bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid detection of hepatitis B virus mutations using real-time PCR and melting curve analysis
Authors: Zhang Manna , Gong Yuewen , Osiowy Carla , Minuk Gerald Y.
Published: March 2004

Current methods of detecting hepatitis B virus (HBV) mutations are time consuming, labor intensive, and not suitable for screening large numbers of samples. In the present study, we documented the advantages of a system that exploits differences in thermal stability between perfect match and mismatch hybrids, and thereby distinguishes between wild-type and mutants. Hybridization probes were designed complementary to specific wild-type HBV sequences in surface (S), precore, and basal core promoter (BCP) regions of the HBV genome (nt 587, 1896, and 1762/1764, respectively). Two probes were designed for each mutation: anchor probes were 3’ labeled with fluorescein and sensor probes, 5’ labeled with LC-Red 640, and 3’ phosphorylated. Temperatures for each probe melted from amplification products were then determined in a melting program. Sera from 12 patients, each containing identified HBV mutants (6 S-escape, 1 precore, 1 BCP, and 4 mixed precore and BCP), and 5 control sera from patients with wild-type virus were analyzed. Genomic sequences of mutant and wild-type viruses were confirmed by direct sequencing. Real-time polymerase chain reaction (PCR) with fluorescent hybridization probes accurately identified each mutant and wild-type genome. Melting temperatures obtained from probe-product duplexes for the 3 mutants were distinguished from wild-type (>4.0°C, minimal) within 45 minutes. The sensitivity of the system was 100 copies/mL and as few as 5% of mutant among wild-type virus were detected. In conclusion, real-time PCR with fluorescent hybridization probes is a specific, sensitive, quantitative, and rapid means of detecting clinically relevant HBV mutants.
Pretreatment with FK506 up-regulates insulin receptors in regenerating rat liver
Authors: Escribano Oscar , Fernández-Moreno María Dolores , Piña María Jesús , Fueyo Jesús , Menor César , Román Irene Dolores , Guijarro Luis G.
Published: March 2004

This report examines the effect of FK506 pretreatment on liver insulin receptor expression in partially (70%) hepatectomized rats. FK506 pretreatment led to an increased insulin receptor number 24 hours after hepatectomy, detected by means of insulin binding and cross-linking procedures. This increase was related to enhanced insulin receptor expression determined by in vitro mRNA translation and Western blot techniques. We also tested the functionality of the expressed insulin receptors by [3H] thymidine incorporation into DNA in insulin-stimulated hepatocytes. The results show that FK506 pretreatment elicits an increase in the amount of insulin receptor α-subunits as measured by Western blot. Maximum α-subunit expression recorded 24 hours after surgery was preceded by increased insulin receptor mRNA levels, which were detected 6 hours after hepatectomy. Moreover, in FK506-pretreated rat hepatocytes, obtained from remnant livers 24 hours after partial hepatectomy (PH), the increase in insulin receptor number was associated with improved sensitivity to the hormone. However, in both experimental groups (FK506-pretreated and nonpretreated rats), the sensitivity of hepatocytes toward epidermal growth factor (EGF) showed no significant change, which suggests a specific effect of FK506 on insulin receptor expression. In conclusion, our findings suggest that FK506 pretreatment induces insulin receptor expression in regenerating rat liver and promotes liver regeneration in hepatectomized rats.
Effect of tauroursodeoxycholic acid on endoplasmic reticulum stress-induced caspase-12 activation
Authors: Xie Qing , Khaoustov Vladimir I. , Chung Charles C. , Sohn Joohyun , Krishnan Bhuvaneswari , Lewis Dorothy E. , Yoffe Boris
Published: March 2004

Activation of death receptors and mitochondrial damage are well-described common apoptotic pathways. Recently, a novel pathway via endoplasmic reticulum (ER) stress has been reported. We assessed the role of tauroursodeoxycholic acid (TUDCA) in inhibition of caspase-12 activation and its effect on calcium homeostasis in an ER stress-induced model of apoptosis. The human liver-derived cell line, Huh7, was treated with thapsigargin (TG) to induce ER stress. Typical morphologic changes of ER stress preceded development of apoptotic changes, including DNA fragmentation and cleavage of poly (adenosine diphosphate-ribose) polymerase (PARP), as well as activation of caspase-3 and -7. Elevation of intracellular calcium levels without loss of mitochondrial membrane potential (MMP) was shown using Fluo-3/Fura-red labeling and flow cytometry, and confirmed by induction of Bip/GRP78, a calcium-dependent chaperon of ER lumen. These changes were accompanied by procaspase-12 processing. TUDCA abolished TG-induced markers of ER stress; reduced calcium efflux, induction of Bip/GRP78, and caspase-12 activation; and subsequently inhibited activation of effector caspases and apoptosis. In conclusion, we propose that mitochondria play a secondary role in ER-mediated apoptosis and that TUDCA prevents apoptosis by blocking a calcium-mediated apoptotic pathway as well as caspase-12 activation. This novel mechanism of TUDCA action suggests new intervention methods for ER stress-induced liver disease.
Hyperosmolarity triggers CD95 membrane trafficking and sensitizes rat hepatocytes toward CD95L-induced apoptosis
Authors: Reinehr Roland , Graf Dirk , Fischer Richard , Schliess Freimut , Häussinger Dieter
Published: March 2004

