bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-localized states in chain molecules of finite lengths
Authors: Dinter Manfred
Published: February 2003

Chain molecules such as aggregates of pseudoisocyanine dye have long been known to develop a very high and narrow peak at the low energy end of the absorption spectrum commonly regarded as a typical indicator for aggregation of long polymers. Contrary to the usual interpretation of this so-called J band by an in-phase excitation of transition dipoles along the chain (giant dipole), the present publication puts forward the thesis that, in chains of finite length, the J band rather originates from bound states due to strong exciton–phonon interaction. These polaronic states (which bear a close relationship to Holstein’s and Davydov’s solitons) are situated immediately below the excitonic continuum. They are visible in light scattering experiments above a chain length threshold L>L0, where L0 is determined by electronic and elastic energies and the magnitude of the exciton–phonon coupling. These length-dependent effects are smeared out in solutions on account of the presence of polymers with variable lengths with distributions which depend on concentration and temperature and have been derived in a prior publication.
Sub-Doppler laser spectroscopy of SO2 in a supersonic beam
Authors: Kullmer R. , Demtröder W.
Published: February 2003

Sub-Doppler excitation spectra of the E band of SO2 around 304 nm have been measured with a spectral resolution down to 10 MHz, by crossing the frequency doubled output beam of a single mode cw dye laser perpendicularly with a supersonic molecular SO2 beam. Although the spectral line density is so large that the mean line separation becomes smaller than the Doppler width, there is no true background continuum. The analysis of the spectra proves that several upper vibrational levels are excited within the E band. A model explaining the observed phenomena is discussed.
Optical spectroscopy of ordered dyes in aqueous lyotropic nematic liquid crystals
Authors: Kuzma M. R. , Skarda V. , Labes M. M.
Published: February 2003

Aqueous lyotropic nematic liquid crystals can be uniformly ordered by magnetic fields of ∼20 kG in flat glass capillaries up to ∼1 mm in path length. Once removed from the field the orientation decays very slowly, and optical spectra of the oriented samples can easily be recorded in conventional instruments. In this manner, the visible spectra of a substituted porphine (TPPS4) and the dye Congo Red were recorded in three nematic lyotropics which consist of rod-shaped micelles. The polarization of the absorption bands can easily be assigned. TPPS4 orients with its plane perpendicular to the optic axis of the lyotropic rods with a low order parameter, and the long axis of Congo Red also orients perpendicular to the optic axis with a considerably higher order parameter. In the nematic system (potassium laurate/decanol/D2O) addition of TPPS4 at a sufficiently high concentration stabilizes a disk-like nematic phase.
Deuterium nuclear quadrupole coupling constants in vibrationally excited C2HD: Evidence for electron reorganization
Authors: Marshall Mark D. , Klemperer W.
Published: February 2003

The l-doubling spectra of monodeuteroacetylene have been obtained in the ν4=1 (C–D bend) and ν5=1 (C–H bend) states of the molecule with resolution sufficient to determine the deuterium nuclear quadrupole coupling constants. The spectroscopic constants obtained from the J=1 rotational level are UFRULE2 ν4=1 ν5=1 UFRULE1 eqQDaa (kHz) 207.(6) 221.(2) eqQDbb−eqQD cc (kHz)  −31.(22)   −6.(4) CD (kHz)   −6.(2)   −1.5(3) CH (kHz) ⋅⋅⋅  −20.0(5) μ (D)   0.023 59(11)   0.056 24(3) q (MHz) 133.050 6(9) 105.699 3(1) UFRULE2 These results are interpreted in terms of the electron distribution surrounding the deuterium nucleus and are shown to be inconsistent with the assumption of a cylindrical distribution about the C–D bond axis in these states. This deviation from the symmetry appropriate for the molecule at equilibrium is shown to arise from a distortion in the cross section of the electron distribution that is unaccompanied by changes along the bond axis.
The 1S level of Pr3+ in LaCl3
Authors: Rana R. S. , Cordero-Montalvo C. D. , Bloembergen N.
Published: February 2003

The 1S0 level of Pr3+:LaC13 has been located in the wavelength region inaccessible to the single-photon absorption method. It was observed at 46 450.6±5 cm−1 by using the two-photon absorption technique. All 13 levels of the 4f2 configuration are now known with high precision and a new parametric fit of the ground configuration levels is presented. Since the reported position of this level in the free ion is doubtful, a suggestion is made on finding the correct value.
Investigation of several low-lying levels of X 2Π NCO using argon laser excited fluorescence
Authors: Wong K. N. , Anderson W. R. , Kotlar A. J. , Vanderhoff J. A.
Published: February 2003

The laser excited fluorescence spectrum of NCO from an atmospheric pressure CH4/N2O/N2 flame is reinvestigated with a more sensitive apparatus than used previously. The NCO is pumped from the X 2Π (1,01,0) level to the A 2Σ+ (0, 00, 0) level. Emissions to (0, 01, 0)2Π, (1, 01, 0)2Π, (0, 01, 1)2Π, and (0, 10, 0)2Σ+ in the X state are observed. The previous tentative assignment of pumping transition as Q231 is confirmed. The confirmation of pumping transition solidifies our earlier interpretation that excited state spin relaxation in the flame is much faster than electronic quenching. In addition, analysis of the fluorescence spectra yields the first reported constants for the X(1, 01, 0)2Π level and spin splitting for X(0, 01, 1)2Π level in the gas phase.
Unimolecular decay paths of electronically excited species. V. The Ã 2B1 state of H2CO+
Authors: Barbier C. , Galloy C. , Lorquet J. C.
Published: February 2003

