bluuebunny/crossref_metadata_2025 huggingface dataset:
The bifurcated hydrogen-bond model of water and amorphous ice
Authors: Giguère Paul A.
Published: July 2002

The existence of bifurcated hydrogen bonds (BHB) between three molecules as a major feature of the structure of liquid water was postulated recently to account for the remarkable effect of temperature on the O–H stretching bands in the Raman spectra. As a corollary, there should be two kinds of H⋅⋅⋅O distances in water: one, 1.85 Å, for the well-known linear bonds (LHB), prevalent in cold water, the other, 2.3 Å, for the weaker BHB. This is evident in the neutron diffraction studies of heavy water, which reveal important structural changes with temperature. For instance, the atom pair correlation functions, both in the first-order difference, and the isochoric temperature derivative methods, show two peaks at 1.8 and 2.3 Å, with inverse temperature dependence similar to that of the Raman bands at 3220 (LHB) and 3420 cm−1 (BHB). In the BHB the nearest-neighbor O⋅⋅⋅O distances are the same as in the LHB, but the apex angle is much smaller than the tetrahedral, between 95° and 100°. This allows slightly shorter second neighbor O⋅⋅⋅O distances, and a closer packing of the molecules. The increased average coordination of the H and O atoms creates an imbalance in the stoichiometry of hydrogen bonding. As a result, a few percent of the water molecules are left with one ‘‘free,’’ i.e., nonhydrogen-bonded OH group (NHB). The energy of the BHB is estimated at 2.5 kcal mol−1, i.e., half that of the LHB, and its proportion in the liquid, at nearly 30% at 0 °C. Amorphous ice prepared from the vapor may also contain BHB according to x-ray and neutron diffraction data. The BHB appears as a common feature of hydroxylic compounds; e.g., hydrogen peroxide, alcohols, etc.
Kinetics of the polymerization of alkenes on zeolites
Authors: Alberty Robert A.
Published: July 2002

The polymerization of alkenes at temperatures in the neighborhood of 600 K on a zeolite catalyst can be described in terms of a mechanism with bimolecular polymerization reactions and cracking reactions of isomer groups. The rate equations for the formation of isomer groups up to C13H26 have been integrated using the fourth-order Runge–Kutta method for polymerizations at constant temperature and pressure. In the absence of data on rate constants, calculations have been made on the basis of the assumption that all the bimolecular rate constants are equal or all the cracking constants are equal. In each case the rate constants for the reverse reactions have been calculated using the equilibrium constants for the steps in the mechanism. Under some circumstances the plots of weight fractions of isomer groups vs time have nearly the same shape for the two assumptions. However, it is possible to distinguish between the two assumptions by using experiments at sufficiently high pressures. The calculations show that it is of interest to examine the compositions arising from different starting materials, even though the equilibrium composition depends only upon temperature and pressure.
Bending and twisting dynamics of short linear DNAs. Analysis of the triplet anisotropy decay of a 209 base pair fragment by Brownian simulation
Authors: Allison Stuart , Austin Robert , Hogan Mike
Published: July 2002

Brownian dynamics is used to simulate the decay anisotropy of short linear DNA fragments modeled as a string of beads. The model is sufficiently general to allow for static bends, anisotropic bending, and elastic constants for bending and twisting which can vary along the chain. In limiting cases, simulations are found to be in excellent agreement with analytic theory down to a correlation length of at least 500 Å. This model is then used to analyze the 0–2.5 μs triplet depletion anisotropy decay of a 209 base pair sea urchin DNA fragment. It is concluded that the conventional worm-like chain model, in which bending is isotropic and/or there are no static bends along the chain, is unable to account for the experimental results unless a correlation length of 1000 Å is assumed. A worm-like chain with anisotropic bending requires a similar but slightly larger correlation length.
Diffusion-controlled reactions. I. Molecular dynamics simulation of a noncontinuum model
Authors: Dong W. , Baros F. , Andre J. C.
Published: July 2002

The molecular dynamics simulation method is extended to study a model of diffusion-controlled reactions. This allows a molecular description of solvent at an equal footing of reactants. Nondiffusional dynamic behavior of reactive molecules is found at short times. It enhances the rate of reactive encounter in comparison to the prediction of Smoluchowski theory. The model studied in this work can be regarded as a theoretical prototype of fluorescence quenching. In this context it is shown that the nondiffusional dynamics is mainly responsible for the discrepancy between Stern–Volmer plots measured in a continuous excitation experiment or obtained by integrating the time resolved fluorescence intensity. The other aspects such as the long-time behavior of survival probability, solvent effect as well as competing effect from finite concentration of one reactive species are also studied in some detail.
Electronic structure of phthalocyanines: Theoretical investigation of the optical properties of phthalocyanine monomers, dimers, and crystals
Authors: Ortí E. , Brédas J. L. , Clarisse C.
Published: July 2002

We present valence effective Hamiltonian (VEH) calculations on the optical absorptions of a series of phthalocyanine compounds: the metal-free phthalocyanine molecule, a model system for the lithium phthalocyanine molecule, the metal-free phthalocyanine dimer, and model systems for the lutetium diphthalocyanine and the lithium phthalocyanine crystal. For these compounds, it is found that the major factor influencing the evolution of the optical transitions is not the electronic structure of the metal but rather the geometric structure: phthalocyanine intraring geometry and, in the dimers and crystals, interring separation and staggering angle. The origin of the so-called Soret or B absorption band is calculated to be significantly more complex than was previously thought on the basis of the simple four-orbital model.
A comparative study of density functional models to estimate molecular atomization energies
Authors: Clementi Enrico , Chakravorty Subhas J.
Published: July 2002

