The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.

PubMed

Drawert, Brian; Lawson, Michael J; Petzold, Linda; Khammash, Mustafa

2010-02-21

We have developed a computational framework for accurate and efficient simulation of stochastic spatially inhomogeneous biochemical systems. The new computational method employs a fractional step hybrid strategy. A novel formulation of the finite state projection (FSP) method, called the diffusive FSP method, is introduced for the efficient and accurate simulation of diffusive transport. Reactions are handled by the stochastic simulation algorithm.

State-to-state reactive scattering in six dimensions using reactant-product decoupling: OH + H2 → H2O + H (J = 0).

PubMed

Cvitaš, Marko T; Althorpe, Stuart C

2011-01-14

We extend to full dimensionality a recently developed wave packet method [M. T. Cvitaš and S. C. Althorpe, J. Phys. Chem. A 113, 4557 (2009)] for computing the state-to-state quantum dynamics of AB + CD → ABC + D reactions and also increase the computational efficiency of the method. This is done by introducing a new set of product coordinates, by applying the Crank-Nicholson approximation to the angular kinetic energy part of the split-operator propagator and by using a symmetry-adapted basis-to-grid transformation to evaluate integrals over the potential energy surface. The newly extended method is tested on the benchmark OH + H(2) → H(2)O + H reaction, where it allows us to obtain accurately converged state-to-state reaction probabilities (on the Wu-Schatz-Fang-Lendvay-Harding potential energy surface) with modest computational effort. These methodological advances will make possible efficient calculations of state-to-state differential cross sections on this system in the near future.

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks.

PubMed

Salis, Howard; Kaznessis, Yiannis N

2005-12-01

Stochastic chemical kinetics more accurately describes the dynamics of "small" chemical systems, such as biological cells. Many real systems contain dynamical stiffness, which causes the exact stochastic simulation algorithm or other kinetic Monte Carlo methods to spend the majority of their time executing frequently occurring reaction events. Previous methods have successfully applied a type of probabilistic steady-state approximation by deriving an evolution equation, such as the chemical master equation, for the relaxed fast dynamics and using the solution of that equation to determine the slow dynamics. However, because the solution of the chemical master equation is limited to small, carefully selected, or linear reaction networks, an alternate equation-free method would be highly useful. We present a probabilistic steady-state approximation that separates the time scales of an arbitrary reaction network, detects the convergence of a marginal distribution to a quasi-steady-state, directly samples the underlying distribution, and uses those samples to accurately predict the state of the system, including the effects of the slow dynamics, at future times. The numerical method produces an accurate solution of both the fast and slow reaction dynamics while, for stiff systems, reducing the computational time by orders of magnitude. The developed theory makes no approximations on the shape or form of the underlying steady-state distribution and only assumes that it is ergodic. We demonstrate the accuracy and efficiency of the method using multiple interesting examples, including a highly nonlinear protein-protein interaction network. The developed theory may be applied to any type of kinetic Monte Carlo simulation to more efficiently simulate dynamically stiff systems, including existing exact, approximate, or hybrid stochastic simulation techniques.

Dynamics Sampling in Transition Pathway Space.

PubMed

Zhou, Hongyu; Tao, Peng

2018-01-09

The minimum energy pathway contains important information describing the transition between two states on a potential energy surface (PES). Chain-of-states methods were developed to efficiently calculate minimum energy pathways connecting two stable states. In the chain-of-states framework, a series of structures are generated and optimized to represent the minimum energy pathway connecting two states. However, multiple pathways may exist connecting two existing states and should be identified to obtain a full view of the transitions. Therefore, we developed an enhanced sampling method, named as the direct pathway dynamics sampling (DPDS) method, to facilitate exploration of a PES for multiple pathways connecting two stable states as well as addition minima and their associated transition pathways. In the DPDS method, molecular dynamics simulations are carried out on the targeting PES within a chain-of-states framework to directly sample the transition pathway space. The simulations of DPDS could be regulated by two parameters controlling distance among states along the pathway and smoothness of the pathway. One advantage of the chain-of-states framework is that no specific reaction coordinates are necessary to generate the reaction pathway, because such information is implicitly represented by the structures along the pathway. The chain-of-states setup in a DPDS method greatly enhances the sufficient sampling in high-energy space between two end states, such as transition states. By removing the constraint on the end states of the pathway, DPDS will also sample pathways connecting minima on a PES in addition to the end points of the starting pathway. This feature makes DPDS an ideal method to directly explore transition pathway space. Three examples demonstrate the efficiency of DPDS methods in sampling the high-energy area important for reactions on the PES.