The formaldehyde ion in its first excited state (Ã 2B1) dissociates to CO++H2 by an electronically adiabatic mechanism. Ab initio calculations reveal, however, that the reaction path corresponds to a low energy trough around a conical intersection between the Ã 2B1/2A′ and a 2A1/2A′ states. This path is characterized by an energy barrier of 0.8 eV. The reaction mechanism is intrinsically multidimensional. Curvature of the reaction path brings about a strong coupling between the coordinate and the orthogonal degrees of freedom. For this reason, the final energy partitioning does not reflect the internal energy distribution at the top of the potential barrier. Energy is presumably released preferentially as translation and rotation. The criterion for reactivity is not purely energetic: the genuine bottleneck is not located at the top of the energy barrier but rather in the region where curvature of the reaction path is largest. The  Ã 2B1 state also dissociates to HCO+ +H fragments. A low-lying quartet state (ã 4B2) was studied but was found to play no role in the reaction. Direct coupling between state Ã and the dissociation continuum of the ground state X̃ is suggested.
Radiative rates of singlet–triplet transitions in nitrogen halide diatomics
Authors: Coombe R. D. , Van Benthem M. H.
Published: February 2003

Near infrared emissions from the a 1Δ→X 3Σ− transitions in NCl and NBr are observed following pulsed laser photolysis of gaseous ClN3 and BrN3, respectively. From the time decay of the NCl emission, the radiative rate of the a→X transition is found to be (4.87±0.37)×102 s−1. Rate constants for collisional quenching of NCl(a 1Δ) by ClN3 and N2 are determined to be (1.27±0.13)×10−13 and 5×10−16 cm3 s−1, respectively. From the NBr emission, the radiative rate of the a→X transition in this molecule is found to be (1.24±0.34)×103 s−1, and the rate constant for collisional quenching of NBr (a 1Δ) by BrN3 is (1.76±0.04)×10−11 cm3 s−1. The radiative rates of the a 1Δ→X 3Σ− and b 1Σ+→X 3Σ− transitions in NF, NCl, and NBr are discussed in terms of spin-orbit mixing of states of the π4π*2, π3π*3, and π4π*σ* electronic configurations. Approximate spin-orbit matrix elements for the individual interactions are calculated based on one electron integrals. Although the calculations present a reasonable model for the a→X transitions, the results conflict with spectroscopic data for the b→X systems.
Observation of the ν1 fundamental band of H2D+
Authors: Amano Takayoshi , Watson J. K. G.
Published: February 2003

The ν1 fundamental band of H2D+ has been observed in absorption in a discharge with a difference frequency laser spectrometer in the range 2830–3200 cm−1. The 27 observed lines are assigned and the transition wave numbers are fit to an effective Hamiltonian to determine the molecular constants. The band origin (2992.488±0.016 cm−1) and the rotational constants are in good agreement with those from ab initio calculations. The dependence of the concentration of H2D+ on the D2/H2 mixing ratio, which can be used to identify absorption lines of this ion, is discussed.
Tunneling of methyl groups in toluquinone: Dependence on the electronic state of the molecule
Authors: Clough S. , Heidemann A. , Lichtenbelt J. H. , Paley M. N. J. , Silbey R. , Trommsdorff H. P. , Wiersma Douwe A.
Published: February 2003

The torsional frequency and the tunneling splitting of the methyl group of crystalline toluquinone are reported for different electronic states of the molecule. Whereas in the ground state both values can be derived from a conventional cos 3φ potential with a barrier height of approximately 8 kJ/mol, the values in the lowest excited triplet state cannot be reconciled with such a simple potential. It is suggested that a chemical interaction between the methyl protons and the adjacent oxygen of the excited carbonyl group is responsible for the modification of the potential. Numerical calculations based on a simple modeling of this chemical interaction support this idea.
Absorption and emission spectroscopies of homogeneous and inhomogeneously broadened multilevel systems in strong light fields
Authors: Dick B. , Hochstrasser Robin M.
Published: February 2003

A method is introduced to calculate for a model set of molecular levels the spectral line shapes expected for a variety of conventional laser experiments including absorption, hole burning, fluorescence line narrowing, and Raman scattering. The method allows the incident laser field to have arbitrary intensity. Furthermore, the effects of model Gaussian or Lorenzian inhomogeneous distributions are readily incorporated. Earlier results for a two-level system are easily obtained and new results are presented for inhomogeneously broadened two and three level systems, and for the effects of pure dephasing on the strong field spectra. In particular we have described the differences between fluorescence and Raman in strong fields, and the effect of strong fields on the spontaneous emission of inhomogeneously broadened transitions. Some predictions are made regarding line narrowing experiments in the strong-field limit.
Matrix-isolation studies on metal coordinated oxyanions. The shape of molecular MClO4, MClO3, MReO4, and EuWO4 systems
Authors: Bencivenni L. , Nagarathna H. M. , Gingerich K. A. , Teghil R.
Published: February 2003

