bluuebunny/crossref_metadata_2025 huggingface dataset:
High pressure reactivity of solid furan probed by infrared and Raman spectroscopy
Authors: Ceppatelli Matteo , Santoro Mario , Bini Robert , Schettino Vincenzo
Published: January 2003

The behavior of crystalline furan has been investigated, at room temperature, along the 0–47–0 GPa pressure cycle by using IR and Raman spectroscopy. These data, joint to high pressure low temperature IR data, allow the identification of two solid phases in the 1.2–12 GPa pressure range: the low-pressure orientationally disordered phase IV and the high-pressure ordered phase III. Above 10–12 GPa solid furan starts to chemically transform. The threshold pressure for the transformation is much lower than in benzene, as expected according to the minor stability of the heteroaromatic ring. The reaction proceeds continuously along the compression path, but it becomes complete only with releasing pressure, and a yellow–brownish sample is recovered. This compound was identified as an amorphous hydrogenated carbon (a-C:H) containing alkylpolyether type segments, alcoholic functions, and C=O bonds. The presence of these new chemical species attests to the opening of the original furan rings and to the transfer of hydrogen atoms. The reaction seems to be very similar to that induced in crystalline benzene. This comparison indicates a general behavior for the reactivity under ultrahigh pressures of the whole class of aromatic compounds.
Erratum: “Transition strengths and potential curves for the valence transitions in Br2 from a reanalysis of the ultraviolet-visible absorption at low resolution” [J. Chem. Phys. 115, 10417 (2001)]
Authors: Tellinghuisen Joel
Published: January 2003

The least-squares analysis has been redone after correction for an error in the conversion of air wavelengths to vacuum, and with inclusion of a scaling parameter to allow for more recent observations that indicate molar absorptivities smaller by ∼1% for the new spectra included in the data set. The revised analysis yields B←X and C←X components that are weaker (by <1%) and an A←X contribution that is stronger (∼2%). The calculated contribution of B←X to the total absorption below 510 nm does not agree well with results from a recent but previously overlooked experimental study of atomic products in photodissociation.
Intermolecular vibrations of the hydrogen bonded OH–CO reactant complex
Authors: Marshall Mark D. , Pond Bethany V. , Lester Marsha I.
Published: January 2003

Intermolecular vibrations of the linear OH–CO reactant complex have been observed as combination bands in the OH overtone region using infrared action spectroscopy. Rotational analyses and simulations of the band structures have been carried out for transitions to geared bend, excited spin–orbit, and H-atom bend states with 50–250 cm−1 of intermolecular excitation. The projection quantum number associated with each of these upper states is identified through the intensity profile of the band contour, missing rotational lines, and/or parity splitting of individual rotational lines. Intermolecular states with projection quantum numbers P=1/2 and 5/2 are observed for each of the two bending modes, arising from coupling of the unquenched angular momentum of OH with the vibrational angular momentum associated with the bending motion of the complex. An additional P=1/2 state is attributed to spin–orbit excitation, which shifts to higher energy than in free OH and gains infrared transition strength through the spin-decoupling interaction. The intermolecular energy level pattern is also examined in the context of the Renner-Teller interaction and spin–orbit coupling. The intermolecular bends of the OH–CO complex are of special interest because they probe portions of the reaction path leading to trans-HOCO formation.
Understanding highly excited states via parametric variations
Authors: Semparithi Aravindan , Charulatha Venkataraman , Keshavamurthy Srihari
Published: January 2003

Highly excited vibrational states of an isolated molecule encode the vibrational energy flow pathways in the molecule. Recent studies have had spectacular success in understanding the nature of the excited states mainly due to the extensive studies of the classical phase space structures and their bifurcations. Such detailed classical-quantum correspondence studies are presently limited to two- or quasi-two-dimensional systems. One of the main reasons for such a constraint has to do with the problem of visualization of relevant objects like surface of sections and Wigner or Husimi distributions associated with an eigenstate. This necessitates various alternative techniques which are more algebraic than geometric in nature. In this work we introduce one such method based on parametric variation of the eigenvalues of a Hamiltonian. It is shown that the level velocities are correlated with the phase space nature of the corresponding eigenstates. A semiclassical expression for the level velocities of a single resonance Hamiltonian is derived which provides theoretical support for the correlation. We use the level velocities to dynamically assign the highly excited states of a model spectroscopic Hamiltonian in the mixed phase space regime. The effect of bifurcations on the level velocities is briefly discussed using a recently proposed spectroscopic Hamiltonian for the HCP molecule.
Isomerization and intermolecular solute–solvent interactions of ethyl isocyanate: Ultrafast infrared vibrational echoes and linear vibrational spectroscopy
Authors: Levinger Nancy E. , Davis Paul H. , Behera Pradipta Kumar , Myers D. J. , Stromberg Christopher , Fayer M. D.
Published: January 2003