Shape and structure of N=Z 64Ge: electromagnetic transition rates from the application of the recoil distance method to a knockout reaction.

PubMed

Starosta, K; Dewald, A; Dunomes, A; Adrich, P; Amthor, A M; Baumann, T; Bazin, D; Bowen, M; Brown, B A; Chester, A; Gade, A; Galaviz, D; Glasmacher, T; Ginter, T; Hausmann, M; Horoi, M; Jolie, J; Melon, B; Miller, D; Moeller, V; Norris, R P; Pissulla, T; Portillo, M; Rother, W; Shimbara, Y; Stolz, A; Vaman, C; Voss, P; Weisshaar, D; Zelevinsky, V

2007-07-27

Transition rate measurements are reported for the 2(1)+ and 2(2)+ states in N=Z 64Ge. The experimental results are in excellent agreement with large-scale shell-model calculations applying the recently developed GXPF1A interactions. The measurement was done using the recoil distance method (RDM) and a unique combination of state-of-the-art instruments at the National Superconducting Cyclotron Laboratory (NSCL). States of interest were populated via an intermediate-energy single-neutron knockout reaction. RDM studies of knockout and fragmentation reaction products hold the promise of reaching far from stability and providing lifetime information for excited states in a wide range of nuclei.

Shape and Structure of N=Z Ge64: Electromagnetic Transition Rates from the Application of the Recoil Distance Method to a Knockout Reaction

NASA Astrophysics Data System (ADS)

Starosta, K.; Dewald, A.; Dunomes, A.; Adrich, P.; Amthor, A. M.; Baumann, T.; Bazin, D.; Bowen, M.; Brown, B. A.; Chester, A.; Gade, A.; Galaviz, D.; Glasmacher, T.; Ginter, T.; Hausmann, M.; Horoi, M.; Jolie, J.; Melon, B.; Miller, D.; Moeller, V.; Norris, R. P.; Pissulla, T.; Portillo, M.; Rother, W.; Shimbara, Y.; Stolz, A.; Vaman, C.; Voss, P.; Weisshaar, D.; Zelevinsky, V.

2007-07-01

Transition rate measurements are reported for the 21+ and 22+ states in N=Z Ge64. The experimental results are in excellent agreement with large-scale shell-model calculations applying the recently developed GXPF1A interactions. The measurement was done using the recoil distance method (RDM) and a unique combination of state-of-the-art instruments at the National Superconducting Cyclotron Laboratory (NSCL). States of interest were populated via an intermediate-energy single-neutron knockout reaction. RDM studies of knockout and fragmentation reaction products hold the promise of reaching far from stability and providing lifetime information for excited states in a wide range of nuclei.

Improving Upon String Methods for Transition State Discovery.

PubMed

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.

Radiative capture reactions via indirect methods

NASA Astrophysics Data System (ADS)

Mukhamedzhanov, A. M.; Rogachev, G. V.