Alkali-metal perchlorates (MClO4), chlorates (MClO3), perrhenates (MReO4), and EuWO4 were investigated with the aid of matrix-isolation IR spectroscopy. The Raman spectra of the MClO4 and MReO4 molecules were also measured in inert matrices. 18O-substitution experiments were carried out on Li 35ClO4, K 35ClO4, Cs 35ClO3, KReO4, and EuWO4 in order to provide the assignment of the observed spectra and to establish the molecular structure of these molecules in the vapor phase. These experiments indicate a C2v bidentate structure for all the MXO4 molecules. The ClO−4 and ReO−4 anions are slightly distorted tetrahedrons with bond angles close to 109°. The WO=4 anion is a distorted tetrahedron with the OWO bond angles equal to 86° and 109°. Alkali chlorates MClO3 are species of C3v symmetry with the metal cation placed on the C3 axis of the ClO−3 pyramidal anion.
New vibrational assignments for the autoionization bands of O2 based on isotope shifts
Authors: Nishitani Eisuke , Tanaka Ikuzo , Tanaka Kenichiro , Kato Tatsuhisa , Koyano Inosuke
Published: February 2003

The relative photoionization efficiency curves of 16O2, 16O18O, and 18O2 have been obtained in the 660–1035 Å region. Based on the detailed analysis of the observed isotope shifts, the autoionizing peaks in the 855–1010 Å region were newly assigned. The strong peaks in the 900–1010 Å region, which had been classified as belonging to four different (H, H′, M, and M′) progressions, were assigned to a single progression of the 3sσg Rydberg state (H 3Πu) converging to O+2(a 4Πu). Similarly, the peaks in the 855–925 Å region were assigned to a single progression of the 3sσg Rydberg state (J 3Πu) converging to O+2(A 2Πu) . Molecular constants of these two states have been determined as follows, all in the unit of cm−1 except δ and re: H 3Πu; 3sσg, J 3Πu; 3sσg, D0=28 249±26, D0=21 832±33, ωe=1058.5±3.0, ωe=1 010.0±5.5, ωexe=10.56±0.20, ωexe=3.70±0.39, T0=99 639±10, T0=106 053±17, δ=1.096±0.001, δ=1.133±0.002. re=1.37±0.01 Å.
Induced absorption spectra of the infrared fundamental band of molecular deuterium at 77 K: S1( J)+S( J) transitions
Authors: Gillard P. G. , Prasad R. D. G. , Reddy S. Paddi
Published: February 2003

The collision-induced spectra of the fundamental band of normal D2 in the high frequency region 3200–3700 cm−1 were recorded for gas densities in the range 80–140 amagat at 77 K with a 2 m absorption cell. The contribution to the intensity of the band in this region comes from the high frequency wings of quadrupolar transitions S1( J) and Q1( J)+S0( J) with J=0 and 1, and from the group of transitions S1(2) and Q1( J)+S0(2) with J=0, 1, and 2 as well as from the relatively weaker double rotational transitions of the type S1( J)+S0( J); the latter transitions arise from the intermolecular interaction between the anisotropic component of the polarizability of one of the colliding pairs of molecules and the quadrupole field of the other. The experimental profiles were analyzed by assuming appropriate line shape functions and using the theoretical matrix elements of the quadrupole moment, isotropic polarizability, and anisotropy of polarizability of the D2 molecule. From this analysis the characteristic half-width parameters δq2 and δq4 of the quadrupolar transitions and the binary and ternary absorption coefficients of the S1( J)+S0( J) transitions have been obtained. The experimental value of the binary absorption coefficient of S1(0)+S0(0) is (2.2±0.1)×10−9 cm−1 amagat−2 and the corresponding theoretical value is 1.53×10−9 cm−1 amagat−2.
Effects of solvent on TMP photophysics. Transition from no barrier to barrier case, induced by solvent properties
Authors: Sundström Villy , Gillbro Tomas
Published: February 2003

The dynamics of the radiationless relaxation of triphenylmethane (TPM) molecules in the n-alcohols methanol to octadecanol have been studied with picosecond absorption recovery techniques as a function of viscosity, temperature, and wavelength of the exciting and analyzing light. It is shown that the solvent dependence of the relaxation rate in TPM molecules cannot, as is usually done, be described by a viscosity dependence only. In going through the n-alcohol series the excited state potential surface changes from a practically flat one (E0=0) in methanol to a surface having a definitive potential barrier (E0≊15 kJ mol−1) in the higher alcohols. This variation of the potential surface implies that the relaxation is largely controlled by rotational diffusion in methanol and ethanol whereas it is mainly controlled by the potential barrier in the higher alcohols. When the viscosity dependence of the relaxation rate is obtained, by compensating for the contribution from the potential barrier, a turnover behavior such as that predicted by activated barrier crossing theories, is observed. We have fitted the expression of Skinner and Wolynes [J. Chem. Phys. 69, 2143 (1978)] to our experimental results in the solvents where a barrier exists, and obtain a frequency of 550 cm−1 at both the well and the top of the potential. The fit is consistent with a friction that is lower than that corresponding to hydrodynamic slip boundary conditions. A decrease in solute–solvent friction relative the hydrodynamic value is also observed in going from small to large solvent molecules. This effect is attributed to a decreasing solute/solvent molecular volume ratio and to the structure of the TPM molecule which could prevent large solvent molecules from coming into close contact with the relaxing groups. In addition to these features we discuss the wavelength dependence and previously suggested change from single- to bi- and multiexponential decay of the relaxation kinetics. The experimental observations are also discussed in relation to the recent theory of Bagchi et al. [J. Chem. Phys. 78, 7375 (1983)].
The effects of collision energy and vibrational excitation on H+2, HD++He reactions
Authors: Turner T. , Dutuit O. , Lee Yuan T.
Published: February 2003