Thermally induced gauche–trans isomerization and direct solute–solvent interactions of the solute, ethyl isocyanate (EIC), in the solvent, 2-methylpentane (2MP), are investigated using ultrafast infrared vibrational echo experiments and linear vibrational absorption spectroscopy of the isocyanate (N=C=O) antisymmetric stretching mode (2278 cm−1). Both the EIC vibrational echo measured pure vibrational dephasing and the absorption spectra show complex behavior as a function of temperature from room temperature to 8 K. The EIC data are compared to absorption experiments on the same mode of isocyanic acid (HNCO), which cannot undergo isomerization. To describe the observations, a model is presented that involves both intramolecular dynamics and intermolecular dynamical interactions. At room temperature, gauche–trans isomerization is very fast, and the isomerization dynamics contribution to the vibrational echo decay and the absorption line shape is small because it is motionally narrowed. The dominant contribution to both the vibrational echo decay and the absorption spectrum is from direct dynamical interactions of the solute with the solvent. As the temperature is lowered, the direct contribution to vibrational dephasing decreases rapidly, but the contribution from isomerization increases because the extent of motional narrowing diminishes. The combined effect is a very gradual decrease of the rate of pure dephasing as the temperature is initially lowered from room temperature. At very low temperature, below the 2MP glass transition, isomerization cannot occur. The absorption spectrum displays two peaks, interpreted as the distinct gauche and trans absorption bands. Even at 8 K, the pure dephasing is surprisingly fast. The direct solvent-induced dephasing is negligible. The dephasing is caused by motions of the ethyl group without isomerization occuring. At intermediate temperatures (150 K>T>100 K), isomerization takes place, but its contribution to the pure dephasing is not motionally narrowed. The absorption spectral shapes are complex. Dephasing arising from direct interaction with the solvent is small. Both isomerization and fluctuations on the gauche–trans surface contribute to the absorption line shape. The model that is used to describe the results involves a NMR type exchange calculation with additional contributions from the direct solvent interactions that are obtained from the temperature-dependent HNCO IR spectra. From the temperature dependence of the isomerization “jump” rate, the barrier height for the isomerization is found to be ∼400 cm−1.
A general expression for the condensation coefficient based on transition state theory and molecular dynamics simulation
Authors: Nagayama Gyoko , Tsuruta Takaharu
Published: January 2003

A theoretical derivation of condensation coefficient based on transition state theory is presented in this paper by considering the three-dimensional movement of condensing molecules in the liquid–vapor interface region. The theoretical expression is a function of free volume ratio of liquid to vapor and activation energy for condensation. We have developed an evaluation of the activated state conditions in the interface region with the use of molecular dynamics (MD) simulations for argon and water. From the molecular scale consideration, it is found that a characteristic length ratio 3Vl/Vg has an important role in evaluating the condensation coefficient because the restricted translational motion is dominant in the condensation process compared with the rotational motion. Present theoretical values agree well with MD results in both monatomic and polyatomic polar molecules. Finally, we conclude that the condensation coefficient is an inherent physical property of a given pure liquid–vapor interface and the interface structure plays a primary role in condensation.
Photophysics of thiophene based polymers in solution: The role of nonradiative decay processes
Authors: Seixas de Melo J. , Burrows H. D. , Svensson M. , Andersson M. R. , Monkman A. P.
Published: January 2003

An investigation has been undertaken of the photophysics of six thiophene-based polymers. This includes the measurement of fluorescence quantum yields, quantum yields for triplet formation, and determination of fluorescence and triplet lifetimes in benzene solution at room temperature. From the above-mentioned data, the overall set of rates for the deactivation processes (fluorescence, intersystem crossing, and internal conversion), has been evaluated. Mechanisms of nonradiative decay are discussed, and it is shown that both intersystem crossing and internal conversion are important in the decay of the lowest singlet excited state of isolated polythiophenes molecules in solution. Comparison of spectroscopic and photophysical properties of the polymers with analogous oligothiophenes shows that with the polymer, the S1⇝S0 internal conversion deactivation pathway plays a major role, in contrast to the behavior found with the oligomers where this internal conversion deactivation channel is essentially negligible.
Ab initio simulation of the two-dimensional vibrational spectrum of dicarbonylacetylacetonato rhodium(I)
Authors: Moran Andrew M. , Dreyer Jens , Mukamel Shaul
Published: January 2003

The complete anharmonic cubic and quartic force field of the two carbonyl stretching vibrations of a rhodium di-carbonyl complex is calculated at the density functional level and used to simulate the third-order vibrational response function. The infrared photon echo spectrum calculated using the diagonalized resulting exciton Hamiltonian is in qualitative agreement with measured values. Quartic terms in the potential are critical for reproducing the experimental transition energies and transition dipoles.
Infrared emission spectra of BeH and BeD
Authors: Shayesteh A. , Tereszchuk K. , Bernath P. F. , Colin R.
Published: January 2003

High resolution infrared emission spectra of beryllium monohydride and monodeuteride have been recorded. The molecules were generated in a furnace-discharge source, at 1500 °C and 333 mA discharge current, with beryllium metal and a mixture of helium and hydrogen or deuterium gases. Approximately 160 BeH lines and 167 BeD lines for the vibrational bands v=1→0 to v=4→3 were observed in the spectra and spectroscopic constants were determined. The Dunham constants (Yl,m) and Born–Oppenheimer breakdown constants were obtained in a combined fit of the BeH and BeD data. The equilibrium rotational constants (Be) for BeH and BeD were found to be 10.319 59(3) cm−1 and 5.688 29(2) cm−1, respectively, while the equilibrium vibrational constants (ωe) are 2061.416(3) and 1529.956(3) cm−1. The equilibrium distance (Re) was determined to be 1.342 436(2) Å for BeH.
Generating strange magnetic and dielectric interactions: Classical molecules and particle foams
Authors: Martin James E. , Anderson Robert A. , Williamson Rodney L.
Published: January 2003

