First de novo whole genome sequencing and assembly of the pink-footed goose.

Annotated genomes can provide new perspectives on the biology of species. We present the first de novo whole genome sequencing for the pink-footed goose. In order to obtain a high-quality de novo assembly the strategy used was to combine one short insert paired-end library with two mate-pair libraries. The pink-footed goose genome was assembled de novo using three different assemblers and an assembly evaluation was subsequently performed in order to choose the best assembler. For our data, ALLPATHS-LG performed the best, since the assembly produced covers most of the genome, while introducing the fewest errors. A total of 26,134 genes were annotated, with bird species accounting for virtually all BLAST hits. We also estimated the substitution rate in the pink-footed goose, which can be of use in future demographic studies, by using a comparative approach with the genome of the chicken, the mallard and the swan goose. A substitution rate of 1.38×10-7 per nucleotide per generation was obtained when comparing the genomes of the two closely-related goose species (the pink-footed and the swan goose). Altogether, we provide a valuable tool for future genomic studies aiming at particular genes and regions of the pink-footed goose genome as well as other bird species.

Reactive scattering of H2 from Cu(100): comparison of dynamics calculations based on the specific reaction parameter approach to density functional theory with experiment.

We present new experimental and theoretical results for reactive scattering of dihydrogen from Cu(100). In the new experiments, the associative desorption of H(2) is studied in a velocity resolved and final rovibrational state selected manner, using time-of-flight techniques in combination with resonance-enhanced multi-photon ionization laser detection. Average desorption energies and rotational quadrupole alignment parameters were obtained in this way for a number of (v = 0, 1) rotational states, v being the vibrational quantum number. Results of quantum dynamics calculations based on a potential energy surface computed with a specific reaction parameter (SRP) density functional, which was derived earlier for dihydrogen interacting with Cu(111), are compared with the results of the new experiments and with the results of previous molecular beam experiments on sticking of H(2) and on rovibrationally elastic and inelastic scattering of H(2) and D(2) from Cu(100). The calculations use the Born-Oppenheimer and static surface approximations. With the functional derived semi-empirically for dihydrogen + Cu(111), a chemically accurate description is obtained of the molecular beam experiments on sticking of H(2) on Cu(100), and a highly accurate description is obtained of rovibrationally elastic and inelastic scattering of D(2) from Cu(100) and of the orientational dependence of the reaction of (v = 1, j = 2 - 4) H(2) on Cu(100). This suggests that a SRP density functional derived for H(2) interacting with a specific low index face of a metal will yield accurate results for H(2) reactively scattering from another low index face of the same metal, and that it may also yield accurate results for H(2) interacting with a defected (e.g., stepped) surface of that same metal, in a system of catalytic interest. However, the description that was obtained of the average desorption energies, of rovibrationally elastic and inelastic scattering of H(2) from Cu(100), and of the orientational dependence of reaction of (v = 0, j = 3 - 5, 8) H(2) on Cu(100) compares less well with the available experiments. More research is needed to establish whether more accurate SRP-density functional theory dynamics results can be obtained for these observables if surface atom motion is added to the dynamical model. The experimentally and theoretically found dependence of the rotational quadrupole alignment parameter on the rotational quantum number provides evidence for rotational enhancement of reaction at low translational energies.

Diffractive and reactive scattering of H2 from Ru(0001): experimental and theoretical study.