An experimental study of proton and deuteron transfer in H+2 + He and HD+ + He has been carried out as a function of kinetic and vibrational energy. The data gives evidence that at lower kinetic energies, the spectator stripping mechanism indeed plays an important role when H+2 or HD+ is vibrationally excited. The H+2 (v=0) reaction has a much smaller cross section than the v=1–4 reactions and seems to go through intimate, small impact parameter collisions involving all the atoms. Investigation of the competition between both the proton and deuteron transfer channels for the HD+ case, shows that vibrational enhancement towards forming the HeD+ product falls off sooner with increasing kinetic energy than does the HeH+ product again in accordance with the spectator stripping model. The higher yield for HeH+ production at both higher vibrational levels of HD+ and at lower kinetic energy and the behavior of translational energy dependence of HeH+ seems to indicate the importance of the induced orientation of HD+ during the collision with He. Because of the displacement of the center of mass from the center of charge in HD+, the charge induced dipole interaction between He and HD+ tends to swing the H atom more towards He during the approach of He and HD+.
Semiclassical investigation of electron transfer reactions in H+2/H2, H+2/D2, D+2/H2, and D+2/D2 collisions
Authors: Lee Chyuan-Yih , DePristo Andrew E.
Published: February 2003

The semiclassical energy conserving trajectory method has been used to determine state-to-state cross sections for the electron transfer reactions, H+2/H2, and isotopic variants. Accurate diabatic interactions were utilized. Calculations were performed for several reactant orientations, initial ion vibrational states, and relative kinetic energies. The state-to-state cross sections are used to test three simple models: an exponential gap correlation procedure, a Franck–Condon exponential gap correlation procedure, and a two-state calculational method. All three are found to be inadequate, and the failure is ascribed to the strongly coupled multistate nature of symmetric electron transfer reactions. We predict the variation of relative total electron transfer cross section with initial ion vibrational state for all four systems. The D+2/H2 system exhibits very unusual behavior at low kinetic energies.
Phase transitions in metal perchlorate hydrates: The supposed hydrate-to-pseudohydrate transformations
Authors: Falk Michael , Seto Ping F. , White Mary Anne
Published: February 2003

The infrared spectrum of well dried Cd(C1O4)2⋅6H2O showed no abrupt changes near 248 K, such as have been observed by Patel and Bist and attributed to a hydrate-to-pseudohydrate transformation. It is suggested here that the spectral changes, which Patel and Bist also found in the spectra of Hg(C1O4)2⋅6H2O and Zn(C1O4)2⋅6H2O, are in fact due to the crystallization of moisture adhering to their samples.
Ab initio studies on the geometrical and vibrational structures of polymers
Authors: Teramae Hiroyuki , Yamabe Tokio , Imamura Akira
Published: February 2003

The geometrical structures and vibrational spectra of all-trans, cis-transoid and trans-cisoid polyacetylene, and all-trans-polymethineimine have been calculated using the energy gradient scheme for one-dimensional polymers based on the ab initio crystal orbital method. The vibrational spectra of all-trans-polyacetylene reported here are in good agreement with the experimental results. We have proposed a reassignment of the Raman spectra of cis-transoid- polyacetylene. The vibrational spectra of the trans-cisoid polyacetylene are calculated theoretically. The bond alternant structure of all-trans-polymethineimine is more stable than the equidistant one, and the vibrational spectra are calculated for this structure.
A proposal for the proper use of pseudopotentials in molecular orbital cluster model studies of chemisorption
Authors: Bagus Paul S. , Bauschlicher Charles W. , Nelin Constance J. , Laskowski Bernard C. , Seel Max
Published: February 2003

The interaction of CO with Cu5, Ni5, and Al4 are treated as model systems for molecular adsorption on metal surfaces. The effect of the use of pseudopotentials for the metal atoms is studied by considering three types of clusters. In the first case, all of the metal electrons are explicitly included in the wave function; an all electron (AE) treatment. In the second case, the metal atom which directly interacts with the CO is described by as AE but the remaining metal atoms include a pseudopotential for their core electrons. Finally, in the third case, all of the metal atoms in the cluster have a pseudopotential treatment for the core electrons. The AE cluster results are taken as reference values for the two pseudopotential treatments. The mixed cluster results are in excellent agreement with those of the all AE clusters; however, the results for the all pseudopotential cluster of Ni5CO or of Cu5CO are qualitatively different. The pseudopotential treatment for all of the metal atoms often leads to results that contain serious errors and it is not a reliable approach.
Symmetric and nonsymmetric tricritical points in liquid sulfur and ‘‘living polymer’’ solutions
Authors: Wheeler John C.
Published: February 2003

