WorldWideScience

Sample records for surfaces transition-state energies

  1. Wetting transition on patterned surfaces: transition states and energy barriers.

    Science.gov (United States)

    Ren, Weiqing

    2014-03-18

    We study the wetting transition on microstructured hydrophobic surfaces. We use the string method [J. Chem. Phys. 2007, 126, 164103; J. Chem. Phys. 2013, 138, 134105] to accurately compute the transition states, the energy barriers, and the minimum energy paths for the wetting transition from the Cassie-Baxter state to the Wenzel state. Numerical results are obtained for the wetting of a hydrophobic surface textured with a square lattice of pillars. It is found that the wetting of the solid substrate occurs via infiltration of the liquid in a single groove, followed by lateral propagation of the liquid front. The propagation of the liquid front proceeds in a stepwise manner, and a zipping mechanism is observed during the infiltration of each layer. The minimum energy path for the wetting transition goes through a sequence of intermediate metastable states, whose wetted areas reflect the microstructure of the patterned surface. We also study the dependence of the energy barrier on the drop size and the gap between the pillars.

  2. Profiling transition-state configurations on the Trypanosoma cruzi trans-sialidase free-energy reaction surfaces.

    Science.gov (United States)

    Rogers, Ian L; Naidoo, Kevin J

    2015-01-22

    Enzymatically catalyzed reactions pass from reactants to products via transition states that are short-lived and potentially characterized from free-energy reaction surfaces. We compute the reaction surface for Trypanosoma cruzi trans-sialidase using the Free Energy from Adaptive Reaction Coordinate Forces method. The reaction coordinates are the bonds between the sialic acid and the leaving group (TYR342) and the sialic acid and the nucpleophile (ASP59). We are able to track progress of the reaction trajectories up to (incomplete), about (recrossed), and across (crossed) the col that divides the reactant (covalent intermediate) and product (Michaelis complex) surfaces. More than 40 transition state configurations were isolated from these trajectories, and the sialic acid substrate conformations were analyzed as well as the substrate interactions with the nucleophile and catalytic acid/base. A successful barrier crossing requires that the substrate passes through a family of E5, (4)H5, and (6)H5 pucker conformations. These puckers interact slightly differently with the enzyme. The E5 and (4)H5 conformations have a high-frequency hydrogen bonding with Asp96, while (6)H5 puckers show increased hydrogen bonding between sialic acid O-8-Glu230. Our analysis of Trypanosoma cruzi trans-sialidase configurations that populate the col separating the reactant from product surfaces brings new evidence to the prevailing premise that there are several pathways from reactant to product passing through the saddle and successful product formation is not restricted to the minimum energy path and transition state.

  3. Transition State Theory for dissipative systems without a dividing surface

    CERN Document Server

    Revuelta, F; Benito, R M; Borondo, F

    2015-01-01

    Transition State Theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when the reactive system is coupled to an environment. The calculations made in this way then overestimate the reaction rate and the results depend critically on the choice of the dividing surface. In this Letter, we study the phase space of a stochastically driven system close to an energetic barrier in order to identify the geometric structure unambiguously determining the reactive trajectories, which is then incorporated in a simple rate formula for reactions in condensed phase that is both independent of the dividing surface and exact.

  4. Use of scaled external correlation, a double many-body expansion, and variational transition state theory to calibrate a potential energy surface for FH2

    Science.gov (United States)

    Lynch, Gillian C.; Steckler, Rozeanne; Varandas, Antonio J. C.; Truhlar, Donald G.; Schwenke, David W.

    1991-01-01

    New ab initio results and a double many-body expansion formalism have been used to parameterize a new FH2 potential energy surface with improved properties near the saddle point and in the region of long-range attraction. The functional form of the new surface includes dispersion forces by a double many-body expansion. Stationary point properties for the new surface are calculated along with the product-valley barrier maxima of vibrationally adiabatic potential curves for F + H2 - HF(nu-prime = 3) + H, F + HD - HF(nu-prime = 3) + D, and F + D2 - DF(nu-prime = 4) + D. The new surface should prove useful for studying the effect on dynamics of a low, early barrier with a wide, flat bend potential.

  5. Discovering Unique, Low-Energy Transition States Using Evolutionary Molecular Memetic Computing

    DEFF Research Database (Denmark)

    Ellabaan, Mostafa M Hashim; Ong, Y.S.; Handoko, S.D.

    2013-01-01

    be accurately identified through the transition states. Transition states describe the paths of molecular systems in transiting across stable states. In this article, we present the discovery of unique, low-energy transition states and showcase the efficacy of their identification using the memetic computing......In the last few decades, identification of transition states has experienced significant growth in research interests from various scientific communities. As per the transition states theory, reaction paths and landscape analysis as well as many thermodynamic properties of biochemical systems can...... of several state-of-the-art algorithms. Not only did the MMC uncover the largest number of transition states, but it also incurred the least amount of computational costs....

  6. Crossing the dividing surface of transition state theory. III. Once and only once. Selecting reactive trajectories

    Energy Technology Data Exchange (ETDEWEB)

    Lorquet, J. C., E-mail: jc.lorquet@ulg.ac.be [Department of Chemistry, University of Liège, Sart-Tilman (Bâtiment B6), B-4000 Liège 1 (Belgium)

    2015-09-14

    The purpose of the present work is to determine initial conditions that generate reacting, recrossing-free trajectories that cross the conventional dividing surface of transition state theory (i.e., the plane in configuration space passing through a saddle point of the potential energy surface and perpendicular to the reaction coordinate) without ever returning to it. Local analytical equations of motion valid in the neighborhood of this planar surface have been derived as an expansion in Poisson brackets. We show that the mere presence of a saddle point implies that reactivity criteria can be quite simply formulated in terms of elements of this series, irrespective of the shape of the potential energy function. Some of these elements are demonstrated to be equal to a sum of squares and thus to be necessarily positive, which has a profound impact on the dynamics. The method is then applied to a three-dimensional model describing an atom-diatom interaction. A particular relation between initial conditions is shown to generate a bundle of reactive trajectories that form reactive cylinders (or conduits) in phase space. This relation considerably reduces the phase space volume of initial conditions that generate recrossing-free trajectories. Loci in phase space of reactive initial conditions are presented. Reactivity is influenced by symmetry, as shown by a comparative study of collinear and bent transition states. Finally, it is argued that the rules that have been derived to generate reactive trajectories in classical mechanics are also useful to build up a reactive wave packet.

  7. Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier.

    Science.gov (United States)

    Mökkönen, Harri; Ala-Nissila, Tapio; Jónsson, Hannes

    2016-09-07

    The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates is found. The use of a sequence of hyperplanes in the evaluation of the recrossing correction speeds up the calculation by an order of magnitude as compared with the traditional approach. As the temperature is lowered, the direct Langevin dynamics simulations as well as the forward flux simulations become computationally too demanding, while the harmonic transition state theory estimate corrected for recrossings can be calculated without significant increase in the computational effort.

  8. Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier

    Science.gov (United States)

    Mökkönen, Harri; Ala-Nissila, Tapio; Jónsson, Hannes

    2016-09-01

    The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates is found. The use of a sequence of hyperplanes in the evaluation of the recrossing correction speeds up the calculation by an order of magnitude as compared with the traditional approach. As the temperature is lowered, the direct Langevin dynamics simulations as well as the forward flux simulations become computationally too demanding, while the harmonic transition state theory estimate corrected for recrossings can be calculated without significant increase in the computational effort.

  9. Crossing the dividing surface of transition state theory. IV. Dynamical regularity and dimensionality reduction as key features of reactive trajectories

    Science.gov (United States)

    Lorquet, J. C.

    2017-04-01

    The atom-diatom interaction is studied by classical mechanics using Jacobi coordinates (R, r, θ). Reactivity criteria that go beyond the simple requirement of transition state theory (i.e., PR* > 0) are derived in terms of specific initial conditions. Trajectories that exactly fulfill these conditions cross the conventional dividing surface used in transition state theory (i.e., the plane in configuration space passing through a saddle point of the potential energy surface and perpendicular to the reaction coordinate) only once. Furthermore, they are observed to be strikingly similar and to form a tightly packed bundle of perfectly collimated trajectories in the two-dimensional (R, r) configuration space, although their angular motion is highly specific for each one. Particular attention is paid to symmetrical transition states (i.e., either collinear or T-shaped with C2v symmetry) for which decoupling between angular and radial coordinates is observed, as a result of selection rules that reduce to zero Coriolis couplings between modes that belong to different irreducible representations. Liapunov exponents are equal to zero and Hamilton's characteristic function is planar in that part of configuration space that is visited by reactive trajectories. Detailed consideration is given to the concept of average reactive trajectory, which starts right from the saddle point and which is shown to be free of curvature-induced Coriolis coupling. The reaction path Hamiltonian model, together with a symmetry-based separation of the angular degree of freedom, provides an appropriate framework that leads to the formulation of an effective two-dimensional Hamiltonian. The success of the adiabatic approximation in this model is due to the symmetry of the transition state, not to a separation of time scales. Adjacent trajectories, i.e., those that do not exactly fulfill the reactivity conditions have similar characteristics, but the quality of the approximation is lower. At higher

  10. Vibrational energy transfer near a dissociative adsorption transition state: State-to-state study of HCl collisions at Au(111).

    Science.gov (United States)

    Geweke, Jan; Shirhatti, Pranav R; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M

    2016-08-07

    In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed-presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]-50 times smaller than those reported here-were influenced by erroneous assignment of spectroscopic lines used in the data analysis.

  11. Vibrational energy transfer near a dissociative adsorption transition state: State-to-state study of HCl collisions at Au(111)

    Science.gov (United States)

    Geweke, Jan; Shirhatti, Pranav R.; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M.

    2016-08-01

    In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed—presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]—50 times smaller than those reported here—were influenced by erroneous assignment of spectroscopic lines used in the data analysis.

  12. State-to-State Mode Specificity: Energy Sequestration and Flow Gated by Transition State.

    Science.gov (United States)

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2015-12-23

    Energy flow and sequestration at the state-to-state level are investigated for a prototypical four-atom reaction, H2 + OH → H + H2O, using a transition-state wave packet (TSWP) method. The product state distribution is found to depend strongly on the reactant vibrational excitation, indicating mode specificity at the state-to-state level. From a local-mode perspective, it is shown that the vibrational excitation of the H2O product derives from two different sources, one attributable to the energy flow along the reaction coordinate into the newly formed OH bond and the other due to the sequestration of the vibrational energy in the OH spectator moiety during the reaction. The analysis provided a unified interpretation of some seemingly contradicting experimental observations. It is further shown that the transfer of vibrational energy from the OH reactant to H2O product is gated by the transition state, accomplished coherently by multiple TSWPs with the corresponding OH vibrational excitation.

  13. Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier

    CERN Document Server

    Mökkönen, Harri; Jónsson, Hannes

    2016-01-01

    The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates i...

  14. Nudged-elastic band method with two climbing images: finding transition states in complex energy landscapes

    CERN Document Server

    Zarkevich, Nikolai A

    2014-01-01

    The nudged-elastic band (NEB) method is modified with concomitant two climbing images (C2-NEB) to find a transition state (TS) in complex energy landscapes, such as those with serpentine minimal energy path (MEP). If a single climbing image (C1-NEB) successfully finds the TS, C2-NEB finds it with higher stability and accuracy. However, C2-NEB is suitable for more complex cases, where C1-NEB misses the TS because the MEP and NEB directions near the saddle point are different. Generally, C2-NEB not only finds the TS but guarantees that the climbing images approach it from the opposite sides along the MEP, and it estimates accuracy from the three images: the highest-energy one and its climbing neighbors. C2-NEB is suitable for fixed-cell NEB and the generalized solid-state NEB (SS-NEB).

  15. Free-end adaptive nudged elastic band method for locating transition states in minimum energy path calculation.

    Science.gov (United States)

    Zhang, Jiayong; Zhang, Hongwu; Ye, Hongfei; Zheng, Yonggang

    2016-09-07

    A free-end adaptive nudged elastic band (FEA-NEB) method is presented for finding transition states on minimum energy paths, where the energy barrier is very narrow compared to the whole paths. The previously proposed free-end nudged elastic band method may suffer from convergence problems because of the kinks arising on the elastic band if the initial elastic band is far from the minimum energy path and weak springs are adopted. We analyze the origin of the formation of kinks and present an improved free-end algorithm to avoid the convergence problem. Moreover, by coupling the improved free-end algorithm and an adaptive strategy, we develop a FEA-NEB method to accurately locate the transition state with the elastic band cut off repeatedly and the density of images near the transition state increased. Several representative numerical examples, including the dislocation nucleation in a penta-twinned nanowire, the twin boundary migration under a shear stress, and the cross-slip of screw dislocation in face-centered cubic metals, are investigated by using the FEA-NEB method. Numerical results demonstrate both the stability and efficiency of the proposed method.

  16. Free-end adaptive nudged elastic band method for locating transition states in minimum energy path calculation

    Science.gov (United States)

    Zhang, Jiayong; Zhang, Hongwu; Ye, Hongfei; Zheng, Yonggang

    2016-09-01

    A free-end adaptive nudged elastic band (FEA-NEB) method is presented for finding transition states on minimum energy paths, where the energy barrier is very narrow compared to the whole paths. The previously proposed free-end nudged elastic band method may suffer from convergence problems because of the kinks arising on the elastic band if the initial elastic band is far from the minimum energy path and weak springs are adopted. We analyze the origin of the formation of kinks and present an improved free-end algorithm to avoid the convergence problem. Moreover, by coupling the improved free-end algorithm and an adaptive strategy, we develop a FEA-NEB method to accurately locate the transition state with the elastic band cut off repeatedly and the density of images near the transition state increased. Several representative numerical examples, including the dislocation nucleation in a penta-twinned nanowire, the twin boundary migration under a shear stress, and the cross-slip of screw dislocation in face-centered cubic metals, are investigated by using the FEA-NEB method. Numerical results demonstrate both the stability and efficiency of the proposed method.

  17. Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates

    DEFF Research Database (Denmark)

    Stegelmann, Carsten; Andreasen, Anders; Campbell, Charles T.

    2009-01-01

    For many decades, the concept of a “rate-determining step” has been of central importance in understanding chemical kinetics in multistep reaction mechanisms and using that understanding to advantage. Yet a rigorous method for identifying the rate-determining step in a reaction mechanism was only...... model for any reaction mechanism. Thus, it is very important to identify these rate-controlling transition states and rate-controlling intermediates for both applied and basic research. Here, we present a method for doing that....

  18. TOPICAL REVIEW: Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments

    Science.gov (United States)

    Hyeon, Changbong; Thirumalai, D.

    2007-03-01

    Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the experimental measurements (the force-extension curves, the mechanical unfolding trajectories, force or loading rate dependent unfolding rates) with sound theoretical models and simulations. Here, we show how by using temperature as a variable in mechanical unfolding of biomolecules in laser optical tweezer or AFM experiments the roughness of the energy landscape can be measured without making any assumptions about the underlying reaction coordinate. The efficacy of the formalism is illustrated by reviewing experimental results that have directly measured roughness in a protein-protein complex. The roughness model can also be used to interpret experiments on forced unfolding of proteins in which temperature is varied. Estimates of other aspects of the energy landscape such as free energy barriers or the transition state (TS) locations could depend on the precise model used to analyse the experimental data. We illustrate the inherent difficulties in obtaining the transition state location from loading rate or force dependent unfolding rates. Because the transition state moves as the force or the loading rate is varied it is in general difficult to invert the experimental data unless the curvature at the top of the one dimensional free energy profile is large, i.e. the barrier is sharp. The independence of the TS location of the force holds good only for brittle or hard biomolecules whereas the TS location changes considerably if the molecule is soft or plastic. We also comment on the usefulness of extension of the molecule as a surrogate reaction coordinate especially in the context of force-quench refolding of proteins and RNA.

  19. Locating transition states using double-ended classical trajectories

    CERN Document Server

    Matro, A; Doll, J D

    1994-01-01

    In this paper we present a method for locating transition states and higher-order saddles on potential energy surfaces using double-ended classical trajectories. We then apply this method to 7- and 8-atom Lennard-Jones clusters, finding one previously unreported transition state for the 7-atom cluster and two for the 8-atom cluster.

  20. The Differential Gibbs Free Energy of Activation and its Implications in the Transition-State of Enzymatic Reactions

    Science.gov (United States)

    Maggi, F.; Riley, W. J.

    2016-12-01

    We propose a mathematical framework to introduce the concept of differential free energy of activation in enzymatically catalyzed reactions, and apply it to N uptake by microalgae and bacteria. This framework extends the thermodynamic capabilities of the classical transition-state theory in and harmonizes the consolidated definitions of kinetic parameters with their thermodynamic and physical meaning. Here, the activation energy is assumed to be a necessary energetic level for equilibrium complexation between reactants and activated complex; however, an additional energy contribution is required for the equilibrium activated complex to release reaction products. We call this "differential free energy of activation"; it can be described by a Boltzmann distribution, and corresponds to a free energy level different from that of complexation. Whether this level is above or below the free energy of activation depends on the reaction, and defines energy domains that correspond to "superactivated", "activated", and "subactivated" complexes. The activated complex reaching one of those states will eventually release the products from an energy level different than that of activation. The concept of differential free energy of activation was tested on 57 independent experiments of NH­4+ and NO3- uptake by various microalgae and bacteria at temperatures ranging between 1 and 45oC. Results showed that the complexation equilibrium always favored the activated complex, but the differential energy of activation led to an apparent energy barrier consistent with observations. Temperature affected all energy levels within this framework but did not alter substantially these thermodynamic features. Overall the approach: (1) provides a thermodynamic and mathematical link between Michaelis-Menten and rate constants; (2) shows that both kinetic parameters can be described or approximated by Arrhenius' like equations; (3) describes the likelihood of formation of sub-, super-, and

  1. Crossing the dividing surface of transition state theory. II. Recrossing times for the atom-diatom interaction

    Science.gov (United States)

    Lorquet, J. C.

    2014-04-01

    We consider a triatomic system with zero total angular momentum and demonstrate that, no matter how complicated the anharmonic part of the potential energy function, classical dynamics in the vicinity of a saddle point is constrained by symmetry properties. At short times and at not too high energies, recrossing dynamics is largely determined by elementary local structural parameters and thus can be described in configuration space only. Conditions for recrossing are given in the form of inequalities involving structural parameters only. Explicit expressions for recrossing times, valid for microcanonical ensembles, are shown to obey interesting regularities. In a forward reaction, when the transition state is nonlinear and tight enough, one-fourth of the trajectories are expected to recross the plane R = R* (where R* denotes the position of the saddle point) within a short time. Another fourth of them are expected to have previously recrossed at a short negative time, i.e., close to the saddle point. These trajectories do not contribute to the reaction rate. The reactive trajectories that obey the transition state model are to be found in the remaining half. However, no conclusion can be derived for them, except that if recrossings occur, then they must either take place in the distant future or already have taken place in the remote past, i.e., far away from the saddle point. Trajectories that all cross the plane R = R* at time t = 0, with the same positive translational momentum P_{R_* } can be partitioned into two sets, distinguished by the parity of their initial conditions; both sets have the same average equation of motion up to and including terms cubic in time. Coordination is excellent in the vicinity of the saddle point but fades out at long (positive or negative) times, i.e., far away from the transition state.

  2. Virtual screening of mandelate racemase mutants with enhanced activity based on binding energy in the transition state.

    Science.gov (United States)

    Gu, Jiali; Liu, Min; Guo, Fei; Xie, Wenping; Lu, Wenqiang; Ye, Lidan; Chen, Zhirong; Yuan, Shenfeng; Yu, Hongwei

    2014-02-05

    Mandelate racemase (MR) is a promising candidate for the dynamic kinetic resolution of racemates. However, the poor activity of MR towards most of its non-natural substrates limits its widespread application. In this work, a virtual screening method based on the binding energy in the transition state was established to assist in the screening of MR mutants with enhanced catalytic efficiency. Using R-3-chloromandelic acid as a model substrate, a total of 53 mutants were constructed based on rational design in the two rounds of screening. The number of mutants for experimental validation was brought down to 17 by the virtual screening method, among which 14 variants turned out to possess improved catalytic efficiency. The variant V26I/Y54V showed 5.2-fold higher catalytic efficiency (k(cat)/K(m)) towards R-3-chloromandelic acid than that observed for the wild-type enzyme. Using this strategy, mutants were successfully obtained for two other substrates, R-mandelamide and R-2-naphthylglycolate (V26I and V29L, respectively), both with a 2-fold improvement in catalytic efficiency. These results demonstrated that this method could effectively predict the trend of mutational effects on catalysis. Analysis from the energetic and structural assays indicated that the enhanced interactions between the active sites and the substrate in the transition state led to improved catalytic efficiency. It was concluded that this virtual screening method based on the binding energy in the transition state was beneficial in enzyme rational redesign and helped to better understand the catalytic properties of the enzyme.

  3. Which Is Better at Predicting Quantum-Tunneling Rates: Quantum Transition-State Theory or Free-Energy Instanton Theory?

    Science.gov (United States)

    Zhang, Yanchuan; Stecher, Thomas; Cvitaš, Marko T; Althorpe, Stuart C

    2014-11-20

    Quantum transition-state theory (QTST) and free-energy instanton theory (FEIT) are two closely related methods for estimating the quantum rate coefficient from the free-energy at the reaction barrier. In calculations on one-dimensional models, FEIT typically gives closer agreement than QTST with the exact quantum results at all temperatures below the crossover to deep tunneling, suggesting that FEIT is a better approximation than QTST in this regime. Here we show that this simple trend does not hold for systems of greater dimensionality. We report tests on several collinear and three-dimensional reactions, in which QTST outperforms FEIT over a range of temperatures below crossover, which can extend down to half the crossover temperature (below which FEIT outperforms QTST). This suggests that QTST-based methods such as ring-polymer molecular dynamics (RPMD) may often give closer agreement with the exact quantum results than FEIT.

  4. Density functional theory calculations on the complexation of p-arsanilic acid with hydrated iron oxide clusters: structures, reaction energies, and transition states.

    Science.gov (United States)

    Adamescu, Adrian; Hamilton, Ian P; Al-Abadleh, Hind A

    2014-07-31

    Aromatic organoarsenicals, such as p-arsanilic acid (pAsA), are still used today as feed additives in the poultry and swine industries in developing countries. Through the application of contaminated litter as a fertilizer, these compounds enter the environment and interact with reactive soil components such as iron and aluminum oxides. Little is known about these surface interactions at the molecular level. We report density functional theory (DFT) calculations on the energies, optimal geometries, and vibrational frequencies for hydrated pAsA/iron oxide complexes, as well as changes in Gibbs free energy, enthalpy, and entropy for various types of ligand exchange reactions leading to both inner- and outer-sphere complexes. Similar calculations using arsenate are also shown for comparison, along with activation barriers and transition state geometries between inner-sphere complexes. Minimum energy calculations show that the formation of inner- and outer-sphere pAsA/iron oxide complexes is thermodynamically favorable, with the monodentate mononuclear complexes being the most favorable. Interatomic As-Fe distances are calculated to be between 3.3 and 3.5 Å for inner-sphere complexes and between 5.2 and 5.6 Å for outer-sphere complexes. In addition, transition state calculations show that activation energies greater than 23 kJ/mol are required to form the bidentate binuclear pAsA/iron oxide complexes, and that formation of arsenate bidentate binuclear complexes is thermodynamically -rather than kinetically- driven. Desorption thermodynamics using phosphate ions show that reactions are most favorable using HPO4(2-) species. The significance of our results for the overall surface complexation mechanism of pAsA and arsenate is discussed.

  5. Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates

    DEFF Research Database (Denmark)

    Stegelmann, Carsten; Andreasen, Anders; Campbell, Charles T.

    2009-01-01

    electronic or steric control on the relative energies of the key species. Since these key species are the ones whose relative energies most strongly influence the net reaction rate, they also identify the species whose energetics must be most accurately measured or calculated to achieve an accurate kinetic...

  6. Non-uniqueness of quantum transition state theory and general dividing surfaces in the path integral space.

    Science.gov (United States)

    Jang, Seogjoo; Voth, Gregory A

    2017-05-07

    Despite the fact that quantum mechanical principles do not allow the establishment of an exact quantum analogue of the classical transition state theory (TST), the development of a quantum TST (QTST) with a proper dynamical justification, while recovering the TST in the classical limit, has been a long standing theoretical challenge in chemical physics. One of the most recent efforts of this kind was put forth by Hele and Althorpe (HA) [J. Chem. Phys. 138, 084108 (2013)], which can be specified for any cyclically invariant dividing surface defined in the space of the imaginary time path integral. The present work revisits the issue of the non-uniqueness of QTST and provides a detailed theoretical analysis of HA-QTST for a general class of such path integral dividing surfaces. While we confirm that HA-QTST reproduces the result based on the ring polymer molecular dynamics (RPMD) rate theory for dividing surfaces containing only a quadratic form of low frequency Fourier modes, we find that it produces different results for those containing higher frequency imaginary time paths which accommodate greater quantum fluctuations. This result confirms the assessment made in our previous work [Jang and Voth, J. Chem. Phys. 144, 084110 (2016)] that HA-QTST does not provide a derivation of RPMD-TST in general and points to a new ambiguity of HA-QTST with respect to its justification for general cyclically invariant dividing surfaces defined in the space of imaginary time path integrals. Our analysis also offers new insights into similar path integral based QTST approaches.

  7. Gold(I)-catalyzed Claisen rearrangement of allenyl vinyl ethers: missing transition states revealed through evolution of aromaticity, Au(I) as an oxophilic Lewis acid, and lower energy barriers from a high energy complex.

    Science.gov (United States)

    Vidhani, Dinesh V; Cran, John W; Krafft, Marie E; Manoharan, Mariappan; Alabugin, Igor V

    2013-03-01

    Curtin-Hammett analysis of four alternative mechanisms of the gold(I)-catalyzed [3,3] sigmatropic rearrangement of allenyl vinyl ethers by density functional theory calculations reveals that the lowest energy pathway (cation-accelerated oxonia Claisen rearrangement) originates from the second most stable of the four Au(I)-substrate complexes in which gold(I) coordinates to the lone pair of oxygen. This pathway proceeds via a dissociative transition state where the C-O bond cleavage precedes C1-C6 bond formation. The alternative Au(I) coordination at the vinyl π-system produces a more stable but less reactive complex. The two least stable modes of coordination at the allenyl π-system display reactivity that is intermediate between that of the Au(I)-oxygen and the Au(I)-vinyl ether complexes. The unusual electronic features of the four potential energy surfaces (PESs) associated with the four possible mechanisms were probed with intrinsic reaction coordinate calculations in conjunction with nucleus independent chemical shift (NICS(0)) evaluation of aromaticity of the transient structures. The development of aromatic character along the "6-endo" reaction path is modulated via Au-complexation to the extent where both the cyclic intermediate and the associated fragmentation transition state do not correspond to stationary points at the reaction potential energy surface. This analysis explains why the calculated PES for cyclization promoted by coordination of gold(I) to allenyl moiety lacks a discernible intermediate despite proceeding via a highly asynchronous transition state with characteristics of a stepwise "cyclization-mediated" process. Although reaction barriers can be strongly modified by aryl substituents of varying electronic demand, direct comparison of experimental and computational substituent effects is complicated by formation of Au-complexes with the Lewis-basic sites of the substrates.

  8. Quantum Transition-State Theory

    CERN Document Server

    Hele, Timothy J H

    2014-01-01

    This dissertation unifies one of the central methods of classical rate calculation, `Transition-State Theory' (TST), with quantum mechanics, thereby deriving a rigorous `Quantum Transition-State Theory' (QTST). The resulting QTST is identical to ring polymer molecular dynamics transition-state theory (RPMD-TST), which was previously considered a heuristic method, and whose results we thereby validate. The key step in deriving a QTST is alignment of the flux and side dividing surfaces in path-integral space to obtain a quantum flux-side time-correlation function with a non-zero $t\\to 0_+$ limit. We then prove that this produces the exact quantum rate in the absence of recrossing by the exact quantum dynamics, fulfilling the requirements of a QTST. Furthermore, strong evidence is presented that this is the only QTST with positive-definite Boltzmann statistics and therefore the pre-eminent method for computation of thermal quantum rates in direct reactions.

  9. Spectroscopic analysis of transition state energy levels - Bending-rotational spectrum and lifetime analysis of H3 quasibound states

    Science.gov (United States)

    Zhao, Meishan; Mladenovic, Mirjana; Truhlar, Donald G.; Schwenke, David W.; Sharafeddin, Omar

    1989-01-01

    Converged quantum mechanical calculations of scattering matrices and transition probabilities are reported for the reaction of H with H2 with total angular momentum 0, 1, and 4 as functions of total energy in the range 0.85-1.15 eV on an accurate potential energy surface. The resonance structure is illustrated with Argand diagrams. State-to-state reactive collision delay times and lifetimes are presented. For J = 0, 1, and 4, the lowest-energy H3 resonance is at total energies of 0.983, 0.985, and 1.01 eV, respectively, with lifetimes of about 16-17 fs. For J = 1 and 4 there is a higher-energy resonance at 1.10-1.11 eV. For J = 1 the lifetime is about 4 fs and for J = 4 it is about 1 fs.

  10. Linear Free Energy Relationship Analysis of Transition State Mimicry by 3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) Oxime, a DAHP Synthase Inhibitor and Phosphate Mimic.

    Science.gov (United States)

    Balachandran, Naresh; To, Frederick; Berti, Paul J

    2017-01-31

    3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) synthase catalyzes an aldol-like reaction of phosphoenolpyruvate (PEP) with erythrose 4-phosphate (E4P) to form DAHP in the first step of the shikimate biosynthetic pathway. DAHP oxime, in which an oxime replaces the ketone, is a potent inhibitor, with Ki = 1.5 μM. Linear free energy relationship (LFER) analysis of DAHP oxime inhibition using DAHP synthase mutants revealed an excellent correlation between transition state stabilization and inhibition. The equations of LFER analysis were rederived to formalize the possibility of proportional, rather than equal, changes in the free energies of transition state stabilization and inhibitor binding, in accord with the fact that the majority of LFER analyses in the literature demonstrate nonunity slopes. A slope of unity, m = 1, indicates that catalysis and inhibitor binding are equally sensitive to perturbations such as mutations or modified inhibitor/substrate structures. Slopes 1 indicate that inhibitor binding is less sensitive or more sensitive, respectively, to perturbations than is catalysis. LFER analysis using the tetramolecular specificity constant, that is, plotting log(KM,MnKM,PEPKM,E4P/kcat) versus log(Ki), revealed a slope, m, of 0.34, with r(2) = 0.93. This provides evidence that DAHP oxime is mimicking the first irreversible transition state of the DAHP synthase reaction, presumably phosphate departure from the tetrahedral intermediate. This is evidence that the oxime group can act as a functional, as well as structural, mimic of phosphate groups.

  11. Morse bifurcations of transition states in bimolecular reactions

    CERN Document Server

    MacKay, Robert S

    2015-01-01

    The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo qualitative changes, known as Morse bifurcations, and to exist for a large range of energies, not just immediately above the critical energy for first connection between reactants and products. Specifically, we consider capture between two molecules and the associated transition states for the case of non-zero angular momentum and general attitudes. The capture between an atom and a diatom, and then a general molecule are presented, providing concrete examples of Morse bifurcations of transition states and dividing surfaces. The reduction of the $n$-body systems representing the reactions is discussed and reviewed with comments on the difficulties associated with choosing appropriate charts and the global geometry of the reduced spaces.

  12. Variational Transition State Theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, Donald G. [Univ. of Minnesota, Minneapolis, MN (United States)

    2016-09-29

    This is the final report on a project involving the development and applications of variational transition state theory. This project involved the development of variational transition state theory for gas-phase reactions, including optimized multidimensional tunneling contributions and the application of this theory to gas-phase reactions with a special emphasis on developing reaction rate theory in directions that are important for applications to combustion. The development of variational transition state theory with optimized multidimensional tunneling as a useful computational tool for combustion kinetics involved eight objectives.

  13. Communication: State-to-state dynamics of the Cl + H2O → HCl + OH reaction: Energy flow into reaction coordinate and transition-state control of product energy disposal.

    Science.gov (United States)

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2015-06-28

    Quantum state-to-state dynamics of a prototypical four-atom reaction, namely, Cl + H2O → HCl + OH, is investigated for the first time in full dimensionality using a transition-state wave packet method. The state-to-state reactivity and its dependence on the reactant internal excitations are analyzed and found to share many similarities both energetically and dynamically with the H + H2O → H2 + OH reaction. The strong enhancement of reactivity by the H2O stretching vibrational excitations in both reactions is attributed to the favorable energy flow into the reaction coordinate near the transition state. On the other hand, the insensitivity of the product state distributions with regard to reactant internal excitation stems apparently from the transition-state control of product energy disposal.

  14. Final Technical Report: Variational Transition State Theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, Donald G. [University of Minnesota; Truhlar, Donald G. [University of Minnesota

    2016-09-15

    Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupledmode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multidimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MPVTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EAVTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical—reactions with 4, 6, and 14 saddle points.

  15. Combining active-space coupled-cluster methods with moment energy corrections via the CC(P;Q) methodology, with benchmark calculations for biradical transition states

    Science.gov (United States)

    Shen, Jun; Piecuch, Piotr

    2012-04-01

    We have recently suggested the CC(P;Q) methodology that can correct energies obtained in the active-space coupled-cluster (CC) or equation-of-motion (EOM) CC calculations, which recover much of the nondynamical and some dynamical electron correlation effects, for the higher-order, mostly dynamical, correlations missing in the active-space CC/EOMCC considerations. It is shown that one can greatly improve the description of biradical transition states, both in terms of the resulting energy barriers and total energies, by combining the CC approach with singles, doubles, and active-space triples, termed CCSDt, with the CC(P;Q)-style correction due to missing triple excitations defining the CC(t;3) approximation.

  16. Variational transition state theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, D.G. [Univ. of Minnesota, Minneapolis (United States)

    1993-12-01

    This research program involves the development of variational transition state theory (VTST) and semiclassical tunneling methods for the calculation of gas-phase reaction rates and selected applications. The applications are selected for their fundamental interest and/or their relevance to combustion.

  17. Dipole moment surfaces of the CH4 + •X → CH3• + HX (X = F, Cl) reactions from atomic dipole moment surfaces, and the origins of the sharp extrema of the dipole moments near the transition states.

    Science.gov (United States)

    Matta, Chérif F; Sowlati-Hashjin, Shahin; Bandrauk, André D

    2013-08-15

    The partitioning of the dipole moment of an isolated molecule or that of a reacting system is reviewed and applied to a dynamic reacting system whereby the system's dipole moment surface is constructed in parallel to its potential energy surface. The dipole moment surface is then decomposed into two origin-independent surfaces: (1) an atomic polarization (AP) surface and a charge transfer (CT) surface. The dipole moment surface as well as its two composing AP and CT surfaces are all further broken down into atomic and/or group contributions with the aid of the quantum theory of atoms in molecules (QTAIM). This approach is applied to the title's laser-induced chemical reactions [CH4 + (•)X → CH3(•) + HX (X = F, Cl)] previously studied by Bandrauk et al. [ J. Chem. Phys. 2004 , 121 , 7764 - 7775 ], and which were found to exhibit marked peaks in the dipole moment and in the polarizability tensor component at (or near) the transition state. These peaks afford a means to control the kinetics of these reactions with the proper adjustment of an external laser field intensity and phase. The entrance channel potentials of these reactions have recently been probed by photodetachment spectroscopy by Bowman and collaborators [ J. Chem. Phys. 2011 , 134 , 191102_1 - 4 ]. The understanding of the origin of the peaks in the dipole moment can provide, eventually, an additional layer of control in the design of reactions tunable by external fields through the proper selection of the reactants to maximize the field-molecule interaction.

  18. Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments

    OpenAIRE

    2006-01-01

    Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the experimental measurements with sound theoretical models and simulations. Here, we show how by using temperature as a variable in mechanical unfolding of biomolecules in laser optical tweezer or AFM experiments the roughness of the energy landscape can be m...

  19. Quantum Transition State Theory for proton transfer reactions in enzymes

    CERN Document Server

    Bothma, Jacques P; McKenzie, Ross H

    2009-01-01

    We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We use a path integral approach which provides a general framework to understand tunneling in a quantum system which interacts with an environment at non-zero temperature. Here the quantum system is the active site of the enzyme and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature $T_0$ which is determined by the curvature of potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. For physically reasonable parameters quantum transition state theory gives a quantitative descr...

  20. Communication: Photodissociation of CH{sub 3}CHO at 308 nm: Observation of H-roaming, CH{sub 3}-roaming, and transition state pathways together along the ground state surface

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hou-Kuan; Tsai, Po-Yu; Hung, Kai-Chan; Kasai, Toshio; Lin, King-Chuen, E-mail: kclin@ntu.edu.tw [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China)

    2015-01-28

    Following photodissociation of acetaldehyde (CH{sub 3}CHO) at 308 nm, the CO(v = 1–4) fragment is acquired using time-resolved Fourier-transform infrared emission spectroscopy. The CO(v = 1) rotational distribution shows a bimodal feature; the low- and high-J components result from H-roaming around CH{sub 3}CO core and CH{sub 3}-roaming around CHO radical, respectively, in consistency with a recent assignment by Kable and co-workers (Lee et al., Chem. Sci. 5, 4633 (2014)). The H-roaming pathway disappears at the CO(v ≥ 2) states, because of insufficient available energy following bond-breaking of H + CH{sub 3}CO. By analyzing the CH{sub 4} emission spectrum, we obtained a bimodal vibrational distribution; the low-energy component is ascribed to the transition state (TS) pathway, consistent with prediction by quasiclassical trajectory calculations, while the high-energy component results from H- and CH{sub 3}-roamings. A branching fraction of H-roaming/CH{sub 3}-roaming/TS contribution is evaluated to be (8% ± 3%)/(68% ± 10%)/(25% ± 5%), in which the TS pathway was observed for the first time. The three pathways proceed concomitantly along the electronic ground state surface.

  1. Biosynthetic consequences of multiple sequential post-transition-state bifurcations

    Science.gov (United States)

    Hong, Young Joo; Tantillo, Dean J.

    2014-02-01

    Selectivity in chemical reactions that form complex molecular architectures from simpler precursors is usually rationalized by comparing competing transition-state structures that lead to different possible products. Herein we describe a system for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations. The reaction network described connects the pimar-15-en-8-yl cation to miltiradiene, a tricyclic diterpene natural product, and isomers via cyclizations and/or rearrangements. The results suggest that the selectivity of the reaction is controlled by (post-transition-state) dynamic effects, that is, how the carbocation structure changes in response to the distribution of energy in its vibrational modes. The inherent dynamical effects revealed herein (characterized through quasiclassical direct dynamics calculations using density functional theory) have implications not only for the general principles of selectivity prediction in systems with complex potential energy surfaces, but also for the mechanisms of terpene synthase enzymes and their evolution. These findings redefine the challenges faced by nature in controlling the biosynthesis of complex natural products.

  2. 3D Printed Potential and Free Energy Surfaces for Teaching Fundamental Concepts in Physical Chemistry

    Science.gov (United States)

    Kaliakin, Danil S.; Zaari, Ryan R.; Varganov, Sergey A.

    2015-01-01

    Teaching fundamental physical chemistry concepts such as the potential energy surface, transition state, and reaction path is a challenging task. The traditionally used oversimplified 2D representation of potential and free energy surfaces makes this task even more difficult and often confuses students. We show how this 2D representation can be…

  3. Transition state trajectory stability determines barrier crossing rates in chemical reactions induced by time-dependent oscillating fields

    CERN Document Server

    Craven, Galen T; Hernandez, Rigoberto

    2015-01-01

    When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product -for example, an energy barrier- becomes time-dependent. We show that for periodic forcing the rate of barrier crossing can be determined through stability analysis of the non-autonomous transition state. Specifically, strong agreement is observed between the difference in the Floquet exponents describing stability of the transition state trajectory, which defines a recrossing-free dividing surface [G. T. Craven, T. Bartsch, and R. Hernandez, Phys. Rev. E 89, 040801(R) (2014)], and the rates calculated by simulation of ensembles of trajectories. This result opens the possibility to extract rates directly from the intrinsic stability of the transition state, even when it is time-dependent, without requiring a numerically-expensive simulation of the long-time dynamics of a large ensemble of trajectories.

  4. A New Exploration of the Torsional Energy Surface of N-Pentane Using Molecular Modeling Software

    Science.gov (United States)

    Galembeck, Sergio E.; Caramori, Giovanni F.; Romero, Jose Ricardo

    2005-01-01

    The torsional potential energy surface of a chemical compounds, the accessible conformations at a specified temperature and the transition states that connect these confirmations establishes many chemical properties such as dynamic behavior, reactivity and biological activity. A conformational search of n-pentane is presented using computational…

  5. Relating transition-state spectroscopy to standard chemical spectroscopic processes

    Science.gov (United States)

    Reimers, Jeffrey R.; Hush, Noel S.

    2017-09-01

    Transition-state spectra are mapped out using generalized adiabatic electron-transfer theory. This simple model depicts diverse chemical properties, from aromaticity, through bound reactions such as isomerizations and atom-transfer processes with classic transition states, to processes often described as being ;non-adiabatic;, to those in the ;inverted; region that become slower as they are made more exothermic. Predictably, the Born-Oppenheimer approximation is found inadequate for modelling transition-state spectra in the weak-coupling limit. In this limit, the adiabatic Born-Huang approximation is found to perform much better than non-adiabatic surface-hopping approaches. Transition-state spectroscopy is shown to involve significant quantum entanglement between electronic and nuclear motion.

  6. Studies of transition states and radicals by negative ion photodetachment

    Energy Technology Data Exchange (ETDEWEB)

    Metz, R.B.

    1991-12-01

    Negative ion photodetachment is a versatile tool for the production and study of transient neutral species such as reaction intermediates and free radicals. Photodetachment of the stable XHY{sup {minus}} anion provides a direct spectroscopic probe of the transition state region of the potential energy surface for the neutral hydrogen transfer reaction X + HY {yields} XH + Y, where X and Y are halogen atoms. The technique is especially sensitive to resonances, which occur at a specific energy, but the spectra also show features due to direct scattering. We have used collinear adiabatic simulations of the photoelectron spectra to evaluate trail potential energy surfaces for the biomolecular reactions and have extended the adiabatic approach to three dimensions and used it to evaluate empirical potential energy surfaces for the I + Hl and Br + HI reactions. In addition, we have derived an empirical, collinear potential energy surface for the Br + HBr reaction that reproduces our experimental results and have extended this surface to three dimensions. Photodetachment of a negative ion can be also used to study neutral free radicals. We have studied the vibrational and electronic spectroscopy of CH{sub 2}NO{sub 2} by photoelectron spectroscopy of CH{sub 2}NO{sub 2}{sup {minus}}, determining the electron affinity of CH{sub 2}NO{sub 2}, gaining insight on the bonding of the {sup 2}B{sub 1} ground state and observing the {sup 2}A{sub 2} excited state for the first time. Negative ion photodetachment also provides a novel and versatile source of mass-selected, jet-cooled free radicals. We have studied the photodissociation of CH{sub 2}NO{sub 2} at 270, 235, and 208 nm, obtaining information on the dissociation products by measuring the kinetic energy release in the photodissociation.

  7. Studies of transition states and radicals by negative ion photodetachment

    Energy Technology Data Exchange (ETDEWEB)

    Metz, R.B.

    1991-12-01

    Negative ion photodetachment is a versatile tool for the production and study of transient neutral species such as reaction intermediates and free radicals. Photodetachment of the stable XHY{sup {minus}} anion provides a direct spectroscopic probe of the transition state region of the potential energy surface for the neutral hydrogen transfer reaction X + HY {yields} XH + Y, where X and Y are halogen atoms. The technique is especially sensitive to resonances, which occur at a specific energy, but the spectra also show features due to direct scattering. We have used collinear adiabatic simulations of the photoelectron spectra to evaluate trail potential energy surfaces for the biomolecular reactions and have extended the adiabatic approach to three dimensions and used it to evaluate empirical potential energy surfaces for the I + Hl and Br + HI reactions. In addition, we have derived an empirical, collinear potential energy surface for the Br + HBr reaction that reproduces our experimental results and have extended this surface to three dimensions. Photodetachment of a negative ion can be also used to study neutral free radicals. We have studied the vibrational and electronic spectroscopy of CH{sub 2}NO{sub 2} by photoelectron spectroscopy of CH{sub 2}NO{sub 2}{sup {minus}}, determining the electron affinity of CH{sub 2}NO{sub 2}, gaining insight on the bonding of the {sup 2}B{sub 1} ground state and observing the {sup 2}A{sub 2} excited state for the first time. Negative ion photodetachment also provides a novel and versatile source of mass-selected, jet-cooled free radicals. We have studied the photodissociation of CH{sub 2}NO{sub 2} at 270, 235, and 208 nm, obtaining information on the dissociation products by measuring the kinetic energy release in the photodissociation.

  8. Surface Meteorology and Solar Energy

    Data.gov (United States)

    National Aeronautics and Space Administration — Surface Meteorology and Solar Energy data - over 200 satellite-derived meteorology and solar energy parameters, monthly averaged from 22 years of data, global solar...

  9. Potential energy surfaces and reaction dynamics of polyatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Yan-Tyng.

    1991-11-01

    A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.

  10. Transition State Theory: Variational Formulation, Dynamical Corrections, and Error Estimates

    Science.gov (United States)

    vanden-Eijnden, Eric

    2009-03-01

    Transition state theory (TST) is discussed from an original viewpoint: it is shown how to compute exactly the mean frequency of transition between two predefined sets which either partition phase space (as in TST) or are taken to be well separate metastable sets corresponding to long-lived conformation states (as necessary to obtain the actual transition rate constants between these states). Exact and approximate criterions for the optimal TST dividing surface with minimum recrossing rate are derived. Some issues about the definition and meaning of the free energy in the context of TST are also discussed. Finally precise error estimates for the numerical procedure to evaluate the transmission coefficient κS of the TST dividing surface are given, and it shown that the relative error on κS scales as 1/√κS when κS is small. This implies that dynamical corrections to the TST rate constant can be computed efficiently if and only if the TST dividing surface has a transmission coefficient κS which is not too small. In particular the TST dividing surface must be optimized upon (for otherwise κS is generally very small), but this may not be sufficient to make the procedure numerically efficient (because the optimal dividing surface has maximum κS, but this coefficient may still be very small).

  11. Communication: Transition state trajectory stability determines barrier crossing rates in chemical reactions induced by time-dependent oscillating fields.

    Science.gov (United States)

    Craven, Galen T; Bartsch, Thomas; Hernandez, Rigoberto

    2014-07-28

    When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product--for example, an energy barrier--becomes time-dependent. We show that for periodic forcing the rate of barrier crossing can be determined through stability analysis of the non-autonomous transition state. Specifically, strong agreement is observed between the difference in the Floquet exponents describing stability of the transition state trajectory, which defines a recrossing-free dividing surface [G. T. Craven, T. Bartsch, and R. Hernandez, "Persistence of transition state structure in chemical reactions driven by fields oscillating in time," Phys. Rev. E 89, 040801(R) (2014)], and the rates calculated by simulation of ensembles of trajectories. This result opens the possibility to extract rates directly from the intrinsic stability of the transition state, even when it is time-dependent, without requiring a numerically expensive simulation of the long-time dynamics of a large ensemble of trajectories.

  12. Surface energies of elemental crystals

    Science.gov (United States)

    Tran, Richard; Xu, Zihan; Radhakrishnan, Balachandran; Winston, Donald; Sun, Wenhao; Persson, Kristin A.; Ong, Shyue Ping

    2016-09-01

    The surface energy is a fundamental property of the different facets of a crystal that is crucial to the understanding of various phenomena like surface segregation, roughening, catalytic activity, and the crystal’s equilibrium shape. Such surface phenomena are especially important at the nanoscale, where the large surface area to volume ratios lead to properties that are significantly different from the bulk. In this work, we present the largest database of calculated surface energies for elemental crystals to date. This database contains the surface energies of more than 100 polymorphs of about 70 elements, up to a maximum Miller index of two and three for non-cubic and cubic crystals, respectively. Well-known reconstruction schemes are also accounted for. The database is systematically improvable and has been rigorously validated against previous experimental and computational data where available. We will describe the methodology used in constructing the database, and how it can be accessed for further studies and design of materials.

  13. Transition state ensemble optimization for reactions of arbitrary complexity

    Science.gov (United States)

    Zinovjev, Kirill; Tuñón, Iñaki

    2015-10-01

    In the present work, we use Variational Transition State Theory (VTST) to develop a practical method for transition state ensemble optimization by looking for an optimal hyperplanar dividing surface in a space of meaningful trial collective variables. These might be interatomic distances, angles, electrostatic potentials, etc. Restrained molecular dynamics simulations are used to obtain on-the-fly estimates of ensemble averages that guide the variations of the hyperplane maximizing the transmission coefficient. A central result of our work is an expression that quantitatively estimates the importance of the coordinates used for the localization of the transition state ensemble. Starting from an arbitrarily large set of trial coordinates, one can distinguish those that are indeed essential for the advance of the reaction. This facilitates the use of VTST as a practical theory to study reaction mechanisms of complex processes. The technique was applied to the reaction catalyzed by an isochorismate pyruvate lyase. This reaction involves two simultaneous chemical steps and has a shallow transition state region, making it challenging to define a good reaction coordinate. Nevertheless, the hyperplanar transition state optimized in the space of 18 geometrical coordinates provides a transmission coefficient of 0.8 and a committor histogram well-peaked about 0.5, proving the strength of the method. We have also tested the approach with the study of the NaCl dissociation in aqueous solution, a stringest test for a method based on transition state theory. We were able to find essential degrees of freedom consistent with the previous studies and to improve the transmission coefficient with respect to the value obtained using solely the NaCl distance as the reaction coordinate.

  14. The surface energy of metals

    DEFF Research Database (Denmark)

    Vitos, Levente; Ruban, Andrei; Skriver, Hans Lomholt

    1998-01-01

    We have used density functional theory to establish a database of surface energies for low index surfaces of 60 metals in the periodic table. The data may be used as a consistent starting point for models of surface science phenomena. The accuracy of the database is established in a comparison...... with other density functional theory results and the calculated surface energy anisotropies are applied in a determination of the equilibrium shape of nano-crystals of Fe, Cu, Mo, Ta, Pt and Ph. (C) 1998 Elsevier Science B.V. All rights reserved....

  15. Perimenopause as a neurological transition state.

    Science.gov (United States)

    Brinton, Roberta D; Yao, Jia; Yin, Fei; Mack, Wendy J; Cadenas, Enrique

    2015-07-01

    Perimenopause is a midlife transition state experienced by women that occurs in the context of a fully functioning neurological system and results in reproductive senescence. Although primarily viewed as a reproductive transition, the symptoms of perimenopause are largely neurological in nature. Neurological symptoms that emerge during perimenopause are indicative of disruption in multiple estrogen-regulated systems (including thermoregulation, sleep, circadian rhythms and sensory processing) and affect multiple domains of cognitive function. Estrogen is a master regulator that functions through a network of estrogen receptors to ensure that the brain effectively responds at rapid, intermediate and long timescales to regulate energy metabolism in the brain via coordinated signalling and transcriptional pathways. The estrogen receptor network becomes uncoupled from the bioenergetic system during the perimenopausal transition and, as a corollary, a hypometabolic state associated with neurological dysfunction can develop. For some women, this hypometabolic state might increase the risk of developing neurodegenerative diseases later in life. The perimenopausal transition might also represent a window of opportunity to prevent age-related neurological diseases. This Review considers the importance of neurological symptoms in perimenopause in the context of their relationship to the network of estrogen receptors that control metabolism in the brain.

  16. Inequivalent models of irreversible dimer filling: ``Transition state'' dependence

    Science.gov (United States)

    Nord, R. S.; Evans, J. W.

    1990-12-01

    Irreversible adsorption of diatomics on crystalline surfaces is sometimes modeled as random dimer filling of adjacent pairs of sites on a lattice. We note that this process can be implemented in two distinct ways: (i) randomly pick adjacent pairs of sites, jj', and fill jj' only if both are empty (horizontal transition state); or (ii) randomly pick a single site, j, and if j and at least one neighbor are empty, then fill j and a randomly chosen empty neighbor (vertical transition state). Here it is instructive to consider processes which also include competitive random monomer filling of single sites. We find that although saturation (partial) coverages differ little between the models for pure dimer filling, there is a significant difference for comparable monomer and dimer filling rates. We present exact results for saturation coverage behavior for a linear lattice, and estimates for a square lattice. Ramifications for simple models of CO oxidation on surfaces are indicated.

  17. Iterative minimization algorithm for efficient calculations of transition states

    Science.gov (United States)

    Gao, Weiguo; Leng, Jing; Zhou, Xiang

    2016-03-01

    This paper presents an efficient algorithmic implementation of the iterative minimization formulation (IMF) for fast local search of transition state on potential energy surface. The IMF is a second order iterative scheme providing a general and rigorous description for the eigenvector-following (min-mode following) methodology. We offer a unified interpretation in numerics via the IMF for existing eigenvector-following methods, such as the gentlest ascent dynamics, the dimer method and many other variants. We then propose our new algorithm based on the IMF. The main feature of our algorithm is that the translation step is replaced by solving an optimization subproblem associated with an auxiliary objective function which is constructed from the min-mode information. We show that using an efficient scheme for the inexact solver and enforcing an adaptive stopping criterion for this subproblem, the overall computational cost will be effectively reduced and a super-linear rate between the accuracy and the computational cost can be achieved. A series of numerical tests demonstrate the significant improvement in the computational efficiency for the new algorithm.

  18. Transition-state theory and dynamical corrections

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm; Hansen, Flemming Yssing

    2002-01-01

    . The correction factor due to non-adiabatic dynamics is considered in relation to the non-activated dissociative sticking of N-2 on Fe(111). For this process, conventional transition-state theory gives a sticking probability which is about 10 times too large (at T = 300 K). We estimate that the sticking......We consider conventional transition-state theory, and show how quantum dynamical correction factors can be incorporated in a simple fashion, as a natural extension of the fundamental formulation. Corrections due to tunneling and non-adiabatic dynamics are discussed, with emphasis on the latter...

  19. Kinetic study on the H + SiH4 abstraction reaction using an ab initio potential energy surface.

    Science.gov (United States)

    Cao, Jianwei; Zhang, Zhijun; Zhang, Chunfang; Bian, Wensheng; Guo, Yin

    2011-01-14

    Variational transition state theory calculations with the correction of multidimensional tunneling are performed on a 12-dimensional ab initio potential energy surface for the H + SiH(4) abstraction reaction. The surface is constructed using a dual-level strategy. For the temperature range 200-1600 K, thermal rate constants are calculated and kinetic isotope effects for various isotopic species of the title reaction are investigated. The results are in very good agreement with available experimental data.

  20. Sampling saddle points on a free energy surface.

    Science.gov (United States)

    Samanta, Amit; Chen, Ming; Yu, Tang-Qing; Tuckerman, Mark; E, Weinan

    2014-04-28

    Many problems in biology, chemistry, and materials science require knowledge of saddle points on free energy surfaces. These saddle points act as transition states and are the bottlenecks for transitions of the system between different metastable states. For simple systems in which the free energy depends on a few variables, the free energy surface can be precomputed, and saddle points can then be found using existing techniques. For complex systems, where the free energy depends on many degrees of freedom, this is not feasible. In this paper, we develop an algorithm for finding the saddle points on a high-dimensional free energy surface "on-the-fly" without requiring a priori knowledge the free energy function itself. This is done by using the general strategy of the heterogeneous multi-scale method by applying a macro-scale solver, here the gentlest ascent dynamics algorithm, with the needed force and Hessian values computed on-the-fly using a micro-scale model such as molecular dynamics. The algorithm is capable of dealing with problems involving many coarse-grained variables. The utility of the algorithm is illustrated by studying the saddle points associated with (a) the isomerization transition of the alanine dipeptide using two coarse-grained variables, specifically the Ramachandran dihedral angles, and (b) the beta-hairpin structure of the alanine decamer using 20 coarse-grained variables, specifically the full set of Ramachandran angle pairs associated with each residue. For the alanine decamer, we obtain a detailed network showing the connectivity of the minima obtained and the saddle-point structures that connect them, which provides a way to visualize the gross features of the high-dimensional surface.

  1. Surface meteorology and Solar Energy

    Science.gov (United States)

    Stackhouse, Paul W. (Principal Investigator)

    The Release 5.1 Surface meteorology and Solar Energy (SSE) data contains parameters formulated for assessing and designing renewable energy systems. Parameters fall under 11 categories including: Solar cooking, solar thermal applications, solar geometry, tilted solar panels, energy storage systems, surplus product storage systems, cloud information, temperature, wind, other meteorological factors, and supporting information. This latest release contains new parameters based on recommendations by the renewable energy industry and it is more accurate than previous releases. On-line plotting capabilities allow quick evaluation of potential renewable energy projects for any region of the world. The SSE data set is formulated from NASA satellite- and reanalysis-derived insolation and meteorological data for the 10-year period July 1983 through June 1993. Results are provided for 1 degree latitude by 1 degree longitude grid cells over the globe. Average daily and monthly measurements for 1195 World Radiation Data Centre ground sites are also available. [Mission Objectives] The SSE project contains insolation and meteorology data intended to aid in the development of renewable energy systems. Collaboration between SSE and technology industries such as the Hybrid Optimization Model for Electric Renewables ( HOMER ) may aid in designing electric power systems that employ some combination of wind turbines, photovoltaic panels, or diesel generators to produce electricity. [Temporal_Coverage: Start_Date=1983-07-01; Stop_Date=1993-06-30] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180].

  2. Theoretical studies of potential energy surfaces and computational methods

    Energy Technology Data Exchange (ETDEWEB)

    Shepard, R. [Argonne National Laboratory, IL (United States)

    1993-12-01

    This project involves the development, implementation, and application of theoretical methods for the calculation and characterization of potential energy surfaces involving molecular species that occur in hydrocarbon combustion. These potential energy surfaces require an accurate and balanced treatment of reactants, intermediates, and products. This difficult challenge is met with general multiconfiguration self-consistent-field (MCSCF) and multireference single- and double-excitation configuration interaction (MRSDCI) methods. In contrast to the more common single-reference electronic structure methods, this approach is capable of describing accurately molecular systems that are highly distorted away from their equilibrium geometries, including reactant, fragment, and transition-state geometries, and of describing regions of the potential surface that are associated with electronic wave functions of widely varying nature. The MCSCF reference wave functions are designed to be sufficiently flexible to describe qualitatively the changes in the electronic structure over the broad range of geometries of interest. The necessary mixing of ionic, covalent, and Rydberg contributions, along with the appropriate treatment of the different electron-spin components (e.g. closed shell, high-spin open-shell, low-spin open shell, radical, diradical, etc.) of the wave functions, are treated correctly at this level. Further treatment of electron correlation effects is included using large scale multireference CI wave functions, particularly including the single and double excitations relative to the MCSCF reference space. This leads to the most flexible and accurate large-scale MRSDCI wave functions that have been used to date in global PES studies.

  3. Specificity in transition state binding: the Pauling model revisited.

    Science.gov (United States)

    Amyes, Tina L; Richard, John P

    2013-03-26

    Linus Pauling proposed that the large rate accelerations for enzymes are caused by the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogues of the transition states for enzymatic reactions often act as tight-binding inhibitors provided early support for this simple and elegant proposal. We review experimental results that support the proposal that Pauling's model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high-energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies that aimed to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-coenzyme A:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of coenzyme A (CoA) are responsible for a rate increase of 3 × 10(12)-fold, which is close to the estimated total 5 × 10(13)-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide an ~12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5'-monophosphate decarboxylase, and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6-8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme-transition

  4. Variational Identification of Markovian Transition States

    Directory of Open Access Journals (Sweden)

    Linda Martini

    2017-09-01

    Full Text Available We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular dynamics (MD trajectories. Our algorithm is presented by using both analytical models and examples from MD simulations of the benchmark system helix-forming peptide Ala_{5}, and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2, the epidermal growth factor receptor (EGFR protein, and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT quantum mechanics/molecular mechanics (QM/MM level of theory. In all cases, our method automatically identifies the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy-to-implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate-limiting transition states occurring along conformational transition paths in complex dynamical systems such as molecular trajectories.

  5. Determining Transition State Geometries in Liquids Using 2D-IR

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Charles; Cahoon, James F.; Sawyer, Karma R.; Schlegel, Jacob P.; Harris, Charles B.

    2007-12-11

    Many properties of chemical reactions are determined by the transition state connecting reactant and product, yet it is difficult to directly obtain any information about these short-lived structures in liquids. We show that two-dimensional infrared (2D-IR) spectroscopy can provide direct information about transition states by tracking the transformation of vibrational modes as a molecule crossed a transition state. We successfully monitored a simple chemical reaction, the fluxional rearrangement of Fe(CO)5, in which the exchange of axial and equatorial CO ligands causes an exchange of vibrational energy between the normal modes of the molecule. This energy transfer provides direct evidence regarding the time scale, transition state, and mechanism of the reaction.

  6. TRANSITION STATE FOR THE GAS-PHASE REACTION OF URANIUM HEXAFLUORIDE WITH WATER

    Energy Technology Data Exchange (ETDEWEB)

    Garrison, S; James Becnel, J

    2008-03-18

    Density Functional Theory and small-core, relativistic pseudopotentials were used to look for symmetric and asymmetric transitions states of the gas-phase hydrolysis reaction of uranium hexafluoride, UF{sub 6}, with water. At the B3LYP/6-31G(d,p)/SDD level, an asymmetric transition state leading to the formation of a uranium hydroxyl fluoride, U(OH)F{sub 5}, and hydrogen fluoride was found with an energy barrier of +77.3 kJ/mol and an enthalpy of reaction of +63.0 kJ/mol (both including zero-point energy corrections). Addition of diffuse functions to all atoms except uranium led to only minor changes in the structure and relative energies of the reacting complex and transition state. However, a significant change in the product complex structure was found, significantly reducing the enthalpy of reaction to +31.9 kJ/mol. Similar structures and values were found for PBE0 and MP2 calculations with this larger basis set, supporting the B3LYP results. No symmetric transition state leading to the direct formation of uranium oxide tetrafluoride, UOF{sub 4}, was found, indicating that the reaction under ambient conditions likely includes several more steps than the mechanisms commonly mentioned. The transition state presented here appears to be the first published transition state for the important gas-phase reaction of UF{sub 6} with water.

  7. Energy conservation potential of surface modification technologies

    Energy Technology Data Exchange (ETDEWEB)

    Le, H.K.; Horne, D.M.; Silberglitt, R.S.

    1985-09-01

    This report assesses the energy conservation impact of surface modification technologies on the metalworking industries. The energy conservation impact of surface modification technologies on the metalworking industries is assessed by estimating their friction and wear tribological sinks and the subsequent reduction in these sinks when surface modified tools are used. Ion implantation, coatings, and laser and electron beam surface modifications are considered.

  8. Prediction of Tetraoxygen Reaction Mechanism with Sulfur Atom on the Singlet Potential Energy Surface

    Directory of Open Access Journals (Sweden)

    Ashraf Khademzadeh

    2014-01-01

    Full Text Available The mechanism of S+O4 (D2h reaction has been investigated at the B3LYP/6-311+G(3df and CCSD levels on the singlet potential energy surface. One stable complex has been found for the S+O4 (D2h reaction, IN1, on the singlet potential energy surface. For the title reaction, we obtained four kinds of products at the B3LYP level, which have enough thermodynamic stability. The results reveal that the product P3 is spontaneous and exothermic with −188.042 and −179.147 kcal/mol in Gibbs free energy and enthalpy of reaction, respectively. Because P1 adduct is produced after passing two low energy level transition states, kinetically, it is the most favorable adduct in the 1S+1O4 (D2h atmospheric reactions.

  9. Stalking Higher Energy Conformers on the Potential Energy Surface of Charged Species.

    Science.gov (United States)

    Brites, Vincent; Cimas, Alvaro; Spezia, Riccardo; Sieffert, Nicolas; Lisy, James M; Gaigeot, Marie-Pierre

    2015-03-10

    Combined theoretical DFT-MD and RRKM methodologies and experimental spectroscopic infrared predissociation (IRPD) strategies to map potential energy surfaces (PES) of complex ionic clusters are presented, providing lowest and high energy conformers, thresholds to isomerization, and cluster formation pathways. We believe this association not only represents a significant advance in the field of mapping minima and transition states on the PES but also directly measures dynamical pathways for the formation of structural conformers and isomers. Pathways are unraveled over picosecond (DFT-MD) and microsecond (RRKM) time scales while changing the amount of internal energy is experimentally achieved by changing the loss channel for the IRPD measurements, thus directly probing different kinetic and isomerization pathways. Demonstration is provided for Li(+)(H2O)3,4 ionic clusters. Nonstatistical formation of these ionic clusters by both direct and cascade processes, involving isomerization processes that can lead to trapping of high energy conformers along the paths due to evaporative cooling, has been unraveled.