We present a combined experimental and theoretical study of the diffraction of H(2) from Ru(0001) in the incident energy range 78-150 meV, and a theoretical study of dissociative chemisorption of H(2) in the same system. Pronounced out-of-plane diffraction was observed in the whole energy range studied. The energy dependence of the elastic diffraction intensities was measured along the two main symmetry directions for a fixed parallel translational energy. The data were compared with quantum dynamics calculations performed by using DFT-based, six-dimensional potential energy surfaces calculated with both the PW91 and RPBE functionals, as well as with a functional obtained from a weighted average of both (the MIX functional, which was earlier shown to perform quite well for H(2) + Cu(111)). Our results show that the PW91 functional describes the H(2) diffraction intensities more accurately than the RPBE and the MIX functionals, although the absolute values of these intensities are overestimated in the calculations. For the reaction probabilities a preference for one or the other functional cannot be given over the entire energy range probed by the sticking experiments. The PW91 functional yields too high reaction probabilities over the entire investigated energy range, but is better than RPBE at low collision energies (<0.1 eV). The RPBE functional gives too low reaction probabilities at low energy and somewhat too high reaction probabilities at high energy, but agrees better with experiment than PW91 for energies >0.1 eV. The results suggest that, in order to get a better description of both H(2) diffraction and dissociative chemisorption for this system, a specific reaction parameter functional for H(2) + Ru(0001) is needed that is a weighted average of functionals other than PW91 and RPBE. We speculate that differences between the H(2) + Ru(0001) system (early and low reaction barrier) and H(2) + Cu(111) (late and high reaction barrier) may well lead to fundamentally different specific reaction parameter functionals, and that including a reasonable accurate description of the van der Waals interaction might be important for H(2) + Ru(0001) which has barriers localised far away from the surface. Based on our results we advocate new, systematic combined theoretical and experimental studies of H(2) interacting with transition metals in early and late barrier systems, with the aim of determining whether specific reaction parameter functionals for these systems might differ in a systematic way.

Six-dimensional dynamics study of reactive and non reactive scattering of H(2) from Cu(111) using a chemically accurate potential energy surface.

We have studied the interaction of H(2) on Cu(111) using quasi-classical and quantum dynamics, and a chemically accurate six-dimensional potential energy surface (PES). The PES was computed using the specific reaction parameter (SRP) approach to density functional theory (DFT), in an implementation adapted to molecules interacting with metal surfaces. To perform this study we have applied the Born-Oppenheimer static surface (BOSS) approximation, i.e., we used both the Born-Oppenheimer (BO) and the static surface (SS) approximations. We show that our theoretical approach accurately describes experiments on dissociative adsorption, the effect of molecular vibrational and rotational motion on dissociative (associative) adsorption (desorption), and rotational excitation upon scattering. More specifically, dynamics calculations on reactive scattering of H(2) reproduce reaction probabilities measured in molecular beam experiments, effective barrier heights describing the dependence of reaction on the initial rovibrational state, and data on rotationally inelastic scattering with chemical accuracy (i.e., within 1 kcal mol(-1) approximately 4.2 kJ mol(-1)). These processes are not affected much by surface motion, either because they were measured using a low surface temperature, T(s), or because the computed observable is independent of T(s). However, we show that to account for the dependence of molecular orientation on a reaction the inclusion of surface motion is required. We have also found that vibrational excitation is poorly described within the BOSS approximation, suggesting a breakdown of this approximation.

A theoretical study of H(2) dissociation on (sq.rt(3) x sq.rt(3))R30 degrees CO/Ru(0001).