In the present study the molecular atomization energies have been computed with some of the recent density functionals and with a semiempirical model developed in the IBM laboratory. In particular, the Lie–Clementi (LC), the Colle–Salvetti (CS), the Gunnarson–Lundqvist (GL), the Vosko, Wilk, and Nusair (VWN), the Perdew–Zunger (PZ), the Becke (B), and the Lee, Yang, and Parr (LYP) functionals have been considered. For GL and VWN the self-interaction correction of Stoll, Pavlidou, and Preuss (SPP) has been included. For the PZ the gradient correction of Perdew has been included. For the LYP a new and simpler form as proposed by Michlich et al. has been implemented. More than 50 small to fairly large molecules have been chosen at test cases. The results obtained with the present semiempirical model are gratifying and indicate that further improvement and calibration is still possible. From the computed data it is concluded that the density functionals in most cases do provide a pragmatic solution to the determination molecular atomization energy.
Time-dependent dynamics of methyl iodide photodissociation in the first continuum
Authors: Guo Hua , Schatz George C.
Published: July 2002

The photodissociation dynamics of methyl iodide (CH3I) and its deuterated counterpart (CD3I) in the A band is studied using a time-dependent quantum mechanical method, based on the fast Fourier transform (FFT) method of Kosloff and Kosloff. The calculation uses a pseudotriatomic approximation in which the umbrella mode of CH3 (CD3) is approximated by a C–X (X=H3, D3) stretch. In addition, the I–C–X dissociation is assumed collinear and angular momentum is ignored. The wave packet is propagated on coupled electronic potential surfaces which we have developed by revising Shapiro’s potentials to fit recent experimental data. Good agreement between our calculations and experiment has been obtained for the absorption spectrum, the vibrational distributions for the methyl umbrella mode, and I*/I branching ratios for both CH3I and CD3I at 248 nm. According to our model, the CH3 fragment in the I* channel at 266 nm is predominantly at its ground vibrational state, while the vibrational distribution in the lower I channel extends to v=6 and has a peak at v=1.
Perturbative calculations of vibrational (J=0) energy levels of linear molecules in normal coordinate representations
Authors: McCoy Anne B. , Sibert Edwin L.
Published: July 2002

Canonical Van Vleck perturbation theory is used to transform curvilinear and rectilinear normal coordinate vibrational Hamiltonians of HCN, C2H2, and CO2 to block-diagonal effective Hamiltonians. Accurate energies as high as 11 000 cm−1 above the zero point are reported for all three molecules. In the absence of off-diagonal coupling terms in the effective Hamiltonians, these two coordinate systems yield identical perturbative expansions for the vibrational energies. Only when coupling terms are introduced do differences between the calculated energies in the two representations become apparent. In CO2, where there is pronounced configuration interaction between nearly degenerate states, we find that the perturbative energies obtained from the curvilinear normal coordinate Hamiltonian are converging significantly faster than those obtained in the rectilinear normal coordinate representation.
Elastic model of DNA supercoiling in the infinite-length limit
Authors: Hunt Nathaniel G. , Hearst John E.
Published: July 2002

The energies of plectonemic and toroidal supercoiled DNA are calculated by treating DNA as an elastic rod with a finite radius. End effects are ignored and all extensive quantities (e.g., writhe, bend energy) are treated as linear densities (writhe per unit length, bend energy per unit length). Minimum energy configurations are found. For plectonemic DNA, the superhelical pitch angle α is in the range 45°<α≤90°. For low values of specific linking difference, most superhelicity is in writhe. As specific linking difference increases, a greater proportion of superhelicity is in twist. Under physiological conditions, roughly 88% of superhelicity is in writhe. Ionic strength effects are discussed, and it is found that variation of excluded volume with ionic strength has a large effect, resulting in significantly greater torsional stress in supercoiled DNA at low ionic strength. For biologically relevant values of specific linking difference, the plectonemic conformation is energetically favored over toroidal conformations. Results are compared with electron microscopy data. The application of the model to DNA conformational transitions is discussed.
Reaction paths and free energy profiles for conformational transitions: An internal coordinate approach
Authors: Lazaridis Themis , Tobias Douglas J. , Brooks Charles L. , Paulaitis Michael E.
Published: July 2002

A new approach is proposed for the determination of transition states and reaction paths for conformational transitions. The method makes use of adiabatic energy surfaces in the space of ‘‘essential’’ degrees of freedom of the molecule. The reduced dimensionality of this space, compared to the full Cartesian space, offers improved computational efficiency and should allow determination of exact reaction paths in systems much larger than those currently amenable to study in Cartesian space. A procedure to obtain reaction paths and free energy profiles in solution is also proposed. The free energy profile along the path in solution is calculated utilizing a free energy perturbation method with constrains and perturbations in internal coordinate space. Applications to a conformational transition of the alanine dipeptide and the folding transition of a model reverse turn in water are presented. For the reverse turn, the sequential flip of dihedral angles reported by Czerminsky and Elber on a similar peptide [J. Chem. Phys. 92, 5580 (1990)] is also observed in the present calculations. The free energy of the extended form of the reverse turn in water is found to be lower than that for the folded conformation by about 3 Kcal/mol, in qualitative accord with previous umbrella sampling calculations.
Glass transition of polymer melts: A two-dimensional Monte Carlo study in the framework of the bond fluctuation method
Authors: Wittmann Hans-Peter , Kremer Kurt , Binder Kurt
Published: July 2002