When a soft magnetic particle suspension is subjected to a vertical uniaxial magnetic field the particles polarize, the positive dipolar interactions causing particle chain formation. If instead an audio-frequency rotating magnetic field is applied in a horizontal plane, the particles experience an average interaction that to first order is a negative dipolar interaction, causing particle sheet formation in the biaxial field plane. When a vertical uniaxial field and a horizontal biaxial field are simultaneously applied with the field amplitudes balanced, the positive and negative dipolar interactions cancel to first order, and one might expect no dipolar interactions at all. But in this balanced triaxial field an isotropic second-order dipolar interaction of surprising magnitude remains. This triaxial interaction can be attractive or repulsive, and exhibits strong many-body interactions that lead to a variety of unexpected effects, including stable clusters with molecular geometries, the emergence of a particle foam, and the production of vortices in the fluid. By manipulating the triaxial field, a variety of particle structures can be made that cannot be produced by any other known means.
The dynamics of the H+D2O→OD+HD reaction at 2.5 eV: Experiment and theory
Authors: Brouard M. , Burak I. , Minayev D. , O’Keeffe P. , Vallance C. , Aoiz F. J. , Bañares L. , Castillo J. F. , Zhang Dong H. , Collins Michael A.
Published: January 2003

The title reaction has been studied both experimentally and computationally at a mean collision energy of 2.48 eV. OD quantum state populations, rotational alignment parameters, rovibrational quantum state-resolved center-of-mass angular scattering distributions and HD co-product internal energy release distributions have been determined, along with OD quantum state averaged energy disposals. The experiments employ pulsed laser photolysis coupled with polarized Doppler-resolved laser induced fluorescence detection of the radical products. The OD angular scattering distributions show a preference for scattering in the forward direction, and are quite different from those observed previously at the lower collision energy of 1.4 eV. So too are the kinetic energy release distributions, which reveal that the HD co-products are born significantly more internally excited at 2.48 eV than at 1.4 eV. The HD internal energy distributions obtained from analysis of the Doppler resolved profiles are in reasonable accord with that derived from the direct HD population measurements performed by Zare and co-workers [J. Chem. Phys. 98, 4636 (1993)] at collision energies around 2.7 eV. The data are compared in detail with the results of new quasi-classical trajectory (QCT) calculations employing two alternative potential energy surfaces (PESs), as well as with the results from previous QCT studies of the title reaction by other workers. Refinements to the most recent of the PESs employed here, that developed using the iterative methods of Collins and Zhang and co-workers [J. Chem. Phys. 115, 174 (2001)], are also described. The theoretical results obtained using this refined PES agree very well with many of the experimental observables, and the surface appears to be a significant improvement on those previously developed. However, even with this new PES, the QCT calculations at 2.48 eV overestimate the internal excitation of the HD products.
Photolysis of the OC⋯HONO complex in low temperature matrices: Infrared detection and ab initio calculations of nitrosoformic acid, HOC(O)NO
Authors: Mielke Zofia , Olbert-Majkut Adriana , Tokhadze Konstantin G.
Published: January 2003

Photochemistry of OC⋯HONO complexes in nitrogen matrices has been investigated using λ>340 nm radiation of a medium pressure mercury arc. Reaction of the OH radicals from HONO photolysis with CO within the nitrogen lattice site has led to formation of trans and cis-HOCO radicals. The HOCO radicals reacted further with NO via two reaction channels yielding trans and cis-HOC(O)NO or HNO+CO2. Comparison of the observed infrared frequencies and isotope shifts (C13, O18, and H2) with the computed frequencies confirmed the assignment of the cis and trans conformers of nitrosoformic acid that have been identified for the first time. In matrices with higher CO concentration the complexes between cis-HOC(O)NO molecule and carbon monoxide were also identified.
Derivation of expressions for the spontaneous curvature, mean and Gaussian bending constants of thermodynamically open surfactant monolayers and bilayers
Authors: Bergström Magnus
Published: January 2003

We have derived expressions for the spontaneous curvature H0, the mean and Gaussian bending constants, kc and k̄c, respectively, for a surfactant film of finite thickness that is open in a thermodynamic sense. Geometrical packing constraints are taken into account and give rise to explicit large and important contributions to kc, k̄c, and kcH0. From its contribution to the latter quantity we may deduce that surfactant aggregates (micelles, vesicles, microemulsion droplets) are expected to dramatically increase their size with increasing surfactant tail length. Moreover, the coupling between free energy contributions related to surfactant head group and tail with geometrical packing constraints give rise to dominant terms on the form 2ξpH0, where ξp is the thickness of a planar film, in the expressions for kc. In the case of repulsive head group effects that favor a large spontaneous curvature, such as electrostatics, these terms raise kc and thus increase the rigidity of the film. Due to the constraint of constant free monomer chemical potentials, the composition of the film becomes a function of curvature. As a result, the ability of a surfactant film to have different surfactant compositions in differently curved parts (e.g., inner and outer layer of a vesicle, central parts and end caps of rod or threadlike micelles, etc.) may considerably reduce kc, whereas k̄c and kcH0 are mainly unaffected by mixing. The magnitude of the reduction of kc of a binary surfactant film increases with increasing asymmetry between the two surfactants with respect to charge number, head group size, and tail volume.
Separating contributions from multiple structural isomers in anion photoelectron spectra: Al3O3− beam hole burning
Authors: Akin F. Ahu , Jarrold Caroline Chick
Published: January 2003