The effect of hyperosmolarity on CD95 membrane targeting and CD95 ligand (CD95L)-induced apoptosis was studied in rat hepatocytes. CD95 showed a predominant intracellular localization in normoosmotically exposed rat hepatocytes, whereas hyperosmotic exposure induced, within 1 hour, CD95 trafficking to the plasma membrane followed by activation of caspase-3 and -8. Hyperosmotic CD95 membrane targeting was sensitive to inhibition of c-Jun-N-terminal kinase (JNK), protein kinase C (PKC), and cyclic adenosine monophosphate, but not to inhibition of extracellular regulated kinases (Erks) or p38 mitogen activated protein kinase (p38MAPK). Hyperosmotic CD95 targeting to the plasma membrane was dose-dependently diminished by glutamine or taurine, probably caused by an augmentation of volume regulatory increase. Despite CD95 trafficking to the plasma membrane and caspase activation, hyperosmolarity per se did not induce apoptosis. Hyperosmolarity, however, sensitized hepatocytes toward CD95L-induced apoptosis, as assessed by annexin V staining and terminal deoxynucleotidyl transferase-mediated X-dUTP nick-end labeling (TUNEL) assay. This sensitization was abolished when hyperosmotic CD95 membrane trafficking was prevented by cyclic adenosine monophosphate, PKC, or JNK inhibition, whereas these effectors had no effect on CD95L-induced apoptosis in normoosmotically exposed hepatocytes. CD95L addition under normoosmotic conditions caused CD95 membrane trafficking, which was sensitive to JNK inhibition, but not to cyclic adenosine monophosphate or inhibition of PKC, Erks, and p38MAPK. In conclusion, multiple signaling pathways are involved in CD95 membrane trafficking. Hyperosmotic hepatocyte shrinkage induces CD95 trafficking to the plasma membrane, which involves JNK-, PKA-, and PKC-dependent mechanisms and sensitizes hepatocytes toward CD95L-mediated apoptosis.
Insulin inhibits secretin-induced ductal secretion by activation of PKC alpha and inhibition of PKA activity
Authors: LeSage Gene D. , Marucci Luca , Alvaro Domenico , Glaser Shannon S. , Benedetti Antonio , Marzioni Marco , Patel Tushar , Francis Heather , Phinizy Jo Lynne , Alpini Gianfranco
Published: March 2004

Insulin stimulates canalicular bile flow by interaction with hepatocytes. Insulin regulates the function of a number of epithelia through activation and membrane translocation of Ca2+-dependent PKC isoforms. No information exists regarding insulin regulation of ductal bile secretion. The aim of the study was to determine the role and mechanisms of action of insulin in the regulation of cholangiocyte secretion in BDL rats. We determined the subcellular localization of insulin receptor in cholangiocytes. We measured the effect of insulin on (1) secretin-stimulated cAMP levels in cholangiocytes and duct expansion in intrahepatic bile duct units (IBDUs) in the absence or presence of BAPTA/AM, H7 or rottlerin and (2) bile flow. We evaluated (1) if insulin effects are associated with activation of PKC alpha and (2) if activation of PKC causes inhibition of secretin-stimulated cAMP levels and PKA activity. We found insulin receptors only in the apical domain of cholangiocytes. Insulin inhibited secretin-induced choleresis and secretin-stimulated cholangiocyte cAMP levels. Insulin inhibited secretin-induced secretion in IBDUs when applied at the basolateral membrane or microinjected into IBDU lumen. Insulin inhibitory effects on cholangiocyte secretion were blocked by BAPTA/AM and H7. Insulin induced activation of PKC alpha, which decreased secretin-stimulated cAMP and PKA activity. In conclusion, insulin inhibited secretin-induced ductal secretion of BDL rats through activation of PKC and inhibition of secretin-stimulated cAMP and PKA activity. In conclusion, insulin counter-regulates cholangiocyte secretory processes in the BDL model, which is characterized by cholangiocyte proliferation.
Demonstration of direct lineage between hepatocytes and hepatocellular carcinoma in diethylnitrosamine-treated rats
Authors: Bralet Marie-Pierre , Pichard Virginie , Ferry Nicolas
Published: March 2004

The question whether hepatocellular carcinoma (HCC) arises from dedifferentiation of mature hepatocytes or from proliferation of liver stem cells is still debated. In the present study, we used retroviral-mediated genetic labeling to investigate the fate of mature hepatocytes in rats after administration of diethylnitrosamine (DEN). Mature hepatocytes were genetically labeled by intravenous injection of retroviral vectors containing the Escherichia coli β-galactosidase gene coupled to a nuclear localization signal (nls-LacZ) 1 day after partial hepatectomy. Liver biopsies performed after completion of hepatic regeneration showed that 18.3% of hepatocytes expressed the nls-LacZ transgene. Rats were then treated with DEN in drinking water for 12 weeks and sacrificed between 98 and 151 days after the onset of DEN administration. Clones of β-galactosidase positive cells were observed, half of which (53%) also expressed the placental form of glutathione-S-transferase (GSTp), a marker of preneoplastic cells. HCCs of various sizes expressing GSTp were present in all animals. Careful examination of 90 HCCs revealed that 16 (17.7%) also expressed nls-LacZ. This figure precisely matched the proportion of labeled hepatocytes before DEN treatment (18.3%). In conclusion, a random clonal origin of HCC from mature hepatocytes is seen in the DEN model of hepatocarcinogenesis.
Ursodeoxycholic acid in cholestatic liver disease: Mechanisms of action and therapeutic use revisited
Authors: Paumgartner Gustav , Beuers Ulrich
Published: March 2004