We have studied the influence of preadsorbed CO on the dissociative adsorption of H(2) on Ru(0001) with density functional theory calculations. For a coverage of 1/3 ML CO, we investigated different possible reaction paths for hydrogen dissociation using nudged elastic band and adaptive nudged elastic band calculations. One reaction path was studied in detail through an energy decomposition and molecular orbital type of analysis. The minimum barrier for H(2) dissociation is found to be 0.29 eV. At the barrier the H-H bond is hardly stretched. Behind this barrier a molecular chemisorption minimum is present. Next, the molecule overcomes a second barrier, with a second local chemisorption minimum behind it. To finally dissociate to chemisorbed atoms, the molecule has to overcome a third barrier. To move along the reaction path from reactants to products, the hydrogen molecule needs to rotate, and to significantly change its center-of-mass position. The procedure of mapping out reaction paths for H(2) reacting on low-index surfaces of bare metals (computing two-dimensional elbow plots for fixed impact high-symmetry sites and H(2) orientations parallel to the surface) does not work for H(2)+CO/Ru. The first barrier in the path is recovered, but the features of the subsequent stretch to the dissociative chemisorption minimum are not captured, because the molecule is not allowed to change its center-of-mass position or to rotate. The dissociative chemisorption of H(2) on CO/Ru(0001) is endoergic, in contrast to the case of H(2) on bare Ru(0001). The zero-point energy corrected energies of molecularly and dissociatively chemisorbed H(2) are very close, suggesting that it may be possible to detect molecularly chemisorbed H(2) on (sq.rt(3) x sq.rt(3))R30 degrees CO/Ru(0001). The presence of CO on the surface increases the barrier height to dissociation compared with bare Ru(0001). Based on an energy decomposition and molecular orbital analysis we attribute the increase in the barrier height mainly to an occupied-occupied interaction between the bonding H(2) sigma(g) orbital and the (surface-hybridized) CO 1pi orbitals, i.e., to site blocking. There is a small repulsive contribution to the barrier from the interaction between the H(2) molecule and the Ru part of the CO covered Ru surface, but it is smaller than one might expect based on the calculations of H(2) interacting with a clean Ru surface, and on calculations of H(2) interacting with the CO overlayer only. Actually, the analysis suggests that the Ru surface as a subsystem is (slightly) more reactive for the reaction path studied with CO preadsorbed on it than without it. Thus, the results indicate that the influence of CO on H(2) dissociation on Ru is not only a simple site-blocking effect, the electronic structure of the underlying Ru is changed.

Quantum dynamics of dissociative chemisorption of CH(4) on Ni(111): Influence of the bending vibration.

Two-dimensional, three-dimensional, and four-dimensional quantum dynamic calculations are performed on the dissociative chemisorption of CH(4) on Ni(111) using the multiconfiguration time-dependent Hartree (MCTDH) method. The potential energy surface used for these calculations is 15-dimensional (15D) and was obtained with density functional theory for points which are concentrated in the region that is dynamically relevant to reaction. Many reduced dimensionality calculations were already performed on this system, but the molecule was generally treated as pseudodiatomic. The main improvement of our model is that we try to describe CH(4) as a polyatomic molecule by including a degree of freedom describing a bending vibration in our three-dimensional and four-dimensional models. Using a polyspherical coordinate system, a general expression for the 15D kinetic energy operator is derived, which discards all the singularities in the operator and includes rotational and Coriolis coupling. We use seven rigid constraints to fix the CH(3) umbrella of the molecule to its gas phase equilibrium geometry and to derive two-dimensional, three-dimensional, and four-dimensional Hamiltonians, which were used in the MCTDH method. Only four degrees of freedom evolve strongly along the 15D minimum energy path: the distance of the center of mass of the molecule to the surface, the dissociative C[Single Bond]H bond distance, the polar orientation of the molecule, and the bending angle between the dissociative C[Single Bond]H bond and the umbrella. A selection of these coordinates is included in each of our models. The polar rotation is found to be important in determining the mode selective behavior of the reaction. Furthermore, our calculations are in good agreement with the finding of Xiang et al. [J. Chem. Phys. 117, 7698 (2002)] in their reduced dimensional calculation that the helicopter motion of the umbrella symmetry axis is less efficient than its cartwheel motion for promoting the reaction. The effect of pre-exciting the bend modes is qualitatively incorrect at higher energies, suggesting the necessity of including additional rotational and vibrational degrees of freedom in the model.

A note on the vibrational efficacy in molecule-surface reactions.