Contributions from two structural isomers in the photoelectron spectrum of Al3O3− have been isolated using an anion beam hole-burning technique. A kite-shaped structure having a lower electron affinity than the bent rectangle isomer was partially bleached from the ion beam just prior to the photoelectron spectroscopy interaction region. Further, we have performed studies varying the time allowed for cluster formation along with density functional calculations on a feasible structural intermediate that suggest that the kite structure may actually be a precursor to the rectangle structure.
Quantum dynamics study of the isotopic effect on capture reactions: HD, D2+CH3
Authors: Wang Dunyou
Published: January 2003

Time-dependent wave-packet-propagation calculations are reported for the isotopic reactions, HD+CH3 and D2+CH3, in six degrees of freedom and for zero total angular momentum. Initial-state-selected reaction probabilities for different initial rotational-vibrational states are presented in this study. This study shows that excitations of the HD(D2) enhances the reactivities, whereas the excitations of the CH3 umbrella mode have the opposite effects. This is consistent with the reaction of H2+CH3. The comparison of these three isotopic reactions also shows the isotopic effects in the initial-state-selected reaction probabilities. The cumulative reaction probabilities (CRPs) are obtained by summing over initial-state-selected reaction probabilities. Theenergy-shift approximation to account for the contribution of degrees of freedom missing in the six dimensionality calculation is employed to obtain approximate full dimensional CRPs. The rate constant comparison shows the H2+CH3 reaction has the biggest reactivity, then HD+CH3, and D2+CH3 has the smallest.
Quenching of an excitation moving on a flexible polymer
Authors: Jun Park Pyeong , Lee Sangyoub
Published: January 2003

We study theoretically the irreversible quenching of an excitation migrating on a polymer by small quencher molecules. Using a simplified superposition approximation, we solve the hierarchical reaction-diffusion equations and obtain the quenching rate and survival probability of the excitation. Depending upon the excitation mobility as well as upon the chain length, the quenching rate shows various behaviors, which is absent in the small molecular quenching reaction. In the diffusion-controlled limit, the quenching rate is found to increase as the excitation mobility increases and converge, for sufficiently large excitation mobility, to a constant value proportional to the radius of gyration of the polymer. This means that fast migration of single excitation, assisted by the dynamics of the polymer, enhance the reaction rate as much as that of the reaction of a static polymer where all the monomers are reactive.
Dielectric hole burning in the high frequency wing of supercooled glycerol
Authors: Duvvuri Kalyan , Richert Ranko
Published: January 2003

We have performed dielectric hole burning experiments on supercooled glycerol at frequencies up to five decades above the peak frequency of the dielectric loss. While most observations of heterogeneous dynamics refer to the slower than average relaxation times, this study confirms the existence of independent relaxation time scales across the high frequency wing of the relaxation time distribution. In this short time regime, the persistence time of the spectrally selective modifications is solely a matter of the burn frequency and no longer determined by the structural relaxation time. For a fixed value of the burn field, the amplitudes of the relaxation pattern changes measured along the log t scale (horizontal holes) are independent of the burn frequency ωb and dielectric loss ε″(ωb). This latter feature is observed in a range of burn frequencies which exceed the loss peak frequency by a factor of 10 to 3×105, where ε″(ωb) varies between 16 and 0.17.
Laser fluorescence excitation spectroscopy of the GeAr van der Waals complex
Authors: Tao Chong , Dagdigian Paul J.
Published: January 2003

Laser fluorescence excitation spectra of the GeAr van der Waals complex, in the vicinity of the individual fine-structure lines of the Ge 4s24p5s 3P°←4s24p2 3P atomic resonance transition in the region 275–260 nm are reported. Excited-state (v′,0) progressions of bands built upon the individual J′←J″ fine-structure atomic lines were observed. In all cases, the progressions terminated with a broad, unstructured band characteristic of the existence of a barrier in the excited-state potential energy curves. Assignment of the v′ vibrational quantum numbers for the resolved bands was successfully carried out through analysis of the GeAr70,72,74,76 isotope splittings of the bands. Rotational analyses of the resolved bands were carried out, and upper- and lower-state Ω assignments and determination of the rotational constants could be performed. Transitions out of lower Ω″=0+, 1, and 0+ levels associated with the asymptotic Ge(4s24p2 3P) J″=0, 1, and 2 atomic fine-structure levels, respectively, were observed. To derive information on the relevant Ge+Ar interactions, the observed spectra were interpreted through model potential energy curves based on the isoelectronic SiAr system. The large spin–orbit interaction of the Ge atom has a strong effect on the nonbonding interactions of the fine-structure levels with the Ar atom.
Model for chemical effects in non-steady-state radiation enhanced diffusion of Ti in MgO
Authors: Lu M. , Lupu C. , Rabalais J. W.
Published: January 2003