2017-10-01

Many radiative capture reactions of astrophysical interest occur at such low energies that their direct measurement is hardly possible. Until now the only indirect method, which was used to determine the astrophysical factor of the astrophysical radiative capture process, was the Coulomb dissociation. In this paper we address another indirect method, which can provide information about resonant radiative capture reactions at astrophysically relevant energies. This method can be considered an extension of the Trojan horse method for resonant radiative capture reactions. The idea of the suggested indirect method is to use the indirect reaction A (a ,s γ )F to obtain information about the radiative capture reaction A (x ,γ )F , where a =(s x ) and F =(x A ) . The main advantage of using the indirect reactions is the absence of the penetrability factor in the channel x +A , which suppresses the low-energy cross sections of the A (x ,γ )F reactions and does not allow one to measure these reactions at astrophysical energies. A general formalism to treat indirect resonant radiative capture reactions is developed when only a few intermediate states contribute and a statistical approach cannot be applied. The indirect method requires coincidence measurements of the triple differential cross section, which is a function of the photon scattering angle, energy, and the scattering angle of the outgoing spectator particle s . Angular dependence of the triple differential cross section at fixed scattering angle of the spectator s is the angular γ -s correlation function. Using indirect resonant radiative capture reactions, one can obtain information about important astrophysical resonant radiative capture reactions such as (p ,γ ) , (α ,γ ) , and (n ,γ ) on stable and unstable isotopes. The indirect technique makes accessible low-lying resonances, which are close to the threshold, and even subthreshold bound states located at negative energies. In this paper, after developing the general formalism, we demonstrate the application of the indirect reaction 12C(6Li,d γ )16O proceeding through 1- and 2+ subthreshold bound states and resonances to obtain the information about the 12C(α ,γ )16O radiative capture at the astrophysically most effective energy 0.3 MeV, which is impossible using standard direct measurements. Feasibility of the suggested approach is discussed.

Photochemical transformations of diazocarbonyl compounds: expected and novel reactions

NASA Astrophysics Data System (ADS)

Galkina, O. S.; Rodina, L. L.

2016-05-01

Photochemical reactions of diazocarbonyl compounds are well positioned in synthetic practice as an efficient method for ring contraction and homologation of carboxylic acids and as a carbene generation method. However, interpretation of the observed transformations of diazo compounds in electronically excited states is incomplete and requires a careful study of the fine mechanisms of these processes specific to different excited states of diazo compounds resorting to modern methods of investigation, including laser technology. The review is devoted to analysis of new data in the chemistry of excited states of diazocarbonyl compounds. The bibliography includes 155 references.

Automated Transition State Theory Calculations for High-Throughput Kinetics.

PubMed

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

2017-09-21

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.

Diels–Alder Reactions of Allene with Benzene and Butadiene: Concerted, Stepwise, and Ambimodal Transition States

PubMed Central

2015-01-01

Multiconfigurational complete active space methods (CASSCF and CASPT2) have been used to investigate the (4 + 2) cycloadditions of allene with butadiene and with benzene. Both concerted and stepwise radical pathways were examined to determine the mechanism of the Diels–Alder reactions with an allene dienophile. Reaction with butadiene occurs via a single ambimodal transition state that can lead to either the concerted or stepwise trajectories along the potential energy surface, while reaction with benzene involves two separate transition states and favors the concerted mechanism relative to the stepwise mechanism via a diradical intermediate. PMID:25216056

Displacement method and apparatus for reducing passivated metal powders and metal oxides

DOEpatents

Morrell,; Jonathan S. , Ripley; Edward, B [Knoxville, TN

2009-05-05

A method of reducing target metal oxides and passivated metals to their metallic state. A reduction reaction is used, often combined with a flux agent to enhance separation of the reaction products. Thermal energy in the form of conventional furnace, infrared, or microwave heating may be applied in combination with the reduction reaction.

Solid state synthesis of poly(dichlorophosphazene)

DOEpatents

Allen, Christopher W.; Hneihen, Azzam S.; Peterson, Eric S.

2001-01-01

A method for making poly(dichlorophosphazene) using solid state reactants is disclosed and described. The present invention improves upon previous methods by removing the need for chlorinated hydrocarbon solvents, eliminating complicated equipment and simplifying the overall process by providing a "single pot" two step reaction sequence. This may be accomplished by the condensation reaction of raw materials in the melt phase of the reactants and in the absence of an environmentally damaging solvent.

