bluuebunny/crossref_metadata_2025 huggingface dataset:
Director reorientation processes in a monodomain thin nematic liquid crystal film: A deuterium NMR spectroscopy study
Authors: Luckhurst G. R. , Miyamoto T. , Sugimura A. , Timimi B. A.
Published: September 2002

Deuterium nuclear magnetic resonance (NMR) spectroscopy has been used to investigate the director dynamics in the nematic liquid crystal, 4-pentyl-4′-cyanobiphenyl (5CB), confined between two glass plates and subject to magnetic and electric fields. The nematic cell was held in the NMR probe head so that the electric field, whose direction is normal to the substrate surface, makes an angle of about 45° with the magnetic field. This experimental geometry avoids the degeneracy in the field-induced alignment pathway for the director found for larger angles. A series of deuterium NMR spectra, obtained using a quadrupolar echo sequence, was acquired as a function of time. When the electric field, whose intensity is controlled so that the director makes an angle with the magnetic field is applied to the nematic film, the director moves from being parallel to the magnetic field to being at an angle with respect to the magnetic field because Δε̃ and Δχ̃ are both positive for 5CB. After the electric field is switched off, the director relaxes back to being parallel to the magnetic field. Deuterium NMR spectra were recorded during the turn-on and the turn-off alignment processes as a function of time. The realignment pathway of the director was monitored by measuring Δν̃, the deuterium quadrupolar splitting. We have studied the time dependence of the director orientation for the turn-on and turn-off processes at different temperatures in the nematic phase. The temperature independence of Δχ̃/Δε̃ is also discussed on the basis of experiment and theory. The diamagnetic anisotropy and the rotational viscosity coefficient were also determined as a function of temperature. The deuterium NMR spectra corresponding to the field-induced director dynamics were predicted by an analysis based on hydrodynamic theory.
A second generation multistate empirical valence bond model for proton transport in aqueous systems
Authors: Day Tyler J. F. , Soudackov Alexander V. , Čuma Martin , Schmitt Udo W. , Voth Gregory A.
Published: September 2002

Building on the previously developed multistate empirical valence bond model [U. W. Schmitt and G. A. Voth, J. Chem. Phys 111, 9361 (1999)] for the dynamics and energetics of an excess proton in bulk phase water, a second generation model is described. This model is shown to produce similar dynamic and structural properties to the previous model, while allowing for the use of the full hydronium charge. This characteristic of the model is required for its implementation in a host of realistic applications beyond bulk water. An improved state selection algorithm is also presented, resulting in a significantly reduced energy drift during microcanonical molecular dynamics simulations. The unusually high self diffusion constant of an excess proton in water due to the proton hopping (Grotthuss) process is observed in the simulation data and is found to be quantitatively in the same range as the experimental value if a quantum correction is taken into consideration. Importantly, a more complete analysis of proton transport process is also presented.
Double Rydberg anions: Photoelectron spectroscopy of NH4−, N2H7−, N3H10−, N4H13−, and N5H16−
Authors: Xu S.-J. , Nilles J. M. , Hendricks J. H. , Lyapustina S. A. , Bowen K. H.
Published: September 2002

We report the discovery and photoelectron spectroscopic study of the four double Rydberg anions: N2H7−, N3H10−, N4H13−, and N5H16−; of three solvated double Rydberg anions; and of a previously unseen feature in the spectrum of the double Rydberg anion, NH4−. In each case, vertical detachment energies were measured and vibrational features tentatively assigned. In the case of solvated double Rydberg anions, anion–neutral interaction energies were also determined.
Direct diabatization of electronic states by the fourfold way. II. Dynamical correlation and rearrangement processes
Authors: Nakamura Hisao , Truhlar Donald G.
Published: September 2002

Diabatic representation of coupled potential energy surfaces and their scalar couplings provides a compact and convenient starting point for dynamics calculations carried out in either the adiabatic or diabatic representation. In a previous paper we presented a general, path-independent scheme, called the fourfold way, for calculating diabatic surfaces and their scalar couplings from adiabatic surfaces and electronic density matrices such that the manifold of diabatic states spans the variationally optimized space of a finite number of adiabatic states. In the present paper we extend that scheme in these ways: (1) We show how to include dynamical electronic correlation energy by multireference perturbation theory or configuration interaction based on a complete active reference space. (2) We present a more general strategy for treating rearrangements. (3) We present consistency criteria for testing the validity of the assumptions for a particular choice of reference geometries, diabatic molecular orbital (DMO) ordering, dominant configuration-state-function lists, and choice(s) for reference DMO(s) for systems involving rearrangements. The first extension is illustrated by multiconfiguration quasidegenerate perturbation theory (MC-QDPT) calculations on LiF, and all three extensions are illustrated by MC-QDPT calculations on the reaction Li(2 2S,2 2P)+HF→LiF+H.
Reactive and diffractive scattering of H2 from Pt(111) studied using a six-dimensional wave packet method
Authors: Pijper E. , Kroes G. J. , Olsen R. A. , Baerends E. J.
Published: September 2002