The dilute n→0 vector model recently used to model the phase equilibria in sulfur solutions and living polymers possesses a nonsymmetrical tricritical point, of the sort found in three- and more-component solutions, at a small nonzero value of the magnetic field as well as the symmetric tricritical point at zero field. This has interesting consequences for the phase diagrams of both living polymers and sulfur solutions and suggests a resolution of a number of discrepancies between the earlier (zero field) theory of Scott and experiments on sulfur solutions.
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o description of large amplitude motions in solid N2. I. Librons in the ordered α and γ phases
Authors: Jansen A. P. J. , Briels W. J. , van der Avoird Ad
Published: February 2003

Starting from an ab initio intermolecular potential, we have calculated the mean field states for the librations in the ordered α and γ phases of solid N2, using a basis of spherical harmonics up to lmax=12. The correlation between the mean field solutions was then taken into account via a libron model based on the random-phase approximation or time-dependent Hartree method. The calculated librational frequencies are rather accurate, showing that the discrepancies in earlier results with the ab initio potential are mainly due to the breakdown of (quasi-)harmonic models for the librations, even in the ordered phases.
Solvation and dielectric dispersion in optical electron transfer
Authors: Delahay Paul , Dziedzic Andrew
Published: February 2003

The effect of dielectric dispersion of the solvent on the energetics of optical electron transfer is determined quantitatively by variations of the free energy of solvation of the species being photoionized. The solvation free energy varies because the solvent polarizability in the inner-sphere region of the photon absorbing species changes with photon energy on account of dispersion. The solvation free energy is computed for a varying polarizability of the solvent in the inner-sphere region and a fixed nuclear configuration of the solvent. The following interaction energies are considered: charge–induced dipole, dipole–induced dipole, induced dipole–induced dipole, formation of induced dipoles, solute–solvent London dispersion, solvent–solvent London dispersion, and solute–solvent and solvent–solvent Born repulsion. The change of solvation free energy in aqueous solution is computed in the 7 to 11 eV range from data on the refractive index of water obtained by reflectance spectroscopy. The theory accounts quantitatively for the effect of dispersion on photoelectron emission by aqueous solutions of anions, cations, and molecules.
Dynamical atom/surface effects: Quantum mechanical scattering and desorption
Authors: Kosloff R. , Cerjan Charles
Published: February 2003

Desorption and scattering of a helium atom from dynamic surfaces are studied using a generalized Langevin equation formalism for the bulk solid and time dependent quantum mechanical propagation of the helium. The motion of the bulk solid enters the Schrödinger equation as a time dependent potential coupling the solid surface to the atom. The propagation of the atomic wave packet is then followed in coordinate space using a Fourier transform technique to evaluate the kinetic energy operator. An attenuating grid is used to remove the wave packet in the asymptotic region thus permitting stable calculations for long duration times. Rates for one dimensional desorption from tungsten as a function of temperature are computed which display a change in mechanism. Three dimensional scattering from platinum at two temperatures shows significant nonspecular amplitude. These results indicate the utility of this time dependent technique.
Experimental observation of the negatively charged water dimer and other small (H2O)−n clusters
Authors: Haberland Hellmut , Ludewigt Christoph , Schindler Hans-Georg , Worsnop Douglas R.
Published: February 2003

Beams of (H2O)−n and (D2O)−n have been produced by injecting low energy electrons into a supersonic expansion of water and heavy water seeded in rare gases. Clusters with n≥2, with the exception of n=4, have been observed. The size distribution can be separated into three groups (n=2, n=6–7, and n≥10), which may be associated with different types of electron binding. The n<10 result gives a new lower limit for the number of water molecules necessary to bind an electron; the n≥10 correspond to the n=11 threshold observed earlier in pure H2O expansions.
The energy of the lowest triplet state of gas phase benzene
Authors: Sharpe Steven , Johnson Philip
Published: February 2003

The 3B1 state in benzene was observed in a supersonic beam by using one-photon ionization. (AIP)
A simple DWBA (‘‘Franck–Condon’’) treatment of H-atom transfers between two heavy particles
Authors: Lopez Vicente , Babamov Vasil K. , Marcus R. A.
Published: February 2003

A simple DWBA (Franck–Condon) method for calculating the probability of transferring a light particle between two heavy ones in a collinear collision at energies below and around the reaction threshold is presented. The region is the important one for the thermal reaction rates. The method is tested for two different model LEPS surfaces for H-atom transfer with moderately high barriers. The results are in good agreement with those of accurate multichannel calculations.The transition probability is calculated as an overlap integral over the reactants’ and products’ wave functions and the interaction potential. The reactants’ and products’ wave functions are calculated from their respective distortion potentials as one-term adiabatically separable approximations. Both the distortion potentials and the interaction potentials are extracted straightforwardly from the LEPS surface. The novel feature of the approach is that for the first time accurate results for the absolute values of the reaction probability are obtained from a simple overlap of single-channel approximate wave functions obtained directly from the respective parts of the potential energy surface for the reaction.
Translational drag coefficients of assemblies of spheres with higher-order hydrodynamic interactions
Authors: Phillies George D. J.
Published: February 2003