The effectiveness of vibrational energy in promoting dissociation of molecules colliding with surfaces can be measured through the so-called vibrational efficacy. It is thought by many to be a pure "energetic" measure and therefore believed to be limited from below by zero (in the case that there is no increase in dissociation probability upon vibrational excitation) and from above by one (in the case that all of the vibrational excitation energy is used to promote reaction). However, the quantity vibrational efficacy is clearly linked to the detailed dynamics of the system, and straightforward considerations lead to the conclusion that it is not limited either from below or above. Here we discuss these considerations together with a quasiclassical dynamics study of a molecule-surface system, N(2)/Ru(0001), for which a vibrational efficacy bigger than one has been found both experimentally and theoretically. We show that an analysis of the vibrational efficacy only in terms of energy transfer from vibration to translation can be too simple to describe the behavior of systems for which the potential energy surfaces present (high) reaction barriers, potential corrugation and anisotropy, and curved reaction paths.

Predicting catalysis: understanding ammonia synthesis from first-principles calculations.

Here, we give a full account of a large collaborative effort toward an atomic-scale understanding of modern industrial ammonia production over ruthenium catalysts. We show that overall rates of ammonia production can be determined by applying various levels of theory (including transition state theory with or without tunneling corrections, and quantum dynamics) to a range of relevant elementary reaction steps, such as N(2) dissociation, H(2) dissociation, and hydrogenation of the intermediate reactants. A complete kinetic model based on the most relevant elementary steps can be established for any given point along an industrial reactor, and the kinetic results can be integrated over the catalyst bed to determine the industrial reactor yield. We find that, given the present uncertainties, the rate of ammonia production is well-determined directly from our atomic-scale calculations. Furthermore, our studies provide new insight into several related fields, for instance, gas-phase and electrochemical ammonia synthesis. The success of predicting the outcome of a catalytic reaction from first-principles calculations supports our point of view that, in the future, theory will be a fully integrated tool in the search for the next generation of catalysts.

Inhibition of growth factor-dependent inositol phosphate Ca2+ signaling by antitumor ether lipid analogues.

Cytotoxic ether lipid analogues have been studied for their ability to inhibit growth factor-dependent [Ca2+]i signaling in Swiss 3T3 fibroblasts. 1-Octadecyl-2-methyl-rac-glycero-3-phosphocholine (ET-18-OCH3) inhibited 45Ca2+ uptake and inositol(1,4,5)trisphosphate-induced 45Ca2+ release in saponin permeabilized cells with concentration producing 50% inhibition values of 55 and 360 microM, respectively. When cells were exposed to ET-18-OCH3 for 18 h before permeabilization there was selective inhibition of inositol(1,4,5)trisphosphate-induced 45Ca2+ release with a concentration producing 50% inhibition value of 20 microM, but no effect on 45Ca2+ uptake, or on 45Ca2+ release by arachidonic acid. The concentration of ET-18-OCH3 with continuous exposure to inhibit cell growth 50% was 19 microM. The ether lipid analogues 1-hexadecylthio-2-ethyl-rac-glycero-3- phosphocholine and 1-S-octadecyl-2-O-methylthiopropyl-3-N,N-dimethyl-gamma-hydroxy pro pyl ammonium iodide had effects similar to those of ET-18-OCH3 but the noncytotoxic analogue 1-alkyl-2-hydroxy-sn-glycero-3- phosphocholine was without effect. Exposure of cells to 10 microM ET-18-OCH3 produced 81% inhibition of platelet-derived growth factor-stimulated inositol phosphate formation and 66% inhibition of fluoroaluminate anion-stimulated inositol phosphate formation. Addition of ET-18-OCH3 to cells in medium with 10% fetal calf serum gave a transient increase in [Ca2+]i without causing an increase in resting [Ca2+]i, while the addition of ET-18-OCH3 to cells in medium without serum gave a sustained increase in resting [Ca2+]i. Cells exposed to 5 microM ET-18-OCH3 for 18 h showed no increase in resting [Ca2+]i but there was 95% inhibition of the [Ca2+]i response to platelet-derived growth factor, 63% inhibition of the response to bradykinin, and 55% inhibition of the response to vasopressin. The block by ether lipid analogues of inositol phosphate-mediated [Ca2+]i signaling suggests a mechanism for preventing the action of growth factors that could contribute to the inhibition of cell proliferation by the agents.