We present results of calculations on dissociative and rotationally (in)elastic diffractive scattering of H2 from Pt(111), treating all six molecular degrees of freedom quantum mechanically. The six-dimensional (6D) potential energy surface was taken from density functional theory calculations using the generalized gradient approximation and a slab representation of the metal surface. The 6D calculations show that out-of-plane diffraction is very efficient, at the cost of in-plane diffraction, as was the case in previous four-dimensional (4D) calculations. This could explain why so little in-plane diffraction was found in scattering experiments, suggesting the surface to be flat, whereas experiments on reaction suggested a corrugated surface. Results of calculations for off-normal incidence of (v=0,j=0) H2 show that initial parallel momentum inhibits dissociation at low normal translational energies, in agreement with experiment, but has little effect for higher energies. Reaction of initial (v=1,j=0) H2 is predicted to be vibrationally enhanced with respect to (v=0,j=0) H2, as was also found in three-dimensional (3D) and 4D calculations, even though H2+Pt(111) is an early barrier system.
Monte Carlo simulation and phase behavior of nonadditive hard-core mixtures in two dimensions
Authors: Saija F. , Giaquinta P. V.
Published: September 2002

We report Monte Carlo results for the thermodynamic and structural properties of a mixture of equally sized hard discs that are characterized by a nonadditive collision diameter for particles belonging to unlike species. We calculated the phase-coexistence lines relative to fluid–fluid demixing using a first-order perturbation theory. We also analyzed the onset of structural ordering in the mixture within a one-phase scheme based on the multiparticle correlation expansion of the statistical entropy, an approach that has been already used to study demixing in three dimensions.
From weak to strong interactions: A comprehensive analysis of the topological and energetic properties of the electron density distribution involving X–H⋯F–Y systems
Authors: Espinosa Enrique , Alkorta Ibon , Elguero José , Molins Elies
Published: September 2002

The topological and energetic properties of the electron density distribution ρ(r) of the isolated pairwise H⋯F interaction have been theoretically calculated at several geometries (0.8<d<2.5 Å) and represented against the corresponding internuclear distances. From long to short geometries, the results presented here lead to three characteristic regions, which correspond to three different interaction states. While the extreme regions are associated to pure closed-shell (CS) and shared-shell (SS) interactions, the middle one has been related to the redistribution of ρ(r) between those electronic states. The analysis carried out with this system has permitted to associate the transit region between pure CS and SS interactions to internuclear geometries involved in the building of the H–F bonding molecular orbital. A comparative analysis between the formation of this orbital and the behavior of some characteristic ρ(r) properties has indicated their intrinsic correspondence, leading to the definition of a bond degree parameter [BD=HCP/ρCP; HCP and ρCP being the total electron energy density and the electron density value at the H⋯F (3,−1) critical point]. Along with the isolated pairwise H⋯F interaction, 79 X–H⋯F–Y (neutral, positively and negatively charged) complexes have been also theoretically considered and analyzed in terms of relevant topological and energetic properties of ρ(r) found at their H⋯F critical points. In particular, the interaction energies of X–H⋯F–Y pure CS interactions have been estimated by using the bond degree parameter. On the other hand, the [F⋯H⋯F]− proton transfer geometry has been related to the local maximum of the electron kinetic energy density (GCP)max.
H
1
,
Li7, and F19 nuclear magnetic resonance and ionic conductivity studies for liquid electrolytes composed of glymes and polyetheneglycol dimethyl ethers of CH3O(CH2CH2O)nCH3 (n=3–50) doped with LiN(SO2CF3)2
Authors: Hayamizu Kikuko , Akiba Etsuo , Bando Toshinori , Aihara Yuichi
Published: September 2002

Solid polyethyleneoxides (PEO) are in effect “polymer liquids” due to their flexibility and high solubility for alkaline salts. To clarify the role of PEO in electrolyte systems, electrolytes composed of members of the “glyme family” [i.e., diglyme(DG), triglyme(TG), tetraglyme(TeG), pentaglyme(PG), and polyethyleneglycol dimethyl ethers(PEGDM)] doped with LiN(SO2CF3)2 were investigated. PEGDMs form a series of low molecular weight PEO-like homologues with molecular weights between 400 and 2500. Electrolytes of the glymes and PEGDMs were prepared for two salt concentrations (ether oxygen: lithium; O:Li) 20:1 and 10:1. The ionic conductivities and the self-diffusion coefficients of the solvent, anion and lithium ions in the electrolytes were measured using pulsed-field gradient spin-echo (PGSE) H1, F19, and Li7 NMR, respectively. From the spin-lattice relaxation times (T1) it was found that the segmental motions of the CH2CH2O moiety and the lithium hopping motions are correlated and that the rate of the segmental motions decreases as the molecular size of the solvent increases. The ionic conductivities calculated from the diffusion coefficients are compared with the experimental ac ionic conductivities. The diffusion and ion conduction mechanisms are discussed and the lithium ion–solvent interactions are shown to depend on the solvent size.
Molecular dynamics simulation of interfacial electrolyte behaviors in nanoscale cylindrical pores
Authors: Cui S. T. , Cochran H. D.
Published: September 2002

Molecular simulations have been carried out on aqueous electrolytes in cylindrical pores a few nanometers in diameter, with uncharged wall or with dispersed, discrete charges modeling silica. The results show a classical Stern layer of adsorbed counterions near the wall, and then a diffuse layer with depleted ion concentration in the interfacial region. The depletion region coincides roughly with the more ordered water structure in the interface. Examination of the interaction energy shows that hydration energy of the ions disfavors the interior, suggesting the importance of the solvent structure near the wall. Comparison with the linearized Poisson–Boltzmann theory indicates qualitative differences in the predicted interfacial behavior.
Time-dependent quantum wave packet study of the H+DCN→HD+CN reaction
Authors: Ma Wan-Yong , Han Ke-Li , Zhang John Z. H.
Published: September 2002