Ursodeoxycholic acid (UCDA) is increasingly used for the treatment of cholestatic liver diseases. Experimental evidence suggests three major mechanisms of action: (1) protection of cholangiocytes against cytotoxicity of hydrophobic bile acids, resulting from modulation of the composition of mixed phospholipid-rich micelles, reduction of bile acid cytotoxicity of bile and, possibly, decrease of the concentration of hydrophobic bile acids in the cholangiocytes; (2) stimulation of hepatobiliary secretion, putatively via Ca2+- and protein kinase C-α-dependent mechanisms and/or activation of p38MAPK and extracellular signal-regulated kinases (Erk) resulting in insertion of transporter molecules (e.g., bile salt export pump, BSEP, and conjugate export pump, MRP2) into the canalicular membrane of the hepatocyte and, possibly, activation of inserted carriers; (3) protection of hepatocytes against bile acid-induced apoptosis, involving inhibition of mitochondrial membrane permeability transition (MMPT), and possibly, stimulation of a survival pathway. In primary biliary cirrhosis, UDCA (13-15 mg/kg/d) improves serum liver chemistries, may delay disease progression to severe fibrosis or cirrhosis, and may prolong transplant-free survival. In primary sclerosing cholangitis, UDCA (13-20 mg/kg/d) improves serum liver chemistries and surrogate markers of prognosis, but effects on disease progression must be further evaluated. Anticholestatic effects of UDCA have also been reported in intrahepatic cholestasis of pregnancy, liver disease of cystic fibrosis, progressive familial intrahepatic cholestasis, and chronic graft-versus-host disease. Future efforts will focus on definition of additional clinical uses of UDCA, on optimized dosage regimens, as well as on further elucidation of mechanisms of action of UDCA at the molecular level.
Hydrogen atom formation from the photodissociation of water ice at 193 nm
Authors: Yabushita Akihiro , Hashikawa Yuichi , Ikeda Atsushi , Kawasaki Masahiro , Tachikawa Hiroto
Published: March 2004

The TOF spectra of photofragment hydrogen atoms from the 193 nm photodissociation of amorphous ice at 90–140 K have been measured. The spectra consist of both a fast and a slow components that are characterized by average translational energies of 2kBTtrans=0.39±0.04 eV (2300±200 K) and 0.02 eV (120±20 K), respectively. The incident laser power dependency of the hydrogen atom production suggests one-photon process. The electronic excitation energy of a branched cluster, (H2O)6+1, has been theoretically calculated, where (H2O)6+1 is a (H2O)6 cyclic cluster attached by a water molecule with the hydrogen bond. The photoabsorption of this branched cluster is expected to appear at around 200 nm. The source of the hydrogen atoms is attributed to the photodissociation of the ice surface that is attached by water molecules with the hydrogen bond. Atmospheric implications are estimated for the photodissociation of the ice particles (Noctilucent clouds) at 190–230 nm in the region between 80 and 85 km altitude.
Ab initio potential energy surface, variational transition state theory, and quasiclassical trajectory studies of the F+CH4→HF+CH3 reaction
Authors: Troya Diego , Millán Judith , Baños Irene , González Miguel
Published: March 2004

In this work we present a study of the F+CH4→HF+CH3 reaction (ΔH298 K∘=−32.0kcal mol−1) using different methods of the chemical reaction theory. The ground potential energy surface (PES) is characterized using several ab initio methods. Full-dimensional rate constants have been calculated employing the variational transition state theory and using directly ab initio data. A triatomic analytical representation of the ground PES was derived from ab initio points calculated at the second- and fourth-order Møller–Plesset levels with the 6-311+G(2df,2pd) basis set, assuming the CH3 fragment to be a 15 a.m.u. pseudoatom in the fitting process. This is suggested from experiments that indicate that the methyl group is uncoupled to the reaction coordinate. A dynamics study by means of the quasiclassical trajectory (QCT) method and employing this analytical surface was also carried out. The experimental data available on the HF internal states distributions are reproduced by the QCT results. Very recent experimental information about the reaction stereodynamics is also borne out by our QCT calculations. Comparisons with the benchmark F+H2 and analogous Cl+CH4 reactions are established throughout.
The relationship between crystal structure and methyl and t-butyl group dynamics in van der Waals organic solids
Authors: Beckmann Peter A. , Paty Carol , Allocco Elizabeth , Herd Maria , Kuranz Carolyn , Rheingold Arnold L.
Published: March 2004