The glass transition of a two-dimensional melt of lattice polymers is discussed. The glass temperature Tg is determined by the free volume approach, by the isothermal compressibility as well as by other methods. The decay of the bond autocorrelation function displays typical glasslike behavior. The time temperature superposition law detected in the dynamical polymer structure factor and in orientational autocorrelation functions can be explained by simple dynamical scaling arguments. Mean square displacements observed over more than five decades in time yield very precise diffusion constants as a function of temperature.
Intrapore field-dependent micropore filling of supercritical N2 in slit-shaped micropores
Authors: Kaneko Katsumi , Shimizu Kazuyuki , Suzuki Takaomi
Published: July 2002

The micropore filling of supercritical N2 on micrographitic carbon fibers having slit-shaped micropores of different micropore widths from 0.7 to 1.4 nm was examined at 303 K under the high pressure of N2 up to 10 MPa. Supercritical N2 in the micropore was presumed to be transformed into quasivapor by strong micropore field; the Dubinin–Radushkevich equation for a vapor was extended to the quasivapor in the micropore. The determination method of the saturated vapor pressure Psq of the quasi-N2 vapor in the micropore was proposed and was applied to the experimental results on N2/micrographitic carbon fiber systems; the determined Psq increases with the micropore width. The relationship between the extent of micropore filling of a supercritical gas through the quasivapor state and the interaction energy between a molecule and two parallel micrographites from the Lennard-Jones potential was theoretically derived, which was evidenced by the simple experimental relationship between the amount of high pressure N2 adsorption at 303 K and the micropore width.
Pore-end effects on adsorption hysteresis in cylindrical and slitlike pores
Authors: Papadopoulou Aphrodite , van Swol Frank , Marini Bettolo Marconi Umberto
Published: July 2002

We present grand canonical and canonical simulation results for the adsorption hysteresis in cylindrical and slitlike pores. Simulations for cylindrical symmetry were carried out for a continuous potential model, whereas the lattice gas was used to investigate the slitlike pores. In particular, we have studied the effects of pore ends on pore filling and pore emptying mechanism. We find that while the pore filling is unaffected, pore emptying is very sensitive to the presence of pore ends. Our findings confirm earlier lattice gas density functional theory results and indicate that fluctuations do not basically alter the mean field picture.
The structure of water determined by microwave dielectric study on water mixtures with glucose, polysaccharides, and L-ascorbic acid
Authors: Mashimo Satoru , Miura Nobuhiro , Umehara Toshihiro
Published: July 2002

Dielectric relaxation measurements over an extremely wide frequency region from 1 MHz to 20 GHz were performed on water mixtures with glucose, polysaccharides, and L-xylo ascorbic acid by the use of time domain reflectometry. For mixtures of polysaccharides bigger than maltotriose, two relaxation peaks were definitely observed. The high frequency relaxation is the water relaxation and the low frequency one is due to orientation of polysaccharide molecules. In the case of glucose, only one relaxation peak could be observed. It is shown that a hexagonal cluster in the lattice of ice can be replaced easily by the glucose molecule, where the lattice is distorted slightly, but stabilized by several hydrogen bonds between the glucose molecule and the lattice. Although the cluster can be replaced by the L-ascorbic acid molecule too, the lattice cannot be kept stable. Its water mixture shows two relaxation peaks clearly. It is suggested that water has a structure of the distorted lattice of ice. Fluctuation of the lattice breaks the hydrogen bonds and the lattice is decomposed. Orientation of the water molecules released gives rise to the relaxation concerned.
Variable-angle correlation spectroscopy in solid-state nuclear magnetic resonancea)
Authors: Frydman Lucio , Chingas Gerard C. , Lee Young K. , Grandinetti Philip J. , Eastman Margaret A. , Barrall Geoffrey A. , Pines Alexander
Published: July 2002

We describe here a new solid-state nuclear-magnetic-resonance (NMR) experiment for correlating anisotropic and isotropic chemical shifts of inequivalent nuclei in powdered samples. Spectra are obtained by processing signals arising from a spinning sample, acquired in independent experiments as a function of the angle between the axis of macroscopic rotation and the external magnetic field. This is in contrast to previously proposed techniques, which were based on sudden mechanical flippings or multiple-pulse sequences. We show that the time evolution of variable-angle-spinning signals is determined by a distribution relating the isotropic frequencies of the spins with their corresponding chemical shift anisotropies. Fourier transformation of these data therefore affords a two-dimensional NMR spectrum, in which line shapes of isotropic and anisotropic interactions are correlated. Theoretical and experimental considerations involved in the extraction of this spectral information are discussed, and the technique is illustrated by an analysis of 13C NMR anisotropy in glycine, cysteine, and p-anisic acid.
Gas sorption and transport in polyisobutylene: Equilibrium and nonequilibrium molecular dynamics simulations
Authors: Müller-Plathe Florian , Rogers Stephen C. , van Gunsteren Wilfred F.
Published: July 2002