Calculations were made of the anisotropic translation drag coefficients of rigid assemblies of spheres in a variety of arrays, including lines, circular equilateral polygons, disks (polygons with a central sphere), and stacked squares. The objective was to compare results obtained using polynomial expansions for the two-body hydrodynamic interaction tensor truncated at the (a/r)1, (a/r)3, (a/r)5, and (a/r)7 levels. Calculations were also made with the three- and four-body hydrodynamic interaction tensors recently obtained by Mazur and van Saarlos, thereby examining the relative importance of two-, three-, and four-body interactions. There are substantial cancellations between terms of order (a/r)5 and (a/r)7, and between the three- and four-body hydrodynamic interactions. For the arrays studied here the Rotne–Prager [two-body, (a/r)3] hydrodynamic interaction tensor gives results which are at least as satisfactory as the results obtained from the full Mazur–van Saarlos [four-body, (a/r)7] interaction tensors.
Modified hypernetted chain approximation for a two component charged hard sphere system
Authors: Caccamo C. , Malescio G. , Reatto L.
Published: February 2003

The symmetric two component system of charged hard spheres is studied in the molten salt regime on the basis of a modified hypernetted chain (MHNC) equation. The two bridge functions E++(r) and E+−(r) are modeled in terms of the bridge function of hard spheres with two different diameters S++ and S+−, respectively. Unequal values for S++ and S+− lead to a significant improvement for thermodynamic and structural quantities with respect to HNC and RHNC results. However the radial distribution function for like charges is still not quantitatively correct.
Two particle cluster calculation of the binodal and spinodal in ternary mixtures of the symmetrical type
Authors: Van der Haegen R. , Stroobants A.
Published: February 2003

The binodal and spinodal for demixing in ternary mixtures of the symmetrical type are calculated using the two-particle cluster approximation. It is found that the width of the metastable region and the two phase area in the phase diagram are significantly smaller than as predicted by regular solution theory. Also contrary to the mean-field result the binodal is not only function of the interaction between dissolved molecules but depends also on the interaction between dissolved and solvent molecules. Consequently, the same conclusion holds for the calculated diminution of the critical dissolution temperature of the binary mixture when introducing a small amount of a third component.
Nascent internal energy distributions of MgH produced in the reaction of Mg(3s3p 1P1) with a variety of polyatomic molecules
Authors: Breckenridge W. H. , Umemoto H.
Published: February 2003

Nascent rotational quantum state distributions of MgH(v=0,1) produced in the reactions of excited Mg(3s3p 1P1) with a variety of polyatomic molecules have been determined using the laser pump-and-probe technique. The distributions are generally bimodal, with one component peaked at low rotational energy and another component at high values of the rotational quantum number N. Except for (CH3)2O, and (C2H5)2O, which produced very little rotationally excited MgH, all compounds with C–H, N–H, and or O–H bonds showed microscopic branching ratios for the ‘‘high-N’’ component of 0.5±0.1. For the reactants SiH4, GeH4, and PH3, the high-N branching ratio was ≥0.9. The results are interpreted in terms of competition between side-on, insertive, and end-on, abstractive attack of the reagent bonds. Little vibrational energy was found in MgH product for any molecule, consistent with extremely ‘‘late’’ energy release for these heavy–light–heavy kinematic conditions. The results are compared to those from similar studies of the reactions of O(3P), O(1D), and F(2P).
The infrared spectrum of KH
Authors: Haese Nathan N. , Liu Di-Jia , Altman Robert S.
Published: February 2003

Reported here is the first observation of the infrared spectrum of KH. Fundamental bands and first hotbands of the 39KH and 41KH isotopic forms were measured at high resolution using a diode laser based spectrometer. An ac glow discharge through potassium vapor and hydrogen gas was used to produce KH. A combined isotopic Dunham coefficient analysis was used to fit all the spectra, with the Dunham coefficients for 39KH coming out as Y10=985.6714(30) cm−1, Y20=−14.9013(10) cm−1, Y01=3.416 40(10) cm−1, Y11=−0.085 313(26) cm−1, Y21=5.41(60)×10−4 cm−1, Y02=−1.6354(36)×10−4 cm−1, Y12=1.13(10)×10−6 cm−1, Y03=7.6(8)×10−9 cm−1, (quoted at 2σ error limits). A bond length of 2.241 152(16) Å and a Dunham corrected value for ωe of 986.0505(30) cm−1 are obtained. The pressure broadening of KH by H2 and the chemistry of KH formation in the glow discharge plasma are also discussed.
Tridiagonal Fermi resonance structure in the IR spectrum of the excited CH chromophore in CF3H
Authors: Dübal Hans-Rolf , Quack Martin
Published: February 2003

The absorption spectrum of trifluoromethane has been recorded between 900 and 14 000 cm−1 with resolutions between 0.004 and 0.5 cm−1 (pressure broadened). 22 bands were assigned as arising from the interacting CH stretching and bending manifolds, which account for most of the absorption in the overtone region. The results can be understood quantitatively with an effective, tridiagonal many-level Fermi resonance Hamiltonian. The experimental and theoretical results are summarized in Table II. The Hamiltonian is given in Table III and shows a very large stretching–bending interaction constant ‖ksbb‖=106 cm−1, which is even larger than the diagonal anharmonic constant for the stretching vibration ‖x′ss‖=62 cm−1. This leads to extensive vibrational redistribution between stretching and bending motions at high levels of excitation. The time dependent redistribution is calculated with the spectroscopic Hamiltonian. A rotational analysis is presented for some of the bands involved in the Fermi resonance. The effect of the Fermi resonance on hot bands is investigated using the same Hamiltonian in comparison with experiment. The results are discussed in relation to the universal local dynamics of the isolated alkyl CH-stretching chromophore and in relation to the vibrational dynamics of highly excited polyatomic molecules as a function of certain elements of molecular structure.
Photoabsorption cross section of OD at 115–180 nm
Authors: Nee Jan B. , Lee L. C.
Published: February 2003