  10. Relationship of wood surface energy to surface composition

    Science.gov (United States)

    Feipeng P. Liu; Timothy G. Rials; John Simonsen

    1998-01-01

    The wood cell wall is composed of cellulose, lignin, hemicelluloses, and extractives. Thus, the surface energy of the wood material must be some combination of the surface energies of these components. The influence of extractives on wood surface chemistry can be important in diverse industrial applications, such as coating, pulping, and wood-based composites. In this...

  11. On apparent quantized transition-state thresholds in the photofragmentation of acetaldehyde

    Energy Technology Data Exchange (ETDEWEB)

    King, Rollin A. [Center for Computational Quantum Chemistry, Department of Chemistry, The University of Georgia, Athens, Georgia 30602-2525 (United States); Allen, Wesley D. [Center for Computational Quantum Chemistry, Department of Chemistry, The University of Georgia, Athens, Georgia 30602-2525 (United States); Schaefer, Henry F. III [Center for Computational Quantum Chemistry, Department of Chemistry, The University of Georgia, Athens, Georgia 30602-2525 (United States)

    2000-04-01

    Recent photofragmentation experiments have observed stepwise increases in the dissociation rate for CH{sub 3}CHO (T{sub 1}){yields}CH{sub 3} (X(tilde sign) {sup 2}A{sub 2}{sup ''})+HCO (X(tilde sign) {sup 2}A{sup '}) as a function of excitation energy. In accord with the Rice-Ramsperger-Kassel-Marcus (RRKM) form of transition-state theory, these steps were interpreted as corresponding to vibrational levels of the fragmentation transition state on the triplet surface. We have investigated this acetaldehyde dissociation using coupled cluster (CC) and density functional (DFT) methods with [C,O/H] atomic-orbital basis sets ranging in quality from [4s2p1d/2s1p] to [6s5p4d3f2g1h/5s4p3d2 f1g]. A high-level focal point analysis, along with harmonic force field computations, results in predictions of the dissociation energy, D{sub 0}=1583 cm{sup -1}, and the association barrier height, V{sub 0}{sup *}=3149 cm{sup -1}. With a basis set of triple-{zeta} plus double-polarization plus f(TZ2Pf ) quality, the DFT method UB3LYP and the CC method RCCSD predict barrier frequencies of 355i cm{sup -1} and 516i cm{sup -1}, respectively, while the empirical value inferred from RRKM models is only 60i cm{sup -1}. The RRKM-derived frequencies for the degrees of freedom orthogonal to the reaction path are more reasonable but still not in convincing agreement with electronic structure theory. Thus, while the experimental steps in the dissociation rate of acetaldehyde (as well as ketene) have yet to be satisfactorily explained, proven ab initio methods provide strong evidence that simple RRKM fits to the k(E) profile provide misleading vibrational frequencies of the transition state on the corresponding triplet potential energy surface. (c) 2000 American Institute of Physics.

  12. Fluoroalkylated Silicon-Containing Surfaces - Estimation of Solid Surface Energy

    Science.gov (United States)

    2010-10-20

    oleophobicity , solid surface energy, Zisman analysis, Girifalco-Good method 4 Introduction In the recent past, there have been a number of reports on...surfaces that are not wetted by liquid droplets, i. e. superhydrophobic,1-4 oleophobic ,5-15 hygrophobic,16 omniphobic7, 12 surfaces. These surfaces have

  13. Transition states for the dimerization of 1,3-cyclohexadiene: a DFT, CASPT2, and CBS-QB3 quantum mechanical investigation.

    Science.gov (United States)

    Ess, Daniel H; Hayden, Amy E; Klärner, Frank-Gerrit; Houk, K N

    2008-10-03

    Quantum mechanical calculations using restricted and unrestricted B3LYP density functional theory, CASPT2, and CBS-QB3 methods for the dimerization of 1,3-cyclohexadiene (1) reveal several highly competitive concerted and stepwise reaction pathways leading to [4 + 2] and [2 + 2] cycloadducts, as well as a novel [6 + 4] ene product. The transition state for endo-[4 + 2] cycloaddition (endo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 28.7 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 19.0 kcal/mol) is not bis-pericyclic, leading to nondegenerate primary and secondary orbital interactions. However, the C(s) symmetric second-order saddle point on the B3LYP energy surface is only 0.3 kcal/mol above endo-2TS. The activation enthalpy for the concerted exo-[4 + 2] cycloaddition (exo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 30.1 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 21.1 kcal/mol) is 1.4 kcal/mol higher than that of the endo transition state. Stepwise pathways involving diallyl radicals are formed via two different C-C forming transition states (rac-5TS and meso-5TS) and are predicted to be competitive with the concerted cycloaddition. Transition states were located for cyclization from intermediate rac-5 leading to the endo-[4 + 2] (endo-2) and exo-[2 + 2] (anti-3) cycloadducts. Only the endo-[2 + 2] (syn-3) transition state was located for cyclization of intermediate meso-5. The novel [6 + 4] "concerted" ene transition state (threo-4TS, DeltaH(double dagger)(UB3LYP(0K)) = 28.3 kcal/mol) is found to be unstable with respect to an unrestricted calculation. This diradicaloid transition state closely resembles the cyclohexadiallyl radical rather than the linked cyclohexadienyl radical. Several [3,3] sigmatropic rearrangement transition states were also located and have activation enthalpies between 27 and 31 kcal/mol.

  14. A New Approach toward Transition State Spectroscopy

    CERN Document Server

    Prozument, Kirill; Ciuba, Monika A; Muenter, John S; Park, G Barratt; Stanton, John F; Guo, Hua; Wong, Bryan M; Perry, David S; Field, Robert W

    2013-01-01

    Chirped-Pulse millimetre-Wave (CPmmW) rotational spectroscopy provides a new class of information about photolysis transition state(s). Measured intensities in rotational spectra determine species-isomer-vibrational populations, provided that rotational populations can be thermalized. The formation and detection of S0 vinylidene is discussed in the limits of low and high initial rotational excitation. CPmmW spectra of 193 nm photolysis of Vinyl Cyanide (Acrylonitrile) contain J=0-1 transitions in more than 20 vibrational levels of HCN, HNC, but no transitions in vinylidene or highly excited local-bender vibrational levels of acetylene. Reasons for the non-observation of the vinylidene co-product of HCN are discussed.

  15. Reactivity trends of hydroxide ion attack on high spin Fe(II complexes including bromosalicylidene amino acid ligands in some mixed aqueous solvents: Gibb’s Free Energy of Transfer and initial-transition state analysis

    Directory of Open Access Journals (Sweden)

    Laila H. Abdel-Rahman

    2017-05-01

    Full Text Available The kinetics of hydroxide ion attack on bis(bromosalicylidene alanateiron (II (bsali, bis(bromosalicylidene phenylalanateiron(II (bsphali, bis(bromosalicylidene aspartateiron(II (bsasi, (bromosalicylidene histidinateiron(II (bshi, bis(bromosalicylidene arginateiron(II (bsari have been reported in different binary aqueous solvent mixtures at 298 K. The observed reactivity trends are discussed in terms of the hydrophilic and hydrophobic forms of the complexes investigated, as well as the transfer chemical potentials of hydroxide ion and the complex. Both the solvent–solute and solvent–solvent interactions have been considered. The hydrophobic character of the complexes studied was manifested by decreasing in reactivity. Solvent effect on reactivity trends of the investigated complexes has been analyzed into initial and transition state components by using the transfer chemical potentials of the reactants and the kinetic data of the studied compounds. The decrease in the observed rate constant values (kobs of the base hydrolysis of the investigated complexes with increasing of solvent % is dominated by the initial state (IS.

  16. Hydroxyl radical reactions with adenine: reactant complexes, transition states, and product complexes.

    Science.gov (United States)

    Cheng, Qianyi; Gu, Jiande; Compaan, Katherine R; Schaefer, Henry F

    2010-10-18

    In order to address problems such as aging, cell death, and cancer, it is important to understand the mechanisms behind reactions causing DNA damage. One specific reaction implicated in DNA oxidative damage is hydroxyl free-radical attack on adenine (A) and other nucleic acid bases. The adenine reaction has been studied experimentally, but there are few theoretical results. In the present study, adenine dehydrogenation at various sites, and the potential-energy surfaces for these reactions, are investigated theoretically. Four reactant complexes [A···OH]* have been found, with binding energies relative to A+OH* of 32.8, 11.4, 10.7, and 10.1 kcal mol(-1). These four reactant complexes lead to six transition states, which in turn lie +4.3, -5.4, (-3.7 and +0.8), and (-2.3 and +0.8) kcal mol(-1) below A+OH*, respectively. Thus the lowest lying [A···OH]* complex faces the highest local barrier to formation of the product (A-H)*+H(2)O. Between the transition states and the products lie six product complexes. Adopting the same order as the reactant complexes, the product complexes [(A-H)···H(2)O]* lie at -10.9, -22.4, (-24.2 and -18.7), and (-20.5 and -17.5) kcal mol(-1), respectively, again relative to separated A+OH*. All six A+OH* → (A-H)*+H(2)O pathways are exothermic, by -0.3, -14.7, (-17.4 and -7.8), and (-13.7 and -7.8) kcal mol(-1), respectively. The transition state for dehydrogenation at N(6) lies at the lowest energy (-5.4 kcal mol(-1) relative to A+OH*), and thus reaction is likely to occur at this site. This theoretical prediction dovetails with the observed high reactivity of OH radicals with the NH(2) group of aromatic amines. However, the high barrier (37.1 kcal mol(-1)) for reaction at the C(8) site makes C(8) dehydrogenation unlikely. This last result is consistent with experimental observation of the imidazole ring opening upon OH radical addition to C(8). In addition, TD-DFT computed electronic transitions of the N(6) product around 420 nm

  17. Adhesion energy, surface traction and surface tension in liquid xenon

    Indian Academy of Sciences (India)

    B Mathew; G A Adebayo

    2011-12-01

    We calculated the adhesion energy, the surface traction and the surface energy of liquid xenon using molecular dynamics (MD) simulation. The value of the adhesion energy for liquid xenon at a reduced density of 0.630 was found to be 0.591 J/m2 and the surface traction has a peak at = 3.32 Å. It was observed that the attraction of the molecules in the liquid surface which produces a resistance to penetration decreases with temperature. This may be attributed to the greater average separation of molecules at higher temperature.

  18. H+CH4 → H2 + CH3 initial state-selected reaction probabilities on different potential energy surfaces

    Science.gov (United States)

    Ellerbrock, Roman; Manthe, Uwe

    2017-01-01

    Initial state-selected reaction probabilities for the H +CH4 →H2 +CH3 reaction on a recently developed potential energy surface which employs neutral network fitting based on permutational invariant polynomials are reported. The quantum dynamics calculations use the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach and study the reaction process in full-dimensionality for vanishing total angular momentum. A detailed comparison with previous results obtained on other high-level potential energy surfaces is given. The connection between the level of quantum state resolution and the sensitivity of the results on differences in the potential energy surfaces is highlighted. Employing a decomposition of the total reactivity into contributions of the different vibrational states of the activated complex, it is found that differences between the potential energy surfaces are mainly related to the umbrella motion of the methyl group.

  19. Surface Energy and Setting Process of Contacting Surfaces

    Directory of Open Access Journals (Sweden)

    M. V. Musokhranov

    2014-01-01

    Full Text Available The paper deals with a challenge in terms of ensuring an accuracy of the relative position of the conjugated surfaces that is to determine a coefficient of friction. To solve it, there is a proposal to use the surface energy, as a tool that influences the contacting parts nature. Presently, energy of the surface layers at best is only stated, but not used in practice.Analysis of the conditions of interaction between two contacting surfaces, such as seizing and setting cannot be explained only from the position of the roughness parameters. It is found that these phenomena are explained by the appearing gripe (setting bridges, which result from the energy of interaction between two or more adjacent surfaces. The emerging phenomenon such as micro welding, i.e. occurring bonds, is caused by the overflow of energy, according to the theory of physics, from the surface with a high level of energy to the surface with the smaller one to balance the system as a whole.The paper shows that through the use of process, controlling the depth of the surface layer and creating a certain structure, the energy level of the material as a whole can be specified. And this will allow us to provide the necessary performance and mechanical properties. It means to create as many gripe bridges as possible to ensure continuous positioning i.e. a fixed connection of the contacting surfaces.It was determined that to increase a value of the friction coefficient, the physical and mechanical properties of the surface layer of the parts material must be taken into account, namely, in the part body accumulate the energy to be consumed for forming the surface.The paper gives recommendations for including the parts of the surface energy in the qualitative indicators of characteristics. This will make a technologist, when routing a process, to choose such operations and modes to provide the designer-specified parameters not only of the accuracy and surface finish, but also of the

  20. Multi-path variational transition state theory for chemical reaction rates of complex polyatomic species: ethanol + OH reactions.

    Science.gov (United States)

    Zheng, Jingjing; Truhlar, Donald G

    2012-01-01

    Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.

  1. Modified Transition State Theory for Evaporation and Condensation

    Institute of Scientific and Technical Information of China (English)

    王遵敬; 陈民; 过增元

    2002-01-01

    A modification of the transition state theory for evaporation and condensation is presented by analysing the kinetic characteristics of liquid-vapour interphase transport. In the modified transition state theory, the moving orientation of molecules is introduced into the calculation of the free volume of the activated complex. The condensation coefficients of argon at different temperatures are calculated with the modified transition state theory. The results agree well with those from molecular dynamics simulations.

  2. NATO Advanced Research Workshop on Geometrical Derivatives of Energy Surfaces and Molecular Properties

    CERN Document Server

    Simons, Jack

    1986-01-01

    The development and computational implementation of analytical expres­ sions for the low-order derivatives of electronic energy surfaces and other molecular properties has undergone rapid growth in recent years. It is now fairly routine for chemists to make use of energy gradient information in locating and identifying stable geometries and transition states. The use of second analytical derivative (Hessian or curvature) expressions is not yet routine, and third and higher energy derivatives as well as property (e.g., dipole moment, polarizability) derivatives are just beginning to be applied to chemical problems. This NATO Advanced Research Workshop focused on analyzing the re­ lative merits of various strategies for deriving the requisite analyti­ cal expressions, for computing necessary integral derivatives and wave­ function parameter derivatives, and for efficiently coding these expres­ sions on conventional scalar machines and vector-oriented computers. The participant list contained many scientist...

  3. A generalized force-modified potential energy surface for mechanochemical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Subramanian, Gopinath, E-mail: Gopinath.Subramanian@usm.edu [School of Polymers and High Performance Materials, University of Southern Mississippi, Hattiesburg, Mississippi 39402 (United States); Mathew, Nithin [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211 (United States); Leiding, Jeff [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

    2015-10-07

    We describe the modifications that a spatially varying external load produces on a Born-Oppenheimer potential energy surface (PES) by calculating static quantities of interest. The effects of the external loads are exemplified using electronic structure calculations (at the HF/6-31G{sup ∗∗} level) of two different molecules: ethane and hexahydro-1,3,5-trinitro-s-triazine (RDX). The calculated transition states and Hessian matrices of stationary points show that spatially varying external loads shift the stationary points and modify the curvature of the PES, thereby affecting the harmonic transition rates by altering both the energy barrier as well as the prefactor. The harmonic spectra of both molecules are blueshifted with increasing compressive “pressure.” Some stationary points on the RDX-PES disappear under application of the external load, indicating the merging of an energy minimum with a saddle point.

  4. Durable, Low-Surface-Energy Treatments

    Science.gov (United States)

    Willis, Paul B.; Mcelroy, Paul M.; Hickey, Gregory S.

    1992-01-01

    Chemical treatment for creation of durable, low-surface-energy coatings for glass, ceramics and other protonated surfaces easily applied, and creates very thin semipermanent film with extremely low surface tension. Exhibits excellent stability; surfaces retreated if coating becomes damaged or eroded. Uses include water-repellent surfaces, oil-repellent surfaces, antimigration barriers, corrosion barriers, mold-release agents, and self-cleaning surfaces. Film resists wetting by water, alcohols, hydrocarbon solvents, and silicone oil. Has moderate resistance to abrasion, such as rubbing with cloths, and compression molding to polymers and composite materials.

  5. Liquid droplet movement on horizontal surface with gradient surface energy

    Institute of Scientific and Technical Information of China (English)

    LIAO Qiang; WANG Hong; ZHU Xun; LI Mingwei

    2006-01-01

    A surface with gradient surface energy was fabricated on a silicon wafer by using the chemical vapor deposition (CVD) technology with the dodecyltrichlorosilane (C12H25Cl3Si) vapor which was adsorbed chemically on the surface of the silicon wafer to form a self-assemble monolayer (ASM) and thus a gradient profile of wettability. The microscopic contours of the gradient surface were measured with Seiko SPA400 atom force microscope (AFM). And the surface wettability profile was characterized by the sessile drop method, measuring the contact angle of fine water droplets that lay on the gradient surface, to represent the distribution of the surface energy on the surface. Using a high-speed video imaging system, the motion of water droplet on the horizontal gradient surface was visualized and the transient velocity was measured under ambient condition. The experimental results show that the liquid droplets can be driven to move from hydrophobic side to hydrophilic side on the horizontal gradient surface and the velocity of droplet can reach up to 40 mm/s. In addition, the motion of the water droplet can be generally divided into two stages: an acceleration stage and a deceleration stage. The droplet presents a squirming movement on the surface with a lower peak velocity and a larger extent of deceleration motion. And the static advancing contact angle of the droplet is obviously larger than the dynamic advancing contact angle on the gradient energy surface.

  6. Solar energy converter using surface plasma waves

    Science.gov (United States)

    Anderson, L. M. (Inventor)

    1984-01-01

    Sunlight is dispersed over a diffraction grating formed on the surface of a conducting film on a substrate. The angular dispersion controls the effective grating period so that a matching spectrum of surface plasmons is excited for parallel processing on the conducting film. The resulting surface plasmons carry energy to an array of inelastic tunnel diodes. This solar energy converter does not require different materials for each frequency band, and sunlight is directly converted to electricity in an efficient manner by extracting more energy from the more energetic photons.

  7. A Quantum Version of Wigner's Transition State Theory

    NARCIS (Netherlands)

    Schubert, R.; Waalkens, H.; Wiggins, S.

    2009-01-01

    A quantum version of a recent realization of Wigner's transition state theory in phase space is presented. The theory developed builds on a quantum normal form which locally decouples the quantum dynamics near the transition state to any desired order in (h) over bar. This leads to an explicit algor

  8. A Quantum Version of Wigner’s Transition State Theory

    NARCIS (Netherlands)

    Schubert, R.; Waalkens, H.; Wiggins, S.

    2009-01-01

    A quantum version of a recent realization of Wigner’s transition state theory in phase space is presented. The theory developed builds on a quantum normal form which locally decouples the quantum dynamics near the transition state to any desired order in ħ. This leads to an explicit algorithm to com

  9. Periodic-orbit formula for quantum reactions through transition states

    NARCIS (Netherlands)

    Schubert, Roman; Waalkens, Holger; Goussev, Arseni; Wiggins, Stephen

    2010-01-01

    Transition state theory forms the basis of computing reaction rates in chemical and other systems. Recently, it has been shown how transition state theory can rigorously be realized in phase space by using an explicit algorithm. The quantization has been demonstrated to lead to an efficient procedur

  10. Dissociation of N2, NO, and CO on transition metal surfaces

    DEFF Research Database (Denmark)

    Mavrikakis, Manos; Hansen, Lars Bruno; Mortensen, Jens Jørgen;

    1999-01-01

    Using density functional theory we study the dissociation of N2, NO, and CO on transition metal surfaces. We discuss an efficient method to locate the minimum energy path and the transition state, and review recent calculations using this method to determine the transition state for dissociation...

  11. Surface energy of metal alloy nanoparticles

    Science.gov (United States)

    Takrori, Fahed M.; Ayyad, Ahmed

    2017-04-01

    The measurement of surface energy of alloy nanoparticles experimentally is still a challenge therefore theoretical work is necessary to estimate its value. In continuation of our previous work on the calculation of the surface energy of pure metallic nanoparticles we have extended our work to calculate the surface energy of different alloy systems, namely, Co-Ni, Au-Cu, Cu-Al, Cu-Mg and Mo-Cs binary alloys. It is shown that the surface energy of metallic binary alloy decreases with decreasing particle size approaching relatively small values at small sizes. When both metals in the alloy obey the Hume-Rothery rules, the difference in the surface energy is small at the macroscopic as well as in the nano-scale. However when the alloy deviated from these rules the difference in surface energy is large in the macroscopic and in the nano scales. Interestingly when solid solution formation is not possible at the macroscopic scale according to the Hume-Rothery rules, it is shown it may form at the nano-scale. To our knowledge these findings here are presented for the first time and is challenging from fundamental as well as technological point of views.

  12. Feet on the potential energy surface, head in the pi clouds

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Quentin [Iowa State Univ., Ames, IA (United States)

    2011-01-01

    This work presents explorations of the potential energy surface of clusters of atoms and of the interactions between molecules. First, structures of small aluminum clusters are examined and classified as ground states, transition states, or higher-order saddle points. Subsequently, the focus shifts to dispersion-dominated π-π interactions when the potential energy surfaces of benzene, substituted benzene, and pyridine dimers are explored. Because DNA nucleotide bases can be thought of as substituted heterocycles, a natural extension of the substituted benzene and pyridine investigations is to model paired nucleotide bases. Finally, the success of the dispersion studies inspires the development of an extension to the computational method used, which will enable the dispersion energy to be modeled – and the potential energy surface explored – in additional chemical systems. The effective fragment potential (EFP) method is described, as well as various quantum mechanical methods. An ab inito quantum mechanical study of 13-atom aluminum clusters is described. EFP studies of aromatic dimers are reported in which dispersion energy makes a significant contribution to the attraction between monomers. Theory and code development toward a means of computing dispersion energy in mixed ab inito-EFP systems are described.

  13. Sorption Energy Maps of Clay Mineral Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Cygan, Randall T.; Kirkpatrick, R. James

    1999-07-19

    A molecular-level understanding of mineral-water interactions is critical for the evaluation and prediction of the sorption properties of clay minerals that may be used in various chemical and radioactive waste disposal methods. Molecular models of metal sorption incorporate empirical energy force fields, based on molecular orbital calculations and spectroscopic data, that account for Coulombic, van der Waals attractive, and short-range repulsive energies. The summation of the non-bonded energy terms at equally-spaced grid points surrounding a mineral substrate provides a three dimensional potential energy grid. The energy map can be used to determine the optimal sorption sites of metal ions on the exposed surfaces of the mineral. By using this approach, we have evaluated the crystallographic and compositional control of metal sorption on the surfaces of kaolinite and illite. Estimates of the relative sorption energy and most stable sorption sites are derived based on a rigid ion approximation.

  14. Improving Upon String Methods for Transition State Discovery.

    Science.gov (United States)

    Chaffey-Millar, Hugh; Nikodem, Astrid; Matveev, Alexei V; Krüger, Sven; Rösch, Notker

    2012-02-14

    Transition state discovery via application of string methods has been researched on two fronts. The first front involves development of a new string method, named the Searching String method, while the second one aims at estimating transition states from a discretized reaction path. The Searching String method has been benchmarked against a number of previously existing string methods and the Nudged Elastic Band method. The developed methods have led to a reduction in the number of gradient calls required to optimize a transition state, as compared to existing methods. The Searching String method reported here places new beads on a reaction pathway at the midpoint between existing beads, such that the resolution of the path discretization in the region containing the transition state grows exponentially with the number of beads. This approach leads to favorable convergence behavior and generates more accurate estimates of transition states from which convergence to the final transition states occurs more readily. Several techniques for generating improved estimates of transition states from a converged string or nudged elastic band have been developed and benchmarked on 13 chemical test cases. Optimization approaches for string methods, and pitfalls therein, are discussed.

  15. Transition State Structure of RNA Depurination by Saporin L3.

    Science.gov (United States)

    Yuan, Hongling; Stratton, Christopher F; Schramm, Vern L

    2016-05-20

    Saporin L3 from the leaves of the common soapwort is a catalyst for hydrolytic depurination of adenine from RNA. Saporin L3 is a type 1 ribosome inactivating protein (RIP) composed only of a catalytic domain. Other RIPs have been used in immunotoxin cancer therapy, but off-target effects have limited their development. In the current study, we use transition state theory to understand the chemical mechanism and transition state structure of saporin L3. In favorable cases, transition state structures guide the design of transition state analogues as inhibitors. Kinetic isotope effects (KIEs) were determined for an A14C mutant of saporin L3. To permit KIE measurements, small stem-loop RNAs that contain an AGGG tetraloop structure were enzymatically synthesized with the single adenylate bearing specific isotopic substitutions. KIEs were measured and corrected for forward commitment to obtain intrinsic values. A model of the transition state structure for depurination of stem-loop RNA (5'-GGGAGGGCCC-3') by saporin L3 was determined by matching KIE values predicted via quantum chemical calculations to a family of intrinsic KIEs. This model indicates saporin L3 displays a late transition state with the N-ribosidic bond to the adenine nearly cleaved, and the attacking water nucleophile weakly bonded to the ribosyl anomeric carbon. The transition state retains partial ribocation character, a feature common to most N-ribosyl transferases. However, the transition state geometry for saporin L3 is distinct from ricin A-chain, the only other RIP whose transition state is known.

  16. Computational analysis of the mechanism of chemical reactions in terms of reaction phases: hidden intermediates and hidden transition States.

    Science.gov (United States)

    Kraka, Elfi; Cremer, Dieter

    2010-05-18

    Computational approaches to understanding chemical reaction mechanisms generally begin by establishing the relative energies of the starting materials, transition state, and products, that is, the stationary points on the potential energy surface of the reaction complex. Examining the intervening species via the intrinsic reaction coordinate (IRC) offers further insight into the fate of the reactants by delineating, step-by-step, the energetics involved along the reaction path between the stationary states. For a detailed analysis of the mechanism and dynamics of a chemical reaction, the reaction path Hamiltonian (RPH) and the united reaction valley approach (URVA) are an efficient combination. The chemical conversion of the reaction complex is reflected by the changes in the reaction path direction t(s) and reaction path curvature k(s), both expressed as a function of the path length s. This information can be used to partition the reaction path, and by this the reaction mechanism, of a chemical reaction into reaction phases describing chemically relevant changes of the reaction complex: (i) a contact phase characterized by van der Waals interactions, (ii) a preparation phase, in which the reactants prepare for the chemical processes, (iii) one or more transition state phases, in which the chemical processes of bond cleavage and bond formation take place, (iv) a product adjustment phase, and (v) a separation phase. In this Account, we examine mechanistic analysis with URVA in detail, focusing on recent theoretical insights (with a variety of reaction types) from our laboratories. Through the utilization of the concept of localized adiabatic vibrational modes that are associated with the internal coordinates, q(n)(s), of the reaction complex, the chemical character of each reaction phase can be identified via the adiabatic curvature coupling coefficients, A(n,s)(s). These quantities reveal whether a local adiabatic vibrational mode supports (A(n,s) > 0) or resists

  17. A periodic orbit formula for quantum reactions through transition states

    CERN Document Server

    Schubert, Roman; Goussev, Arseni; Wiggins, Stephen

    2010-01-01

    Transition State Theory forms the basis of computing reaction rates in chemical and other systems. Recently it has been shown how transition state theory can rigorously be realized in phase space using an explicit algorithm. The quantization has been demonstrated to lead to an efficient procedure to compute cumulative reaction probabilities and the associated Gamov-Siegert resonances. In this letter these results are used to express the cumulative reaction probability as an absolutely convergent sum over periodic orbits contained in the transition state.

  18. Classical trajectory simulations of post-transition state dynamics

    Science.gov (United States)

    Lourderaj, Upakarasamy; Park, Kyoyeon; Hase, William L.

    Classical chemical dynamics simulations of post-transition state dynamics are reviewed. Most of the simulations involve direct dynamics for which the potential energy and gradient are obtained directly from an electronic structure theory. The chemical reaction attributes and chemical systems presented are product energy partitioning for Cl- ··· CH3Br → ClCH3 + Br- and C2H5F → C2H4 + HF dissociation, non-RRKM dynamics for cyclopropane stereomutation and the Cl- ··· CH3Cl complexes mediating the Cl- + CH3Cl SN2 nucleophilic substitution reaction, and non-IRC dynamics for the OH- + CH3F and F- + CH3OOH chemical reactions. These studies illustrate the important role of chemical dynamics simulations in understanding atomic-level reaction dynamics and interpreting experiments. They also show that widely used paradigms and model theories for interpreting reaction kinetics and dynamics are often inaccurate and are not applicable.

  19. Probing the NO2 --> NO+O transition state via time resolved unimolecular decomposition

    Science.gov (United States)

    Ionov, S. I.; Brucker, G. A.; Jaques, C.; Chen, Y.; Wittig, C.

    1993-09-01

    Time resolved, subpicosecond resolution measurements of photoinitiated NO2 unimolecular decomposition rates are reported for expansion cooled and room temperature samples. The molecules are excited by 375-402 nm tunable subpicosecond pulses having bandwidths ≥20 cm-1 to levels which are known to be thorough admixtures of the 2B2 electronically excited state and the 2A1 ground electronic state. Subsequent decomposition is probed by a 226 nm subpicosecond pulse that excites laser-induced fluorescence (LIF) in the NO product. When increasing the amount of excitation over the dissociation threshold, an uneven, ``step-like'' increase of the decomposition rate vs energy is observed for expansion cooled samples. The steps are spaced by ˜100 cm-1 and can be assigned ad hoc to bending at the transition state. Relying on experimental estimates for the near threshold density of states, we point out that simple transition state theory predictions give rates that are consistent with these measured values. The rates are sufficiently rapid to question the assumption of rapid intramolecular vibrational redistribution, which is implicit in transition state theories. In contrast to expansion cooled samples, room temperature samples exhibit a smooth variation of the reaction rate vs photon energy. By comparing rates for rotationally cold and room temperature NO2, the ON-O bond is estimated to be ˜40% longer in the transition state than in the parent molecule.

  20. Ionic and Covalent Stabilization of Intermediates and Transition States in Catalysis by Solid Acids

    Energy Technology Data Exchange (ETDEWEB)

    Deshlahra, Prashant; Carr, Robert T.; Iglesia, Enrique

    2014-10-29

    Reactivity descriptors describe catalyst properties that determine the stability of kinetically relevant transition states and adsorbed intermediates. Theoretical descriptors, such as deprotonation energies (DPE), rigorously account for Brønsted acid strength for catalytic solids with known structure. Here, mechanistic interpretations of methanol dehydration turnover rates are used to assess how charge reorganization (covalency) and electrostatic interactions determine DPE and how such interactions are recovered when intermediates and transition states interact with the conjugate anion in W and Mo polyoxometalate (POM) clusters and gaseous mineral acids. Turnover rates are lower and kinetically relevant species are less stable on Mo than W POM clusters with similar acid strength, and such species are more stable on mineral acids than that predicted from W-POM DPE–reactivity trends, indicating that DPE and acid strength are essential but incomplete reactivity descriptors. Born–Haber thermochemical cycles indicate that these differences reflect more effective charge reorganization upon deprotonation of Mo than W POM clusters and the much weaker reorganization in mineral acids. Such covalency is disrupted upon deprotonation but cannot be recovered fully upon formation of ion pairs at transition states. Predictive descriptors of reactivity for general classes of acids thus require separate assessments of the covalent and ionic DPE components. Here, we describe methods to estimate electrostatic interactions, which, taken together with energies derived from density functional theory, give the covalent and ionic energy components of protons, intermediates, and transition states. In doing so, we provide a framework to predict the reactive properties of protons for chemical reactions mediated by ion-pair transition states.

  1. Ionic and covalent stabilization of intermediates and transition states in catalysis by solid acids.

    Science.gov (United States)

    Deshlahra, Prashant; Carr, Robert T; Iglesia, Enrique

    2014-10-29

    Reactivity descriptors describe catalyst properties that determine the stability of kinetically relevant transition states and adsorbed intermediates. Theoretical descriptors, such as deprotonation energies (DPE), rigorously account for Brønsted acid strength for catalytic solids with known structure. Here, mechanistic interpretations of methanol dehydration turnover rates are used to assess how charge reorganization (covalency) and electrostatic interactions determine DPE and how such interactions are recovered when intermediates and transition states interact with the conjugate anion in W and Mo polyoxometalate (POM) clusters and gaseous mineral acids. Turnover rates are lower and kinetically relevant species are less stable on Mo than W POM clusters with similar acid strength, and such species are more stable on mineral acids than that predicted from W-POM DPE-reactivity trends, indicating that DPE and acid strength are essential but incomplete reactivity descriptors. Born-Haber thermochemical cycles indicate that these differences reflect more effective charge reorganization upon deprotonation of Mo than W POM clusters and the much weaker reorganization in mineral acids. Such covalency is disrupted upon deprotonation but cannot be recovered fully upon formation of ion pairs at transition states. Predictive descriptors of reactivity for general classes of acids thus require separate assessments of the covalent and ionic DPE components. Here, we describe methods to estimate electrostatic interactions, which, taken together with energies derived from density functional theory, give the covalent and ionic energy components of protons, intermediates, and transition states. In doing so, we provide a framework to predict the reactive properties of protons for chemical reactions mediated by ion-pair transition states.

  2. Surface Plasmon-Assisted Solar Energy Conversion.

    Science.gov (United States)

    Dodekatos, Georgios; Schünemann, Stefan; Tüysüz, Harun

    2016-01-01

    The utilization of localized surface plasmon resonance (LSPR) from plasmonic noble metals in combination with semiconductors promises great improvements for visible light-driven photocatalysis, in particular for energy conversion. This review summarizes the basic principles of plasmonic photocatalysis, giving a comprehensive overview about the proposed mechanisms for enhancing the performance of photocatalytically active semiconductors with plasmonic devices and their applications for surface plasmon-assisted solar energy conversion. The main focus is on gold and, to a lesser extent, silver nanoparticles in combination with titania as semiconductor and their usage as active plasmonic photocatalysts. Recent advances in water splitting, hydrogen generation with sacrificial organic compounds, and CO2 reduction to hydrocarbons for solar fuel production are highlighted. Finally, further improvements for plasmonic photocatalysts, regarding performance, stability, and economic feasibility, are discussed for surface plasmon-assisted solar energy conversion.

  3. Energy flow and energy dissipation in a free surface.

    Science.gov (United States)

    Goldburg, Walter; Cressman, John

    2005-11-01

    Turbulent flows on a free surface are strongly compressible [1] and do not conserve energy in the absence of viscosity as bulk fluids do. Despite violation of assumptions essential to Kolmogorov's theory of 1941 (K41) [2, 3], surface flows show strong agreement with Kolmogorov scaling, though intermittency is larger there. Steady state turbulence is generated in a tank of water, and the spatially averaged energy flux is measured from the four-fifth's law at each instant of time. Likewise, the energy dissipation rate as measured from velocity gradients is also a random variable in this experiment. The energy flux - dissipation rate cross-correlation is measured to be correlated in incompressible bulk flows, but strongly anti-correlated on the surface. We argue that the reason for this discrepancy between surface and bulk flows is due to compressible effects present on the surface. [1] J. R. Cressman, J. Davoudi, W. I. Goldburg, and J. Schumacher, New Journal of Physics, 6, 53, 2004. [2] U. Frisch. Turbulence: The legacy of A. N. Kolmogorov, Cambridge University Press, Cambridge, 1995. [3] A. N. Kolmogorov, Doklady Akad. Nauk SSSR, 32, 16, 1941.

  4. Transition state theory and the dynamics of hard disks.

    Science.gov (United States)

    Barnett-Jones, M; Dickinson, P A; Godfrey, M J; Grundy, T; Moore, M A

    2013-11-01

    The dynamics of two- and five-disk systems confined in a square has been studied using molecular dynamics simulations and compared with the predictions of transition state theory. We determine the partition functions Z and Z(‡) of transition state theory using a procedure first used by Salsburg and Wood for the pressure. Our simulations show this procedure and transition state theory are in excellent agreement with the simulations. A generalization of the transition state theory to the case of a large number of disks N is made and shown to be in full agreement with simulations of disks moving in a narrow channel. The same procedure for hard spheres in three dimensions leads to the Vogel-Fulcher-Tammann formula for their alpha relaxation time.

  5. The Immucillins: Design, Synthesis and Application of Transition- State Analogues.

    Science.gov (United States)

    Evans, Gary B; Schramm, Vern L; Tyler, Peter C

    2015-01-01

    Transition-state analysis based on kinetic isotope effects and computational chemistry provides electrostatic potential maps to serve as blueprints for the design and chemical synthesis of transition-state analogues. The utility of these molecules is exemplified by potential clinical applications toward leukemia, autoimmune disorders, gout, solid tumors, bacterial quorum sensing and bacterial antibiotics. In some cases, transition-state analogues have chemical features that have allowed them to be repurposed for new indications, including potential antiviral use. Three compounds from this family have entered clinical trials. The transition-state analogues bind to their target proteins with high affinity and specificity. The physical and structural properties of binding teach valuable and often surprising lessons about the nature of tight-binding inhibitors.

  6. Scaling law of Wolff cluster surface energy

    Science.gov (United States)

    Hsiao, Pai-Yi; Monceau, Pascal

    2003-05-01

    We study the scaling properties of the clusters grown by the Wolff algorithm on seven different Sierpinski-type fractals of Hausdorff dimension 1Wolff cluster follows a power law with respect to the lattice size. Moreover, we investigate the probability density distribution of the surface energy of the Wolff cluster and are able to establish a different scaling relation. It enables us to introduce an exponent that is associated to the surface energy of the Wolff cluster. Finally, this exponent is linked to a dynamical exponent via an inequality.

  7. Scaling law of Wolff cluster surface energy

    OpenAIRE

    Hsiao, Pai-Yi; Monceau, Pascal

    2003-01-01

    We study the scaling properties of the clusters grown by the Wolff algorithm on seven different Sierpinski-type fractals of Hausdorff dimension $1 < d_f \\le 3$ in the framework of the Ising model. The mean absolute value of the surface energy of Wolff cluster follows a power law with respect to the lattice size. Moreover, we investigate the probability density distribution of the surface energy of Wolff cluster and are able to establish a new scaling relation. It enables us to introduce a new...

  8. Study of hair surface energy and conditioning.

    Science.gov (United States)

    Gao, Timothy; He, Yingxia; Landa, Peter; Tien, Jung-Mei

    2011-01-01

    A new test method has been developed to determine surface energy of hair fibers through measurements of contact angles at two hair/liquid interfaces. By measuring changes in surface energy of the same hair fiber before and after a cosmetic treatment, effects of active ingredients and the performance of tested formulations can be evaluated.The establishment of the method is based on Fowkes theory (1,2) described with two components, a dispersive and a non-dispersive component. The non-polar liquid used in this study was diiodomethane, and the polar liquid was benzyl alcohol. A Kruss 100 Tensiometer was used to measure contact angles of hair fibers. Virgin dark brown and regular bleached hairs were treated with selected conditioner formulations. Reductions in combing forces of hair tresses before and after respective treatments were correlated with decreases in average surface energy of hair fibers obtained from the corresponding tresses.Experimental results indicate that the average surface energy of hair fibers treated with conditioners decreases and the hydrophobicity of the hair surface increases, the results correlate well with the reduction in combing forces after respective treatments. This research work provides a new methodology to evaluate/screen conditioning performance of hair care ingredients and formulations for development of better products.

  9. Metal surfaces: Surface, step and kink formation energies

    DEFF Research Database (Denmark)

    Kollár, J.; Vitos, Levente; Johansson, B.;

    2000-01-01

    We review the surface, step, and kink energies in monoatomic metallic systems. A systematic comparison is given between the theoretical results based on density functional theory and available experimental data. Our calculated values are used to predict the equilibrium shapes of small metal...

  10. SURFACE ENERGY BALANCE OVER ORANGE ORCHARD USING SURFACE RENEWAL ANALYSIS

    Directory of Open Access Journals (Sweden)

    Salvatore Barbagallo

    2009-12-01

    Full Text Available Reliable estimation of surface sensible and latent heat flux is the most important process to appraise energy and mass exchange among atmosphere and biosphere. In this study the surface energy fluxes were measured over an irrigated orange orchard during 2005-2008 monitoring periods using a Surface Renewal- Energy Balance approach. The experimental area is located in a representative orchard growing area of eastern Sicily (Italy. The performance of Surface Renewal (SR analysis for estimating sensible heat flux (H was analysed and evaluated in terms of correlation with H fluxes from the eddy covariance (EC method. Study revealed that the mean available energy (RN- G and latent heat flux (LE were of about 300 W m-2 and 237 W m-2, respectively, during dry periods and unstable-case atmospheric conditions. The estimated crop coefficient Kc values for the orchard crop averaged close to 0.80, which is considerably higher than previous FAO studies that found the value to be 0.65 for citrus with 70% of ground cover. The intercepted photosynthetically active radiation (LI PAR by the crop was measured and relationships between LAI and crop coefficient (Kc were established.

  11. Transition States from Empirical Force Fields

    DEFF Research Database (Denmark)

    Jensen, Frank; Norrby, Per-Ola

    2003-01-01

    This is an overview of the use of empirical force fields in the study of reaction mechanisms. EVB-type methods (including RFF and MCMM) produce full reaction surfaces by mixing, in the simplest case, known force fields describing reactants and products. The SEAM method instead locates approximate...

  12. Design of biomimetic catalysts by molecular imprinting in synthetic polymers: the role of transition state stabilization.

    Science.gov (United States)

    Wulff, Günter; Liu, Junqiu

    2012-02-21

    The impressive efficiency and selectivity of biological catalysts has engendered a long-standing effort to understand the details of enzyme action. It is widely accepted that enzymes accelerate reactions through their steric and electronic complementarity to the reactants in the rate-determining transition states. Thus, tight binding to the transition state of a reactant (rather than to the corresponding substrate) lowers the activation energy of the reaction, providing strong catalytic activity. Debates concerning the fundamentals of enzyme catalysis continue, however, and non-natural enzyme mimics offer important additional insight in this area. Molecular structures that mimic enzymes through the design of a predetermined binding site that stabilizes the transition state of a desired reaction are invaluable in this regard. Catalytic antibodies, which can be quite active when raised against stable transition state analogues of the corresponding reaction, represent particularly successful examples. Recently, synthetic chemistry has begun to match nature's ability to produce antibody-like binding sites with high affinities for the transition state. Thus, synthetic, molecularly imprinted polymers have been engineered to provide enzyme-like specificity and activity, and they now represent a powerful tool for creating highly efficient catalysts. In this Account, we review recent efforts to develop enzyme models through the concept of transition state stabilization. In particular, models for carboxypeptidase A were prepared through the molecular imprinting of synthetic polymers. On the basis of successful experiments with phosphonic esters as templates to arrange amidinium groups in the active site, the method was further improved by combining the concept of transition state stabilization with the introduction of special catalytic moieties, such as metal ions in a defined orientation in the active site. In this way, the imprinted polymers were able to provide both an

  13. SURFACE SYMMETRY ENERGY OF NUCLEAR ENERGY DENSITY FUNCTIONALS

    Energy Technology Data Exchange (ETDEWEB)

    Nikolov, N; Schunck, N; Nazarewicz, W; Bender, M; Pei, J

    2010-12-20

    We study the bulk deformation properties of the Skyrme nuclear energy density functionals. Following simple arguments based on the leptodermous expansion and liquid drop model, we apply the nuclear density functional theory to assess the role of the surface symmetry energy in nuclei. To this end, we validate the commonly used functional parametrizations against the data on excitation energies of superdeformed band-heads in Hg and Pb isotopes, and fission isomers in actinide nuclei. After subtracting shell effects, the results of our self-consistent calculations are consistent with macroscopic arguments and indicate that experimental data on strongly deformed configurations in neutron-rich nuclei are essential for optimizing future nuclear energy density functionals. The resulting survey provides a useful benchmark for further theoretical improvements. Unlike in nuclei close to the stability valley, whose macroscopic deformability hangs on the balance of surface and Coulomb terms, the deformability of neutron-rich nuclei strongly depends on the surface-symmetry energy; hence, its proper determination is crucial for the stability of deformed phases of the neutron-rich matter and description of fission rates for r-process nucleosynthesis.

  14. Divacancy binding energy, formation energy and surface energy of BCC transition metals using MEAM potentials

    Science.gov (United States)

    Uniyal, Shweta; Chand, Manesh; Joshi, Subodh; Semalty, P. D.

    2016-05-01

    The modified embedded atom method (MEAM) potential parameters have been employed to calculate the unrelaxed divacancy formation energy, binding energy and surface energies for low index planes in bcc transition metals. The calculated results of divacancy binding energy and vacancy formation energy compare well with experimental and other available calculated results.

  15. Potential energy surface of alanine polypeptide chains

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.

    2006-01-01

    The multidimensional potential energy surfaces of the peptide chains consisting of three and six alanine (Ala) residues have been studied with respect to the degrees of freedom related to the twist of these molecules relative to the peptide backbone (these degrees of freedom are responsible...

  16. Phase space barriers and dividing surfaces in the absence of critical points of the potential energy

    CERN Document Server

    Ezra, Gregory S

    2010-01-01

    We consider the existence of invariant manifolds in phase space governing reaction dynamics in situations where there are no saddle points on the potential energy surface in the relevant regions of configuration space. We point out that such situations occur in a number of important classes of chemical reactions, and we illustrate this concretely by considering a model for transition state switching in an ion-molecule association reaction due to Chesnavich (J. Chem. Phys. {\\bf 84}, 2615 (1986)). For this model we show that, in the region of configuration space relevant to the reaction, there are no saddle points on the potential energy surface, but that in phase space there is a normally hyperbolic invariant manifold (NHIM) bounding a dividing surface having the property that the reactive flux through this dividing surface is a minimum. We then describe two methods for finding NHIMs and their associated phase space structures in systems with more than two degrees-of-freedom. These methods do not rely on the e...

  17. Temperature and pressure dependent rate coefficients for the reaction of C2H4 + HO2 on the C2H4O2H potential energy surface.

    Science.gov (United States)

    Guo, JunJiang; Xu, JiaQi; Li, ZeRong; Tan, NingXin; Li, XiangYuan

    2015-04-02

    The potential energy surface (PES) for reaction C2H4 + HO2 was examined by using the quantum chemical methods. All rates were determined computationally using the CBS-QB3 composite method combined with conventional transition state theory(TST), variational transition-state theory (VTST) and Rice-Ramsberger-Kassel-Marcus/master-equation (RRKM/ME) theory. The geometries optimization and the vibrational frequency analysis of reactants, transition states, and products were performed at the B3LYP/CBSB7 level. The composite CBS-QB3 method was applied for energy calculations. The major product channel of reaction C2H4 + HO2 is the formation C2H4O2H via an OH(···)π complex with 3.7 kcal/mol binding energy which exhibits negative-temperature dependence. We further investigated the reactions related to this complex, which were ignored in previous studies. Thermochemical properties of the species involved in the reactions were determined using the CBS-QB3 method, and enthalpies of formation of species were compared with literature values. The calculated rate constants are in good agreement with those available from literature and given in modified Arrhenius equation form, which are serviceable in combustion modeling of hydrocarbons. Finally, in order to illustrate the effect for low-temperature ignition of our new rate constants, we have implemented them into the existing mechanisms, which can predict ethylene ignition in a shock tube with better performance.

  18. Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations.

    Science.gov (United States)

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

    Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

  19. Post-Transition State Dynamics in Gas Phase Reactivity: Importance of Bifurcations and Rotational Activation.

    Science.gov (United States)

    Martín-Sómer, Ana; Yáñez, Manuel; Hase, William L; Gaigeot, Marie-Pierre; Spezia, Riccardo

    2016-03-01

    Beyond the established use of thermodynamic vs kinetic control to explain chemical reaction selectivity, the concept of bifurcations on a potential energy surface (PES) is proving to be of pivotal importance with regard to selectivity. In this article, we studied by means of post-transition state (TS) direct dynamics simulations the effect that vibrational and rotational excitation at the TS may have on selectivity on a bifurcating PES. With this aim, we studied the post-TS unimolecular reactivity of the [Ca(formamide)](2+) ion, for which Coulomb explosion and neutral loss reactions compete. The PES exhibits different kinds of nonintrinsic reaction coordinate (IRC) dynamics, among them PES bifurcations, which direct the trajectories to multiple reaction paths after passing the TS. Direct dynamics simulations were used to distinguish between the bifurcation non-IRC dynamics and non-IRC dynamics arising from atomistic motions directing the trajectories away from the IRC. Overall, we corroborated the idea that kinetic selectivity often does not reduce to a simple choice between paths with different barrier heights and instead dynamical behavior after passing the TS may be crucial. Importantly, rotational excitation may play a pivotal role on the reaction selectivity favoring nonthermodynamic products.

  20. Sparse representation for a potential energy surface

    Science.gov (United States)

    Seko, Atsuto; Takahashi, Akira; Tanaka, Isao

    2014-07-01

    We propose a simple scheme to estimate the potential energy surface (PES) for which the accuracy can be easily controlled and improved. It is based on model selection within the framework of linear regression using the least absolute shrinkage and selection operator (LASSO) technique. Basis functions are selected from a systematic large set of candidate functions. The sparsity of the PES significantly reduces the computational cost of evaluating the energy and force in molecular dynamics simulations without losing accuracy. The usefulness of the scheme for describing the elemental metals Na and Mg is clearly demonstrated.

  1. Determination of Energy Fluxes Over Agricultural Surfaces

    OpenAIRE

    Josefina Argete

    1994-01-01

    An energy budget was conducted over two kinds if surfaces: grass and corn canopy. The net radiative flux and the soil heat flux were directly measured while the latent and sensible heat flux were calculated from the vertical profiles if wet and dry-bulb temperature and wind speed. The crop storage flux was also estimated. Using the gradient or aerodynamic equations, the calculated fluxes when compared to the measured fluxes in the context of an energy budget gave an SEE = 63 Wm-2 over grass a...

  2. Multiple Transition States and Roaming in Ion-Molecule Reactions: a Phase Space Perspective

    CERN Document Server

    Mauguiere, Frederic A L; Ezra, Gregory S; Farantos, Stavros C; Wiggins, Stephen

    2013-01-01

    We provide a dynamical interpretation of the recently identified `roaming' mechanism for molecular dissociation reactions in terms of geometrical structures in phase space. These are NHIMs (Normally Hyperbolic Invariant Manifolds) and their stable/unstable manifolds that define transition states for ion-molecule association or dissociation reactions. The associated dividing surfaces rigorously define a roaming region of phase space, in which both reactive and nonreactive trajectories can be trapped for arbitrarily long times.

  3. Computationally Efficient Characterization of Potential Energy Surfaces Based on Fingerprint Distances

    CERN Document Server

    Schaefer, Bastian

    2016-01-01

    An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic, dynamic and structural properties. Unfortunately computing the transition states and reaction pathways in addition to the significant energetically low-lying local minima is a computationally demanding task. We here introduce a computationally efficient method that is based on a combination of the minima hopping global optimization method and the insight that uphill barriers tend to increase with increasing structural distances of the educt and product states. This method allows to replace the exact connectivity information and transition state energies with alternative and approximate concepts. Without adding any significant additional cost to the minima hopping global optimization approach, this method allows to generate an approximate network of the minima, their connectivit...

  4. Fast Shepard interpolation on graphics processing units: potential energy surfaces and dynamics for H + CH4 → H2 + CH3.

    Science.gov (United States)

    Welsch, Ralph; Manthe, Uwe

    2013-04-28

    A strategy for the fast evaluation of Shepard interpolated potential energy surfaces (PESs) utilizing graphics processing units (GPUs) is presented. Speed ups of several orders of magnitude are gained for the title reaction on the ZFWCZ PES [Y. Zhou, B. Fu, C. Wang, M. A. Collins, and D. H. Zhang, J. Chem. Phys. 134, 064323 (2011)]. Thermal rate constants are calculated employing the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach. Results for the ZFWCZ PES are compared to rate constants obtained for other ab initio PESs and problems are discussed. A revised PES is presented. Thermal rate constants obtained for the revised PES indicate that an accurate description of the anharmonicity around the transition state is crucial.

  5. Applications of Molecular Modeling to Transition State Energies and Conformations

    Science.gov (United States)

    1992-05-08

    reactivity trends for similar systems are known. Illuminati and Mandolini have done research on the lactone formation from w-bromoalkane-carboxylate...strikingly similar to that determined for Illuminati and Mandolini’s similar lactonization system (see Figure 20). The AE, for the 4- 69 membered ring...Brown, F.K.; Spellmeyer, D.C.; Metz, J.T.; Li, Y.; Loncharich, R.L. Science. 1986, 231, 1108-17. Illuminati , G.; Mandolini, L. Accts. of Chem. Res. 1981

  6. Computed potential energy surfaces for chemical reactions

    Science.gov (United States)

    Walch, Stephen P.

    1994-01-01

    Quantum mechanical methods have been used to compute potential energy surfaces for chemical reactions. The reactions studied were among those believed to be important to the NASP and HSR programs and included the recombination of two H atoms with several different third bodies; the reactions in the thermal Zeldovich mechanism; the reactions of H atom with O2, N2, and NO; reactions involved in the thermal De-NO(x) process; and the reaction of CH(squared Pi) with N2 (leading to 'prompt NO'). These potential energy surfaces have been used to compute reaction rate constants and rates of unimolecular decomposition. An additional application was the calculation of transport properties of gases using a semiclassical approximation (and in the case of interactions involving hydrogen inclusion of quantum mechanical effects).

  7. Surface spectroscopy using high energy heavy ions

    Energy Technology Data Exchange (ETDEWEB)

    Doyle, B.L.; Cocke, C.L.; Gray, T.J.; Justiniano, E.; Peercy, P.S.

    1983-04-01

    Surface atoms ionized by high energy heavy ions have been detected by time-of-flight and quadrupole mass spectroscopic techniques. The experimental arrangements are described and potential applications are suggested. Both techniques are demonstrated to produce significant improvements in the detection of atomic hydrogen, with the TOF method producing a nine order of magnitude increase in the sensitivity of atomic hydrogen compared to standard nuclear analysis methods.

  8. Determination of Energy Fluxes Over Agricultural Surfaces

    Directory of Open Access Journals (Sweden)

    Josefina Argete

    1994-12-01

    Full Text Available An energy budget was conducted over two kinds if surfaces: grass and corn canopy. The net radiative flux and the soil heat flux were directly measured while the latent and sensible heat flux were calculated from the vertical profiles if wet and dry-bulb temperature and wind speed. The crop storage flux was also estimated. Using the gradient or aerodynamic equations, the calculated fluxes when compared to the measured fluxes in the context of an energy budget gave an SEE = 63 Wm-2 over grass and SEE = 81 Wm-2 over corn canopy. The calculated fluxes compared reasonably well with those obtained using the Penman equations.For an energy budget research with limited instrumentation, the aerodynamic method performed satisfactorily in estimating the daytime fluxes, when atmospheric conditions are fully convective, but failed when conditions were stably stratified as during nighttime.

  9. Liberation of H2 from (o-C6H4Me)3P—H(+) + (-)H—B(p-C6F4H)3 ion-pair: A transition-state in the minimum energy path versus the transient species in Born-Oppenheimer molecular dynamics

    Science.gov (United States)

    Pu, Maoping; Heshmat, Mojgan; Privalov, Timofei

    2017-07-01

    Using Born-Oppenheimer molecular dynamics (BOMD) with density functional theory, transition-state (TS) calculations, and the quantitative energy decomposition analysis (EDA), we examined the mechanism of H2-liberation from LB—H(+) + (-)H—LA ion-pair, 1, in which the Lewis base (LB) is (o-C6H4Me)3P and the Lewis acid (LA) is B(p-C6F4H)3. BOMD simulations indicate that the path of H2 liberation from the ion-pair 1 goes via the short-lived transient species, LB⋯H2⋯LA, which are structurally reminiscent of the TS-structure in the minimum-energy-path describing the reversible reaction between H2 and (o-C6H4Me)3P/B(p-C6F4H)3 frustrated Lewis pair (FLP). With electronic structure calculations performed on graphics processing units, our BOMD data-set covers more than 1 ns of evolution of the ion-pair 1 at temperature T ≈ 400 K. BOMD simulations produced H2-recombination events with various durations of H2 remaining fully recombined as a molecule within a LB/LA attractive "pocket"—from very short vibrational-time scale to time scales in the range of a few hundred femtoseconds. With the help of perturbational approach to trajectory-propagation over a saddle-area, we directly examined dynamics of H2-liberation. Using EDA, we elucidated interactions between the cationic and anionic fragments in the ion-pair 1 and between the molecular fragments in the TS-structure. We have also considered a model that qualitatively takes into account the potential energy characteristics of H—H recombination and H2-release plus inertia of molecular motion of the (o-C6H4Me)3P/B(p-C6F4H)3 FLP.

  10. Methane dissociation on Ni(111): A fifteen-dimensional potential energy surface using neural network method

    Science.gov (United States)

    Shen, Xiangjian; Chen, Jun; Zhang, Zhaojun; Shao, Kejie; Zhang, Dong H.

    2015-10-01

    In the present work, we develop a highly accurate, fifteen-dimensional potential energy surface (PES) of CH4 interacting on a rigid flat Ni(111) surface with the methodology of neural network (NN) fit to a database consisted of about 194 208 ab initio density functional theory (DFT) energy points. Some careful tests of the accuracy of the fitting PES are given through the descriptions of the fitting quality, vibrational spectrum of CH4 in vacuum, transition state (TS) geometries as well as the activation barriers. Using a 25-60-60-1 NN structure, we obtain one of the best PESs with the least root mean square errors: 10.11 meV for the entrance region and 17.00 meV for the interaction and product regions. Our PES can reproduce the DFT results very well in particular for the important TS structures. Furthermore, we present the sticking probability S0 of ground state CH4 at the experimental surface temperature using some sudden approximations by Jackson's group. An in-depth explanation is given for the underestimated sticking probability.

  11. A comparison of transition state of phenol in H-atom abstraction by methyl and methylperoxyl radicals

    Institute of Scientific and Technical Information of China (English)

    SUN YouMin; WU JunSen; LIU ChengBu

    2007-01-01

    DFT method was employed to locate transition state for H-atom transfer from phenol by methyl radical and methylperoxyl radical. The reaction pathway energy profiles and the structure of transition state show that a common feature is the out-of-plane structure of the transition state: in contrast to the energetic minima of a hydrogen-bonded intermediate, the hydrogen bond in transition structures is considerably twisted out of the aromatic ring. From the values of enthalpy (△H) and activation energy (Ea)obtained, it is found that the rate of the reaction of peroxyl radical with phenolic antioxidant is higher than that of alkyl radical with antioxidant. Spin density distributions show that the electron transmission is between methyl (methylperoxyl) radical and phenol.

  12. Large-Scale Density Functional Theory Transition State Searching in Enzymes.

    Science.gov (United States)

    Lever, Greg; Cole, Daniel J; Lonsdale, Richard; Ranaghan, Kara E; Wales, David J; Mulholland, Adrian J; Skylaris, Chris-Kriton; Payne, Mike C

    2014-11-06

    Linear-scaling quantum mechanical density functional theory calculations have been applied to study the rearrangement of chorismate to prephenate in large-scale models of the Bacillus subtilis chorismate mutase enzyme. By treating up to 2000 atoms at a consistent quantum mechanical level of theory, we obtain an unbiased, almost parameter-free description of the transition state geometry and energetics. The activation energy barrier is calculated to be lowered by 10.5 kcal mol(-1) in the enzyme, compared with the equivalent reaction in water, which is in good agreement with experiment. Natural bond orbital analysis identifies a number of active site residues that are important for transition state stabilization in chorismate mutase. This benchmark study demonstrates that linear-scaling density functional theory techniques are capable of simulating entire enzymes at the ab initio quantum mechanical level of accuracy.

  13. Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates.

    Science.gov (United States)

    Svensson, Fredrik; Engen, Karin; Lundbäck, Thomas; Larhed, Mats; Sköld, Christian

    2015-09-28

    Transition state and high energy intermediate mimetics have the potential to be very potent enzyme inhibitors. In this study, a model of peptide hydrolysis in the active site of insulin-regulated aminopeptidase (IRAP) was developed using density functional theory calculations and the cluster approach. The 3D structure models of the reaction coordinates were used for virtual screening to obtain new chemical starting points for IRAP inhibitors. This mechanism-based virtual screening process managed to identify several known peptidase inhibitors from a library of over 5 million compounds, and biological testing identified one compound not previously reported as an IRAP inhibitor. This novel methodology for virtual screening is a promising approach to identify new inhibitors mimicking key transition states or intermediates of an enzymatic reaction.

  14. An alternative derivation of ring-polymer molecular dynamics transition-state theory

    CERN Document Server

    Hele, Timothy J H

    2016-01-01

    In a previous article [J. Chem. Phys. 138, 084108 (2013)], we showed that the transition-state-theory ($t\\rightarrow 0_+$) limit of ring-polymer molecular dynamics rate-theory (RPMD-TST) is also the $t\\rightarrow 0_+$ limit of a new type of quantum flux-side time-correlation function, in which the dividing surfaces are invariant to imaginary-time translation; in other words, that RPMD-TST is a $t\\rightarrow 0_+$ quantum transition-state theory (QTST). Recently, Jang and Voth [J. Chem. Phys. 144, 084110 (2016)] rederived this quantum $t\\rightarrow 0_+$ limit, and claimed that it gives instead the centroid-density approximation. Here we show that the $t\\rightarrow 0_+$ limit derived by Jang and Voth is in fact RPMD-TST.

  15. Planar Homotropenylium Cation : A Transition State with Reversed Aromaticity

    NARCIS (Netherlands)

    Gibson, Christopher M.; Havenith, Remco W. A.; Fowler, Patrick W.; Jenneskens, Leonardus W.

    2015-01-01

    In contrast to the equilibrium structure of the homoaromatic C-s homotropenylium cation, C8H9+ (1), which supports a pinched diatropic ring current, the C(2)v transition state (2) for inversion of the methylene bridge of 1 is antiaromatic and supports a two-lobe paratropic pi current, as detected by

  16. Reaction dynamics: The view from a transition state

    Science.gov (United States)

    Continetti, Robert E.

    2017-10-01

    Ejecting electrons from negative ions using light can create structures that very closely resemble the transition states of bimolecular reactions. Now, using this technique, trapped quantum states, or 'resonances', have been observed in a seven-atom reaction, and theory has been shown to be up to the task of capturing such complex phenomena.

  17. Phase space barriers and dividing surfaces in the absence of critical points of the potential energy: Application to roaming in ozone

    Energy Technology Data Exchange (ETDEWEB)

    Mauguière, Frédéric A. L., E-mail: frederic.mauguiere@bristol.ac.uk; Collins, Peter, E-mail: peter.collins@bristol.ac.uk; Wiggins, Stephen, E-mail: stephen.wiggins@mac.com [School of Mathematics, University of Bristol, Bristol BS8 1TW (United Kingdom); Kramer, Zeb C., E-mail: zebcolterkramer@gmail.com; Ezra, Gregory S., E-mail: gse1@cornell.edu [Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853 (United States); Carpenter, Barry K., E-mail: carpenterb1@cardiff.ac.uk [School of Chemistry, Cardiff University, Cardiff CF10 3AT (United Kingdom); Farantos, Stavros C., E-mail: farantos@iesl.forth.gr [Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, and Department of Chemistry, University of Crete, Iraklion 711 10, Crete (Greece)

    2016-02-07

    We examine the phase space structures that govern reaction dynamics in the absence of critical points on the potential energy surface. We show that in the vicinity of hyperbolic invariant tori, it is possible to define phase space dividing surfaces that are analogous to the dividing surfaces governing transition from reactants to products near a critical point of the potential energy surface. We investigate the problem of capture of an atom by a diatomic molecule and show that a normally hyperbolic invariant manifold exists at large atom-diatom distances, away from any critical points on the potential. This normally hyperbolic invariant manifold is the anchor for the construction of a dividing surface in phase space, which defines the outer or loose transition state governing capture dynamics. We present an algorithm for sampling an approximate capture dividing surface, and apply our methods to the recombination of the ozone molecule. We treat both 2 and 3 degrees of freedom models with zero total angular momentum. We have located the normally hyperbolic invariant manifold from which the orbiting (outer) transition state is constructed. This forms the basis for our analysis of trajectories for ozone in general, but with particular emphasis on the roaming trajectories.