Molecular dynamics calculations are reported on the sorption and diffusion of small gas molecules (He, H2, and O2) in amorphous polyisobutylene. An all-atom force field (with explicit hydrogen atoms) was used. In addition to the standard method of obtaining the diffusion coefficient from an equilibrium calculation via the mean-square displacement we used a nonequilibrium technique that applies a fictitious external field selectively to the gas molecules. To our knowledge, nonequilibrium MD is, for the first time, applied to the problem of gas diffusion in polymers. Results of both techniques are compared. Energy profiles of the jump events underlying gas diffusion through polymers are studied. We also discuss the possible presence of anomalous (non-Einstein) behavior of gas molecules diffusing through an amorphous polymer. Gas solubilities in polyisobutylene are calculated by particle-insertion techniques.
Electric dipole interactions of chain molecules in nematics: The analysis of segmental ordering in α, ω-dibromoalkanes
Authors: Photinos D. J. , Samulski E. T.
Published: July 2002

The residual electric dipole interactions recently detected in the deuterium NMR spectra of α,ω-dibromoalkanes dissolved in nematic liquid crystalline solvents [J. Phys. Chem. 96, 8176 (1992)] are analyzed in the context of the modular formulation of flexible molecule ordering. The chord model realization of this formulation, previously applied to the study of n-alkanes, is minimally extended to include the additional coupling of the dipole carrying segments of the solute molecules to the dipolar bias produced by the solvent. The ensuing simple model successfully reproduces the observed segmental order parameter profiles of the solute over the entire nematic temperature range of the solvents. Three types of solvents are considered (Phase V, 5CB, 5OCB) differing in their molecular dipole moment constitutions. It is found that in all solvent cases the orientational ordering is suppressed at the dipole moment carrying ends of the solute molecules whereas the ordering in the main body could either be reduced or elevated depending on the configuration of the dipole moments on the solvent molecules. Quantitative results for the effects of the dipolar bias on the potential of mean torque are presented and the mechanism of electric dipole driven ordering in these solvent–solute systems is discussed.
A model for nonadiabatic coupling in the photodissociation of I2–solvent complexes
Authors: Dardi Peter S. , Dahler John S.
Published: July 2002

Experiments performed on moderately dense gases indicate that the absorption of photons with energies in excess of the dissociation energy of I2 often fails to cause dissociation and, instead, results in the direct production of iodine molecules in the ground electronic state. To account for this, Otto, Schroeder, and Troe (OST) proposed that the photons are absorbed by I2–solvent complexes from which the solvent subsequently is ejected and the I2 simultaneously deposited in the electronic ground state. Our earlier calculations (for solvent ethane) already have established that the concentrations of I2–solvent complexes are, indeed, large enough to satisfy the requirements of the OST model. What we now propose is a dynamic mechanism that accounts for the photoabsorptive dissociation of the complex into a solvent fragment and a vibrationally excited I2 molecule in the ground electronic state. The occurrence of such an event is surprising because, at first glance, it appears to violate commonly accepted notions about the interconversion of electronic and nuclear, kinetic energy.
Translational diffusion of a transient radical studied by the transient grating method, pyrazinyl radical in 2-propanol
Authors: Terazima Masahide , Hirota Noboru
Published: July 2002

A translational diffusion coefficient (Ddiff) of a transient radical created by a photochemical reaction of pyrazine in 2-propanol is measured by the transient grating technique. The rise and decay curves of the transient grating signal on the millisecond time scale are attributed to the diffusion of the pyrazinyl radical and the parent molecule (pyrazine). Ddiff of both species are determined. The measured Ddiff of the radical is four times smaller than that of pyrazine even though the molecular size is similar to each other. The small Ddiff suggests that the radical–solvent interaction is stronger than the parent molecule–solvent interaction.
Molecular recognition at self-assembled monolayers: Optimization of surface functionalization
Authors: Spinke J. , Liley M. , Schmitt F.-J. , Guder H.-J. , Angermaier L. , Knoll W.
Published: July 2002

Sulfur-based molecules containing biotin and hydroxyl groups have been used to create a wide variety of self-assembled monolayers on gold surfaces. Surface plasmon resonance has been used to study in situ the binding of streptavidin to these monolayers from solution. The self-assembled monolayers allow a high degree of control over the surface properties. The choice of an appropriate biotin-containing molecule, with a spacer segment, and the dilution of this molecule within the monolayer by hydroxythiols, allows optimization of the binding properties of the monolayer—nonspecific interactions between streptavidin and the surface are below detection limits, and specific binding between the streptavidin and biotin groups can be maximized.
On the orbital picture of shape resonances using Feynman–Dyson amplitudes from different decouplings of the dilated electron propagator
Authors: Medikeri Milan N. , Nair Jayraman , Mishra Manoj K.
Published: July 2002