Time-dependent wave packet calculation for the reaction H+DCN→HD+CN is carried out using the semirigid vibrating rotor target model [J. Z. H. Zhang, J. Chem. Phys. 111, 3929 (1999)] on the TSH3 potential energy surface [J. Chem. Phys. 105, 558 (1996)]. Reaction probabilities are calculated from various initial rovibrational states of the reagent. Reaction cross sections and rate constants are calculated and are compared with the previous results for the isotopic reaction H+HCN on the same potential energy surface.
A connection between quantum critical points and classical separatracies of electronic states
Authors: Hopkinson Brian M. , Kwee Edgar D. , Knudson Stephen K.
Published: September 2002

Wave functions for one-electron diatomic molecules such as H2+ and HeH2+ are analyzed by Bader’s atoms in molecules method. The locations of the degenerate axial critical points in the electron density generated from sigma states arising from the n=1–6 united atom manifolds are shown to correspond well with the boundaries of domains obtained solely from a classical description of the electron motion. The relationship clarifies the connection between the atomic and molecular regimes of classical trajectories and the quantum description of the states. In particular, the classical transition from atomic to molecular character roughly corresponds to the appearance of a critical point in the electron density located on the internuclear axis between the nuclei. The global aspects of the relationship between the classical and quantum descriptions helps to demonstrate the classical framework of the quantum picture.
First-principles study of systematics of high-pressure elasticity in rare gas solids, Ne, Ar, Kr, and Xe
Authors: Tsuchiya Taku , Kawamura Katsuyuki
Published: September 2002

Elastic properties and their pressure dependence of rare gas solids (RGSs) Ne, Ar, Kr, and Xe are calculated using the ab initio full-potential linear muffin-tin-orbital method to study their systematics. Though the local density approximation (LDA) underestimates volume of these substances, especially Ne, equations of state and elastic constants are well reproduced in the entire pressure range up to a megabar. The Cauchy deviation, the Zener anisotropy ratio, and the normalized elastic constant are investigated as a function of pressure. It is found that many-body contribution to the interatomic force surprisingly increases with increasing pressure even in all RGSs and it is larger in the heavier element. The elastic anisotropy of all four RGSs gradually decreases with increasing pressure. The normalized elastic constants c11′ and c12′ largely deviate from the ideal values, and cij′’s are remarkably insensitive to pressure over 10 GPa. Moreover, no elastic instability appears under high pressure in all RGSs. Consequently, LDA is sufficiently valid even for RGS since the van der Waals interaction becomes minor with increasing pressure. These trends of high-pressure elastic property are quite different from those of ionic solid and metal.
Relativistic density functional theory using Gaussian basis sets
Authors: Quiney H. M. , Belanzoni P.
Published: September 2002

A four-component formulation of relativistic density functional theory is presented together with the details of its implemention using a G-spinor basis set. The technical features of this approach are compared to those found in the nonrelativistic density functional theory of quantum chemistry which employ scalar basis sets of Gaussian-type functions. Numerical results of the G-spinor expansion method are presented for a sequence of closed-shell atoms, and for a selection of relativistic density functionals, and are compared with finite difference benchmarks.
Scaling of demixing curves and crossover from critical to tricritical behavior in polymer solutions
Authors: Hager J. S. , Anisimov M. A. , Sengers J. V. , Gorodetskiı̆ E. E.
Published: September 2002

In this paper we show that the virial expansion up to third order for the osmotic pressure of a dilute polymer solution, including first-order perturbative corrections to the virial coefficients, allows for a scaling description of phase-separation data for polymer solutions in reduced variables. This scaling description provides a method to estimate the Θ-temperature, where demixing occurs in the limit of vanishing polymer volume fraction φ and infinite chain length N, without explicit assumptions concerning the chain-length dependence of the critical parameters Tc and φc. The scaling incorporates three limiting regimes: The Ising limit asymptotically close to the critical point of phase separation, the pure-solvent limit, and the tricritical limit for the polymer-rich phase asymptotically close to the theta point. We incorporate the effects of critical and tricritical fluctuations on the coexistence-curve scaling by using renormalization-group methods. We present a detailed comparison with experimental and simulation data for coexistence curves and compare our estimates for the Θ-temperatures of several systems with those obtained from different extrapolation schemes.
Effect of CH4 addition on excess electron mobility in liquid Kr
Authors: Borghesani A. F. , Folegani M. , Frabetti P. L. , Piemontese L.
Published: September 2002

The mobility μ of excess electrons has been measured in liquid mixtures of Kr and CH4 as a function of the electric field up to E≈104 V/cm and of the CH4 concentration x up to x≈10%, at a temperature T≈125 K, fairly close to the normal boiling point of Kr (Tb≈120 K) [Nucl. Instrum. Methods Phys. Res. A 430, 277 (1997)]. We present here new data extending the previous set in the low E region. At small E, μ appears to be quite independent of x. CH4 impurities prove to be less efficient in enhancing momentum transfer than liquified rare gas impurities Kr and Xe in liquid Ar. The dependence of μ on E at higher strengths is complicated. On the one hand, the addition of CH4 extends the range of E in which μ is field independent, by efficiently thermalizing the electrons. On the other hand, at the highest field, the presence of the impurities accomplishes a large increase of the electron drift velocity with respect to the pure liquid (up to a factor of 7 for the highest x). Moreover, at intermediate values of E, where electrons are epithermal, there appears to be a crossover between two different behaviors of μ as a function of E. The electric field strength at the crossover, E⋆, is well correlated with x. The behavior of μ can be rationalized in terms of a gas-kinetic model proposed to explain its concentration dependence in the liquified rare gas mixtures Ar–Kr and Ar–Xe. This analysis suggests that the observed crossover is related to the excitation of the first vibrational level of CH4.
Examination of the viability of the Smoluchowski–Collins–Kimball model in fluorescence quenching of S2-xanthione
Authors: Krystkowiak Ewa , Maciejewski Andrzej
Published: September 2002