The non-steady-state radiation enhanced diffusion of Ti in MgO(100) prebombarded with 7 keV Ar+ and Cl+ has been studied and the data have been first interpreted quantitatively in terms of a diffusion-reaction mechanism. Secondary ion mass spectroscopy was used for depth profiling and mass spectral measurements. The results revealed an unrealistic stoichiometry for formation of a volatile TiClx compound, indicating the failure of the hypothesis of volatile species formation during diffusion. A modified Kapinos–Platonov model [Rad. Eff. 103, 45 (1987)] was developed which provides a consistent interpretation of the data. The model purports that during the thermal relaxation stage of the energetic collision cascade, the initially identical defect structures induced by Ar+ and Cl+ implantation undergo different chemical reaction processes, leading to different Mg vacancy cluster distributions. Statistically, Mg vacancy clusters in the Cl+ prebombarded MgO are larger in size than those in Ar+ prebombarded MgO. The difference in these defect structures is the reason for the difference in the subsequent Ti diffusion in MgO as we observed previously [J. Chem. Phys. 115, 446 (2001)]. From this model it is derived that after diffusion for an extended time period, Ti diffusion in Cl+ prebombarded MgO is greater than that in Ar+ prebombarded MgO due to the complete release of monovacancies stored in the vacancy clusters. This trend is just opposite of the case of short-time diffusion as in the previous case. This prediction was conformed by using prolonged diffusion experiments.
Control of vortex breakdown by addition of near-axis swirl
Authors: Husain Hyder S. , Shtern Vladimir , Hussain Fazle
Published: January 2003

We present a new method for controlling vortex breakdown (VB) via addition of co- or counter-rotation near the axis. Co-rotation is adequate to totally suppress VB, whereas counter-rotation increases the number and size of VB “bubbles” and makes the flow unsteady. We study these effects in a closed cylindrical container, in which a rotating end disc drives the base flow; an independently rotating central rod (with rod radius≪disk radius) is employed to control VB. This flow, being free of ambient disturbances, is well suited for understanding both the VB mechanism and its control; the present work appears to be the first to study VB control. We develop and explain our control strategy using flow visualization and simple analytical reasoning. Our results suggest that an additional co- or counter-rotation, applied near the vortex axis, can be effective in suppressing or enhancing VB in practical flows.
The high-pressure chemistry of butadiene crystal
Authors: Citroni Margherita , Ceppatelli Matteo , Bini Roberto , Schettino Vincenzo
Published: January 2003

FTIR spectroscopy was applied to the study of the high-pressure reactivity of solid butadiene. The chemical transformation from the ordered phase I was observed to occur only above 270 K. The existence of a threshold temperature for the reaction reveals the central role of the lattice phonons in the activation of the transformation. Below 4.0 GPa only dimerization to 4-vinylcyclohexene occurs, while above this pressure an increasing amount of polymer forms with rising pressure. Room temperature kinetic studies have been performed at different pressures, from 2.1 up to 6.6 GPa, and the sign of the activation volume for the dimerization has been obtained. The dimerization reaction is found to follow a first-order mechanism. A reaction pathway for this process is proposed where the internal rearrangement of a diradical intermediate specie is identified as the rate limiting step. An acceleration of the dimerization process is observed above 4.0 GPa and is ascribed to the simultaneous polymer formation. This effect causes the laser assisted reaction, where a large amount of polymer is produced at any pressure, to be not as selective on polymerization as it is in the liquid phase, since also the dimerization rate is enhanced.
Theoretical calculations of the electroabsorption spectra of perylenetetracarboxylic dianhydride
Authors: Mazur Grzegorz , Petelenz Piotr , Slawik Michał
Published: January 2003

A three-dimensional analog of the Merrifield model is proposed to study excitons in solid perylenetetracarboxylic dianhydride (PTCDA). Its relevant parameters are estimated by independent calculations, and finally determined by fitting the experimental absorption and electroabsorption spectra of PTCDA films; the optimum values obtained from the fit correspond well with the calculated values. The results justify description of PTCDA excitons within a one-dimensional model, as proposed in the literature. The calculated spectra are generally in good agreement with the experimental ones, with the exception of the directional properties of the electroabsorption signal. A possible reason for this discrepancy is suggested. Generally, the results highlight the prominent role of charge-transfer excitons in the electroabsorption spectrum of PTCDA by showing the experimental features that are difficult to explain without invoking these states.
Common Hamiltonian structure of the shallow water equations with horizontal temperature gradients and magnetic fields
Authors: Dellar Paul J.
Published: January 2003

The Hamiltonian structure of the inhomogeneous layer models for geophysical fluid dynamics devised by Ripa [Geophys. Astrophys. Fluid Dyn. 70, 85 (1993)] involves the same Poisson bracket as a Hamiltonian formulation of shallow water magnetohydrodynamics in velocity, height, and magnetic flux function variables. This Poisson bracket becomes the Lie–Poisson bracket for a semidirect product Lie algebra under a change of variables, giving a simple and direct proof of the Jacobi identity in place of Ripa’s long outline proof. The same bracket has appeared before in compressible and relativistic magnetohydrodynamics. The Hamiltonian is the integral of the three dimensional energy density for both the inhomogeneous layer and magnetohydrodynamic systems, which provides a compact derivation of Ripa’s models.
Computer simulation of anisotropic diffusion in monolayer films in mica slit pores
Authors: Su Zhen , Cushman John H. , Curry Joan E.
Published: January 2003