We report x-ray diffractometry in a single crystal of 2-t-butyl-4-methylphenol (TMP) and low-frequency solid state nuclear magnetic resonance (NMR) proton relaxometry in a polycrystalline sample of TMP. The x-ray data show TMP to have a monoclinic, P21/c, structure with eight molecules per unit cell and two crystallographically inequivalent t-butyl group (C(CH3)3) sites. The proton spin-lattice relaxation rates were measured between 90 and 310 K at NMR frequencies of 8.50, 22.5, and 53.0 MHz. The relaxometry data is fitted with two models characterizing the dynamics of the t-butyl groups and their constituent methyl groups, both of which are consistent with the determined x-ray structure. In addition to presenting results for TMP, we review previously reported x-ray diffractometry and low-frequency NMR relaxometry in two other van der Waals solids which have a simpler structure. In both cases, a unique model for the reorientational dynamics was found. Finally, we review a similar previously reported analysis in a van der Waals solid with a very complex structure in which case fitting the NMR relaxometry requires very many parameters and serves mainly as a flag for a careful x-ray diffraction study.
Principal instabilities of large amplitude inertio-gravity waves
Authors: Yau K.-H. , Klaassen G. P. , Sonmor L. J.
Published: March 2004

We analyze the three-dimensional stability properties of monochromatic, large-amplitude, nonhydrostatic inertio-gravity waves propagating in a rotating stratified fluid with no mean shear. The ratio of Coriolis parameter f to the Brunt-Väisälä frequency N is fixed at a value f/N=0.01, chosen to be representative of the Earth’s atmosphere and upper oceans in extra-tropical latitudes. By using Floquet theory combined with suitable coordinate transformations, our analysis provides an exact representation of the spatial and temporal periodicity of the basic wave state. Growth rates are computed for several discrete phase-elevation angles 80°⩽θ⩽89.7°, spanning the frequency range in which rotational effects become important, and the basic wave state changes from fully overturned to suboverturned. For each basic wave, we identify the growth rate peaks in disturbance wavenumber space—these are the principal modes. At the lowest phase-elevation angle considered, θ=80°, the dominant principal mode is similar to its low-frequency nonrotating counterpart, with disturbance roll axes aligned in, or nearly in, the direction of the largest component of basic wave shear. As θ increases to values where the effects of rotation are more strongly manifested, the dominant rotating mode shifts to oblique orientation. At still higher values of θ, the fastest-growing modes have roll axes oriented orthogonal to the main shear component of the basic wave. At the highest values of θ considered in this study, the waves are no longer vertically overturned, but still feature minimum Richardson numbers below 14. We find that such low-frequency waves are subject to wave-scale instabilities: for the largest amplitude considered, the instability shows no preferred orientation, while at a somewhat lower amplitude, the dominant instability prefers an oblique orientation. Dominant oblique instabilities have not been reported in previous approximate stability analyses of inertio-gravity waves, although they have been found in nonlinear simulations. Our analysis resolves this discrepancy.
Quantum control of molecular orientation by two-color laser fields
Authors: Ohmura Hideki , Nakanaga Taisuke
Published: March 2004

We demonstrate molecular orientation by using phase-controlled two-color ω+2ω laser pulses with an intensity of 1.0×1012 W/cm2 and a pulse duration of 130 fs. The orientation of three iodine-containing molecules (IBr, CH3I, and C3H5I) was monitored by the directional asymmetries of the photofragment angular distribution in dissociative ionization. In all three molecules, the directional asymmetry showed an oscillating behavior dependent on the relative phase difference between ω and 2ω pulses. The phase dependence of the directional asymmetry observed in iodine ions and counterpart ions were out of phase with each other. This result shows that a phase-controlled ω+2ω optical field discriminates between parallel and antiparallel configurations of aligned molecules that have a permanent dipole. This method performed well because (1) molecular orientation can be achieved by all-optical fields; (2) the direction of orientation is easily switched by changing the sign of the quantum interference; and (3) this method is free from any resonance constraint and thus can be applied to any molecule.
Hydrogen desorption kinetics from the Si(1−x)Gex(100)-(2×1) surface
Authors: Tok E. S. , Ong S. W. , Kang H. Chuan
Published: March 2004

We study the influence of germanium atoms upon molecular hydrogen desorption energetics using density functional cluster calculations. A three-dimer cluster is used to model the Si(1−x)Gex(100)-(2×1) surface. The relative stabilities of the various monohydride and clean surface configurations are computed. We also compute the energy barriers for desorption from silicon, germanium, and mixed dimers with various neighboring configurations of silicon and germanium atoms. Our results indicate that there are two desorption channels from mixed dimers, one with an energy barrier close to that for desorption from germanium dimers and one with an energy barrier close to that for desorption from silicon dimers. Coupled with the preferential formation of mixed dimers over silicon or germanium dimers on the surface, our results suggest that the low barrier mixed dimer channel plays an important role in hydrogen desorption from silicon–germanium surfaces. A simple kinetics model is used to show that reasonable thermal desorption spectra result from incorporating this channel into the mechanism for hydrogen desorption. Our results help to resolve the discrepancy between the surface germanium coverage found from thermal desorption spectra analysis, and the results of composition measurements using photoemission experiments. We also find from our cluster calculations that germanium dimers exert little influence upon the hydrogen desorption barriers of neighboring silicon or germanium dimers. However, a relatively larger effect upon the desorption barrier is observed in our calculations when germanium atoms are present in the second layer.
The evaporation/condensation transition of liquid droplets
Authors: MacDowell Luis G. , Virnau Peter , Müller Marcus , Binder Kurt
Published: March 2004

