dependent electron localization functions in the case of parallel spin and of the time-dependent antiparallel spin electron localization functions for antiparallel spin. With the help of these functions, it becomes possible to illustrate how electronic localization is modified through the vibrational wave-packet motion of the nucleus.
The effect of surface roughness on the adhesion of solid surfaces for systems with and without liquid lubricant
Authors: Samoilov V. N. , Sivebaek I. M. , Persson B. N. J.
Published: November 2004

We present molecular dynamics results for the interaction between two solid elastic walls during pull-off for systems with and without octane (C8H18) lubricant. We used two types of substrate—flat and corrugated—and varied the lubricant coverage from ∼1/8 to ∼4 ML (monolayers) of octane. For the flat substrate without lubricant the maximum adhesion was found to be approximately three times larger than for the system with the corrugated substrate. As a function of the octane coverage (for the corrugated substrate) the pull-off force first increases as the coverage increases from 0 to ∼1 ML, and then decreases as the coverage is increased beyond monolayer coverage. It is shown that at low octane coverage, the octane molecules located in the substrate corrugation wells during squeezing are pulled out of the wells during pull-off, forming a network of nanocapillary bridges around the substrate nanoasperities, thus increasing the adhesion between two surfaces. For greater lubricant coverages a single capillary bridge is formed. The adhesion force saturates for lubricant coverages greater than 3 ML. For the flat substrate, during pull-off we observe discontinuous, thermally activated changes in the number n of lubricant layers (n−1→n layering transitions), whereas for the corrugated substrate these transitions are “averaged” by the substrate surface roughness.
Particle connectedness and cluster formation in sequential depositions of particles: Integral-equation theory
Authors: Danwanichakul Panu , Glandt Eduardo D.
Published: November 2004

We applied the integral-equation theory to the connectedness problem. The method originally applied to the study of continuum percolation in various equilibrium systems was modified for our sequential quenching model, a particular limit of an irreversible adsorption. The development of the theory based on the (quenched-annealed) binary-mixture approximation includes the Ornstein-Zernike equation, the Percus-Yevick closure, and an additional term involving the three-body connectedness function. This function is simplified by introducing a Kirkwood-like superposition approximation. We studied the three-dimensional (3D) system of randomly placed spheres and 2D systems of square-well particles, both with a narrow and with a wide well. The results from our integral-equation theory are in good accordance with simulation results within a certain range of densities.
DNA-psoralen interaction: A single molecule experiment
Authors: Rocha M. S. , Viana N. B. , Mesquita O. N.
Published: November 2004

By attaching one end of a single λ-DNA molecule to a microscope coverslip and the other end to a polystyrene microsphere trapped by an optical tweezers, we can study the entropic elasticity of the λ-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particulary interested in the effects of the photosensitive drug psoralen on the elasticity of the DNA molecule. We have illuminated the sample with different light sources, studying how the different wavelengths affect the psoralen-DNA linkage. To do this, we measure the persistence length of individual DNA-psoralen complexes.