Transient increases of intracellular Ca2+ induced by volatile anesthetics in rat hepatocytes.

The affects of volatile anesthetics on mobilization of intracellular Ca2+ was monitored in primary cultures of rat hepatocytes using the fluorescent Ca2+ probe Fura-2. The use of Fura-2 was limited by several factors which complicated the quantitative analysis of the results, such as: (i) a high rate of dye leakage; (ii) changes in the redox state of the hepatocytes which interfered with the fluorescence produced by the dye at various excitation wavelengths; (iii) compartmentalization of the dye producing high local intracellular concentrations; and, of particular importance for this study, (iv) enhanced photobleaching of the dye in the presence of halothane. To aid in the interpretation of the Fura-2 data, the Ca2(+)-sensitive photoprotein aequorin was also used to monitor changes in [Ca2+]i. The aequorin and Fura-2 techniques qualitatively yielded the same result, that the volatile anesthetic agents halothane, enflurane, and isoflurane induce an immediate and transient increase of [Ca2+]i. The durations of these transients were approximately between 5 and 10 min and were not related to any evident acute cell toxicity. The [Ca2+]i increases induced by the volatile anesthetic agents were dose-dependent, with halothane the most potent. The exact mechanism governing these increases in [Ca2+]i induced by these anesthetics in rat hepatocytes is unknown, but is likely to involve effects on both the cell surface membrane and endoplasmic reticulum components of the signal transducing system.

Synthesis, absolute configuration, and antibacterial activity of 6,7-dihydro-5,8-dimethyl-9-fluoro-1-oxo-1H,5H- benzo[ij]quinolizine-2-carboxylic acid.

The tricyclic quinolone antibacterial agent 6,7-dihydro-5,8-dimethyl-9-fluoro-1-oxo-1H,5H-benzo[ij]quinolizine -2-carboxylic acid has an asymmetric center at position 5 of the molecule. The R and S isomers of the compound have been prepared from the corresponding (R)- and (S)-2,5-dimethyl-6-fluoro-1,2,3,4-tetrahydroquinolines, which were separated via their diastereomeric amides of N-tosyl-(S)-proline. The absolute configuration was established by X-ray analysis of one of the diastereomeric amides. The 5-desmethyl analogue was prepared for antibacterial comparison with the isomers and the racemic mixture. It has now been established that the S isomer is much more active than the R isomer. The 5-desmethyl analogue was found to be more active than the R isomer but not as active as the S isomer or the racemic mixture. The importance of stereochemistry at position 5 in this system has been established.

Suramin blocks intracellular Ca2+ release and growth factor-induced increases in cytoplasmic free Ca2+ concentration.

Suramin, a polysulfonated naphthylurea with antitumor activity, has been shown to be an inhibitor of the release of Ca2+ from non-mitochondrial stores induced by the putative intracellular second messengers inositol 1, 4, 5-trisphosphate and GTP in saponin permeabilized Swiss 3T3 fibroblasts. The IC50 for the effect of suramin was about 40 microM in both cases. Suramin did not block Ca2+ release induced by the Ca2+ ionophore 4-bromo A23187 or by the membrane perturbing agent halothane. Suramin, 7 x 10(-5) M, caused a 49% decrease in the elevation of intracellular free Ca2+ concentration ([Ca2+]i) caused by platelet derived growth factor (PDGF) in intact Swiss 3T3 fibroblasts but did not block the increases in [Ca2+]i caused by bradykinin or vasopressin. Suramin decreased PDGF binding to its receptor on intact Swiss 3T3 fibroblasts but had no effect on the binding of bradykinin and vasopressin. The results show that the effect of suramin in decreasing the [Ca2+]i response to growth factors may be mediated by a block of growth factor-receptor binding, but an effect on intracellular Ca2+ release cannot be ruled out.