The condensation of a supersaturated vapor enclosed in a finite system is considered. A phenomenological analysis reveals that the vapor is found to be stable at densities well above coexistence. The system size at which the supersaturated vapor condenses into a droplet is found to be governed by a typical length scale which depends on the coexistence densities, temperature and surface tension. When fluctuations are neglected, the chemical potential is seen to show a discontinuity at an effective spinodal point, where the inhomogeneous state becomes more stable than the homogeneous state. If fluctuations are taken into account, the transition is rounded, but the slope of the chemical potential versus density isotherm develops a discontinuity in the thermodynamic limit. In order to test the theoretical predictions, we perform a simulation study of droplet condensation for a Lennard-Jones fluid and obtain loops in the chemical potential versus density and pressure. By computing probability distributions for the cluster size, chemical potential, and internal energy, we confirm that the effective spinodal point may be identified with the occurrence of a first order phase transition, resulting in the condensation of a droplet. An accurate equation of state is employed in order to estimate the droplet size and the coexisting vapor density and good quantitative agreement with the simulation data is obtained. The results highlight the need of an accurate equation of state data for the Laplace equation to have predictive power.
Energy partitioning for “fuzzy” atoms
Authors: Salvador P. , Mayer I.
Published: March 2004

The total energy of a molecule is presented as a sum of one- and two-atomic energy components in terms of “fuzzy” atoms, i.e., such divisions of the three-dimensional physical space into atomic regions in which the regions assigned to the individual atoms have no sharp boundaries but exhibit a continuous transition from one to another. By proper definitions the energy components are on the chemical energy scale. The method is realized by using Becke’s integration scheme and weight function permitting very effective numerical integrations.
Local chemical reaction of benzene on Cu(110) via STM-induced excitation
Authors: Komeda T. , Kim Y. , Fujita Y. , Sainoo Y. , Kawai Maki
Published: March 2004

We have investigated the mechanism of the chemical reaction of the benzene molecule adsorbed on Cu(110) surface induced by the injection of tunneling electrons using scanning tunneling microscopy (STM). With the dosing of tunneling electrons of the energy 2–5 eV from the STM tip to the molecule, we have detected the increase of the height of the benzene molecule by 40% in the STM image and the appearance of the vibration feature of the ν(C–H) mode in the inelastic tunneling spectroscopy (IETS) spectrum. It can be understood with a model in which the dissociation of C–H bonds occurs in a benzene molecule that induces a bonding geometry change from flat-lying to up-right configuration, which follows the story of the report of Lauhon and Ho on the STM-induced change of benzene on the Cu(100) surface. [L. J. Lauhon and W. Ho, J. Phys. Chem. A 104, 2463 (2000)]. The reaction probability shows a sharp rise at the sample bias voltage at 2.4 V, which saturates at 3.0 V, which is followed by another sharp rise at the voltage of 4.3 V. No increase of the reaction yield is observed for the negative sample voltage up to 5 eV. In the case of a fully deuterated benzene molecule, it shows the onset at the same energy of 2.4 eV, but the reaction probability is 103 smaller than the case of the normal benzene molecule. We propose a model in which the dehydrogenation of the benzene molecule is induced by the formation of the temporal negative ion due to the trapping of the electrons at the unoccupied resonant states formed by the π orbitals. The existence of the resonant level close to the Fermi level (∼2.4 eV) and multiple levels in less than ∼5 eV from the Fermi level, indicates a fairly strong interaction of the Cu-π* state of the benzene molecule. We estimated that the large isotope effect of ∼103 can be accounted for with the Menzel–Gomer–Redhead (MGR) model with an assumption of a shallow potential curve for the excited state.
Interfacial glass transition profiles in ultrathin, spin cast polymer films
Authors: Sills Scott , Overney René M. , Chau Wilson , Lee Victor Y. , Miller Robert D. , Frommer Jane
Published: March 2004

Interfacial glass transition temperature (Tg) profiles in spin cast, ultrathin films of polystyrene and derivatives were investigated using shear-modulated scanning force microscopy. The transitions were measured as a function of film thickness (δ), molecular weight, and crosslinking density. The Tg(δ) profiles were nonmonotonic and exhibited two regimes: (a) a sublayer extending about 10 nm from the substrate, with Tg values lowered up to ∼10 °C below the bulk value, and (b) an intermediate regime extending over 200 nm beyond the sublayer, with Tg values exceeding the bulk value by up to 10 °C. Increasing the molecular weight was found to shift the Tg(δ) profiles further from the substrate interface, on the order of 10 nm/kDa. Crosslinking the precast films elevated the absolute Tg values, but had no effect on the spatial length scale of the Tg(δ) profiles. These results are explained in the context of film preparation history and its influence on molecular mobility. Specifically, the observed rheological anisotropy is interpreted based on the combined effects of shear-induced structuring and thermally activated interdiffusion.
Translational and rotational diffusion of SF6 in zeolite NaY
Authors: Ghorai Pradip Kr. , Yashonath S.
Published: March 2004