  18. Surface Energy Balance System (SEBS) Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Cook, D. R. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2016-01-01

    A Surface Energy Balance System (SEBS) has been installed collocated with each deployed Eddy Correlation Flux Measurement System (ECOR) at the Atmospheric Radiation Measurement (ARM) Climate Research Facility’s Southern Great Plains (SGP) site, North Slope of Alaska (NSA) site, first ARM Mobile Facility (AMF1), second ARM Mobile Facility (AMF2), and third ARM Mobile Facility (AMF3) at Oliktok Point (OLI). A SEBS was also deployed with the Tropical Western Pacific (TWP) site, before it was decommissioned. Data from these sites, including the retired TWP, are available in the ARM Data Archive. The SEBS consists of upwelling and downwelling solar and infrared radiometers within one net radiometer, a wetness sensor, and soil measurements. The SEBS measurements allow the comparison of ECOR sensible and latent heat fluxes with the energy balance determined from the SEBS and provide information on wetting of the sensors for data quality purposes.

  19. Theoretical studies of potential energy surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Harding, L.B. [Argonne National Laboratory, IL (United States)

    1993-12-01

    The goal of this program is to calculate accurate potential energy surfaces (PES) for both reactive and nonreactive systems. To do this the electronic Schrodinger equation must be solved. Our approach to this problem starts with multiconfiguration self-consistent field (MCSCF) reference wavefunctions. These reference wavefunctions are designed to be sufficiently flexible to accurately describe changes in electronic structure over a broad range of geometries. Electron correlation effects are included via multireference, singles and doubles configuration interaction (MRSDCI) calculations. With this approach, the authors are able to provide useful predictions of the energetics for a broad range of systems.

  20. Constrained Broyden Dimer Method with Bias Potential for Exploring Potential Energy Surface of Multistep Reaction Process.

    Science.gov (United States)

    Shang, Cheng; Liu, Zhi-Pan

    2012-07-10

    To predict the chemical activity of new matter is an ultimate goal in chemistry. The identification of reaction pathways using modern quantum mechanics calculations, however, often requires a high demand in computational power and good chemical intuition on the reaction. Here, a new reaction path searching method is developed by combining our recently developed transition state (TS) location method, namely, the constrained Broyden dimer method, with a basin-filling method via bias potentials, which allows the system to walk out from the energy traps at a given reaction direction. In the new method, the reaction path searching starts from an initial state without the need for preguessing the TS-like or final state structure and can proceed iteratively to the final state by locating all related TSs and intermediates. In each elementary reaction step, a reaction direction, such as a bond breaking, needs to be specified, the information of which is refined and preserved as a normal mode through biased dimer rotation. The method is tested successfully on the Baker reaction system (50 elementary reactions) with good efficiency and stability and is also applied to the potential energy surface exploration of multistep reaction processes in the gas phase and on the surface. The new method can be applied for the computational screening of new catalytic materials with a minimum requirement of chemical intuition.

  1. Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis.

    Science.gov (United States)

    Burschowsky, Daniel; van Eerde, André; Ökvist, Mats; Kienhöfer, Alexander; Kast, Peter; Hilvert, Donald; Krengel, Ute

    2014-12-09

    For more than half a century, transition state theory has provided a useful framework for understanding the origins of enzyme catalysis. As proposed by Pauling, enzymes accelerate chemical reactions by binding transition states tighter than substrates, thereby lowering the activation energy compared with that of the corresponding uncatalyzed process. This paradigm has been challenged for chorismate mutase (CM), a well-characterized metabolic enzyme that catalyzes the rearrangement of chorismate to prephenate. Calculations have predicted the decisive factor in CM catalysis to be ground state destabilization rather than transition state stabilization. Using X-ray crystallography, we show, in contrast, that a sluggish variant of Bacillus subtilis CM, in which a cationic active-site arginine was replaced by a neutral citrulline, is a poor catalyst even though it effectively preorganizes chorismate for the reaction. A series of high-resolution molecular snapshots of the reaction coordinate, including the apo enzyme, and complexes with substrate, transition state analog and product, demonstrate that an active site, which is only complementary in shape to a reactive substrate conformer, is insufficient for effective catalysis. Instead, as with other enzymes, electrostatic stabilization of the CM transition state appears to be crucial for achieving high reaction rates.

  2. Rational design of catalysts for asymmetric diamination reaction using transition state modeling.

    Science.gov (United States)

    Jindal, Garima; Sunoj, Raghavan B

    2014-05-07

    The stereoselective synthesis of 1,2-diamines has remained a formidable challenge. A recent palladium-catalyzed asymmetric diamination of conjugated double bonds using di-tert-butyldiaziridinone appears promising. The axially chiral binol phosphoramidite ligands are successful in offering high enantioselectivity. The density functional theory investigations revealed that the energies of the stereocontrolling transition states for the C-N bond formation depend on a number of weak non-covalent interactions such as C-H···π, C-H···O and anagostic interactions. We envisaged that the modulation in these interactions in the transition states, through subtle changes in chiral phosphoramidite substituents, could be exploited toward steering the stereoselectivity. The effect of systematic modifications on both 3,3' positions of the binol as well as on the amido nitrogen on the stereochemical outcome is predicted. It is identified that high enantioselectivity requires a balance between the nature of the substituents on binol and amido groups. The reduced size of the amido substituents demands increased bulk on the binol whereas lowering the size on the binol demands increased bulk on the amido for higher stereoselectivity. The substituent at the α-position of the amido group is found to be vital and appears to be a hot spot for modifications. These insights derived from studies on the stereocontrolling transition states could help improve the catalytic efficacies in palladium-catalyzed asymmetric diamination reactions.

  3. Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions.

    Science.gov (United States)

    Zhou, G; Somasundaram, T; Blanc, E; Parthasarathy, G; Ellington, W R; Chapman, M S

    1998-07-21

    Arginine kinase belongs to the family of enzymes, including creatine kinase, that catalyze the buffering of ATP in cells with fluctuating energy requirements and that has been a paradigm for classical enzymological studies. The 1.86-A resolution structure of its transition-state analog complex, reported here, reveals its active site and offers direct evidence for the importance of precise substrate alignment in the catalysis of bimolecular reactions, in contrast to the unimolecular reactions studied previously. In the transition-state analog complex studied here, a nitrate mimics the planar gamma-phosphoryl during associative in-line transfer between ATP and arginine. The active site is unperturbed, and the reactants are not constrained covalently as in a bisubstrate complex, so it is possible to measure how precisely they are pre-aligned by the enzyme. Alignment is exquisite. Entropic effects may contribute to catalysis, but the lone-pair orbitals are also aligned close enough to their optimal trajectories for orbital steering to be a factor during nucleophilic attack. The structure suggests that polarization, strain toward the transition state, and acid-base catalysis also contribute, but, in contrast to unimolecular enzyme reactions, their role appears to be secondary to substrate alignment in this bimolecular reaction.

  4. Surface Pyrolysis of High Energy Materials

    Directory of Open Access Journals (Sweden)

    Luigi Deluca

    1998-10-01

    Full Text Available The Arrhenius zero-order phenomenological pyrolysis law, commonly used in conjunction with the Vieille ballistic law to study pressure-driven burning of energetic materials, is revisited. Motivated by experimental and theoretical work performed in 1984 in this Laboratory , a relationship among several interplaying parameters is found under steady-state conditions. This relationship corresponds to the Jacobian of the pyrolysis sensitivity parameters used in the Zeldovich-Novozhilov approach. The Arrhenius pyrolysis is still expressed in terms of a global surface activation energy, but consistency with the experimental ballistic law may require an explicit pressure dependence as well. This conclusion is supported by a variety of arguments drawn from different areas. The linear dependence of the pre-exponential factor on surface activation energy (known as kinetic compensation is proved and extended to the pressure exponent, for any given experimental data set under steady burning. Experimental results are reported for about a dozen solid propellants of different nature. The effects of surface pyrolysis explicit pressure dependence, although modest on steady-state burning, are potentially far-reaching for unsteady regime and/or unstable burning. The paper is mainly focussed on pressure-driven burning and Arrhenius pyrolysis, but the implemented method is believed to apply in general. Thus, enforcing KTSS zero-order phenomenological pyrolysis with the Vieille ballistic law yields similar results and requires an explicit pressure dependence. In case, the Zeldovich ballistic law is enforced instead of the classical Vieille law, no explicit pressure dependence is required. The unifying concept for these different trends is the pyrolysis Jacobian as a consistency requirement between the implemented steady pyrolysis and ballistic laws."

  5. Computationally efficient characterization of potential energy surfaces based on fingerprint distances

    Science.gov (United States)

    Schaefer, Bastian; Goedecker, Stefan

    2016-07-01

    An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows us to understand important characteristics like thermodynamic, dynamic, and structural properties. Unfortunately computing the transition states and reaction pathways in addition to the significant energetically low-lying local minima is a computationally demanding task. We here introduce a computationally efficient method that is based on a combination of the minima hopping global optimization method and the insight that uphill barriers tend to increase with increasing structural distances of the educt and product states. This method allows us to replace the exact connectivity information and transition state energies with alternative and approximate concepts. Without adding any significant additional cost to the minima hopping global optimization approach, this method allows us to generate an approximate network of the minima, their connectivity, and a rough measure for the energy needed for their interconversion. This can be used to obtain a first qualitative idea on important physical and chemical properties by means of a disconnectivity graph analysis. Besides the physical insight obtained by such an analysis, the gained knowledge can be used to make a decision if it is worthwhile or not to invest computational resources for an exact computation of the transition states and the reaction pathways. Furthermore it is demonstrated that the here presented method can be used for finding physically reasonable interconversion pathways that are promising input pathways for methods like transition path sampling or discrete path sampling.

  6. Deformed transition-state theory: Deviation from Arrhenius behavior and application to bimolecular hydrogen transfer reaction rates in the tunneling regime.

    Science.gov (United States)

    Carvalho-Silva, Valter H; Aquilanti, Vincenzo; de Oliveira, Heibbe C B; Mundim, Kleber C

    2017-01-30

    A formulation is presented for the application of tools from quantum chemistry and transition-state theory to phenomenologically cover cases where reaction rates deviate from Arrhenius law at low temperatures. A parameter d is introduced to describe the deviation for the systems from reaching the thermodynamic limit and is identified as the linearizing coefficient in the dependence of the inverse activation energy with inverse temperature. Its physical meaning is given and when deviation can be ascribed to quantum mechanical tunneling its value is calculated explicitly. Here, a new derivation is given of the previously established relationship of the parameter d with features of the barrier in the potential energy surface. The proposed variant of transition state theory permits comparison with experiments and tests against alternative formulations. Prescriptions are provided and implemented to three hydrogen transfer reactions: CH4  + OH → CH3  + H2 O, CH3 Cl + OH → CH2 Cl + H2 O and H2  + CN → H + HCN, widely investigated both experimentally and theoretically. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Correlation between surface free energy and anchoring energy of 6CHBT on polyimide surface

    Science.gov (United States)

    Borycki, Jerzy; Okulska-Bozek, Malgorzata; Kedzierski, Jerzy; Kojdecki, Marek A.

    2002-06-01

    Polyimides were prepared in the classical two-step method via poly(amic acids). Poly(amic acids) were obtained from 3,3',4,4'-biphenyltetracarboxylic dianhydride (BPDA), 4,4'- (hexafluoroisopropylidene)diphthalic anhydride (6FDA), pyromellitic dianhydride (PMDA), 3,3',4,4'- diphenylsulfonetetracarboxylic dianhydride (DSDA), 4,4'- oxydiphthalic anhydride (ODPA) and amines 4,4'-oxydianiline (ODA), 1,3-phenylenediamine (MPD), 1,4-phenylenediamine (PPD), 4,4'-diaminodiphenylmethane (MDA), 4,4'- ethylenedianiline (DAB), 2,4,6-trimethyl-1,3- phenylenediamine (TMPD), 4-methyl-1,3-phenylenediamine (MMPD) and 2,3,5,6-tetramethyl-1,4-phenylenediamine (DAD) in dimethylformamide. The indium tin oxide (ITO)-glass plates were spin-coated with the poly(amic acids) solutions and dried. A thermal imidization process was then carried out at 250 degree(s)C for 4 h. In this study the anchoring energies of 6CHBT molecules were evaluated on rubbing aligning layers of PI films. The polar anchoring energy coefficient was determined by wedge cell method. The surface free energy and its components of polyimide layers were determined by measuring the contact angles of water, ethylene glycol, formamide and diiodomethane drops on the rubbing polymer surfaces. The Lifshitz-van der Waals and acidic-basic components of surface free energies were found from van Oss equation.

  8. Reactions of 1-naphthyl radicals with ethylene. Single pulse shock tube experiments, quantum chemical, transition state theory, and multiwell calculations.

    Science.gov (United States)

    Lifshitz, Assa; Tamburu, Carmen; Dubnikova, Faina

    2008-02-07

    The reactions of 1-naphthyl radicals with ethylene were studied behind reflected shock waves in a single pulse shock tube, covering the temperature range 950-1200 K at overall densities behind the reflected shocks of approximately 2.5 x 10(-5) mol/cm3. 1-Iodonaphthalene served as the source for 1-naphthyl radicals as its C-I bond dissociation energy is relatively small. It is only approximately 65 kcal/mol as compared to the C-H bond strength in naphthalene which is approximately 112 kcal/mol and can thus produce naphthyl radicals at rather low reflected shock temperatures. The [ethylene]/[1-iodo-naphthalene] ratio in all of the experiments was approximately 100 in order to channel the free radicals into reactions with ethylene rather than iodonaphthalene. Four products resulting from the reactions of 1-naphthyl radicals with ethylene were found in the post shock samples. They were vinyl naphthalene, acenaphthene, acenaphthylene, and naphthalene. Some low molecular weight aliphatic products at rather low concentrations, resulting from the attack of various free radicals on ethylene were also found in the shocked samples. In view of the relatively low temperatures employed in the present experiments, the unimolecular decomposition rate of ethylene is negligible. Three potential energy surfaces describing the production of vinyl naphthalene, acenaphthene, and acenaphthylene were calculated using quantum chemical methods and rate constants for the elementary steps on the surfaces were calculated using transition state theory. Naphthalene is not part of the reactions on the surfaces. Acenaphthylene is obtained only from acenaphthene. A kinetics scheme containing 27 elementary steps most of which were obtained from the potential energy surfaces was constructed and computer modeling was performed. An excellent agreement between the experimental yields of the four major products and the calculated yields was obtained.

  9. Explicit correlation treatment of the potential energy surface of CO{sub 2} dimer

    Energy Technology Data Exchange (ETDEWEB)

    Kalugina, Yulia N., E-mail: kalugina@phys.tsu.ru [Tomsk State University, 36 Lenin Ave., Tomsk 634050 (Russian Federation); Buryak, Ilya A. [Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, Moscow (Russian Federation); Chemistry Department, Lomonosov Moscow State University, Moscow (Russian Federation); Ajili, Yosra [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 Bd Descartes, 77454 Marne-La-Vallée (France); Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA Université de Tunis El Manar (Tunisia); Vigasin, Andrei A. [Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, Moscow (Russian Federation); Jaidane, Nejm Eddine [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA Université de Tunis El Manar (Tunisia); Hochlaf, Majdi [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 Bd Descartes, 77454 Marne-La-Vallée (France)

    2014-06-21

    We present an extensive study of the four-dimensional potential energy surface (4D-PES) of the carbon dioxide dimer, (CO{sub 2}){sub 2}. This PES is developed over the set of intermolecular coordinates. The electronic computations are carried out at the explicitly correlated coupled cluster method with single, double, and perturbative triple excitations [CCSD(T)-F12] level of theory in connection with the augmented correlation-consistent aug-cc-pVTZ basis set. An analytic representation of the 4D-PES is derived. Our extensive calculations confirm that “Slipped Parallel” is the most stable form and that the T-shaped structure corresponds to a transition state. Later on, this PES is employed for the calculations of the vibrational energy levels of the dimer. Moreover, the temperature dependence of the dimer second virial coefficient and of the first spectral moment of rototranslational collision-induced absorption spectrum is derived. For both quantities, a good agreement is found between our values and the experimental data for a wide range of temperatures. This attests to the high quality of our PES. Generally, our PES and results can be used for modeling CO{sub 2} supercritical fluidity and examination of its role in planetary atmospheres. It can be also incorporated into dynamical computations of CO{sub 2} capture and sequestration. This allows deep understanding, at the microscopic level, of these processes.

  10. Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

    Science.gov (United States)

    García-Meseguer, Rafael; Martí, Sergio; Ruiz-Pernía, J. Javier; Moliner, Vicent; Tuñón, Iñaki

    2013-07-01

    Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We show that the structure of the protein provides an adequate environment for the progress of the reaction, although a certain degree of flexibility is needed to attain the full catalytic effect. However, these motions do not introduce significant dynamical corrections to the rate constant and can be described as equilibrium fluctuations.

  11. State-to-state reaction probabilities within the quantum transition state framework.

    Science.gov (United States)

    Welsch, Ralph; Huarte-Larrañaga, Fermín; Manthe, Uwe

    2012-02-14

    Rigorous quantum dynamics calculations of reaction rates and initial state-selected reaction probabilities of polyatomic reactions can be efficiently performed within the quantum transition state concept employing flux correlation functions and wave packet propagation utilizing the multi-configurational time-dependent Hartree approach. Here, analytical formulas and a numerical scheme extending this approach to the calculation of state-to-state reaction probabilities are presented. The formulas derived facilitate the use of three different dividing surfaces: two dividing surfaces located in the product and reactant asymptotic region facilitate full state resolution while a third dividing surface placed in the transition state region can be used to define an additional flux operator. The eigenstates of the corresponding thermal flux operator then correspond to vibrational states of the activated complex. Transforming these states to reactant and product coordinates and propagating them into the respective asymptotic region, the full scattering matrix can be obtained. To illustrate the new approach, test calculations study the D + H(2)(ν, j) → HD(ν', j') + H reaction for J = 0. © 2012 American Institute of Physics

  12. The energy balance of the earth' surface : a practical approach

    NARCIS (Netherlands)

    Bruin, de H.A.R.

    1982-01-01

    This study is devoted to the energy balance of the earth's surface with a special emphasis on practical applications. A simple picture of the energy exchange processes that take place at the ground is the following. Per unit time and area an amount of radiant energy is supplied to the surface. This

  13. The energy balance of the earth's surface : a practical approach

    NARCIS (Netherlands)

    Bruin, de H.A.R.

    1982-01-01

    This study is devoted to the energy balance of the earth's surface with a special emphasis on practical applications. A simple picture of the energy exchange processes that take place at the ground is the following. Per unit time and area an amount of radiant energy is supplied to the surface. This

  14. The radiation of surface wave energy: Implications for volcanic tremor

    Science.gov (United States)

    Haney, M. M.; Denolle, M.; Lyons, J. J.; Nakahara, H.

    2015-12-01

    The seismic energy radiated by active volcanism is one common measurement of eruption size. For example, the magnitudes of individual earthquakes in volcano-tectonic (VT) swarms can be summed and expressed in terms of cumulative magnitude, energy, or moment release. However, discrepancies exist in current practice when treating the radiated energy of volcano seismicity dominated by surface waves. This has implications for volcanic tremor, since eruption tremor typically originates at shallow depth and is made up of surface waves. In the absence of a method to compute surface wave energy, estimates of eruption energy partitioning between acoustic and seismic waves typically assume seismic energy is composed of body waves. Furthermore, without the proper treatment of surface wave energy, it is unclear how much volcanic tremor contributes to the overall seismic energy budget during volcanic unrest. To address this issue, we derive, from first principles, the expression of surface wave radiated energy. In contrast with body waves, the surface wave energy equation is naturally expressed in the frequency domain instead of the time domain. We validate our result by reproducing an analytical solution for the radiated power of a vertical force source acting on a free surface. We further show that the surface wave energy equation leads to an explicit relationship between energy and the imaginary part of the surface wave Green's tensor at the source location, a fundamental property recognized within the field of seismic interferometry. With the new surface wave energy equation, we make clear connections to reduced displacement and propose an improved formula for the calculation of surface wave reduced displacement involving integration over the frequency band of tremor. As an alternative to reduced displacement, we show that reduced particle velocity squared is also a valid physical measure of tremor size, one based on seismic energy rate instead of seismic moment rate. These

  15. Obtaining evapotranspiration and surface energy fluxes with ...

    African Journals Online (AJOL)

    ... energy fluxes with remotely sensed data to improve agricultural water management. ... Remote sensing based energy balance models are presently most suited for ... concern the validation of the used model for spatial distribution analysis of

  16. Kinetics study of the CN + CH4 hydrogen abstraction reaction based on a new ab initio analytical full-dimensional potential energy surface.

    Science.gov (United States)

    Espinosa-Garcia, Joaquin; Rangel, Cipriano; Suleimanov, Yury V

    2017-07-26

    We have developed an analytical full-dimensional potential energy surface, named PES-2017, for the gas-phase hydrogen abstraction reaction between the cyano radical and methane. This surface is fitted using high-level ab initio information as input. Using the PES-2017 surface, a kinetics study was performed via two theoretical approaches: variational transition-state theory with multidimensional tunnelling (VTST-MT) and ring polymer molecular dynamics (RPMD). The results are compared with the experimental data. In the whole temperature range analysed, 300-1500 K, both theories agree within a factor of kinetic isotope effects are important, reproducing the scarce experimental evidence. The good agreement with the ab initio information used in the fitting process (self-consistency test) and with the kinetic behaviour in a wide temperature range gives confidence and strength to the new surface.

  17. Thermal isomerization of azobenzenes: on the performance of Eyring transition state theory

    Science.gov (United States)

    Rietze, Clemens; Titov, Evgenii; Lindner, Steven; Saalfrank, Peter

    2017-08-01

    The thermal Z\\to E (back-)isomerization of azobenzenes is a prototypical reaction occurring in molecular switches. It has been studied for decades, yet its kinetics is not fully understood. In this paper, quantum chemical calculations are performed to model the kinetics of an experimental benchmark system, where a modified azobenzene (AzoBiPyB) is embedded in a metal-organic framework (MOF). The molecule can be switched thermally from cis to trans, under solvent-free conditions. We critically test the validity of Eyring transition state theory for this reaction. As previously found for other azobenzenes (albeit in solution), good agreement between theory and experiment emerges for activation energies and activation free energies, already at a comparatively simple level of theory, B3LYP/6-31G* including dispersion corrections. However, theoretical Arrhenius prefactors and activation entropies are in qualitiative disagreement with experiment. Several factors are discussed that may have an influence on activation entropies, among them dynamical and geometric constraints (imposed by the MOF). For a simpler model—Z\\to E isomerization in azobenzene—a systematic test of quantum chemical methods from both density functional theory and wavefunction theory is carried out in the context of Eyring theory. Also, the effect of anharmonicities on activation entropies is discussed for this model system. Our work highlights capabilities and shortcomings of Eyring transition state theory and quantum chemical methods, when applied for the Z\\to E (back-)isomerization of azobenzenes under solvent-free conditions.

  18. Inequivalent models of irreversible dimer filling: Transition state'' dependence

    Energy Technology Data Exchange (ETDEWEB)

    Nord, R.S. (Department of Chemistry, Eastern Michigan University, Ypsilanti, MI (USA)); Evans, J.W. (Ames Laboratory, Ames IA (USA) Department of Physics, Iowa State Univ., Ames, IA (USA) Department of Mathematics, Iowa State Univ., Ames, IA (USA))

    1990-12-01

    Irreversible adsorption of diatomics on crystalline surfaces is sometimes modeled as random dimer filling of adjacent pairs of sites on a lattice. We note that this process can be implemented in two distinct ways: (i) randomly pick adjacent pairs of sites, {ital jj}{prime}, and fill {ital jj}{prime} only if both are empty (horizontal transition state); or (ii) randomly pick a single site, {ital j}, and if {ital j} and at least one neighbor are empty, then fill {ital j} and a randomly chosen empty neighbor (vertical transition state). Here it is instructive to consider processes which also include competitive random monomer filling of single sites. We find that although saturation (partial) coverages differ little between the models for pure dimer filling, there is a significant difference for comparable monomer and dimer filling rates. We present exact results for saturation coverage behavior for a linear lattice, and estimates for a square lattice. Ramifications for simple models of CO oxidation on surfaces are indicated.

  19. Energy quantization for approximate H-surfaces and applications

    Directory of Open Access Journals (Sweden)

    Shenzhou Zheng

    2013-07-01

    Full Text Available We consider weakly convergent sequences of approximate H-surface maps defined in the plane with their tension fields bounded in $L^p$ for p> 4/3, and establish an energy quantization that accounts for the loss of their energies by the sum of energies over finitely many nontrivial bubbles maps on $mathbb{R}^2$. As a direct consequence, we establish the energy identity at finite singular time to their H-surface flows.

  20. New hybrid method for reactive systems from integrating molecular orbital or molecular mechanics methods with analytical potential energy surfaces.

    Science.gov (United States)

    Espinosa-Garciá, Joaquín; Rangel, Cipriano; Navarrete, Marta; Corchado, José C

    2004-09-15

    A computational approach to calculating potential energy surfaces for reactive systems is presented and tested. This hybrid approach is based on integrated methods where calculations for a small model system are performed by using analytical potential energy surfaces, and for the real system by using molecular orbital or molecular mechanics methods. The method is tested on a hydrogen abstraction reaction by using the variational transition-state theory with multidimensional tunneling corrections. The agreement between the calculated and experimental information depends on the quality of the method chosen for the real system. When the real system is treated by accurate quantum mechanics methods, the rate constants are in excellent agreement with the experimental measurements over a wide temperature range. When the real system is treated by molecular mechanics methods, the results are still good, which is very encouraging since molecular mechanics itself is not at all capable of describing this reactive system. Since no experimental information or additional fits are required to apply this method, it can be used to improve the accuracy of molecular orbital methods or to extend the molecular mechanics method to treat any reactive system with the single constraint of the availability of an analytical potential energy surface that describes the model system.

  1. Study of radicals, clusters and transition state species by anion photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, D.W.

    1994-08-01

    Free radicals, elemental and van der Waals clusters and transition state species for bimolecular chemical reactions are investigated using anion photoelectron spectroscopy. Several low-lying electronic states of ozone have been identified via photoelectron spectroscopy of O{sub 3}{sup {minus}}. A characterization of these states is important to models for atmospheric ozone reaction kinetics. The fluoroformyloxyl radical, FCO{sub 2}, has been investigated, providing vibrational frequencies and energies for two electronic states. The technique has also been employed to make the first direct observation and characterization of the NNO{sub 2} molecule. Several electronic states are observed for this species which is believed to play a role as a reactive intermediate in the N + NO{sub 2} reaction. The experimental results for all three of these radicals are supplemented by ab initio investigations of their molecular properties. The clusters investigations include studies of elemental carbon clusters (C{sub 2}{sup {minus}} {minus} C{sub 11}{sup {minus}}), and van der Waals clusters (X{sup {minus}}(CO{sub 2}){sub n}, X = I, Br, Cl; n {le} 13 and I{sup {minus}} (N{sub 2}O){sub n=1--11}). Primarily linear clusters are observed for the smaller carbon clusters, while the spectra of the larger clusters contain contribution from cyclic anion photodetachment. Very interesting ion-solvent interactions are observed in the X{sup {minus}}(CO{sub 2})n clusters. The transition state regions for several bimolecular chemical reactions have also been investigated by photodetachment of a negative ion precursor possessing a geometry similar to that of the transition state species. These spectra show features which are assigned to motions of the unstable neutral complex existing between reactants and products.

  2. Study of radicals, clusters and transition state species by anion photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, Don Wesley [Univ. of California, Berkeley, CA (United States)

    1994-08-01

    Free radicals, elemental and van der Waals clusters and transition state species for bimolecular chemical reactions are investigated using anion photoelectron spectroscopy. Several low-lying electronic states of ozone have been identified via photoelectron spectroscopy of O3-. A characterization of these states is important to models for atmospheric ozone reaction kinetics. The fluoroformyloxyl radical, FCO2, has been investigated, providing vibrational frequencies and energies for two electronic states. The technique has also been employed to make the first direct observation and characterization of the NNO2 molecule. Several electronic states are observed for this species which is believed to play a role as a reactive intermediate in the N + NO2 reaction. The experimental results for all three of these radicals are supplemented by ab initio investigations of their molecular properties. The clusters investigations include studies of elemental carbon clusters (C2- - C11-), and van der Waals clusters (X-(CO2)n, X = I, Br, Cl; n {le} 13 and I- (N2O)n=1--11). Primarily linear clusters are observed for the smaller carbon clusters, while the spectra of the larger clusters contain contribution from cyclic anion photodetachment. Very interesting ion-solvent interactions are observed in the X-(CO2)n clusters. The transition state regions for several bimolecular chemical reactions have also been investigated by photodetachment of a negative ion precursor possessing a geometry similar to that of the transition state species. These spectra show features which are assigned to motions of the unstable neutral complex existing between reactants and products.

  3. Vinylidene: a very shallow minimum on the C2H2 potential energy surface

    Energy Technology Data Exchange (ETDEWEB)

    Osamura, Yoshihiro [Univ. of Texas, Austin, TX (United States); Schaefer, III, Henry F. [Univ. of Texas, Austin, TX (United States); Gray, Stephen K. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Miller, William H. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

    1981-04-01

    The potential energy surface for the singlet vinylidene → acetylene rearrangement has been investigated in this study by using nonempirical molecular electronic structure theory. A double-ζ plus polarization basis set was used in conjunction with configuration interaction (CI) including single and double excitations, a total of 13,861 configurations. Newly developed analytic CI gradient techniques were used to locate precisely the vinylidene and acetylene minima and the transition state connecting them. Single point calculations were carried out with a larger triple-ζ plus polarization basis. The classical barrier height is calculated to be 6.4 kcal, or 5.4 kcal after correction for the effects of higher excitations, and our best estimate of the true classical barrier is 4 kcal. Harmonic vibrational analyses were carried out about each of the three stationary points, and zero-point energy effects lower the effective barrier by 1.8 kcal. Even for energies below this, however, tunneling through the barrier is found to be extremely rapid; for instance, with no vibrational excitation energy (above its zero point energy) the lifetime of vinylidene with respect to rearrangement to acetylene is calculated to be only ~ 10-9 s, and with 2 kcal of excitation energy this decreases to ~ 10-12 s. In addition, these predictions appear to be consistent with the experimental findings of Skell (1972) and Steinfeld (1980).

  4. Study of Surface Cell Madelung Constant and Surface Free Energy of Nanosized Crystal Grain

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-Jia; WANG Tian-Min; CUI Min

    2005-01-01

    Surface cell Madelung constant is firstly defined in calculating surface free energy of nanosized crystal grains, which explains the physical performance of small crystals and may be great benefit to make surface analysis and study dynamics of crystal nucleus growth. A new ap- proximative expression of surface energy and relevant thermodynamic data was used in this cal- culation. A new formula and computing method for calculating the Madelung constant α of any complex crystals is proposed, and surface free energies and surface electrostatic energies of nano- sized crystal grains as well as Madelung constant of some complex crystals are theoretically cal- culated in this paper. The surface free energy of nanosized crystal grain TiO2 and surface elec- trostatic energy(absolute value) of nanosized crystal grain α-Al2O3 are found to be the biggest among other crystal grains.

  5. Study of surface cell Madelung constant and surface free energy of nanosized crystal grain

    Institute of Scientific and Technical Information of China (English)

    Zhang Wei-Jia; Wang Tian-Min; Rong Ai-Lun; Cui Min

    2006-01-01

    Surface cell Madelung constant is firstly defined for calculating the surface free energy of nanosized crystal grains,which explains the physical performance of small crystals and may be greatly beneficial to the analysis of surface states and the study of the dynamics of crystal nucleation and growth.A new approximative expression of the surface energy and relevant thermodynamic data are used in this calculation.New formula and computing method for calculating the Madelung constant α of any complex crystals are proposed,and the surface free energies and surface electrostatic energies of nanosized crystal grains and the Madelung constant of some complex crystals are theoretically calculated in this paper.The surface free energy of nanosized-crystal-grain TiO2 and the surface electrostatic energy (absolute value) of nanosized-crystal-grain α-A12O3 are found to be the biggest among all the crystal grains including those of other species.

  6. Metastability of the Nonlinear Wave Equation: Insights from Transition State Theory

    Science.gov (United States)

    Newhall, Katherine A.; Vanden-Eijnden, Eric

    2017-06-01

    This paper is concerned with the longtime dynamics of the nonlinear wave equation in one-space dimension, u_{tt} - κ ^2 u_{xx} +V'(u) =0 \\quad x\\in [0,1] where κ >0 is a parameter and V( u) is a potential bounded from below and growing at least like u^2 as |u|→ ∞. Infinite energy solutions of this equation preserve a natural Gibbsian invariant measure, and when the potential is double-welled, for example when V(u) = 1/4 (1-u^2)^2, there is a regime such that two small disjoint sets in the system's phase-space concentrate most of the mass of this measure. This suggests that the solutions to the nonlinear wave equation can be metastable over these sets, in the sense that they spend long periods of time in these sets and only rarely transition between them. Here, we quantify this phenomenon by calculating exactly via transition state theory (TST) the mean frequency at which the solutions of the nonlinear wave equation with initial conditions drawn from its invariant measure cross a dividing surface lying in between the metastable sets. We also investigate numerically how the mean TST frequency compares to the rate at which a typical solution crosses this dividing surface. These numerical results suggest that the dynamics of the nonlinear wave equation is ergodic and rapidly mixing with respect to the Gibbs invariant measure when the parameter κ in small enough. In this case, successive transitions between the two regions are roughly uncorrelated and their dynamics can be coarse-grained to jumps in a two-state Markov chain whose rate can be deduced from the mean TST frequency. This is a regime in which the dynamics of the nonlinear wave equation displays a metastable behavior that is not fundamentally different from that observed in its stochastic counterpart in which random noise and damping terms are added to the equation. For larger κ , however, the dynamics either stops being ergodic, or its mixing time becomes larger than the inverse of the TST frequency

  7. Metastability of the Nonlinear Wave Equation: Insights from Transition State Theory

    Science.gov (United States)

    Newhall, Katherine A.; Vanden-Eijnden, Eric

    2017-01-01

    This paper is concerned with the longtime dynamics of the nonlinear wave equation in one-space dimension, u_{tt} - κ^2 u_{xx} +V'(u) =0 quad xin [0,1] where κ >0 is a parameter and V(u) is a potential bounded from below and growing at least like u^2 as |u|→ ∞. Infinite energy solutions of this equation preserve a natural Gibbsian invariant measure, and when the potential is double-welled, for example when V(u) = 1/4 (1-u^2)^2 , there is a regime such that two small disjoint sets in the system's phase-space concentrate most of the mass of this measure. This suggests that the solutions to the nonlinear wave equation can be metastable over these sets, in the sense that they spend long periods of time in these sets and only rarely transition between them. Here, we quantify this phenomenon by calculating exactly via transition state theory (TST) the mean frequency at which the solutions of the nonlinear wave equation with initial conditions drawn from its invariant measure cross a dividing surface lying in between the metastable sets. We also investigate numerically how the mean TST frequency compares to the rate at which a typical solution crosses this dividing surface. These numerical results suggest that the dynamics of the nonlinear wave equation is ergodic and rapidly mixing with respect to the Gibbs invariant measure when the parameter κ in small enough. In this case, successive transitions between the two regions are roughly uncorrelated and their dynamics can be coarse-grained to jumps in a two-state Markov chain whose rate can be deduced from the mean TST frequency. This is a regime in which the dynamics of the nonlinear wave equation displays a metastable behavior that is not fundamentally different from that observed in its stochastic counterpart in which random noise and damping terms are added to the equation. For larger κ, however, the dynamics either stops being ergodic, or its mixing time becomes larger than the inverse of the TST frequency

  8. Bond-Energy and Surface-Energy Calculations in Metals

    Science.gov (United States)

    Eberhart, James G.; Horner, Steve

    2010-01-01

    A simple technique appropriate for introductory materials science courses is outlined for the calculation of bond energies in metals from lattice energies. The approach is applied to body-centered cubic (bcc), face-centered cubic (fcc), and hexagonal-closest-packed (hcp) metals. The strength of these bonds is tabulated for a variety metals and is…

  9. Surface free energy of copper-zinc alloy for energy-saving of boiler

    Institute of Scientific and Technical Information of China (English)

    WANG Man; LIANG Jinsheng; TANG Qingguo; MING Xing; MENG Junping; DING Yan

    2006-01-01

    Cu-Zn, Cu-Zn-Sn, Cu-Zn-Ni alloys were melted by vacuum smelter. The effect factors to the surface free energy of the alloys such as chemical composition, crystal structure and surface crystal lattice distortion etc. were investigated by OCA30 automatic contact angle test instrument, metallography microscope and XRD instrument etc. Results suggests: adding alloy element to Cu may increase its surface free energy, and the more kinds of alloy elements are added, the more surface free energy increases; the alloy element Sn an increase the surface free energy of Cu-Zn alloy; Cu-Zn alloy with fir-tree crystal structure, great phase discrepancy and obvious composition aliquation has greater surface free energy; Cu-Zn alloy with compounds and serious surface crystal lattice distortion has greater surface free energy.

  10. Evaluation of wettability and surface energy of native Nitinol surfaces in relation to hemocompatibility

    Energy Technology Data Exchange (ETDEWEB)

    Shabalovskaya, Svetlana A. [Ames Laboratory-DOE, Iowa State University, Ames, IA 50011 (United States); Institute of Materials Science and Technology, Friedrich-Schiller University, Loebdergraben 32, 07743 Jena (Germany); Siegismund, Daniel [Institute of Materials Science and Technology, Friedrich-Schiller University, Loebdergraben 32, 07743 Jena (Germany); Department of Bioinformatics, Friedrich-Schiller University, Ernst-Abbe-Platz 2, 07743 Jena (Germany); Heurich, Erik [Institute of Materials Science and Technology, Friedrich-Schiller University, Loebdergraben 32, 07743 Jena (Germany); Rettenmayr, Markus, E-mail: M.Rettenmayr@uni-jena.de [Institute of Materials Science and Technology, Friedrich-Schiller University, Loebdergraben 32, 07743 Jena (Germany)

    2013-01-01

    In the present study the dependence of Nitinol contact angles and surface energy on surface treatment is explored in order to better understand the material hemocompatibility that was evaluated in our previous studies. It is found that in the group of surfaces: (1) mechanically polished, (2) additionally heat treated, (3) chemically etched, and (4) additionally boiled in water, and (5) further heat treated, the contact angle could vary in the 50 Degree-Sign -80 Degree-Sign hydrophobic range and the total surface free energy in the 34-53 mN/m range. The polar surface energy, varying from 5 to 29 mN/m, constitutes a decisive contribution to the total energy change, and it seems to be a direct function of the Nitinol surface chemistry. Based on the complex analysis of surface energy together with the earlier results on electrochemistry and hemocompatibility it is concluded that the alteration of the polar component of surface energy and thrombogenicity is due to changes of the electron-acceptor/electron-donor character of native Nitinol surfaces during surface treatments. - Highlights: Black-Right-Pointing-Pointer Wettability experiments on differently pretreated Nitinol surfaces provide new information about hemocompatibility. Black-Right-Pointing-Pointer Protein adsorption, platelet activation and the polar surface energy of the different surfaces are correlated. Black-Right-Pointing-Pointer Specifically designed implant surfaces for the respective application within the human body should be chosen.

  11. Finding the transition state of quasi-barrierless reactions by a growing string method for newton trajectories: application to the dissociation of methylenecyclopropene and cyclopropane.

    Science.gov (United States)

    Quapp, Wolfgang; Kraka, Elfi; Cremer, Dieter

    2007-11-08

    A method for finding a transition state (TS) between a reactant minimum and a quasi-flat, high dissociation plateau on the potential energy surface is described. The method is based on the search of a growing string (GS) along reaction pathways defined by different Newton trajectories (NT). Searches with the GS-NT method always make it possible to identify the TS region because monotonically increasing NTs cross at the TS or, if not monotonically increasing, possess turning points that are located in the TS region. The GS-NT method is applied to quasi-barrierless and truly barrierless chemical reactions. Examples are the dissociation of methylenecyclopropene to acetylene and vinylidene, for which a small barrier far out in the exit channel is found, and the cycloaddition of singlet methylene and ethene, which is barrierless for a broad reaction channel with Cs-symmetry reminiscent of a mountain cirque formed by a glacier.

  12. Modeling of a nanoscale flexoelectric energy harvester with surface effects

    Science.gov (United States)

    Yan, Zhi

    2017-04-01

    This work presents the modeling of a beam energy harvester scavenging energy from ambient vibration based on the phenomenon of flexoelectricity. By considering surface elasticity, residual surface stress, surface piezoelectricity and bulk flexoelectricity, a modified Euler-Bernoulli beam model for the energy harvester is developed. After deriving the requisite energy expressions, the extended Hamilton's principle and the assumed-modes method are employed to obtain the discrete electromechanical Euler-Lagrange's equations. Then, the expressions of the steady-state electromechanical responses are given for harmonic base excitation. Numerical simulations are conducted to show the output voltage and the output power of the flexoelectric energy harvesters with different materials and sizes. Particular emphasis is given to the surface effects on the performance of the energy harvesters. It is found that the surface effects are sensitive to the beam geometries and the surface material constants, and the effect of residual surface stress is more significant than that of the surface elasticity and the surface piezoelectricity. The axial deformation of the beam is also considered in the model to account for the electromechanical coupling due to piezoelectricity, and results indicate that piezoelectricity will diminish the output electrical quantities for the case investigated. This work could lead to the development of flexoelectric energy harvesters that can make the micro- and nanoscale sensor systems autonomous.

  13. Physiologic Measures of Animal Stress during Transitional States of Consciousness

    Directory of Open Access Journals (Sweden)

    Robert E. Meyer

    2015-08-01

    Full Text Available Determination of the humaneness of methods used to produce unconsciousness in animals, whether for anesthesia, euthanasia, humane slaughter, or depopulation, relies on our ability to assess stress, pain, and consciousness within the contexts of method and application. Determining the subjective experience of animals during transitional states of consciousness, however, can be quite difficult; further, loss of consciousness with different agents or methods may occur at substantially different rates. Stress and distress may manifest behaviorally (e.g., overt escape behaviors, approach-avoidance preferences [aversion] or physiologically (e.g., movement, vocalization, changes in electroencephalographic activity, heart rate, sympathetic nervous system [SNS] activity, hypothalamic-pituitary axis [HPA] activity, such that a one-size-fits-all approach cannot be easily applied to evaluate methods or determine specific species applications. The purpose of this review is to discuss methods of evaluating stress in animals using physiologic methods, with emphasis on the transition between the conscious and unconscious states.

  14. Automated Transition State Theory Calculations for High-Throughput Kinetics.

    Science.gov (United States)

    Bhoorasingh, Pierre L; Slakman, Belinda L; Seyedzadeh Khanshan, Fariba; Cain, Jason Y; West, Richard Henry

    2017-08-18

    A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and improve the accuracy of predictive kinetic models, we have developed a high-throughput, fully automated, reaction rate calculation method, AutoTST. The algorithm integrates automated saddle-point geometry search methods and a canonical transition state theory kinetics calculator. The automatically calculated reaction rates compare favorably to existing estimated rates. Comparison against high level theoretical calculations show the new automated method performs better than rate estimates when the estimate is made by a poor analogy. The method will improve by accounting for internal rotor contributions and by improving methods to determine molecular symmetry.

  15. Immigration Control in Transit States: The Case of Turkey

    Directory of Open Access Journals (Sweden)

    Zeynep Sahin Mencutek

    2016-02-01

    Full Text Available Transit countries exhibit many similarities with respect to state-led anti-transit and more restrictive actions toward contemporary transit migration flows. This paper examines the changes after 1990s in state concerns, behaviors, and policies regarding transit migration by taking Turkey as a case study. Which factors led to Turkey's increased attention to immigration, specifically transit migration in spite of its long history of immigration, emigration and the transit migration. Why has Turkey employed restrictive policies and projects to regularize immigration since 1993? How can we explain the anti-transit immigration projects in Turkey? I argue that two driving forces can explain the restrictive policies of Turkey as a transit state. First, Turkey attempts to reconfigure its state authority in different forms to respond to the challenges of irregular migration through immigration control. Second, the Turkish state`s concern is based upon the externalization/adoption of European Union's immigration control policies.

  16. Immigration Control in Transit States: The Case of Turkey

    Directory of Open Access Journals (Sweden)

    Zeynep Sahin-Mencütek

    2012-05-01

    Full Text Available Transit countries exhibit many similarities with respect to state-led anti-transit and more restrictive actions toward contemporary transit migration flows. This paper examines the changes after 1990s in state concerns, behaviors, and policies regarding transit migration by taking Turkey as a case study. Which factors led to Turkey’s increased attention to immigration, specifically transit migration in spite of its long history of immigration, emigration and the transit migration. Why has Turkey employed restrictive policies and projects to regularize immigration since 1993? How can we explain the anti-transit immigration projects in Turkey? I argue that two driving forces can explain the restrictive policies of Turkey as a transit state. First, Turkey attempts to reconfigure its state authority in different forms to respond to the challenges of irregular migration through immigration control. Second, the Turkish state`s concern is based upon the externalization/adoption of European Union’s immigration control policies.

  17. Accurate potential energy surfaces with a DFT+U(R) approach.

    Science.gov (United States)

    Kulik, Heather J; Marzari, Nicola

    2011-11-21

    We introduce an improvement to the Hubbard U augmented density functional approach known as DFT+U that incorporates variations in the value of self-consistently calculated, linear-response U with changes in geometry. This approach overcomes the one major shortcoming of previous DFT+U studies, i.e., the use of an averaged Hubbard U when comparing energies for different points along a potential energy surface is no longer required. While DFT+U is quite successful at providing accurate descriptions of localized electrons (e.g., d or f) by correcting self-interaction errors of standard exchange correlation functionals, we show several diatomic molecule examples where this position-dependent DFT+U(R) provides a significant two- to four-fold improvement over DFT+U predictions, when compared to accurate correlated quantum chemistry and experimental references. DFT+U(R) reduces errors in binding energies, frequencies, and equilibrium bond lengths by applying the linear-response, position-dependent U(R) at each configuration considered. This extension is most relevant where variations in U are large across the points being compared, as is the case with covalent diatomic molecules such as transition-metal oxides. We thus provide a tool for deciding whether a standard DFT+U approach is sufficient by determining the strength of the dependence of U on changes in coordinates. We also apply this approach to larger systems with greater degrees of freedom and demonstrate how DFT+U(R) may be applied automatically in relaxations, transition-state finding methods, and dynamics.

  18. Determination of Surface Exciton Energies by Velocity Resolved Atomic Desorption

    Energy Technology Data Exchange (ETDEWEB)

    Hess, Wayne P.; Joly, Alan G.; Beck, Kenneth M.; Sushko, Petr V.; Shluger, Alexander L.

    2004-08-20

    We have developed a new method for determining surface exciton band energies in alkali halides based on velocity-resolved atomic desorption (VRAD). Using this new method, we predict the surface exciton energies for K1, KBr, KC1, and NaC1 within +0.15 eV. Our data, combined with the available EELS data for alkali fluorides, demonstrate a universal linear correlation with the inverse inter-atomic distance in these materials. The results suggest that surface excitons exist in all alkali halides and their excitation energies can be predicted from the known bulk exciton energies and the obtained correlation plot.

  19. Transition states and modeling for Co9S8/MoS 2 catalysis

    Science.gov (United States)

    Gonzalez, Gabriel Angel

    Transition state computational studies of the sulfur removal from dibenzothiophene (DBT) molecule have herein been performed considering the Co9S8/MoS2 interface existing on unsupported Co/MoS2 catalysts. The linear synchronous transit (LST) and quadratic synchronous transit (QST) methods integrated in a density functional theory (DFT) program such as Dmol3 were used for the calculations of energy barriers of the transition states. Three different configurations present on the Co9S8/MoS2 interface have been envisaged as possible catalytic sites: sulfur-sulfur (S, S) sites, and molybdenum-sulfur (Mo, S) and molybdenum-molybdenum (Mo, Mo) edge sites. This study revealed that the (Mo, Mo) edge site is the most catalytically active site for the hydrodesulfurization (HDS) reaction followed by the (Mo, S) edge site while the (S, S) site shows almost inertness for the HDS reaction. This information allows us to propose clues to design new catalysts based on bulk Co9S8/MoS2 phases with higher efficiency by increasing the proportion of (Mo, Mo) edge sites.

  20. Curvature-dependent surface energy and implications for nanostructures

    Science.gov (United States)

    Chhapadia, P.; Mohammadi, P.; Sharma, P.

    2011-10-01

    At small length scales, several size-effects in both physical phenomena and properties can be rationalized by invoking the concept of surface energy. Conventional theoretical frameworks of surface energy, in both the mechanics and physics communities, assume curvature independence. In this work we adopt a simplified and linearized version of a theory proposed by Steigmann-Ogden to capture curvature-dependence of surface energy. Connecting the theory to atomistic calculations and the solution to an illustrative paradigmatical problem of a bent cantilever beam, we catalog the influence of curvature-dependence of surface energy on the effective elastic modulus of nanostructures. The observation in atomistic calculations that the elastic modulus of bent nanostructures is dramatically different than under tension - sometimes softer, sometimes stiffer - has been a source of puzzlement to the scientific community. We show that the corrected surface mechanics framework provides a resolution to this issue. Finally, we propose an unambiguous definition of the thickness of a crystalline surface.

  1. The roles of entropy and enthalpy in stabilizing ion-pairs at transition states in zeolite acid catalysis.

    Science.gov (United States)

    Gounder, Rajamani; Iglesia, Enrique

    2012-02-21

    Acidic zeolites are indispensable catalysts in the petrochemical industry because they select reactants and their chemical pathways based on size and shape. Voids of molecular dimensions confine reactive intermediates and transition states that mediate chemical reactions, stabilizing them by van der Waals interactions. This behavior is reminiscent of the solvation effects prevalent within enzyme pockets and has analogous consequences for catalytic specificity. Voids provide the "right fit" for certain transition states, reflected in their lower free energies, thus extending the catalytic diversity of zeolites well beyond simple size discrimination. This catalytic diversity is even more remarkable because acid strength is essentially unaffected by confinement among known crystalline aluminosilicates. In this Account, we discuss factors that determine the "right fit" for a specific chemical reaction, exploring predictive criteria that extend the prevailing discourse based on size and shape. We link the structures of reactants, transition states, and confining voids to chemical reactivity and selectivity. Confinement mediates enthalpy-entropy compromises that determine the Gibbs free energies of transition states and relevant reactants; these activation free energies determine turnover rates via transition state theory. At low temperatures (400-500 K), dimethyl ether carbonylation occurs with high specificity within small eight-membered ring (8-MR) voids in FER and MOR zeolite structures, but at undetectable rates within larger voids (MFI, BEA, FAU, and SiO(2)-Al(2)O(3)). More effective van der Waals stabilization within 8-MR voids leads to lower ion-pair enthalpies but also lower entropies; taken together, carbonylation activation free energies are lower within 8-MR voids. The "right fit" is a "tight fit" at low temperatures, a consequence of how temperature appears in the defining equation for Gibbs free energy. In contrast, entropy effects dominate in high

  2. Improving Energy Efficiency In Thermal Oil Recovery Surface Facilities

    Energy Technology Data Exchange (ETDEWEB)

    Murthy Nadella, Narayana

    2010-09-15

    Thermal oil recovery methods such as Cyclic Steam Stimulation (CSS), Steam Assisted Gravity Drainage (SAGD) and In-situ Combustion are being used for recovering heavy oil and bitumen. These processes expend energy to recover oil. The process design of the surface facilities requires optimization to improve the efficiency of oil recovery by minimizing the energy consumption per barrel of oil produced. Optimization involves minimizing external energy use by heat integration. This paper discusses the unit processes and design methodology considering thermodynamic energy requirements and heat integration methods to improve energy efficiency in the surface facilities. A design case study is presented.

  3. Using a Family of Dividing Surfaces Normal to the Minimum EnergyPath for Quantum Instanton Rate Constants

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yimin; Miller, Wlliam H.

    2006-02-22

    One of the outstanding issues in the quantum instanton (QI) theory (or any transition state-type theory) for thermal rate constants of chemical reactions is the choice of an appropriate ''dividing surface'' (DS) that separates reactants and products. (In the general version of the QI theory, there are actually two dividing surfaces involved.) This paper shows one simple and general way for choosing DS's for use in QI Theory, namely using the family of (hyper) planes normal to the minimum energy path (MEP) on the potential energy surface at various distances s along it. Here the reaction coordinate is not one of the dynamical coordinates of the system (which will in general be the Cartesian coordinates of the atoms), but rather simply a parameter which specifies the DS. It is also shown how this idea can be implemented for an N-atom system in 3d space in a way that preserves overall translational and rotational invariance. Numerical application to a simple system (the colliner H + H{sub 2} reaction) is presented to illustrate the procedure.

  4. Enhancement of surface processes with low energy ions

    Energy Technology Data Exchange (ETDEWEB)

    Chason, E.

    1995-05-01

    Continuing trends in device fabrication towards smaller feature sizes, lower thermal budgets and advanced device structures put greater emphasis on controlling the surface structure and reactivity during processing. Since the evolution of the semiconductor surface during processing is determined by the interaction of multiple surface processes, understanding how to control and modify these processes on the atomic level would enable us to exert greater control over the resulting morphology and composition. Low energy ions represent one method for bringing controlled amounts of energy to the surface to modify surface structure and kinetics. The kinetic energy deposited by the ions can break bonds and displace atoms, creating defect populations significantly in excess of the equilibrium concentration. Consequences of these non-equilibrium conditions include the enhancement of surface kinetic processes, increased surface reactivity and formation of metastable structures and compositions. These effects can be beneficial (ion enhanced mass transport can lead to surface smoothing) or they can be detrimental (residual defects can degrade electrical properties or lead to amorphization). The net results depend on a complex balance that depends on many parameters including ion mass, energy, flux and temperature. In the following section, we review progress both in our fundamental understanding of the production of low-energy ion-induced defects and in the use of low energy ions to enhance surface morphology, stimulate low temperature growth and obtain non-equilibrium structures and compositions.

  5. Towards a standardized setup for surface energy calculations

    Science.gov (United States)

    Kaminski, Jakub W.; Kratzer, Peter; Ratsch, Christian

    2017-02-01

    High-throughput design of new materials with desired electronic properties, based on screening of large collections of crystal structures organized in the from of libraries or databases require fast, widely applicable, consistent and unsupervised methods to calculate the property of interest. In this work we present an approach for the calculation of surface energies of two-dimensional periodic crystal lattices which meets all these requirements. For materials slabs which are terminated with two identical surfaces, the task of calculating the surface energy is trivial. More problematic are the cases where both terminating surfaces are different, as there is no single established method allowing for equal treatment of a wide range of surface morphologies and orientations. Our proposed approach addresses this problem. It relies on appropriately chosen capping atoms, whose bonding energy contributions are used to approximate the total energy of the surface. The choice of the capping atoms is governed by a set of simple guidelines that are applicable for surfaces with different terminations. We present the results for different semiconductor materials and show that our approach leads to surface energies with errors that are below 10%, and that are as low as 2% in many cases. We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations.

  6. Potential energy surfaces of Polonium isotopes

    Science.gov (United States)

    Nerlo-Pomorska, B.; Pomorski, K.; Schmitt, C.; Bartel, J.

    2015-11-01

    The evolution of the potential energy landscape is analysed in detail for ten even-even polonium isotopes in the mass range 188\\lt A\\lt 220 as obtained within the macroscopic-microscopic approach, relying on the Lublin-Strasbourg drop model and the Yukawa-folded single-particle energies for calculating the microscopic shell and pairing corrections. A variant of the modified Funny-Hills nuclear shape parametrization is used to efficiently map possible fission paths. The approach explains the main features of the fragment partition as measured in low-energy fission along the polonium chain. The latter lies in a transitional region of the nuclear chart, and will be essential to consistently understand the evolution of fission properties from neutron-deficient mercury to heavy actinides. The ability of our method to predict fission observables over such an extended region looks promising.

  7. High level theoretical study of binding and of the potential energy surface in benzene-hydride system

    Energy Technology Data Exchange (ETDEWEB)

    Coletti, Cecilia, E-mail: ccoletti@unich.it [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy); Re, Nazzareno [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy)

    2012-04-04

    Graphical abstract: In-plane minimum geometries for benzene-H{sup -} non-covalent adducts: linear adduct (left) with the hydride ion hydrogen bonded to one aromatic hydrogen; bifurcated adduct (right), with the hydride ion hydrogen bonded to two adjacent aromatic hydrogens. Highlights: Black-Right-Pointing-Pointer Theoretical study on covalent and non-covalent binding in benzene-hydride. Black-Right-Pointing-Pointer Two non-covalent stable adducts were characterized in the in-plane geometry. Black-Right-Pointing-Pointer Significant sections of the potential energy surface were determined. Black-Right-Pointing-Pointer Formation of a very stable C{sub 6}H{sub 7}{sup -} anion upon covalent binding to carbon. - Abstract: High level ab initio calculations were performed on the interaction of the hydride anion with benzene, a system of potential interest for modelling the interactions occurring in hydrogen rich planetary atmospheres. We investigated both non-covalent and covalent binding, exploring the complete basis set limit using highly correlated MP2 and CCSD(T) levels of theory. Two non-covalent minima on the potential energy surface have been characterized, and found to correspond to moderately strong hydrogen bonding interactions. To gain further insight on the nature of binding, the total interaction energy was decomposed into its physically meaningful components and selected sections of the potential energy surface were calculated. Moreover, we found that H{sup -} can easily covalently bind to one of the carbon atoms of benzene to form a stable C{sub 6}H{sub 7}{sup -} anion, a global minimum on the potential energy surface, characterized by a puckered geometry, with a carbon atom bending out of the benzene plane. A slightly less stable planar C{sub 6}H{sub 7}{sup -} structure was also identified, corresponding to the transition state for the flipping motion of the puckered species.

  8. A hierarchy of potential energy surfaces constructed from energies and energy derivatives calculated on grids

    Science.gov (United States)

    Matito, Eduard; Toffoli, Daniele; Christiansen, Ove

    2009-04-01

    In this work we develop and test a methodology for the generation of Born-Oppenheimer potential energy surfaces (PES) for use in vibrational structure calculations. The method relies on the widely used restricted-mode-coupling expansion of the fully coupled potential surface where only up to n or less vibrational coordinates are coupled in the potential. Low-order derivatives of the energy are then used to extrapolate the higher mode-coupling potential terms; derivative information is thus used in a convenient way for the evaluation of higher mode couplings avoiding their explicit calculation on multidimensional grids. The formulation, which is a variant of the popular modified Shepard interpolation, is general for any extrapolation of (n +p)-mode-coupling terms from n-mode couplings and can be applied to the energy or any other molecular property surface for which derivative information is available. The method depends only on analytical parameter-free weight functions that satisfy important limiting conditions and control the contribution from each direction of extrapolation. The procedure has been applied on a representative set of 13 molecules, and its accuracy has been tested using only gradients and using both gradients and Hessians. The results provide evidence for the importance of higher mode couplings and illustrate the cost efficiency of the proposed approach.

  9. Calabi Energies of Extremal Toric Surfaces

    CERN Document Server

    LeBrun, Claude

    2011-01-01

    We derive a formula for the L^2 norm of the scalar curvature of any extremal Kaehler metric on a compact complex toric surface, stated purely in terms of the geometry of the corresponding moment polygon. We then describe some applications of this formula to the construction of 4-manifolds with vanishing Bach tensor.

  10. What is the Role of the Transition State in Soret and Chemical Diffusion Induced Isotopic Fractionation?

    Science.gov (United States)

    Dominguez, G.

    2013-12-01

    For over six decades, Urey's (1) statistical mechanical model of isotopic fractionation based on partition functions with quantized energy levels have enjoyed enormous success in quantitatively explaining equilibrium isotopic fractionation in a wide variety of geochemical systems For example, the interpretation of oxygen isotopic variations in carbonate systems (e.g. foraminiferas), in terms of partition functions with quantized energy levels, forms the basis for paleothermometry (2). Recent observations of isotopic fractionation from chemical and thermal (Soret) diffusion (3-7) appear to challenge our theoretical understanding of mass-transport and isotopic fractionation (8, 9). For example, a recently proposed quantum mechanical model of Soret diffusion, which correctly predicts the isotopic fractionation in thermal gradients for isotopes of Mg, Ca, Fe, Si, and possibly oxygen, was critiqued as being unphysical. First, it was argued that the zero point energies needed to explain the magnitude of isotopic fractionation in basalt melts were unrealistically high based on infrared spectra of these melts. Second, it was argued that the chemical diffusion isotopic fractionation (beta) factors expected from these zero-point energies were also unphysical (10). A recently proposed collision-momentum transfer model partially explains observed fractionation factors, although it fails miserably (by a factor of 3) to account for the isotopic fractionation of Mg isotopes (11). In this presentation, I will review recent observations and models of isotopic fractionation in geochemical melts with thermal gradients and expand upon previous work (8, 12) to show how transition state theory can simultaneously explain mass-transport induced isotopic fractionation, including kinetic, equilibrium, and Soret isotopic fractionation. I show this by providing a few example calculations of the kinetic fractionation factors (a.k.a. beta factors) expected in chemical diffusion as well as

  11. Surface technologies 2006 - Alternative energies and policy options

    Energy Technology Data Exchange (ETDEWEB)

    Rose, Lars [University of British Columbia, Vancouver (Canada). Department of Materials Engineering

    2007-12-15

    Surfaces are the immediate contact between anything in our world. Literally, every industry utilizes coatings and surface modifications in order to create surfaces tailored to specific needs, protect underlying substrates, or modify their behavior. Surface and coating technologies are essential to a large variety of different industrial sectors, including transportation, manufacturing, food and biomedical engineering, energy, resources, and materials science and technology. The present paper explains the limitations for alternative energy technologies, with a focus on fuel cell technology development and the alternative energy sector, based on the outcomes of presentations and facilitated discussion groups during a Canadian national workshop series. Options for technological improvements of alternative energy systems are presented in combination with national and international policy choices, which could positively influence research and development in the alternative energy sector. (author)

  12. OGO-6 gas-surface energy transfer experiment

    Science.gov (United States)

    Mckeown, D.; Dummer, R. S.; Bowyer, J. M., Jr.; Corbin, W. E., Jr.

    1973-01-01

    The kinetic energy flux of the upper atmosphere was analyzed using OGO-6 data. Energy transfer between 10 microwatts/sq cm and 0.1 W/sq cm was measured by short-term frequency changes of temperature-sensitive quartz crystals used in the energy transfer probe. The condition of the surfaces was continuously monitored by a quartz crystal microbalance to determine the effect surface contamination had on energy accommodation. Results are given on the computer analysis and laboratory tests performed to optimize the operation of the energy transfer probe. Data are also given on the bombardment of OGO-6 surfaces by high energy particles. The thermoelectrically-cooled quartz crystal microbalance is described in terms of its development and applications.

  13. Diabatic potential energy surfaces of H+ + CO

    Indian Academy of Sciences (India)

    F George D X; Sanjay Kumar

    2007-09-01

    Ab initio adiabatic and diabatic surfaces of the ground and the first excited electronic states have been computed for the H+ + CO system for the collinear ( = 0°) and the perpendicular ( = 90°) geometries employing the multi-reference configuration interaction method and Dunning's -VTZ basis set. Other properties such as mixing angle before coupling potential and before coupling matrix elements have also been obtained in order to provide an understanding of the coupling dynamics of inelastic and charge transfer process.

  14. Energy and water cycle over the Tibetan plateau : surface energy balance and turbulent heat fluxes

    NARCIS (Netherlands)

    Su, Zhongbo; Zhang, Ting; Ma, Yaoming; Jia, Li; Wen, Jun

    2006-01-01

    This contribution presents an overview and an outlook of studies on energy and water cycle over the Tibetan plateau with focuses on the estimation of energy balance terms and turbulent heat fluxes. On the basis of the surface energy balance calculations, we show that the phenomena of the energy imba

  15. Energy and water cycle over the Tibetan Plateau: surface energy balance and turbulent heat fluxes

    NARCIS (Netherlands)

    Su, Z.; Zhang, T.; Ma, Y.; Jia, L.; Wen, J.