The photoabsorption cross sections of OD in the 115–180 nm region were measured. The OD radicals were produced from a pulsed discharge in a mixture containing a trace of D2O in a few Torr of argon. Results are compared with the photoabsorption of OH previously measured.
Photolysis quantum yields and atom recombination rates of bromine in compressed gases. Experiments up to 7 kbar
Authors: Hippler H. , Schubert V. , Troe J.
Published: February 2003

Photolysis quantum yields of Br2 and recombination rates of bromine atoms have been measured by nanosecond laser flash photolysis at 532 nm. The influence of the pressure of the bath gases He, Ne, Ar, and N2 was studied over the range 1–7000 bar. Measurements in CO2 were performed up to 60 bar, in C3F8 up to 8 bar. Diffusion control of the atom recombination, with decreasing recombination rates at increasing bath gas densities, could be established for Ar and N2. Photolytic cage effect, i.e., decreasing photolysis quantum yields with increasing densities, was observed for all gases. The results are expressed in terms of simple models applied earlier to similar phenomena in iodine photolysis. The combination of quantum yield and recombination data allows for separation and semiquantitative representation of two mechanisms for geminate recombination, i.e., stabilization in clusters and cage energy relaxation.
Effect of added sodium chloride on the molecular environment and photoionization of N,N,N′,N′-tetramethylbenzidine in micellar solutions as studied by electron spin echo and electron spin resonance spectroscopy
Authors: Maldonado René , Kevan Larry , Szajdzinska-Piȩtek Ewa , Jones Richard R. M.
Published: February 2003

The electron spin echo modulation (ESEM) and electron spin resonance (ESR) spectra of the cation radical of N,N,N′,N′-tetramethylbenzidine (TMB) in frozen sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) micelles were studied as a function of sodium chloride concentration. TMB+⋅ was produced by photoionization at 350 nm of the parent compound in the micelles at 77 K. From the ESEM analysis it is found that the cation–water interactions increase with salt addition in both anionic and cationic micelles to a maximum near 0.2 M NaCl and then decrease somewhat. The increase is interpreted in terms of an increase in the water density at the micellar surface due to an increased surface concentration of hydrated counterions. The decrease may be due to TMB moving further from the polar micellar surface with added salt. From ESR spectra the photoionization yields of TMB at 77 K were determined. For DTAC micelles the yields are found to decrease with salt addition as expected from electrostatic considerations. For SDS micelles the photoionization yields increase for salt concentrations up to about 0.15 M and decrease for greater salt concentrations up to 0.5 M. The initial increase in cation yield correlates with electrostatic expectations. The decrease may be due to TMB moving further from the polar micellar surface with added salt. The possible effect of differing TMB protonation equilibria between anionic and cationic micelles on the photoionization yields was found to be unimportant by adjusting the bulk solution pH. An important conclusion is that salt addition can be used to optimize charge separation for photoionized solutes in anionic micelles.
Estimating the diversity of peptide populations from limited sequence data
Authors: Makowski Lee , Soares Alexei
Published: February 2003

Motivation: Combinatorial libraries of peptides such as those displayed on the surface of a bacteriophage particle have become widely used tools for characterizing protein–protein and protein–small molecule interactions. The quality of a library frequently depends on its completeness, or diversity—the proportion of possible sequences actually present in the library. The diversity of these libraries is frequently quoted on the basis of phage titers that provide little information about their completeness.

Results: Here, an analytical expression for diversity is introduced and a method for estimating the diversity of a peptide library from the sequences of a limited number of the members of the library is demonstrated. The diversities of a number of computationally constructed and actual peptide libraries are estimated using this method.

Contact: lmakowski@anl.gov

* To whom correspondence should be addressed.
Clustering of time-course gene expression data
using a mixed-effects model with B-splines
Authors: Luan Yihui , Li Hongzhe
Published: February 2003

Motivation: Time-course gene expression data are often measured to study dynamic biological systems and gene regulatory networks. To account for time dependency of the gene expression measurements over time and the noisy nature of the microarray data, the mixed-effects model using B-splines was introduced. This paper further explores such mixed-effects model in analyzing the time-course gene expression data and in performing clustering of genes in a mixture model framework.

Results: After fitting the mixture model in the framework of the mixed-effects model using an EM algorithm, we obtained the smooth mean gene expression curve for each cluster. For each gene, we obtained the best linear unbiased smooth estimate of its gene expression trajectory over time, combining data from that gene and other genes in the same cluster. Simulated data indicate that the methods can effectively cluster noisy curves into clusters differing in either the shapes of the curves or the times to the peaks of the curves. We further demonstrate the proposed method by clustering the yeast genes based on their cell cycle gene expression data and the human genes based on the temporal transcriptional response of fibroblasts to serum. Clear periodic patterns and varying times to peaks are observed for different clusters of the cell-cycle regulated genes. Results of the analysis of the human fibroblasts data show seven distinct transcriptional response profiles with biological relevance.

Availability: Matlab programs are available on request from the authors.