The orbital picture of shape resonances is investigated by examining the radial charge density distributions calculated from resonant Feynman–Dyson amplitudes for the 2P shape resonances in e-Be, e-Mg, and e-Ca scattering using the zeroth (bivariational self-consistent field), second order and the diagonal two particle one hole-Tamm–Dancoff approximation decouplings of the dilated electron propagator. A comparison between the radial density distributions from the highest occupied and the resonant orbital/Feynman–Dyson amplitude(s) reveals an accumulation of the electron density near the target for optimal value of the complex scaling parameter. The nodal pattern of the radial distributions differs from that expected for the lowest unoccupied p orbitals but their dominant contribution to the charge density distribution is clearly seen. A study of the difference between the radial densities obtained from various decoupling schemes highlights the role of correlation and relaxation in the characterization of these resonances. The role of coordinate space span of the primitive Gaussian-type orbital basis in characterization of these resonances is discussed.
Nonempirical intermolecular potentials for urea–water systems
Authors: Åstrand P.-O. , Wallqvist A. , Karlström G.
Published: July 2002

In this work, we present ab initio derived intermolecular potentials for the urea–water system. Our method of calculation, which is termed NEMO, is based on intermolecular perturbation theory. Dipole moment fluctuations as well as many-body effects in an assembly of molecules are described by including atomic polarizabilities in the potential. For the urea dimer we found a cyclic minimum with an energy of −21.9 kcal/mol and two equivalent hydrogen bonds of length 1.77 Å. Noteworthy is that this interaction energy is more than four times larger than the water dimer minimum energy. To be able to satisfactorily model the interaction between two urea molecules we have improved the NEMO approach in the description of the repulsion energy and we have also included a more accurate damping on the dispersion energy. With this improved model we reinvestigated the water dimer and urea–water potentials and found good agreement with earlier potentials derived with similar approaches. From simulations of liquid water we investigated the sensitivity of structural properties resulting from small changes in repulsion parameters. Qualitative changes of the tetrahedral hydrogen bonding may occur for inappropriate parameter choices of the same potential surface.
Interaction of an aluminum atom with an alkaline earth atom: Spectroscopic and ab initio investigations of AlCa
Authors: Behm Jane M. , Morse Michael D. , Boldyrev Alexander I. , Simons Jack
Published: July 2002

A spectroscopic analysis of diatomic AlCa generated by laser vaporization of a 2:1 Al:Ca metal alloy followed by supersonic expansion has been completed using resonant two-photon ionization spectroscopy. Four excited electronic states have been identified and investigated in the energy region from 13 500 to 17 900 cm−1. These are the [13.5] 2Πr, the [15.8] 2Σ, the [17.0] 2Δ3/2(?), and the [17.6] 2Δ3/2 states. From rotational analysis excited state bond lengths have been measured for three of the four excited states, and the ground state has been unambiguously determined as a 2Πr state with a weighted least squares value of the ground state bond length of r0″ = 3.1479± 0.0010 Å. The ionization energy of the molecule has also been directly determined as 5.072±0.028 eV. Ab initio calculations for the potential energy curves of seven low-lying states of AlCa [X 2Πr, 2Σ+, 4Σ−, 4Πr, 2Πr(2), 2Δ, and 2Σ−] and for the X 1Σ+ ground electronic state of AlCa+ have been carried out. In agreement with experiment, 2Πr is calculated to be the ground electronic state of the neutral molecule. The dissociation energies of AlCa (X 2Πr) into Al(3s23p1,2P0)+Ca(4s2,1S) and for AlCa+ (X 1Σ+) into Al+(3s2,1S)+Ca(4s2,1S) are calculated to be 0.47 and 1.50 eV, respectively. The excited 2Σ+, 4Σ−, 4Πr, 2Πr(2), 2Δ, and 2Σ− states are calculated to lie 0.2, 0.7, 0.7, 1.1, 1.1, and 1.1 eV above X 2Πr, respectively, and the vertical and adiabatic ionization energies of AlCa have been calculated to be 5.03 and 4.97 eV, respectively.
Phase transitions in mixed Langmuir films of 8CB and stearic acid
Authors: Enderle Th. , Meixner A. J. , Zschokke-Gränacher I.
Published: July 2002

Pure and mixed monolayers of 4-n-octyl-4′-cyanobiphenyl (8CB) and stearic acid (SA) at the air–water interface have been investigated by a combination of surface balance measurements and polarization sensitive, optical second harmonic spectroscopy. These measurements make it possible to carry out in situ studies of the formation of the monolayer and to identify different regimes upon compression of the film. These regimes cover the whole range from an isotropic monolayer, a highly oriented phase, up to phase separation at a critical surface pressure π*. It is shown that the polarization dependence of the second harmonic intensity is a very sensitive method to investigate the orientation of the optically nonlinear 8CB chromophores in the mixed film as a function of surface pressure as well as concentration. A comparison of monolayers of different mole fractions of 8CB and SA shows that the alignment of the 8CB molecules in the mixed film depends on the surface pressure and not on their concentration in the monolayer only. This behavior can be explained by assuming an ideal mixed monolayer, where the orientation of the 8CB chromophores is due only to the hydrophobic interaction with the alkyl chains of the SA. In addition, the critical surface pressure of the mixed film πmix* can be calculated as a function of the 8CB mole fraction x8CB.
Electronic absorption spectroscopy of matrix-isolated polycyclic aromatic hydrocarbon cations. II. The phenanthrene cation (C14H10+) and its 1-methyl derivative
Authors: Salama F. , Joblin C. , Allamandola L. J.
Published: July 2002