    2006-01-01

    This contribution presents an overview and an outlook of studies on energy and water cycle over the Tibetan plateau with focuses on the estimation of energy balance terms and turbulent heat fluxes. On the basis of the surface energy balance calculations, we show that the phenomena of the energy imba

  16. Surface free energy for systems with integrable boundary conditions

    Energy Technology Data Exchange (ETDEWEB)

    Goehmann, Frank [Fachbereich C-Physik, Bergische Universitaet Wuppertal, 42097 Wuppertal (Germany); Bortz, Michael [Department of Theoretical Physics, Australian National University, Canberra ACT 0200 (Australia); Frahm, Holger [Institut fuer Theoretische Physik, Universitaet Hannover, 30167 Hannover (Germany)

    2005-12-16

    The surface free energy is the difference between the free energies for a system with open boundary conditions and the same system with periodic boundary conditions. We use the quantum transfer matrix formalism to express the surface free energy in the thermodynamic limit of systems with integrable boundary conditions as a matrix element of certain projection operators. Specializing to the XXZ spin-1/2 chain we introduce a novel 'finite temperature boundary operator' which characterizes the thermodynamical properties of surfaces related to integrable boundary conditions.

  17. Study on Surface Free Energy of Thermochromic Wood

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Thermochromic wood is a kind of new functional materials. It is significant for thermochromic wood development to study surface free energy. Samples of Chinese white poplar were colored using thermochromic agent though the method of ultrasonic impregnation and its surface free energy was investigated in the experiment. The results showed that the surface free energy for untreated, black-red, orange-yellow and blue thermochromic wood was 40.25, 29.85, 28.30 and 21.05 mN/m, respectively. The FTIR results show...

  18. Derivation of a true (t → 0+) quantum transition-state theory. I. Uniqueness and equivalence to ring-polymer molecular dynamics transition-state-theory.

    Science.gov (United States)

    Hele, Timothy J H; Althorpe, Stuart C

    2013-02-28

    Surprisingly, there exists a quantum flux-side time-correlation function which has a non-zero t → 0+ limit and thus yields a rigorous quantum generalization of classical transition-state theory (TST). In this Part I of two articles, we introduce the new time-correlation function and derive its t → 0+ limit. The new ingredient is a generalized Kubo transform which allows the flux and side dividing surfaces to be the same function of path-integral space. Choosing this function to be a single point gives a t → 0+ limit which is identical to an expression introduced on heuristic grounds by Wigner in 1932; however, this expression does not give positive-definite quantum statistics, causing it to fail while still in the shallow-tunnelling regime. Positive-definite quantum statistics is obtained only if the dividing surface is invariant to imaginary-time translation, in which case the t → 0+ limit is identical to ring-polymer molecular dynamics (RPMD) TST. The RPMD-TST rate is not a strict upper bound to the exact quantum rate, but is a good approximation to one if real-time coherence effects are small. Part II will show that the RPMD-TST rate is equal to the exact quantum rate in the absence of recrossing.

  19. Cohesion and coordination effects on transition metal surface energies

    Science.gov (United States)

    Ruvireta, Judit; Vega, Lorena; Viñes, Francesc

    2017-10-01

    Here we explore the accuracy of Stefan equation and broken-bond model semiempirical approaches to obtain surface energies on transition metals. Cohesive factors are accounted for either via the vaporization enthalpies, as proposed in Stefan equation, or via cohesive energies, as employed in the broken-bond model. Coordination effects are considered including the saturation degree, as suggested in Stefan equation, employing Coordination Numbers (CN), or as the ratio of broken bonds, according to the bond-cutting model, considering as well the square root dependency of the bond strength on CN. Further, generalized coordination numbers CN bar are contemplated as well, exploring a total number of 12 semiempirical formulations on the three most densely packed surfaces of 3d, 4d, and 5d Transition Metals (TMs) displaying face-centered cubic (fcc), body-centered cubic (bcc), or hexagonal close-packed (hcp) crystallographic structures. Estimates are compared to available experimental surface energies obtained extrapolated to zero temperature. Results reveal that Stefan formula cohesive and coordination dependencies are only qualitative suited, but unadvised for quantitative discussion, as surface energies are highly overestimated, favoring in addition the stability of under-coordinated surfaces. Broken-bond cohesion and coordination dependencies are a suited basis for quantitative comparison, where square-root dependencies on CN to account for bond weakening are sensibly worse. An analysis using Wulff shaped averaged surface energies suggests the employment of broken-bond model using CN to gain surface energies for TMs, likely applicable to other metals.

  20. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

    Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...... by various electronic structure methods, where part of the enzyme is represented by a force field description and the effects of the solvent are represented by a continuum model. The relative energies vary by several hundreds of kJ/mol between the transition structures, and tests showed that a large part...... of this variation is due to changes in the enzyme structure at distances more than 5 Å from the active site. There are significant differences between the results obtained by pure quantum methods and those from mixed quantum and molecular mechanics methods....

  1. Probing the transition state region in catalytic CO oxidation on Ru

    Energy Technology Data Exchange (ETDEWEB)

    Ostrom, H. [Stockholm Univ. (Sweden); Oberg, H. [Stockholm Univ. (Sweden); Xin, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); LaRue, J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Beye, M. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Dell' Angela, M. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Gladh, J. [Stockholm Univ. (Sweden); Ng, M. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Sellberg, J. A. [Stockholm Univ. (Sweden); SLAC National Accelerator Lab., Menlo Park, CA (United States); Kaya, S. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Mercurio, G. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Nordlund, D. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Hantschmann, M. [Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Hieke, F. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Kuhn, D. [Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Schlotter, W. F. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Dakovski, G. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Turner, J. J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Minitti, M. P. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Mitra, A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Moeller, S. P. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Fohlisch, A. [Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Univ. Potsdam, Potsdam (Germany); Wolf, M. [Fritz-Haber Institute of the Max-Planck-Society, Berlin (Germany); Wurth, W. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); DESY Photon Science, Hamburg (Germany); Persson, M. [The Univ. of Liverpool, Liverpool (United Kingdom); Norskov, J. K. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Abild-Pedersen, F. [Stanford Univ., Stanford, CA (United States); Ogasawara, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Pettersson, L. G. M. [Stockholm Univ. (Sweden); Nilsson, A. [Stockholm Univ. (Sweden); SLAC National Accelerator Lab., Menlo Park, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-02-12

    Femtosecond x-ray laser pulses are used to probe the CO oxidation reaction on ruthenium (Ru) initiated by an optical laser pulse. On a time scale of a few hundred femtoseconds, the optical laser pulse excites motions of CO and O on the surface, allowing the reactants to collide, and, with a transient close to a picosecond (ps), new electronic states appear in the O K-edge x-ray absorption spectrum. Density functional theory calculations indicate that these result from changes in the adsorption site and bond formation between CO and O with a distribution of OC–O bond lengths close to the transition state (TS). After 1 ps, 10% of the CO populate the TS region, which is consistent with predictions based on a quantum oscillator model.

  2. Fourth-Order Vibrational Transition State Theory and Chemical Kinetics

    Science.gov (United States)

    Stanton, John F.; Matthews, Devin A.; Gong, Justin Z.

    2015-06-01

    Second-order vibrational perturbation theory (VPT2) is an enormously successful and well-established theory for treating anharmonic effects on the vibrational levels of semi-rigid molecules. Partially as a consequence of the fact that the theory is exact for the Morse potential (which provides an appropriate qualitative model for stretching anharmonicity), VPT2 calculations for such systems with appropriate ab initio potential functions tend to give fundamental and overtone levels that fall within a handful of wavenumbers of experimentally measured positions. As a consequence, the next non-vanishing level of perturbation theory -- VPT4 -- offers only slight improvements over VPT2 and is not practical for most calculations since it requires information about force constants up through sextic. However, VPT4 (as well as VPT2) can be used for other applications such as the next vibrational correction to rotational constants (the ``gammas'') and other spectroscopic parameters. In addition, the marriage of VPT with the semi-classical transition state theory of Miller (SCTST) has recently proven to be a powerful and accurate treatment for chemical kinetics. In this talk, VPT4-based SCTST tunneling probabilities and cumulative reaction probabilities are give for the first time for selected low-dimensional model systems. The prospects for VPT4, both practical and intrinsic, will also be discussed.

  3. Transition-state theory predicts clogging at the microscale

    Science.gov (United States)

    Laar, T. Van De; Klooster, S. Ten; Schroën, K.; Sprakel, J.

    2016-06-01

    Clogging is one of the main failure mechanisms encountered in industrial processes such as membrane filtration. Our understanding of the factors that govern the build-up of fouling layers and the emergence of clogs is largely incomplete, so that prevention of clogging remains an immense and costly challenge. In this paper we use a microfluidic model combined with quantitative real-time imaging to explore the influence of pore geometry and particle interactions on suspension clogging in constrictions, two crucial factors which remain relatively unexplored. We find a distinct dependence of the clogging rate on the entrance angle to a membrane pore which we explain quantitatively by deriving a model, based on transition-state theory, which describes the effect of viscous forces on the rate with which particles accumulate at the channel walls. With the same model we can also predict the effect of the particle interaction potential on the clogging rate. In both cases we find excellent agreement between our experimental data and theory. A better understanding of these clogging mechanisms and the influence of design parameters could form a stepping stone to delay or prevent clogging by rational membrane design.

  4. Surface Immobilization of Molecular Electrocatalysts for Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Bullock, R. Morris [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, Richland WA 99352 USA; Das, Atanu K. [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, Richland WA 99352 USA; Appel, Aaron M. [Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, Richland WA 99352 USA

    2017-03-22

    Electrocatalysts are critically important for a secure energy future, as they facilitate the conversion between electrical energy and chemical energy. Molecular catalysts offer precise control of their structure, and the ability to modify the substituents to understand structure-reactivity relationships that are more difficult to achieve with heterogeneous catalysts. Molecular electrocatalysts can be immobilized on surfaces by covalent bonds or through non-covalent interactions. Advantages of surface immobilization include the need for less catalyst, avoidance of bimolecular decomposition pathways, and easier determination of catalyst lifetime. Copper-catalyzed click reactions are often used to form covalent bonds to surfaces, and pi-pi stacking of pyrene substituents appended to the ligand of a molecular complex is a frequently used method to achieve non-covalent surface immobilization. This mini-review highlights surface confinement of molecular electrocatalysts for reduction of O2, oxidation of H2O, production of H2, and reduction of CO2.

  5. Surface energy and work function of elemental metals

    DEFF Research Database (Denmark)

    Skriver, Hans Lomholt; Rosengaard, N. M.

    1992-01-01

    are in excellent agreement with a recent full-potential, all-electron, slab-supercell calculation of surface energies and work functions for the 4d metals. The present calculations explain the trend exhibited by the surface energies of the alkali, alkaline earth, divalent rare-earth, 3d, 4d, and 5d transition......We have performed an ab initio study of the surface energy and the work function for six close-packed surfaces of 40 elemental metals by means of a Green’s-function technique, based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations. The results...... and noble metals, as derived from the surface tension of liquid metals. In addition, they give work functions which agree with the limited experimental data obtained from single crystals to within 15%, and explain the smooth behavior of the experimental work functions of polycrystalline samples...

  6. An energy dispersive time resolved liquid surface reflectometer

    CERN Document Server

    Garrett, R F; King, D J; Dowling, T L; Fullagar, W

    2001-01-01

    Two designs are presented for an energy dispersive liquid surface reflectometer with time resolution in the milli-second domain. The designs utilise rotating crystal and Laue analyser optics respectively to energy analyse a pink synchrotron X-ray beam after reflection from a liquid surface. Some performance estimates are presented, along with results of a test experiment using a laboratory source and solid state detector.

  7. Ab Initio Calculations for the Surface Energy of Silver Nanoclusters

    Science.gov (United States)

    Medasani, Bharat; Vasiliev, Igor; Park, Young Ho

    2007-03-01

    We apply first principles computational methods to study the surface energy and the surface stress of silver nanoparticles. The structures, energies and lattice contractions of spherical Ag nanoclusters are calculated in the framework of density functional theory combined with the generalized gradient approximation. Our calculations predict the surface energies of Ag nanoclusters to be in the range of 1-2 J/m^2. These values are close to the bulk surface energy of silver, but are significantly lower than the recently reported value of 7.2 J/m^2 derived from the Kelvin equation for free Ag nanoparticles. From the lattice contraction and the nearest neighbor interatomic distance, we estimate the surface stress of the silver nanoclusters to be in the the range of 1-1.45 N/m. This result suggests that a liquid droplet model can be employed to evaluate the surface energy and the surface stress of Ag nanoparticles. K. K. Nanda et al., Phys. Rev. Lett. 91, 106102 (2003).

  8. Effect of milling temperatures on surface area, surface energy and cohesion of pharmaceutical powders.

    Science.gov (United States)

    Shah, Umang V; Wang, Zihua; Olusanmi, Dolapo; Narang, Ajit S; Hussain, Munir A; Tobyn, Michael J; Heng, Jerry Y Y

    2015-11-10

    Particle bulk and surface properties are influenced by the powder processing routes. This study demonstrates the effect of milling temperatures on the particle surface properties, particularly surface energy and surface area, and ultimately on powder cohesion. An active pharmaceutical ingredient (API) of industrial relevance (brivanib alaninate, BA) was used to demonstrate the effect of two different, but most commonly used milling temperatures (cryogenic vs. ambient). The surface energy of powders milled at both cryogenic and room temperatures increased with increasing milling cycles. The increase in surface energy could be related to the generation of surface amorphous regions. Cohesion for both cryogenic and room temperature milled powders was measured and found to increase with increasing milling cycles. For cryogenic milling, BA had a surface area ∼ 5× higher than the one obtained at room temperature. This was due to the brittle nature of this compound at cryogenic temperature. By decoupling average contributions of surface area and surface energy on cohesion by salinization post-milling, the average contribution of surface energy on cohesion for powders milled at room temperature was 83% and 55% at cryogenic temperature.

  9. A new (multi-reference configuration interaction) potential energy surface for H2CO and preliminary studies of roaming

    Science.gov (United States)

    Wang, Xiaohong; Houston, Paul L.; Bowman, Joel M.

    2017-03-01

    We report a new global potential energy surface (PES) for H2CO, based on precise fitting of roughly 67 000 MRCI/cc-pVTZ energies. This PES describes the global minimum, the cis- and trans-HCOH isomers, and barriers relevant to isomerization, formation of the molecular (H2+CO) and radical (H+HCO) products, and the loose so-called roaming transition-state saddle point. The key features of the PES are reviewed and compared with a previous PES, denoted by PES04, based on five local fits that are `stitched' together by switching functions (Zhang et al. 2004 J. Phys. Chem. A 108, 8980-8986 (doi:10.1021/jp048339l)). Preliminary quasi-classical trajectory calculations are performed at the total energy of 36 233 cm-1 (103 kcal mol-1), relative to the H2CO global minimum, using the new PES, with a particular focus on roaming dynamics. When compared with the results from PES04, the new PES findings show similar rotational distributions, somewhat more roaming and substantially higher H2 vibrational excitation. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

  10. Surface energy and work function of the light actinides

    DEFF Research Database (Denmark)

    Kollár, J.; Vitos, Levente; Skriver, Hans Lomholt

    1994-01-01

    We have calculated the surface energy and work function of the light actinides Fr, Ra, Ac, Th, Pa, U, Np, and Pu by means of a Green's-function technique based on the linear-muffin-tin-orbitals method within the tight-binding representation. In these calculations we apply an energy functional which...

  11. He-, Ne-, and Ar-phosgene intermolecular potential energy surfaces

    DEFF Research Database (Denmark)

    Munteanu, Cristian R.; Henriksen, Christian; Felker, Peter M.

    2013-01-01

    Using the CCSD(T) model, we evaluated the intermolecular potential energy surfaces of the He-, Ne-, and Ar-phosgene complexes. We considered a representative number of intermolecular geometries for which we calculated the corresponding interaction energies with the augmented (He complex) and double...

  12. Ultralow energy ion beam surface modification of low density polyethylene.

    Science.gov (United States)

    Shenton, Martyn J; Bradley, James W; van den Berg, Jaap A; Armour, David G; Stevens, Gary C

    2005-12-01

    Ultralow energy Ar+ and O+ ion beam irradiation of low density polyethylene has been carried out under controlled dose and monoenergetic conditions. XPS of Ar+-treated surfaces exposed to ambient atmosphere show that the bombardment of 50 eV Ar+ ions at a total dose of 10(16) cm(-2) gives rise to very reactive surfaces with oxygen incorporation at about 50% of the species present in the upper surface layer. Using pure O+ beam irradiation, comparatively low O incorporation is achieved without exposure to atmosphere (approximately 13% O in the upper surface). However, if the surface is activated by Ar+ pretreatment, then large oxygen contents can be achieved under subsequent O+ irradiation (up to 48% O). The results show that for very low energy (20 eV) oxygen ions there is a dose threshold of about 5 x 10(15) cm(-2) before surface oxygen incorporation is observed. It appears that, for both Ar+ and O+ ions in this regime, the degree of surface modification is only very weakly dependent on the ion energy. The results suggest that in the nonequilibrium plasma treatment of polymers, where the ion flux is typically 10(18) m(-2) s(-1), low energy ions (<50 eV) may be responsible for surface chemical modification.

  13. Surface energy balance of shrub vegetation in the Sahel

    NARCIS (Netherlands)

    Verhoef, A.

    1995-01-01

    Recently, the development and use of Global Circulation Models, employed for climate change prediction, has taken off. These models provide us with the current and future status of the surface, expressed by the surface energy and water balances. In order to obtain reliable

  14. DLVO interaction energies between hollow spherical particles and collector surfaces

    Science.gov (United States)

    The surface element integration technique was used to systematically study Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energies/forces between hollow spherical particles (HPs) and a planar surface or two intercepting half planes under different ionic strength conditions. The inner and outer ...

  15. PyCPR - a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures.

    Science.gov (United States)

    Gisdon, Florian J; Culka, Martin; Ullmann, G Matthias

    2016-10-01

    Conjugate peak refinement (CPR) is a powerful and robust method to search transition states on a molecular potential energy surface. Nevertheless, the method was to the best of our knowledge so far only implemented in CHARMM. In this paper, we present PyCPR, a new Python-based implementation of the CPR algorithm within the pDynamo framework. We provide a detailed description of the theory underlying our implementation and discuss the different parts of the implementation. The method is applied to two different problems. First, we illustrate the method by analyzing the gauche to anti-periplanar transition of butane using a semiempirical QM method. Second, we reanalyze the mechanism of a glycyl-radical enzyme, namely of 4-hydroxyphenylacetate decarboxylase (HPD) using QM/MM calculations. In the end, we suggest a strategy how to use our implementation of the CPR algorithm. The integration of PyCPR into the framework pDynamo allows the combination of CPR with the large variety of methods implemented in pDynamo. PyCPR can be used in combination with quantum mechanical and molecular mechanical methods (and hybrid methods) implemented directly in pDynamo, but also in combination with external programs such as ORCA using pDynamo as interface. PyCPR is distributed as free, open source software and can be downloaded from http://www.bisb.uni-bayreuth.de/index.php?page=downloads . Graphical Abstract PyCPR is a search tool for finding saddle points on the potential energy landscape of a molecular system.

  16. Energy loss in grazing proton-surface collisions

    Energy Technology Data Exchange (ETDEWEB)

    Juaristi, J.I. (Dept. Fisica de Materiales, Facultad de Quimicas, UPV/EHU, San Sebastian (Spain)); Garcia de Abajo, F.J. (Dept. Ciencias de la Computacion e Inteligencia Artificial, Facultad de Informatica, UPV/EHU, San Sebastian (Spain))

    1994-05-01

    The energy loss of fast protons, with energy E > 100 keV, specularly reflected on a solid surface with glancing angle of incidence of the order of a mrad is analysed on theoretical grounds. Two different contributions can be distinguished: (i) energy losses originating from the interaction with the valence band, accounted for through an induced force, and (ii) the excitation of electron bound states of the target atoms. The results are compared with available experimental data. (orig.)

  17. Stabilisation of liquid-air surfaces by particles of low surface energy.

    Science.gov (United States)

    Binks, Bernard P; Rocher, Anaïs

    2010-08-28

    We describe the stabilisation of liquid-air surfaces by microparticles of a low surface energy solid. By varying the surface tension of the liquid, various particle-stabilised materials from oil dispersions to air-in-oil foams to dry water can be prepared.

  18. Microscopic Calculation of IBM Parameters by Potential Energy Surface Mapping

    CERN Document Server

    Bentley, I

    2011-01-01

    A coherent state technique is used to generate an Interacting Boson Model (IBM) Hamiltonian energy surface that simulates a mean field energy surface. The method presented here has some significant advantages over previous work. Specifically, that this can be a completely predictive requiring no a priori knowledge of the IBM parameters. The technique allows for the prediction of the low lying energy spectra and electromagnetic transition rates which are of astrophysical interest. Results and comparison with experiment are included for krypton, molybdenum, palladium, cadmium, gadolinium, dysprosium and erbium nuclei.

  19. Surface Immobilization of Molecular Electrocatalysts for Energy Conversions.

    Science.gov (United States)

    Bullock, Morris; Das, Atanu K; Appel, Aaron M

    2017-02-08

    Electrocatalysts are critically important for a secure energy future, as they facilitate the conversion between electrical and chemical energy. Molecular catalysts offer precise control of structure that enables understanding of structure-reactivity relationships, which can be difficult to achieve with heterogeneous catalysts. Molecular electrocatalysts can be immobilized on surfaces by covalent bonds or through non-covalent interactions. Advantages of surface immobilization include the need for less catalyst, avoidance of bimolecular decomposition pathways, and easier determination of catalyst lifetime. This mini-review highlights surface immobilization of molecular electrocatalysts for reduction of O2, oxidation of H2O, production of H2, and reduction of CO2.

  20. Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching.

    Science.gov (United States)

    Glowacki, David R; Rodgers, W J; Shannon, Robin; Robertson, Struan H; Harvey, Jeremy N

    2017-04-28

    The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of

  1. Information Exchange via Surface Modified Resonance Energy Transfer

    CERN Document Server

    Boström, Mathias; Huang, Dan; Ninham, Barry W; Sernelius, Bo E

    2013-01-01

    The theory is presented for resonance interaction between two atoms in an excited configuration: one atom, the "receptor" of information (i.e. energy), adsorbed on a phospholipid surface and the other atom, the "emitter" of information (i.e. energy), a long distance away. The dielectric function for a specific phospholipid membrane is obtained from density functional theory calculations. We present numerical results comparing the range and magnitude of non-specific Casimir-Polder interactions with the much more long-ranged, and highly specific, resonance interaction. A study of the resonance interaction with one or both atoms adsorbed on a phospholipid membrane surface reveals a possibility to have a cross over from attraction to repulsion or from repulsion to attraction at separations between receptor and emitter atoms exceeding several hundred {\\AA}ngstr\\"oms. The energy transfer and the observed transitions in the sign of the interaction energies near surfaces provide potential new ways to start recognitio...

  2. Liquid-drop model for the surface energy of nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Nanda, Karuna Kar, E-mail: nanda@mrc.iisc.ernet.in [Materials Research Centre, Indian Institute of Science, Bangalore 560012 (India)

    2012-04-09

    Based on the liquid-drop model, we have evaluated the Tolman length and surface energy of nanoparticles for different elements and compared with other theoretical models as well as the available simulated data. The predictions of the model show good agreement with the simulated results. Like the cohesive energy and melting temperature, the size-dependency of surface energy is also shape-dependent. -- Highlights: ► Derivation of size-dependent surface energy based on a liquid-drop model. ► Evaluated the Tolman length for different elements. ► Predictions of the model show good agreement with the simulated results. ► Shape-dependent Tolman's length.

  3. The energy loss of medium-energy He+ ions backscattered from a Cu(100) surface

    NARCIS (Netherlands)

    Alkemade, P.F.A.; Turkenburg, W.C.; Weg, W.F. van der

    1987-01-01

    A model is presented for the shape of the surface peak in the energy spectrum of backscattered ions in a channeling and blocking experiment. The elastic energy loss distribution of the ions is calculated by use of Monte Carlo simulation. The inelastic energy loss distribution is calculated by use of

  4. Catalytic Efficiency Is a Function of How Rhodium(I) (5 + 2) Catalysts Accommodate a Conserved Substrate Transition State Geometry: Induced Fit Model for Explaining Transition Metal Catalysis.

    Science.gov (United States)

    Mustard, Thomas J L; Wender, Paul A; Cheong, Paul Ha-Yeon

    2015-03-06

    The origins of differential catalytic reactivities of four Rh(I) catalysts and their derivatives in the (5 + 2) cycloaddition reaction were elucidated using density functional theory. Computed free energy spans are in excellent agreement with known experimental rates. For every catalyst, the substrate geometries in the transition state remained constant (Catalytic efficiency is shown to be a function of how well the catalyst accommodates the substrate transition state geometry and electronics. This shows that the induced fit model for explaining biological catalysis may be relevant to transition metal catalysis. This could serve as a general model for understanding the origins of efficiencies of catalytic reactions.

  5. Critical evaluation of the potential energy surface of the CH3 + HO2reaction system

    Science.gov (United States)

    Faragó, E. P.; Szőri, M.; Owen, M. C.; Fittschen, C.; Viskolcz, B.

    2015-02-01

    The CH3 + HO2 reaction system was studied theoretically by a newly developed, HEAT345-(Q) method based CHEAT1 protocol and includes the combined singlet and triplet potential energy surfaces. The main simplification is based on the CCSDT(Q)/cc-pVDZ calculation which is computationally inexpensive. Despite the economic and black-box treatment of higher excitations, the results are within 0.6 kcal/mol of the highly accurate literature values. Furthermore, the CHEAT1 surpassed the popular standard composite methods such as CBS-4M, CBS-QB3, CBS-APNO, G2, G3, G3MP2B3, G4, W1U, and W1BD mainly due to their poor performance in characterizing transition states (TS). For TS structures, various standard DFT and MP2 method have also been tested against the resulting CCSD/cc-pVTZ geometry of our protocol. A fairly good agreement was only found in the cases of the B2PLYP and BHandHLYP functionals, which were able to reproduce the structures of all TS studied within a maximum absolute deviation of 7%. The complex reaction mechanism was extended by three new low lying reaction channels. These are indirect water elimination from CH3OOH resulted formaldehyde, H2 elimination yielded methylene peroxide, and methanol and reactive triplet oxygen were formed via H-shift in the third channel. CHEAT1 protocol based on HEAT345-(Q) method is a robust, general, and cheap alternative for high accurate kinetic calculations.

  6. Potential Energy Surfaces of Nitrogen Dioxide for the Ground State

    Institute of Scientific and Technical Information of China (English)

    SHAO Ju-Xiang; ZHU Zheng-He; CHENG Xin-Lu; YANG Xiang-Dong

    2007-01-01

    The potential energy function of nitrogen dioxide with the C2v symmetry in the ground state is represented using the simplified Sorbie-Murrell many-body expansion function in terms of the symmetry of NO2. Using the potential energy function, some potential energy surfaces of NO2(C2v, X2A1), such as the bond stretching contour plot for a fixed equilibrium geometry angle θ and contour for O moving around N-O (R1), in which R1 is fixed at the equilibrium bond length, are depicted. The potential energy surfaces are analysed. Moreover, the equilibrium parameters for NO2 with the C2v, Cs and D8h symmetries, such as equilibrium geometry structures and energies, are calculated by the ab initio (CBS-Q) method.

  7. Energy budget of surface waves in the global ocean

    Institute of Scientific and Technical Information of China (English)

    TENG Yong; YANG Yongzeng; QIAO Fangli; LU Jing; YIN Xunqiang

    2009-01-01

    Mechanical energy input from atmosphere and losses from wave-breaking dissipation of sea surface waves are estimated by a direct scheme. This scheme is based on the integration in the wavenumber space of the wind input and breaking dissipation source functions of the MASNUM wave model.The global amount of wind energy input, averaged in 2005, is about 57 TW, and the wave-breaking dissipation summed in deep-water is about 33 TW, over a half of the wind energy input. The residual may be dissipated by beach processes. Global distributions of the energy input and breaking dissipation concentrate in the westerlies of the Southern Hemisphere.

  8. Kinetic or Dynamic Control on a Bifurcating Potential Energy Surface? An Experimental and DFT Study of Gold-Catalyzed Ring Expansion and Spirocyclization of 2-Propargyl-β-tetrahydrocarbolines.

    Science.gov (United States)

    Zhang, Lei; Wang, Yi; Yao, Zhu-Jun; Wang, Shaozhong; Yu, Zhi-Xiang

    2015-10-21

    In classical transition state theory, a transition state is connected to its reactant(s) and product(s). Recently, chemists found that reaction pathways may bifurcate after a transition state, leading to two or more sets of products. The product distribution for such a reaction containing a bifurcating potential energy surface (bPES) is usually determined by the shape of the bPES and dynamic factors. However, if the bPES leads to two intermediates (other than two products), which then undergo further transformations to give different final products, what factors control the selectivity is still not fully examined. This missing link in transition state theory is founded in the present study. Aiming to develop new methods for the synthesis of azocinoindole derivatives, we found that 2-propargyl-β-tetrahydrocarbolines can undergo ring expansion and spirocyclization under gold catalysis. DFT study revealed that the reaction starts with the intramolecular cyclization of the gold-activated 2-propargyl-β-tetrahydrocarboline with a bPES. The cyclization intermediates can not only interconvert into each other via a [1,5]-alkenyl shift, but also undergo ring expansion (through fragmentation/protodeauration mechanism) or spirocyclization (through deprotonation/protodeauration mechanism). Detailed analysis of the complex PESs for substrates with different substituents indicated that the reaction selectivity is under dynamic control if the interconversion of the intermediates is slower than the ring expansion and spirocyclization processes. Otherwise, the chemical outcome is under typical kinetic control and determined by the relative preference of ring expansion versus spirocyclization pathways. The present study may enrich chemist's understanding of the determinants for selectivities on bPESs.

  9. Influences of tidal energy advection on the surface energy balance in a mangrove forest

    Directory of Open Access Journals (Sweden)

    J. G. Barr

    2012-08-01

    Full Text Available Mangrove forests are ecosystems susceptible to changing water levels and temperatures due to climate change as well as perturbations resulting from tropical storms. Numerical models can be used to project mangrove forest responses to regional and global environmental changes, and the reliability of these models depends on surface energy balance closure. However, for tidal ecosystems, the surface energy balance is complex because the energy transport associated with tidal activity remains poorly understood. This study aimed to quantify impacts of tidal flows on energy dynamics within a mangrove ecosystem. To address the research objective, an intensive study was conducted in a mangrove forest located along the Shark River in the Everglades National Park, FL. Forest-atmosphere energy exchanges were quantified with an eddy covariance system deployed on a flux tower. The lateral energy transport associated with tidal activity was calculated based on a coupled mass and energy balance approach. The mass balance included tidal flows and accumulation of water on the forest floor. The energy balance included temporal changes in enthalpy, resulting from tidal flows and temperature changes in the water column. By serving as a net sink or a source of available energy, tidal flows reduced the impact of high radiational loads on the mangrove forest. Including tidal energy advection in the surface energy balance improved the 30-min daytime energy closure from 73% to 82% over the study period. Also, the cumulative sum of energy output improved from 79% to 91% of energy input during the study period. Results indicated that tidal inundation provides an important mechanism for heat removal and that tidal exchange should be considered in surface energy budgets of coastal ecosystems. Results also demonstrated the importance of including tidal energy advection in mangrove biophysical models that are used for predicting ecosystem response to changing climate and

  10. Surface energies and self-assembly of block copolymers on grafted surfaces.

    Science.gov (United States)

    Trombly, David M; Pryamitsyn, Victor; Ganesan, Venkat

    2011-09-30

    We present a theoretical analysis of the self-assembly of diblock copolymers on surfaces grafted with random copolymers. Our results demonstrate that the surface energies of homopolymeric components on grafted surfaces differ from the corresponding values for self-assembled morphologies. Moreover, grafted random copolymers are shown to adapt their conformations in response to the morphology of the overlaying block copolymer film to create chemical inhomogeneities which modulate the interfacial interactions. Consequently, the surface energy differences between the different components on the grafted substrate do not serve as a useful measure to predict the stability of self-assembly of the diblock copolymer film.

  11. Sub-Facet Heterogeneity of the Urban Surface Energy Budget

    Science.gov (United States)

    Ramamurthy, P.; Bou-Zeid, E.; Smith, J. A.; Baeck, M. L.; Welty, C.

    2013-12-01

    The Princeton Urban Canopy Model (PUCM) and observational data are combined to understand the influence of urban sub-facet heterogeneity, and the associated influence of material properties, on the urban surface energy budget. This heterogeneity is related to the different surfaces and materials (asphalt, concrete, grass, black roofs, green roofs, etc.) that are typically found within one urban facet (roof, wall, and ground). Of particular interest is the role of water storage and evaporation from urban surfaces in modulating the energy budget. The PUCM is evaluated at sites of various urban densities. Subsequently, one densely-built site is selected for in-depth analysis and the model is applied, with sub-facet resolution, to simulate the water and energy budgets. Our analyses show that while all built surfaces convert most of the incoming energy into sensible rather than latent heat, sensible heat fluxes from asphalt and non-reflective rooftops are twice as high as those from concrete surfaces and light colored roofs. Another important and commonly observed characteristic of urban areas- the shift in peak time of sensible heat compared to rural areas, is shown to be mainly linked to concrete's high heat storage capacity. Our results also indicate that while evaporation from built surfaces is discontinuous and intermittent, overall, these surfaces accounted for nearly 16% of latent heat fluxes (LE) at the study site during the study period. More importantly, this contribution is mainly concentrated during the 48 hours following a rain event and thus its accurate representation is critical to our understanding of the urban surface energy budget during wet periods.

  12. Evaluation of the surface free energy of plant surfaces: toward standardizing the procedure.

    Science.gov (United States)

    Fernández, Victoria; Khayet, Mohamed

    2015-01-01

    Plant surfaces have been found to have a major chemical and physical heterogeneity and play a key protecting role against multiple stress factors. During the last decade, there is a raising interest in examining plant surface properties for the development of biomimetic materials. Contact angle measurement of different liquids is a common tool for characterizing synthetic materials, which is just beginning to be applied to plant surfaces. However, some studies performed with polymers and other materials showed that for the same surface, different surface free energy values may be obtained depending on the number and nature of the test liquids analyzed, materials' properties, and surface free energy calculation methods employed. For 3 rough and 3 rather smooth plant materials, we calculated their surface free energy using 2 or 3 test liquids and 3 different calculation methods. Regardless of the degree of surface roughness, the methods based on 2 test liquids often led to the under- or over-estimation of surface free energies as compared to the results derived from the 3-Liquids method. Given the major chemical and structural diversity of plant surfaces, it is concluded that 3 different liquids must be considered for characterizing materials of unknown physico-chemical properties, which may significantly differ in terms of polar and dispersive interactions. Since there are just few surface free energy data of plant surfaces with the aim of standardizing the calculation procedure and interpretation of the results among for instance, different species, organs, or phenological states, we suggest the use of 3 liquids and the mean surface tension values provided in this study.

  13. Zero-point Energy is Needed in Molecular Dynamics Calculations to Access the Saddle Point for H+HCN→H2CN* and cis/trans-HCNH* on a New Potential Energy Surface.

    Science.gov (United States)

    Wang, Xiaohong; Bowman, Joel M

    2013-02-12

    We calculate the probabilities for the association reactions H+HCN→H2CN* and cis/trans-HCNH*, using quasiclassical trajectory (QCT) and classical trajectory (CT) calculations, on a new global ab initio potential energy surface (PES) for H2CN including the reaction channels. The surface is a linear least-squares fit of roughly 60 000 CCSD(T)-F12b/aug-cc-pVDZ electronic energies, using a permutationally invariant basis with Morse-type variables. The reaction probabilities are obtained at a variety of collision energies and impact parameters. Large differences in the threshold energies in the two types of dynamics calculations are traced to the absence of zero-point energy in the CT calculations. We argue that the QCT threshold energy is the realistic one. In addition, trajectories find a direct pathway to trans-HCNH, even though there is no obvious transition state (TS) for this pathway. Instead the saddle point (SP) for the addition to cis-HCNH is evidently also the TS for direct formation of trans-HCNH.

  14. Phase space barriers and dividing surfaces in the absence of critical points of the potential energy: Application to roaming in ozone

    CERN Document Server

    Mauguière, Frédéric A L; Kramer, Zeb C; Carpenter, Barry K; Ezra, Gregory S; Farantos, Stavros C; Wiggins, Stephen

    2015-01-01

    We examine the phase space structures that govern reaction dynamics in the absence of critical points on the potential energy surface. We show that in the vicinity of hyperbolic invariant tori it is possible to define phase space dividing surfaces that are analogous to the dividing surfaces governing transition from reactants to products near a critical point of the potential energy surface. We investigate the problem of capture of an atom by a diatomic molecule and show that a normally hyperbolic invariant manifold exists at large atom-diatom distances, away from any critical points on the potential. This normally hyperbolic invariant manifold is the anchor for the construction of a dividing surface in phase space, which defines the outer or loose transition state governing capture dynamics. We present an algorithm for sampling an approximate capture dividing surface, and apply our methods to the recombination of the ozone molecule. We treat both 2 and 3 degree of freedom models with zero total angular momen...

  15. Surface energy budget and turbulent fluxes at Arctic terrestrial sites

    Science.gov (United States)

    Grachev, Andrey; Persson, Ola; Uttal, Taneil; Konopleva-Akish, Elena; Crepinsek, Sara; Cox, Christopher; Fairall, Christopher; Makshtas, Alexander; Repina, Irina

    2017-04-01

    Determination of the surface energy budget (SEB) and all SEB components at the air-surface interface are required in a wide variety of applications including atmosphere-land/snow simulations and validation of the surface fluxes predicted by numerical models over different spatial and temporal scales. Here, comparisons of net surface energy budgets at two Arctic sites are made using long-term near-continuous measurements of hourly averaged surface fluxes (turbulent, radiation, and soil conduction). One site, Eureka (80.0 N; Nunavut, Canada), is located in complex topography near a fjord about 200 km from the Arctic Ocean. The other site, Tiksi (71.6 N; Russian East Siberia), is located on a relatively flat coastal plain less than 1 km from the shore of Tiksi Bay, a branch of the Arctic Ocean. We first analyzed diurnal and annual cycles of basic meteorological parameters and key SEB components at these locations. Although Eureka and Tiksi are located on different continents and at different latitudes, the annual course of the surface meteorology and SEB components are qualitatively similar. Surface energy balance closure is a formulation of the conservation of energy principle. Our direct measurements of energy balance for both Arctic sites show that the sum of the turbulent sensible and latent heat fluxes and the ground (conductive) heat flux systematically underestimate the net radiation by about 25-30%. This lack of energy balance closure is a fundamental and pervasive problem in micrometeorology. We discuss a variety of factors which may be responsible for the lack of SEB closure. In particular, various storage terms (e.g., air column energy storage due to radiative and/or sensible heat flux divergence, ground heat storage above the soil flux plate, energy used in photosynthesis, canopy biomass heat storage). For example, our observations show that the photosynthesis storage term is relatively small (about 1-2% of the net radiation), but about 8-12% of the

  16. Transition state models for probing stereoinduction in Evans chiral auxiliary-based asymmetric aldol reactions.

    Science.gov (United States)

    Shinisha, C B; Sunoj, Raghavan B

    2010-09-08

    The use of chiral auxiliaries is one of the most fundamental protocols employed in asymmetric synthesis. In the present study, stereoselectivity-determining factors in a chiral auxiliary-based asymmetric aldol reaction promoted by TiCl(4) are investigated by using density functional theory methods. The aldol reaction between chiral titanium enolate [derived from Evans propionyl oxazolidinone (1a) and its variants oxazolidinethione (1b) and thiazolidinethione (1c)] and benzaldehyde is examined by using transition-state modeling. Different stereochemical possibilities for the addition of titanium enolates to aldehyde are compared. On the basis of the coordination of the carbonyl/thiocarbonyl group of the chiral auxiliary with titanium, both pathways involving nonchelated and chelated transition states (TSs) are considered. The computed relative energies of the stereoselectivity-determining C-C bond formation TSs in the nonchelated pathway, for both 1a and 1c, indicate a preference toward Evans syn aldol product. The presence of a ring carbonyl or thiocarbonyl group in the chiral auxiliary renders the formation of neutral TiCl(3)-enolate, which otherwise is energetically less favored as compared to the anionic TiCl(4)-enolate. Hence, under suitable conditions, the reaction between titanium enolate and aldehyde is expected to be viable through chelated TSs leading to the selective formation of non-Evans syn aldol product. Experimentally known high stereoselectivity toward Evans syn aldol product is effectively rationalized by using the larger energy differences between the corresponding diastereomeric TSs. In both chelated and nonchelated pathways, the attack by the less hindered face of the enolate on aldehyde through a chair-like TS with an equatorial disposition of the aldehydic substituent is identified as the preferred mode. The steric hindrance offered by the isopropyl group and the possible chelation are identified as the key reasons behind the interesting

  17. Energy loss of low energy ion N+q grazing on the Al(111) surface

    Institute of Scientific and Technical Information of China (English)

    Hu Bi-Tao; Chen Chun-Hua; Song Yu-Shou; Gu Jian-Gang

    2007-01-01

    The total energy loss of N+q ions (for v < Bohr velocity) grazing on the Al(111) has been simulated without any 'fit' parameter and compared with the experimental data. The energy loss due to the charge exchange, happening before the N+q hits the Al(111) surface, is studied. The present simulation shows that the energy loss strongly depends on the charge state of the projectile and the lattice orientation of Al(111) surface. The calculated total energy loss agrees with experimental data very well.

  18. Relative Efficiency of Surface Energy Budgets Over Different Land Covers

    Science.gov (United States)

    Yang, Jiachuan

    The partitioning of available solar energy into different fluxes at the Earth's surface is important in determining different physical processes, such as turbulent transport, subsurface hydrology, land-atmospheric interactions, etc. Direct measurements of these turbulent fluxes were carried out using eddy-covariance (EC) towers. However, the distribution of EC towers is sparse due to relatively high cost and practical difficulties in logistics and deployment. As a result, data is temporally and spatially limited and is inadequate to be used for researches at large scales, such as regional and global climate modeling. Besides field measurements, an alternative way is to estimate turbulent fluxes based on the intrinsic relations between surface energy budget components, largely through thermodynamic equilibrium. These relations, referred as relative efficiency, have been included in several models to estimate the magnitude of turbulent fluxes in surface energy budgets such as latent heat and sensible heat. In this study, three theoretical models based on the lumped heat transfer model, the linear stability analysis and the maximum entropy principle respectively, were investigated. Model predictions of relative efficiencies were compared with turbulent flux data over different land covers, viz. lake, grassland and suburban surfaces. Similar results were observed over lake and suburban surface but significant deviation is found over vegetation surface. The relative efficiency of outgoing longwave radiation is found to be orders of magnitude deviated from theoretic predictions. Meanwhile, results show that energy partitioning process is influenced by the surface water availability to a great extent. The study provides insight into what property is determining energy partitioning process over different land covers and gives suggestion for future models.

  19. An adaptive interpolation scheme for molecular potential energy surfaces

    Science.gov (United States)

    Kowalewski, Markus; Larsson, Elisabeth; Heryudono, Alfa

    2016-08-01

    The calculation of potential energy surfaces for quantum dynamics can be a time consuming task—especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm based on polyharmonic splines combined with a partition of unity approach. The adaptive node refinement allows to greatly reduce the number of sample points by employing a local error estimate. The algorithm and its scaling behavior are evaluated for a model function in 2, 3, and 4 dimensions. The developed algorithm allows for a more rapid and reliable interpolation of a potential energy surface within a given accuracy compared to the non-adaptive version.

  20. An adaptive interpolation scheme for molecular potential energy surfaces

    CERN Document Server

    Kowalewski, Markus; Heryudono, Alfa

    2016-01-01

    The calculation of potential energy surfaces for quantum dynamics can be a time consuming task -- especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm based on polyharmonic splines combined with a partition of unity approach. The adaptive node refinement allows to greatly reduce the number of sample points by employing a local error estimate. The algorithm and its scaling behavior is evaluated for a model function in 2, 3 and 4 dimensions. The developed algorithm allows for a more rapid and reliable interpolation of a potential energy surface within a given accuracy compared to the non-adaptive version.

  1. A surface-scattering model satisfying energy conservation and reciprocity

    CERN Document Server

    Sasihithlu, Karthik; Hugonin, Jean-Paul; Greffet, Jean-Jacques

    2015-01-01

    In order for surface scattering models to be accurate they must necessarily satisfy energy conservation and reciprocity principles. Roughness scattering models based on Kirchoff's approximation or perturbation theory do not satisfy these criteria in all frequency ranges. Here we present a surface scattering model based on analysis of scattering from a layer of particles on top of a substrate in the dipole approximation which satisfies both energy conservation and reciprocity and is thus accurate in all frequency ranges. The model takes into account the absorption in the substrate induced by the particles but does not take into account the near-field interactions between the particles.

  2. Locating landmarks on high-dimensional free energy surfaces.

    Science.gov (United States)

    Chen, Ming; Yu, Tang-Qing; Tuckerman, Mark E

    2015-03-17

    Coarse graining of complex systems possessing many degrees of freedom can often be a useful approach for analyzing and understanding key features of these systems in terms of just a few variables. The relevant energy landscape in a coarse-grained description is the free energy surface as a function of the coarse-grained variables, which, despite the dimensional reduction, can still be an object of high dimension. Consequently, navigating and exploring this high-dimensional free energy surface is a nontrivial task. In this paper, we use techniques from multiscale modeling, stochastic optimization, and machine learning to devise a strategy for locating minima and saddle points (termed "landmarks") on a high-dimensional free energy surface "on the fly" and without requiring prior knowledge of or an explicit form for the surface. In addition, we propose a compact graph representation of the landmarks and connections between them, and we show that the graph nodes can be subsequently analyzed and clustered based on key attributes that elucidate important properties of the system. Finally, we show that knowledge of landmark locations allows for the efficient determination of their relative free energies via enhanced sampling techniques.

  3. Engineering of surfaces for energy-related applications

    Science.gov (United States)

    Umeda, Grant Asano

    Finding solutions to today's energy challenges will be spearheaded by the development of novel materials systems. This dissertation examines the engineering of surfaces for both energy collection and energy storage. Energy collection research, such as the development of more efficient photovoltaic devices, has received much attention in recent literature, however, achieving inexpensive efficiency improvements in other parts of the photovoltaic system has not been well documented. The first part of this dissertation examines the possibility of utilizing a sol-gel approach to fabricate a single-layer abrasion-resistant antireflective coating for cover glass for solar cell arrays. By controlling the porosity of the film to reduce reflection from the substrate, and by controlling the chemistry of the sol-gel formation, we have achieved a film that is both durable and exhibits excellent antireflection properties. The second part of this dissertation examines a novel approach to the protection of lithium metal for use in secondary batteries. Current lithium-ion technologies utilize carbon anodes which have a low energy density compared to lithium metal. However, the interaction between lithium metal and commercially available non-aqueous electrolytes produces an inhomogeneous layer on the surface of the lithium which results in poor cycle life. A novel coating is presented which uses sol-gel precursors to stabilize the surface of lithium metal and results in a film that protects a lithium metal surface for over 100 cycles of stripping and plating.

  4. Free energy surfaces in the superconducting mixed state

    Science.gov (United States)

    Finnemore, D. K.; Fang, M. M.; Bansal, N. P.; Farrell, D. E.

    1989-01-01

    The free energy surface for Tl2Ba2Ca2Cu3O1O has been measured as a function of temperature and magnetic field to determine the fundamental thermodynamic properties of the mixed state. The change in free energy, G(H)-G(O), is found to be linear in temperature over a wide range indicating that the specific heat is independent of field.

  5. Calculated surface-energy anomaly in the 3d metals

    DEFF Research Database (Denmark)

    Aldén, M.; Skriver, Hans Lomholt; Mirbt, S.

    1992-01-01

    Local-spin-density theory and a Green’s-function technique based on the linear muffin-tin orbitals method have been used to calculate the surface energy of the 3d metals. The theory explains the variation of the values derived from measurements of the surface tension of liquid metals including...... the pronounced anomaly occurring between vanadium and nickel in terms of a decrease in the d contribution caused by spin polarization....

  6. Methods for the calculation of surface free energy of solids

    OpenAIRE

    M. Żenkiewicz

    2007-01-01

    Purpose: The main purpose of this paper is the analysis of the most common methods for the calculation of the surface free energy (SFE) of solids, utilising the results of the contact angle measurements. The calculation deals also with the SFE at the interface, especially that at the surface of polymers and polymeric materials. The survey has been meant to ease the understanding of physical processes occurring at the solid-liquid interface and to help to find proper measuring methods with res...

  7. Surface free energy analysis of adsorbents used for radioiodine adsorption

    Energy Technology Data Exchange (ETDEWEB)

    González-García, C.M. [Departamento de Física Aplicada, Universidad de Extremadura, Avda. Elvas s/n, 06006 Badajoz (Spain); Román, S., E-mail: sroman@unex.es [Departamento de Física Aplicada, Universidad de Extremadura, Avda. Elvas s/n, 06006 Badajoz (Spain); González, J.F.; Sabio, E. [Departamento de Física Aplicada, Universidad de Extremadura, Avda. Elvas s/n, 06006 Badajoz (Spain); Ledesma, B. [Departamento de Ingeniería Mecánica, Energética y de los Materiales, Universidad de Extremadura, Avda. Elvas s/n, 06006 Badajoz (Spain)

    2013-10-01

    In this work, the surface free energy of biomass-based activated carbons, both fresh and impregnated with triethylenediamine, has been evaluated. The contribution of Lifshitz van der Waals components was determined by the model proposed by van Oss et al. The results obtained allowed predicting the most probable configurations of the impregnant onto the carbon surface and its influence on the subsequent adsorption of radioactive methyl iodide.

  8. Theoretical exploration of the potential energy surface of the HOI → HIO isomerization reaction

    Science.gov (United States)

    Sun, Q.; Mackie, J. C.; Dlugogorski, B. Z.; Kennedy, E. M.

    2007-02-01

    The isomerization reaction HOI → HIO has been investigated using quantum mechanical techniques. The activation energy of the reaction at the CCSD(T) level of theory is 77.0 kcal/mol. Molecular parameters and relative energies of HOI, HIO, five HOI-H 2O complexes, three HIO-H 2O complexes and four transition states have been calculated by the B3LYP method. For isomerization assisted by a single water molecule, the activation energy whereby the water molecule directly facilitates proton transfer during isomerization, reduces to 48.4 kcal/mol. Where the water molecule interacts with the HOI/HIO system by forming hydrogen-bond and/or van der Waals complexes, the activation energy is not significantly reduced.

  9. Scattered surface wave energy in the seismic coda

    Science.gov (United States)

    Zeng, Y.

    2006-01-01

    One of the many important contributions that Aki has made to seismology pertains to the origin of coda waves (Aki, 1969; Aki and Chouet, 1975). In this paper, I revisit Aki's original idea of the role of scattered surface waves in the seismic coda. Based on the radiative transfer theory, I developed a new set of scattered wave energy equations by including scattered surface waves and body wave to surface wave scattering conversions. The work is an extended study of Zeng et al. (1991), Zeng (1993) and Sato (1994a) on multiple isotropic-scattering, and may shed new insight into the seismic coda wave interpretation. The scattering equations are solved numerically by first discretizing the model at regular grids and then solving the linear integral equations iteratively. The results show that scattered wave energy can be well approximated by body-wave to body wave scattering at earlier arrival times and short distances. At long distances from the source, scattered surface waves dominate scattered body waves at surface stations. Since surface waves are 2-D propagating waves, their scattered energies should in theory follow a common decay curve. The observed common decay trends on seismic coda of local earthquake recordings particular at long lapse times suggest that perhaps later seismic codas are dominated by scattered surface waves. When efficient body wave to surface wave conversion mechanisms are present in the shallow crustal layers, such as soft sediment layers, the scattered surface waves dominate the seismic coda at even early arrival times for shallow sources and at later arrival times for deeper events.

  10. Surface properties of Ti-6Al-4V alloy part I: Surface roughness and apparent surface free energy.

    Science.gov (United States)

    Yan, Yingdi; Chibowski, Emil; Szcześ, Aleksandra

    2017-01-01

    Titanium (Ti) and its alloys are the most often used implants material in dental treatment and orthopedics. Topography and wettability of its surface play important role in film formation, protein adhesion, following osseointegration and even duration of inserted implant. In this paper, we prepared Ti-6Al-4V alloy samples using different smoothing and polishing materials as well the air plasma treatment, on which contact angles of water, formamide and diiodomethane were measured. Then the apparent surface free energy was calculated using four different approaches (CAH, LWAB, O-W and Neumann's Equation of State). From LWAB approach the components of surface free energy were obtained, which shed more light on the wetting properties of samples surface. The surface roughness of the prepared samples was investigated with the help of optical profilometer and AFM. It was interesting whether the surface roughness affects the apparent surface free energy. It was found that both polar interactions the electron donor parameter of the energy and the work of water adhesion increased with decreasing roughness of the surfaces. Moreover, short time plasma treatment (1min) caused decrease in the surface hydrophilic character, while longer time (10min) treatment caused significant increase in the polar interactions and the work of water adhesion. Although Ti-6Al-4V alloy has been investigated many times, to our knowledge, so far no paper has been published in which surface roughness and changes in the surface free energy of the alloy were compared in the quantitative way in such large extent. This novel approach deliver better knowledge about the surface properties of differently smoothed and polished samples which may be helpful to facilitate cell adhesion, proliferation and mineralization. Therefore the results obtained present also potentially practical meaning.

  11. Summertime influences of tidal energy advection on the surface energy balance in a mangrove forest

    Directory of Open Access Journals (Sweden)

    J. G. Barr

    2013-01-01

    Full Text Available Mangrove forests are ecosystems susceptible to changing water levels and temperatures due to climate change as well as perturbations resulting from tropical storms. Numerical models can be used to project mangrove forest responses to regional and global environmental changes, and the reliability of these models depends on surface energy balance closure. However, for tidal ecosystems, the surface energy balance is complex because the energy transport associated with tidal activity remains poorly understood. This study aimed to quantify impacts of tidal flows on energy dynamics within a mangrove ecosystem. To address the research objective, an intensive 10-day study was conducted in a mangrove forest located along the Shark River in the Everglades National Park, FL, USA. Forest–atmosphere turbulent exchanges of energy were quantified with an eddy covariance system installed on a 30-m-tall flux tower. Energy transport associated with tidal activity was calculated based on a coupled mass and energy balance approach. The mass balance included tidal flows and accumulation of water on the forest floor. The energy balance included temporal changes in enthalpy, resulting from tidal flows and temperature changes in the water column. By serving as a net sink or a source of available energy, flood waters reduced the impact of high radiational loads on the mangrove forest. Also, the regression slope of available energy versus sink terms increased from 0.730 to 0.754 and from 0.798 to 0.857, including total enthalpy change in the water column in the surface energy balance for 30-min periods and daily daytime sums, respectively. Results indicated that tidal inundation provides an important mechanism for heat removal and that tidal exchange should be considered in surface energy budgets of coastal ecosystems. Results also demonstrated the importance of including tidal energy advection in mangrove biophysical models that are used for predicting ecosystem

  12. Fluctuations of collective coordinates and convexity theorems for energy surfaces

    CERN Document Server

    Giraud, B G; Sami, T

    2016-01-01

    Constrained energy minimizations of a many-body Hamiltonian return energy landscapes e(b) where b= representes the average value(s) of one (or several) collective operator(s), B, in an "optimized" trial state Phi_b, and e = is the average value of the Hamiltonian in this state Phi_b. It is natural to consider the uncertainty, Delta e, given that Phi_b usually belongs to a restricted set of trial states. However, we demonstrate that the uncertainty, Delta b, must also be considered, acknowledging corrections to theoretical models. We also find a link between fluctuations of collective coordinates and convexity properties of energy surfaces.

  13. Modulation of multiple photon energies by use of surface plasmons

    Science.gov (United States)

    Passian, A.; Lereu, A. L.; Arakawa, E. T.; Wig, A.; Thundat, T.; Ferrell, T. L.

    2005-01-01

    A form of optical modulation at low pulse rates is reported in the case of surface plasmons excited by 1.55-µm photons in a thin gold foil. Several visible-photon energies are shown to be pulsed by the action of the infrared pulses, the effect being maximized when each visible beam also excites surface plasmons. The infrared surface plasmons are implicated as the primary cause of thermally induced changes in the foil. The thermal effects dissipate in sufficiently small times so that operation up to the kilohertz range in pulse repetition frequency is obtained. Unlike direct photothermal phenomena, no phase change is necessary for the effect to be observed.

  14. Evaluation of surface energy and radiation balance systems for FIFE

    Science.gov (United States)

    Fritschen, Leo J.; Qian, Ping

    1988-01-01

    The energy balance and radiation balance components were determined at six sites during the First International Satellite Land Surface Climatology Project Field Experiment (FIFE) conducted south of Manhattan, Kansas during the summer of 1987. The objectives were: to determine the effect of slope and aspect, throughout a growing season, on the magnitude of the surface energy balance fluxes as determined by the Energy Balance Method (EBM); to investigate the calculation of the soil heat flux density at the surface as calculated from the heat capacity and the thermal conductivity equations; and to evaluate the performance of the Surface Energy and Radiation Balance System (SERBS). A total of 17 variables were monitored at each site. They included net, solar (up and down), total hemispherical (up and down), and diffuse radiation, soil temperature and heat flux density, air and wet bulb temperature gradients, wind speed and direction, and precipitation. A preliminary analysis of the data, for the season, indicate that variables including net radiation, air temperature, vapor pressure, and wind speed were quite similar at the sites even though the sites were as much as 16 km apart and represented four cardinal slopes and the top of a ridge.

  15. Kinetic-energy functionals studied by surface calculations

    DEFF Research Database (Denmark)

    Vitos, Levente; Skriver, Hans Lomholt; Kollár, J.

    1998-01-01

    The self-consistent jellium model of metal surfaces is used to study the accuracy of a number of semilocal kinetic-energy functionals for independent particles. It is shown that the poor accuracy exhibited by the gradient expansion approximation and most of the semiempirical functionals in the low...

  16. Surface energy, CO2 fluxes and sea ice

    CSIR Research Space (South Africa)

    Gulev, SK

    2009-09-01

    Full Text Available , there are serious concerns about the recent decline in the number of VOS observations. Closure of global and regional energy balances still cannot be achieved without adjustments to the flux fields and/or the underlying surface meteorological variables. The impact...

  17. Surface segregation energies in transition-metal alloys

    DEFF Research Database (Denmark)

    Ruban, Andrei; Skriver, Hans Lomholt; Nørskov, Jens Kehlet

    1999-01-01

    We present a database of 24 x 24 surface segregation energies of single transition metal impurities in transition-metal hosts obtained by a Green's-function linear-muffin-tin-orbitals method in conjunction with the coherent potential and atomic sphere approximations including a multipole correction...

  18. The Transition States for CO2 Capture by Substituted Ethanolamines

    NARCIS (Netherlands)

    Gangarapu, S.; Marcelis, A.T.M.; Alhamed, Y.A.; Zuilhof, H.

    2015-01-01

    Quantum chemical studies are used to understand the electronic and steric effects on the mechanisms of the reaction of substituted ethanolamines with CO2. SCS-MP2/6-311+G(2d,2p) calculations are used to obtain the activation energy barriers and reaction energies for both the carbamate and bicarbonat

  19. The Transition States for CO2 Capture by Substituted Ethanolamines

    NARCIS (Netherlands)

    Gangarapu, S.; Marcelis, A.T.M.; Alhamed, Y.A.; Zuilhof, H.

    2015-01-01

    Quantum chemical studies are used to understand the electronic and steric effects on the mechanisms of the reaction of substituted ethanolamines with CO2. SCS-MP2/6-311+G(2d,2p) calculations are used to obtain the activation energy barriers and reaction energies for both the carbamate and

  20. Rotational Energy Transfer of N2 Gas Determined Using a New Ab Initio Potential Energy Surface

    Science.gov (United States)

    Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Rotational energy transfer between two N2 molecules is a fundamental process of some importance. Exchange is expected to play a role, but its importance is somewhat uncertain. Rotational energy transfer cross sections of N2 also have applications in many other fields including modeling of aerodynamic flows, laser operations, and linewidth analysis in nonintrusive laser diagnostics. A number of N2-N2 rigid rotor potential energy surface (PES) has been reported in the literature.

  1. Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction.

    Science.gov (United States)

    Monge-Palacios, M; Rangel, C; Espinosa-Garcia, J

    2013-02-28

    A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200-2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.

  2. Surface Energy Fluxes During Arctic Freeze-Up

    Science.gov (United States)

    Persson, Ola; Blomquist, Byron; Guest, Peter; Fairall, Christopher; Stammerjohn, Sharon; Brooks, Ian; Björk, Göran; Tjernström, Michael; Inoue, Jun

    2016-04-01

    This presentation will use atmospheric and ocean mixed-layer observations from three cruises during the past two years to examine the magnitude and variability of the air-ocean energy fluxes, the sources of the variability, the impact of the fluxes on the ocean mixed-layer thermal structure, and how these surface energy fluxes impact the initial ice formation. The measurements were made during the ACSE, Mirai, and Sea State field programs, the first two obtaining measurements near the ice edge in the Laptev and Chukchi Seas in September 2014 and the last along the advancing ice edge in the Beaufort/Chukchi Sea in October 2015. These time periods include the onset of continuous ocean heat loss, the initial episodic ice formation, and the core period for southward advance of the ice. Frequent atmospheric soundings and continuous remote-sensor measurements provide the vertical kinematic and thermodynamic structure in the lower troposphere. Broadband radiometers, turbulent flux sensors, surface temperature sensors, surface characterization instruments, and basic meteorological instrumentation provide continuous measurements of all surface energy flux terms (shortwave/longwave radiation, sensible/latent turbulent heat fluxes), allowing the quantification of the total energy exchange between the ocean and the atmosphere. Furthermore, each cruise provided continuous measurements of the upper-ocean temperature and salinity and frequent CTD measurements of the ocean temperature and salinity profiles, providing estimates of upper-ocean energy evolution. Various methods for characterizing the ocean surface (open ocean, ice cover, ice thickness, wave state, etc.) allow linking energy changes with changes in ocean surface conditions. Analyses of the September and October conditions show persistent ocean heat loss after Sep. 15 because of the reduction of downwelling shortwave radiation and strong impacts of off-ice airflow on turbulent heat fluxes and downwelling longwave

  3. Communication: Fitting potential energy surfaces with fundamental invariant neural network

    Science.gov (United States)

    Shao, Kejie; Chen, Jun; Zhao, Zhiqiang; Zhang, Dong H.

    2016-08-01

    A more flexible neural network (NN) method using the fundamental invariants (FIs) as the input vector is proposed in the construction of potential energy surfaces for molecular systems involving identical atoms. Mathematically, FIs finitely generate the permutation invariant polynomial (PIP) ring. In combination with NN, fundamental invariant neural network (FI-NN) can approximate any function to arbitrary accuracy. Because FI-NN minimizes the size of input permutation invariant polynomials, it can efficiently reduce the evaluation time of potential energy, in particular for polyatomic systems. In this work, we provide the FIs for all possible molecular systems up to five atoms. Potential energy surfaces for OH3 and CH4 were constructed with FI-NN, with the accuracy confirmed by full-dimensional quantum dynamic scattering and bound state calculations.

  4. Potential energy surface of the photolysis of isocyanic acid HNCO

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The dissociation curves of the photolysis of the isocyanic acidHNCOHN+CO corresponding to the ground state (S0), the first triplet excited state (T1) and the first singlet excited state (S1) have been studied respectively at the UHF/6-311G** and CIS/6-311G** levels using ab initio method. The energy surface crossing points, S1/T1, T1/S0 and S1/S0, have been found and the characteristics of the energy minimum crossing point were given, based on which, the changes of the crossing points' geometries along the lower electronic energy surface and its end-result have been located according to the steepest descent principle. The computational result indicates that the photolysis of the isocyanic acid HNCOHN+CO has three competitive reaction channels ((A)-(C)), and from the kinetic piont of view, channel (A) is the most advantageous.