Molecular dynamics computer simulations are used to study diffusion of monolayer octamethylcyclotetrasiloxane and cyclohexane films confined between atomically structured uncharged mica surfaces. Diffusion parallel to the walls is found to be anisotropic due to the influence of the atomically structured surfaces. If the surfaces are aligned perfectly the fluid occupies isolated regions of the pore space and diffusion is the same in all lateral directions and is a minimum. If one of the surfaces is shifted laterally in the x-direction by one-half unit cell diffusion is enhanced in the x-direction along conduits formed by the overlapping potential energy fields of the surfaces. This work augments earlier work by the authors and confirms that diffusion of a confined simple fluid in a nanoscale slit-pore is tunable in terms of direction and magnitude through control of the relative alignment of the surfaces.
Theoretical investigation of glycine–2Ben+ (n=0,1,2) complexes in gas phase: Origin of negative dissociation energies
Authors: Ai Hongqi , Bu Yuxiang , Chen Zhida
Published: January 2003

The negative dissociation energies (or positive binding energies) have first been found in seven different glycine–2Be2+ conformers, one glycine–Be2+Be+ complex, and one glycine–2Be2+ complex. For the seven glycine–2Be2+ conformers, the negative dissociation energies originate from the contributions of electrostatic, dipolar, charge transfer and deformed terms. All of these terms play important roles for the negative dissociation energy during separating one Be2+ from the corresponding complex. Also two dissociation energy barriers have been observed in the course of separating each of the two Be2+ ions from the most stable glycine–2Be2+ conformer. One barrier derives from the deformed effect and another is mainly from electronic effect. For the glycine–Be2+Be+, the positive binding energy (or negative dissociation energy) is also observed when Be+ ion interacts with the oxygen end of zwitterionic glycine. Binding energy contribution analysis (BECA) shows that it mainly stems from the electrostatic effect. For the glycine–2Be+ with two possible multiplicities, only the triplet state tautomer has positive binding energy. BECA indicates that its binding energy results from the contribution of the deformation energy, and from the spin repulsion of two single electrons over three different atoms of the glycine–2Be+ complex. In the course of studying these interesting binding energies, geometries of the seven glycine–2Be2+ conformers, five different glycine–2Ben+ complexes, and seven different glycine–2Ben+ (n=0, 1, or 2) complexes are optimized and characterized at HF(B3LYP)/6-31G* level. The results indicate that the most stable glycine–2Be2+ isomer in the seven glycine–2Be2+ complexes has a Cs symmetry, in which two Be2+ ions are bound to two oxygen ends of the zwitterionic glycine, respectively. For the five glycine–2Ben+ complexes with different valence states, which are yielded according to the coordination mode of the most stable glycine–2Be2+ complex, the geometries of three lower valence-state complexes suffer serious deformation due to the repulsion of lone pairs or parallel electron spin. The distance of two Be ions becomes longer and longer with the increase of their valence states in these complexes. For the separated species of these glycine–2Ben+ complexes, their characteristic geometries are presented and the binding energy of one glycine–Be2+ complex is calculated and compared with other theoretical values.
Water structure and dynamics in phosphate fluorosurfactant based reverse micelle: A computer simulation study
Authors: Senapati Sanjib , Berkowitz Max L.
Published: January 2003

We performed a molecular dynamics simulation on a system containing a water pool inside the reverse micelle made up of an assembly of phosphate fluorosurfactant molecules dissolved in supercritical carbon dioxide. The water molecules in the first solvation shell of the headgroup lose the water to water tetrahedral hydrogen bonded network but are strongly bonded to the surfactant headgroups. This change in inter-water hydrogen bonding in connection with the confined geometry of the reverse micelle slows down the translational and especially the rotational dynamics of water.
Theory for the rate of contact formation in a polymer chain with local conformational transitions
Authors: Zhou Huan-Xiang
Published: January 2003

I derive an expression for the rate of contact formation between two residues in a polymer chain when both residues undergo native to non-native conformational transitions. A contact can only form when the two residues are brought into contact by interresidue diffusion and are in the native conformations at the same time. The entropy of the chain connecting the two residues are accounted for by the potential of mean force for the interresidue distance. Both the equilibrium probabilities of the native conformations and the time scales of the transitions between the native and non-native conformations are important in determining the contact formation rate. For protein residues, transitions between native and non-native conformations occur in the picoseconds time scale. In comparison, the average time for traversing the distance of a few Å by interresidue diffusion is in the nanoseconds time scale. This separation of time scales between residue conformational transitions and interresidue diffusion ensures that the rate of contact formation is much higher than what is expected from the equilibrium probability for both residues to be in the native conformations.
Molecular dynamics simulations of ionic concentration gradients across model bilayers
Authors: Sachs Jonathan N. , Petrache Horia I. , Zuckerman Daniel M. , Woolf Thomas B.
Published: January 2003