The ultraviolet, visible, and near infrared absorption spectra of phenanthrene (C14H10), 1-methylphenanthrene [(CH3)C14H9], and their radical ions [C14H+10; (CH3)C14H+9], formed by vacuum-ultraviolet irradiation, were measured in neon matrices at 4.2 K. The associated vibronic band systems and their spectroscopic assignments are discussed. The oscillator strengths were calculated for the phenanthrene ion and found lower than the theoretical predictions. This study presents the first spectroscopic data for phenanthrene and its methyl derivative trapped in a neon matrix where the perturbation of the isolated species by its environment is minimum; a condition crucial to astrophysical applications.
Ab initio calculation of vibration frequencies, infrared intensities, and structures for H+4, LiH+3, Li2H+2, and Li+4, and deuterated analogs
Authors: Pan Zhifang , Borkman R. F.
Published: July 2002

The six normal mode vibration frequencies and infrared intensities for H+4 and three tetra-atomic lithium–hydrogen ion clusters have been calculated using ab initio SCF, MP2, and CISD methods. Vibration frequencies are also reported for all possible deuterated analogs of the four ions. The normal mode vibrational characteristics and structures of the ions are discussed and compared to each other. The H+4 ion can reasonably be regarded as a strongly bonded, triangular H+3 core with an additional H atom less strongly bound to one of the ring hydrogens in a planar C2v arrangement. The calculated normal mode vibration frequencies for H+4 and its deuterated analogs confirm this picture. The hydrogen–lithium clusters, LiH+3, Li2H+2, and Li+4, had structures and normal mode frequencies which did not yield the same ring/ligand picture as H+4. Instead, these ions behaved like two interacting diatomic fragments (e.g., H2 and LiH+ subunits in LiH+3) oriented perpendicular to each other in a planar arrangement. The potential energy surfaces for the hydrogen–lithium cluster ions displayed two extremely low frequency vibrational modes corresponding to angular motion of these diatomic subunits relative to each other.
Fourier-transform microwave spectroscopy of triplet carbon monoxides, C2O, C4O, C6O, and C8O
Authors: Ohshima Yasuhiro , Endo Yasuki , Ogata Teruhiko
Published: July 2002

Rotational spectra of CnO with n=2, 4, 6, and 8 have been observed by using a Fabry–Perot type Fourier-transform microwave spectrometer cooperated with a pulsed discharge nozzle. The molecules have been generated by an electric discharge of carbon suboxide diluted in Ar, and adiabatically cooled to ≊2 K in a subsequent supersonic expansion. All the observed spectra for these species are characterized as linear molecules in the 3Σ− electronic ground state. Since all the three spin sublevels have been detected even in the free-jet condition, the spin–spin coupling constants have been determined precisely as well as other spectroscopic constants. The coupling constants show rapid increase as n becomes larger, indicating smaller energy gaps between the excited 1Σ+ state and the 3Σ− ground state for the longer species. Along with the recent observation of singlet CnO (n=5, 7, and 9) [Ogata, Ohshima, and Endo, J. Am. Chem. Soc. (submitted)], the present study has established the existence of a complete set of the linear carbon-chain series CnO up to n=9 in the gas phase. The effective C=C bond lengths evaluated from the rotational constants decrease gradually to a converging value of ≊1.28 Å as n becomes larger. No apparent quasilinearity has been observed in the centrifugal-distortion constants of all the members, in contrast to the relevant series of the pure carbon clusters, Cn, some of which (n=3 and 7) have shown substantial nonrigidity for the bending vibration.
Structural and thermodynamic properties of end-grafted polymers on curved surfaces
Authors: Carignano M. A. , Szleifer I.
Published: July 2002

Conformational and thermodynamic properties of polymer chains end-grafted to cylindrical and spherical surfaces under good solvent conditions have been studied using the single-chain mean-field theory. We have considered chains of 50, 100, and 150 segments, and five different radii from R=2 up to R=100. We have found excellent quantitative agreement with all the available molecular dynamics and Monte Carlo simulations for the conformational properties at all curvatures. Further, the chemical potential of the chains for planar geometries is found to be in excellent agreement with recent Monte Carlo simulations. In the limit of strong curvature for the cylindrical geometry our findings qualitatively agree with the analytical prediction of Li and Witten for the structure but not for the polymer free energy. The chemical potential of the grafted chains was calculated as a function of the surface coverage and the radius of curvature of the surface. Our findings suggest that for all curvatures and surface coverage the chemical potential has to be properly calculated to obtain realistic adsorption isotherms.
Photoionization of hydrogen and deuterium
Authors: Latimer C. J. , Dunn K. F. , O’Neill F. P. , MacDonald M. A. , Kouchi N.
Published: July 2002

Cross sections for the formation of slow molecular and energetic fragment ions in the photoionization of hydrogen and deuterium have been determined using synchrotron radiation within the energy range 25–40 eV. Superexcited states have been shown to play an important role in the photoionization process but recently predicted resonance effects have not been observed.
Integrating the Car–Parrinello equations. III. Techniques for ultrasoft pseudopotentials
Authors: Hutter Jürg , Tuckerman Mark , Parrinello Michele
Published: July 2002