The fluorescence quenching of S2-xanthione by five different hydrocarbon quenchers in perfluoro-1,3-dimethylcyclohexane has been studied assuming the Smoluchowski–Collins–Kimball (SCK) model. The fluorescence decay curves were measured by means of a picosecond time-resolved, single-photon counting technique. The model used has been shown to satisfactorily describe the process of S2-thioketones fluorescence quenching for six donor–quencher–solvent systems best fitting the model assumption [Krystkowiak and Maciejewski, J. Chem. Phys. 117, 2246 (2002)]. The systems studied were characterized by a short lifetime of an excited donor (equal to 152±2 ps in perfluoro-1,3-dimethylcyclohexane), the quenching process mechanism demanding a direct contact of reacting molecules and at the end the inert solvent. The influence of the shape, size, reactivity anisotropy of quencher molecules on the possibility of the SCK model application, and the values of molecular parameters: R (the sum of the molecular radii), D (the sum of diffusion coefficients), and the specific rate constant of the process (κ) was studied for S2-xanthione–n-hexane, S2-xanthione–n-decane, S2-xanthione–n-hexadecane, and S2-xanthione–longicyclene systems. The system with benzene as a quencher was studied for comparative reasons because of a different mechanism of the S2-xanthione fluorescence quenching process, which does not need a direct contact of reagent molecules. We have confirmed that the fluorescence quenching process of S2-xanthione by hydrocarbons could be described by a Smoluchowski–Collins–Kimball model only when the quencher molecules are characterized by a well-defined shape (not necessarily spherical) and isotropic reactivity and when the excited donor and quencher molecules are in direct contact within the contact pair. A satisfactory fit of the Smoluchowski–Collins–Kimball function the donor fluorescence decay in the presence of the quencher cannot be a sufficient criterion of the correctness of the model application. The parameters R, D, and κ determined for electronically excited donor–quencher pairs should be compared with these obtained from an independent study.
Fourier transform microwave spectroscopy of the CH2CP(X̃  2B1) radical
Authors: Ozeki H. , Habara H. , Ahmad I. K. , Saito S. , Yamamoto S.
Published: September 2002

The hyperfine resolved rotational spectrum of the CH2CP radical in the X̃ 2B1 ground electronic state has been observed for the first time using a Fourier transform microwave spectrometer in combination with a pulsed discharge nozzle. The radical was produced by discharging a mixture of PH3 and C2H2 diluted in either Ar or Ne. A total of 25 hyperfine components of the 202–101 and 303–202 transitions have been measured which enabled us to precisely determine hyperfine coupling constants for both phosphorus and hydrogen nuclei. Spin densities on the phosphorus and β-carbon atoms, estimated from the hyperfine coupling constants, suggest that the radical forms an allenic structure (CP double bond) that is modified by a phosphoryl structure (CP triple bond), which is consistent with the theoretical estimation obtained previously by an ab initio calculation. The nature of the CP chemical bond in the radical is investigated in comparison with the corresponding nitrogen bearing counterparts.
Reactions of N2(a′ 1Σu−) with H2, CH4, and their isotopic variants: Rate constants and the production yields of H(D) atoms
Authors: Umemoto Hironobu , Ozeki Ryoji , Ueda Masashi , Oku Mizuki
Published: September 2002

The reactions of N2(a′ 1Σu−, v=0) with H2, CH4, and their isotopic variants were examined. N2(a′, v=0) was produced by energy transfer from N2(a 1Πg, v=0), while N2(a, v=0) was produced by two-photon excitation of ground state N2. The rate constant for the deactivation of N2(a′,v=0) can be determined by measuring the decay profiles of N2(a, v=0) under the conditions that equilibration between N2(a, v=0) and N2(a′, v=0) can be assumed. The detection of N2(a, v=0) was accomplished by a laser-induced fluorescence technique by utilizing the N2(b′ 1Σu+, v=7) state as an upper state. The rate constants for the quenching of N2(a′, v=0) by N2, H2, D2, CH4, CH2D2, and CD4 were determined to be (2.0±0.1)×10−13, (2.8±0.1)×10−11, (1.7±0.1)×10−11, (2.9±0.2)×10−10, (2.4±0.3)×10−10, and (2.6±0.2)×10−10 cm3 molecule−1 s−1, respectively. H(D) atoms were identified as reaction products by a two-photon laser-induced fluorescence technique. The yields for the production of H(D) atoms from CH4 and CD4 were both determined to be 0.7±0.2 under the assumption that the only exit for H2(D2) is the production of two H(D) atoms. No preferential production of H or D atoms was observed in the reaction with CH2D2, suggesting that the reaction proceeds via bound intermediate complexes.
The rotational spectra of oxirane⋯xenon (129Xe, Xe131, Xe132 Xe134, Xe136 isotopomers): Bond energy and dynamics of Xe
Authors: Velino Biagio , Favero Paolo G. , Caminati Walther
Published: September 2002