  5. Three-dimensional potential energy surface of Ar–CO

    Energy Technology Data Exchange (ETDEWEB)

    Sumiyoshi, Yoshihiro, E-mail: y-sumiyoshi@gunma-u.ac.jp [Division of Pure and Applied Science, Graduate School of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510 (Japan); Endo, Yasuki [Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

    2015-01-14

    A three-dimensional intermolecular potential energy surface of the Ar–CO complex has been determined by fitting most of the previously reported spectroscopic data, where observed transition frequencies by microwave, millimeter-wave, submillimeter-wave, and infrared spectroscopy were reproduced simultaneously within their experimental accuracies. A free rotor model Hamiltonian considering all the freedom of motions for an atom-diatom system was applied to calculate vibration-rotation energies. A three-dimensional potential energy surface obtained by ab initio calculations at the CCSD(T)-F12b/aug-cc-pV5Z level of theory was parameterized by a model function consisting of 46 parameters. They were used as initial values for the least-squares analysis of the experimental data. A total of 20 parameters were optimized to reproduce all the spectroscopic data.

  6. Nanometer polymer surface features: the influence on surface energy, protein adsorption and endothelial cell adhesion

    Science.gov (United States)

    Carpenter, Joseph; Khang, Dongwoo; Webster, Thomas J.

    2008-12-01

    Current small diameter (require an eight-week in vitro culture period prior to implantation—too long for immediate clinical bedside applications. Previous in vitro studies have shown that nanostructured poly(lactic-co-glycolic acid) (PLGA) surfaces elevated endothelial cell adhesion, proliferation, and extracellular matrix synthesis when compared to nanosmooth surfaces. Nonetheless, these studies failed to address the importance of lateral and vertical surface feature dimensionality coupled with surface free energy; nor did such studies elicit an optimum specific surface feature size for promoting endothelial cell adhesion. In this study, a series of highly ordered nanometer to submicron structured PLGA surfaces of identical chemistry were created using a technique employing polystyrene nanobeads and poly(dimethylsiloxane) (PDMS) molds. Results demonstrated increased endothelial cell adhesion on PLGA surfaces with vertical surface features of size less than 18.87 nm but greater than 0 nm due to increased surface energy and subsequently protein (fibronectin and collagen type IV) adsorption. Furthermore, this study provided evidence that the vertical dimension of nanometer surface features, rather than the lateral dimension, is largely responsible for these increases. In this manner, this study provides key design parameters that may promote vascular graft efficacy.

  7. Revisiting the global surface energy budgets with maximum-entropy-production model of surface heat fluxes

    Science.gov (United States)

    Huang, Shih-Yu; Deng, Yi; Wang, Jingfeng

    2016-10-01

    The maximum-entropy-production (MEP) model of surface heat fluxes, based on contemporary non-equilibrium thermodynamics, information theory, and atmospheric turbulence theory, is used to re-estimate the global surface heat fluxes. The MEP model predicted surface fluxes automatically balance the surface energy budgets at all time and space scales without the explicit use of near-surface temperature and moisture gradient, wind speed and surface roughness data. The new MEP-based global annual mean fluxes over the land surface, using input data of surface radiation, temperature data from National Aeronautics and Space Administration-Clouds and the Earth's Radiant Energy System (NASA CERES) supplemented by surface specific humidity data from the Modern-Era Retrospective Analysis for Research and Applications (MERRA), agree closely with previous estimates. The new estimate of ocean evaporation, not using the MERRA reanalysis data as model inputs, is lower than previous estimates, while the new estimate of ocean sensible heat flux is higher than previously reported. The MEP model also produces the first global map of ocean surface heat flux that is not available from existing global reanalysis products.

  8. Revisiting the global surface energy budgets with maximum-entropy-production model of surface heat fluxes

    Science.gov (United States)

    Huang, Shih-Yu; Deng, Yi; Wang, Jingfeng

    2017-09-01

    The maximum-entropy-production (MEP) model of surface heat fluxes, based on contemporary non-equilibrium thermodynamics, information theory, and atmospheric turbulence theory, is used to re-estimate the global surface heat fluxes. The MEP model predicted surface fluxes automatically balance the surface energy budgets at all time and space scales without the explicit use of near-surface temperature and moisture gradient, wind speed and surface roughness data. The new MEP-based global annual mean fluxes over the land surface, using input data of surface radiation, temperature data from National Aeronautics and Space Administration-Clouds and the Earth's Radiant Energy System (NASA CERES) supplemented by surface specific humidity data from the Modern-Era Retrospective Analysis for Research and Applications (MERRA), agree closely with previous estimates. The new estimate of ocean evaporation, not using the MERRA reanalysis data as model inputs, is lower than previous estimates, while the new estimate of ocean sensible heat flux is higher than previously reported. The MEP model also produces the first global map of ocean surface heat flux that is not available from existing global reanalysis products.

  9. Comparison of surface energy fluxes with satellite-derived surface energy flux estimates from a shrub-steppe

    Energy Technology Data Exchange (ETDEWEB)

    Kirkham, Randy R. [Univ. of Washington, Seattle, WA (United States)

    1993-12-01

    This thesis relates the components of the surface energy balance (i.e., net radiation, sensible and latent heat flux densities, soil heat flow) to remotely sensed data for native vegetation in a semi-arid environment. Thematic mapper data from Landsat 4 and 5 were used to estimate net radiation, sensible heat flux (H), and vegetation amount. Several sources of ground truth were employed. They included soil water balance using the neutron thermalization method and weighing lysimeters, and the measurement of energy fluxes with the Bowen ratio energy balance (BREB) technique. Sensible and latent heat flux were measured at four sites on the U.S. Department of Energy`s Hanford Site using a weighing lysimeter and/or BREB stations. The objective was to calibrate an aerodynamic transport equation that related H to radiant surface temperature. The transport equation was then used with Landsat thermal data to generate estimates of H and compare these estimates against H values obtained with BREB/lysimeters at the time of overflight. Landsat and surface meteorologic data were used to estimate the radiation budget terms at the surface. Landsat estimates of short-wave radiation reflected from the surface correlate well with reflected radiation measured using inverted Eppley pyranometers. Correlation of net radiation estimates determined from satellite data, pyranometer, air temperature, and vapor pressure compared to net radiometer values obtained at time of overflight were excellent for a single image, but decrease for multiple images. Soil heat flux, GT, is a major component of the energy balance in arid systems and G{sub T} generally decreases as vegetation cover increases. Normalized difference vegetation index (NDVI) values generated from Landsat thermatic mapper data were representative of field observations of the presence of green vegetation, but it was not possible to determine a single relationship between NDVI and GT for all sites.

  10. Finding possible transition states of defects in silicon-carbide and alpha-iron using the dimer method

    CERN Document Server

    Gao Fei; Weber, W J; Corrales, L R; Jonsson, H

    2003-01-01

    Energetic primary recoil atoms from ion implantation or fast neutron irradiation produce isolated point defects and clusters of both vacancies and interstitials. The migration energies and mechanisms for these defects are crucial to successful multiscale modeling of microstructural evolution during ion-implantation, thermal annealing, or under irradiation over long periods of time. The dimer method is employed to search for possible transition states of interstitials and small interstitial clusters in SiC and alpha-Fe. The method uses only the first derivatives of the potential energy to find saddle points without knowledge of the final state of the transition. In SiC, the possible migration pathway for the C interstitial is found to consist of the first neighbor jump via a Si site or second neighbor jump, but the relative probability for the second neighbor jump is very low. In alpha-Fe, the possible transition states are studied as a function of interstitial cluster size, and the lowest energy barriers corr...

  11. Triangulating Nucleic Acid Conformations Using Multicolor Surface Energy Transfer.

    Science.gov (United States)

    Riskowski, Ryan A; Armstrong, Rachel E; Greenbaum, Nancy L; Strouse, Geoffrey F

    2016-02-23

    Optical ruler methods employing multiple fluorescent labels offer great potential for correlating distances among several sites, but are generally limited to interlabel distances under 10 nm and suffer from complications due to spectral overlap. Here we demonstrate a multicolor surface energy transfer (McSET) technique able to triangulate multiple points on a biopolymer, allowing for analysis of global structure in complex biomolecules. McSET couples the competitive energy transfer pathways of Förster Resonance Energy Transfer (FRET) with gold-nanoparticle mediated Surface Energy Transfer (SET) in order to correlate systematically labeled points on the structure at distances greater than 10 nm and with reduced spectral overlap. To demonstrate the McSET method, the structures of a linear B-DNA and a more complex folded RNA ribozyme were analyzed within the McSET mathematical framework. The improved multicolor optical ruler method takes advantage of the broad spectral range and distances achievable when using a gold nanoparticle as the lowest energy acceptor. The ability to report distance information simultaneously across multiple length scales, short-range (10-50 Å), mid-range (50-150 Å), and long-range (150-350 Å), distinguishes this approach from other multicolor energy transfer methods.

  12. Nano Sensing and Energy Conversion Using Surface Plasmon Resonance (SPR

    Directory of Open Access Journals (Sweden)

    Iltai (Isaac Kim

    2015-07-01

    Full Text Available Nanophotonic technique has been attracting much attention in applications of nano-bio-chemical sensing and energy conversion of solar energy harvesting and enhanced energy transfer. One approach for nano-bio-chemical sensing is surface plasmon resonance (SPR imaging, which can detect the material properties, such as density, ion concentration, temperature, and effective refractive index in high sensitivity, label-free, and real-time under ambient conditions. Recent study shows that SPR can successfully detect the concentration variation of nanofluids during evaporation-induced self-assembly process. Spoof surface plasmon resonance based on multilayer metallo-dielectric hyperbolic metamaterials demonstrate SPR dispersion control, which can be combined with SPR imaging, to characterize high refractive index materials because of its exotic optical properties. Furthermore, nano-biophotonics could enable innovative energy conversion such as the increase of absorption and emission efficiency and the perfect absorption. Localized SPR using metal nanoparticles show highly enhanced absorption in solar energy harvesting. Three-dimensional hyperbolic metamaterial cavity nanostructure shows enhanced spontaneous emission. Recently ultrathin film perfect absorber is demonstrated with the film thickness is as low as ~1/50th of the operating wavelength using epsilon-near-zero (ENZ phenomena at the wavelength close to SPR. It is expected to provide a breakthrough in sensing and energy conversion applications using the exotic optical properties based on the nanophotonic technique.

  13. Energy minimization calculations for diamond (111) surface reconstructions

    Energy Technology Data Exchange (ETDEWEB)

    Vanderbilt, D.; Louie, S.G.

    1984-08-01

    A remarkable variety of surface reconstructions occur on the (111) surfaces of the tetrahedral elements C, Si and Ge. A possible common denominator may be the occurrence of a similar 2 x 1 reconstruction on all three elemental surfaces. While clear 2 x 1 LEED patterns are observed for Si and Ge (111) surfaces, LEED cannot distinguish between a true 2 x 2 or disordered domains of 2 x 1 for the diamond (111) surface. However, the similarity of the angle-resolved photoemission (ARUPS) results for C, Si, and Ge suggests that a common 2 x 1 structure may be responsible. The 2 x 1 structure disappears upon annealing for Si and Ge but appears upon annealing for C, indicating that it may be thermodynamically stable only for C. Thus the study of the diamond 2 x 2/2 x 1 surface is of particular interest. Here, we report direct energy minimization calculations for these models. A first principles linear combination of atomic orbitals approach has been used to calculate total energies in the pseudopotential and local density (LDA) approximations. 27 refs., 3 figs., 2 tabs.

  14. Excited state potential energy surfaces and their interactions in Fe(IV)=O active sites.

    Science.gov (United States)

    Srnec, Martin; Wong, Shaun D; Solomon, Edward I

    2014-12-21

    The non-heme ferryl active sites are of significant interest for their application in biomedical and green catalysis. These sites have been shown to have an S = 1 or S = 2 ground spin state; the latter is functional in biology. Low-temperature magnetic circular dichroism (LT MCD) spectroscopy probes the nature of the excited states in these species including ligand-field (LF) states that are otherwise difficult to study by other spectroscopies. In particular, the temperature dependences of MCD features enable their unambiguous assignment and thus determination of the low-lying excited states in two prototypical S = 1 and S = 2 NHFe(IV)[double bond, length as m-dash]O complexes. Furthermore, some MCD bands exhibit vibronic structures that allow mapping of excited-state interactions and their effects on the potential energy surfaces (PESs). For the S = 2 species, there is also an unusual spectral feature in both near-infrared absorption and MCD spectra - Fano antiresonance (dip in Abs) and Fano resonance (sharp peak in MCD) that indicates the weak spin-orbit coupling of an S = 1 state with the S = 2 LF state. These experimental data are correlated with quantum-chemical calculations that are further extended to analyze the low-lying electronic states and the evolution of their multiconfigurational characters along the Fe-O PESs. These investigations show that the lowest-energy states develop oxyl Fe(III) character at distances that are relevant to the transition state (TS) for H-atom abstraction and define the frontier molecular orbitals that participate in the reactivity of S = 1 vs. S = 2 non-heme Fe(IV)[double bond, length as m-dash]O active sites. The S = 1 species has only one available channel that requires the C-H bond of a substrate to approach perpendicular to the Fe-oxo bond (the π channel). In contrast, there are three channels (one σ and two π) available for the S = 2 non-heme Fe(IV)[double bond, length as m-dash]O system allowing C-H substrate approach

  15. Theoretical Studies on CH3SiH3+H→CH3SiH2+H2 Reaction with the Variational Transitional State Theory

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    In this paper, the abstraction reaction of CH3SiH3 with H has been studied by using the "direct dynamics" method of variational transition-state theory, which is based on the information on geometries, frequencies and energies calculated by ab initio along the minimum energy path. The rate constants of the title reaction were calculated for the range of temperature 298-1700 K. The rate constants calculated match well with the experimental values.

  16. An algorithm to locate optimal bond breaking points on a potential energy surface for applications in mechanochemistry and catalysis

    Science.gov (United States)

    Bofill, Josep Maria; Ribas-Ariño, Jordi; García, Sergio Pablo; Quapp, Wolfgang

    2017-10-01

    The reaction path of a mechanically induced chemical transformation changes under stress. It is well established that the force-induced structural changes of minima and saddle points, i.e., the movement of the stationary points on the original or stress-free potential energy surface, can be described by a Newton Trajectory (NT). Given a reactive molecular system, a well-fitted pulling direction, and a sufficiently large value of the force, the minimum configuration of the reactant and the saddle point configuration of a transition state collapse at a point on the corresponding NT trajectory. This point is called barrier breakdown point or bond breaking point (BBP). The Hessian matrix at the BBP has a zero eigenvector which coincides with the gradient. It indicates which force (both in magnitude and direction) should be applied to the system to induce the reaction in a barrierless process. Within the manifold of BBPs, there exist optimal BBPs which indicate what is the optimal pulling direction and what is the minimal magnitude of the force to be applied for a given mechanochemical transformation. Since these special points are very important in the context of mechanochemistry and catalysis, it is crucial to develop efficient algorithms for their location. Here, we propose a Gauss-Newton algorithm that is based on the minimization of a positively defined function (the so-called σ -function). The behavior and efficiency of the new algorithm are shown for 2D test functions and for a real chemical example.

  17. Allylic H-Abstraction Mechanism:  The Potential Energy Surface of the Reaction of Propene with OH Radical.

    Science.gov (United States)

    Szori, Milan; Fittschen, Christa; Csizmadia, Imre G; Viskolcz, Bela

    2006-11-01

    The allylic H-atom abstraction reaction plays a more dominant role, especially at lower temperature, than addition reactions in the case of the CH2 [Formula: see text] CH-CH3 + •OH system. Different computational methods including ab initio as well as density functional methods have been used to examine allylic H-abstraction. Both the energetically less favorable direct H-abstraction and the more favorable indirect H-abstractions have been investigated. Using first principles computations, for the indirect abstraction, a stable π- or reactantlike as well as a late productlike complex were found on the potential energy surface. Based on higher level single point calculations (QCISD(T)/6-311+G(3df,2p)), a new activation enthalpy value, Δ(⧧)H° = 0.3 ± 2 kJ/mol, is suggested for the title reaction. The computed reaction enthalpy ΔrH° = -124.7 ± 2 kJ/mol is in good agreement with the experimental value. The stability of the initial π-complex was found to be ΔH°π-complex = -7.1 kJ/mol. The product complex between the transition state and the product was found with the stability of -127.2 kJ/mol.

  18. Potential energy surface of the CO{sub 2}–N{sub 2} van der Waals complex

    Energy Technology Data Exchange (ETDEWEB)

    Nasri, Sameh; Ajili, Yosra [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El Manar, Tunis (Tunisia); Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France); Jaidane, Nejm-Eddine [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El Manar, Tunis (Tunisia); Kalugina, Yulia N. [Department of Optics and Spectroscopy, Tomsk State University, 36 Lenin Ave., Tomsk 634050 (Russian Federation); Halvick, Philippe; Stoecklin, Thierry [Institut des Sciences Moléculaires, Université de Bordeaux, CNRS UMR 5255, 33405 Talence Cedex (France); Hochlaf, Majdi, E-mail: hochlaf@univ-mlv.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France)

    2015-05-07

    Four-dimensional potential energy surface (4D-PES) of the atmospherically relevant CO{sub 2}–N{sub 2} van der Waals complex is generated using the explicitly correlated coupled cluster with single, double, and perturbative triple excitation (CCSD(T)-F12) method in conjunction with the augmented correlation consistent triple zeta (aug-cc-pVTZ) basis set. This 4D-PES is mapped along the intermonomer coordinates. An analytic fit of this 4D-PES is performed. Our extensive computations confirm that the most stable form corresponds to a T-shape structure where the nitrogen molecule points towards the carbon atom of CO{sub 2}. In addition, we located a second isomer and two transition states in the ground state PES of CO{sub 2}–N{sub 2}. All of them lay below the CO{sub 2} + N{sub 2} dissociation limit. This 4D-PES is flat and strongly anisotropic along the intermonomer coordinates. This results in the possibility of the occurrence of large amplitude motions within the complex, such as the inversion of N{sub 2}, as suggested in the recent spectroscopic experiments. Finally, we show that the experimentally established deviations from the C{sub 2v} structure at equilibrium for the most stable isomer are due to the zero-point out-of-plane vibration correction.

  19. Harvesting electrostatic energy using super-hydrophobic surfaces

    Science.gov (United States)

    Pociecha, Dominik; Zylka, Pawel

    2016-11-01

    Almost all environments are now being extensively populated by miniaturized, nano-powered electronic sensor devices communicated together through wireless sensor networks building Internet of Things (IoT). Various energy harvesting techniques are being more and more frequently proposed for battery-less powering of such remote, unattended, implantable or wearable sensors or other low-power electronic gadgets. Energy harvesting relays on extracting energy from the ambient sources readily accessible at the sensor location and converting it into electrical power. The paper exploits possibility of generating electric energy safely accessible for nano-power electronics using tribo-electric and electrostatic induction phenomena displayed at super-hydrophobic surfaces impinged by water droplets. Mechanism of such interaction is discussed and illustrated by experimental results.

  20. ANISOTROPY OF (1× 1)-SURFACE FREE ENERGIES OF CRYSTALS

    Institute of Scientific and Technical Information of China (English)

    Z.M.Yu; A. Flodstrom

    2001-01-01

    The surface free energy (SFE) of (1× 1)-surfaces of crystals, without reconstructionand adsorption, is calculated using a bond-broken mode. In the mode, the potentialenergy of the crystals is treated as a sum of the energies of the bonds connectingpair-wise atoms (u-bonds). The SFE is calculated based on the bond energy and thearea density of dangling bonds which depends on the structure of the surface. Theresults provide a general expression for the SFE in terms of the bond energy (E)and the bond length (do) of the crystal and Miller indices hkl. The anisotropy ofthe SFE is therefore completely determined with the expression. As the examples,considering the nearest-neighboring bonding, the SFEs of sc, fcc, bcc and cth (cubictetrahedral) crystals are discussed, respectively. Wulff plots of bcc and fcc crystalsare then obtained. The equilibrium forms (EFs) of these crystals ave consequentlygot from their Wulff plots, respectively. It is found that the EFs of bcc and fcc arerespectively the rhombic dodecahedron and the truncated-octahedron that are their firstBrillouin zones, respectively.

  1. A Novel Energy efficient Surface water Wireless Sensor Network Algorithm

    Directory of Open Access Journals (Sweden)

    B.Meenakshi

    2012-07-01

    Full Text Available Maintaining the energy of sensors in Wireless Sensor Network (WSN is important in critical applications. It has been a challenge to design wireless sensor networks to enable applications for oceanographicdata collection, pollution monitoring, offshore exploration, disaster prevention, assisted navigation and tactical surveillance applications. WSN consists of sensor nodes which sense the physical parameters such as temperature, humidity, pressure and light etc and send them to a fusion center namely Base Station (BS from where one can get the value of physical parameters at any time. Requirement of monitoring the environment might be anywhere, like middle of the sea or under the earth where man cannot go often to recharge the batterieswhich supplies the sensing device, transceiver and memory unit in the sensor node. So the usage of the battery power must be judicious in WSN. Earlier attempts have been made to prolong the network lifetime, but still it is a challenging task. In this paper we propose a Novel Energy efficient Surface water Wireless Sensor Network Algorithm (NES-WSN to optimize the energy consumption by WSN. The present work concentrates on energy saving of sensor nodes when they are deployed in the surface of the sea water. Whenever the sea surface temperature increases there will be a power loss which is reduced by clustering the nodes and by transferring data through multihop routing. Experimental results show that due to increase in temperature there is a definite power loss and it can be minimized by using NES-WSN algorithm definitely.

  2. Predicting pressure-dependent unimolecular rate constants using variational transition state theory with multidimensional tunneling combined with system-specific quantum RRK theory: a definitive test for fluoroform dissociation.

    Science.gov (United States)

    Bao, Junwei Lucas; Zhang, Xin; Truhlar, Donald G

    2016-06-22

    Understanding the falloff in rate constants of gas-phase unimolecular reaction rate constants as the pressure is lowered is a fundamental problem in chemical kinetics, with practical importance for combustion, atmospheric chemistry, and essentially all gas-phase reaction mechanisms. In the present work, we use our recently developed system-specific quantum RRK theory, calibrated by canonical variational transition state theory with small-curvature tunneling, combined with the Lindemann-Hinshelwood mechanism, to model the dissociation reaction of fluoroform (CHF3), which provides a definitive test for falloff modeling. Our predicted pressure-dependent thermal rate constants are in excellent agreement with experimental values over a wide range of pressures and temperatures. The present validation of our methodology, which is able to include variational transition state effects, multidimensional tunneling based on the directly calculated potential energy surface along the tunneling path, and torsional and other vibrational anharmonicity, together with state-of-the-art reaction-path-based direct dynamics calculations, is important because the method is less empirical than models routinely used for generating full mechanisms, while also being simpler in key respects than full master equation treatments and the full reduced falloff curve and modified strong collision methods of Troe.

  3. Evidence for a transition state model compound of in-plane vinylic SN2 reaction.

    Science.gov (United States)

    Yamaguchi, Torahiko; Yamamoto, Yohsuke; Fujiwara, Yoshihisa; Tanimoto, Yoshifumi

    2005-06-23

    [reaction: see text] To isolate a transition state model compound of an in-plane vinylic S(N)2 reaction, vinyl bromide 6 bearing a newly synthesized tridentate ligand derived from 1,8-dimethoxythioxanthen-9-one (5) was prepared as a precursor. Although irradiation of 6 gave demethylated benzofuran 12, a transient broad peak which indicates formation of the desired transition state model compound was observed in the laser flash photolytic study.

  4. Monte Carlo simulations on atropisomerism of thienotriazolodiazepines applicable to slow transition phenomena using potential energy surfaces by ab initio molecular orbital calculations.

    Science.gov (United States)

    Morikami, Kenji; Itezono, Yoshiko; Nishimoto, Masahiro; Ohta, Masateru

    2014-01-01

    Compounds with a medium-sized flexible ring often show atropisomerism that is caused by the high-energy barriers between long-lived conformers that can be isolated and often have different biological properties to each other. In this study, the frequency of the transition between the two stable conformers, aS and aR, of thienotriazolodiazepine compounds with flexible 7-membered rings was estimated computationally by Monte Carlo (MC) simulations and validated experimentally by NMR experiments. To estimate the energy barriers for transitions as precisely as possible, the potential energy (PE) surfaces used in the MC simulations were calculated by molecular orbital (MO) methods. To accomplish the MC simulations with the MO-based PE surfaces in a practical central processing unit (CPU) time, the MO-based PE of each conformer was pre-calculated and stored before the MC simulations, and then only referred to during the MC simulations. The activation energies for transitions calculated by the MC simulations agreed well with the experimental ΔG determined by the NMR experiments. The analysis of the transition trajectories of the MC simulations revealed that the transition occurred not only through the transition states, but also through many different transition paths. Our computational methods gave us quantitative estimates of atropisomerism of the thienotriazolodiazepine compounds in a practical period of time, and the method could be applicable for other slow-dynamics phenomena that cannot be investigated by other atomistic simulations.

  5. Influence of Surface Energy Effects on Elastic Fields of a Layered Elastic Medium under Surface Loading

    Directory of Open Access Journals (Sweden)

    Supakorn Tirapat

    2017-01-01

    Full Text Available This paper presents the analysis of a layered elastic half space under the action of axisymmetric surface loading and the influence of the surface energy effects. The boundary value problems for the bulk and the surface are formulated based on classical linear elasticity and a complete Gurtin-Murdoch constitutive relation. An analytical technique using Love’s representation and the Hankel integral transform is employed to derive an integral-form solution for both displacement and stress fields. An efficient numerical quadrature is then applied to accurately evaluate all involved integrals. Selected numerical results are presented to portray the influence of various parameters on elastic fields. Numerical results indicate that the surface stress displays a significant influence on both displacement and stress fields. It is also found that the layered half space becomes stiffer with the presence of surface stresses. In addition, unlike the classical elasticity solution, size-dependent behavior of elastic fields is noted. The present analytical solutions provide fundamental understanding of the influence of surface energy on layered elastic materials. It can also be used as a benchmark solution for the development of numerical techniques such as FEM and BEM, for analysis of more complex problems involving a layered medium under the influence of surface energy effects.

  6. Surface energy budget responses to radiative forcing at Summit, Greenland

    Science.gov (United States)

    Miller, Nathaniel B.; Shupe, Matthew D.; Cox, Christopher J.; Noone, David; Persson, P. Ola G.; Steffen, Konrad

    2017-02-01

    Greenland Ice Sheet surface temperatures are controlled by an exchange of energy at the surface, which includes radiative, turbulent, and ground heat fluxes. Data collected by multiple projects are leveraged to calculate all surface energy budget (SEB) terms at Summit, Greenland, for the full annual cycle from July 2013 to June 2014 and extend to longer periods for the radiative and turbulent SEB terms. Radiative fluxes are measured directly by a suite of broadband radiometers. Turbulent sensible heat flux is estimated via the bulk aerodynamic and eddy correlation methods, and the turbulent latent heat flux is calculated via a two-level approach using measurements at 10 and 2 m. The subsurface heat flux is calculated using a string of thermistors buried in the snow pack. Extensive quality-control data processing produced a data set in which all terms of the SEB are present 75 % of the full annual cycle, despite the harsh conditions. By including a storage term for a near-surface layer, the SEB is balanced in this data set to within the aggregated uncertainties for the individual terms. November and August case studies illustrate that surface radiative forcing is driven by synoptically forced cloud characteristics, especially by low-level, liquid-bearing clouds. The annual cycle and seasonal diurnal cycles of all SEB components indicate that the non-radiative terms are anticorrelated to changes in the total radiative flux and are hence responding to cloud radiative forcing. Generally, the non-radiative SEB terms and the upwelling longwave radiation component compensate for changes in downwelling radiation, although exact partitioning of energy in the response terms varies with season and near-surface characteristics such as stability and moisture availability. Substantial surface warming from low-level clouds typically leads to a change from a very stable to a weakly stable near-surface regime with no solar radiation or from a weakly stable to neutral

  7. Surface wind energy trends near Taiwan in winter since 1871

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    2017-01-01

    Full Text Available The tropical surface wind speed in boreal winter reaches a maximum near Taiwan. This stable wind resource may be used for future clean energy development. How this surface wind energy source has changed in past 141 years is investigated using the 20th century reanalysis dataset and CMIP5 models. Our observational analysis shows that the surface wind speed experienced a weakening trend in the past 141 years (1871 - 2010. The average decreasing rate is around -1.4 m s-1 per century. The decrease is primarily attributed to the relative sea surface temperature (SST cooling in the subtropical North Pacific, which forces a large-scale low-level anti-cyclonic circulation anomaly in situ and is thus responsible for the southerly trend near Taiwan. The relative SST trend pattern is attributed mainly to the greenhouse gas effect associated with anthropogenic activities. The southerly trend near Taiwan is more pronounced in the boreal winter than in summer. Such seasonal difference is attributed to the reversed seasonal mean wind, which promotes more efficient positive feedback in the boreal winter. The CMIP5 historical run analysis reveals that climate models capture less SST warming and large-scale anti-cyclonic circulation in the subtropical North Pacific, but the simulated weakening trend of the surface wind speed near Taiwan is too small.

  8. The Global Energy Balance Archive (GEBA): A database for the worldwide measured surface energy fluxes

    Science.gov (United States)

    Wild, Martin; Ohmura, Atsumu; Schär, Christoph; Müller, Guido; Hakuba, Maria Z.; Mystakidis, Stefanos; Arsenovic, Pavle; Sanchez-Lorenzo, Arturo

    2017-02-01

    The Global Energy Balance Archive (GEBA) is a database for the worldwide measured energy fluxes at the Earth's surface. GEBA is maintained at ETH Zurich (Switzerland) and has been founded in the 1980s by Prof. Atsumu Ohmura. It has continuously been updated and currently contains around 2500 stations with 500`000 monthly mean entries of various surface energy balance components. Many of the records extend over several decades. The most widely measured quantity available in GEBA is the solar radiation incident at the Earth's surface ("global radiation"). The data sources include, in addition to the World Radiation Data Centre (WRDC) in St. Petersburg, data reports from National Weather Services, data from different research networks (BSRN, ARM, SURFRAD), data published in peer-reviewed publications and data obtained through personal communications. Different quality checks are applied to check for gross errors in the dataset. GEBA is used in various research applications, such as for the quantification of the global energy balance and its spatiotemporal variation, or for the estimation of long-term trends in the surface fluxes, which enabled the detection of multi-decadal variations in surface solar radiation, known as "global dimming" and "brightening". GEBA is further extensively used for the evaluation of climate models and satellite-derived surface flux products. On a more applied level, GEBA provides the basis for engineering applications in the context of solar power generation, water management, agricultural production and tourism. GEBA is publicly accessible over the internet via www.geba.ethz.ch.

  9. Artificial ocean upwelling utilizing the energy of surface waves

    Science.gov (United States)

    Soloviev, Alexander

    2016-04-01

    Artificial upwelling can bring cold water from below the thermocline to the sea surface. Vershinsky, Pshenichnyy, and Soloviev (1987) developed a prototype device, utilizing the energy of surface waves to create an upward flow of water in the tube. This is a wave-inertia pump consisting of a vertical tube, a valve, and a buoy to keep the device afloat. An outlet valve at the top of the unit synchronizes the operation of the device with surface waves and prevents back-splashing. A single device with a 100 m long and 1.2 m diameter tube is able to produce up to 1 m3s-1 flow of deep water to the surface. With a 10 oC temperature difference over 100 m depth, the negative heat supply rate to the sea surface is 42 MW, which is equivalent to a 42 Wm-2 heat flux, if distributed over 1 km2 area. Such flux is comparable to the average net air-sea flux. A system of artificial upwelling devices can cool down the sea surface, modify climate on a regional scale and possibly help mitigate hurricanes. The cold water brought from a deeper layer, however, has a larger density than the surface water and therefore has a tendency to sink back down. In this work, the efficiency of wave-inertia pumps and climatic consequences are estimated for different environmental conditions using a computational fluid dynamics model.

  10. Radiation exchange between persons and surfaces for building energy simulations

    DEFF Research Database (Denmark)

    Vorre, Mette Havgaard; Jensen, Rasmus Lund; Dreau, Jerome Le

    2015-01-01

    intersection points with the edges of the surface, making the method applicable to rooms with complex geometry. The method for calculating view factors is robust and applicable to building energy simulation tools. Calculation time can be long depending on the complexity of geometry, grid-size and the choice...... energy simulations. The method calculates view factors by numerical integration of projected area factor. Over time the projected area factor of a person has been simplified by geometrical shapes. These shapes were compared with more complex equations on precision and calculation time. The same was done...

  11. Calculating vibrational spectra using modified Shepard interpolated potential energy surfaces.

    Science.gov (United States)

    Evenhuis, Christian R; Manthe, Uwe

    2008-07-14

    A potential energy interpolation approach based on modified Shepard interpolation and specifically designed for calculation of vibrational states is presented. The importance of the choice of coordinates for the rate of convergence is demonstrated. Studying the vibrational states of the water molecule as a test case, a coordinate system comprised of inverse bond distances and trigonometric functions of the bond angle is found to be particularly efficient. Different sampling schemes used to locate the reference points in the modified Shepard interpolation are investigated. A final scheme is recommended, which allows the construction of potential energy surfaces to sub-wave-number accuracy.

  12. Weissenberg reflection high-energy electron diffraction for surface crystallography.

    Science.gov (United States)

    Abukawa, Tadashi; Yamazaki, Tomoyuki; Yajima, Kentaro; Yoshimura, Koji

    2006-12-15

    The principle of a Weissenberg camera is applied to surface crystallographic analysis by reflection high-energy electron diffraction. By removing inelastic electrons and measuring hundreds of patterns as a function of sample rotation angle phi, kinematical analysis can be performed over a large volume of reciprocal space. The data set is equivalent to a three-dimensional stack of Weissenberg photographs. The method is applied to analysis of an Si(111)-square root of 3 x square root of 3-Ag surface, and the structural data obtained are in excellent agreement with the known atomic structure.

  13. Can quantum transition state theory be defined as an exact t = 0+ limit?

    Science.gov (United States)

    Jang, Seogjoo; Voth, Gregory A

    2016-02-28

    The definition of the classical transition state theory (TST) as a t → 0+ limit of the flux-side time correlation function relies on the assumption that simultaneous measurement of population and flux is a well defined physical process. However, the noncommutativity of the two measurements in quantum mechanics makes the extension of such a concept to the quantum regime impossible. For this reason, quantum TST (QTST) has been generally accepted as any kind of quantum rate theory reproducing the TST in the classical limit, and there has been a broad consensus that no unique QTST retaining all the properties of TST can be defined. Contrary to this widely held view, Hele and Althorpe (HA) [J. Chem. Phys. 138, 084108 (2013)] recently suggested that a true QTST can be defined as the exact t → 0+ limit of a certain kind of quantum flux-side time correlation function and that it is equivalent to the ring polymer molecular dynamics (RPMD) TST. This work seeks to question and clarify certain assumptions underlying these suggestions and their implications. First, the time correlation function used by HA as a starting expression is not related to the kinetic rate constant by virtue of linear response theory, which is the first important step in relating a t = 0+ limit to a physically measurable rate. Second, a theoretical analysis calls into question a key step in HA's proof which appears not to rely on an exact quantum mechanical identity. The correction of this makes the true t = 0+ limit of HA's QTST different from the RPMD-TST rate expression, but rather equal to the well-known path integral quantum transition state theory rate expression for the case of centroid dividing surface. An alternative quantum rate expression is then formulated starting from the linear response theory and by applying a recently developed formalism of real time dynamics of imaginary time path integrals [S. Jang, A. V. Sinitskiy, and G. A. Voth, J. Chem. Phys. 140, 154103 (2014)]. It is shown

  14. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

    Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...

  15. Rate constants of chemical reactions from semiclassical transition state theory in full and one dimension.

    Science.gov (United States)

    Greene, Samuel M; Shan, Xiao; Clary, David C

    2016-06-28

    Semiclassical Transition State Theory (SCTST), a method for calculating rate constants of chemical reactions, offers gains in computational efficiency relative to more accurate quantum scattering methods. In full-dimensional (FD) SCTST, reaction probabilities are calculated from third and fourth potential derivatives along all vibrational degrees of freedom. However, the computational cost of FD SCTST scales unfavorably with system size, which prohibits its application to larger systems. In this study, the accuracy and efficiency of 1-D SCTST, in which only third and fourth derivatives along the reaction mode are used, are investigated in comparison to those of FD SCTST. Potential derivatives are obtained from numerical ab initio Hessian matrix calculations at the MP2/cc-pVTZ level of theory, and Richardson extrapolation is applied to improve the accuracy of these derivatives. Reaction barriers are calculated at the CCSD(T)/cc-pVTZ level. Results from FD SCTST agree with results from previous theoretical and experimental studies when Richardson extrapolation is applied. Results from our implementation of 1-D SCTST, which uses only 4 single-point MP2/cc-pVTZ energy calculations in addition to those for conventional TST, agree with FD results to within a factor of 5 at 250 K. This degree of agreement and the efficiency of the 1-D method suggest its potential as a means of approximating rate constants for systems too large for existing quantum scattering methods.

  16. Calculating rate constants with updated Hessians using variational transition state theory with multidimensional tunneling.

    Science.gov (United States)

    Chuang, Yao-Yuan

    2007-08-01

    Variational transition state theory with multidimensional tunneling (VTST/MT) has been used for calculating the rate constants of reactions. The updated Hessians have been used to reduce the computational costs for both geometry optimization and trajectory following procedures. In this paper, updated Hessians are used to reduce the computational costs while calculating the rate constants applying VTST/MT. Although we found that directly applying the updated Hessians will not generate good vibrational frequencies along the minimum energy path (MEP), however, we can either re-compute the full Hessian matrices at fixed intervals or calculate the Block Hessians, which is constructed by numerical one-side difference for the Hessian elements in the "critical" region and Bofill updating scheme for the rest of the Hessian elements. Due to the numerical instability of the Bofill update method near the saddle point region, we have suggested a simple strategy in which we follow the MEP until certain percentage of the classical barrier height from the barrier top with full Hessians computed and then performing rate constant calculation with the extended MEP using Block Hessians. This strategy results a mean unsigned percentage deviation (MUPD) around 10% with full Hessians computed till the point with 80% classical barrier height for four studied reactions. This proposed strategy is attractive not only it can be implemented as an automatic procedure but also speeds up the VTST/MT calculation via embarrassingly parallelization to a personal computer cluster.

  17. Intermittency and energy fluxes in the surface layer of free-surface turbulence

    CERN Document Server

    Troiani, Guido; Olivieri, Angelo; Casciola, Carlo Massimo

    2016-01-01

    By analyzing hot-wire velocity data taken in an open channel flow, an unambiguous definition of surface-layer thickness is here provided in terms of the cross-over scale between backward and forward energy fluxes. It is shown that the turbulence in the surface layer does not conform to the classical description of two-dimensional turbulence, since the direct energy cascade persists at scales smaller than the cross-over scale, comparable with the distance from the free-surface. The multifractal analysis of the one-dimensional surrogate of the turbulent kinetic energy dissipation rate in terms of generalized dimensions and singularity spectrum indicates that intermittency is strongly depleted in the surface layer, as shown by the singularity spectrum contracted to a single point. The combination of intermittency indicators and energy fluxes allowed to identify the specific nature of the surface layer as alternative to classical paradigms of three- and two-dimensional turbulence which cannot fully capture the gl...

  18. Calculation of the surface energy of fcc metals with modified embedded-atom method

    Institute of Scientific and Technical Information of China (English)

    Zhang Jian-Min; Ma Fei; Xu Ke-Wei

    2004-01-01

    The surface energies for 38 surfaces of fcc metals Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Rh and Ir have been calculated by using the modified embedded-atom method. The results show that, for Cu, Ag, Ni, Al, Pb and Ir, the average values of the surface energies are very close to the polycrystalline experimental data. For all fcc metals, as predicted, the close-packed (111) surface has the lowest surface energy. The surface energies for the other surfaces increase linearly with increasing angle between the surfaces (hkl) and (111). This can be used to estimate the relative values of the surface energy.

  19. Embedded atom calculations of unstable stacking fault energies and surface energies in intermetallics

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Department of Materials Science and Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (United States); Zhou, S.J. [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Vailhe, C.; Mutasa, B.; Panova, J. [Department of Materials Science and Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (United States)

    1997-01-01

    We performed embedded atom method calculations on surface energies and unstable stacking fault energies for a series of intermetallics for which interatomic potentials of the embedded atom type have recently been developed. These results were analyzed and applied to the prediction of relative ductility of these materials using the various current theories. Series of alloys with the B2 ordered structure were studied, and the results were compared to those in pure body-centered cubic (bcc) Fe. Ordered compounds with L1{sub 2} and L1{sub 0} structures based on the face-centered cubic (fcc) lattice were also studied. It was found that there is a correlation between the values of the antiphase boundary (APB) energies in B2 alloys and their unstackable stacking fault energies. Materials with higher APB energies tend to have higher unstable stacking fault energies, leading to an increased tendency to brittle fracture. {copyright} {ital 1997 Materials Research Society.}

  20. Electronic structure, molecular bonding and potential energy surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ruedenberg, K. [Ames Laboratory, IA (United States)

    1993-12-01

    By virtue of the universal validity of the generalized Born-Oppenheimer separation, potential energy surfaces (PES`) represent the central conceptual as well as quantitative entities of chemical physics and provide the basis for the understanding of most physicochemical phenomena in many diverse fields. The research in this group deals with the elucidation of general properties of PES` as well as with the quantitative determination of PES` for concrete systems, in particular pertaining to reactions involving carbon, oxygen, nitrogen and hydrogen molecules.

  1. Surface Free Energy Determination of APEX Photosensitive Glass

    OpenAIRE

    William R. Gaillard; Emanuel Waddell; Williams, John D.

    2016-01-01

    Surface free energy (SFE) plays an important role in microfluidic device operation. Photosensitive glasses such as APEX offer numerous advantages over traditional glasses for microfluidics, yet the SFE for APEX has not been previously reported. We calculate SFE with the Owens/Wendt geometric method by using contact angles measured with the Sessile drop technique. While the total SFE for APEX is found to be similar to traditional microstructurable glasses, the polar component is lower, which i...

  2. An accurate determination of the surface energy of solid selenium

    Science.gov (United States)

    Guisbiers, G.; Arscott, S.; Snyders, R.

    2012-12-01

    Selenium is currently a key element for developing nano and micro-technologies. Nevertheless, the surface energy of solid selenium (γSe) reported in the literature is still questionable. In this work, we have measured γSe = 0.291 ± 0.025 J/m2 at 293 K using the sessile drop technique with different probe liquids, namely ethylene glycol, de-ionized water, mercury, and gallium. This value is in excellent agreement with theoretical predictions.

  3. Evolution of the potential-energy surface of amorphous silicon

    OpenAIRE

    Kallel, Houssem; Mousseau, Normand; Schiettekatte, François

    2010-01-01

    The link between the energy surface of bulk systems and their dynamical properties is generally difficult to establish. Using the activation-relaxation technique (ART nouveau), we follow the change in the barrier distribution of a model of amorphous silicon as a function of the degree of relaxation. We find that while the barrier-height distribution, calculated from the initial minimum, is a unique function that depends only on the level of distribution, the reverse-barrier height distributio...

  4. Dropwise condensation rate of water breath figures on polymer surfaces having similar surface free energies

    Science.gov (United States)

    Ucar, Ikrime O.; Erbil, H. Yildirim

    2012-10-01

    This study investigates the effect of surface roughness, wettability, water contact angle hysteresis (CAH) and wetting hysteresis (WH) of polymeric substrates to the water drop condensation rate. We used five polyolefin coatings whose surface free energies were in a close range of 30-37 mJ/m2 but having different surface roughness and CAH. The formation of water breath figures was monitored at a temperature just below the dew point. The initial number of the condensed droplets per unit area (N0) and droplet surface coverage were determined during the early stage of drop condensation where the droplet coalescence was negligible. It was found that the mean drop diameter of condensed droplets on these polymer surfaces grow according to a power law with exponent 1/3 of time, similar to the previous reports given in the literature. It was determined that surface roughness and corresponding CAH and WH properties of polymers have important effects on the number of nucleation sites and growth rate of the condensed water droplets. N0 values and the surface coverage increased with the increase in surface roughness, CAH and WH of the polymer surfaces. The total condensed water drop volume also increased with the increase in surface roughness in accordance with the increase of the number of nucleated droplets.

  5. Surface free energy of a solid from contact angle hysteresis.

    Science.gov (United States)

    Chibowski, Emil

    2003-04-25

    Nature of contact angle hysteresis is discussed basing on the literature data (Colloids Surf. A 189 (2001) 265) of dynamic advancing and receding contact angles of n-alkanes and n-alcohols on a very smooth surface of 1,1,2,-trichloro-1,2,2,-trifluoroethane (FC-732) film deposited on a silicon plate. The authors considered the liquid absorption and/or retention (swelling) processes responsible for the observed hysteresis. In this paper hysteresis is considered to be due to the liquid film left behind the drop during retreating of its contact line. Using the contact angle hysteresis an approach is suggested for evaluation of the solid surface free energy. Molecular spacing and the film structure are discussed to explain the difference in n-alkanes and n-alcohols behaviour as well as to explain the difference between dispersion free energy gamma(s)(d) and total surface free energy gamma(s)(tot) of FC-732, as determined from the advancing contact angles and the hysteresis, respectively.

  6. Effect of surface energy of solid surfaces on the micro- and macroscopic properties of adsorbed BSA and lysozyme.

    Science.gov (United States)

    Sharma, Indu; Pattanayek, Sudip K

    2017-07-01

    The surface energy, a macroscopic property, depends on the chemical functionality and micro- and macroscopic roughness of the surface. The adsorption of two widely used proteins bovine serum albumin (BSA) and lysozyme on surfaces of four different chemical functionalities were done to find out the interrelation between macroscopic and microscopic properties. We have observed the secondary structure of protein after its adsorption. In addition, we observed the variation of surface energy of proteins due to variation in adsorption time, change in protein concentration and effect of a mixture of proteins. Surfaces of three different chemical functionalities namely, amine, hydroxyl and octyl were obtained through self-assembled monolayer on silica surfaces and were tested for responses towards adsorption of lysozyme and BSA. The adsorbed lysozyme has higher surface energy than the adsorbed BSA on amine and octyl surfaces. On hydroxyl functional surface, the surface energy due to the adsorbed lysozyme or BSA increases slowly with time. The surface energy of the adsorbed protein increases gradually with increasing protein concentration on hydrophobic surfaces. On hydrophilic surfaces, with increasing BSA concentration in bulk solution, the surface energy of the adsorbed protein on GPTMS and amine surfaces is maximum at 1μM concentration. During the adsorption from a mixture of BSA and lysozyme on octyl surface, first lysozyme adsorbs and subsequent BSA adsorption leads to a high surface energy. Copyright © 2016. Published by Elsevier B.V.

  7. Surface energy and relaxation in boron carbide (101¯1) from first principles

    Science.gov (United States)

    Beaudet, Todd D.; Smith, John R.; Adams, Jane W.

    2015-10-01

    The surface energy of the boron carbide polytype B11Cp(CBC) for planar separations along {101¯1} was determined to be 3.21 J/m2 via first-principles density-functional computations. Surface atomic relaxations are relatively large, thereby lowering the surface energy significantly. The icosahedra are not intact on the surface, i.e., severed polyhedra are the lowest energy surface configuration. Good agreement was found with an experimental average fracture surface energy.

  8. Supramolecular Surface Photochemistry: Cascade Energy Transfer between Encapsulated Dyes Aligned on a Clay Nanosheet Surface.

    Science.gov (United States)

    Tsukamoto, Takamasa; Ramasamy, Elamparuthi; Shimada, Tetsuya; Takagi, Shinsuke; Ramamurthy, V

    2016-03-29

    Three coumarin derivatives (7-propoxy coumarin, coumarin-480, and coumarin-540a, 2, 3, and 4, respectively) having different absorption and emission spectra were encapsulated within a water-soluble organic capsule formed by the two positively charged ammonium-functionalized cavitand octaamine (OAm, 1). Guests 2, 3, and 4 absorb in ultraviolet, violet, and blue regions and emit in violet, blue, and green regions, respectively. Energy transfer between the above three coumarin@(OAm)2 complexes assembled on the surface of a saponite clay nanosheet was investigated by steady-state and time-resolved emission techniques. Judging from their emission and excitation spectra, we concluded that the singlet-singlet energy transfer proceeded from 2 to 3, from 2 to 4, and from 3 to 4 when OAm-encapsulated 2, 3, and 4 were aligned on a clay surface as two-component systems. Under such conditions, the energy transfer efficiencies for the paths 2* to 3, 2* to 4, and 3* to 4 were calculated to be 33, 36, and 50% in two-component systems. When all three coumarins were assembled on the surface and 2 was excited, the energy transfer efficiencies for the paths 2* to 3, 2* to 4, and 3* to 4 were estimated to be 32, 34, and 33%. A comparison of energy transfer efficiencies of the two-component and three-component systems revealed that excitation of 2 leads to emission from 4. Successful merging of supramolecular chemistry and surface chemistry by demonstrating novel multi-step energy transfer in a three-component dye encapsulated system on a clay surface opens up newer opportunities for exploring such systems in an artificial light-harvesting phenomenon.

  9. Study on the energy performance of glazing surfaces

    Directory of Open Access Journals (Sweden)

    Ligia MOGA

    2014-12-01

    Full Text Available A proper thermal design of the building envelope represents an important factor for the energy economics. Glazing surfaces represent one of the important elements in the hygrothermal design activity of a building envelope. The window’s thermal performance has also a strong influence on the thermal performance of the opaque area of the wall. This fact imposed the research of the real interaction, of cooperation and of mutual influences of the characteristics between the two components of the wall of the building envelope, respectively the opaque and the glazing area. Optimal constructive details for the opaque and glazing area of the wall need to be properly designed in order to achieve the required thermal and energy performances imposed for new types of buildings, e.g. passive houses, zero energy buildings.

  10. Marangoni driven turbulence in high energy surface melting processes

    CERN Document Server

    Kidess, Anton; Righolt, Bernhard W; Kleijn, Chris R

    2016-01-01

    Experimental observations of high-energy surface melting processes, such as laser welding, have revealed unsteady, often violent, motion of the free surface of the melt pool. Surprisingly, no similar observations have been reported in numerical simulation studies of such flows. Moreover, the published simulation results fail to predict the post-solidification pool shape without adapting non-physical values for input parameters, suggesting the neglect of significant physics in the models employed. The experimentally observed violent flow surface instabilities, scaling analyses for the occurrence of turbulence in Marangoni driven flows, and the fact that in simulations transport coefficients generally have to be increased by an order of magnitude to match experimentally observed pool shapes, suggest the common assumption of laminar flow in the pool may not hold, and that the flow is actually turbulent. Here, we use direct numerical simulations (DNS) to investigate the role of turbulence in laser melting of a st...

  11. Adhesion on Nanoorganized Multilayers: Surface Thermodynamics and Local Energy Dissipation

    Directory of Open Access Journals (Sweden)

    Yolla Kazzi

    2010-01-01

    Full Text Available Nanostructured multilayers, composed of alternate organic (3-mercaptopropyltrimethoxysilane, alkylthiols, polydimethylsiloxane and metallic (gold layers, are grafted onto glass and prepared in order to modify the mechanical and dissipative properties of a thin surface layer of the substrate. The external face is constituted either of gold or alkyl groups, allowing us to study two types of surfaces exhibiting different chemical and thermodynamic properties. The formation and the structure of the nanostructured multilayers are first examined by means of various techniques such as atomic force microscopy (AFM, wettability, X-ray photoelectron spectroscopy (XPS, and conductivity measurements. All the results concerning the structure of the systems studied are used to understand the adhesive properties at short contact times (tack of the multi-layers and an elastomer (polyisoprene. The influence of the structural aspects of gold layers, the length of the alkyl chains of the top layer, the terminal functionality, and the length of the confined organic layer between two gold layers on the energy of adhesion regarding the polyisoprene are clearly demonstrated. The influence of the nano-structured surface layers on adhesion phenomena is explained in terms of either the surface thermodynamics or local energy dissipation during the propagation of a fracture according to complex mechanisms.

  12. Inverse scattering at fixed energy on asymptotically hyperbolic Liouville surfaces

    Science.gov (United States)

    Daudé, Thierry; Kamran, Niky; Nicoleau, Francois

    2015-12-01

    In this paper, we study an inverse scattering problem on Liouville surfaces having two asymptotically hyperbolic ends. The main property of Liouville surfaces consists of the complete separability of the Hamilton-Jacobi equations for the geodesic flow. An important related consequence is the fact that the stationary wave equation can be separated into a system of radial and angular ODEs. The full scattering matrix at fixed energy associated to a scalar wave equation on asymptotically hyperbolic Liouville surfaces can be thus simplified by considering its restrictions onto the generalized harmonics corresponding to the angular separated ODE. The resulting partial scattering matrices consists in a countable set of 2 × 2 matrices whose coefficients are the so called transmission and reflection coefficients. It is shown that the reflection coefficients are nothing but generalized Weyl-Titchmarsh (WT) functions for the radial ODE in which the generalized angular momentum is seen as the spectral parameter. Using the complex angular momentum method and recent results on 1D inverse problem from generalized WT functions, we show that the knowledge of the reflection operators at a fixed non-zero energy is enough to determine uniquely the metric of the asymptotically hyperbolic Liouville surface under consideration.

  13. The importance of surface finish to energy performance

    Directory of Open Access Journals (Sweden)

    Smith Geoff B.

    2017-01-01

    Full Text Available Power generation in solar energy systems, thermal control in buildings and mitigation of the Urban Heat Island problem, are all sensitive to directional response to incoming radiation. The radiation absorption and emission profile also plays a crucial role in each system's response and depends strongly on surface finish. This important sensitivity needs wider recognition in materials data sheets, system modeling, plus in materials and environmental engineering. The impact of surface roughness on thermal response of natural and man-made external environments is examined. Important examples will be given of the role of surface finish within each class. Total emittance links to the way surface finish influences directional emittance E(θ. Smooth surface thermal emittance on PV module covers, many solar absorbers, some roof paints, polished concrete, and glass windows can be up to 15% different from insulator results based on fully diffuse models of the same material. Widespread evidence indicates smooth metals and low-E solar absorber surfaces cool faster, and smooth insulators slower than previously thought. Matt paint is cooler than low sheen paint under the same solar heating impacts and normal concrete cooler than polished. Emittance for water is the prime environmental example of oblique impacts as it reflects strongly at oblique incidence, which leads to a significant drop in E(θ. Ripples or waves however raise water's average emittance. A surprise in this work was the high sensitivity of total E and its angular components to roughness in the depth range of 0.1–0.8 μm, which are well under ambient thermal IR wavelengths of 3–30 μm but common in metal finishing. Parallel energy flows such as evaporation and convective cooling vary if emittance varies. Thermal image analysis can provide insights into angular radiative effects.

  14. Ab initio surface core-level shifts and surface segregation energies

    DEFF Research Database (Denmark)

    Aldén, Magnus; Skriver, Hans Lomholt; Johansson, Börje

    1993-01-01

    We have calculated the surface core-level energy shifts of the 4d and 5d transition metals by means of local-density theory and a Green’s-function technique based on the linear muffin-tin orbitals method. Final-state effects are included by treating the core-ionized atom as an impurity located...

  15. Estudio teórico de la isomerización del ácido maleico en ácido fumárico: un enfoque basado en el concepto de superficie de energía potencial Theoretical study of the isomerization of maleic acid into fumaric acid: an approach based on the concept of potential energy surface

    Directory of Open Access Journals (Sweden)

    Ricardo Ugarte

    2010-01-01

    Full Text Available A comparative study based on potential energy surfaces (PES of 2-butanedioic and hypothetic 2-butanedioic/HCl acids is useful for understanding the maleic acid isomerization. The PES enables locating conformers of minimum energy, intermediates of reactions and transition states. From contour diagrams, a set of possible reaction paths are depicted interconnecting the proposed structures. The study was carried out in absentia and in the presence of the catalyst (HCl, using an solvatation model provided by the Gaussian software package. Clearly, the effect of HCl is given by new reaction paths with lower energetic barriers in relation to the reaction without catalyzing.

  16. Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems.

    Science.gov (United States)

    Olsson, Mats H M; Mavri, Janez; Warshel, Arieh

    2006-08-29

    The idea that enzyme catalysis involves special factors such as coherent fluctuations, quantum mechanical tunnelling and non-equilibrium solvation (NES) effects has gained popularity in recent years. It has also been suggested that transition state theory (TST) cannot be used in studies of enzyme catalysis. The present work uses reliable state of the art simulation approaches to examine the above ideas. We start by demonstrating that we are able to simulate any of the present catalytic proposals using the empirical valence bond (EVB) potential energy surfaces, the dispersed polaron model and the quantized classical path (QCP) approach, as well as the approximate vibronic method. These approaches do not treat the catalytic effects by phenomenological treatments and thus can be considered as first principles approaches (at least their ability to compare enzymatic reaction to the corresponding solution reactions). This work will consider the lipoxygenase reaction, and to lesser extent other enzymes, for specific demonstration. It will be pointed out that our study of the lipoxygenase reaction reproduces the very large observed isotope effect and the observed rate constant while obtaining no catalytic contribution from nuclear quantum mechanical (NQM) effects. Furthermore, it will be clarified that our studies established that the NQM effect decreases rather than increases when the donor-acceptor distance is compressed. The consequences of these findings in terms of the temperature dependence of the kinetic isotope effect and in terms of different catalytic proposals will be discussed. This paper will also consider briefly the dynamical effects and conclude that such effects do not contribute in a significant way to enzyme catalysis. Furthermore, it will be pointed out that, in contrast to recent suggestions, NES effects are not dynamical effects and should therefore be part of the activation free energy rather than the transmission factor. In view of findings of the

  17. Measuring surface energy and evapotranspiration across Caribbean mangrove forests

    Science.gov (United States)

    Lagomasino, D.; Fatoyinbo, T. E.; Price, R.

    2014-12-01

    Coastal mangroves lose large amounts of water through evapotranspiration (ET) that can be equivalent to the amount of annual rainfall in certain years. Satellite remote sensing has been used to estimate surface energy and ET variability in many forested ecosystems, yet has been widely overlooked in mangrove forests. Using a combination of long-term datasets (30-year) acquired from the NASA Landsat 5 and 7 satellite databases, the present study investigated ET and surface energy balance variability between two mangrove forest sites in the Caribbean: 1) Everglades National Park (ENP; Florida, USA) and 2) Sian Ka'an Biosphere Reserve (SKBR; Quintana Roo, Mexico). A satellite-derived surface energy balance model was used to estimate ET in tall and scrub mangroves environments at ENP and SKBR. Results identified significant differences in soil heat flux measurements and ET between the tall and scrub mangrove environments. Scrub mangroves exhibited the highest soil heat flux coincident with the lowest biophysical indices (i.e., Fractional Vegetation Cover, Normalized Difference Vegetation Index, and Soil-Adjusted Vegetation Index) and ET rates. Mangrove damage and mortality was observed on the satellite images following strong tropical storms and associated with anthropogenic modifications and resulted in low values in spectral vegetation indices, higher soil heat flux, and higher ET. Recovery of the spectral characteristics, soil heat flux and ET was within 1-2 years following hurricane disturbance while, degradation caused by human disturbance persisted for many years. Remotely sensed ET of mangrove forests can provide estimates over a few decades and provide us with some understanding of how these environments respond to disturbances to the landscape in periods where no ground data exists or in locations that are difficult to access. Moreover, relationships between energy and water balance components developed for the coastal mangroves of Florida and Mexico could be

  18. Localized description of surface energy gap effects in the resonant charge exchange between atoms and surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Iglesias-Garcia, A; Garcia, Evelina A; Goldberg, E C, E-mail: aiglesiasg@santafe-conicet.gov.ar [Instituto de Desarrollo Tecnologico para la Industria Quimica (INTEC-CONICET-UNL), Gueemes 3450, CC91, (S3000GLN) Santa Fe (Argentina)

    2011-02-02

    The resonant charge exchange between atoms and surfaces is described by considering a localized atomistic view of the solid within the Anderson model. The presence of a surface energy gap is treated within a simplified tight-binding model of the solid, and a proper calculation of the Hamiltonian terms based on a LCAO expansion of the solid eigenstates is performed. It is found that interference terms jointly with a surface projected gap maximum at the {Gamma} point and the Fermi level inside it, lead to hybridization widths negligible around the Fermi level. This result can explain experimental observations related to long-lived adsorbate states and anomalous neutral fractions of low energy ions in alkali/Cu(111) systems.

  19. Reducing measurement scale mismatch to improve surface energy flux estimation

    Science.gov (United States)

    Iwema, Joost; Rosolem, Rafael; Rahman, Mostaquimur; Blyth, Eleanor; Wagener, Thorsten

    2016-04-01

    Soil moisture importantly controls land surface processes such as energy and water partitioning. A good understanding of these controls is needed especially when recognizing the challenges in providing accurate hyper-resolution hydrometeorological simulations at sub-kilometre scales. Soil moisture controlling factors can, however, differ at distinct scales. In addition, some parameters in land surface models are still often prescribed based on observations obtained at another scale not necessarily employed by such models (e.g., soil properties obtained from lab samples used in regional simulations). To minimize such effects, parameters can be constrained with local data from Eddy-Covariance (EC) towers (i.e., latent and sensible heat fluxes) and Point Scale (PS) soil moisture observations (e.g., TDR). However, measurement scales represented by EC and PS still differ substantially. Here we use the fact that Cosmic-Ray Neutron Sensors (CRNS) estimate soil moisture at horizontal footprint similar to that of EC fluxes to help answer the following question: Does reduced observation scale mismatch yield better soil moisture - surface fluxes representation in land surface models? To answer this question we analysed soil moisture and surface fluxes measurements from twelve COSMOS-Ameriflux sites in the USA characterized by distinct climate, soils and vegetation types. We calibrated model parameters of the Joint UK Land Environment Simulator (JULES) against PS and CRNS soil moisture data, respectively. We analysed the improvement in soil moisture estimation compared to uncalibrated model simulations and then evaluated the degree of improvement in surface fluxes before and after calibration experiments. Preliminary results suggest that a more accurate representation of soil moisture dynamics is achieved when calibrating against observed soil moisture and further improvement obtained with CRNS relative to PS. However, our results also suggest that a more accurate

  20. Energy Crops and their Implications on Soil Carbon Sequestration, Surface Energy and Water Balance

    Science.gov (United States)

    Song, Y.; Barman, R.; Jain, A. K.

    2011-12-01

    The quest to meet growing energy demand with low greenhouse gas emissions has increased attention on the potential of existing and advanced biomass energy crops. Potential energy crops include row crops such as corn, and perennial grasses such as switchgrass. However, a massive expansion of bioenergy crops raises many questions such as: how and where to grow energy crops; and what will be the impacts of growing large scale biofuel crops on the terrestrial hydrological cycle, the surface energy budget, soil carbon sequestration and the concurrent effects on the climate system. An integrated modeling system is being developed with in the framework of a land surface model, the Integrated Science Assessment Model (ISAM), and being applied to address these questions.This framework accounts for the biophysical, physiological and biogeochemical systems governing important processes that regulate crop growth including water, energy and nutrient cycles within the soil-plant-atmosphere system. One row crop (Corn) and two energy crops (Switchgrass and Miscanthus) are studied in current framework. Dynamic phenology processes and parameters for simulating each crop have been developed using observed data from a north to south gradient of field trial sites. This study will specifically focus on the agricultural regions in the US and in Europe. The potential productivity of these three crops will be assessed in terms of carbon sequestration, surface energy and water balance and their spatial variability. This study will help to quantify the importance of various environmental aspects towards modeling bioenergy crops and to better understand the spatial and temporal dynamics of bioenergy crop yields.