A Study of Interactions between Mixing and Chemical Reaction Using the Rate-Controlled Constrained-Equilibrium Method

NASA Astrophysics Data System (ADS)

Hadi, Fatemeh; Janbozorgi, Mohammad; Sheikhi, M. Reza H.; Metghalchi, Hameed

2016-10-01

The rate-controlled constrained-equilibrium (RCCE) method is employed to study the interactions between mixing and chemical reaction. Considering that mixing can influence the RCCE state, the key objective is to assess the accuracy and numerical performance of the method in simulations involving both reaction and mixing. The RCCE formulation includes rate equations for constraint potentials, density and temperature, which allows taking account of mixing alongside chemical reaction without splitting. The RCCE is a dimension reduction method for chemical kinetics based on thermodynamics laws. It describes the time evolution of reacting systems using a series of constrained-equilibrium states determined by RCCE constraints. The full chemical composition at each state is obtained by maximizing the entropy subject to the instantaneous values of the constraints. The RCCE is applied to a spatially homogeneous constant pressure partially stirred reactor (PaSR) involving methane combustion in oxygen. Simulations are carried out over a wide range of initial temperatures and equivalence ratios. The chemical kinetics, comprised of 29 species and 133 reaction steps, is represented by 12 RCCE constraints. The RCCE predictions are compared with those obtained by direct integration of the same kinetics, termed detailed kinetics model (DKM). The RCCE shows accurate prediction of combustion in PaSR with different mixing intensities. The method also demonstrates reduced numerical stiffness and overall computational cost compared to DKM.

Investigation of the triple-α reaction in a full three-body approach

DOE PAGES

Nguyen, N. B.; Nunes, F. M.; Thompson, I. J.

2013-05-22

Here, the triple-alpha reaction is the key to our understanding about the nucleosynthesis and the observed abundance of 12C in stars. The theory of this process is well established at high temperatures but rather ambiguous in the low temperature regime where measurements are impossible. Develop a new three-body method, which tackles properly the scattering boundary condition for three charged particles and takes into account both the resonant and the non-resonant reaction mechanisms on the same footing, to compute the triple-alpha reaction rate at low temperatures. Methods: We combine the R-matrix expansion, the R-matrix propagation method, and the screening technique inmore » the hyperspherical harmonics basis. Both the 2 + 1 bound state and the 0 + 2 resonant state in 12C are well reproduced. We also study the cluster structure of these states. We calculate the triple-alpha reaction rate for T = 0.01 - 0.1 GK. In conclusion, we obtain the same rate as NACRE for temperatures above 0.07 GK, but the new rate is largely enhanced at lower temperatures (≈ 10 12 at 0.02 GK). The differences are caused by the direct capture contribution to the reaction when three alpha particles can not reach the resonant energies.« less

Growing large columnar grains of CH3NH3PbI3 using the solid-state reaction method enhanced by less-crystallized nanoporous PbI2 films

NASA Astrophysics Data System (ADS)

Zheng, Huifeng; Wang, Weiqi; Liu, Yangqiao; Sun, Jing

2017-03-01

Compact, pinhole-free and PbI2-free perovskite films, are desirable for high-performance perovskite solar cells (PSCs), especially if large columnar grains are obtained in which the adverse effects of grain boundaries will be minimized. However, the conventional solid-state reaction methods, originated from the two-step method, failed to grow columnar grains of CH3NH3PbI3 in a facile way. Here, we demonstrate a strategy for growing large columnar grains of CH3NH3PbI3, by less-crystallized nanoporous PbI2 (ln-PbI2) film enhanced solid-state reaction method. We demonstrated columnar grains were obtainable only when ln-PbI2 films were applied. Therefore, the replacement of compact PbI2 by ln-PbI2 in the solid-sate reaction, leads to higher power conversion efficiency, better reproducibility, better stability and less hysteresis. Furthermore, by systematically investigating the effects of annealing temperature and duration, we found that an annealing temperature ≥120 °C was also critical for growing columnar grains. With the optimal process, a champion efficiency of 16.4% was obtained and the average efficiency reached 14.2%. Finally, the mechanism of growing columnar grains was investigated, in which a VPb″ -assisted hooping model was proposed. This work reveals the origins of grain growth in the solid-state reaction method, which will contribute to preparing high quality perovskite films with much larger columnar grains.