Temperature dependence of equilibrium as well as dynamical properties of SF6 in zeolite NaY have been investigated by molecular dynamics simulation. By about 200 K, SF6 begins to have increased mobility. Strong orientational preference is exhibited by SF6 during its passage through the 12-ring window, the bottleneck for diffusion. The preference is for orientation with C3 followed by C2 and then C4 molecular symmetry axis perpendicular to the window plane. Translational motion is diffusive with an activation energy of 5.5 kJ/mol. Rotational-diffusion coefficient has an activation energy of 2.83 kJ/mol. Rotational motion is facile within the α-cage. Translational motion is hindered during passage through the 12-ring window when C4 is perpendicular to the window plane. Orientational correlation functions P1 and P2 around C2, C3 and C4 are reported. Only the long time decay of C4 shows oscillations. This is attributed to the hindered rotation during intercage migration while passing through the 12-ring window.
High pressure reactivity of propene by first principles molecular dynamics calculations
Authors: Mugnai Martina , Cardini Gianni , Schettino Vincenzo
Published: March 2004

The reactivity of propene under high pressure has been investigated in the framework of Car–Parrinello molecular dynamics. Changes in structural and electronic properties due to pressure have been analyzed in systems with a density ranging from 0.855 to 2.151 g/cm3. A ionic collective mechanism which leads to the formation of oligomers has been found by both spin restricted and spin polarized formalism. The maximally localized Wannier centers analysis has allowed us to characterize the addition scheme and to identify a Wannier center with a high spread value involved in the formation of the principal reaction products.
Simple and accurate method to evaluate tunneling splitting in polyatomic molecules
Authors: Mil’nikov Gennady V. , Yagi Kiyoshi , Taketsugu Tetsuya , Nakamura Hiroki , Hirao Kimihiko
Published: March 2004

A practical and accurate semiclassical method for calculating the tunneling splitting of the ground state in polyatomic molecules is presented based on a recent version of the instanton theory [J. Chem. Phys. 115, 6881 (2001)]. The method uses ab initio quantum chemical data for the potential energy surface without any concomitant extrapolation and requires only a small number of ab initio data points to get convergence even for large molecules. This enables one to use an advanced level of electronic structure theory and achieve a high accuracy of the result. The method is applied to the 9-atomic malonaldehyde molecule by making use of the potential energy surface at the level of CCSD(T) with the hybrid basis set of aug-cc-pVTZ (for oxygen atoms and the transferred hydrogen atom) and cc-pVTZ (for other atoms).
Submillimeter-wave spectra of hypoiodous acid
Authors: Ozeki Hiroyuki , Saito Shuji
Published: March 2004

Pure rotational spectra of hypoiodous acid, HOI, and its deuterated species, DOI, were measured in the frequency range of 320–670 GHz. The molecule was efficiently produced by a reaction of atomic oxygen with iodoethane. Rotational constants and centrifugal distortion constants for the molecule were determined accurately. The vibrationally averaged structure for HOI was obtained by taking the isotopic difference of the OH bond length into consideration: rz(OH)=0.967(8) Å, rz(OI)=1.9941(3) Å, and θz(HOI)=103.89°, where the errors were estimated from the residual inertial defect. Equilibrium bond lengths for the OH and OI bonds were derived as 0.959(8) Å and 1.9874(3) Å, respectively, by assuming anharmonic constants of the corresponding diatomic molecules. Electric-quadrupole interaction constants and nuclear-spin–rotation coupling constants for the iodine nucleus were obtained. Nonaxial terms of the electric-quadrupole constant for HOI can be determined as well, which enabled us to derive the principal values of the coupling tensor. The values obtained were used to gauge the ionicity of the X–O bond in the HOX molecular system. The nuclear-spin-rotation coupling constant along the a inertial axis is found to be significantly smaller than others, which may be explained by a contribution from two low-lying singlet excited states.
Covariance nuclear magnetic resonance spectroscopy
Authors: Brüschweiler Rafael , Zhang Fengli
Published: March 2004

Covariance nuclear magnetic resonance (NMR) spectroscopy is introduced, which is a new scheme for establishing nuclear spin correlations from NMR experiments. In this method correlated spin dynamics is directly displayed in terms of a covariance matrix of a series of one-dimensional (1D) spectra. In contrast to two-dimensional (2D) Fourier transform NMR, in a covariance spectrum the spectral resolution along the indirect dimension is determined by the favorable spectral resolution obtainable along the detection dimension, thereby reducing the time-consuming sampling requirement along the indirect dimension. The covariance method neither involves a second Fourier transformation nor does it require separate phase correction or apodization along the indirect dimension. The new scheme is demonstrated for cross-relaxation (NOESY) and J-coupling based magnetization transfer (TOCSY) experiments.
How much can an intermediate state influence competing reactive pathways?
Authors: Despa Florin , Berry R. Stephen
Published: March 2004

A molecule undergoing reaction may form a short-lived intermediate. Under certain conditions, the rate at which the reaction proceeds toward the product state via the intermediate may exceed that of a simple, direct path. The competition of two alternative reactive pathways is analyzed here in terms of a stochastic model. The approach allows one to diagnose this competition as a function of the energy of the intermediate relative to the barrier heights of the potential surface and values of the reactive vibrational modes. The result has applications to a variety of problems in chemical physics, ranging from the “lock-and-key” mechanism for the enzymatic activity to control of temporal evolution of complex systems by optimal laser fields.
Ground state, growth, and electronic properties of small lanthanum clusters
Authors: Zhang Dong-Bo , Shen Jiang
Published: March 2004