Supplementary Information: http://dna/ucdavis.edu/~hli/bioinforsupp.pdf

Contact: hli@ucdavis.edu

* To whom correspondence should be addressed.
A multivariate approach applied to microarray data for
identification of genes with cell cycle-coupled transcription
Authors: Johansson Daniel , Lindgren Petter , Berglund Anders
Published: February 2003

We have analyzed microarray data using a modeling approach based on the multivariate statistical method partial least squares (PLS) regression to identify genes with periodic fluctuations in expression levels coupled to the cell cycle in the budding yeast, Saccharomyces cerevisiae. PLS has major advantages for analyzing microarray data since it can model data sets with large numbers of variables and with few observations.

A response model was derived describing the expression profile over time expected for periodically transcribed genes, and was used to identify budding yeast transcripts with similar profiles. PLS was then used to interpret the importance of the variables (genes) for the model, yielding a ranking list of how well the genes fitted the generated model. Application of an appropriate cutoff value, calculated from randomized data, allows the identification of genes whose expression appears to be synchronized with cell cycling. Our approach also provides information about the stage in the cell cycle where their transcription peaks.

Three synchronized yeast cell microarray data sets were analyzed, both separately and combined. Cell cycle-coupled periodicity was suggested for 455 of the 6,178 transcripts monitored in the combined data set, at a significance level of 0.5%. Among the candidates, 85% of the known periodic transcripts were included. Analysis of the three data sets separately yielded similar ranking lists, showing that the method is robust.

Contact: anders.berglund@chem.umu.se

Supplementary material: Available at: http://www.chem.umu.se/dep/orgchem/forskning/chemometrics/bioinformatic.stm

* To whom correspondence should be addressed.

† The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Room temperature Cu–Cu direct bonding using surface activated bonding method
Authors: Kim T. H. , Howlader M. M. R. , Itoh T. , Suga T.
Published: February 2003

Thin copper (Cu) films of 80 nm thickness deposited on a diffusion barrier layered 8 in. silicon wafers were directly bonded at room temperature using the surface activated bonding method. A low energy Ar ion beam of 40–100 eV was used to activate the Cu surface prior to bonding. Contacting two surface-activated wafers enables successful Cu–Cu direct bonding. The bonding process was carried out under an ultrahigh vacuum condition. No thermal annealing was required to increase the bonding strength since the bonded interface was strong enough at room temperature. The chemical constitution of the Cu surface was examined by Auger electron spectroscope. It was observed that carbon-based contaminations and native oxides on copper surface were effectively removed by Ar ion beam irradiation for 60 s without any wet cleaning processes. An atomic force microscope study shows that the Ar ion beam process causes no surface roughness degradation. Tensile test results show that high bonding strength equivalent to bulk material is achieved at room temperature. The cross-sectional transmission electron microscope observations reveal the presence of void-free bonding interface without intermediate layer at the bonded Cu surfaces.
Diamond-like carbon films deposited on polyethylene terephthalate substrates by radio frequency plasma chemical vapor deposition method
Authors: Kimura Ayako , Kodama Hideyuki , Suzuki Tetsuya
Published: February 2003

Diamond-like carbon (DLC) films were deposited on polyethylene terephthalate (PET) substrates with the rf plasma chemical vapor deposition method using C2H2 gas and were investigated on the chemical bonding characteristics and microstructures, comparing with those on Si substrates. At the initial stage of deposition (∼10 s), the DLC films deposited on PET substrates contained more sp2 bonds and the growth rate was higher. Then, the number of sp3 bonds increased and became unchanged after 10 s of deposition. Similar results were observed for DLC films on Si substrates. When the input power of rf plasma equipment was higher, the C 1s x-ray photoelectron spectra from DLC films shifted to higher binding energy, but this shift was not observed for the films on Si substrates. Transmission electron microscope observation showed that the films were uniformly deposited on PET substrates and had amorphous structure without graphitic structure even in the restricted area.
Current–pressure–voltage characteristics in a planar magnetron discharge
Authors: Escrivão M. L. , Pereira P. J. S. , Cabral M. H. , Teixeira M. R. , Maneira M. J. P.
Published: February 2003

An experimental study of the dependence of current intensity with pressure, at different constant voltages, Va⩽450 V, in the pressure range between 3.3 and 66.7 Pa, is made for an argon–copper planar magnetron discharge. At Va⩽360 V, the current increases with pressure, until approximately 12 Pa, where a maximum is observed and then decreases leading the discharge almost to extinction. At intermediate voltages, the relative current maximum, at approximately the same pressure, is followed by a local minimum after which a linear increase is observed. At higher voltages, the structure of maxima and minima tends to fade out. An empirical relation with two terms is proposed for the current intensity dependence on pressure and voltage. The first term suggests an electron scattering effect. The second term is linearly dependent on pressure. This empirical model is discussed and compared with a theoretical model from literature. From this analysis, the first term is interpreted as the contribution of electrons generated inside the cathode dark space, while the second term represents the contributions to the current of ions striking the target and of secondary electrons. Results indicate the occurrence of significant ionization in the cathode dark space for the pressure range from 3 to 30 Pa. For higher pressure values and Va>360 V, the cathode sheath is relatively thin and most ionization takes place outside of it. Using both models, theoretical calculations, and experimental parameters, the thickness of the dark space as a function of pressure at several discharge voltages is obtained.