Hydrogen generation systems utilizing sodium silicide and sodium silica gel materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wallace, Andrew P.; Melack, John M.; Lefenfeld, Michael

Systems, devices, and methods combine reactant materials and aqueous solutions to generate hydrogen. The reactant materials can sodium silicide or sodium silica gel. The hydrogen generation devices are used in fuels cells and other industrial applications. One system combines cooling, pumping, water storage, and other devices to sense and control reactions between reactant materials and aqueous solutions to generate hydrogen. Multiple inlets of varied placement geometries deliver aqueous solution to the reaction. The reactant materials and aqueous solution are churned to control the state of the reaction. The aqueous solution can be recycled and returned to the reaction. One systemmore » operates over a range of temperatures and pressures and includes a hydrogen separator, a heat removal mechanism, and state of reaction control devices. The systems, devices, and methods of generating hydrogen provide thermally stable solids, near-instant reaction with the aqueous solutions, and a non-toxic liquid by-product.« less

Hydrogen generation systems utilizing sodium silicide and sodium silica gel materials

DOEpatents

Wallace, Andrew P.; Melack, John M.; Lefenfeld, Michael

2015-07-14

Systems, devices, and methods combine reactant materials and aqueous solutions to generate hydrogen. The reactant materials can sodium silicide or sodium silica gel. The hydrogen generation devices are used in fuels cells and other industrial applications. One system combines cooling, pumping, water storage, and other devices to sense and control reactions between reactant materials and aqueous solutions to generate hydrogen. Multiple inlets of varied placement geometries deliver aqueous solution to the reaction. The reactant materials and aqueous solution are churned to control the state of the reaction. The aqueous solution can be recycled and returned to the reaction. One system operates over a range of temperatures and pressures and includes a hydrogen separator, a heat removal mechanism, and state of reaction control devices. The systems, devices, and methods of generating hydrogen provide thermally stable solids, near-instant reaction with the aqueous solutions, and a non-toxic liquid by-product.

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

PubMed

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.

Uncovering the Geometry of Barrierless Reactions Using Lagrangian Descriptors.

PubMed

Junginger, Andrej; Hernandez, Rigoberto

2016-03-03

Transition-state theories describing barrierless chemical reactions, or more general activated problems, are often hampered by the lack of a saddle around which the dividing surface can be constructed. For example, the time-dependent transition-state trajectory uncovering the nonrecrossing dividing surface in thermal reactions in the framework of the Langevin equation has relied on perturbative approaches in the vicinity of the saddle. We recently obtained an alternative approach using Lagrangian descriptors to construct time-dependent and recrossing-free dividing surfaces. This is a nonperturbative approach making no reference to a putative saddle. Here we show how the Lagrangian descriptor can be used to obtain the transition-state geometry of a dissipated and thermalized reaction across barrierless potentials. We illustrate the method in the case of a 1D Brownian motion for both barrierless and step potentials; however, the method is not restricted and can be directly applied to different kinds of potentials and higher dimensional systems.

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

PubMed Central

Gunner, MR; Baker, Nathan A.

2017-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding their underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. PMID:27497160

Reaction Event Counting Statistics of Biopolymer Reaction Systems with Dynamic Heterogeneity.

PubMed

Lim, Yu Rim; Park, Seong Jun; Park, Bo Jung; Cao, Jianshu; Silbey, Robert J; Sung, Jaeyoung

2012-04-10

We investigate the reaction event counting statistics (RECS) of an elementary biopolymer reaction in which the rate coefficient is dependent on states of the biopolymer and the surrounding environment and discover a universal kinetic phase transition in the RECS of the reaction system with dynamic heterogeneity. From an exact analysis for a general model of elementary biopolymer reactions, we find that the variance in the number of reaction events is dependent on the square of the mean number of the reaction events when the size of measurement time is small on the relaxation time scale of rate coefficient fluctuations, which does not conform to renewal statistics. On the other hand, when the size of the measurement time interval is much greater than the relaxation time of rate coefficient fluctuations, the variance becomes linearly proportional to the mean reaction number in accordance with renewal statistics. Gillespie's stochastic simulation method is generalized for the reaction system with a rate coefficient fluctuation. The simulation results confirm the correctness of the analytic results for the time dependent mean and variance of the reaction event number distribution. On the basis of the obtained results, we propose a method of quantitative analysis for the reaction event counting statistics of reaction systems with rate coefficient fluctuations, which enables one to extract information about the magnitude and the relaxation times of the fluctuating reaction rate coefficient, without a bias that can be introduced by assuming a particular kinetic model of conformational dynamics and the conformation dependent reactivity. An exact relationship is established between a higher moment of the reaction event number distribution and the multitime correlation of the reaction rate for the reaction system with a nonequilibrium initial state distribution as well as for the system with the equilibrium initial state distribution.