  1. Potential energy surface and rovibrational energy levels of the H2-CS van der Waals complex.

    Science.gov (United States)

    Denis-Alpizar, Otoniel; Stoecklin, Thierry; Halvick, Philippe; Dubernet, Marie-Lise; Marinakis, Sarantos

    2012-12-21

    Owing to its large dipole, astrophysicists use carbon monosulfide (CS) as a tracer of molecular gas in the interstellar medium, often in regions where H(2) is the most abundant collider. Predictions of the rovibrational energy levels of the weakly bound complex CS-H(2) (not yet observed) and also of rate coefficients for rotational transitions of CS in collision with H(2) should help to interpret the observed spectra. This paper deals with the first goal, i.e., the calculation of the rovibrational energy levels. A new four-dimensional intermolecular potential energy surface for the H(2)-CS complex is presented. Ab initio potential energy calculations were carried out at the coupled-cluster level with single and double excitations and a perturbative treatment of triple excitations, using a quadruple-zeta basis set and midbond functions. The potential energy surface was obtained by an analytic fit of the ab initio data. The equilibrium structure of the H(2)-CS complex is found to be linear with the carbon pointing toward H(2) at the intermolecular separation of 8.6 a(o). The corresponding well depth is -173 cm(-1). The potential was used to calculate the rovibrational energy levels of the para-H(2)-CS and ortho-H(2)-CS complexes. The present work provides the first theoretical predictions of these levels. The calculated dissociation energies are found to be 35.9 cm(-1) and 49.9 cm(-1), respectively, for the para and ortho complexes. The second virial coefficient for the H(2)-CS pair has also been calculated for a large range of temperature. These results could be used to assign future experimental spectra and to check the accuracy of the potential energy surface.

  2. Concrete with carpet recyclates: suitability assessment by surface energy evaluation.

    Science.gov (United States)

    Schmidt, H; Cieślak, M

    2008-01-01

    Worn out textile floor coverings are burdensome wastes that are degraded in landfill sites after a very long period of time. One of the ways to manage this kind of waste may be the use of carpet recyclate (CR) as an additive for concrete reinforcement. Therefore, an attempt was made to predict the effects of recyclate additives on the durability a concrete-carpet mixture by employing the method of assessing surface properties of components in the concrete-carpet recyclates composite. Testing was performed on carpet wastes, containing polyamide (PA) and polypropylene (PP) piles and butadiene-styrene resin with chalk filler (BSC) as back coating, to assess the suitability of CR additive for concrete reinforcement by surface energy evaluation. Based on the measurements of contact angles, the free surface energy of recyclate components was determined. The reversible work of adhesion at the interface between these components in dry and wet states was also calculated. The results show that CR with both PA and PP fibers form a strong and water-resistant bond with concrete.

  3. Treatment of surfaces with low-energy electrons

    Science.gov (United States)

    Frank, L.; Mikmeková, E.; Lejeune, M.

    2017-06-01

    Electron-beam-induced deposition of various materials from suitable precursors has represented an established branch of nanotechnology for more than a decade. A specific alternative is carbon deposition on the basis of hydrocarbons as precursors that has been applied to grow various nanostructures including masks for subsequent technological steps. Our area of study was unintentional electron-beam-induced carbon deposition from spontaneously adsorbed hydrocarbon molecules. This process traditionally constitutes a challenge for scanning electron microscopy practice preventing one from performing any true surface studies outside an ultrahigh vacuum and without in-situ cleaning of samples, and also jeopardising other electron-optical devices such as electron beam lithographs. Here we show that when reducing the energy of irradiating electrons sufficiently, the e-beam-induced deposition can be converted to e-beam-induced release causing desorption of hydrocarbons and ultimate cleaning of surfaces in both an ultrahigh and a standard high vacuum. Using series of experiments with graphene samples, we demonstrate fundamental features of e-beam-induced desorption and present results of checks for possible radiation damage using Raman spectroscopy that led to optimisation of the electron energy for damage-free cleaning. The method of preventing carbon contamination described here paves the way for greatly enhanced surface sensitivity of imaging and substantially reduced demands on vacuum systems for nanotechnological applications.

  4. Transition-state-guided drug design for treatment of parasitic neglected tropical diseases.

    Science.gov (United States)

    Murkin, A S; Moynihan, M M

    2014-01-01

    Many of the deadliest neglected tropical diseases are caused by protozoan and helminthic parasites. These organisms have evolved several enzymes to exploit their host's metabolic resources and evade immune responses. Because these essential proteins are absent in humans, they are targets for antiparasitic drug development. Despite decades of investigation, no therapy has been successful in the eradication of these diseases, so new approaches are desired. Chemically stable analogues of the transition states of enzymatic reactions are often potent inhibitors, and several examples of clinically effective compounds are known for other diseases. The design of transition-state analogues is aided by structural models of the transition state, which are obtained by complementing experimental measurement of kinetic isotope effects with theoretical calculations. Such transition-state-guided inhibitor design has been demonstrated for human, bovine, malarial, and trypanosomal enzymes of the purine salvage pathway, including purine nucleoside phosphorylase, nucleoside hydrolases, and adenosine deaminase. Cysteine proteases, trans-sialidase, 1-deoxy-d-xylulose-5-phosphate reductoisomerase, and trypanothione synthetase are presented as additional candidates for application of transition-state analysis with the goal of identifying new leads for the treatment of parasitic neglected tropical diseases.

  5. The role of the transition state in polyatomic reactions: Initial state-selected reaction probabilities of the H + CH4 → H2 + CH3 reaction

    Science.gov (United States)

    Welsch, Ralph; Manthe, Uwe

    2014-11-01

    Full-dimensional calculations of initial state-selected reaction probabilities on an accurate ab initio potential energy surface (PES) have been communicated recently [R. Welsch and U. Manthe, J. Chem. Phys. 141, 051102 (2014)]. These calculations use the quantum transition state concept, the multi-layer multi-configurational time-dependent Hartree approach, and graphics processing units to speed up the potential evaluation. Here further results of these calculations and an extended analysis are presented. State-selected reaction probabilities are given for many initial ro-vibrational states. The role of the vibrational states of the activated complex is analyzed in detail. It is found that rotationally cold methane mainly reacts via the ground state of the activated complex while rotationally excited methane mostly reacts via H-H-CH3-bending excited states of the activated complex. Analyzing the different contributions to the reactivity of the vibrationally states of methane, a complex pattern is found. Comparison with initial state-selected reaction probabilities computed on the semi-empirical Jordan-Gilbert PES reveals the dependence of the results on the specific PES.

  6. The role of the transition state in polyatomic reactions: initial state-selected reaction probabilities of the H + CH₄ → H₂ + CH₃ reaction.

    Science.gov (United States)

    Welsch, Ralph; Manthe, Uwe

    2014-11-07

    Full-dimensional calculations of initial state-selected reaction probabilities on an accurate ab initio potential energy surface (PES) have been communicated recently [R. Welsch and U. Manthe, J. Chem. Phys. 141, 051102 (2014)]. These calculations use the quantum transition state concept, the multi-layer multi-configurational time-dependent Hartree approach, and graphics processing units to speed up the potential evaluation. Here further results of these calculations and an extended analysis are presented. State-selected reaction probabilities are given for many initial ro-vibrational states. The role of the vibrational states of the activated complex is analyzed in detail. It is found that rotationally cold methane mainly reacts via the ground state of the activated complex while rotationally excited methane mostly reacts via H-H-CH3-bending excited states of the activated complex. Analyzing the different contributions to the reactivity of the vibrationally states of methane, a complex pattern is found. Comparison with initial state-selected reaction probabilities computed on the semi-empirical Jordan-Gilbert PES reveals the dependence of the results on the specific PES.

  7. An ab initio potential energy surface and vibrational energy levels of HXeBr

    Institute of Scientific and Technical Information of China (English)

    Zheng Guo Huang; En Cui Yang; Dai Qian Xie

    2008-01-01

    A three-dimensional global potential energy surface for the electronic ground state of HXeBr molecule is constructed from morethan 4200 ab initio points. These points are generated using an internally contracted multi-reference configuration interactionmethod with the Davidson correction (icMRCI + Q) and large basis sets. The stabilities and dissociation barriers are identified fromthe potential energy surfaces. The three-body dissociation channel is found to be the dominate dissociation channel for HXeBr.Based on the obtained potentials, low-lying vibrational energy levels of HXeBr calculated using the Lanczos algorithm is found tobe in good agreement with the available experimental band origins.2008 Zheng Guo Huang. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.

  8. The Global Energy Balance Archive (GEBA) version 2017: a database for worldwide measured surface energy fluxes

    Science.gov (United States)

    Wild, Martin; Ohmura, Atsumu; Schär, Christoph; Müller, Guido; Folini, Doris; Schwarz, Matthias; Zyta Hakuba, Maria; Sanchez-Lorenzo, Arturo

    2017-08-01

    The Global Energy Balance Archive (GEBA) is a database for the central storage of the worldwide measured energy fluxes at the Earth's surface, maintained at ETH Zurich (Switzerland). This paper documents the status of the GEBA version 2017 dataset, presents the new web interface and user access, and reviews the scientific impact that GEBA data had in various applications. GEBA has continuously been expanded and updated and contains in its 2017 version around 500 000 monthly mean entries of various surface energy balance components measured at 2500 locations. The database contains observations from 15 surface energy flux components, with the most widely measured quantity available in GEBA being the shortwave radiation incident at the Earth's surface (global radiation). Many of the historic records extend over several decades. GEBA contains monthly data from a variety of sources, namely from the World Radiation Data Centre (WRDC) in St. Petersburg, from national weather services, from different research networks (BSRN, ARM, SURFRAD), from peer-reviewed publications, project and data reports, and from personal communications. Quality checks are applied to test for gross errors in the dataset. GEBA has played a key role in various research applications, such as in the quantification of the global energy balance, in the discussion of the anomalous atmospheric shortwave absorption, and in the detection of multi-decadal variations in global radiation, known as global dimming and brightening. GEBA is further extensively used for the evaluation of climate models and satellite-derived surface flux products. On a more applied level, GEBA provides the basis for engineering applications in the context of solar power generation, water management, agricultural production and tourism. GEBA is publicly accessible through the internet via http://www.geba.ethz.ch. Supplementary data are available at https://doi.org/10.1594/PANGAEA.873078.

  9. Bioresponse to polymeric substrates: Effect of surface energy, modulus, topography, and surface graft copolymers

    Science.gov (United States)

    Wilson, Leslie Hoipkemeier

    Biofouling is the accumulation of biological matter on a substrate. It is essential to elucidate and model the major factors that affect both biological settlement and adhesion to substrates in order to develop coatings that minimize initial fouling or ease the removal of this fouling. To date, models that have estimated adhesion strength to coatings primarily included bulk elastic modulus and surface energy. Topography, however, has been found to dominate both these terms in the reduction of settlement and has been found to affect the adhesion strength as well. Silicone foul release coatings have demonstrated moderate success in the prevention of marine biofouling because of their low modulus and low surface energy. Problems exist with durability and eventual fouling of the coating due to the overgrowth of foulants that prefer hydrophobic substrates. This research details the characterization and the surface and bulk modification of a commercially available silicone elastomer. The modifications include bulk additives, surface topography, and surface graft copolymers. The effect of these modifications on biological response was then assayed using the alga Ulva as a model for marine biofouling. The unmodified silicone elastomer has a bulk modulus of approximately 1 MPa. The addition of vinyl functional polydimethylsiloxane oils allowed for a greater than 200% increase or a 90% decrease in the bulk modulus of the material. The addition of non-reactive polydimethylsiloxane oils allowed for a change in the surface lubricity of the elastomer without a significant change in the mechanical properties. Topographical modifications of the surface show a profound effect on the bioresponse. Appropriately scaled engineered microtopographies replicated in the silicone elastomer can produce a 250% increase in algal zoospore fouling or an 85% reduction in settlement relative to a smooth silicone elastomer. Finally, the modification of the surface energy of this material was

  10. Permutation invariant polynomial neural network approach to fitting potential energy surfaces. III. Molecule-surface interactions

    Science.gov (United States)

    Jiang, Bin; Guo, Hua

    2014-07-01

    The permutation invariant polynomial-neural network (PIP-NN) method for constructing highly accurate potential energy surfaces (PESs) for gas phase molecules is extended to molecule-surface interaction PESs. The symmetry adaptation in the NN fitting of a PES is achieved by employing as the input symmetry functions that fulfill both the translational symmetry of the surface and permutation symmetry of the molecule. These symmetry functions are low-order PIPs of the primitive symmetry functions containing the surface periodic symmetry. It is stressed that permutationally invariant cross terms are needed to avoid oversymmetrization. The accuracy and efficiency are demonstrated in fitting both a model PES for the H2 + Cu(111) system and density functional theory points for the H2 + Ag(111) system.

  11. Accurate global potential energy surface for the H + OH+ collision

    Science.gov (United States)

    Gannouni, M. A.; Jaidane, N. E.; Halvick, P.; Stoecklin, T.; Hochlaf, M.

    2014-05-01

    We mapped the global three-dimensional potential energy surface (3D-PES) of the water cation at the MRCI/aug-cc-pV5Z including the basis set superposition (BSSE) correction. This PES covers the molecular region and the long ranges close to the H + OH+(X3Σ-), the O + H2+(X2Σg+), and the hydrogen exchange channels. The quality of the PES is checked after comparison to previous experimental and theoretical results of the spectroscopic constants of H2O+(tilde X2B1) and of the diatomic fragments, the vibronic spectrum, the dissociation energy, and the barrier to linearity for H2O+(tilde X2B1). Our data nicely approach those measured and computed previously. The long range parts reproduce quite well the diatomic potentials. In whole, a good agreement is found, which validates our 3D-PES.

  12. Stabilized Quasi-Newton Optimization of Noisy Potential Energy Surfaces

    CERN Document Server

    Schaefer, Bastian; Roy, Shantanu; Goedecker, Stefan

    2014-01-01

    Optimizations of atomic positions belong to the most commonly performed tasks in electronic structure calculations. Many simulations like global minimum searches or characterizations of chemical reactions require performing hundreds or thousands of minimizations or saddle computations. To automatize these tasks, optimization algorithms must not only be efficient, but also very reliable. Unfortunately computational noise in forces and energies is inherent to electronic structure codes. This computational noise poses a sever problem to the stability of efficient optimization methods like the limited-memory Broyden-Fletcher-Goldfarb-Shanno algorithm. We here present a technique that allows obtaining significant curvature information of noisy potential energy surfaces. We use this technique to construct both, a stabilized quasi-Newton minimization method and a stabilized quasi-Newton saddle finding approach. We demonstrate with the help of benchmarks that both the minimizer and the saddle finding approach are sup...

  13. Novel mixture model for the representation of potential energy surfaces

    Science.gov (United States)

    Pham, Tien Lam; Kino, Hiori; Terakura, Kiyoyuki; Miyake, Takashi; Dam, Hieu Chi

    2016-10-01

    We demonstrate that knowledge of chemical physics on a materials system can be automatically extracted from first-principles calculations using a data mining technique; this information can then be utilized to construct a simple empirical atomic potential model. By using unsupervised learning of the generative Gaussian mixture model, physically meaningful patterns of atomic local chemical environments can be detected automatically. Based on the obtained information regarding these atomic patterns, we propose a chemical-structure-dependent linear mixture model for estimating the atomic potential energy. Our experiments show that the proposed mixture model significantly improves the accuracy of the prediction of the potential energy surface for complex systems that possess a large diversity in their local structures.

  14. New molecular species of potential interest to atmospheric chemistry: isomers on the [H, S2, Br] potential energy surface.

    Science.gov (United States)

    de Oliveira-Filho, Antonio Gustavo S; Aoto, Yuri Alexandre; Ornellas, Fernando R

    2009-02-19

    This work reports a state-of-the-art theoretical characterization of four new sulfur-bromine species and five transition states on the [H, S(2), Br] potential energy surface. Our highest level theoretical approach employed the method coupled cluster singles and doubles with perturbative contributions of connected triples, CCSD(T), along with the series of correlation-consistent basis sets and with extrapolation to the complete basis set (CBS) limit in the optimization of the geometrical parameters and to quantify the energetic quantities. The structural and vibrational frequencies here reported are unique and represent the most accurate investigation to date of these species. The global minimum corresponds to a skewed structure HSSBr with a disulfide bond; this is followed by a pyramidal-like structure, SSHBr, 18.85 kcal/mol above the minimum. Much higher in energy, we found another skewed structure, HSBrS (50.29 kcal/mol), with one S-Br dative-type bond, and another pyramidal-like one, HBrSS (109.80 kcal/mol), with two S-Br dative-type bonds. The interconversion of HSSBr into SSHBr can occur via a transfer of either the hydrogen or the bromine atom but involves a very high barrier of about 43 kcal/mol. These molecules are potentially a new route of coupling the sulfur and bromine chemistry in the atmosphere, and conditions of high concentration of H(2)S like in volcanic eruptions might contribute to their formation. We note that HSSBr can act as a reservoir molecule for the reaction between the radicals HSS and Br. Also, an assessment of the methods DFT/B3LYP/CBS and MP2/CBS relative to CCSD(T)/CBS provides insights on the expected performance of these methods on the characterization of polysulfides and also of more complex systems containing disulfide bridges.

  15. Surface Free Energy Determination of APEX Photosensitive Glass

    Directory of Open Access Journals (Sweden)

    William R. Gaillard

    2016-02-01

    Full Text Available Surface free energy (SFE plays an important role in microfluidic device operation. Photosensitive glasses such as APEX offer numerous advantages over traditional glasses for microfluidics, yet the SFE for APEX has not been previously reported. We calculate SFE with the Owens/Wendt geometric method by using contact angles measured with the Sessile drop technique. While the total SFE for APEX is found to be similar to traditional microstructurable glasses, the polar component is lower, which is likely attributable to composition. The SFE was modified at each stage of device fabrication, but the SFE of the stock and fully processed glass was found to be approximately the same at a value of 51 mJ·m−2. APEX exhibited inconsistent wetting behavior attributable to an inhomogeneous surface chemical composition. Means to produce more consistent wetting of photosensitive glass for microfluidic applications are discussed.

  16. Oxidation of nickel surfaces by low energy ion bombardment

    Energy Technology Data Exchange (ETDEWEB)

    Saric, Iva [Faculty of Civil Engineering, University of Rijeka (Croatia); Center for Micro and Nano Sciences and Technologies, University of Rijeka (Croatia); Peter, Robert; Kavre, Ivna; Badovinac, Ivana Jelovica; Petravic, Mladen [Center for Micro and Nano Sciences and Technologies, University of Rijeka (Croatia); Department of Physics, University of Rijeka (Croatia)

    2016-03-15

    We have studied formation of oxides on Ni surfaces by low energy oxygen bombardment using X-ray photoemission spectroscopy (XPS) and secondary ion mass spectrometry (SIMS). Different oxidation states of Ni ions have been identified in XPS spectra measured around Ni 2p and O 1s core-levels. We have compared our results with thermal oxidation of Ni and shown that ion bombardment is more efficient in creating thin oxide films on Ni surfaces. The dominant Ni-oxide in both oxidation processes is NiO (Ni{sup 2+} oxidation state), while some Ni{sub 2}O{sub 3} contributions (Ni{sup 3+} oxidation state) are still present in all oxidised samples. The oxide thickness of bombarded Ni samples, as determined by SIMS, was shown to be related to the penetration depth of oxygen ions in Ni.

  17. Potential Energy Surfaces Using Algebraic Methods Based on Unitary Groups

    Directory of Open Access Journals (Sweden)

    Renato Lemus

    2011-01-01

    Full Text Available This contribution reviews the recent advances to estimate the potential energy surfaces through algebraic methods based on the unitary groups used to describe the molecular vibrational degrees of freedom. The basic idea is to introduce the unitary group approach in the context of the traditional approach, where the Hamiltonian is expanded in terms of coordinates and momenta. In the presentation of this paper, several representative molecular systems that permit to illustrate both the different algebraic approaches as well as the usual problems encountered in the vibrational description in terms of internal coordinates are presented. Methods based on coherent states are also discussed.

  18. Potential Energy Surfaces and Quantum Yields for Photochromic Diarylethene Reactions

    Directory of Open Access Journals (Sweden)

    Makoto Hatakeyama

    2013-05-01

    Full Text Available Photochromic diarylethenes (DAEs are among the most promising molecular switching systems for future molecular electronics. Numerous derivatives have been synthesized recently, and experimental quantum yields (QYs have been reported for two categories of them. Although the QY is one of the most important properties in various applications, it is also the most difficult property to predict before a molecule is actually synthesized. We have previously reported preliminary theoretical studies on what determines the QYs in both categories of DAE derivatives. Here, reflecting theoretical analyses of potential energy surfaces and recent experimental results, a rational explanation of the general guiding principle for QY design is presented for future molecular design.

  19. Taboo search by successive confinement: Surveying a potential energy surface

    Science.gov (United States)

    Chekmarev, Sergei F.

    2001-09-01

    A taboo search for minima on a potential energy surface (PES) is performed by means of confinement molecular dynamics: the molecular dynamics trajectory of the system is successively confined to various basins on the PES that have not been sampled yet. The approach is illustrated for a 13-atom Lennard-Jones cluster. It is shown that the taboo search radically accelerates the process of surveying the PES, with the probability of finding a new minimum defined by a propagating Fermi-like distribution.

  20. Low-energy electron scattering from molecules, biomolecules and surfaces

    CERN Document Server

    Carsky, Petr

    2011-01-01

    Since the turn of the 21st century, the field of electron molecule collisions has undergone a renaissance. The importance of such collisions in applications from radiation chemistry to astrochemistry has flowered, and their role in industrial processes such as plasma technology and lighting are vital to the advancement of next generation devices. Furthermore, the development of the scanning tunneling microscope highlights the role of such collisions in the condensed phase, in surface processing, and in the development of nanotechnology.Low-Energy Electron Scattering from Molecules, Biomolecule

  1. Tuning surface porosity on vanadium surface by low energy He{sup +} ion irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Tripathi, J.K., E-mail: jtripat@purdue.edu; Novakowski, T.J.; Hassanein, A.

    2016-08-15

    Highlights: • Surface nanostructuring on vanadium surface using novel He{sup +} ion irradiation process. • Tuning surface-porosity using high-flux, low-energy He{sup +} ion irradiation at constant elevated sample temperature (823–173 K). • Presented top-down approach guarantees good contact between different crystallites. • Sequential significant enhancement in surface-pore edge size (and corresponding reduction in surface-pore density) with increasing sample temperature. - Abstract: In the present study, we report on tuning the surface porosity on vanadium surfaces using high-flux, low-energy He{sup +} ion irradiation as function of sample temperature. Polished, mirror-finished vanadium samples were irradiated with 100 eV He{sup +} ions at a constant ion-flux of 7.2 × 10{sup 20} ions m{sup −2} s{sup −1} for 1 h duration at constant sample temperatures in the wide range of 823–1173 K. Our results show that the surface porosity of V{sub 2}O{sub 5} (naturally oxidized vanadium porous structure, after taking out from UHV) is strongly correlated to the sample temperature and is highly tunable. In fact, the surface porosity significantly increases with reducing sample temperature and reaches up to ∼87%. Optical reflectivity on these highly porous V{sub 2}O{sub 5} surfaces show ∼0% optical reflectivity at 670 nm wavelength, which is very similar to that of “black metal”. Combined with the naturally high melting point of V{sub 2}O{sub 5}, this very low optical reflectivity suggests potential application in solar power concentration technology. Additionally, this top-down approach guarantees relatively good contact between the different crystallites and avoids electrical conductivity limitations (if required). Since V{sub 2}O{sub 5} is naturally a potential photocatalytic material, the resulting sub-micron-sized cube-shaped porous structures could be used in solar water splitting for hydrogen production in energy applications.

  2. Tuning surface porosity on vanadium surface by low energy He+ ion irradiation

    Science.gov (United States)

    Tripathi, J. K.; Novakowski, T. J.; Hassanein, A.

    2016-08-01

    In the present study, we report on tuning the surface porosity on vanadium surfaces using high-flux, low-energy He+ ion irradiation as function of sample temperature. Polished, mirror-finished vanadium samples were irradiated with 100 eV He+ ions at a constant ion-flux of 7.2 × 1020 ions m-2 s-1 for 1 h duration at constant sample temperatures in the wide range of 823-1173 K. Our results show that the surface porosity of V2O5 (naturally oxidized vanadium porous structure, after taking out from UHV) is strongly correlated to the sample temperature and is highly tunable. In fact, the surface porosity significantly increases with reducing sample temperature and reaches up to ∼87%. Optical reflectivity on these highly porous V2O5 surfaces show ∼0% optical reflectivity at 670 nm wavelength, which is very similar to that of "black metal". Combined with the naturally high melting point of V2O5, this very low optical reflectivity suggests potential application in solar power concentration technology. Additionally, this top-down approach guarantees relatively good contact between the different crystallites and avoids electrical conductivity limitations (if required). Since V2O5 is naturally a potential photocatalytic material, the resulting sub-micron-sized cube-shaped porous structures could be used in solar water splitting for hydrogen production in energy applications.

  3. Visualization of the Differential Transition State Stabilization within the Active Site Environment

    Directory of Open Access Journals (Sweden)

    Jerzy Leszczynski

    2004-05-01

    Full Text Available Abstract: Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new interactive method to investigate catalytic effects using differential transition state stabilization approach (DTSS [1, 2] is presented. The catalytic properties of the active site of cytidine deaminase (E.C. 3.5.4.5 is visualized in the form of differential electrostatic properties. The visualization was implemented using scripting interface of VMD [3]. Cumulative Atomic Multipole Moments (CAMM [4,5,6] were utilized for efficient yet accurate evaluation of the electrostatic properties. The implementation is efficient enough for interactive presentation of catalytic effects in the active site of the enzyme due to transition state or substrate movement. This system of visualization of DTTS approach can be potentially used to validate hypotheses regarding the catalytic mechanism or to study binding properties of transition state analogues.

  4. Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

    Science.gov (United States)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

  5. Transition state for the NSD2-catalyzed methylation of histone H3 lysine 36.

    Science.gov (United States)

    Poulin, Myles B; Schneck, Jessica L; Matico, Rosalie E; McDevitt, Patrick J; Huddleston, Michael J; Hou, Wangfang; Johnson, Neil W; Thrall, Sara H; Meek, Thomas D; Schramm, Vern L

    2016-02-02

    Nuclear receptor SET domain containing protein 2 (NSD2) catalyzes the methylation of histone H3 lysine 36 (H3K36). It is a determinant in Wolf-Hirschhorn syndrome and is overexpressed in human multiple myeloma. Despite the relevance of NSD2 to cancer, there are no potent, selective inhibitors of this enzyme reported. Here, a combination of kinetic isotope effect measurements and quantum chemical modeling was used to provide subangstrom details of the transition state structure for NSD2 enzymatic activity. Kinetic isotope effects were measured for the methylation of isolated HeLa cell nucleosomes by NSD2. NSD2 preferentially catalyzes the dimethylation of H3K36 along with a reduced preference for H3K36 monomethylation. Primary Me-(14)C and (36)S and secondary Me-(3)H3, Me-(2)H3, 5'-(14)C, and 5'-(3)H2 kinetic isotope effects were measured for the methylation of H3K36 using specifically labeled S-adenosyl-l-methionine. The intrinsic kinetic isotope effects were used as boundary constraints for quantum mechanical calculations for the NSD2 transition state. The experimental and calculated kinetic isotope effects are consistent with an SN2 chemical mechanism with methyl transfer as the first irreversible chemical step in the reaction mechanism. The transition state is a late, asymmetric nucleophilic displacement with bond separation from the leaving group at (2.53 Å) and bond making to the attacking nucleophile (2.10 Å) advanced at the transition state. The transition state structure can be represented in a molecular electrostatic potential map to guide the design of inhibitors that mimic the transition state geometry and charge.

  6. Heat Capacity Changes for Transition-State Analogue Binding and Catalysis with Human 5'-Methylthioadenosine Phosphorylase.

    Science.gov (United States)

    Firestone, Ross S; Cameron, Scott A; Karp, Jerome M; Arcus, Vickery L; Schramm, Vern L

    2017-02-17

    Human 5'-methylthioadenosine phosphorylase (MTAP) catalyzes the phosphorolysis of 5'-methylthioadenosine (MTA). Its action regulates cellular MTA and links polyamine synthesis to S-adenosylmethionine (AdoMet) salvage. Transition state analogues with picomolar dissociation constants bind to MTAP in an entropically driven process at physiological temperatures, suggesting increased hydrophobic character or dynamic structure for the complexes. Inhibitor binding exhibits a negative heat capacity change (-ΔCp), and thus the changes in enthalpy and entropy upon binding are strongly temperature-dependent. The ΔCp of inhibitor binding by isothermal titration calorimetry does not follow conventional trends and is contrary to that expected from the hydrophobic effect. Thus, ligands of increasing hydrophobicity bind with increasing values of ΔCp. Crystal structures of MTAP complexed to transition-state analogues MT-DADMe-ImmA, BT-DADMe-ImmA, PrT-ImmA, and a substrate analogue, MT-tubercidin, reveal similar active site contacts and overall protein structural parameters, despite large differences in ΔCp for binding. In addition, ΔCp values are not correlated with Kd values. Temperature dependence of presteady state kinetics revealed the chemical step for the MTAP reaction to have a negative heat capacity for transition state formation (-ΔCp(‡)). A comparison of the ΔCp(‡) for MTAP presteady state chemistry and ΔCp for inhibitor binding revealed those transition-state analogues most structurally and thermodynamically similar to the transition state. Molecular dynamics simulations of MTAP apoenzyme and complexes with MT-DADMe-ImmA and MT-tubercidin show small, but increased dynamic motion in the inhibited complexes. Variable temperature CD spectroscopy studies for MTAP-inhibitor complexes indicate remarkable protein thermal stability (to Tm = 99 °C) in complexes with transition-state analogues.

  7. Nanoscale control of energy and matter in plasma-surface interactions: towards energy-efficient nanotech

    Science.gov (United States)

    Ostrikov, Kostya

    2010-11-01

    This presentation focuses on the plasma issues related to the solution of the grand challenge of directing energy and matter at nanoscales. This ability is critical for the renewable energy and energy-efficient technologies for sustainable future development. It will be discussed how to use environmentally and human health benign non-equilibrium plasma-solid systems and control the elementary processes of plasma-surface interactions to direct the fluxes of energy and matter at multiple temporal and spatial scales. In turn, this makes it possible to achieve the deterministic synthesis of self- organised arrays of metastable nanostructures in the size range beyond the reach of the present-day nanofabrication. Such structures have tantalising prospects to enhance performance of nanomaterials in virtually any area of human activity yet remain almost inaccessible because the Nature's energy minimisation rules allow only a small number of stable equilibrium states. By using precisely controlled and kinetically fast nanoscale transfer of energy and matter under non-equilibrium conditions and harnessing numerous plasma- specific controls of species creation, delivery to the surface, nucleation and large-scale self-organisation of nuclei and nanostructures, the arrays of metastable nanostructures can be created, arranged, stabilised, and further processed to meet the specific requirements of the envisaged applications. These approaches will eventually lead to faster, unprecedentedly- clean, human-health-friendly, and energy-efficient nanoscale synthesis and processing technologies for the next-generation renewable energy and light sources, biomedical devices, information and communication systems, as well as advanced functional materials for applications ranging from basic food, water, health and clean environment needs to national security and space missions.

  8. Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

    Directory of Open Access Journals (Sweden)

    Vicente Martí-Centelles

    2012-01-01

    competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

  9. VTST/MT studies of the catalytic mechanism of C-H activation by transition metal complexes with [Cu2(μ-O2)], [Fe2(μ-O2)] and Fe(IV)-O cores based on DFT potential energy surfaces.

    Science.gov (United States)

    Kim, Yongho; Mai, Binh Khanh; Park, Sumin

    2017-04-01

    High-valent Cu and Fe species, which are generated from dioxygen activation in metalloenzymes, carry out the functionalization of strong C-H bonds. Understanding the atomic details of the catalytic mechanism has long been one of the main objectives of bioinorganic chemistry. Large H/D kinetic isotope effects (KIEs) were observed in the C-H activation by high-valent non-heme Cu or Fe complexes in enzymes and their synthetic models. The H/D KIE depends significantly on the transition state properties, such as structure, energies, frequencies, and shape of the potential energy surface, when the tunneling effect is large. Therefore, theoretical predictions of kinetic parameters such as rate constants and KIEs can provide a reliable link between atomic-level quantum mechanical mechanisms and experiments. The accurate prediction of the tunneling effect is essential to reproduce the kinetic parameters. The rate constants and HD/KIE have been calculated using the variational transition-state theory including multidimensional tunneling based on DFT potential energy surfaces along the reaction coordinate. Excellent agreement was observed between the predicted and experimental results, which assures the validity of the DFT potential energy surfaces and, therefore, the proposed atomic-level mechanisms. The [Cu2(μ-O)2], [Fe2(μ-O)2], and Fe(IV)-oxo species were employed for C-H activation, and their role as catalysts was discussed at an atomic level.

  10. Front instability and energy of the free surface

    Science.gov (United States)

    Beltrame, Philippe

    2014-05-01

    In recent years, there has been a proliferation of research devoted to the formation of preferential flow paths occurring without macroscopic heterogeneity of the porous media. DiCarlo (2013) points out the connection between "overshoot" and the front instability. Extension of the standard Richards equation is required to capture this phenomenon. In most of the improvements, interfacial phenomena as the triple line at the front are considered. For instance, velocity dependent contact angle (Wang et al., 2013) or contact angle hysteresis (Rätz and Schweizer, 2012) allow to simulate successfully the instability. Another approach proposed by Cueto-Felgueroso and Juanes (2009) introduces a macroscopic surface tension related to the existence of the water/air interface. As previously, the simulation of an advancing front displays physical looking fingering displacements. The goal of this contribution is to better understand the role of the different surface energies in the emergence of the front instability. We propose a model involving both the macroscopic surface tension and the soil wettability. This latter allows to define a contact angle and possibly hysteresis using heterogeneous wettability (Beltrame et al., 2011). Therefore, we employ the phase field approach developed by Felgueroso and Juanes, 2009 to which we add a free energy term corresponding to the wettability: a disjoining or conjoining pressure resulting from effective molecular interactions between the substrate and the free surface (DeGennes, 1985). The difference with the classical suction pressure is the hydrophobic behavior for ultra-thin film (small water saturation). Such a water repellency was recently estimated in the soil (Diamantopoulos et al. 2013). Stability analysis of an advancing front in an uniform porous media shows that macroscopic surface tension and wettability may independently produce the instability growth. In contrast, for a front stopping when reaching the layers interface of

  11. Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Lipi Thukral

    2011-09-01

    Full Text Available Small globular proteins and peptides commonly exhibit two-state folding kinetics in which the rate limiting step of folding is the surmounting of a single free energy barrier at the transition state (TS separating the folded and the unfolded states. An intriguing question is whether the polypeptide chain reaches, and leaves, the TS by completely random fluctuations, or whether there is a directed, stepwise process. Here, the folding TS of a 15-residue β-hairpin peptide, Peptide 1, is characterized using independent 2.5 μs-long unbiased atomistic molecular dynamics (MD simulations (a total of 15 μs. The trajectories were started from fully unfolded structures. Multiple (spontaneous folding events to the NMR-derived conformation are observed, allowing both structural and dynamical characterization of the folding TS. A common loop-like topology is observed in all the TS structures with native end-to-end and turn contacts, while the central segments of the strands are not in contact. Non-native sidechain contacts are present in the TS between the only tryptophan (W11 and the turn region (P7-G9. Prior to the TS the turn is found to be already locked by the W11 sidechain, while the ends are apart. Once the ends have also come into contact, the TS is reached. Finally, along the reactive folding paths the cooperative loss of the W11 non-native contacts and the formation of the central inter-strand native contacts lead to the peptide rapidly proceeding from the TS to the native state. The present results indicate a directed stepwise process to folding the peptide.

  12. Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory.

    Science.gov (United States)

    Westaway, Kenneth C; Fang, Yao-ren; MacMillar, Susanna; Matsson, Olle; Poirier, Raymond A; Islam, Shahidul M

    2008-10-16

    Nucleophile (11)C/ (14)C [ k (11)/ k (14)] and secondary alpha-deuterium [( k H/ k D) alpha] kinetic isotope effects (KIEs) were measured for the S N2 reactions between tetrabutylammonium cyanide and ethyl iodide, bromide, chloride, and tosylate in anhydrous DMSO at 20 degrees C to determine whether these isotope effects can be used to determine the structure of S N2 transition states. Interpreting the experimental KIEs in the usual fashion (i.e., that a smaller nucleophile KIE indicates the Nu-C alpha transition state bond is shorter and a smaller ( k H/ k D) alpha is found when the Nu-LG distance in the transition state is shorter) suggests that the transition state is tighter with a slightly shorter NC-C alpha bond and a much shorter C alpha-LG bond when the substrate has a poorer halogen leaving group. Theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion. The results show that the experimental nucleophile (11)C/ (14)C KIEs can be used to determine transition-state structure in different reactions and that the usual method of interpreting these KIEs is correct. The magnitude of the experimental secondary alpha-deuterium KIE is related to the nucleophile-leaving group distance in the S N2 transition state ( R TS) for reactions with a halogen leaving group. Unfortunately, the calculated and experimental ( k H/ k D) alpha's change oppositely with leaving group ability. However, the calculated ( k H/ k D) alpha's duplicate both the trend in the KIE with leaving group ability and the magnitude of the ( k H/ k D) alpha's for the ethyl halide reactions when different scale factors are used for the high and the low energy vibrations. This suggests it is critical that different scaling factors for the low and high energy vibrations be used if one wishes to duplicate experimental ( k H/ k D) alpha's. Finally, neither the experimental nor the theoretical secondary alpha-deuterium KIEs for the ethyl tosylate reaction fit the trend found

  13. On the measurement of the surface energy budget over a land surface during the summer monsoon

    Indian Academy of Sciences (India)

    G S Bhat; S C Arunchandra

    2008-12-01

    The measurement of surface energy balance over a land surface in an open area in Bangalore is reported. Measurements of all variables needed to calculate the surface energy balance on time scales longer than a week are made. Components of radiative fluxes are measured while sensible and latent heat fluxes are based on the bulk method using measurements made at two levels on a micrometeorological tower of 10 m height. The bulk flux formulation is verified by comparing its fluxes with direct fluxes using sonic anemometer data sampled at 10 Hz.Soil temperature is measured at 4 depths. Data have been continuously collected for over 6 months covering pre-monsoon and monsoon periods during the year 2006. The study first addresses the issue of getting the fluxes accurately.It is shown that water vapour measurements are the most crucial. A bias of 0.25% in relative humidity,which is well above the normal accuracy assumed by the manufacturers but achievable in the field using a combination of laboratory calibration and field intercomparisons, results in about 20 W m−2 change in the latent heat flux on the seasonal time scale. When seen on the seasonal time scale,the net longwave radiation is the largest energy loss term at the experimental site. The seasonal variation in the energy sink term is small compared to that in the energy source term.

  14. New Material Development for Surface Layer and Surface Technology in Tribology Science to Improve Energy Efficiency

    Science.gov (United States)

    Ismail, R.; Tauviqirrahman, M.; Jamari, Jamari; Schipper, D. J.

    2009-09-01

    This paper reviews the development of new material and surface technology in tribology and its contribution to energy efficiency. Two examples of the economic benefits, resulted from the optimum tribology in the transportation sector and the manufacturing industry are discussed. The new materials are proposed to modify the surface property by laminating the bulk material with thin layer/coating. Under a suitable condition, the thin layer on a surface can provide a combination of good wear, a low friction and corrosion resistance for the mechanical components. The innovation in layer technology results molybdenum disulfide (MoS2), diamond like carbon (DLC), cubic boron nitride (CBN) and diamond which perform satisfactory outcome. The application of the metallic coatings to carbon fibre reinforced polymer matrix composites (CFRP) has the capacity to provide considerable weight and power savings for many engineering components. The green material for lubricant and additives such as the use of sunflower oil which possesses good oxidation resistance and the use of mallee leaves as bio-degradable solvent are used to answer the demand of the environmentally friendly material with good performance. The tribology research implementation for energy efficiency also touches the simple things around us such as: erasing the laser-print in a paper with different abrasion techniques. For the technology in the engineering surface, the consideration for generating the suitable surface of the components in running-in period has been discussed in order to prolong the components life and reduce the machine downtime. The conclusion, tribology can result in reducing manufacturing time, reducing the maintenance requirements, prolonging the service interval, improving durability, reliability and mechanical components life, and reducing harmful exhaust emission and waste. All of these advantages will increase the energy efficiency and the economic benefits.

  15. Delta self-consistent field method to obtain potential energy surfaces of excited molecules on surfaces

    DEFF Research Database (Denmark)

    Gavnholt, Jeppe; Olsen, Thomas; Engelund, Mads;

    2008-01-01

    We present a modification of the Delta self-consistent field (Delta SCF) method of calculating energies of excited states in order to make it applicable to resonance calculations of molecules adsorbed on metal surfaces, where the molecular orbitals are highly hybridized. The Delta SCF approximation...... is a density-functional method closely resembling standard density-functional theory (DFT), the only difference being that in Delta SCF one or more electrons are placed in higher lying Kohn-Sham orbitals instead of placing all electrons in the lowest possible orbitals as one does when calculating the ground......-state energy within standard DFT. We extend the Delta SCF method by allowing excited electrons to occupy orbitals which are linear combinations of Kohn-Sham orbitals. With this extra freedom it is possible to place charge locally on adsorbed molecules in the calculations, such that resonance energies can...

  16. Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface

    Science.gov (United States)

    Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.

  17. A land surface scheme for atmospheric and hydrologic models: SEWAB (Surface Energy and Water Balance)

    Energy Technology Data Exchange (ETDEWEB)

    Mengelkamp, H.T.; Warrach, K.; Raschke, E. [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Atmosphaerenphysik

    1997-12-31

    A soil-vegetation-atmosphere-transfer scheme is presented here which solves the coupled system of the Surface Energy and Water Balance (SEWAB) equations considering partly vegetated surfaces. It is based on the one-layer concept for vegetation. In the soil the diffusion equations for heat and moisture are solved on a multi-layer grid. SEWAB has been developed to serve as a land-surface scheme for atmospheric circulation models. Being forced with atmospheric data from either simulations or measurements it calculates surface and subsurface runoff that can serve as input to hydrologic models. The model has been validated with field data from the FIFE experiment and has participated in the PILPS project for intercomparison of land-surface parameterization schemes. From these experiments we feel that SEWAB reasonably well partitions the radiation and precipitation into sensible and latent heat fluxes as well as into runoff and soil moisture Storage. (orig.) [Deutsch] Ein Landoberflaechenschema wird vorgestellt, das den Transport von Waerme und Wasser zwischen dem Erdboden, der Vegetation und der Atmosphaere unter Beruecksichtigung von teilweise bewachsenem Boden beschreibt. Im Erdboden werden die Diffusionsgleichungen fuer Waerme und Feuchte auf einem Gitter mit mehreren Schichten geloest. Das Schema SEWAB (Surface Energy and Water Balance) beschreibt die Landoberflaechenprozesse in atmosphaerischen Modellen und berechnet den Oberflaechenabfluss und den Basisabfluss, die als Eingabedaten fuer hydrologische Modelle genutzt werden koennen. Das Modell wurde mit Daten des FIFE-Experiments kalibriert und hat an Vergleichsexperimenten fuer Landoberflaechen-Schemata im Rahmen des PILPS-Projektes teilgenommen. Dabei hat sich gezeigt, dass die Aufteilung der einfallenden Strahlung und des Niederschlages in den sensiblen und latenten Waermefluss und auch in Abfluss und Speicherung der Bodenfeuchte in SEWAB den beobachteten Daten recht gut entspricht. (orig.)

  18. High surface area aerogels for energy storage and efficiency

    Science.gov (United States)

    Maloney, Ryan Patrick

    ADAI are demonstrated in a third-generation prototypical thermoelectric generator for automotive waste heat recovery. The second chapter then details two different aerogel-based materials for electrochemical energy storage. It begins with lithium titanate aerogel, which takes advantage of the high surface area of the aerogel morphology to display a batt-cap behavior. This should allow the lithium titanate aerogel to perform at higher rates than would normally be expected for the bulk oxide material. Additionally, the flexibility of the sol-gel process is demonstrated through the incorporation of electrically conductive high-surface area exfoliated graphite nanoplatelets in the oxide. The last section describes the characterization of a LiMn2O 4 spinel coated carbon nanofoam in a non-aqueous electrolyte. The short diffusion path, high surface area and intimately wired architecture of the nanofoam allows the oxide to retain its capacity at significantly higher rates when compared with literature values for the bulk oxide. Additionally, the nanometric length scale improves cycle life, and the high surface area dramatically increases the insertion capacity by providing a higher concentration of surface defects. Taken together, it is clear that aerogels are an extremely attractive class of material for applications pertaining to energy and efficiency, and further research in this area will provide valuable solutions for pressing societal needs. (Abstract shortened by UMI.).

  19. Pseudospectral Gaussian quantum dynamics: Efficient sampling of potential energy surfaces

    Science.gov (United States)

    Heaps, Charles W.; Mazziotti, David A.

    2016-04-01

    Trajectory-based Gaussian basis sets have been tremendously successful in describing high-dimensional quantum molecular dynamics. In this paper, we introduce a pseudospectral Gaussian-based method that achieves accurate quantum dynamics using efficient, real-space sampling of the time-dependent basis set. As in other Gaussian basis methods, we begin with a basis set expansion using time-dependent Gaussian basis functions guided by classical mechanics. Unlike other Gaussian methods but characteristic of the pseudospectral and collocation methods, the basis set is tested with N Dirac delta functions, where N is the number of basis functions, rather than using the basis function as test functions. As a result, the integration for matrix elements is reduced to function evaluation. Pseudospectral Gaussian dynamics only requires O ( N ) potential energy calculations, in contrast to O ( N 2 ) evaluations in a variational calculation. The classical trajectories allow small basis sets to sample high-dimensional potentials. Applications are made to diatomic oscillations in a Morse potential and a generalized version of the Henon-Heiles potential in two, four, and six dimensions. Comparisons are drawn to full analytical evaluation of potential energy integrals (variational) and the bra-ket averaged Taylor (BAT) expansion, an O ( N ) approximation used in Gaussian-based dynamics. In all cases, the pseudospectral Gaussian method is competitive with full variational calculations that require a global, analytical, and integrable potential energy surface. Additionally, the BAT breaks down when quantum mechanical coherence is particularly strong (i.e., barrier reflection in the Morse oscillator). The ability to obtain variational accuracy using only the potential energy at discrete points makes the pseudospectral Gaussian method a promising avenue for on-the-fly dynamics, where electronic structure calculations become computationally significant.

  20. Selectivity for CO2 over CH4 on a functionalized periodic mesoporous phenylene-silica explained by transition state theory

    Science.gov (United States)

    Kunkel, Christian; Viñes, Francesc; Lourenço, Mirtha A. O.; Ferreira, Paula; Gomes, José R. B.; Illas, Francesc

    2017-03-01

    Efficient separation of CO2/CH4 is critical in biogas upgrading, requiring highly selective adsorbents. Based on the adsorption energies of -0.30 and -0.14 eV, previously calculated by dispersion corrected density functional theory for adsorption/desorption of CO2 and CH4 on the functionalized periodic mesoporous phenylene-silica material APTMS@Ph-PMO, respectively, transition state theory rates were derived and used to simulate the adsorption/desorption rates of these two gases on APTMS@Ph-PMO. The latter yielded an estimation of initial CO2/CH4 selectivity at various temperatures. At T = 298 K, selectivity of 32.2 agrees to an experimental value of 26.1, which validates the method used for evaluating CO2/CH4 adsorption selectivities.

  1. Estimation of surface energy fluxes under complex terrain of Mt. Qomolangma over the Tibetan Plateau

    NARCIS (Netherlands)

    Chen, Xuelong; Su, Zhongbo; Ma, Y.; Yang, K.; Wang, B.

    2013-01-01

    Surface solar radiation is an important parameter in surface energy balance models and in estimation of evapotranspiration. This study developed a DEM based radiation model to estimate instantaneous clear sky solar radiation for surface energy balance system to obtain accurate energy absorbed by the

  2. Efficient Computation of Transition State Resonances and Reaction Rates from a Quantum Normal Form

    NARCIS (Netherlands)

    Schubert, Roman; Waalkens, Holger; Wiggins, Stephen

    2006-01-01

    A quantum version of a recent formulation of transition state theory in phase space is presented. The theory developed provides an algorithm to compute quantum reaction rates and the associated Gamov-Siegert resonances with very high accuracy. The algorithm is especially efficient for multi-degree-o

  3. Wigner's dynamical transition state theory in phase space : classical and quantum

    NARCIS (Netherlands)

    Waalkens, Holger; Schubert, Roman; Wiggins, Stephen

    2008-01-01

    We develop Wigner's approach to a dynamical transition state theory in phase space in both the classical and quantum mechanical settings. The key to our development is the construction of a normal form for describing the dynamics in the neighbourhood of a specific type of saddle point that governs t

  4. Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

    NARCIS (Netherlands)

    Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.

    2007-01-01

    A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which expe

  5. Synthesis, surface characterization, and biointeraction studies of low-surface energy side-chain polyetherurethanes

    Science.gov (United States)

    Porter, Stephen Christopher

    1999-10-01

    New segmented polyetherurethanes (PEUs) with low surface energy hydrocarbon and fluorocarbon side-chains attached to the polymer hard segments were synthesized. The surface chemistry of solvent cast polymer films was studied using X-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectrometry, and dynamic contact angle (DCA) measurements. Increases in the overall density and length of the alkyl side-chains within the PEUs resulted in greater side-chain concentrations at the polymer surface. PEUs bearing long alkyl (> C10 ) and perfluorocarbon side-chains were found to posses surfaces with highly enriched side-chain concentrations relative to the bulk polymer. In PEUs with significant side-chain surface enrichment, the relatively polar hard segment blocks were shown to reside in high concentrations just below the side-chain enriched surface layer. Furthermore, DCA measurements demonstrated that the surface of the alkyl side-chain PEUs did not undergo significant rearrangement when placed into an aqueous environment, whereas the surface of a hard segment model polymer bearing C18 sidechains (PEU-C18-HS) did. Hydrogen bonding within the PEUs was examined using FTIR and was shown to be disrupted by the addition of side-chains; an effect dependent on the density but not on the length of the side-chains. Heteropolymer blends comprised of mixtures of high side-chain density and side-chain free PEUs were compared with homopolymers having the same overall side-chain concentration as the blends. Significantly more surface enrichment of side-chains was found in the heteropolymer blends whereas hydrogen bonding nearly the same as in the homopolymers. Adsorption of native and delipidized human serum albumin (HSA) from pure solution and blood plasma; the elutabilty of adsorbed HSA; and static platelet adhesion to plasma preadsorbed surfaces, were all examined on alkyl side-chain PEUs. Several polymers with high C18 side-chain densities displayed increased

  6. Accuracy of Low-level Surface in Hierarchical Construction of Potential Energy Surface

    Institute of Scientific and Technical Information of China (English)

    Chun-rui Wang; Dong H. Zhang

    2012-01-01

    The effects of low-level PES on the overall accuracy of the final surface constructed by using hierarchical construction were investigated with the constructions of a number of global surfaces for the H3 system at UHF (UMP2,DFT-B3LYP,UCCSD(T))/vtz,and UCCSD(T)/avqz levels of theory.The total reaction probabilities for the H+H2 reaction calculated on these surfaces revealed that the accuracy of UCCSD(T)/avqz surface is very close to the well-known BKMP2 surface,while the UCCSD(T)/vtz PES has a slightly higher barrier.In contrast,the low-level theories (UHF,UMP2,DFT-B3LYP) with vtz basis set can only provide a qualitative description of this simplest reaction despite the fact that they are widely used to study reactions in complex systems.On the other hand,although these theories are not accurate on describing the reaction,they can be used to provide the lowlevel PESs for hierarchical construction of the UCCSD(T)/avqz PES with the number of UCCSD(T)/avqz energies substantially reduced.

  7. Effects of Zr doping on the surface energy and surface structure of UO{sub 2}: Atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Hongxing, E-mail: xiaohongxing2003@163.com [Science and Technology on Reactor Fuel and Materials Laboratory, Nuclear Power Institute of China, Chengdu (China); Long, Chongsheng; Chen, Hongsheng [Science and Technology on Reactor Fuel and Materials Laboratory, Nuclear Power Institute of China, Chengdu (China); Tian, Xiaofeng [The College of Nuclear Technology and Automation Engineering, Chengdu University of Technology, Chengdu (China); Wei, Tianguo; Zhao, Yi; Gao, Wen [Science and Technology on Reactor Fuel and Materials Laboratory, Nuclear Power Institute of China, Chengdu (China)

    2015-10-01

    A shell-core model is applied to investigate the effects of Zr doping on the surface energies and surface structures of the three low Miller index surfaces in UO{sub 2} using the molecular dynamics (MD) technique. The surface energies and atomic structures of the Zr-doped and undoped UO{sub 2} (1 0 0), (1 1 0) and (1 1 1) surfaces are compared. Simulation results indicate that (i) the surface energy of (U{sub 1−y}Zr{sub y})O{sub 2} depend on the crystallographic orientation, as well as of undoped UO{sub 2}. The (1 0 0) surface exhibits the highest surface energy, followed by the (1 1 0) surface, and the (1 1 1) surface; (ii) Zr doping will significantly increase the surface energy of UO{sub 2} by approximately 20% on (1 0 0) surface, 10% on (1 1 0) surface and 15% on (1 1 1) surface with the ZrO{sub 2} contents ranging from 0 to 12.5 mol%, respectively; (iii) the surface energies of the three low Miller index surfaces decrease with increasing temperature both in undoped UO{sub 2} and in (U{sub 1−y}Zr{sub y})O{sub 2}; (iv) the addition of Zr induces a severe distortion of the (U{sub 1−y}Zr{sub y})O{sub 2} surface structure, and the outermost top layer exhibits the strongest rumpling; (v) the considerable reconstructions can be observed in the two top layers of Zr-doped and undoped UO{sub 2} surfaces when the temperature is elevated to 900–1500 K.

  8. High Accuracy Potential Energy Surface, Dipole Moment Surface, Rovibrational Energies and Line List Calculations for ^{14}NH_3

    Science.gov (United States)

    Coles, Phillip; Yurchenko, Sergei N.; Polyansky, Oleg; Kyuberis, Aleksandra; Ovsyannikov, Roman I.; Zobov, Nikolay Fedorovich; Tennyson, Jonathan

    2017-06-01

    We present a new spectroscopic potential energy surface (PES) for ^{14}NH_3, produced by refining a high accuracy ab initio PES to experimental energy levels taken predominantly from MARVEL. The PES reproduces 1722 matched J=0-8 experimental energies with a root-mean-square error of 0.035 cm-1 under 6000 cm^{-1} and 0.059 under 7200 cm^{-1}. In conjunction with a new DMS calculated using multi reference configuration interaction (MRCI) and H=aug-cc-pVQZ, N=aug-cc-pWCVQZ basis sets, an infrared (IR) line list has been computed which is suitable for use up to 2000 K. The line list is used to assign experimental lines in the 7500 - 10,500 cm^{-1} region and previously unassigned lines in HITRAN in the 6000-7000 cm^{-1} region. Oleg L. Polyansky, Roman I. Ovsyannikov, Aleksandra A. Kyuberis, Lorenzo Lodi, Jonathan Tennyson, Andrey Yachmenev, Sergei N. Yurchenko, Nikolai F. Zobov, J. Mol. Spec., 327 (2016) 21-30 Afaf R. Al Derzia, Tibor Furtenbacher, Jonathan Tennyson, Sergei N. Yurchenko, Attila G. Császár, J. Quant. Spectrosc. Rad. Trans., 161 (2015) 117-130

  9. Experimental cross-sections energy dependence and an ab initio electronic structure survey of the ground singlet potential surface for reactive Li(+) + n-C(3)H(7)Cl collisions at low energies.

    Science.gov (United States)

    Lucas, José María; de Andrés, Jaime; Albertí, Margarita; Bofill, Josep Maria; Bassi, Davide; Aguilar, Antonio

    2010-11-07

    Reactive collisions between n-C(3)H(7)Cl molecules and lithium ions both in their ground electronic state have been studied in the 0.05-7.00 eV center of mass energy range using an octopole radio frequency guided-ion beam apparatus developed in our laboratory and recently modified. At low collision energies, dehydrohalogenation reactions leading to Li(C(3)H(6))(+) and Li(HCl)(+) are the main reaction channels, while on increasing energies C(3)H(7)(+) and C(2)H(3)(+) formation become dominant. Cross section energy dependences in arbitrary units for all these reactions have been measured. Also, ab initio electronic structure calculations at the MP2 level have been performed to obtain information about the potential energy surface on which the reactive processes take place. The reactants' entrance channel leads to the formation of a stable [Li-n-C(3)H(7)Cl](+) ion-molecule adduct that, following an intrinsic-reaction-coordinate pathway and surmounting a transition state, isomerizes to [Li-i-C(3)H(7)Cl](+). From this second minimum, dehydrohalogenation reactions for both n-C(3)H(7)Cl and i-C(3)H(7)Cl share a common reaction pathway leading to the same products. All potential barriers explored by reactions always lie below the reactants' energy. The entrance reaction channel [Li-n-C(3)H(7)Cl](+) adduct also leads adiabatically to C(3)H(7)(+) formation which, on increasing collision energy generates C(2)H(3)(+)via a unimolecular decomposition. A qualitative interpretation of the experimental results based on our ab initio calculations is also given.

  10. Improved DFT Potential Energy Surfaces via Improved Densities.

    Science.gov (United States)

    Kim, Min-Cheol; Park, Hansol; Son, Suyeon; Sim, Eunji; Burke, Kieron

    2015-10-01

    Density-corrected DFT is a method that cures several failures of self-consistent semilocal DFT calculations by using a more accurate density instead. A novel procedure employs the Hartree-Fock density to bonds that are more severely stretched than ever before. This substantially increases the range of accurate potential energy surfaces obtainable from semilocal DFT for many heteronuclear molecules. We show that this works for both neutral and charged molecules. We explain why and explore more difficult cases, for example, CH(+), where density-corrected DFT results are even better than sophisticated methods like CCSD. We give a simple criterion for when DC-DFT should be more accurate than self-consistent DFT that can be applied for most cases.

  11. Identification of Swell in Nearshore Surface Wave Energy Spectra

    Directory of Open Access Journals (Sweden)

    Paul A. Work

    2010-06-01

    Full Text Available An approach for routine identification of swell and sea in nominally fully developed, omnidirectional, surface water wave energy spectra measured in arbitrary water depth is developed, applied, and discussed. The methodology is an extension of earlier work with deepwater spectra and involves identifying the frequency at which wave steepness is maximized and relating this to the swell separation frequency. The TMA parameterized spectrum is employed to establish a relationship between the two frequencies so that the methodology can be used when wind data are unavailable. The methodology is developed for finite water depth and tested using a dataset that includes both acoustic Doppler current profiler and wave buoy data, recorded simultaneously at the same location. For cases where the sea and swell are clearly, visually distinguishable in the omnidirectional spectra, the new method accurately distinguishes between the two, but it can also be used to identify sea and swell in unimodal spectra.

  12. A global potential energy surface and dipole moment surface for silane.

    Science.gov (United States)

    Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Thiel, Walter

    2015-12-28

    A new nine-dimensional potential energy surface (PES) and dipole moment surface (DMS) for silane have been generated using high-level ab initio theory. The PES, CBS-F12(HL), reproduces all four fundamental term values for (28)SiH4 with sub-wavenumber accuracy, resulting in an overall root-mean-square error of 0.63 cm(-1). The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit, and incorporates a range of higher-level additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, and scalar relativistic effects. Systematic errors in computed intra-band rotational energy levels are reduced by empirically refining the equilibrium geometry. The resultant Si-H bond length is in excellent agreement with previous experimental and theoretical values. Vibrational transition moments, absolute line intensities of the ν3 band, and the infrared spectrum for (28)SiH4 including states up to J = 20 and vibrational band origins up to 5000 cm(-1) are calculated and compared with available experimental results. The DMS tends to marginally overestimate the strength of line intensities. Despite this, band shape and structure across the spectrum are well reproduced and show good agreement with experiment. We thus recommend the PES and DMS for future use.

  13. A global potential energy surface and dipole moment surface for silane

    Energy Technology Data Exchange (ETDEWEB)

    Owens, Alec, E-mail: owens@mpi-muelheim.mpg.de [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Yurchenko, Sergei N.; Yachmenev, Andrey [Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Thiel, Walter [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)

    2015-12-28

    A new nine-dimensional potential energy surface (PES) and dipole moment surface (DMS) for silane have been generated using high-level ab initio theory. The PES, CBS-F12{sup HL}, reproduces all four fundamental term values for {sup 28}SiH{sub 4} with sub-wavenumber accuracy, resulting in an overall root-mean-square error of 0.63 cm{sup −1}. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit, and incorporates a range of higher-level additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, and scalar relativistic effects. Systematic errors in computed intra-band rotational energy levels are reduced by empirically refining the equilibrium geometry. The resultant Si–H bond length is in excellent agreement with previous experimental and theoretical values. Vibrational transition moments, absolute line intensities of the ν{sub 3} band, and the infrared spectrum for {sup 28}SiH{sub 4} including states up to J = 20 and vibrational band origins up to 5000 cm{sup −1} are calculated and compared with available experimental results. The DMS tends to marginally overestimate the strength of line intensities. Despite this, band shape and structure across the spectrum are well reproduced and show good agreement with experiment. We thus recommend the PES and DMS for future use.

  14. Surface layer scintillometry for estimating the sensible heat flux component of the surface energy balance

    Directory of Open Access Journals (Sweden)

    M. J. Savage

    2010-01-01

    Full Text Available The relatively recently developed scintillometry method, with a focus on the dual-beam surface layer scintillometer (SLS, allows boundary layer atmospheric turbulence, surface sensible heat and momentum flux to be estimated in real-time. Much of the previous research using the scintillometer method has involved the large aperture scintillometer method, with only a few studies using the SLS method. The SLS method has been mainly used by agrometeorologists, hydrologists and micrometeorologists for atmospheric stability and surface energy balance studies to obtain estimates of sensible heat from which evaporation estimates representing areas of one hectare or larger are possible. Other applications include the use of the SLS method in obtaining crucial input parameters for atmospheric dispersion and turbulence models. The SLS method relies upon optical scintillation of a horizontal laser beam between transmitter and receiver for a separation distance typically between 50 and 250 m caused by refractive index inhomogeneities in the atmosphere that arise from turbulence fluctuations in air temperature and to a much lesser extent the fluctuations in water vapour pressure. Measurements of SLS beam transmission allow turbulence of the atmosphere to be determined, from which sub-hourly, real-time and in situ path-weighted fluxes of sensible heat and momentum may be calculated by application of the Monin-Obukhov similarity theory. Unlike the eddy covariance (EC method for which corrections for flow distortion and coordinate rotation are applied, no corrections to the SLS measurements, apart from a correction for water vapour pressure, are applied. Also, path-weighted SLS estimates over the propagation path are obtained. The SLS method also offers high temporal measurement resolution and usually greater spatial coverage compared to EC, Bowen ratio energy balance, surface renewal and other sensible heat measurement methods. Applying the shortened surface

  15. Selective Covalent Chemistry via Gas-Phase Ion/ion Reactions: An Exploration of the Energy Surfaces Associated with N-Hydroxysuccinimide Ester Reagents and Primary Amines and Guanidine Groups

    Science.gov (United States)

    Bu, Jiexun; Fisher, Christine M.; Gilbert, Joshua D.; Prentice, Boone M.; McLuckey, Scott A.

    2016-06-01

    Selective covalent bond forming reactions (referred to as covalent reactions) can occur in gas-phase ion/ion reactions and take place via the formation of a long-lived chemical complex. The gas-phase ion/ion reactivity between sulfo- N-hydroxysuccinimide (sulfo-NHS) ester reagent anions and peptide cations containing a primary amine or guanidine group has been examined via DFT calculations and complex dissociation rate measurements. The results reveal insights regarding the roles of the barriers of competing processes within the complex. When the covalent reaction is exothermic, two prototypical cases, determined by the nature of the energy surface, are apparent. The product partitioning between covalent reaction and simple proton transfer upon dissociation of the long-lived complex is sensitive to activation conditions when the transition state barrier for covalent reaction is relatively high ( case 1) but is insensitive to activation conditions when the transition state barrier is relatively low ( case 2). Covalent reaction efficiencies are very high in case 2 scenarios, such as when the reactive site is a guanidine and the anion attachment site is a guanidinium ion. Covalent reaction efficiencies are variable, and generally low, in case 1 scenarios, such as when an amine is the reactive site and an ammonium ion is the site of anion attachment. A relatively long slow-heating step prior to the complex dissociation step, however, can dramatically increase covalent reaction yield in case 1 scenarios.