The pulsed jet millimeter wave spectra of five isotopomers of the weakly bonded oxirane⋯Xe complex have been measured. Information on the equilibrium conformation, dynamics and dissociation energy have been deduced. The equilibrium distance of Xe with respect to the center-of-mass of the molecules is 3.82 Å, with Xe tilted 15° from the perpendicular to the center-of-mass of the ring toward the oxygen atom. The dissociation energy is estimated, from the centrifugal distortion constant DJ, to be ≈3.9 kJ/mol.
Deviations from the Boltzmann distribution in small microcanonical quantum systems: Two approximate one-particle energy distributions
Authors: Shirts Randall B. , Shirts Michael R.
Published: September 2002

The Boltzmann distribution, which accurately describes the exponential energy dependence of the canonical ensemble, only describes the distribution of one-particle energies for a microcanonical system in the large system limit. We present two distribution functions which closely approximate the distribution of allowed one-particle energies in weakly coupled microcanonical quantum systems. One function is exact for a set of identical harmonic oscillators. The second function is a generalization of work by Andersen et al. [J. Chem. Phys. 114, 6518 (2001)] and is exact for a system with constant microcanonical heat capacity. We compare these two functions with enumerated probabilities for three model systems. The model system distributions and both approximate functions become exponential for large systems but differ from the Boltzmann distribution most dramatically at high energy, for which states can be considerably less populated than predicted by the Boltzmann distribution. Corrections to the Boltzmann distribution may be important in unimolecular reactions, fragmentation dynamics, and in the spectroscopy of nanoclusters.
Photodissociation dynamics of CH2I2 molecules in the ultraviolet range studied by ion imaging
Authors: Xu Haifeng , Guo Ying , Liu Shilin , Ma Xingxiao , Dai Dongxu , Sha Guohe
Published: September 2002

The photodissociation dynamics of diiodomethane molecules has been investigated in the wavelength range of 277–305 nm by an ion imaging spectrometer operated under optimal conditions for velocity mapping, where the ions were generated from (2+1) multiphoton ionization of I(2P3/2) and I*(2P1/2) fragments with the same laser as that to dissociate the parent molecules. The speed and angular distributions of I* and I fragments were determined from the images. The translational energy distribution of I*(2P1/2) fragment consists of a single Gaussian component (named G*), while that of I(2P3/2) consists of two Gaussian components (named G1 and G2). It was found that the component G* and G2 show similar angular distributions and similar fragmentation energy partitioning ratios, indicating that these two components originate from dissociation at the same electronically excited state, while the component G1 is from another state. Three fragmentation pathways were employed to account for the experimental observations, the adiabatic dissociation from the 1B1 state to form I(2P3/2) with component G1, the adiabatic dissociation from the 2B1 state to form I*(2P1/2) with component G*, and the nonadiabatic dissociation from the 2B1 state caused by coupling with the higher 2A1 state to form I(2P3/2) with component G2.
Phase III of methane: Crystal structure and rotational tunneling
Authors: Prager M. , Press W. , Asmussen B. , Combet J.
Published: September 2002

On the basis of the recently determined low temperature crystal structure of phase III of methane new high resolution tunneling spectra on 1.5% CH4 dissolved in CD4 are successfully described by two tunneling systems at sites with two-fold and mirror symmetry, respectively. The analysis is based on tunneling matrix elements. The octopole moments of the CH4 impurities are found to agree with those of the CD4 host molecules. T levels of molecules at m sites show different spin conversion times. Spectra of pure CD4 III are reanalyzed and consistently explained assuming the presence of a small contamination of CD3H.
Full dimensionality quantum calculations of acetylene/vinylidene isomerization
Authors: Zou Shengli , Bowman Joel M.
Published: September 2002

The isomerization of acetylene to vinylidene is examined theoretically in full dimensionality using a recent global potential energy surface. Eigenfunctions and eigenvalues of the exact Hamiltonian, for zero total angular momentum, are obtained using a series of truncation/recoupling procedures that begins with the eigenfunctions of a three degree-of-freedom Hamiltonian for the angular motion. By examining expectation values of the eigenfunctions a number of states are definitely identified with vinylidenelike characteristics.
Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation
Authors: Diehn Maximilian , Alizadeh Ash A. , Rando Oliver J. , Liu Chih Long , Stankunas Kryn , Botstein David , Crabtree Gerald R. , Brown Patrick O.
Published: September 2002

Optimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic expression program in human peripheral T cells responding to stimulation of these receptors. We found that CD28 agonists alone elicited few, but reproducible, changes in gene expression, whereas CD3 agonists elicited a multifaceted temporally choreographed gene expression program. The principal effect of simultaneous engagement of CD28 was to increase the amplitude of the CD3 transcriptional response. The induced genes whose expression was most enhanced by costimulation were significantly enriched for known targets of nuclear factor of activated T cells (NFAT) transcription factors. This enhancement was nearly abolished by blocking the nuclear translocation of NFATc by using the calcineurin inhibitor FK506. CD28 signaling promoted phosphorylation, and thus inactivation, of the NFAT nuclear export kinase glycogen synthase kinase-3 (GSK3), coincident with enhanced dephosphorylation of NFATc proteins. These results provide a detailed picture of the transcriptional program of T cell activation and suggest that enhancement of transcriptional activation by NFAT, through inhibition of its nuclear export, plays a key role in mediating the CD28 costimulatory signal.
Dynamic and clustering model of bacterial chemotaxis receptors: Structural basis for signaling and high sensitivity
Authors: Kim Sung-Hou , Wang Weiru , Kim Kyeong Kyu
Published: September 2002