New methods for integrating the Car–Parrinello equations with ultrasoft pseudopotentials are introduced. In particular, the difficulties associated with the generalized orthonormality constraint condition 〈φi‖Ŝ({RI})‖φj〉=δij are addressed. It is shown that the equations of motion can be integrated using the velocity Verlet/RATTLE scheme, and a new method, the constrained nonorthogonal orbital method, that eliminates the need to enforce this constraint explicitly is introduced. In this new scheme, the generalized orthonormality constraint is satisfied implicitly, thus allowing the freedom to choose simpler constraint conditions. We show that usual N3 scaling associated with the calculation of the Lagrange multipliers in the constraint force can be reduced to an N2 calculation by the use of a simple set of norm or length constraints on the electronic orbitals without sacrificing accuracy. The constrained nonorthogonal orbital method is shown to be considerably simpler to implement and more efficient than the standard approach to the ultrasoft pseudopotential problem.
Mid-infrared vibrational spectrum of CO after photodissociation from heme: Evidence for a ligand docking site in the heme pocket of hemoglobin and myoglobin
Authors: Lim Manho , Jackson Timothy A. , Anfinrud Philip A.
Published: July 2002

Time-resolved mid-ir absorption spectra of CO at 283 K have been measured 100 ps after photodissociation from human hemoglobin A, horse myoglobin, and sperm whale myoglobin. The spectra reveal two vibrational features that are narrower than any reported for CO in the condensed phase near room temperature, indicating that CO becomes localized in a rotationally constrained environment. The integrated absorbance under these narrow features is 0.53±0.05 times that found for sperm whale myoglobin in low temperature glasses. A model is developed that relates this reduction of integrated absorbance to molecular motion in a rotationally constrained environment. From this model, the barrier to CO rotation is found to be 1.5±0.25 kcal/mol. The two vibrational features are tentatively assigned to CO oriented oppositely in the same site within the heme pocket. Evidently, the residues circumscribing the heme pocket in hemoglobin and myoglobin fashion a cavity near the binding site that accommodates the dissociated CO and restricts its rotational motion. This ‘‘docking’’ site mediates ligand transport to and from the active binding site and may be important to the function of ligand-binding heme proteins.
Coherent isotropic averaging in zero-field nuclear magnetic resonance. I. General theory and icosahedral sequences
Authors: Llor A. , Olejniczak Z. , Pines A.
Published: July 2002

We present a general theory of coherent isotropic averaging in nuclear magnetic resonance (NMR). In a zero external field, magnetic-field pulses can selectively average the internal spin Hamiltonians, while preserving the intrinsic invariance of the spectrum with respect to the sample orientation. The theory predicts the limits of the scaling factors for tensor interactions of different ranks. Time reversal is found to be possible for first- and second-rank tensors with scaling factors of −1/3 and −1/4, respectively. Explicit sequences, based on icosahedral symmetry, are given for a number of optimal scaling factors. To illustrate the theory, an experiment is also presented in the special case of rank-selective decoupling. As in high-field NMR, applications can be expected from the introduction of coherent averaging schemes for zero-field techniques: for example, decouplings (by rank or nuclear species), time reversal, and multipolar experiments (zero-field analog of multiple-quantum NMR).
Area dependence of the surface tension of a Lennard-Jones fluid from molecular dynamics simulations
Authors: Chen Li-Jen
Published: July 2002

Molecular dynamics simulations are used to study the structure of the vapor–liquid interface of three-dimensional fluids. Particles interact via a truncated Lennard-Jones pair potential in the absence of external fields. The effect of the surface area on the surface tension is investigated. It is found that the surface tension increases with the decrease of the surface area. However, this finite-size effect is pronounced only in small surface areas. In addition, our simulation results show that the finite-size correction of the surface tension is directly proportional to the reciprocal of the surface area, in accord with the prediction of the Gaussian model of capillary waves.
Passages in lamellar phases of highly charged fluid membranes
Authors: de Vries Renko
Published: July 2002

The free energy is calculated of a single passage defect in a lamellar phase of highly charged fluid membranes. The limit is considered in which the curvature energy of the membranes and the curvature energy of the surrounding electric double layers dominate. It is found that in the regime 10 ≤χD≤ 60, with D the distance between the membranes in the lamellar phase and χ−1 a length scale of the order of the Debye length, the free energy of a passage decreases rapidly with dilution.
Calculation of nuclear spin–spin couplings. VIII. Vicinal proton–proton coupling constants in ethane
Authors: Fukui H. , Inomata H. , Baba T. , Miura K. , Matsuda H.
Published: July 2002

Ab initio self-consistent-field (SCF) and electron correlation calculations have been carried out for the dihedral angle dependence of the vicinal proton–proton coupling constants, 3JHH, in ethane molecule. The four contributions to 3JHH, (JFC, JSD, JOP, and JOD) have been computed with the three different basis sets, [5s2p1d/2s1p], [5s3p1d/3s1p], and [7s4p2d/5s2p]. The Fermi contact (FC) contribution was largest and the spin–dipole (SD) contribution was smallest. The FC and orbital paramagnetic (OP) contributions showed large basis set dependence, but the SD and orbital diamagnetic (OD) contributions presented little basis set dependence. The calculated total SCF contribution to 3JHH was higher than the experimental coupling. Using the Mo/ller–Plesset perturbation theory we have introduced electron correlation effects on the FC and OP terms. The correlation effects on the OP term was shown to be negligible. The second-order correlation in the FC term was very large and amounted to half of its SCF value in magnitude with opposite sign. However, the third-order correlation in the FC contribution was small. Unfortunately, the calculated 3JHH value including correlation corrections through third order was too small compared to the experimental one. The poor agreement between calculation and experiment is claimed to be due to higher than third-order correlations in the FC term.
Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique
Authors: Socci Nicholas D. , Onuchic José Nelson
Published: July 2002