To model a concentration gradient across a biomembrane, we have performed all-atom molecular dynamics simulations of NaCl solutions separated by two oppositely charged plates. We have employed the recently formulated three-dimensional Ewald summation with correction (EW3DC) technique for calculations of long-range electrostatics in two-dimensionally periodic systems, allowing for different salt concentrations on the two sides of the plates. Six simulations were run, varying the salt concentrations and plate surface charge density in a biologically relevant range. The simulations reveal well-defined, atomic-level asymmetries between the two sides: distinct translational and rotational orderings of water molecules; differing ion residency times; a clear wetting layer adjacent only to the negative plate; and marked differences in charge density/potential profiles which reflect the microscopic behavior. These phenomena, which may play important roles in membrane and ion channel physiology, result primarily from the electrostatics and asymmetry of water molecules, and not from the salt ions. In order to establish that EW3DC can accurately capture fundamental electrostatic interactions important to asymmetric biomembrane systems, the CHARMM force-field (with the corrected Ewald sum) has been used. Comparison of the results with previously published simulations of electrolyte near charged surfaces, which employed different force-fields, shows the robustness of the CHARMM potential and gives confidence in future all-atom bilayer simulations using EW3DC and CHARMM.
Thermodynamically consistent description of the work to form a nucleus of any size
Authors: Kashchiev Dimo
Published: January 2003

A thermodynamically consistent formula for the work W to form homogeneously a one-component gaseous, liquid, or solid nucleus is derived in the scope of the Gibbs theory of capillarity. This formula is applicable to nuclei constituted of whatever number of molecules, because it is valid in the entire range of conditions between the binodal and the spinodal (when such exists) of the nucleating system. Analysis is based on a newly introduced dividing surface called conservative, because its specific surface energy is independent of the nucleus size. The thermodynamically consistent formula for W accounts for the annulment of the nucleation work at the spinodal. For spinodal-unlimited systems it turns into the classical formula for W, thereby justifying the application of the latter to such systems even when the nuclei are of a few molecules only. It is shown that for systems with spinodal, classically, the nucleation rate is lower than that calculated with the aid of the thermodynamically consistent formula for W. The correction is practically only temperature-dependent and vanishes for spinodal-unlimited systems. Expressions are obtained for the excess or deficiency number Δn of molecules in the density fluctuation and for the number nC of molecules constituting the corresponding nucleus defined by the conservative dividing surface. These expressions are valid for any value of Δn and nC and reveal why, as found in experiments and computer simulations, the classical Gibbs–Thomson equation is able to predict the size of nuclei built up of less than a few tens of molecules. The general results are applied to homogeneous one-component nucleation of solids, liquids or gases under isothermal or isobaric conditions.
Thermocapillary migration of long bubbles in polygonal tubes. II. Experiments
Authors: Lajeunesse E. , Homsy G. M.
Published: January 2003

We study experimentally the thermocapillary migration of a long gas bubble in a horizontal pipe of rectangular cross section. An imposed axial temperature gradient produces a gradient of surface tension leading to a steady migration of the bubble towards the hotter region. The bubble velocity is found to be independent of bubble length for sufficiently long bubbles, and to vary linearly with the temperature gradient. For pipes of small vertical dimension, gravity is negligible and the measurements of the bubble velocity are in good agreement with the zero gravity theory of Mazouchi and Homsy [Phys. Fluids 13, 1594 (2001)]. In larger pipes, gravity is no longer negligible and the bubble is observed to move faster than that theory predicts. A simple calculation taking into account the combined effect of buoyant rise and thermocapillary stress accounts for these results.
Discovery of the optically forbidden S1–S transition of silylidene (H2C=Si)
Authors: Smith Tony C. , Evans Corey J. , Clouthier Dennis J.
Published: January 2003

The electronically forbidden Ã 1A2–X̃ 1A1 band system of jet-cooled silylidene (H2CSi and D2CSi) has been detected for the first time using laser-induced fluorescence (LIF) and stimulated emission pumping (SEP) techniques. The very weak, vibronically induced 401 and 301401 bands were detected by LIF along with the corresponding 601 and 301601 bands which gain intensity through excited state Coriolis coupling. SEP spectra, obtained by pumping the 000 band of the S2 state and stimulating transitions down to the S1 state through the allowed S2–S1 transition, revealed many more bands, including the 000 bands, which were studied at high resolution and rotationally analyzed. From the upper state rotational constants of H2CSi and D2CSi, the excited state structure was obtained as r0′ (SiC)=1.873(2) Å, r0′(CH)=1.099(5) Å, and θ0′(HCH)=113.9(3)°. The four lowest energy excited state vibrational frequencies of both isotopomers have also been determined. High level ab initio predictions of the ground and excited state properties of silylidene are also reported and found to be in good agreement with the experimentally determined values.
Primary charge separation in the bacterial reaction center: Validity of incoherent sequential model
Authors: Pudlak Michal
Published: January 2003

A description of electron transfer (ET) by the incoherent sequential model was employed to elucidate the unidirectionality of the primary charge separation process in bacterial reaction centers (RC). The model assumes that the vibrational relaxation of the medium modes is sufficiently fast and that the system relaxes to thermal equilibrium after each ET step. ET was investigated for 5-sites (molecules) arranged in two branches. Beginning at molecule 1, ET can proceed in two directions with each branch composed of two molecules. Analysis shows that the model can successfully explain the asymmetry of primary electron transfer both in the wild type and several mutants of Rb capsulatus RC. In these cases the dependence of ET asymmetry on temperature was also evaluated. It was shown that in order to obtain the correct temperature dependence of ET asymmetry in the mutants, the superexchange mechanism operating in parallel with the sequential process must be used.
Full configuration interaction potential energy curves for breaking bonds to hydrogen: An assessment of single-reference correlation methods
Authors: Dutta Antara , Sherrill C. David
Published: January 2003