  16. Microscopically derived potential energy surfaces from mostly structural considerations

    Energy Technology Data Exchange (ETDEWEB)

    Ermamatov, M.J. [Instituto de Física, Universidade Federal Fluminense, 24210-340, Niterói, Rio de Janeiro (Brazil); Institute of Nuclear Physics, Ulughbek, Tashkent 100214 (Uzbekistan); Hess, Peter O., E-mail: hess@nucleares.unam.mx [Instituto de Ciencias Nucleares, UNAM, Circuito Exterior, C.U., A.P. 70-543, 04510, Mexico D.F. (Mexico)

    2016-08-15

    A simple procedure to estimate the quadrupole Potential-Energy-Surface (PES) is presented, using mainly structural information, namely the content of the shell model space and the Pauli exclusion principle. Further microscopic properties are implicitly contained through the use of results from the Möller and Nix tables or experimental information. A mapping to the geometric potential is performed yielding the PES. The General Collective Model is used in order to obtain an estimate on the spectrum and quadrupole transitions, adjusting only the mass parameter. First, we test the conjecture on known nuclei, deriving the PES and compare them to known data. We will see that the PES approximates very well the structure expected. Having acquired a certain confidence, we predict the PES of several chain of isotopes of heavy and super-heavy nuclei and at the end we investigate the structure of nuclei in the supposed island of stability. One of the main points to show is that simple assumptions can provide already important information on the structure of nuclei outside known regions and that spectra and electromagnetic transitions can be estimated without using involved calculations and assumptions. The procedure does not allow to calculate binding energies. The method presented can be viewed as a starting point for further improvements.

  17. A metamaterial electromagnetic energy rectifying surface with high harvesting efficiency

    Science.gov (United States)

    Duan, Xin; Chen, Xing; Zhou, Lin

    2016-12-01

    A novel metamaterial rectifying surface (MRS) for electromagnetic energy capture and rectification with high harvesting efficiency is presented. It is fabricated on a three-layer printed circuit board, which comprises an array of periodic metamaterial particles in the shape of mirrored split rings, a metal ground, and integrated rectifiers employing Schottky diodes. Perfect impedance matching is engineered at two interfaces, i.e. one between free space and the surface, and the other between the metamaterial particles and the rectifiers, which are connected through optimally positioned vias. Therefore, the incident electromagnetic power is captured with almost no reflection by the metamaterial particles, then channeled maximally to the rectifiers, and finally converted to direct current efficiently. Moreover, the rectifiers are behind the metal ground, avoiding the disturbance of high power incident electromagnetic waves. Such a MRS working at 2.45 GHz is designed, manufactured and measured, achieving a harvesting efficiency up to 66.9% under an incident power density of 5 mW/cm2, compared with a simulated efficiency of 72.9%. This high harvesting efficiency makes the proposed MRS an effective receiving device in practical microwave power transmission applications.

  18. A finite difference Davidson procedure to sidestep full ab initio hessian calculation: application to characterization of stationary points and transition state searches.

    Science.gov (United States)

    Sharada, Shaama Mallikarjun; Bell, Alexis T; Head-Gordon, Martin

    2014-04-28

    The cost of calculating nuclear hessians, either analytically or by finite difference methods, during the course of quantum chemical analyses can be prohibitive for systems containing hundreds of atoms. In many applications, though, only a few eigenvalues and eigenvectors, and not the full hessian, are required. For instance, the lowest one or two eigenvalues of the full hessian are sufficient to characterize a stationary point as a minimum or a transition state (TS), respectively. We describe here a method that can eliminate the need for hessian calculations for both the characterization of stationary points as well as searches for saddle points. A finite differences implementation of the Davidson method that uses only first derivatives of the energy to calculate the lowest eigenvalues and eigenvectors of the hessian is discussed. This method can be implemented in conjunction with geometry optimization methods such as partitioned-rational function optimization (P-RFO) to characterize stationary points on the potential energy surface. With equal ease, it can be combined with interpolation methods that determine TS guess structures, such as the freezing string method, to generate approximate hessian matrices in lieu of full hessians as input to P-RFO for TS optimization. This approach is shown to achieve significant cost savings relative to exact hessian calculation when applied to both stationary point characterization as well as TS optimization. The basic reason is that the present approach scales one power of system size lower since the rate of convergence is approximately independent of the size of the system. Therefore, the finite-difference Davidson method is a viable alternative to full hessian calculation for stationary point characterization and TS search particularly when analytical hessians are not available or require substantial computational effort.

  19. Experimental and Theoretical Studies of the F(•) + H-F Transition-State Region by Photodetachment of [F-H-F]().

    Science.gov (United States)

    Hou, Gao-Lei; Wang, Xue-Bin; McCoy, Anne B; Borden, Weston Thatcher

    2017-10-06

    The transition-state (TS) region of the simplest heavy-light-heavy type of reaction, F(•) + H-F → F-H + F(•), is investigated in this work by a joint experimental and theoretical approach. Photodetaching the bifluoride anion, [F···H···F](-), generates a negative ion photoelectron (NIPE) spectrum with three partially resolved bands in the electron binding energy (eBE) range of 5.4-7.0 eV. These bands correspond to the transition from the ground state of the anion to the electronic ground state of [F-H-F](•) neutral, with associated vibrational excitations. The significant increase of eBE of the bifluoride anion, relative to that of F(-), reflects a hydrogen bond energy between F(-) and HF of ∼46 kcal/mol. Theoretical modeling reveals that the antisymmetric motion of H between the two F atoms, near the TS on the neutral [F-H-F](•) surface, dominates the observed three bands, while the F-H-F bending, F-F symmetric stretching modes, and the couplings between them are calculated to account for the breadth of the observed spectrum. From the NIPE spectrum, a lower limit on the activation enthalpy for F(•) + H-F → F-H + F(•) can be estimated to be ΔH(‡) = 12 ± 2 kcal/mol, a value below that of ΔH(‡) = 14.9 kcal/mol, given by our G4 calculations.

  20. Manipulating Surface Energy to form Compound Semiconductor Nanostructures

    Science.gov (United States)

    DeJarld, Matthew T.

    Nanostructures have been lauded for their quantum confinement capabilities and potential applications in future devices. Compound semiconductor nanostructures are being integrated into the next generation of photovoltaic and light emitting devices to take advantage of their unique optical characteristics. Despite their promise, adoption of nanostructure based devices has been slow. This is due in large part to difficulties in effective fabrication and processing steps. By manipulating the surface energy of various components during growth, we can control the final structure and corresponding optoelectronic characteristics. Specifically I will present on GaSb quantum dots embedded in GaAs and GaAs nanowires using novel substrate and catalyst materials. GaSb quantum dots embedded in a GaAs matrix are ideal for devices that require capture of minority carriers as they exhibit a type II band offset with carrier concentration in the valence band. However, during GaAs capping, there is a strong driving force for the dot to demolish into a distribution of intact dots, rings, and GaSb material clusters. We demonstrate the ability to mitigate this effect using both chemical and kinetic means: we alter the surface chemistry via the addition of aluminum, and use droplet epitaxy as an alternative quantum dot formation method. Secondly, the growth of high quality GaAs on silicon has always been restricted due to material incompatibilities. With the emergence of increasingly smaller low power electronics, there is a demand to integrate optoelectronic devices directly on the surface of CMOS sensor stacks. Utilizing the vapor-liquid-solid growth mechanism we are able to demonstrate the growth of high quality GaAs nanowires on polycrystalline substrates at low temperatures. This allows for the growth of III-V nanowire based devices directly on the metal pads of pre-packaged CMOS chips. We also investigate the potential use of bismuth as an alternative to gold for catalyzing

  1. Surface structure and energy of B2 type intermetallic compound NiAl

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Jianmin [College of Physics and Information Technology, Shaanxi Normal University, Xian 710062, Shaanxi (China)], E-mail: jianm_zhang@yahoo.com; Wang Doudou [College of Physics and Information Technology, Shaanxi Normal University, Xian 710062, Shaanxi (China); Institute of Telecommunication Engineering of the Air Force Engineering University (AFEU1), Xian 710077, Shaanxi (China); Chen Guoxiang [School of Science, Xian Shiyou University, Xian 710065, Shaanxi (China); Xu Kewei [State Key Laboratory for Mechanical Behavior of Materials, Xian Jiaotong University, Xian 710049, Shaanxi (China)

    2008-02-15

    The surface structure and energies for 22 surfaces of NiAl, an ordered intermetallic compound of B2 structure, have been studied by using embedded atom method. The results show that, for alternating Ni and Al surfaces with odd numbers of the sum of their three Miller indices, the energy difference between the Ni terminated surface and Al terminated surface increase linearly with increasing the interlayer distance. So from surface energy minimization, the Al terminated surface is favorable for each alternating Ni and Al surface. This is in agreement with experimental results. However, the energy of the (1 1 0) surface belonged to the other kind of the surface consisted of stoichiometric atomic layers and with even numbers of the sum of their three Miller indices, is the lowest in all two kinds of the surfaces. Therefore the (1 1 0) texture of NiAl appears mostly in the experiments.

  2. Vibrational energies for HFCO using a neural network sum of exponentials potential energy surface.

    Science.gov (United States)

    Pradhan, Ekadashi; Brown, Alex

    2016-05-07

    A six-dimensional potential energy surface (PES) for formyl fluoride (HFCO) is fit in a sum-of-products form using neural network exponential fitting functions. The ab initio data upon which the fit is based were computed at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations [CCSD(T)-F12]/cc-pVTZ-F12 level of theory. The PES fit is accurate (RMSE = 10 cm(-1)) up to 10 000 cm(-1) above the zero point energy and covers most of the experimentally measured IR data. The PES is validated by computing vibrational energies for both HFCO and deuterated formyl fluoride (DFCO) using block improved relaxation with the multi-configuration time dependent Hartree approach. The frequencies of the fundamental modes, and all other vibrational states up to 5000 cm(-1) above the zero-point energy, are more accurate than those obtained from the previous MP2-based PES. The vibrational frequencies obtained on the PES are compared to anharmonic frequencies at the MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ levels of theory obtained using second-order vibrational perturbation theory. The new PES will be useful for quantum dynamics simulations for both HFCO and DFCO, e.g., studies of intramolecular vibrational redistribution leading to unimolecular dissociation and its laser control.

  3. Converting chemical energy into electricity through a functionally cooperating device with diving-surfacing cycles.

    Science.gov (United States)

    Song, Mengmeng; Cheng, Mengjiao; Ju, Guannan; Zhang, Yajun; Shi, Feng

    2014-11-05

    A smart device that can dive or surface in aqueous medium has been developed by combining a pH-responsive surface with acid-responsive magnesium. The diving-surfacing cycles can be used to convert chemical energy into electricity. During the diving-surfacing motion, the smart device cuts magnetic flux lines and produces a current, demonstrating that motional energy can be realized by consuming chemical energy of magnesium, thus producing electricity.

  4. Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

    Science.gov (United States)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

  5. Ab Initio Exploration of the Potential Energy Surface of the O_2-SO_2 Open-Shell Complex.

    Science.gov (United States)

    Fawzy, Wafaa M.; Hougen, Jon T.

    2016-06-01

    The O_2-SO_2 complex is believed to be a precursor to acid rain. The previously observed FTMW spectrum suggested internal motions within the complex, but their nature was not identified. Development of an effective Hamiltonian for an open-shell molecule with tunneling requires knowledge of the potential energy surface (PES) and the intrinsic reaction coordinates (IRC) for the paths between minima. A recent ab initio study reported two different nonplanar minima in the ground electronic state of O_2-SO_2. These predictions were based on geometry optimization calculations at the MP2/aug-cc-pVnZ level of theory, with n = 2 and 3. The current work is focused on a highly correlated ab initio investigation of the global PES (a 9-D problem) in the ground triplet electronic state of O_2-SO_2. Because of the high dimensionality in the complex, the PES calculations are partitioned into several two-dimensional cuts through the PES. We have so far explored only a 3-D part of the global PES to look for stable planar configurations. These calculations included geometry optimization, frequency, and single point energy calculations. Calculations were performed using UCCSD(T)/aug-cc-pV(n+D)Z,where n = 2 and 3, level of theory. We used an axis system that defines the radial and the angular van der Waals coordinates for a planar complex as RvW, θ_1, and θ_2. The bond length (RvW) is the distance between the center of mass of the O_2 unit and the S atom. θ_1 and θ_2 are the angles between the van der Waals bond and the O_2 internuclear axis or one of the SO bonds in the SO_2 moiety, respectively. Full geometry optimization calculations predicted a minimum of C_s symmetry in which both the O_2 and SO_2 units are tilted with respect to the van der Waals bond, and RvW = 3.63 {Å}. 3-D PES surface calculations, which involve the RvW, θ_1, and θ_2 vdW coordinates, showed that the optimized structure is the global minimum. In addition, a local minimum at RvW = 3.9 {Å}, which

  6. Origin of the Hawaiian rainforest and its transition states in long-term primary succession

    Science.gov (United States)

    Mueller-Dombois, D.; Boehmer, H. J.

    2013-07-01

    This paper addresses the question of transition states in the Hawaiian rainforest ecosystem with emphasis on their initial developments. Born among volcanoes in the north central Pacific about 4 million years ago, the Hawaiian rainforest became assembled from spores of algae, fungi, lichens, bryophytes, ferns and from seeds of about 275 flowering plants that over the millennia evolved into ca. 1000 endemic species. Outstanding among the forest builders were the tree ferns (Cibotium spp.) and the 'ōhi'a lehua trees (Metrosideros spp.), which still dominate the Hawaiian rainforest ecosystem today. The structure of this forest is simple. The canopy in closed mature rainforests is dominated by cohorts of Metrosideros polymorpha and the undergrowth by tree fern species of Cibotium. When a new lava flow cuts through this forest, kipuka are formed, i.e., islands of remnant vegetation. On the new volcanic substrate, the assemblage of plant life forms is similar to the assemblage during the evolution of this system. In open juvenile forests, a mat-forming fern, the uluhe fern (Dicranopteris linearis), becomes established. It inhibits further regeneration of the dominant 'ōhi'a tree, thereby reinforcing the cohort structure of the canopy guild. In the later part of its life cycle, the canopy guild breaks down often in synchrony. The trigger is hypothesized to be a climatic perturbation. After the disturbance, the forest becomes reestablished in about 30-40 yr. As the volcanic surfaces age, they go from a mesotrophic to a eutrophic phase, reaching a biophilic nutrient climax by about 1-25 K yr. Thereafter, a regressive oligotrophic phase follows; the soils become exhausted of nutrients. The shield volcanoes break down. Marginally, forest habitats change into bogs and stream ecosystems. The broader 'ōhi'a rainforest redeveloping in the more dissected landscapes of the older islands loses stature, often forming large gaps that are invaded by the aluminum tolerant uluhe fern

  7. Origin of the Hawaiian rainforest and its transition states in long-term primary succession

    Directory of Open Access Journals (Sweden)

    D. Mueller-Dombois

    2013-07-01

    Full Text Available This paper addresses the question of transition states in the Hawaiian rainforest ecosystem with emphasis on their initial developments. Born among volcanoes in the north central Pacific about 4 million years ago, the Hawaiian rainforest became assembled from spores of algae, fungi, lichens, bryophytes, ferns and from seeds of about 275 flowering plants that over the millennia evolved into ca. 1000 endemic species. Outstanding among the forest builders were the tree ferns (Cibotium spp. and the 'ōhi'a lehua trees (Metrosideros spp., which still dominate the Hawaiian rainforest ecosystem today. The structure of this forest is simple. The canopy in closed mature rainforests is dominated by cohorts of Metrosideros polymorpha and the undergrowth by tree fern species of Cibotium. When a new lava flow cuts through this forest, kipuka are formed, i.e., islands of remnant vegetation. On the new volcanic substrate, the assemblage of plant life forms is similar to the assemblage during the evolution of this system. In open juvenile forests, a mat-forming fern, the uluhe fern (Dicranopteris linearis, becomes established. It inhibits further regeneration of the dominant 'ōhi'a tree, thereby reinforcing the cohort structure of the canopy guild. In the later part of its life cycle, the canopy guild breaks down often in synchrony. The trigger is hypothesized to be a climatic perturbation. After the disturbance, the forest becomes reestablished in about 30–40 yr. As the volcanic surfaces age, they go from a mesotrophic to a eutrophic phase, reaching a biophilic nutrient climax by about 1–25 K yr. Thereafter, a regressive oligotrophic phase follows; the soils become exhausted of nutrients. The shield volcanoes break down. Marginally, forest habitats change into bogs and stream ecosystems. The broader 'ōhi'a rainforest redeveloping in the more dissected landscapes of the older islands loses stature, often forming large gaps that are invaded by the aluminum

  8. Energy conversion by surface-tension driven charge separation

    CERN Document Server

    Pini, Cesare; Dietzel, Mathias

    2016-01-01

    In this work, the shear-induced electrokinetic streaming potential present in free-surface electrolytic flows subjected to a gradient in surface tension is assessed. Firstly, for a Couette flow with fully resolved electric double layer (EDL), the streaming potential per surface stress as a function of the Debye parameter and surface potential is analyzed. By contrast to the Smoluchowski limit in pressure-driven channel flow, the shear-induced streaming potential vanishes for increasing Debye parameter (infinitely thin EDL), unless the free surface contains (induced) surface charge or the flow at the charged, solid wall is permitted to slip. Secondly, a technical realization of surface-tension induced streaming is proposed, with surface stress acting on the free (slipping) surfaces of a micro-structured, superhydrophobic wall. The streaming potential is analyzed with respect to the slip parameter and surface charge. Finally, the surface tension is assumed to vary with temperature (thermocapillarity) or with su...

  9. Transition state theory thermal rate constants and RRKM-based branching ratios for the N((2)D) + CH(4) reaction based on multi-state and multi-reference ab initio calculations of interest for the Titan's chemistry.

    Science.gov (United States)

    Ouk, Chanda-Malis; Zvereva-Loëte, Natalia; Scribano, Yohann; Bussery-Honvault, Béatrice

    2012-10-30

    Multireference single and double configuration interaction (MRCI) calculations including Davidson (+Q) or Pople (+P) corrections have been conducted in this work for the reactants, products, and extrema of the doublet ground state potential energy surface involved in the N((2)D) + CH(4) reaction. Such highly correlated ab initio calculations are then compared with previous PMP4, CCSD(T), W1, and DFT/B3LYP studies. Large relative differences are observed in particular for the transition state in the entrance channel resolving the disagreement between previous ab initio calculations. We confirm the existence of a small but positive potential barrier (3.86 ± 0.84 kJ mol(-1) (MR-AQCC) and 3.89 kJ mol(-1) (MRCI+P)) in the entrance channel of the title reaction. The correlation is seen to change significantly the energetic position of the two minima and five saddle points of this system together with the dissociation channels but not their relative order. The influence of the electronic correlation into the energetic of the system is clearly demonstrated by the thermal rate constant evaluation and it temperature dependance by means of the transition state theory. Indeed, only MRCI values are able to reproduce the experimental rate constant of the title reaction and its behavior with temperature. Similarly, product branching ratios, evaluated by means of unimolecular RRKM theory, confirm the NH production of Umemoto et al., whereas previous works based on less accurate ab initio calculations failed. We confirm the previous findings that the N((2)D) + CH(4) reaction proceeds via an insertion-dissociation mechanism and that the dominant product channels are CH(2)NH + H and CH(3) + NH.

  10. Transition State Models for Understanding the Origin of Chiral Induction in Asymmetric Catalysis.

    Science.gov (United States)

    Sunoj, Raghavan B

    2016-05-17

    In asymmetric catalysis, a chiral catalyst bearing chiral center(s) is employed to impart chirality to developing stereogenic center(s). A rich and diverse set of chiral catalysts is now available in the repertoire of synthetic organic chemistry. The most recent trends point to the emergence of axially chiral catalysts based on binaphthyl motifs, in particular, BINOL-derived phosphoric acids and phosphoramidites. More fascinating ideas took shape in the form of cooperative multicatalysis wherein organo- and transition-metal catalysts are made to work in concert. At the heart of all such manifestations of asymmetric catalysis, classical or contemporary, is the stereodetermining transition state, which holds a perennial control over the stereochemical outcome of the catalytic process. Delving one step deeper, one would find that the origin of the stereoselectivity is delicately dependent on the relative stabilization of one transition state, responsible for the formation of the predominant stereoisomer, over the other transition state for the minor stereoisomer. The most frequently used working hypothesis to rationalize the experimentally observed stereoselectivity places an undue emphasis on steric factors and tends to regard the same as the origin of facial discrimination between the prochiral faces of the reacting partners. In light of the increasing number of asymmetric catalysts that rely on hydrogen bonding as well as other weak non-covalent interactions, it is important to take cognizance of the involvement of such interactions in the sterocontrolling transition states. Modern density functional theories offer a pragmatic and effective way to capture non-covalent interactions in transition states. Aided by the availability of such improved computational tools, it is quite timely that the molecular origin of stereoselectivity is subjected to more intelligible analysis. In this Account, we describe interesting molecular insights into the stereocontrolling

  11. Global Surface Temperature Response Explained by Multibox Energy Balance Models

    Science.gov (United States)

    Fredriksen, H. B.; Rypdal, M.

    2016-12-01

    We formulate a multibox energy balance model, from which global temperature evolution can be described by convolving a linear response function and a forcing record. We estimate parameters in the response function from instrumental data and historic forcing, such that our model can produce a response to both deterministic forcing and stochastic weather forcing consistent with observations. Furthermore, if we make separate boxes for upper ocean layer and atmosphere over land, we can also make separate response functions for global land and sea surface temperature. By describing internal variability as a linear response to white noise, we demonstrate that the power-law form of the observed temperature spectra can be described by linear dynamics, contrary to a common belief that these power-law spectra must arise from nonlinear processes. In our multibox model, the power-law form can arise due to the multiple response times. While one of our main points is that the climate system responds over a wide range of time scales, we cannot find one set of time scales that can be preferred compared to other choices. Hence we think the temperature response can best be characterized as something that is scale-free, but still possible to approximate by a set of well separated time scales.

  12. Experimental study of breaking and energy dissipation in surface waves

    Science.gov (United States)

    Ruiz Chavarria, Gerardo; Le Gal, Patrice; Le Bars, Michael

    2014-11-01

    We present an experimental study of the evolution of monochromatic waves produced by a parabolic wave maker. Because of the parabolic shape of the wave front, the waves exhibit spatial focusing and their amplitude dramatically increases over distances of a few wavelengths. Unlike linear waves, the amplitude of the free surface deformation cannot exceed a certain threshold and when this happens the waves break. In order to give a criterion for the appearance of breaking, we calculate the steepness defined as ɛ = H/ λ (where H is the wave height and λ their wavelength) for waves of frequencies in the range 4-10 Hz. We found that wave breaking develops when ɛ attains approximately a value of 0.10. We also evaluate the lost of energy carried by the waves during their breaking by a detailed and accurate measurement of their amplitude using an optical Fourier transform profilometry. G. Ruiz Chavarria acknowledges DGAPA-UNAM by support under Project IN 116312 (Vorticidad y ondas no lineales en fluidos).

  13. Exploring the free energy surface using ab initio molecular dynamics

    Science.gov (United States)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  14. Surface Energy Characteristics of Toner Particles by Automated Inverse Gas Chromatography

    NARCIS (Netherlands)

    Segeren, L.H.G.J.; Wouters, M.E.L.; Bos, M.; van den Berg, J.W.A.; Vancso, Gyula J.

    2002-01-01

    Inverse gas chromatography (IGC) was applied to the surface energy study of surfaces of toner particles. The dispersive component of the surface energy was determined for three toner materials by infinite dilution IGC. The values obtained were comparable to the values obtained from contact angle

  15. Correlation of Effective Dispersive and Polar Surface Energies in Heterogeneous Self-Assembled Monolayer Coatings

    DEFF Research Database (Denmark)

    Zhuang, Yanxin; Hansen, Ole

    2009-01-01

    We show, theoretically, that the measured effective dispersive and polar surface energies of a heterogeneous Surface are correlated; the correlation, however, differs whether a Cassic or an Israelachvili and Gee model is assumed. Fluorocarbon self-assembled monolayers with varying coverage were...... grown oil oxidized (100) silicon Surfaces in a vapor phase process using five different precursors. Experimentally, effective surface energy components of the fluorocarbon self-assembled monolayers were determined from measured contact angles using the Owens-Wendt-Rabel-Kaelble method. We show...... that the correlation between the effective surface energy components of the heterogeneous Surfaces coated with fluorocarbon self-assembled monolayers is in agreement with the Cassie model....

  16. Muon-Substituted Malonaldehyde: Transforming a Transition State into a Stable Structure by Isotope Substitution.

    Science.gov (United States)

    Goli, Mohammad; Shahbazian, Shant

    2016-02-12

    Isotope substitutions are usually conceived to play a marginal role on the structure and bonding pattern of molecules. However, a recent study [Angew. Chem. Int. Ed. 2014, 53, 13706-13709; Angew. Chem. 2014, 126, 13925-13929] further demonstrates that upon replacing a proton with a positively charged muon, as the lightest radioisotope of hydrogen, radical changes in the nature of the structure and bonding of certain species may take place. The present report is a primary attempt to introduce another example of structural transformation on the basis of the malonaldehyde system. Accordingly, upon replacing the proton between the two oxygen atoms of malonaldehyde with the positively charged muon a serious structural transformation is observed. By using the ab initio nuclear-electronic orbital non-Born-Oppenheimer procedure, the nuclear configuration of the muon-substituted species is derived. The resulting nuclear configuration is much more similar to the transition state of the proton transfer in malonaldehyde rather than to the stable configuration of malonaldehyde. The comparison of the "atoms in molecules" (AIM) structure of the muon-substituted malonaldehyde and the AIM structure of the stable and the transition-state configurations of malonaldehyde also unequivocally demonstrates substantial similarities of the muon-substituted malonaldehyde to the transition state.

  17. A New Approach for Surface Energy Calculations Applicable to High-throughput Design of New Interfaces

    Science.gov (United States)

    Ratsch, Christian; Kaminski, Jakub

    In this talk we will present a new approach for the calculation of surface energies of periodic crystal. For non-polar materials slabs (which are terminated by two identical surfaces) the task of calculating the surface energy is trivial. But it is more problematic for polar systems where both terminating surfaces are different, as there is no single established method allowing for equal treatment of a wide range of surface morphologies and orientations. Our proposed new approach addresses this problem. It relies on carefully chosen capping atoms and the assumptions that their bond energy contributions can be used to approximate the total energy of the surface. The choice of the capping atoms is governed by a set of simple guidelines that are applicable for surfaces with different terminations. We present the results for different semiconductor materials and show that our approach leads to surfaces energies with errors as low as 2%. We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations. Our approach is suitable for high-throughput screening of new material interfaces, as accurate calculations of surface energies can be performed in an unsupervised algorithm. A New Approach for Surface Energy Calculations Applicable to High-throughput Design of New Interfaces.

  18. Theoretical study of solvent effects on the ground and low-lying excited free energy surfaces of a push-pull substituted azobenzene.

    Science.gov (United States)

    Corchado, Jose C; Sánchez, M Luz; Fdez Galván, Ignacio; Martín, M Elena; Muñoz-Losa, Aurora; Barata-Morgado, Rute; Aguilar, Manuel A

    2014-10-30

    The ground and low-lying excited free energy surfaces of 4-amino-4'-cyano azobenzene, a molecule that has been proposed as building block for chiroptical switches, are studied in gas phase and a variety of solvents (benzene, chloroform, acetone, and water). Solvent effects on the absorption and emission spectra and on the cis-trans thermal and photo isomerizations are analyzed using two levels of calculation: TD-DFT and CASPT2/CASSCF. The solvent effects are introduced using a polarizable continuum model and a QM/MM method, which permits one to highlight the role played by specific interactions. We found that, in gas phase and in agreement with the results found for other azobenzenes, the thermal cis-trans isomerization follows a rotation-assisted inversion mechanism where the inversion angle must reach values close to 180° but where the rotation angle can take almost any value. On the contrary, in polar solvents the mechanism is controlled by the rotation of the CN═NC angle. The change in the mechanism is mainly related to a better solvation of the nitrogen atoms of the azo group in the rotational transition state. The photoisomerization follows a rotational pathway both in gas phase and in polar and nonpolar solvents. The solvent introduces only small modifications in the nπ* free energy surface (S1), but it has a larger effect on the ππ* surface (S2) that, in polar solvents, gets closer to S1. In fact, the S2 band of the absorption spectrum is red-shifted 0.27 eV for the trans isomer and 0.17 eV for the cis. In the emission spectrum the trend is similar: only S2 is appreciably affected by the solvent, but in this case a blue shift is found.

  19. Intersections of potential energy surfaces of short-lived states: the complex analogue of conical intersections.

    Science.gov (United States)

    Feuerbacher, Sven; Sommerfeld, Thomas; Cederbaum, Lorenz S

    2004-02-15

    Whereas conical intersections between potential energy surfaces of bound states are well known, the interaction of short-lived states has been investigated only rarely. Here, we present several systematically constructed model Hamiltonians to study the topology of intersecting complex potential energy surfaces describing short-lived states: We find the general phenomenon of doubly intersecting complex energy surfaces, i.e., there are two points instead of one as in the case of bound states where the potential energy surfaces coalesce. In addition, seams of intersections of the respective real and imaginary parts of the potential energy surfaces emanate from these two points. Using the Sigma* and Pi* resonance states of the chloroethene anion as a practical example, we demonstrate that our complete linear model Hamiltonian is able to reproduce all phenomena found in explicitly calculated ab initio complex potential energy surfaces.

  20. Surface energy evaluation of unhydrogenated DLC thin film deposited by thermionic vacuum arc (TVA) method

    Science.gov (United States)

    Vladoiu, R.; Dinca, V.; Musa, G.

    2009-08-01

    The aim of this paper is concerned with the surface energy evaluation by contact angle measurements of DLC films deposited by thermionic vacuum arc (TVA) on different substrates: glass plate, zinc foil, stainless steel and alumina foil. TVA is an original method based on a combination of the evaporation by electron bombardment and anodic arc. The evaluation of the surface free energy has been carried out by surface energy evaluation system (SEE System). The influence of the experimental conditions is also investigated.

  1. Mussel-inspired block copolymer lithography for low surface energy materials of teflon, graphene, and gold.

    Science.gov (United States)

    Kim, Bong Hoon; Lee, Duck Hyun; Kim, Ju Young; Shin, Dong Ok; Jeong, Hu Young; Hong, Seonki; Yun, Je Moon; Koo, Chong Min; Lee, Haeshin; Kim, Sang Ouk

    2011-12-15

    Mussel-inspired interfacial engineering is synergistically integrated with block copolymer (BCP) lithography for the surface nanopatterning of low surface energy substrate materials, including, Teflon, graphene, and gold. The image shows the Teflon nanowires and their excellent superhydrophobicity.

  2. Electrochemical and mechanical processes at surfaces and interfaces of advanced materials for energy storage

    Science.gov (United States)

    Shi, Feifei

    Energy storage is a rapidly emerging field. In almost all energy storage applications, surfaces and interfaces are playing dominant roles. Examples are fuel cell electrodes, where electro-catalytic reactions occur, Li-ion battery (LIB) electrodes, where electrolyte decomposition and passivation commence simultaneously, and failure (fracture) of battery electrodes, where surface crack initiation greatly affects battery endurance. The most fundamental chemical, electrochemical, and mechanical problems in energy storage applications originate from surfaces and interfaces. This thesis investigates the electrochemical and mechanical processes at surfaces and interfaces of advanced materials for energy applications. The thesis includes the following five main research topics. (Abstract shortened by ProQuest.).

  3. Surface energy balance, melt and sublimation at Neumayer Station, East Antarctica

    NARCIS (Netherlands)

    van den Broeke, M.R.; König-Langlo, G.; Picard, G.; Kuipers Munneke, P.; Lenaerts, J.T.M.

    2009-01-01

    A surface energy balance model is forced by 13 years of high-quality hourly observations from the Antarctic coastal station Neumayer. The model accurately reproduces observed surface temperatures. Surface sublimation is significant in summer, when absorbed solar radiation heats the surface. Includin

  4. Energy Saving Melting and Revert Reduction Technology (Energy-SMARRT): Surface/Near Surface Indication - Characterization of Surface Anomalies from Magnetic Particle and Liquid Penetrant Indications

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, John [university of Alabama - Birmingham

    2014-02-20

    The systematic study and characterization of surface indications has never been conducted. Producers and users of castings do not have any data on which they can reliably communicate the nature of these indications or their effect on the performance of parts. Clearly, the ultimate intent of any work in this area is to eliminate indications that do in fact degrade properties. However, it may be impractical physically and/or financially to eliminate all surface imperfections. This project focused on the ones that actually degrade properties. The initial work was to identify those that degrade properties. Accurate numerical simulations of casting service performance allow designers to use the geometric flexibility of castings and the superior properties of steel to produce lighter weight and more energy efficient components for transportation systems (cars and trucks), construction, and mining. Accurate simulations increase the net melting energy efficiency by improving casting yield and reducing rework and scrap. Conservatively assuming a 10% improvement in yield, approximately 1.33 x 1012 BTU/year can be saved with this technology. In addition, CO2 emissions will be reduced by approximately 117,050 tons per year.

  5. Size Driven Ferroelectric-Paraelectric Phase Transition from the Surface Energy Viewpoint

    Institute of Scientific and Technical Information of China (English)

    钟维烈; 王渊旭; 张沛霖

    2003-01-01

    The size driven ferroelectric-paraelectric phase transition in a ferroelectric of small size is studied within the framework of Landau phase transition theory. The transition is a consequence of the competition between decreasing the volume free energy by polarization and increasing the surface energy of the ferroelectric phase,which has a surface energy density higher than that in the paraelectric phase. A simple expression for the ferroelectric critical size as a function of the Landau free energy coefficients and the surface energy density is derived.

  6. Properties of Low Surface Energy Fluorocarbon Polymers with Fluoro-acrylic Resins

    Institute of Scientific and Technical Information of China (English)

    LIU Xiusheng; WANG Can; LIU Lanxuan; LI Jian; GAO Wanzhen

    2008-01-01

    The low surface energy fluorocarbon polymer from the synthesized fluoro-acrylic resins was developed. Then the molecule orientation principle of nonpolar and polar functional groups in the polymers was analyzed. And the contact angles of pure water drops on the surfaces of various fluoro-monomer homopolymers and interpolymers were measured. So the relation of polymers' fluoro-content with the surface energy was determined. The distribution of fluoric functional groups in the polymers was investigated. And the test results show that though the total fluorine content of the fluorocarbon polymers is relative few, their surface energy is really low due to the enrichment of fluoro-chains on the polymers surface.

  7. The Study of Low Surface Energy Fluorocarbon Coatings with Fluor Content Being Lower

    Institute of Scientific and Technical Information of China (English)

    GAO Wan-zhen; LIU Xiu-sheng; ZHONG Ping

    2004-01-01

    A kind of low surface energy fluorocarbon coatings from the synthesized fluoro-acrylic resin was developed.The molecule orientation principle of nonpolar and polar functional groups in the coatings was analyzed. The contact angles of pure water drops on the surfaces of various fluoro-monomer homopolymers and interpolymers were measured. The relation of coatings' fluoro-content with the surface energy was determined. The distribution of fluoric functional groups in the coatings was investigated. The test results show that though the total content of fluor of the fluorocarbon coatings is relative few, their surface energy is really low due to the enrichment of fluoro-chains on the surfaces.

  8. Kinetics and dynamics of the C((3)P) + H2O reaction on a full-dimensional accurate triplet state potential energy surface.

    Science.gov (United States)

    Li, Jun; Xie, Changjian; Guo, Hua

    2017-08-30

    A full dimensional accurate potential energy surface (PES) for the C((3)P) and H2O reaction is developed based on ∼34 000 data points calculated at the level of the explicitly correlated unrestricted coupled cluster method with single, double, and perturbative triple excitations with the augmented correlation-consistent polarized triple zeta basis set (CCSD(T)-F12a/AVTZ). The PES is invariant with respect to the permutation of the two hydrogen atoms and the total root mean square error (RMSE) of the fit is only 0.31 kcal mol(-1). The PES features two barriers in the entrance channel and several potential minima, as well as multiple product channels. The rate coefficients of this reaction calculated using a transition-state theory and quasi-classical trajectory (QCT) method are small near room temperature, consistent with experiments. The reaction dynamics is also investigated with QCT on the new PES, which found that the reactivity is constrained by the entrance barriers and the final product branching is not statistical.

  9. Estimating changes in heat energy stored within a column of wetland surface water and factors controlling their importance in the surface energy budget

    Science.gov (United States)

    Shoemaker, W.B.; Sumner, D.M.; Castillo, A.

    2005-01-01

    [1] Changes in heat energy stored within a column of wetland surface water can be a considerable component of the surface energy budget, an attribute that is demonstrated by comparing changes in stored heat energy to net radiation at seven sites in the wetland areas of southern Florida, including the Everglades. The magnitude of changes in stored heat energy approached the magnitude of net radiation more often during the winter dry season than during the summer wet season. Furthermore, the magnitude of changes in stored heat energy in wetland surface water generally decreased as surface energy budgets were upscaled temporally. A new method was developed to estimate changes in stored heat energy that overcomes an important data limitation, namely, the limited spatial and temporal availability of water temperature measurements. The new method is instead based on readily available air temperature measurements and relies on the convolution of air temperature changes with a regression-defined transfer function to estimate changes in water temperature. The convolution-computed water temperature changes are used with water depths and heat capacity to estimate changes in stored heat energy within the Everglades wetland areas. These results likely can be adapted to other humid subtropical wetlands characterized by open water, saw grass, and rush vegetation type communities. Copyright 2005 by the American Geophysical Union.

  10. Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution.

    Science.gov (United States)

    Takenaka, Norio; Kitamura, Yukichi; Nagaoka, Masataka

    2016-03-03

    In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface (FES) which is analogous to a Born-Oppenheimer potential energy surface. To survey the FES, an efficient computational research protocol is proposed within the QM/MM framework; (i) we first obtain some stable states (or transition states) involved by optimizing their structures on the FES, in a stepwise fashion, finally using the free energy gradient (FEG) method, and then (ii) we directly obtain the FE differences among any arbitrary states on the FES, efficiently by employing the QM/MM method with energy representation (ER), i.e., the QM/MM-ER method. To validate the calculation accuracy and efficiency, we applied the above FEG-ER methodology to a typical isomerization reaction of glycine in aqueous solution, and reproduced quite satisfactorily the experimental value of the reaction FE. Further, it was found that the structural relaxation of the solute in the QM/MM force field is not negligible to estimate correctly the FES. We believe that the present research protocol should become prevailing as one computational strategy and will play promising and important roles in solution chemistry toward solution reaction ergodography.

  11. Using radiometric surface temperature for surface energy flux estimation in Mediterranean drylands from a two-source perspective

    DEFF Research Database (Denmark)

    Morillas, L.; Garcia Garcia, Monica; Nieto Solana, Hector;

    2013-01-01

    A two-source model (TSM) for surface energy balance, considering explicitly soil and vegetation components, was tested under water stress conditions. The TSM evaluated estimates the sensible heat flux (H) using the surface-air thermal gradient and the latent heat flux (LE) as a residual from the ...

  12. SCANNING ELECTRON-MICROSCOPIC EVALUATION OF THE FRACTURED SURFACES OF CANINE CALCULI FROM SUBSTRATA WITH DIFFERENT SURFACE FREE-ENERGY

    NARCIS (Netherlands)

    UYEN, HMW; JONGEBLOED, WL; BUSSCHER, HJ

    1991-01-01

    The strength of adhesion between dental calculus and enamel or dentin surfaces determines the ease with which the calculus can be removed by brushing or professional dental treatment. In this study, we examined the adhesion of canine calculi formed on substrata with different surface free energies

  13. Minimum action transition paths connecting minima on an energy surface

    Science.gov (United States)

    Koehl, Patrice

    2016-11-01

    Dynamics is essential to the biological functions of many bio-molecules, yet our knowledge of dynamics remains fragmented. Experimental techniques for studying bio-molecules either provide high resolution information on static conformations of the molecule or provide low-resolution, ensemble information that does not shed light on single molecule dynamics. In parallel, bio-molecular dynamics occur at time scale that are not yet attainable through detailed simulation methods. These limitations are especially noticeable when studying transition paths. To address this issue, we report in this paper two methods that derive meaningful trajectories for proteins between two of their conformations. The first method, MinActionPath, uses approximations of the potential energy surface for the molecule to derive an analytical solution of the equations of motion related to the concept of minimum action path. The second method, RelaxPath, follows the same principle of minimum action path but implements a more sophisticated potential, including a mixed elastic potential and a collision term to alleviate steric clashes. Using this new potential, the equations of motion cannot be solved analytically. We have introduced a relaxation method for solving those equations. We describe both the theories behind the two methods and their implementations, focusing on the specific techniques we have used that make those implementations amenable to study large molecular systems. We have illustrated the performance of RelaxPath on simple 2D systems. We have also compared MinActionPath and RelaxPath to other methods for generating transition paths on a well suited test set of large proteins, for which the end points of the trajectories as well as an intermediate conformation between those end points are known. We have shown that RelaxPath outperforms those other methods, including MinActionPath, in its ability to generate trajectories that get close to the known intermediates. We have also shown

  14. Minimum action transition paths connecting minima on an energy surface.

    Science.gov (United States)

    Koehl, Patrice

    2016-11-14

    Dynamics is essential to the biological functions of many bio-molecules, yet our knowledge of dynamics remains fragmented. Experimental techniques for studying bio-molecules either provide high resolution information on static conformations of the molecule or provide low-resolution, ensemble information that does not shed light on single molecule dynamics. In parallel, bio-molecular dynamics occur at time scale that are not yet attainable through detailed simulation methods. These limitations are especially noticeable when studying transition paths. To address this issue, we report in this paper two methods that derive meaningful trajectories for proteins between two of their conformations. The first method, MinActionPath, uses approximations of the potential energy surface for the molecule to derive an analytical solution of the equations of motion related to the concept of minimum action path. The second method, RelaxPath, follows the same principle of minimum action path but implements a more sophisticated potential, including a mixed elastic potential and a collision term to alleviate steric clashes. Using this new potential, the equations of motion cannot be solved analytically. We have introduced a relaxation method for solving those equations. We describe both the theories behind the two methods and their implementations, focusing on the specific techniques we have used that make those implementations amenable to study large molecular systems. We have illustrated the performance of RelaxPath on simple 2D systems. We have also compared MinActionPath and RelaxPath to other methods for generating transition paths on a well suited test set of large proteins, for which the end points of the trajectories as well as an intermediate conformation between those end points are known. We have shown that RelaxPath outperforms those other methods, including MinActionPath, in its ability to generate trajectories that get close to the known intermediates. We have also shown

  15. Deposition of Ultrathin Nano-Hydroxyapatite Films on Laser Micro-Textured Titanium Surfaces to Prepare a Multiscale Surface Topography for Improved Surface Wettability/Energy

    Directory of Open Access Journals (Sweden)

    Maria Surmeneva

    2016-10-01

    Full Text Available The primary aim of this study was to analyse the correlation between topographical features and chemical composition with the changes in wettability and the surface free energy of microstructured titanium (Ti surfaces. Periodic microscale structures on the surface of Ti substrates were fabricated via direct laser interference patterning (DLIP. Radio-frequency magnetron sputter deposition of ultrathin nanostructured hydroxyapatite (HA films was used to form an additional nanoscale grain morphology on the microscale-structured Ti surfaces to generate multiscale surface structures. The surface characteristics were evaluated using atomic force microscopy and contact angle and surface free energy measurements. The structure and phase composition of the HA films were investigated using X-ray diffraction. The HA-coated periodic microscale structured Ti substrates exhibited a significantly lower water contact angle and a larger surface free energy compared with the uncoated Ti substrates. Control over the wettability and surface free energy was achieved using Ti substrates structured via the DLIP technique followed by the deposition of a nanostructured HA coating, which resulted in the changes in surface chemistry and the formation of multiscale surface topography on the nano- and microscale.

  16. Tuning Charge Transfer in Ion-Surface Collisions at Hyperthermal Energies.

    Science.gov (United States)

    Yao, Yunxi; Giapis, Konstantinos P

    2016-05-18

    Charge exchange in ion-surface collisions may be influenced by surface adsorbates to alter the charge state of the scattered projectiles. We show here that the positive-ion yield, observed during ion scattering on metal surfaces at low incident energies, is greatly enhanced by adsorbing electronegative species onto the surface. Specifically, when beams of N(+) and O(+) ions are scattered off of clean Au surfaces at hyperthermal energies, no positive ions are observed exiting. Partial adsorption of F atoms on the Au surface, however, leads to the appearance of positively charged primary ions scattering off of Au, a direct result of the increase in the Au work function. The inelastic energy losses for positive-ion exits are slightly larger than the corresponding ionization energies of the respective N and O atoms, which suggest that the detected positive ions are formed by surface reionization during the hard collision event.

  17. Components of near-surface energy balance derived from satellite soundings – Part 1: Net available energy

    Directory of Open Access Journals (Sweden)

    K. Mallick

    2014-08-01

    Full Text Available This paper introduces a relatively simple method for recovering global fields of near-surface net available energy (the sum of the sensible and latent heat flux or the difference between the net radiation and surface heat accumulation using satellite visible and infra-red products derived from the AIRS (Atmospheric Infrared Sounder and MODIS (MOderate Resolution Imaging Spectroradiometer platforms. The method focuses on first specifying net surface radiation by considering its various shortwave and longwave components. This was then used in a surface energy balance equation in conjunction with satellite day–night surface temperature difference to derive 12 h discrete time estimates of surface, system heat capacity and heat accumulation, leading directly to retrieval for surface net available energy. Both net radiation and net available energy estimates were evaluated against ground truth data taken from 30 terrestrial tower sites affiliated to the FLUXNET network covering 7 different biome classes. This revealed a relatively good agreement between the satellite and tower data, with a pooled root mean square deviation of 98 and 72 W m−2 for net radiation and net available energy, respectively, although both quantities were underestimated by approximately 25 and 10%, respectively relative to the tower observations. Analysis of the individual shortwave and longwave components of the net radiation revealed the downwelling shortwave radiation to be the main source of this systematic underestimation.

  18. Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory.

    Science.gov (United States)

    Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G

    2016-03-02

    Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry. We employ a new calibration procedure for quantum Rice-Ramsperger-Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring. The new theoretical framework is applied to the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. Our system-specific (SS) QRRK approach is adjusted with SS parameters to agree with multistructural canonical variational transition state theory with multidimensional tunneling (MS-CVT/SCT) at the high-pressure limit. The new method avoids the need for the usual empirical estimations of the QRRK parameters, and it eliminates the need for variational transition state theory calculations as a function of energy, although in this first application we do validate the falloff curves by comparing SS-QRRK results without tunneling to multistructural microcanonical variational transition state theory (MS-μVT) rate constants without tunneling. At low temperatures, the two approaches agree well with each other, but at high temperatures, SS-QRRK tends to overestimate falloff slightly. We also show that the variational effect is important in computing the energy-resolved rate constants. Multiple-structure anharmonicity, torsional-potential anharmonicity, and high-frequency-mode vibrational anharmonicity are all included in the rate computations, and torsional anharmonicity effects on the density of states are investigated. Branching fractions, which are both temperature- and pressure-dependent (and for which only limited data is available from experiment), are predicted as a function of pressure.

  19. Behavior of transition state regulator AbrB in batch cultures of Bacillus thuringiensis.

    Science.gov (United States)

    Lozano Goné, Astrid Magdalena; Dinorín Téllez Girón, Jabel; Jiménez Montejo, Fabiola Eloisa; Hidalgo-Lara, María Eugenia; López Y López, Víctor Eric

    2014-11-01

    The transition state regulator AbrB is involved in the regulation of various cellular functions such as exponential growth, transition state and sporulation onset, due to its ability to activate, suppress or prevent the inappropriate expression of various genes in Bacillus subtilis. In order to understand combined behavior in batch cultures of AbrB in Bacillus thuringiensis, we cloned and expressed the abrB gene of B. thuringiensis in Escherichia coli. The deduced sequence of abrB gene coded for a protein consisting of 94 amino acids with ~10.5 kDa protein that shares 100 and 85 % identity with those from Bacillus cereus and Bacillus subtilis. The recombinant AbrB protein was used as antigen for the production of rabbit polyclonal antibodies anti-AbrB. Two media cultures with carbon: nitrogen ratios of 7.0, but varying access to nutrients were tested in batch cultures. In the case of both media, AbrB accumulation occurred from the beginning of the process and was maximal during early exponential growth. Thereafter, the level of AbrB decreased when there were no nutrient limitations and coincided with a decreased value in specific growth rate, although growth continued exponentially. Nonetheless, sporulation onset was determined 3 h and 4 h later, in media with highly metabolizable nutrients clean medium and Farrera medium, respectively. Hence, the maximal level of AbrB accumulation in batch cultures of B. thuringiensis is not influenced by limiting nutrients; however, nutrient availability affects the required time lapse for transition state regulator accumulation.

  20. Kinetic Isotope Effects as a Probe for the Protonolysis Mechanism of Alkylmetal Complexes: VTST/MT Calculations Based on DFT Potential Energy Surfaces.

    Science.gov (United States)

    Mai, Binh Khanh; Kim, Yongho

    2016-10-03

    Protonolysis by platinum or palladium complexes has been extensively studied because it is the microscopic reverse of the C-H bond activation reaction. The protonolysis of (COD)Pt(II)Me2, which exhibits abnormally large kinetic isotope effects (KIEs), is proposed to occur via a concerted pathway (SE2 mechanism) with large tunneling. However, further investigation of KIEs for the protonolysis of ZnMe2 and others led to a conclusion that there is no noticeable correlation between the mechanism and magnitude of KIE. In this study, we demonstrated that variational transition state theory including multidimensional tunneling (VTST/MT) could accurately predict KIEs and Arrhenius parameters of the protonolysis of alkylmetal complexes based on the potential energy surfaces generated by density functional theory. The predicted KIEs, Ea(D) - Ea(H) values, and AH/AD ratios for the protonolysis of (COD)Pt(II)Me2 and Zn(II)Me2 by TFA agreed very well with experimental values. The protonolysis of ZnMe2 with the concerted pathway has a very flat potential energy surface, which produces a very small tunneling effect and therefore a small KIE. The predicted KIE for the stepwise protonolysis (SE(ox) mechanism) of (COD)Pt(II)Me2 was much smaller than that of the concerted pathway, but greater than the KIE of the concerted protonolysis of ZnMe2. A large KIE, which entails a significant tunneling effect, could be used as an experimental probe of the concerted pathway. However, a normal or small KIE should not be used as an indicator of the stepwise mechanism, and the interplay between experiments and reliable theory including tunneling would be essential to uncover the mechanism correctly.

  1. Transition-state structure for the hydronium-ion-promoted hydrolysis of α-d-glucopyranosyl fluoride

    National Research Council Canada - National Science Library

    Tang, Ariel; Chan, Jefferson; Bennet, Andrew J

    2015-01-01

    The transition state for the hydronium-ion-promoted hydrolysis of α- d -glucopyranosyl fluoride in water has been characterized by combining multiple kinetic isotope effect measurements with theoretical modelling...

  2. Transition-state structure for the hydronium-ion-promoted hydrolysis of [alpha]-D-glucopyranosyl fluoride

    National Research Council Canada - National Science Library

    Chan, Jefferson; Tang, Ariel; Bennet, Andrew J

    2015-01-01

    The transition state for the hydronium-ion-promoted hydrolysis of [alpha]-D-glucopyranosyl fluoride in water has been characterized by combining multiple kinetic isotope effect measurements with theoretical modelling...

  3. Surface Energy of C60 and the Interfacial Interactions in Aqueous Systems

    Science.gov (United States)

    The surface free energy components of C60 powder in the form of compressed pellets were determined by sessile drop contact angle measurements. Based on van Oss-Chaudhury-Good model to Young-Dupre equation, the surface energy of C60 and the contributions of the apolar (Lifshitz-v...

  4. Surface energy balance closure in an arid region: role of soil and heat flux

    NARCIS (Netherlands)

    Heusinkveld, B.G.; Jacobs, A.F.G.; Holtslag, A.A.M.; Berkowicz, S.M.

    2004-01-01

    The large soil heat fluxes in hot desert regions are very important in energy balance studies. Surface energy balance (SEB) observations, however, reveal that there is an imbalance in Surface flux measurements and that it is difficult to isolate those flux measurements causing the imbalance errors.

  5. Towards hot electron mediated charge exchange in hyperthermal energy ion-surface interactions

    DEFF Research Database (Denmark)

    Ray, M. P.; Lake, R. E.; Thomsen, Lasse Bjørchmar;

    2010-01-01

    electrons useful for driving chemical reactions at surfaces. Using the binary collision approximation and a nonadiabatic model that takes into account the time-varying nature of the ion–surface interaction, the energy loss of the ions is reproduced. The energy loss for Na + ions incident on the devices...

  6. On the Surface Free Energy of PVC/EVA Polymer Blends: Comparison of Different Calculation Methods.

    Science.gov (United States)

    Michalski; Hardy; Saramago

    1998-12-01

    The surface free energy of polymeric films of polyvinylchloride (PVC) + poly(ethylene-co-vinylacetate) (EVA) blends was calculated using the van Oss treatment (Lifshitz and electron donor-electron acceptor components of surface free energy) and the Owens-Wendt treatment (dispersive and nondispersive components of surface free energy). Surface free energy results were found to be greatly dependent on the calculation method and on the number of standard liquids used for contact angle measurements. The nondispersive/donor-acceptor surface free energy component and the total surface free energy of polymeric films were always higher when the van Oss treatment was used compared to the Owens-Wendt treatment. Conversely, both methods led to similar apolar/Lifshitz components. All the calculation methods were in good agreement for the surface free energy of PVC; however, a discrepancy between the methods arose as EVA content in the blends increased. It seems that there is not yet a definite solution for the calculation of solid surface free energy. Further developments of existing models are needed in order to gain consistency when calculating this important physicochemical quantity. Copyright 1998 Academic Press.

  7. Equilibrium Geometries, Reaction Pathways, and Electronic Structures of Ethanol Adsorbed on the Si (111) Surface

    CERN Document Server

    Gavrilenko, A V; Gavrilenko, V I

    2008-01-01

    Equilibrium atomic configurations and electron energy structure of ethanol adsorbed on the Si (111) surface are studied by the first-principles density functional theory. Geometry optimization is performed by the total energy minimization method. Several equilibrium atomic configurations of ethanol, both undissociated and dissociated, on the Si (111) surface are found. Reaction pathways and predicted transition states are discussed in comparison with available experimental data in terms of the feasibility of the reactions occurring. Analysis of atom and orbital resolved projected density of states indicate substantial modifications of the Si surface valence and conduction bands due to the adsorption of ethanol affecting the electrical properties of the surface.

  8. The effective surface energy of heterogeneous solids measured by inverse gas chromatography at infinite dilution.

    Science.gov (United States)

    Sun, Chenhang; Berg, John C

    2003-04-15

    Inverse gas chromatography (IGC) at infinite dilution has been widely used to access the nonspecific surface free energy of solid materials. Since most practical surfaces are heterogeneous, the effective surface energy given by IGC at infinite dilution is somehow averaged over the whole sample surface, but the rule of averaging has thus far not been established. To address this problem, infinite dilution IGC analysis was carried out on mixtures of known heterogeneity. These materials are obtained by mixing two types of solid particles with significantly different surface energies as characterized individually with IGC, and results are obtained for binary combinations in varying proportions. It is found that when all surface components have the same accessibility by probe molecules, the effective surface energy of such a heterogeneous surface is related to the surface energy distribution by a square root linear relationship, square root sigma(eff)(LW)= summation operator (i)phi(i) square root sigma(i)(LW), where sigma(i)(LW) refers to the nonspecific (Lifshitz-van der Waals) surface energy of patches i, and phi(i) to their area fraction.

  9. The formation energy for steps and kinks on cubic transition metal surfaces

    DEFF Research Database (Denmark)

    Vitos, Levente; Skriver, Hans Lomholt; Kollàr, Janos

    1999-01-01

    We have used our first-principles database of surface energies for metals in conjunction with the concept of vicinal surfaces to derive the energies of formation of monoatomic steps and corresponding kinks on close-packed surface facets of bcc and fee transition metals. The entries in the database...... allow for a direct calculation of the energies of a number of important steps. For the remaining steps and for all the kinks the energies of formation have been estimated from pair potential expansions of the entries in the database. (C) 1999 Elsevier Science B.V. All rights reserved....

  10. Technique for the estimation of surface temperatures from embedded temperature sensing for rapid, high energy surface deposition.

    Energy Technology Data Exchange (ETDEWEB)

    Watkins, Tyson R.; Schunk, Peter Randall; Roberts, Scott Alan

    2014-07-01

    Temperature histories on the surface of a body that has been subjected to a rapid, highenergy surface deposition process can be di cult to determine, especially if it is impossible to directly observe the surface or attach a temperature sensor to it. In this report, we explore two methods for estimating the temperature history of the surface through the use of a sensor embedded within the body very near to the surface. First, the maximum sensor temperature is directly correlated with the peak surface temperature. However, it is observed that the sensor data is both delayed in time and greatly attenuated in magnitude, making this approach unfeasible. Secondly, we propose an algorithm that involves tting the solution to a one-dimensional instantaneous energy solution problem to both the sensor data and to the results of a one-dimensional CVFEM code. This algorithm is shown to be able to estimate the surface temperature 20 C.

  11. Unpolarized radiative cylindrical spacetimes Trapped surfaces and quasilocal energy

    CERN Document Server

    Gonçalves, S M C V

    2003-01-01

    We consider the most general vacuum cylindrical spacetimes, which are defined by two global, spacelike, commuting, non-hypersurface-orthogonal Killing vector fields. The cylindrical waves in such spacetimes contain both + and $\\times$ polarizations, and are thus said to be unpolarized. We show that there are no trapped cylinders in the spacetime, and present a formal derivation of Thorne's C-energy, based on a Hamiltonian reduction approach. Using the Brown-York quasilocal energy prescription, we compute the actual physical energy (per unit Killing length) of the system, which corresponds to the value of the Hamiltonian that generates unit proper-time translations orthogonal to a given fixed spatial boundary. The C-energy turns out to be a monotonic non-polynomial function of the Brown-York quasilocal energy. Finally, we show that the Brown-York energy at spatial infinity is related to an asymptotic deficit angle in exactly the same manner as the specific mass of a straight cosmic string is to the former.

  12. Nucleation at surfaces: the importance of interfacial energy.

    Science.gov (United States)

    Wu, W; Gerard, D E; Nancollas, G H

    1999-11-01

    The nucleation and growth of stone-forming minerals on the surfaces of other crystalline phases, cellular material, and immobilized macromolecules must be important in the formation of stones in the urinary tract. The nucleation and growth of calcium oxalate monohydrate (COM) crystals were studied using the constant composition kinetics technique, in solution supersaturated with respect to COM (sigmaCOM = 1.44). The solid phases during the reaction were examined by x-ray diffraction, scanning electron microscopy, and diffuse reflectance Fourier transform infrared spectroscopy. Human serum albumin was found to nucleate COM crystals when immobilized on hydroxyapatite (HAP) surfaces. The induction period for nucleation of COM on HAP surfaces preadsorbed with albumin significantly decreased to about 65 min from about 230 min for pure HAP particles. The initial growth rate of COM on pure HAP particles, Rm approximately/= 0.56 X 10(-7) mol/min per m2, was slower than that for HAP surfaces preadsorbed with albumin, 2.14 x 10(-7) mol/min per m2. The surface properties were characterized using contact angle measurements by sessile drop and thin layer wicking. The thermodynamic results suggested that surfaces with high Lewis base parameter values (gamma-) and low interfacial tension with water (gammaSL) are more effective in the nucleation and growth of crystal phases.

  13. Surface structure determinations of crystalline ionic thin films grown on transition metal single crystal surfaces by low energy electron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Joel Glenn [Univ. of California, Berkeley, CA (United States)

    2000-05-01

    The surface structures of NaCl(100), LiF(100) and alpha-MgCl2(0001) adsorbed on various metal single crystals have been determined by low energy electron diffraction (LEED). Thin films of these salts were grown on metal substrates by exposing the heated metal surface to a molecular flux of salt emitted from a Knudsen cell. This method of investigating thin films of insulators (ionic salts) on a conducting substrate (metal) circumvents surface charging problems that plagued bulk studies, thereby allowing the use of electron-based techniques to characterize the surface.

  14. High-resolution proton energy-loss spectrometer for surface analysis

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, Noriaki; Kanasaki, Junichi; Matsunami, Noriaki; Matsuda, Kouji; Aoki, Masahiko.

    1988-11-01

    We describe a new ion-beam surface analyzer, proton energy loss spectrometer. It analyzes ions incident at 100 keV and scattered by 180degC at solid surfaces with a resolution of 5eV. The results of computer simulation of the energy spectra of scattered ions and the informations on surface electronic and atomic structures possibly derived by the analysis are described. Application of the spectrometer in several areas of science and technology is briefly discussed.

  15. Influence of transitional states on the microbial ecology of anaerobic digesters treating solid wastes.

    Science.gov (United States)

    Regueiro, Leticia; Veiga, Patricia; Figueroa, Mónica; Lema, Juan M; Carballa, Marta

    2014-03-01

    A better understanding of the microbial ecology of anaerobic processes during transitional states is important to achieve a long-term efficient reactor operation. Five wastes (pig manure, biodiesel residues, ethanol stillage, molasses residues, and fish canning waste) were treated in five anaerobic reactors under the same operational conditions. The influence of the type of substrate and the effect of modifying feeding composition on the microbial community structure was evaluated. The highest biomethanation efficiency was observed in reactors fed with fish canning waste, which also presented the highest active archaeal population and the most diverse microbial communities. Only two Bacteria populations could be directly related to a particular substrate: Ilyobacter with biodiesel residues and Trichococcus with molasses residues. Results showed that the time to achieve steady-state performance after these transitional states was not dependent on the substrate treated. But reactors needed more time to handle the stress conditions derived from the start-up compared to the adaptation to a new feeding. Cluster analyses showed that the type of substrate had a clear influence on the microbiology of the reactors, and that segregation was related to the reactors performance. Finally, we conclude that the previous inoculum history treating solid waste and higher values of active Archaea population are important factors to face a successful change in substrate not entailing stability failure.

  16. A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis.

    Science.gov (United States)

    Liberman, Joseph A; Guo, Man; Jenkins, Jermaine L; Krucinska, Jolanta; Chen, Yuanyuan; Carey, Paul R; Wedekind, Joseph E

    2012-10-17

    One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman crystallography to directly measure pK(a) values for the Ade38 N1 imino group of a hairpin ribozyme in distinct conformational states. A transition-state analogue gave a pK(a) value of 6.27 ± 0.05, which agrees strikingly well with values measured by pH-rate analyses. To identify the chemical attributes that contribute to the shifted pK(a), we determined crystal structures of hairpin ribozyme variants containing single-atom substitutions at the active site and measured their respective Ade38 N1 pK(a) values. This approach led to the identification of a single interaction in the transition-state conformation that elevates the base pK(a) > 0.8 log unit relative to the precatalytic state. The agreement of the microscopic and macroscopic pK(a) values and the accompanying structural analysis supports a mechanism in which Ade38 N1(H)+ functions as a general acid in phosphodiester bond cleavage. Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity.

  17. Computer simulation of reactions in beta-cyclodextrin molecular reactors: transition state recognition.

    Science.gov (United States)

    Yeguas, Violeta; López, Ramón; Lambert, Alexandrine; Monard, Gérald; Ruiz-López, Manuel F

    2010-10-07

    Cyclodextrins have attracted much interest in recent years because of their potential use as molecular reactors allowing organic reactions in aqueous solution. To better understand their effect on reaction mechanisms, we have carried out a computational study of a prototypical process (neutral ester hydrolysis) in a beta-cyclodextrin (beta-CD). Two models have been used for the reactor. The first and simpler one assumes that the medium can be described by a polarizable dielectric continuum. The second one takes into account the discrete nature of the beta-CD and water molecules thanks to a computational approach that combines the use of Quantum Mechanics, Molecular Mechanics and Molecular Dynamics techniques. We focus on neutral pH processes for which either acceleration or inhibition has experimentally been observed depending on ester derivatives. Our calculations rationalize such observations by showing that the two reaction mechanisms usually invoked for hydrolysis, stepwise (involving two transitions states with formation of a -C(OH)(2)OR tetrahedral intermediate) and concerted, undergo opposite effects in the beta-CD environment. The results highlight the role played by molecular shape recognition. Thus, in spite of a higher polarity exhibited by the three transition states with respect to the reactants, the interactions with the beta-CD cavity may either increase or decrease the activation barrier due to different 3D-arrangements of the chemical structures.