Bacterial chemotaxis receptors can detect a small concentration gradient of attractants and repellents in the environment over a wide range of background concentration. The clustering of these receptors to form patches observed
in vivo
and
in vitro
has been suspected as a reason for the high sensitivity, and such wide dynamic range is thought to be due to the resetting of the receptor sensitivity threshold by methylation/demethylation of the receptors. However, the mechanisms by which such high sensitivity is achieved and how the methylation/demethylation resets the sensitivity are not well understood. A molecular modeling of an intact bacterial chemotaxis receptor based on the crystal structures of a cytoplasmic domain and a periplasmic domain suggests an interesting clustering of three dimeric receptors and a two-dimensional, close-packed lattice formation of the clusters, where each receptor dimer contacts two other receptor dimers at the cytoplasmic domain and two yet different receptor dimers at the periplasmic domain. This interconnection of the receptors to form a patch of receptor clusters suggests a structural basis for the high sensitivity of the bacterial chemotaxis receptors. Furthermore, we present crystallographic data suggesting that, in contrast to most molecular signaling by conformational changes and/or oligomerization of the signaling molecules, the changes in dynamic property of the receptors on ligand binding or methylation may be the language of the signaling by the chemotaxis receptors. Taken together, the changes of the dynamic property of one receptor propagating mechanically to many others in the receptor patch provides a plausible, simple mechanism for the high sensitivity and the dynamic range of the receptors.
Arrangement of RecA protein in its active filament determined by polarized-light spectroscopy
Authors: Morimatsu Katsumi , Takahashi Masayuki , Nordén Bengt
Published: September 2002

Linear dichroism (LD) polarized-light spectroscopy is used to determine the arrangement of RecA in its large filamentous complex with DNA, active in homologous recombination. Angular orientation data for two tryptophan and seven tyrosine residues, deduced from differential LD of wild-type RecA vs. mutants that were engineered to attenuate the UV absorption of selected residues, revealed a rotation by some 40° of the RecA subunits relative to the arrangement in crystal without DNA. In addition, conformational changes are observed for tyrosine residues assigned to be involved in DNA binding and in RecA–RecA contacts, thus potentially related to the global structure of the filament and its biological function. The presented spectroscopic approach, called “Site-Specific Linear Dichroism” (SSLD), may find forceful applications also to other biologically important fibrous complexes not amenable to x-ray crystallographic or NMR structural analysis.
Stimulation of the cell cycle and maize transformation by disruption of the plant retinoblastoma pathway
Authors: Gordon-Kamm William , Dilkes Brian P. , Lowe Keith , Hoerster George , Sun Xifan , Ross Margit , Church Laura , Bunde Chris , Farrell Jeff , Hill Patrea , Maddock Sheila , Snyder Jane , Sykes Louisa , Li Zhongsen , Woo Young-min , Bidney Dennis , Larkins Brian A.
Published: September 2002

The genome of the Mastreviruses encodes a replication-associated protein (RepA) that interacts with members of the plant retinoblastoma-related protein family, which are putative cell cycle regulators. Expression of ZmRb1, a maize retinoblastoma-related gene, and RepA inhibited and stimulated, respectively, cell division in tobacco cell cultures. The effect of RepA was mitigated by over-expression of ZmRb1. RepA increased transformation frequency and callus growth rate of high type II maize germplasm. RepA-containing transgenic maize calli remained embryogenic, were readily regenerable, and produced fertile plants that transmitted transgene expression in a Mendelian fashion. In high type II, transformation frequency increased with the strength of the promoter driving RepA expression. When a construct in which RepA was expressed behind its native LIR promoter was used, primary transformation frequencies did not improve for two elite Pioneer maize inbreds. However, when LIR:RepA-containing transgenic embryos were used in subsequent rounds of transformation, frequencies were higher in the RepA+ embryos. These data demonstrate that RepA can stimulate cell division and callus growth in culture, and improve maize transformation.
Structural genomics of the
Thermotoga maritima
proteome implemented in a high-throughput structure determination pipeline
Authors: Lesley Scott A. , Kuhn Peter , Godzik Adam , Deacon Ashley M. , Mathews Irimpan , Kreusch Andreas , Spraggon Glen , Klock Heath E. , McMullan Daniel , Shin Tanya , Vincent Juli , Robb Alyssa , Brinen Linda S. , Miller Mitchell D. , McPhillips Timothy M. , Miller Mark A. , Scheibe Daniel , Canaves Jaume M. , Guda Chittibabu , Jaroszewski Lukasz , Selby Thomas L. , Elsliger Marc-Andre , Wooley John , Taylor Susan S. , Hodgson Keith O. , Wilson Ian A. , Schultz Peter G. , Stevens Raymond C.
Published: September 2002