The DMol cluster method based on density-functional theory has been employed to study the structural stability and electronic structure of Lan (n=2–14) clusters. The ground states have been found out for lanthanum clusters. The Jahn-Teller effect plays an important role in this process because there are many isomers near the ground state. The magnetism is not sensitive to interatomic spacing when the change of interatomic spacing is in a small range. Lanthanum clusters grow in an icosahedral pattern. The results of the mean binding energy, of the second derivative of binding energy, and of the formation energy show strong odd–even alternation and that 7- and 13-atom clusters are magic. Further, the HOMO-LUMO gap, the mean nearest bond lengths, and the mean magnetic moments suggest that the convergence to bulk is slow and it shows an oscillatory behavior for small lanthanum clusters.
Stability of elliptic flow with a horizontal axis under stable stratification
Authors: Itano Toshihisa
Published: March 2004

Effects of stratification on the three dimensional instability of elliptic flow having a horizontal axis are investigated. It is revealed that the stratification works fundamentally to suppress the instability. However, its responses to increasing stratification are different depending on situations of the elliptic flow in a vertical plane. Generally, the instability tends to be dumped further when the longer axis of the elliptic flow is oriented vertical rather than horizontal.
First principles study of the stability and electronic structure of the icosahedral La13, La13−1, and La13+1 clusters
Authors: Zhang Dong-Bo , Shen Jiang
Published: March 2004

The structural stability and electronic-structure of icosahedral La13, La13−1, and La13+1 clusters have been studied by DMOL cluster method based on density-functional theory. The ground state of all-electron with relativity results is shown to be a distorted D2h icosahedron by the Jahn–Teller effect. However, the binding energies of D3d and D5d are very close to that of the D2h structure for La13, La13−1, and La13+1 clusters. The effective core potential results show that the true ground state is D5d structure. The clusters have small magnetic moments and the symmetry of cluster is an important factor in determining the magnetic moments of the clusters. The effects of interatomic spacing and coordination on atomic magnetic moment are discussed. Further, 5d electrons dominate the hybrid orbitals below the Fermi level in the neutral cluster and contribute the main spin of clusters.
Density-functional theory calculations of optical rotatory dispersion in the nonresonant and resonant frequency regions
Authors: Norman Patrick , Ruud Kenneth , Helgaker Trygve
Published: March 2004

The complex linear response function, which can be employed for calculations of second-order molecular properties in regions of strong absorption, is here extended to encompass the mixed electric-dipole–magnetic-dipole polarizability. The mixed electric-dipole–magnetic-dipole polarizability determines the optical rotation and, when absorption is taken into account, the full anomalous optical rotatory dispersion (ORD) spectra of chiral molecules can be calculated using first-principle quantum-chemical methods. Gauge-origin independence of the results is ensured through the use of London atomic orbitals. To illustrate the importance of taking the absorption process properly into account, we here apply this methodology to the study of the anomalous ORD of hydrogen peroxide, 3R-methylcyclohexanone, 4R-1,1-dimethyl-[3]-(1,2)-ferrocenophan-2-on, and the D2 isomer of the C84 fullerene.
Plasmon hybridization in spherical nanoparticles
Authors: Prodan E. , Nordlander P.
Published: March 2004

We show that the plasmon resonances in single metallic nanoshells and multiple concentric metallic shell particles can be understood in terms of interaction between the bare plasmon modes of the individual surfaces of the metallic shells. The interaction of these elementary plasmons results in hybridized plasmons whose energy can be tuned over a wide range of optical and infrared wavelengths. The approach can easily be generalized to more complex systems, such as dimers and small nanoparticle aggregates.
The lattice and rotational dynamics of the methyl halides described by pair potentials based on universal force fields
Authors: Kirstein O. , Prager M.
Published: March 2004

A systematical computational study of the lattice and rotational dynamics of the methyl halides, which belong to the most simple organic molecules containing CH3 groups, was done. Because of their simplicity there might be a chance to understand and model the dynamics of these systems by combining nonbonded pair interactions and crystallographic information. Based on the experimentally determined crystal structure, which was not relaxed during the calculations, interactions were modeled using the transferable parameters of the universal force fields. The lattice dynamical calculation can reproduce with reasonable accuracy the low-energy regime of the lattice excitations as well as the single-particle rotational potential of the CH3 group of the respective halide.
Lattice gas 2D/3D equilibria: Chemical potentials and adsorption isotherms with correct critical points
Authors: Aranovich G. L. , Erickson J. S. , Donohue M. D.
Published: March 2004

A priori information is used to derive the chemical potential as a function of density and temperature for 2D and 3D lattice systems. The functional form of this equation of state is general in terms of lattice type and dimensionality, though it contains critical temperature and critical density as parameters which depend on lattice type and dimensionality. The adsorption isotherm is derived from equilibrium between two-dimensional and three-dimensional phases. Theoretical predictions are in excellent agreement with grand canonical Monte Carlo simulations.
Decoupling quantum dissipation interaction via stochastic fields
Authors: Shao Jiushu
Published: March 2004