Several approximate correlation methods have been assessed for bond breaking reactions in BH, HF, and CH4 by comparison to the full configuration interaction limit. Second-order Møller–Plesset perturbation theory, coupled-cluster singles and doubles (CCSD), coupled-cluster with perturbative triples [CCSD(T)], and the hybrid density-functional method Becke three parameter Lee–Yang–Parr have been considered. Both restricted and unrestricted references have been used along with the basis sets aug-cc-pVQZ, 6-31G**, and 6-31G* for BH, HF, and CH4 respectively. Among the methods considered, unrestricted CCSD and CCSD(T) provide potential energy curves which are the most parallel to the benchmark full CI curves, but the nonparallelity errors are fairly large (up to 6 and 4 kcal mol−1, respectively). Optimized-orbital coupled-cluster methods provide superior results but nevertheless exhibit approximately the same maximum errors.
Molecular structure, vibrational frequencies, energetics, and excited states of the HOONO+ ions
Authors: Watts John D. , Francisco Joseph S.
Published: January 2003

Equilibrium geometries have been optimized and harmonic vibrational frequencies obtained for neutral HOONO and its cation employing quadratic configuration interaction methods and correlation-consistent basis sets. The lowest energy structure of HOONO+ found is a planar conformer on the A'2 potential-energy surface with a cis–trans arrangement [τ(OONO)=0° and τ(HOON)=180°]. This is quite the opposite from neutral HOONO, which prefers a cis–cis arrangement because of hydrogen bonding. The adiabatic ionization potential for HOONO is predicted to be 260.0±1 kcal mol−1 (11.3 eV) at the complete basis set limit. A planar ion–molecule complex formed from HO2 and NO+ was located on the A"2 surface. The binding energy of this complex relative to HO2 and NO+ is estimated to be 18.1±1 kcal mol−1 at the complete basis set limit. Excited states of the HOONO+ ion were also calculated with quasi-restricted Hartree–Fock and unrestricted Hartree–Fock coupled-cluster methods including connected triple excitations.
Kinetics of H2 (D2) desorption from a Ge(100)-2×1:H (D) surface studied using scanning tunneling microscopy and temperature programmed desorption
Authors: Lee Jun Young , Maeng Jae Yeol , Kim Ansoon , Cho Young Eun , Kim Sehun
Published: January 2003

The kinetics of H2 (D2) desorption from a Ge(100)-2×1:H (D) surface was studied using scanning tunneling microscopy (STM) and temperature programmed desorption (TPD). Inspection of STM images of surfaces at the saturation coverage of H (D) (θH(D)≃1.0 ML) revealed a 2×1 monohydride (monodeuteride) phase in which most H (D) atoms were paired on Ge-dimers. By counting the sites of H2 (D2) desorption in STM images taken after desorption of H2 (D2) at temperatures in the range Ts=500−550 K, the desorption of H2 (D2) was found to follow first order kinetics with an activation energy of Ed=1.65±0.1 eV (1.65±0.1 eV) and a pre-exponential factor of νd=(2.7±0.5)×1013 s−1 [(1.2±0.5)×1013 s−1]. These values of Ed and νd were used to simulate TPD spectra for the desorption of H2 (D2) from a Ge(100)-2×1:H (D) surface. The simulated spectra were in good agreement with the experimental TPD spectra. In contrast to the surfaces with saturated H coverage, which are characterized by pairs of H atoms on Ge-dimers, at the low H coverage of θH≃0.05 ML unpaired H atoms as well as paired H atoms were observed on the Ge-dimers on the surface, causing the desorption process to follow second order kinetics. At Ts∼300 K, the singly occupied dimers (SODs) appear to be favored over doubly occupied dimers (DODs). However, upon increasing the temperature (Ts) from 300 to 500 K, most SODs were rapidly converted into the thermodynamically favored DODs by the migration of H atoms. On the other hand, it is observed that even above Ts∼500 K, the onset temperature for H2 desorption from DODs, a non-negligible number of SODs remain on the surface due to the large entropic barrier to pairing. These results suggest that H adsorption in the low coverage is strongly influenced by the energetics of the pairing of H atoms.
The effect of outer cylinder rotation on Taylor–Couette flow at small aspect ratio
Authors: Schulz A. , Pfister G. , Tavener S. J.
Published: January 2003

We present the results of a combined experimental and numerical study of Taylor–Couette flow where both inner and outer cylinders rotate. Excellent quantitative agreement has been obtained between finite-element calculations and experimental measurements for a range of aspect ratios and rotation rates. Counter-rotation was found to enhance the breaking of the reflectional symmetry about the midplane of the apparatus, corotation to suppress symmetry breaking. For the region of parameter space explored, increasing the corotation of the outer cylinder had a qualitatively similar effect to increasing the aspect ratio, and vice versa.