Structural genomics is emerging as a principal approach to define protein structure–function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium
Thermotoga maritima
. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the
T. maritima
proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.
CD8+T cell responses against a dominant cryptic HLA-A2 epitope after NY-ESO-1 peptide immunization of cancer patients
Authors: Gnjatic Sacha , Jäger Elke , Chen Weisan , Altorki Nasser K. , Matsuo Mitsutoshi , Lee Sang-Yull , Chen Qiyuan , Nagata Yasuhiro , Atanackovic Djordje , Chen Yao-Tseng , Ritter Gerd , Cebon Jonathan , Knuth Alexander , Old Lloyd J.
Published: September 2002

NY-ESO-1 is a germ cell antigen aberrantly expressed in different tumor types that elicits strong humoral and cellular immune responses in cancer patients. Monitoring spontaneous CD8+T cell responses against NY-ESO-1 peptides 157–165 (S9C) and 157–167 (S11L) in a series of HLA-A2+cancer patients showed that these two peptides had overlapping antigenic profiles and were equally immunogenic. However, discrepancies between S9C and S11L reactivities were observed upon vaccination with both peptides to generate or boost T cell responses to NY-ESO-1 in cancer patients. We here analyze the fine specificity of these responses and describe an HLA-A2-restricted epitope, NY-ESO-1 peptide 159–167 (L9L), which is strongly recognized by CD8+T cells as a result of peptide vaccination of cancer patients. Responses to L9L were stimulated by S11L and appeared early in the course of vaccination, independently of S9C responses. However, L9L-specific CD8+T cells failed to recognize tumor cells naturally expressing NY-ESO-1 or B lymphoblastoid cells transduced with NY-ESO-1. Processing of L9L could be rescued after IFN-γ treatment of tumor cells or by dendritic cells pulsed with NY-ESO-1 protein/antibody immune complexes. The present results demonstrate a dual specificity within peptide S11L, with S9C as the natural antigenic tumor epitope, and L9L as a cryptic epitope with dominant immunogenicity upon vaccination that diverts the immune response from tumor recognition. These unanticipated findings raise questions about the use of S11L in the clinic and emphasize the importance of analyzing the fine specificity of vaccine-induced T cell responses in patients as a basis for constructing effective cancer vaccines.
Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by
Escherichia coli
RNA polymerase
Authors: Forde Nancy R. , Izhaky David , Woodcock Glenna R. , Wuite Gijs J. L. , Bustamante Carlos
Published: September 2002

Escherichia coli
RNA polymerase translocates along the DNA discontinuously during the elongation phase of transcription, spending proportionally more time at some template positions, known as pause and arrest sites, than at others. Current models of elongation suggest that the enzyme backtracks at these locations, but the dynamics are unresolved. Here, we study the role of lateral displacement in pausing and arrest by applying force to individually transcribing molecules. We find that an assisting mechanical force does not alter the translocation rate of the enzyme, but does reduce the efficiency of both pausing and arrest. Moreover, arrested molecules cannot be rescued by force, suggesting that arrest occurs by a bipartite mechanism: the enzyme backtracks along the DNA followed by a conformational change of the ternary complex (RNA polymerase, DNA and transcript), which cannot be reversed mechanically.
Phytochrome from
Agrobacterium tumefaciens
has unusual spectral properties and reveals an N-terminal chromophore attachment site
Authors: Lamparter Tilman , Michael Norbert , Mittmann Franz , Esteban Berta
Published: September 2002

Phytochromes are photochromic photoreceptors with a bilin chromophore that are found in plants and bacteria. The soil bacterium
Agrobacterium tumefaciens
contains two genes that code for phytochrome-homologous proteins, termed
Agrobacterium
phytochrome 1 and 2 (Agp1 and Agp2). To analyze its biochemical and spectral properties, Agp1 was purified from the clone of an
E. coli
overexpressor. The protein was assembled with the chromophores phycocyanobilin and biliverdin, which is the putative natural chromophore, to photoactive holoprotein species. Like other bacterial phytochromes, Agp1 acts as light-regulated His kinase. The biliverdin adduct of Agp1 represents a previously uncharacterized type of phytochrome photoreceptor, because photoreversion from the far-red absorbing form to the red-absorbing form is very inefficient, a feature that is combined with a rapid dark reversion. Biliverdin bound covalently to the protein; blocking experiments and site-directed mutagenesis identified a Cys at position 20 as the binding site. This particular position is outside the region where plant and some cyanobacterial phytochromes attach their chromophore and thus represents a previously uncharacterized binding site. Sequence comparisons imply that the region around Cys-20 is a ring D binding motif in phytochromes.
The novel Rho-GTPase activating gene
MEGAP
/
srGAP3
has a putative role in severe mental retardation
Authors: Endris Volker , Wogatzky Birgit , Leimer Uwe , Bartsch Dusan , Zatyka Malgorzata , Latif Farida , Maher Eamonn R. , Tariverdian Gholamali , Kirsch Stefan , Karch Dieter , Rappold Gudrun A.
Published: September 2002