Based on the Hubbard–Stratonovich transformation, the dissipative interaction between the system of interest and the heat bath is decoupled and the separated system and bath thus evolve in common classical random fields. This manipulation allows us to establish a novel theoretical methodology by which the reduced density matrix is formulated as an ensemble average of its random realizations in the auxiliary white noise fields. Within the stochastic description, the interaction between the system and the bath is reflected in the mutually induced mean fields. The relationship between the bath-induced field and the influence functional in the path integral framework is revealed. As a demonstration of this approach, we derive the exact master equations for two model systems.
A first principles simulation of rigid water
Authors: Allesch Markus , Schwegler Eric , Gygi François , Galli Giulia
Published: March 2004

We present the results of Car–Parrinello (CP) simulations of water at ambient conditions and under pressure, using a rigid molecule approximation. Throughout our calculations, water molecules were maintained at a fixed intramolecular geometry corresponding to the average structure obtained in fully unconstrained simulations. This allows us to use larger time steps than those adopted in ordinary CP simulations of water, and thus to access longer time scales. In the absence of chemical reactions or dissociation effects, these calculations open the way to ab initio simulations of aqueous solutions that require time scales substantially longer than presently feasible (e.g., simulations of hydrophobic solvation). Our results show that structural properties and diffusion coefficients obtained with a rigid model are in better agreement with experiment than those determined with fully flexible simulations. Possible reasons responsible for this improved agreement are discussed.
Electronic spectroscopy and ionization potential of UO2 in the gas phase
Authors: Han Jiande , Goncharov Vasiliy , Kaledin Leonid A. , Komissarov Anatoly V. , Heaven Michael C.
Published: March 2004

The electronic spectroscopy of UO2 has been examined using multiphoton ionization with mass-selected detection of the UO2+ ions. Supersonic jet cooling was used to reduce the spectral congestion. Twenty-two vibronic bands of neutral UO2 were observed in the range from 17 400 to 32 000 cm−1. These bands originated from the U(5fφu7sσg)O2 X 3Φ(2u) and Φ(3u)3 states. The stronger band systems are attributed to metal-centered 7p←7s transitions. Threshold ionization measurements were used to determine the ionization potentials of UO and UO2. These were found to be higher than the values obtained previously from electron impact measurements but in agreement with the results of recent theoretical calculations.
Excitations, optical absorption spectra, and optical excitonic gaps of heterofullerenes. I. C60, C59N+, and C48N12: Theory and experiment
Authors: Xie Rui-Hua , Bryant Garnett W. , Sun Guangyu , Nicklaus Marc C. , Heringer David , Frauenheim Th. , Manaa M. Riad , Smith Vedene H. , Araki Yasuyuki , Ito Osamu
Published: March 2004

Low-energy excitations and optical absorption spectrum of C60 are computed by using time-dependent (TD) Hartree–Fock, TD-density functional theory (TD-DFT), TD DFT-based tight-binding (TD-DFT-TB), and a semiempirical Zerner intermediate neglect of diatomic differential overlap method. A detailed comparison of experiment and theory for the excitation energies, optical gap, and absorption spectrum of C60 is presented. It is found that electron correlations and correlation of excitations play important roles in accurately assigning the spectral features of C60, and that the TD-DFT method with nonhybrid functionals or a local spin density approximation leads to more accurate excitation energies than with hybrid functionals. The level of agreement between theory and experiment for C60 justifies similar calculations of the excitations and optical absorption spectrum of a monomeric azafullerene cation C59N+, to serve as a spectroscopy reference for the characterization of carborane anion salts. Although it is an isoelectronic analogue to C60, C59N+ exhibits distinguishing spectral features different from C60: (1) the first singlet is dipole-allowed and the optical gap is redshifted by 1.44 eV; (2) several weaker absorption maxima occur in the visible region; (3) the transient triplet–triplet absorption at 1.60 eV (775 nm) is much broader and the decay of the triplet state is much faster. The calculated spectra of C59N+ characterize and explain well the measured ultraviolet–visible (UV–vis) and transient absorption spectra of the carborane anion salt [C59N][Ag(CB11H6Cl6)2] [Kim et al., J. Am. Chem. Soc. 125, 4024 (2003)]. For the most stable isomer of C48N12, we predict that the first singlet is dipole-allowed, the optical gap is redshifted by 1.22 eV relative to that of C60, and optical absorption maxima occur at 585, 528, 443, 363, 340, 314, and 303 nm. We point out that the characterization of the UV–vis and transient absorption spectra of C48N12 isomers is helpful in distinguishing the isomer structures required for applications in molecular electronics. For C59N+ and C48N12 as well as C60, TD-DFT-TB yields reasonable agreement with TD-DFT calculations at a highly reduced cost. Our study suggests that C60, C59N+, and C48N12, which differ in their optical gaps, have potential applications in polymer science, biology, and medicine as single-molecule fluorescent probes, in photovoltaics as the n-type emitter and/or p-type base of a p–n junction solar cell, and in nanoelectronics as fluorescence-based sensors and switches.
Quantum solvation of phthalocyanine in superfluid helium droplets
Authors: Lehnig R. , Slenczka A.
Published: March 2004

We have measured quantum states of the solvent–solute system of phthalocyanine in superfluid helium droplets in a high resolution pump–probe experiment. This provides evidence for the attribution of a splitting effect in the emission spectra of phthalocyanine in helium droplets to the relaxation of the first helium layer upon electronic excitation, measured recently by us. Our experimental results are a strong indication for the first helium layer playing a key roll for the solvation of molecules in helium droplets and, thus, for their spectroscopic features.