Analysis of Classes of Singular Steady State Reaction Diffusion Equations

NASA Astrophysics Data System (ADS)

Son, Byungjae

We study positive radial solutions to classes of steady state reaction diffusion problems on the exterior of a ball with both Dirichlet and nonlinear boundary conditions. We study both Laplacian as well as p-Laplacian problems with reaction terms that are p-sublinear at infinity. We consider both positone and semipositone reaction terms and establish existence, multiplicity and uniqueness results. Our existence and multiplicity results are achieved by a method of sub-supersolutions and uniqueness results via a combination of maximum principles, comparison principles, energy arguments and a-priori estimates. Our results significantly enhance the literature on p-sublinear positone and semipositone problems. Finally, we provide exact bifurcation curves for several one-dimensional problems. In the autonomous case, we extend and analyze a quadrature method, and in the nonautonomous case, we employ shooting methods. We use numerical solvers in Mathematica to generate the bifurcation curves.

Quantum dynamics study of H+NH3-->H2+NH2 reaction.

PubMed

Zhang, Xu Qiang; Cui, Qian; Zhang, John Z H; Han, Ke Li

2007-06-21

We report in this paper a quantum dynamics study for the reaction H+NH3-->NH2+H2 on the potential energy surface of Corchado and Espinosa-Garcia [J. Chem. Phys. 106, 4013 (1997)]. The quantum dynamics calculation employs the semirigid vibrating rotor target model [J. Z. H. Zhang, J. Chem. Phys. 111, 3929 (1999)] and time-dependent wave packet method to propagate the wave function. Initial state-specific reaction probabilities are obtained, and an energy correction scheme is employed to account for zero point energy changes for the neglected degrees of freedom in the dynamics treatment. Tunneling effect is observed in the energy dependency of reaction probability, similar to those found in H+CH4 reaction. The influence of rovibrational excitation on reaction probability and stereodynamical effect are investigated. Reaction rate constants from the initial ground state are calculated and are compared to those from the transition state theory and experimental measurement.

Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions.

PubMed

Landsgesell, Jonas; Holm, Christian; Smiatek, Jens

2017-02-14

We present a novel method for the study of weak polyelectrolytes and general acid-base reactions in molecular dynamics and Monte Carlo simulations. The approach combines the advantages of the reaction ensemble and the Wang-Landau sampling method. Deprotonation and protonation reactions are simulated explicitly with the help of the reaction ensemble method, while the accurate sampling of the corresponding phase space is achieved by the Wang-Landau approach. The combination of both techniques provides a sufficient statistical accuracy such that meaningful estimates for the density of states and the partition sum can be obtained. With regard to these estimates, several thermodynamic observables like the heat capacity or reaction free energies can be calculated. We demonstrate that the computation times for the calculation of titration curves with a high statistical accuracy can be significantly decreased when compared to the original reaction ensemble method. The applicability of our approach is validated by the study of weak polyelectrolytes and their thermodynamic properties.

A numerical fragment basis approach to SCF calculations.

NASA Astrophysics Data System (ADS)

Hinde, Robert J.

1997-11-01

The counterpoise method is often used to correct for basis set superposition error in calculations of the electronic structure of bimolecular systems. One drawback of this approach is the need to specify a ``reference state'' for the system; for reactive systems, the choice of an unambiguous reference state may be difficult. An example is the reaction F^- + HCl arrow HF + Cl^-. Two obvious reference states for this reaction are F^- + HCl and HF + Cl^-; however, different counterpoise-corrected interaction energies are obtained using these two reference states. We outline a method for performing SCF calculations which employs numerical basis functions; this method attempts to eliminate basis set superposition errors in an a priori fashion. We test the proposed method on two one-dimensional, three-center systems and discuss the possibility of extending our approach to include electron correlation effects.

Kinetics of First-Row Transition Metal Cations (V+, Fe+, Co+) with OCS at Thermal Energies.