In the last few years, several genes involved in X-specific mental retardation (MR) have been identified by using genetic analysis. Although it is likely that additional genes responsible for idiopathic MR are also localized on the autosomes, cloning and characterization of such genes have been elusive so far. Here, we report the isolation of a previously uncharacterized gene,
MEGAP
, which is disrupted and functionally inactivated by a translocation breakpoint in a patient who shares some characteristic clinical features, such as hypotonia and severe MR, with the 3p
−
syndrome. By fluorescence
in situ
hybridization and loss of heterozygosity analysis, we demonstrated that this gene resides on chromosome 3p25 and is deleted in 3p
−
patients that present MR.
MEGAP
/
srGAP3
mRNA is predominantly and highly expressed in fetal and adult brain, specifically in the neurons of the hippocampus and cortex, structures known to play a pivotal role in higher cognitive function, learning, and memory. We describe several
MEGAP
/
srGAP3
transcript isoforms and show that MEGAP/srGAP3
a
and -
b
represent functional GTPase-activating proteins (GAP) by an
in vitro
GAP assay. MEGAP/srGAP3 has recently been shown to be part of the Slit-Robo pathway regulating neuronal migration and axonal branching, highlighting the important role of MEGAP/srGAP3 in mental development. We propose that haploinsufficiency of
MEGAP
/
srGAP3
leads to the abnormal development of neuronal structures that are important for normal cognitive function.
Creating nanocavities of tunable sizes: Hollow helices
Authors: Gong Bing , Zeng Huaqiang , Zhu Jin , Yua Lihua , Han Yaohua , Cheng Shizhi , Furukawa Mako , Parra Rubén D. , Kovalevsky Andrey Y. , Mills Jeffrey L. , Skrzypczak-Jankun Ewa , Martinovic Suzana , Smith Richard D. , Zheng Chong , Szyperski Thomas , Zeng Xiao Cheng
Published: September 2002

A general strategy for creating nanocavities with tunable sizes based on the folding of unnatural oligomers is presented. The backbones of these oligomers are rigidified by localized, three-center intramolecular hydrogen bonds, which lead to well-defined hollow helical conformations. Changing the curvature of the oligomer backbone leads to the adjustment of the interior cavity size. Helices with interior cavities of 10 Å to >30 Å across, the largest thus far formed by the folding of unnatural foldamers, are generated. Cavities of these sizes are usually seen at the tertiary and quaternary structural levels of proteins. The ability to tune molecular dimensions without altering the underlying topology is seen in few natural and unnatural foldamer systems.
Cellular inhibitors with Fv1-like activity restrict human and simian immunodeficiency virus tropism
Authors: Cowan Simone , Hatziioannou Theodora , Cunningham Tshaka , Muesing Mark A. , Gottlinger Heinrich G. , Bieniasz Paul D.
Published: September 2002

Many nonhuman primate cells are unable to support the replication of HIV-1, whereas others are nonpermissive for infection by simian immunodeficiency virus from macaques (SIVmac). Here, we show that restricted HIV-1 and SIVmac infection of primate cell lines shares some salient features with Fv1 and Ref1-mediated restriction of murine retrovirus infection. In particular, the nonpermissive phenotype is most evident at low multiplicities of infection, results in reduced accumulation of reverse transcription products, and is dominant in heterokaryons generated by fusion of permissive and nonpermissive target cells. Moreover, in nonpermissive primate cells, HIV-1 and SIVmac infection is cooperative, and enveloped HIV-1 virus-like particles, minimally containing Gag and protease, abrogate restriction. In African green monkey cells, HIV-1 virus-like particles ablate restrictions to HIV-1 and SIVmac, suggesting that both are restricted by the same factor. Finally, a virus that contains an HIV-1 capsid-p2 domain in an SIVmac background exhibits a tropism for primate cells that is HIV-1-like rather than SIVmac-like. These data indicate the existence of one or more saturable inhibitors that are polymorphic in primates and prevent HIV and SIV infection by targeting the capsid of the incoming lentivirus particle.
Modulation of TCR-induced transcriptional profiles by ligation of CD28, ICOS, and CTLA-4 receptors
Authors: Riley James L. , Mao Mao , Kobayashi Sumire , Biery Matt , Burchard Julja , Cavet Guy , Gregson Brian P. , June Carl H. , Linsley Peter S.
Published: September 2002

Signals generated by T cell receptor (TCR) and CD28 engagement are required for optimal T cell activation, but how these signals integrate within the cell is still largely unknown. We have used near genome-scale expression profiling to monitor T cell signal transduction pathways triggered via TCR and/or costimulatory receptors. Ligation of CD28 alone induced a set of short-lived early response transcripts in both Jurkat T cells and primary CD4 T cells, thus providing evidence that CD28 engagement can affect gene regulation independently of TCR engagement. Simultaneous signaling through both the TCR and CD28 resulted in altered expression of several thousand genes following several distinct temporal patterns. Most of these gene regulations were induced by TCR signaling alone and were augmented to varying degrees by CD28 costimulation. CD28 and ICOS costimulation had nearly identical effects on gene regulation, but a few transcripts (e.g., IL2, IL9) were significantly more affected by CD28. Therefore, the distinctive functional outcomes of costimulation via CD28 and ICOS are accompanied by relatively few distinct differences in gene expression. Cytotoxic T lymphocyte antigen 4 (CTLA-4) engagement selectively blocked augmentation of gene regulations by CD28-mediated costimulation, but did not ablate gene regulation induced by TCR triggering alone.
Protein–DNA computation by stochastic assembly cascade
Authors: Bar-Ziv Roy , Tlusty Tsvi , Libchaber Albert
Published: September 2002

The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan DNA sequence through a cascade of random nucleation and disassembly events that is mechanistically similar to the dynamic instability of microtubules. This iterative cascade is a multistage kinetic proofreading process that amplifies minute differences, even a single base change. Our measurements suggest that this stochastic Turing-like machine can compute certain integral transforms.