Platelet-derived growth factor blocks the increase in intracellular free Ca2+ caused by calcium ionophores and a volatile anesthetic agent in Swiss 3T3 fibroblasts without altering toxicity.

Platelet-derived growth factor (PDGF) produced an almost complete block of the increase in intracellular free Ca2+ concentration ([Ca2+]i) in Swiss 3T3 fibroblasts caused by the Ca2(+)-selective ionophores 4-bromo-A23187 and ionomycin, and by the volatile anesthetic agent halothane. The effect of PDGF was similar to the decreased [Ca2+]i response to Ca2(+)-ionophores produced by phorbol 12-myristate 13-acetate, an activator of protein kinase C. There was no effect of PDGF or PMA on the acute or delayed toxicity of the Ca2(+)-ionophores to Swiss 3T3 cells, suggesting that the increase in [Ca2+]i is not the direct cause of toxicity of these agents.

Chemically accurate simulation of a prototypical surface reaction: H2 dissociation on Cu(111).

Methods for accurately computing the interaction of molecules with metal surfaces are critical to understanding and thereby improving heterogeneous catalysis. We introduce an implementation of the specific reaction parameter (SRP) approach to density functional theory (DFT) that carries the method forward from a semiquantitative to a quantitative description of the molecule-surface interaction. Dynamics calculations on reactive scattering of hydrogen from the copper (111) surface using an SRP-DFT potential energy surface reproduce data on the dissociative adsorption probability as a function of incidence energy and reactant state and data on rotationally inelastic scattering with chemical accuracy (within approximately 4.2 kilojoules per mole).

Six-dimensional quantum dynamics of H2 dissociative adsorption on the Pt(211) stepped surface.

Results of experimental studies, and theoretical calculations utilizing classical trajectories, have shown that dissociation of H2 on the Pt(211) stepped surface is enhanced at low energies by a molecular trapping mechanism. Because quantum effects can play a large role at the low energies and long lifetimes that characterize molecular trapping, we have undertaken quantum dynamics calculations for this system, the first to treat all molecular degrees of freedom of a gas molecule reacting on a stepped metallic surface. The calculations show that molecular trapping persists in the quantum system, but only at much lower energies than experimentally seen, pointing to possible deficiencies in the potential energy surface. Classical and quasiclassical trajectory calculations on the same potential provide a reasonable picture of reaction overall, but many of the finer details are inaccurate, and certain classical reaction mechanisms are entirely invalid. We conclude that some skepticism should be shown toward any classical study for which long-lived trapping states play a role.

Six-dimensional potential energy surface for H2 at Ru(0001).

The six-dimensional (6D) potential energy surface (PES) for the H(2) molecule interacting with a clean Ru(0001) surface has been computed accurately for the first time. Density functional theory (DFT) and a pseudopotential based periodic plane-wave approach have been used to calculate the electronic interactions between the molecule and the surface. Two different generalized gradient approximation (GGA) exchange-correlation functionals, PW91 and RPBE, have been adopted. Based on the DFT/GGA calculated potential energies, an analytical 6D PES has been constructed using the corrugation reducing procedure. A very accurate representation of the DFT/GGA data has been achieved, with an average error in the interpolation of about 3 meV and a maximum error not larger than about 30 meV. The top site is found to be the most reactive site for both functionals used, but PW91 predicts a higher reactivity than RPBE, with lower-energy and earlier-located dissociation barriers. The energetic corrugation displayed by the RPBE PES is larger than the PW91 PES while the geometric corrugation is smaller. The differences between the two PESs increase as the distance of the molecular center of mass to the surface decreases. A direct comparison with experimental investigations on H(2)/Ru(0001) could shed light on the suitability of these XC potentials often used in DFT calculations.