  18. Performance of the correlation consistent composite approach for transition states: A comparison to G3B theory

    Science.gov (United States)

    Grimes, Thomas V.; Wilson, Angela K.; DeYonker, Nathan J.; Cundari, Thomas R.

    2007-10-01

    The correlation consistent composite approach (ccCA) was applied to the prediction of reaction barrier heights (i.e., transition state energy relative to reactants and products) for a standard benchmark set of reactions comprised of both hydrogen transfer reactions and nonhydrogen transfer reactions (i.e., heavy-atom transfer, SN2, and unimolecular reactions). The ccCA method was compared against G3B for the same set of reactions. Error metrics indicate that ccCA achieves "chemical accuracy" with a mean unsigned error (MUE) of 0.89kcal/mol with respect to the benchmark data for barrier heights; G3B has a mean unsigned error of 1.94kcal/mol. Further, the greater accuracy of ccCA for predicted reaction barriers is compared to other benchmarked literature methods, including density functional (BB1K, MUE =1.16kcal/mol) and wavefunction-based [QCISD(T), MUE =1.10kcal/mol] methods.

  19. Surface energy of bovine dentin and enamel by means of inverse gas chromatography.

    Science.gov (United States)

    Okulus, Zuzanna; Strzemiecka, Beata; Czarnecka, Beata; Buchwald, Tomasz; Voelkel, Adam

    2015-04-01

    Adhesion between tooth tissues and dental fillings depends on the surface energy of both connected materials. Bond strength can be determined directly or indirectly as a work of adhesion on the basis of values of surface energy of these materials. Inverse gas chromatography (IGC) is one of the methods of surface energy examination. In this study the values of total surface energy components of wet and dry teeth fragments (enamel, crown dentin and root dentin) were determined with the use of inverse gas chromatography. Inverse gas chromatography has never been used for investigation of surface energy of natural tooth tissues. Different storage conditions were examined - wet and dry. Different values of surface energy are observed according to the type of tooth tissue (dentin or enamel), occurring place (crown or root) and storage conditions (dry or wet). The effect of tissue type and occurring place was the greatest, while storage conditions were of secondary importance. Surface energy depends on composition of tissue, its surface area and the presence of pores. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. The dependence of the measured surface energy of graphene on nanosheet size

    Science.gov (United States)

    Ferguson, Auren; Harvey, Andrew; Godwin, Ian J.; Bergin, Shane D.; Coleman, Jonathan N.

    2017-03-01

    The surface energy of graphene nanosheets is surprisingly poorly known, probably due to size effects and energetic heterogeneities. Here we use finite-dilution inverse gas chromatography to measure the surface energy of liquid-exfoliated, few-layer graphene nanosheets of different sizes as a function of probe coverage. In all cases, the surface energy falls with probe coverage from a defect-controlled, low-coverage value to a value that approaches the basal plane surface energy at high coverage. We find an intrinsic basal plane dispersive surface energy of 61 ± 4 mJ m-2, close to the value of 63 mJ m-2 found for graphite. By comparison with similar data measured on graphite and using simple models, we can use the length dependence of the low coverage surface energy to differentiate between the effects of edge and basal plane defects, finding these to contribute ˜130 and 180 mJ m-2 to the surface energy respectively. From this data, we estimate a basal plane defect content of ˜6 × 1014 defects m-2 for both graphite and graphene in reasonable agreement with Raman data. This work shows that, in terms of surface energetics, few-layer graphene nanosheets behave exactly like graphite with the only differences associated with platelet dimensions.

  1. Investigation of the Abstraction and Dissociation Mechanism in the Nitrogen Trifluoride Channels: Combined Post-Hartree-Fock and Transition State Theory Approaches.

    Science.gov (United States)

    Claudino, D; Gargano, R; Carvalho-Silva, Valter H; E Silva, Geraldo M; da Cunha, W F

    2016-07-21

    The present paper concludes our series of kinetics studies on the reactions involved in the complex mechanism of nitrogen trifluoride decomposition. Two other related reactions that, along with this mechanism, take part in an efficient boron nitride growth process are also investigated. We report results concerning two abstraction reactions, namely NF2 + N ⇄ 2NF and NF3 + NF ⇄ 2NF2, and two dissociations, N2F4 ⇄ 2NF2 and N2F3 ⇄ NF2 + NF. State-of-the-art electronic structure calculations at the CCSD(T)/cc-pVTZ level of theory were considered to determine geometries and frequencies of reactants, products, and transition states. Extrapolation of the energies to the complete basis set limit was used to obtain energies of all the species. We applied transition state theory to compute thermal rate constants including Wigner, Eckart, Bell, and deformed theory corrections in order to take tunneling effects into account. The obtained results are in good agreement with the experimental data available in the literature and are expected to provide a better phenomenological understanding of the NF3 decomposition role in the boron nitride growth for a wide range of temperature values.

  2. A three-dimensional He-CO potential energy surface with improved long-range behavior

    Science.gov (United States)

    McBane, George C.

    2016-12-01

    A weakness of the ;CBS + corr; He-CO potential energy surface (Peterson and McBane, 2005) has been rectified by constraining the potential to adopt accurate long-range behavior for He-CO distances well beyond 15a0 . The resulting surface is very similar to the original in the main part of the interaction. Comparison with accurately known bound-state energies indicates that the surface is slightly improved in the region sampled by the highest lying bound states. The positions of shape and Feshbach resonances within a few cm-1 of the j = 1 excitation threshold are essentially unchanged. The low-energy scattering lengths changed noticeably. The revised surface generates a small negative limiting scattering length for collisions with 4He, while the original surface gave a small positive one. Both surfaces yield scattering lengths quite different from the widely used surface of Heijmen et al. (1997) for both He isotopes.

  3. Ab initio ground state phenylacetylene-argon intermolecular potential energy surface and rovibrational spectrum

    DEFF Research Database (Denmark)

    Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian

    2012-01-01

    We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set ...

  4. Methods and apparatus for delivering high power laser energy to a surface

    Energy Technology Data Exchange (ETDEWEB)

    Faircloth, Brian O; Zediker, Mark S; Rinzler, Charles C; Koblick, Yeshaya; Moxley, Joel F

    2013-04-23

    There is provided a system, apparatus and methods for providing a laser beam to borehole surface in a predetermined and energy deposition profile. The predetermined energy deposition profiles may be uniform or tailored to specific downhole applications. Optic assemblies for obtaining these predetermined energy deposition profiles are further provided.

  5. Low energy high current pulsed electron beam treatment for improving surface microstructure and properties

    Energy Technology Data Exchange (ETDEWEB)

    Wu, J; Allain-Bonasso, N; Zhang, X D; Hao, S Z; Grosdider, T; Dong, C [Laboratoire d' Etude des Textures et Applications aux Materiaux (LETAM, UMR-CNRS 3143), Universite Paul Verlaine-Metz, Ile du Saulcy, 57045 Metz (France); Zou, J X, E-mail: jiang.wu@univ-metz.fr, E-mail: thierry.grosdidier@univ-metz.fr [National Engineering Research Center of Light Alloy Net Forming, Shanghai Jiao Tong University, Shanghai 200240 (China)

    2010-06-15

    Low energy high current pulsed electron beam (LEHCPEB) is a fairly new technique for surface modifications authorizing improvement in wear and corrosion properties as well as texture changes and hardening. This contribution highlights some microstructure modifications encountered at the surface of HCPEB treated steels and bulk metallic glasses taking into account the effects of surface melting and the effects of the induced stress.

  6. Physical and chemical nature of the scaling relations between adsorption energies of atoms on metal surfaces

    DEFF Research Database (Denmark)

    Calle-Vallejo, F.; Martínez, J. I.; García Lastra, Juan Maria;

    2012-01-01

    phenomenon between any set of adsorbates bound similarly to the surface. On the example of the near-surface alloys of Pt, we show that scalability is a result of identical variations of adsorption energies with respect to the valence configuration of both the surface components and the adsorbates....

  7. Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design.

    Science.gov (United States)

    Montgomery, Andrew; Szabo, Rémi; Skropeta, Danielle; Yu, Haibo

    2016-05-01

    Human β-galactoside α-2,6-sialyltransferase I (hST6Gal I) catalyses the synthesis of sialylated glycoconjugates involved in cell-cell interactions. Overexpression of hST6Gal I is observed in many different types of cancers, where it promotes metastasis through altered cell surface sialylation. A wide range of sialyltransferase (ST) inhibitors have been developed based on the natural donor, cytidine 5'-monophosphate N-acetylneuraminic acid (CMP-Neu5Ac). Of these, analogues that are structurally similar to the transition state exhibit the highest inhibitory activity. In order to design inhibitors that are readily accessible synthetically and with favourable pharmacokinetic properties, an investigation of the replacement of the charged phosphodiester-linker, present in many ST inhibitors, with a potential neutral isostere such as a carbamate or a 1,2,3-triazole has been undertaken. To investigate this, molecular docking and molecular dynamics simulations were performed. These simulations provided an insight into the binding mode of previously reported phosphodiester-linked ST inhibitors and demonstrated that targeting the proposed sialyl acceptor site is a viable option for producing selective inhibitors. The potential for a carbamate- or triazole-linker as an isosteric replacement for the phosphodiester in transition-state analogue ST inhibitors was established using molecular docking. Molecular dynamics simulations of carbamate- and phosphodiester-linked compounds revealed that both classes exhibit consistent interactions with hST6Gal I. Overall, the results obtained from this study provide a rationale for synthetic and biological evaluation of triazole- and carbamate-linked transition-state analogue ST inhibitors as potential new antimetastatic agents.

  8. Surface Energy and Work Function Control of AlOx/Al Surfaces by Fluorinated Benzylphosphonic Acids.

    Science.gov (United States)

    Abraham, Ffion; Ford, William E; Scholz, Frank; Nelles, Gabriele; Sandford, Graham; von Wrochem, Florian

    2016-05-11

    The performance of organic electronic devices can be significantly improved by modifying metal electrodes with organic monolayers, which alter the physical and chemical nature of the interface between conductor and semiconductor. In this paper we examine a series of 12 phosphonic acid compounds deposited on the native oxide layer of aluminum (AlOx/Al), an electrode material with widespread applications in organic electronics. This series includes dodecylphosphonic acid as a reference and 11 benzylphosphonic acids, seven of which are fluorinated, including five newly synthesized derivatives. The monolayers are experimentally characterized by contact angle goniometry and by X-ray photoemission spectroscopy (XPS), and work function data obtained by low-intensity XPS are correlated with molecular dipoles obtained from DFT calculations. We find that monolayers are formed with molecular areas ranging from 17.7 to 42.9 Å(2)/molecule, and, by the choice of appropriate terminal groups, the surface energy can be tuned from 23.5 mJ/m(2) to 70.5 mJ/m(2). Depending on the number and position of fluorine substituents on the aromatic rings, a variation in the work function of AlOx/Al substrates over a range of 0.91 eV is achieved, and a renormalization procedure based on molecular density yields a surprising agreement of work function changes with interface dipoles as expected from Helmholtz' equation. The ability to adjust energetics and adhesion at organic semiconductor/AlOx interfaces has immediate applications in devices such as OLEDs, OTFTs, organic solar cells, and printed organic circuits.

  9. Surface Energy Determined by Inverse Gas Chromatography as a Tool to Investigate Particulate Interactions in Dry Powder Inhalers.

    Science.gov (United States)

    Das, Shyamal C; Tucker, Ian G; Stewart, Peter J

    2015-01-01

    Dry powder inhalers (DPIs) usually contain drug particles energy of particles. Inverse gas chromatography (IGC) has been used to determine the surface energy of powder particles used in DPI to characterize materials and to understand aerosolization behaviour. Early studies used an infinite dilution technique to determine nonpolar surface energy and free energy of adsorption for polar interactions separately. Although some correlations were observed with the change in nonpolar surface energy before and after micronization, milling and storage, a lack of consistency in the change of free energy of adsorption was common. Moreover, a consistent relationship between complex de-agglomeration behaviour and surface energy has not been established and there are even some examples of negative correlation. In fact, nonpolar surface energy at infinite dilution is an incomplete representation of powder surface characteristics. The techniques for measuring polar surface energy, total surface energy and surface energy distribution have provided more revealing information about surface energetics of powders. Surface energy distributions determined by IGC or surface energy analyser have been successfully used to understand energetic heterogeneity of surfaces, characterize different polymorphs and understand changes due to micronization, structural relaxation, dry coating and storage. Efforts have been made to utilize surface energy distribution data to calculate powder strength distribution and to explain complex de-agglomeration behaviour of DPI formulations.

  10. Microclimatic models. Estimation of components of the energy balance over land surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Heikinheimo, M.; Venaelaeinen, A.; Tourula, T. [Finnish Meteorological Inst., Helsinki (Finland). Air Quality Dept.

    1996-12-31

    Climates at regional scale are strongly dependent on the interaction between atmosphere and its lower boundary, the oceans and the land surface mosaic. Land surfaces influence climate through their albedo, and the aerodynamic roughness, the processes of the biosphere and many soil hydrological properties; all these factors vary considerably geographically. Land surfaces receive a certain portion of the solar irradiance depending on the cloudiness, atmospheric transparency and surface albedo. Short-wave solar irradiance is the source of the heat energy exchange at the earth`s surface and also regulates many biological processes, e.g. photosynthesis. Methods for estimating solar irradiance, atmospheric transparency and surface albedo were reviewed during the course of this project. The solar energy at earth`s surface is consumed for heating the soil and the lower atmosphere. Where moisture is available, evaporation is one of the key components of the surface energy balance, because the conversion of liquid water into water vapour consumes heat. The evaporation process was studied by carrying out field experiments and testing parameterisation for a cultivated agricultural surface and for lakes. The micrometeorological study over lakes was carried out as part of the international `Northern Hemisphere Climatic Processes Experiment` (NOPEX/BAHC) in Sweden. These studies have been aimed at a better understanding of the energy exchange processes of the earth`s surface-atmosphere boundary for a more accurate and realistic parameterisation of the land surface in atmospheric models

  11. Hot electron mediated desorption rates calculated from excited state potential energy surfaces

    CERN Document Server

    Olsen, Thomas; Schiøtz, Jakob

    2008-01-01

    We present a model for Desorption Induce by (Multiple) Electronic Transitions (DIET/DIMET) based on potential energy surfaces calculated with the Delta Self-Consistent Field extension of Density Functional Theory. We calculate potential energy surfaces of CO and NO molecules adsorbed on various transition metal surfaces, and show that classical nuclear dynamics does not suffice for propagation in the excited state. We present a simple Hamiltonian describing the system, with parameters obtained from the excited state potential energy surface, and show that this model can describe desorption dynamics in both the DIET and DIMET regime, and reproduce the power law behavior observed experimentally. We observe that the internal stretch degree of freedom in the molecules is crucial for the energy transfer between the hot electrons and the molecule when the coupling to the surface is strong.

  12. A transitioning Arctic surface energy budget: the impacts of solar zenith angle, surface albedo and cloud radiative forcing

    Energy Technology Data Exchange (ETDEWEB)

    Sedlar, Joseph; Tjernstroem, Michael; Leck, Caroline [Stockholm University, Department of Meteorology, Stockholm (Sweden); Mauritsen, Thorsten [Max-Planck-Institute for Meteorology, Hamburg (Germany); Shupe, Matthew D.; Persson, P.O.G. [University of Colorado, NOAA-ESRL-PSD, Boulder, CO (United States); Brooks, Ian M.; Birch, Cathryn E. [University of Leeds, School of Earth and Environment, Leeds (United Kingdom); Sirevaag, Anders [University of Bergen, Bjerknes Center for Climate Research, Bergen (Norway); Nicolaus, Marcel [Norwegian Polar Institute, Tromsoe (Norway); Alfred Wegener Institute for Polar and Marine Research, Bremerhaven (Germany)

    2011-10-15

    Snow surface and sea-ice energy budgets were measured near 87.5 N during the Arctic Summer Cloud Ocean Study (ASCOS), from August to early September 2008. Surface temperature indicated four distinct temperature regimes, characterized by varying cloud, thermodynamic and solar properties. An initial warm, melt-season regime was interrupted by a 3-day cold regime where temperatures dropped from near zero to -7 C. Subsequently mean energy budget residuals remained small and near zero for 1 week until once again temperatures dropped rapidly and the energy budget residuals became negative. Energy budget transitions were dominated by the net radiative fluxes, largely controlled by the cloudiness. Variable heat, moisture and cloud distributions were associated with changing air-masses. Surface cloud radiative forcing, the net radiative effect of clouds on the surface relative to clear skies, is estimated. Shortwave cloud forcing ranged between -50 W m{sup -2} and zero and varied significantly with surface albedo, solar zenith angle and cloud liquid water. Longwave cloud forcing was larger and generally ranged between 65 and 85 W m{sup -2}, except when the cloud fraction was tenuous or contained little liquid water; thus the net effect of the clouds was to warm the surface. Both cold periods occurred under tenuous, or altogether absent, low-level clouds containing little liquid water, effectively reducing the cloud greenhouse effect. Freeze-up progression was enhanced by a combination of increasing solar zenith angles and surface albedo, while inhibited by a large, positive surface cloud forcing until a new air-mass with considerably less cloudiness advected over the experiment area. (orig.)

  13. Study of Fusion Dynamics Using Skyrme Energy Density Formalism with Different Surface Corrections

    Institute of Scientific and Technical Information of China (English)

    Ishwar Dutt; Narinder K. Dhiman

    2010-01-01

    @@ Within the framework of Skyrme energy density formalism, we investigate the role of surface corrections on the fusion of colliding nuclei. The coefficient of surface correction is varied between 1/36 and 4/36, and its impact is studied on about 180 reactions. The detailed investigations indicate a linear relationship between the fusion barrier heights and strength of the surface corrections. Our analysis of the fusion barriers advocate the strength of surface correction of 1/36.

  14. Energy analysis of the engineering-economic optimization of convective heat-transfer surfaces

    Science.gov (United States)

    Stoyanov, N. M.

    1991-07-01

    The influence of the specific costs of the heat transfer surface, 1 kW of installed power of the blower and motor, 1 kW·h of electrical energy consumption by it, operating time of the surface, and other factors on the optimum specific power expenditure to force heat-transfer fluids through the ducts of heattransfer surfaces is investigated. The minimum engineering-economically justified operating time of the surface is determined.

  15. Bending energy penalty enhances the adhesive strength of functional amyloid curli to surfaces.

    Science.gov (United States)

    Zhang, Yao; Wang, Ao; DeBenedictis, Elizabeth P; Keten, Sinan

    2017-09-27

    The functional amyloid curli fiber, a major proteinaceous component of biofilm extracellular matrices, plays an important role in biofilm formation and enterobacteriaceae adhesion. Curli nanofibers exhibit exceptional underwater adhesion to various surfaces, have high rigidity and strong tensile mechanical properties, and thus hold great promise in biomaterials. The mechanisms of how curli fibers strongly attach to surfaces and detach under force remain elusive. To investigate curli fiber adhesion to surfaces, we developed a coarse-grained curli fiber model, in which the protein subunit CsgA (curli specific gene A) self-assembles into the fiber. The coarse-grained model yields physiologically relevant and tunable bending rigidity and persistence length. The force-induced desorption of a single curli fiber is examined using coarse-grained modeling and theoretical analysis. We find that the bending energy penalty arising from high persistence length enhances the resistance of the curli fiber against desorption and thus strengthens the adhesion of the curli fiber to surfaces. The CsgA-surface adhesion energy and the curli fiber bending rigidity both play crucial roles in the resistance of curli fiber against desorption from surfaces. To enable the desorption process, the applied peeling force must overcome both the interfacial adhesion energy and the energy barrier for bending the curli fiber at the peeling front. We show that the energy barrier to desorption increases with the interfacial adhesion energy, however, the bending induced failure of a single curli fiber limits the work of adhesion if the proportion of the CsgA-surface adhesion energy to the CsgA-CsgA cohesive energy becomes large. These results illustrate that the optimal adhesion performance of nanofibers is dictated by the interplay between bending, surface energy and cohesive energy. Our model provides timely insight into enterobacteriaceae adhesion mechanisms as well as future designs of engineered

  16. Designing superhydrophobic disordered arrays of fibers with hierarchical roughness and low-surface-energy

    Science.gov (United States)

    Rawal, Amit; Sharma, Sumit; Kumar, Vijay; Saraswat, Harshvardhan

    2016-12-01

    Hierarchical roughness and low surface energy are the main criteria for designing superhydrophobic surfaces with extreme water repellency. Herein, we present a step-wise approach to devise three-dimensional (3D) superhydrophobic disordered arrays of fibers in the form of nonwoven mats exhibiting hierarchical surface roughness and low surface energy. Key design parameters in the form of roughness factors at multiple length scales for 3D nonwoven mats have been quantified. The contact angles have been predicted for each of the wetting regimes that exists for nonwoven mats with predefined level of hierarchical surface roughness and surface energy. Experimental realization of superhydrophobic mats was attained by decorating the highly hydrophilic nonwoven viscose fibers with ZnO rods that effectively modulated the surface roughness at multiple length scales and subsequently, the surface energy was lowered using fluorocarbon treatment. Synergistic effects of hierarchical roughness and surface energy have systematically increased the static water contact angle of nonwoven mat (up to 164°) and simultaneously, lowered the roll-off angle (≈11°).

  17. Band energy control of molybdenum oxide by surface hydration

    Energy Technology Data Exchange (ETDEWEB)

    Butler, Keith T., E-mail: k.t.butler@bath.ac.uk; Walsh, Aron [Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom); Crespo-Otero, Rachel [School of Biological and Chemical Sciences, Queen Mary University London, Mile End Road, London E1 4NS (United Kingdom); Buckeridge, John; Scanlon, David O. [University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ (United Kingdom); Bovill, Edward; Lidzey, David [Department of Physics and Astronomy, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH (United Kingdom)

    2015-12-07

    The application of oxide buffer layers for improved carrier extraction is ubiquitous in organic electronics. However, the performance is highly susceptible to processing conditions. Notably, the interface stability and electronic structure is extremely sensitive to the uptake of ambient water. In this study we use density functional theory calculations to asses the effects of adsorbed water on the electronic structure of MoO{sub x}, in the context of polymer-fullerene solar cells based on PCDTBT. We obtain excellent agreement with experimental values of the ionization potential for pristine MoO{sub 3} (010). We find that IP and EA values can vary by as much as 2.5 eV depending on the oxidation state of the surface and that adsorbed water can either increase or decrease the IP and EA depending on the concentration of surface water.

  18. Modeling the surface stored thermal energy in asphalt concrete pavements

    Directory of Open Access Journals (Sweden)

    Matić Bojan J.

    2016-01-01

    Full Text Available Regression analysis is used to develop models for minimal daily pavement surface temperature, using minimal daily air temperature, day of the year, wind speed and solar radiation as predictors, based on data from Awbari, Lybia,. Results were compared with existing SHRP and LTPP models. This paper also presents the models to predict surface pavement temperature depending on the days of the year using neural networks. Four annual periods are defined and new models are formulated for each period. Models using neural networks are formed on the basis of data gathered on the territory of the Republic of Serbia and are valid for that territory. [Projekat Ministarstva nauke Republike Srbije, br. TR 36017

  19. Estimation of surface energy fluxes under complex terrain of Mt. Qomolangma over the Tibetan Plateau

    Directory of Open Access Journals (Sweden)

    X. Chen

    2013-04-01

    Full Text Available Surface solar radiation is an important parameter in surface energy balance models and in estimation of evapotranspiration. This study developed a DEM based radiation model to estimate instantaneous clear sky solar radiation for surface energy balance system to obtain accurate energy absorbed by the mountain surface. Efforts to improve spatial accuracy of satellite based surface energy budget in mountainous regions were made in this work. Based on eight scenes of Landsat TM/ETM+ (Thematic Mapper/Enhanced Thematic Mapper+ data and observations around the Qomolangma region of the Tibetan Plateau, the topographical enhanced surface energy balance system (TESEBS was tested for deriving net radiation, ground heat flux, sensible heat flux and latent heat flux distributions over the heterogeneous land surface. The land surface energy fluxes over the study area showed a wide range in accordance with the surface features and their thermodynamic states. The model was validated by observations at QOMS/CAS site in the research area with a reasonable accuracy. The mean bias of net radiation, sensible heat flux, ground heat flux and latent heat flux is lower than 23.6 W m−2. The surface solar radiation estimated by the DEM based radiation model developed by this study has a mean bias as low as −9.6 W m−2. TESEBS has a decreased mean bias of about 5.9 W m−2 and 3.4 W m−2 for sensible heat and latent heat flux, respectively, compared to the Surface Energy Balance System (SEBS.

  20. Modelled and measured energy exchange at a snow surface

    Science.gov (United States)

    Halberstam, I.

    1979-01-01

    Results of a model developed at JPL for the energy interchange between the atmosphere and the snow are compared with measurements made over a snowfield during a warm period of March, 1978. Both model and measurements show that turbulent fluxes are considerably smaller than the radiative fluxes, especially during the day. The computation of turbulent fluxes for both model and data is apparently lacking because of problems inherent in the stable atmosphere.

  1. Intermolecular potential energy surface and thermophysical properties of ethylene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Crusius, Johann-Philipp, E-mail: johann-philipp.crusius@uni-rostock.de; Hassel, Egon [Lehrstuhl für Technische Thermodynamik, Universität Rostock, 18059 Rostock (Germany); Hellmann, Robert; Bich, Eckard [Institut für Chemie, Universität Rostock, 18059 Rostock (Germany)

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C{sub 2}H{sub 4}O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

  2. Evaluating surface energy components of asphalt binders using Wilhelmy Plate and Sessile Drop Techniques

    OpenAIRE

    Bahramian, Anohe

    2012-01-01

    In this Study, the surface energy was investigated for six penetration grade 70/100 bitumen binders. Wilhelmy Plate and the Sessile Drop were used to determine the contact angles. The purpose of this study was to compare the Wilhelmy Plate method with the Sessile Drop method, and to compare the significance of Owens-Wendt model with the significance of Acid Base model by correlating surface energy components. Better R2 –values were found for surface energy components by using the Owens-Wendt ...

  3. Surface energy balance measurements in the Mexico City: a review

    Energy Technology Data Exchange (ETDEWEB)

    Tejeda Martinez, A. [Universidad Veracruzana, Xalapa, Veracruz (Mexico); Jauregui Ostos, E. [Centro de Ciencias de la Atmosfera, Universidad Nacional Autonoma de Mexico, UNAM, Mexico, D.F. (Mexico)

    2005-01-01

    During the last decade of the 20th Century, diverse campaigns for measuring the atmospheric energy balance were performed in downtown Mexico City (School of Mines and Preparatory School No. 7), in the southern suburbs (University Reserve) and in the surrounding rural areas (Plan Texcoco), in addition to a campaign carried out in 1985 in the Tacubaya district, a suburban western peripheral site. The objective was to obtain data for a better understanding of the climatic alterations due to urbanization, particularly to describe the role that the modification of the natural ground cover has played as a result of paving and the construction of urban canyons. In this paper, a review of these campaigns is presented. Energy partitioning in some areas (Tacubaya and Preparatory School No.7) is similar to that observed in urban centers of middle latitudes, whereas the major contrast was observed between Texcoco, with maximum energy consumption through evaporation, and School of Mines, where the latent heat is as low as in a desert. From the values of the correlations among the different components of energy balance, it may be possible to attempt the modeling of the diverse components of energy balance by means of regression equations starting from the net radiation. Those same coefficients distinguish the type of environment: urban, suburban or rural. [Spanish] Las primeras mediciones de balance energetico en la Ciudad de Mexico se realizaron en 1985 en un suburbio al poniente de la ciudad (el observatorio de Tacubaya). Ya en la decada de los anos noventa del siglo XX, dichas observaciones se multiplicaron tanto en el centro historico (antigua Escuela de Minas y en el edificio de la Preparatoria No. 7), como en otros sitios al sur (en terrenos de Ciudad Universitaria) y en la periferia rural (Plan Texcoco). El proposito de estas mediciones ha sido tener un mejor entendimiento de las alteraciones climaticas debidas a la urbanizacion. En este trabajo se presenta una revision

  4. Apparent Surface Free Energy of Polymer/Paper Composite Material Treated by Air Plasma

    Directory of Open Access Journals (Sweden)

    Konrad Terpiłowski

    2017-01-01

    Full Text Available Surface plasma treatment consists in changes of surface properties without changing internal properties. In this paper composite polymer/paper material is used for production of packaging in cosmetic industry. There are problems with bonding this material at the time of packaging production due to its properties. Composite surface was treated by air plasma for 1, 10, 20, and 30 s. The advancing and receding contact angles of water, formamide, and diiodomethane were measured using both treated and untreated samples. Apparent surface free energy was estimated using the hysteresis (CAH and Van Oss, Good, Chaudhury approaches (LWAB. Surface roughness was investigated using optical profilometry and identification of after plasma treatment emerging chemical groups was made by means of the XPS (X-ray photoelectron spectroscopy technique. After plasma treatment the values of contact angles decreased which is particularly evident for polar liquids. Apparent surface free energy increased compared to that of untreated samples. Changes of energy value are due to the electron-donor parameter of energy. This parameter increases as a result of adding polar groups at the time of surface plasma activation. Changes of surface properties are combination of increase of polar chemical functional groups, increase on the surface, and surface roughness increase.

  5. Soil heat flux and day time surface energy balance closure at astronomical observatory, Thiruvananthapuram, south Kerala

    Indian Academy of Sciences (India)

    M S Roxy; V B Sumithranand; G Renuka

    2014-06-01

    Soil heat flux is an important input component of surface energy balance. Estimates of soil heat flux were made in the year 2008 using soil temperature data at Astronomical Observatory, Thiruvananthapuram, south Kerala. Hourly values of soil heat flux from 00 to 24 LST are presented for selected days typical of the winter, pre-monsoon, SW monsoon and NE monsoon seasons. The diurnal variation is characterized by a cross-over from negative to positive values at 0700 h, occurrence of maximum around noon and return to negative values in the late evening. The energy storage term for the soil layer 0–0.05 m is calculated and the ground heat flux * is estimated in all seasons. Daytime surface energy balance at the surface on wet and dry seasons is investigated. The average Bowen’s ratio during the wet and dry seasons were 0.541 and 0.515, respectively indicating that considerable evaporation takes place at the surface. The separate energy balance components were examined and the mean surface energy balance closure was found to be 0.742 and 0.795 for wet and dry seasons, respectively. When a new method that accounts for both soil thermal conduction and soil thermal convection was adopted to calculate the surface heat flux, the energy balance closure was found to be improved. Thus on the land surface under study, the soil vertical water movement is significant.

  6. Reconnoitering the effect of shallow groundwater on land surface temperature and surface energy balance using MODIS and SEBS

    Directory of Open Access Journals (Sweden)

    F. Alkhaier

    2012-07-01

    Full Text Available The possibility of observing shallow groundwater depth and areal extent using satellite measurements can support groundwater models and vast irrigation systems management. Moreover, these measurements can help to include the effect of shallow groundwater on surface energy balance within land surface models and climate studies, which broadens the methods that yield more reliable and informative results. To examine the capacity of MODIS in detecting the effect of shallow groundwater on land surface temperature and the surface energy balance in an area within Al-Balikh River basin in northern Syria, we studied the interrelationship between in-situ measured water table depths and land surface temperatures measured by MODIS. We, also, used the Surface Energy Balance System (SEBS to calculate surface energy fluxes, evaporative fraction and daily evaporation, and inspected their relationships with water table depths. We found out that the daytime temperature increased while the nighttime temperature decreased when the depth of the water table increased. And, when the water table depth increased, net radiation, latent and ground heat fluxes, evaporative fraction and daily evaporation decreased, while sensible heat flux increased. This concords with the findings of a companion paper (Alkhaier et al., 2012. The observed clear relationships were the result of meeting both conditions that were concluded in the companion paper, i.e. high potential evaporation and big contrast in day-night temperature. Moreover, the prevailing conditions in this study area helped SEBS to yield accurate estimates. Under bare soil conditions and under the prevailing weather conditions, we conclude that MODIS is suitable for detecting the effect of shallow groundwater because it has proper imaging times and adequate sensor accuracy; nevertheless, its coarse spatial resolution is disadvantageous.

  7. Jump Markov models and transition state theory: the quasi-stationary distribution approach.

    Science.gov (United States)

    Di Gesù, Giacomo; Lelièvre, Tony; Le Peutrec, Dorian; Nectoux, Boris

    2016-12-22

    We are interested in the connection between a metastable continuous state space Markov process (satisfying e.g. the Langevin or overdamped Langevin equation) and a jump Markov process in a discrete state space. More precisely, we use the notion of quasi-stationary distribution within a metastable state for the continuous state space Markov process to parametrize the exit event from the state. This approach is useful to analyze and justify methods which use the jump Markov process underlying a metastable dynamics as a support to efficiently sample the state-to-state dynamics (accelerated dynamics techniques). Moreover, it is possible by this approach to quantify the error on the exit event when the parametrization of the jump Markov model is based on the Eyring-Kramers formula. This therefore provides a mathematical framework to justify the use of transition state theory and the Eyring-Kramers formula to build kinetic Monte Carlo or Markov state models.

  8. On the uniqueness of t->0+ quantum transition-state theory

    CERN Document Server

    Hele, Timothy J H

    2013-01-01

    It was shown recently that there exists a true quantum transition-state theory (QTST) corresponding to the t->0+ limit of a (new form of) quantum flux-side time-correlation function. Remarkably, this QTST is identical to ring-polymer molecular dynamics (RPMD) TST. Here we provide evidence which suggests very strongly that this QTST (= RPMD-TST) is unique, in the sense that the t->0+ limit of any other flux-side time-correlation function gives either non-positive-definite quantum statistics or zero. We introduce a generalized flux-side time-correlation function which includes all other (known) flux-side time-correlation functions as special limiting cases. We find that the only non-zero t->0+ limit of this function that contains positive-definite quantum statistics is RPMD-TST.

  9. Molecular wave-packet dynamics on laser-controlled transition states

    CERN Document Server

    Fischer, Andreas; Cörlin, Philipp; Sperl, Alexander; Schönwald, Michael; Mizuno, Tomoya; Sansone, Giuseppe; Senftleben, Arne; Ullrich, Joachim; Feuerstein, Bernold; Pfeifer, Thomas; Moshammer, Robert

    2016-01-01

    Understanding and controlling the electronic as well as ro-vibrational motion and, thus, the entire chemical dynamics in molecules is the ultimate goal of ultrafast laser and imaging science. In photochemistry, laser-induced dissociation has become a valuable tool for modification and control of reaction pathways and kinetics. Here, we present a pump-probe study of the dissociation dynamics of H$_2^+$ using ultrashort extreme-ultraviolet (XUV) and near-infrared (IR) laser pulses. The reaction kinematics can be controlled by varying the pump-probe delay. We demonstrate that the nuclear motion through the transition state can be reduced to isolated pairs of initial vibrational states. The dynamics is well reproduced by intuitive semi-classical trajectories on a time-dependent potential curve. From this most fundamental scenario we gain insight in the underlying mechanisms which can be applied as design principles for molecular quantum control, particularly for ultrafast reactions involving protons.

  10. Jump Markov models and transition state theory: the Quasi-Stationary Distribution approach

    CERN Document Server

    Di Gesù, Giacomo; Peutrec, Dorian Le; Nectoux, Boris

    2016-01-01

    We are interested in the connection between a metastable continuous state space Markov process (satisfying e.g. the Langevin or overdamped Langevin equation) and a jump Markov process in a discrete state space. More precisely, we use the notion of quasi-stationary distribution within a metastable state for the continuous state space Markov process to parametrize the exit event from the state. This approach is useful to analyze and justify methods which use the jump Markov process underlying a metastable dynamics as a support to efficiently sample the state-to-state dynamics (accelerated dynamics techniques). Moreover, it is possible by this approach to quantify the error on the exit event when the parametrization of the jump Markov model is based on the Eyring-Kramers formula. This therefore provides a mathematical framework to justify the use of transition state theory and the Eyring-Kramers formula to build kinetic Monte Carlo or Markov state models.

  11. Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic

    Science.gov (United States)

    Perry, Kay; Hwang, Young; Bushman, Frederic D.; Van Duyne, Gregory D.

    2010-01-01

    Summary Poxviruses encode their own type IB topoisomerases (TopIBs) which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves a novel Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small vs. large enzyme subfamilies. PMID:20152159

  12. Transition state theory: a generalization to nonequilibrium systems with power-law distributions

    CERN Document Server

    Jiulin, Du

    2011-01-01

    Transition state theory (TST) is generalized for the nonequilibrium system with power-law distributions. The stochastic dynamics that gives rise to the power-law distributions for the reaction coordinate and momentum is modeled by the Langevin equations and corresponding Fokker-Planck equations. It is assumed that the system far away from equilibrium has not to relax to a thermal equilibrium state with Boltzmann-Gibbs distribution, but asymptotically approaches to a nonequilibrium stationary-state with power-law distributions. Thus, we obtain a generalization of TST rates to nonequilibrium systems with power-law distributions. Furthermore, we derive the generalized TST rate constants for one-dimension and n-dimension Hamiltonian systems away from equilibrium, and receive a generalized Arrhenius rate for the system with power-law distributions.

  13. Design, Synthesis, and Evaluation of Novel Prodrugs of Transition State Inhibitors of Norovirus 3CL Protease.

    Science.gov (United States)

    Galasiti Kankanamalage, Anushka C; Kim, Yunjeong; Rathnayake, Athri D; Alliston, Kevin R; Butler, Michelle M; Cardinale, Steven C; Bowlin, Terry L; Groutas, William C; Chang, Kyeong-Ok

    2017-07-27

    Ester and carbamate prodrugs of aldehyde bisulfite adduct inhibitors were synthesized in order to improve their pharmacokinetic and pharmacodynamic properties. The inhibitory activity of the compounds against norovirus 3C-like protease in enzyme and cell-based assays was determined. The ester and carbamate prodrugs displayed equivalent potency to those of the precursor aldehyde bisulfite adducts and precursor aldehydes. Furthermore, the rate of ester cleavage was found to be dependent on alkyl chain length. The generated prodrugs exhibited low cytotoxicity and satisfactory liver microsomes stability and plasma protein binding. The methodology described herein has wide applicability and can be extended to the bisulfite adducts of common warheads employed in the design of transition state inhibitors of serine and cysteine proteases of medical relevance.

  14. Inhibition and Structure of Trichomonas vaginalis Purine Nucleoside Phosphorylase with Picomolar Transition State Analogues

    Energy Technology Data Exchange (ETDEWEB)

    Rinaldo-Matthis,A.; Wing, C.; Ghanem, M.; Deng, H.; Wu, P.; Gupta, A.; Tyler, P.; Evans, G.; Furneaux, R.; et al.

    2007-01-01

    Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions in the reverse direction relative to the PNPs in other organisms. Immucillin-A (ImmA) and DADMe-Immucillin-A (DADMe-ImmA) are transition stte mimics of adenosine with geometric and electrostatic features that resemble early and late transition states of adenosine at the transition state stabilized by TvPNP. ImmA demonstrates slow-onset tight-binding inhibition with TvPNP, to give an equilibrium dissociation constant of 87 pM, an inhibitor release half-time of 17.2 min, and a K{sub m}/K{sub d} ratio of 70,100. DADMe-ImmA resembles a late ribooxacarbenium ion transition state for TvPNP to give a dissociation constant of 30 pM, an inhibitor release half-time of 64 min, and a K{sub m}/K{sub d} ratio of 203,300. The tight binding of DADMe-ImmA supports a late S{sub N}1 transition state. Despite their tight binding to TvPNP, ImmA and DADMe-ImmA are weak inhibitors of human and P. falciparum PNPs. The crystal structures of the TvPNP-ImmA{center_dot}PO{sub 4} and TvPNP{center_dot}DADMe-ImmA{center_dot}PO{sub 4} ternary complexes differ from previous structures with substrate anologues. The tight binding with DADMe-ImmA is in part due to a 2.7 {angstrom} ionic interaction between a PO{sub 4} oxygen and the N1 cation of the hydroxypyrrolidine and is weaker in the TvPNP{center_dot}ImmA{center_dot}PO{sub 4} structure at 3.5 {angstrom}. However, the TvPNP{center_dot}ImmA{center_dot}PO{sub 4} structure includes hydrogen bonds between the 2'-hydroxyl and the protein that are not present in TvPNP{center_dot}DADMe-ImmA{center_dot}PO{sub 4}. These structures explain why DADMe-ImmA binds tighter than ImmA. Immucillin-H is a 12 nM inhibitor of TvPNP but a 56 pM inhibitor of human PNP. And this difference is explained by isotope

  15. Implementation of a microcanonical variational transition state theory for direct dynamics calculations of rate constants

    Institute of Scientific and Technical Information of China (English)

    王艳; 钱英; 冯文林; 刘若庄

    2003-01-01

    An implementation of the variational quantum RRKM program is presented to utilize the direct ab initio dynamics approach for calculating k(E, J), k(E) and k(T) within the framework of the microcanonical transition state (μTST) and microcanonical variational TST (μVT) theories. An algorithm including tunneling contributions in Beyer-Swinehart method for calculating microcanonical rate constants is also proposed. An efficient piece-wise interpolation method is developed to evaluate the Boltzmann integral in calculation of thermal rate constants. Calculations on several test reactions, namely the H(D)2CO→H(D)2 + CO, CH2CO→CH2 + CO and CH4 + H→CH3 + H2 reactions, show that the results are in good agreement with the previous rate constants calculations. This approach would require much less computational resource.

  16. Charge exchange of medium energy H and He ions emerging from solid surfaces

    Science.gov (United States)

    Kitsudo, Y.; Shibuya, K.; Nishimura, T.; Hoshino, Y.; Vickridge, I.; Kido, Y.

    2009-02-01

    Charge exchange of medium energy H and He ions emerging from clean solid surfaces is studied extensively using a toroidal electrostatic analyzer with an excellent energy resolution. The charge distributions of He ions scattered from sub-monolayers near a surface are non-equilibrated, resulting in a surface peak even for poly-crystal solids. By solving simultaneous rate equations numerically, we derive electron capture and loss cross sections for Ni and Au surfaces. Based on a free electron gas model, non-equilibrated He+ fractions dependent on emerging angle reveals uniform electronic surfaces for metals and corrugated surfaces for Si and graphite with covalent bonds. It is also found that equilibrium charge fractions of H+ are independent of surface materials (Z2) and in contrast equilibrium He+ fractions depend pronouncedly on Z2. The data obtained are compared with semi-empirical formulas.

  17. Surface relaxation and surface energy of face –centered Cubic ...

    African Journals Online (AJOL)

    DR. MIKE HORSFALL

    were based on perturbation theory or non-perturbative variational methods. ... knowledge for Rh, Ir, Pb, Ca, Sr and Th metal surfaces. ... represented in the ECT by the inclusion of the three – ... the ECT method to an fcc (100) metallic surface,.

  18. Effect of mechanical denaturation on surface free energy of protein powders.

    Science.gov (United States)

    Mohammad, Mohammad Amin; Grimsey, Ian M; Forbes, Robert T; Blagbrough, Ian S; Conway, Barbara R

    2016-10-01

    Globular proteins are important both as therapeutic agents and excipients. However, their fragile native conformations can be denatured during pharmaceutical processing, which leads to modification of the surface energy of their powders and hence their performance. Lyophilized powders of hen egg-white lysozyme and β-galactosidase from Aspergillus oryzae were used as models to study the effects of mechanical denaturation on the surface energies of basic and acidic protein powders, respectively. Their mechanical denaturation upon milling was confirmed by the absence of their thermal unfolding transition phases and by the changes in their secondary and tertiary structures. Inverse gas chromatography detected differences between both unprocessed protein powders and the changes induced by their mechanical denaturation. The surfaces of the acidic and basic protein powders were relatively basic, however the surface acidity of β-galactosidase was higher than that of lysozyme. Also, the surface of β-galactosidase powder had a higher dispersive energy compared to lysozyme. The mechanical denaturation decreased the dispersive energy and the basicity of the surfaces of both protein powders. The amino acid composition and molecular conformation of the proteins explained the surface energy data measured by inverse gas chromatography. The biological activity of mechanically denatured protein powders can either be reversible (lysozyme) or irreversible (β-galactosidase) upon hydration. Our surface data can be exploited to understand and predict the performance of protein powders within pharmaceutical dosage forms. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Dissociative scattering of hyperthermal energy CF3+ ions from modified surfaces.

    Science.gov (United States)

    Rezayat, Talayeh; Shukla, Anil

    2007-02-28

    Dissociative scattering of CF3+ ions in collision with a self-assembled monolayer surface of fluorinated alkyl thiol on a gold 111 crystal has been studied at low ion kinetic energies (from 29 to 159 eV) using a custom built tandem mass spectrometer with a rotatable second stage energy analyzer and mass spectrometer detectors. Energy and intensity distributions of the scattered fragment ions were measured as a function of the fragment ion mass and scattering angle. Inelastically scattered CF3+ ions were not observed even at the lowest energy studied here. All fragment ions, CF2+, CF+, F+, and C+, were observed at all energies studied with the relative intensity of the highest energy pathway, C+, increasing and that of the lowest energy pathway, CF2+, decreasing with collision energy. Also, the dissociation efficiency of CF3+ decreased significantly as the collision energy was increased to 159 eV. Energy distributions of all fragment ions from the alkyl thiol surface showed two distinct components, one corresponding to the loss of nearly all of the kinetic energy and scattered over a broad angular range while the other corresponding to smaller kinetic energy losses and scattered closer to the surface parallel. The latter process is due to delayed dissociation of collisionally excited ions after they have passed the collision region as excited parent ions. A similar study performed at 74 eV using a LiF coated surface on a titanium substrate resulted only in one process for all fragment ions; corresponding to the delayed dissociation process. The intensity maxima for these fragmentation processes were shifted farther away from the surface parallel compared to the thiol surface. A new mechanism is proposed for the delayed dissociation process as proceeding via projectile ions' neutralization to long-lived highly excited Rydberg state(s), reionization by the potential field between the collision region and entrance to the energy analyzer, and subsequent dissociation

  20. Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design.

    Science.gov (United States)

    Nagaraju, Mulpuri; McGowan, Lauren C; Hamelberg, Donald

    2013-02-25

    Human Cyclophilin A (CypA) catalyzes cis-trans isomerization of the prolyl peptide ω-bond in proteins and is involved in many subcellular processes. CypA has, therefore, been identified as a potential drug target in many diseases, and the development of potent inhibitors with high selectivity is a key objective. In computer-aided drug design, selectivity is improved by taking into account the inherent flexibility of the receptor. However, the relevant receptor conformations to focus on in order to develop highly selective inhibitors are not always obvious from available X-ray crystal structures or ensemble of conformations generated using molecular dynamics simulations. Here, we show that the conformation of the active site of CypA varies as the substrate configuration changes during catalytic turnover. We have analyzed the principal modes of the active site dynamics of CypA from molecular dynamics simulations to show that similar ensembles of enzyme conformations recognize diverse inhibitors and bind the different configurations of the peptide substrate. Small nonpeptidomimetic inhibitors with varying activity are recognized by enzyme ensembles that are similar to those that tightly bind the transition state and cis configurations of the substrate. Our results suggest that enzyme-substrate ensembles are more relevant in structure-based drug design for CypA than free enzyme. Of the vast conformational space of the free enzyme, the enzyme conformations of the tightly bound enzyme-substrate complexes are the most important for catalysis. Therefore, functionalizing lead compounds to optimize their interactions with the enzyme's conformational ensemble bound to the substrate in the cis or the transition state could lead to more potent inhibitors.

  1. Prediction of monomer reactivity in radical copolymerizations from transition state quantum chemical descriptors

    Directory of Open Access Journals (Sweden)

    Zhengde Tan

    2013-01-01

    Full Text Available In comparison with the Q-e scheme, the Revised Patterns Scheme: the U, V Version (the U-V scheme has greatly improved both its accessibility and its accuracy in interpreting and predicting the reactivity of a monomer in free-radical copolymerizations. Quantitative structure-activity relationship (QSAR models were developed to predict the reactivity parameters u and v of the U-V scheme, by applying genetic algorithm (GA and support vector machine (SVM techniques. Quantum chemical descriptors used for QSAR models were calculated from transition state species with structures C¹H3 - C²HR³• or •C¹H2 - C²H2R³ (formed from vinyl monomers C¹H²=C²HR³ + H•, using density functional theory (DFT, at the UB3LYP level of theory with 6-31G(d basis set. The optimum support vector regression (SVR model of the reactivity parameter u based on Gaussian radial basis function (RBF kernel (C = 10, ε = 10- 5 and γ = 1.0 produced root-mean-square (rms errors for the training, validation and prediction sets being 0.220, 0.326 and 0.345, respectively. The optimal SVR model for v with the RBF kernel (C = 20, ε = 10- 4 and γ = 1.2 produced rms errors for the training set of 0.123, the validation set of 0.206 and the prediction set of 0.238. The feasibility of applying the transition state quantum chemical descriptors to develop SVM models for reactivity parameters u and v in the U-V scheme has been demonstrated.

  2. Kinetics, reactivity, initial-transition state analysis and thermodynamic parameters of base-catalyzed hydrolysis of coumalic acid in solvents with different polarities

    Directory of Open Access Journals (Sweden)

    Ezz A. Abu-Gharib

    2017-02-01

    Full Text Available Base-catalyzed hydrolysis of coumalic acid (COU in binary aqueous-methanol and aqueous-acetone mixtures has been studied kinetically at a temperature range from 283 to 313 K. Moreover, the change in the activation energy barrier of COU from water to water–methanol and water–acetone mixtures is estimated from the kinetic data. Solvent effects on reactivity trends have been analyzed into initial and transition state components by using transfer chemical potentials of the reactants and kinetic data. The transfer chemical potentials δmμθ for COU− anion are derived from solubility data from its calcium, cerium and lanthanum salts. The decrease in rate constant of the base hydrolysis reaction of COU as the percentage of methanol or acetone increases is dominated by transition state (TS. The base hydrolysis reaction of COU follows a rate law with kobs = k2[OH−] and the reaction mechanism was suggested. The high negative values of entropy of activation support the proposal mechanism, i.e. the investigated reaction takes place via the formation of an intermediate complex. Thus, the ring opening of the intermediate complex would be the rate controlling step.

  3. Surface structures from low energy electron diffraction: Atoms, small molecules and an ordered ice film on metal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Materer, N.F.

    1995-09-01

    We investigated the surface bonding of various adsorbates (0, S, C{sub 2}H{sub 3} and NO) along with the resulting relaxation of the Pt(111) surface using low energy electron diffiraction (LEED). LEED experiments have been performed on these ordered overlayers along with theoretical structural analysis using automated tensor LEED (ATLEED). The resulting surface structures of these ordered overlayers exhibit similar adsorbate-induced relaxations. In all cases the adsorbate occupies the fcc hollow site and induces an approximately 0.1 A buckling of the metal surface. The three metal atoms directly bonded to the adsorbate are ``pulled`` out of the surface and the metal atom that is not bound to the adsorbate is `pushed`` inward. In order to understand the reliability of such details, we have carried out a comprehensive study of various non-structural parameters used in a LEED computation. We also studied the adsorption of water on the Pt(lll) surface. We ordered an ultra thin ice film on this surface. The film`s surface is found to be the (0001) face of hexagonal ice. This surface is apparently terminated by a full-bilayer, in which the uppermost water molecules have large vibrational amplitudes even at temperatures as low as 90 K. We examined two other metal surfaces besides Pt(111): Ni(111) and Fe(lll). On Ni(111), we have studied the surface under a high coverage of NO. On both Ni(111) and Pt(111) NO molecules occupy the hollow sites and the N-0 bond distances are practically identical. The challenging sample preparation of an Fe(111) surface has been investigated and a successful procedure has been obtained. The small interlayer spacing found on Fe(111) required special treatment in the LEED calculations. A new ATLEED program has been developed to handle this surface.

  4. The role of the transition state in polyatomic reactions: Initial state-selected reaction probabilities of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction

    Energy Technology Data Exchange (ETDEWEB)

    Welsch, Ralph, E-mail: rwelsch@uni-bielefeld.de; Manthe, Uwe, E-mail: uwe.manthe@uni-bielefeld.de [Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld (Germany)

    2014-11-07

    Full-dimensional calculations of initial state-selected reaction probabilities on an accurate ab initio potential energy surface (PES) have been communicated recently [R. Welsch and U. Manthe, J. Chem. Phys. 141, 051102 (2014)]. These calculations use the quantum transition state concept, the multi-layer multi-configurational time-dependent Hartree approach, and graphics processing units to speed up the potential evaluation. Here further results of these calculations and an extended analysis are presented. State-selected reaction probabilities are given for many initial ro-vibrational states. The role of the vibrational states of the activated complex is analyzed in detail. It is found that rotationally cold methane mainly reacts via the ground state of the activated complex while rotationally excited methane mostly reacts via H–H–CH{sub 3}-bending excited states of the activated complex. Analyzing the different contributions to the reactivity of the vibrationally states of methane, a complex pattern is found. Comparison with initial state-selected reaction probabilities computed on the semi-empirical Jordan-Gilbert PES reveals the dependence of the results on the specific PES.

  5. Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice-Ramsperger-Kassel theory.

    Science.gov (United States)

    Bao, Junwei Lucas; Zhang, Xin; Truhlar, Donald G

    2016-11-29

    Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C2F4), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice-Ramsperger-Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements.

  6. A temperature-dependent surface free energy model for solid single crystals

    Science.gov (United States)

    Cheng, Tianbao; Fang, Daining; Yang, Yazheng

    2017-01-01

    A temperature-dependent theoretical model for the surface free energy of the solid single crystals is established. This model relates the surface free energy at the elevated temperatures to that at the reference temperature, the temperature-dependent specific heat at constant pressure and coefficient of the linear thermal expansion, the heat of phase transition, the melting heat, and the vapor heat. As examples, the surface free energies of Fe, Cu, Al, Ni, and Pb from 0 K to melting points are calculated and are in reasonable agreement with these from Tyson's theories and the experimental results. This model has obvious advantages compared to Tyson's semi-empirical equations from the aspect of physical meaning, applicable condition, and accuracy. The study shows that the surface free energy of the solid single crystals firstly remains approximately constant and then decreases linearly as temperature increases from 0 K to melting point.

  7. Mixed Potential Energy Surfaces of the Ultrafast Isomerization of Retinal in Bacteriorhodopsin

    Directory of Open Access Journals (Sweden)

    Prokhorenko Valentyn I.

    2013-03-01

    Full Text Available We observe, using electronic two-dimensional photon echo spectroscopy, that the cis and trans potential energy surfaces of the ultrafast isomerization of retinal in bacteriorhodopsin are mixed via the hydrogen out of plane (HOOP mode.

  8. The thermal energy of a scalar field on a unidimensional Riemann surface

    CERN Document Server

    Elizalde, E

    2002-01-01

    We discuss some controverted aspects of the evaluation of the thermal energy of a scalar field on a unidimensional Riemann surface. The calculations are carried out using a generalised zeta function approach.

  9. Study on the Surface Free Energy of Ground CaO by IGC

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    CaO formed by decomposing CaCO3 at 1450℃ was ground in a vibrational mill,then the long-time ground sample was reheated at different temperatures.Inverse Gas Chromatography (IGC) was used to measure the variation of the sample′s surface free energy under grinding and reheating.It is concluded that the total surface free energy and the London dispersive component of the surface free energy increases with grinding,while the polar component first increases with grinding,and then decreases,and finally disappears.When the long-time ground sample was reheated,its total surface free energy decreases,among which the London component decreases,but the polar component appears again.

  10. Nb2O5 Nanostructure Evolution on Nb Surfaces via Low-Energy He(+) Ion Irradiation.

    Science.gov (United States)

    Novakowski, Theodore Joseph; Tripathi, Jitendra Kumar; Hassanein, Ahmed

    2016-12-21

    We propose low-energy, broad-beam He(+) ion irradiation as a novel processing technique for the generation of Nb2O5 surface nanostructures due to its relative simplicity and scalability in a commercial setting. Since there have been relatively few studies involving the interaction of high-fluence, low-energy He(+) ion irradiation and Nb (or its oxidized states), this systematic study explores both effects of fluence and sample temperature during irradiation on resulting surface morphology. Detailed normal and cross-sectional scanning electron microscopy (SEM) studies reveal subsurface He bubble formation and elucidate potential driving mechanisms for nanostructure evolution. A combination of specular optical reflectivity and X-ray photoelectron spectroscopy (XPS) is also used to gain additional information on roughness and stoichiometry of irradiated surfaces. Our investigations show significant surface modification for all tested irradiation conditions; the resulting surface structure size and geometry have a strong dependence on both sample temperature during irradiation and total ion fluence. Optical reflectivity measurements on irradiated surfaces demonstrate increased surface roughening with increasing ion fluence, and XPS shows higher oxidation levels for samples irradiated at lower temperatures, suggesting larger surface roughness and porosity. Overall, it was found that low-energy He(+) ion irradiation is an efficient processing technique for nanostructure formation, and surface structures are highly tunable by adjusting ion fluence and Nb2O5 sample temperature during irradiation. These findings may have excellent potential applications for solar energy conversion through improved efficiency due to effective light absorption.

  11. Volume and surface contributions to the nuclear symmetry energy within the coherent density fluctuation model

    CERN Document Server

    Antonov, A N; Sarriguren, P; de Guerra, E Moya

    2016-01-01

    The volume and surface components of the nuclear symmetry energy (NSE) and their ratio are calculated within the coherent density fluctuation model (CDFM). The estimations use the results of the model for the NSE in finite nuclei based on the Brueckner energy-density functional for nuclear matter. In addition, we present results for the NSE and its volume and surface contributions obtained by using the Skyrme energy-density functional. The CDFM weight function is obtained using the proton and neutron densities from the self-consistent HF+BCS method with Skyrme interactions. We present and discuss the values of the volume and surface contributions to the NSE and their ratio obtained for the Ni, Sn, and Pb isotopic chains studying their isotopic sensitivity. The results are compared with estimations of other approaches which have used available experimental data on binding energies, neutron-skin thicknesses, excitation energies to isobaric analog states (IAS) and also with results of other theoretical methods.

  12. A surface hopping algorithm for nonadiabatic minimum energy path calculations.

    Science.gov (United States)

    Schapiro, Igor; Roca-Sanjuán, Daniel; Lindh, Roland; Olivucci, Massimo

    2015-02-15

    The article introduces a robust algorithm for the computation of minimum energy paths transiting along regions of near-to or degeneracy of adiabatic states. The method facilitates studies of excited state reactivity involving weakly avoided crossings and conical intersections. Based on the analysis of the change in the multiconfigurational wave function the algorithm takes the decision whether the optimization should continue following the same electronic state or switch to a different state. This algorithm helps to overcome convergence difficulties near degeneracies. The implementation in the MOLCAS quantum chemistry package is discussed. To demonstrate the utility of the proposed procedure four examples of application are provided: thymine, asulam, 1,2-dioxetane, and a three-double-bond model of the 11-cis-retinal protonated Schiff base.

  13. Minimum energy surface required by quantum memory devices.

    Science.gov (United States)

    van Dam, Wim; Nguyen, Hieu D

    2013-06-21

    We address the question of what physical resources are required and sufficient to store classical information. While there is no lower bound on the required energy or space to store information, we find that there is a nonzero lower bound for the product P = of these two resources. Specifically, we prove that any physical system of mass m and d degrees of freedom that stores S bits of information will have a lower bound on the product P that is proportional to d2/m(exp(S/d) - 1)2. This result is obtained in a nonrelativistic, quantum mechanical setting, and it is independent of earlier thermodynamical results such as the Bekenstein bound on the entropy of black holes.

  14. The surface magnetization study of Cr2O3 by spin polarized low energy electron microscopy

    Science.gov (United States)

    Cao, Shi; Wu, Ning; Zhang, Xin; N'diaye, Alpha; Chen, Gong; Schmid, Andreas; Echtenkamp, Will; Lauter, Valeria; Binek, Christian; Dowben, Peter

    2014-03-01

    The boundary magnetization at the surface of a Cr2O3 single crystal has been demonstrated by using spin-polarized low-energy electron microscopy (SPLEEM), indicating net surface spin polarization. This work shows that the placement of Cr2O3 single crystal in the single domain state, will result in net Cr2O3 spin polarization at the boundary, even in the presence of a gold overlayer. There are indications that the spin-polarized low-energy electron microscopy (SPLEEM) contrast for the two polarizations states is different. In addition, the boundary magnetization protected by the symmetry exists despite of the surface roughness/softness which was studied by the non-spin neutron reflectometry and low energy electron diffraction. Unoccupied surface oxygen sites and chromium sites are possible mechanism contributing to the surface ``softness,'' which will be discussed.

  15. Study on Surface Energy Characteristics of Poplar and Yellow Pine Strands

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yang; WANG Siqun

    2006-01-01

    The objective of this study was to investigate the surface free energy of poplar and yellow pine strands by Wilhelmy Plate Method.The measurement items included the surface contact angle,surface free energy and change of sample weight.Thirty industrial strands were randomly collected for each condition.The samples were cut down to 25.0-26.0 mm long.7.0-8.0 mm wide.The density and thickness of each sample were also tested.The range of density was from 0.35 to 0.75 g/cm3 and the range of thickness was from 0.5 to 1.0 mm.The research result shows that there is a close relationship between the wettability,mass change and moisture content.Both the density and the thickness of the strand have a small influence on the surface contact angle and the surface free energy.

  16. Intercomparison and interpretation of surface energy fluxes in atmospheric general circulation models

    Science.gov (United States)

    Randall, D. A.; Cess, R. D.; Blanchet, J. P.; Boer, G. J.; Dazlich, D. A.; Del Genio, A. D.; Deque, M.; Dymnikov, V.; Galin, V.; Ghan, S. J.

    1992-01-01

    Responses of the surface energy budgets and hydrologic cycles of 19 atmospheric general circulation models to an imposed, globally uniform sea surface temperature perturbation of 4 K were analyzed. The responses of the simulated surface energy budgets are extremely diverse and are closely linked to the responses of the simulated hydrologic cycles. The response of the net surface energy flux is not controlled by cloud effects; instead, it is determined primarily by the response of the latent heat flux. The prescribed warming of the oceans leads to major increases in the atmospheric water vapor content and the rates of evaporation and precipitation. The increased water vapor amount drastically increases the downwelling IR radiation at the earth's surface, but the amount of the change varies dramatically from one model to another.

  17. A general scheme for the estimation of oxygen binding energies on binary transition metal surface alloys

    DEFF Research Database (Denmark)

    Greeley, Jeffrey Philip; Nørskov, Jens Kehlet

    2005-01-01

    A simple scheme for the estimation of oxygen binding energies on transition metal surface alloys is presented. It is shown that a d-band center model of the alloy surfaces is a convenient and appropriate basis for this scheme; variations in chemical composition, strain effects, and ligand effects...... for the estimation of oxygen binding energies on a wide variety of transition metal alloys. (c) 2005 Elsevier B.V. All rights reserved....

  18. Surface dispersive energy determined with IGC-ID in anti-graffiti-coated building materials

    OpenAIRE

    Carmona-Quiroga, Paula María; Rubio, J; Sánchez, M. J.; Martínez-Ramírez, Sagrario.; Blanco-Varela, María Teresa

    2011-01-01

    Coating building materials with anti-graffiti treatments hinders or prevents spray paint adherence by generating low energy surfaces. This paper describes the effect of coating cement paste, lime mortar, granite, limestone and brick with two anti-graffiti agents (a water-base fluoroalkylsiloxane, “Protectosil Antigraffiti®”, and a Zr ormosil) on the dispersive component of the surface energy of these five construction materials. The agents were rediluted in their respective solvents at concen...

  19. Adhesion Evaluation of Asphalt-Aggregate Interface Using Surface Free Energy Method

    OpenAIRE

    Jie Ji; Hui Yao; Luhou Liu; Zhi Suo; Peng Zhai; Xu Yang; Zhanping You

    2017-01-01

    The influence of organic additives (Sasobit and RH) and water on the adhesion of the asphalt-aggregate interface was studied according to the surface free energy theory. Two asphalt binders (SK-70 and SK-90), and two aggregate types (limestone and basalt) were used in this study. The sessile drop