Using Monte Carlo dynamics and the Monte Carlo histogram method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good and poor folding sequences. The good (fast folding) sequences have sharp well-defined thermodynamic transitions while the slow folding sequences have broad ones. We find two independent transitions: a collapse transition to compact states and a folding transition from compact states to the native state. The collapse transition is second-order-like, while folding is first-order-like. The system is also studied as a function of the energy parameters. In particular, as the average energetic drive toward compactness is reduced, the two transitions approach each other. At zero average drive, collapse and folding occur almost simultaneously; i.e., the chain collapses directly into the native state. At a specific value of this energy drive the folding temperature falls below the glass point, indicating that the chain is now trapped in local minimum. By varying one parameter in this simple model, we obtain a diverse array of behaviors which may be useful in understanding the different folding properties of various proteins.
State-to-state rate constants for the collisional interaction of Xe(7p), Xe(6p′), and Kr(5p′) atoms with He and Ar
Authors: Zikratov G. , Setser D. W.
Published: July 2002

One-photon laser excitation of Xe(6s[3/2]2) and Kr(5s[3/2]2) atoms that were generated in a discharge-flow reactor was used to study the collisional relaxation of the Kr(5p′[3/2]1, [3/2]2, and [1/2]1), the Xe(7p[3/2]2, [3/2]1, [5/2]2, and [5/2]3), and the Xe(6p′[3/2]1, [3/2]2, and [1/2]1) states in He and Ar. Both cw and pulsed laser excitation techniques were utilized to obtain the total deactivation rate constants and product formation rate constants at 300 K. Collisions with He mainly produce Xe* and Kr* product states with small energy defects, but the rate constants can be as large as 20×10−10 cm3 atom−1 s−1, which correspond to thermally averaged cross sections of 150 Å2. Because of the rapid collisional coupling of populations in nearly isoenergetic levels, multicomponent exponential decay of the initially produced state is frequently observed. The deactivation rate constants for Ar are smaller than for He, but the product distributions tend to be more diverse than for He, and arguments based only on energy defects are not necessarily a good guide to the favored product state(s) from Ar collisions. The magnitude of the quenching cross sections for Ar is consistent with the crossing of an entrance channel with several diabatic exit channel potentials. However, the superlarge quenching cross sections for Xe*–He to just one or two product levels require special considerations. The Kr(5p′) and Xe(6p′ and 7p) rate constants with He are discussed with respect to collisional effects upon the use of cw optical pumping to convert populations in the metastable Xe(6s[3/2]2) and Kr(5s[3/2]2) levels to the Xe(6s′[1/2]0) and Kr([5s′[1/2]0) levels.
Adsorption on surfaces with molecular-scale heterogeneities
Authors: Aranovich G. L. , Donohue M. D.
Published: July 2002

The Ono–Kondo lattice model for the density gradient near a surface is applied to surfaces where the adsorbate–adsorbent interactions are not homogeneous. While solving the general equations would be quite complex, relatively simple solutions can be obtained for periodic surfaces such as a checkerboard. It is shown that the adsorption behavior on surfaces with molecular-scale heterogeneities is very different from adsorption on surfaces where the surface heterogeneities are much larger than the size of the adsorbent molecules.
Dynamic polarizabilities and excitation spectra from a molecular implementation of time-dependent density-functional response theory: N2 as a case study
Authors: Jamorski Christine , Casida Mark E. , Salahub Dennis R.
Published: July 2002

We report the implementation of time-dependent density-functional response theory (TD-DFRT) for molecules using the time-dependent local density approximation (TDLDA). This adds exchange and correlation response terms to our previous work which used the density-functional theory (DFT) random phase approximation (RPA) [M. E. Casida, C. Jamorski, F. Bohr, J. Guan, and D. R. Salahub, in Theoretical and Computational Modeling of NLO and Electronic Materials, edited by S. P. Karna and A. T. Yeates (ACS, Washington, D.C., in press)], and provides the first practical, molecular DFT code capable of treating frequency-dependent response properties and electronic excitation spectra based on a formally rigorous approach. The essentials of the method are described, and results for the dynamic mean dipole polarizability and the first eight excitation energies of N2 are found to be in good agreement with experiment and with results from other ab initio methods.
Helix uncoiling modes of sheared cholesteric liquid crystals
Authors: Rey Alejandro D.
Published: July 2002

This work presents an analysis that identifies the two prominent mechanisms that govern the helix uncoiling of sheared cholesteric liquid crystals. In the presence of free surface orientation helix uncoiling proceed by pitch expansion of traveling orientational waves, and in the presence of fixed surface orientation helix uncoiling proceeds via compression of elastic boundary layers.