PubMed

Sweeny, Brendan C; Ard, Shaun G; Shuman, Nicholas S; Viggiano, Albert A

2018-05-03

The temperature-dependent kinetics for reactions of V + , Fe + , and Co + with OCS are measured using a selected ion flow tube apparatus heated to 300-600 K. All three reactions proceed solely by C-S activation at thermal energies, resulting in metal sulfide cation formation. Previously calculated reaction pathways were employed to inform statistical modeling of these reactions for comparison to the data. As surmised previously, all three reactions at thermal energies require spin crossing, with the Fe + reaction crossing once circumventing a prohibitive transition state, before crossing again to form ground state products. The Fe + and Co + reaction efficiencies increase with energy. For the Co + reaction, and to a lesser extent the Fe + reaction, the apparent activation energies are less than the reaction endothermicities, possibly indicating increasing diabatic behavior of the spin crossings with energy. The V + reaction was well modeled assuming an entirely adiabatic spin crossing, such that the resultant avoided crossing behaves similarly to a tight transition state. The subsequent reaction of VS + with OCS producing VS 2 + is also investigated; the rate-limiting transition state energy derived from statistical modeling is poorly reproduced by quantum calculations using a variety of methods, highlighting the large (1-2 eV) uncertainty in calculated energetics of transition-metal containing species.

Shape and structure of N=Z ^64Ge; Electromagnetic transition rates from the application of the Recoil Distance Method to knock-out reactions.

NASA Astrophysics Data System (ADS)

Starosta, K.; Dewald, A.

2007-04-01

Transition rate measurements are reported for the 2^+1 and 2^+2 states in the N=Z nucleus ^64Ge. The measurement was done utilizing the Recoil Distance Method (RDM) and a unique combination of state of the art instruments at the National Superconducting Cyclotron Laboratory (NSCL). States of interest were populated via an intermediate energy single neutron knock-out reaction. RDM studies of knock-out and fragmentation reaction products hold the promise of reaching far from stability and providing lifetime information for intermediate-spin excited states in a wide range of exotic nuclei. The large-scale Shell Model calculations applying the recently developed GXPF1A interaction are in excellent agreement with the above results. Theoretical analysis suggests that ^64Ge is a collective γ-soft anharmonic vibrator.

Transient-state kinetic approach to mechanisms of enzymatic catalysis.

PubMed

Fisher, Harvey F

2005-03-01

Transient-state kinetics by its inherent nature can potentially provide more directly observed detailed resolution of discrete events in the mechanistic time courses of enzyme-catalyzed reactions than its more widely used steady-state counterpart. The use of the transient-state approach, however, has been severely limited by the lack of any theoretically sound and applicable basis of interpreting the virtual cornucopia of time and signal-dependent phenomena that it provides. This Account describes the basic kinetic behavior of the transient state, critically examines some currently used analytic methods, discusses the application of a new and more soundly based "resolved component transient-state time-course method" to the L-glutamate-dehydrogenase reaction, and establishes new approaches for the analysis of both single- and multiple-step substituted transient-state kinetic isotope effects.

Application of one-dimensional semiclassical transition state theory to the CH3OH + H ⇌ CH2OH/CH3O + H2 reactions.

PubMed

Shan, Xiao; Clary, David C

2018-03-13

The rate constants of the two branches of H-abstractions from CH 3 OH by the H-atom and the corresponding reactions in the reverse direction are calculated using the one-dimensional semiclassical transition state theory (1D SCTST). In this method, only the reaction mode vibration of the transition state (TS) is treated anharmonically, while the remaining internal degrees of freedom are treated as they would have been in a standard TS theory calculation. A total of eight ab initio single-point energy calculations are performed in addition to the computational cost of a standard TS theory calculation. This allows a second-order Richardson extrapolation method to be employed to improve the numerical estimation of the third- and fourth-order derivatives, which in turn are used in the calculation of the anharmonic constant. Hindered-rotor (HR) vibrations are identified in the equilibrium states of CH 3 OH and CH 2 OH, and the TSs of the reactions. The partition function of the HRs are calculated using both a simple harmonic oscillator model and a more sophisticated one-dimensional torsional eigenvalue summation (1D TES) method. The 1D TES method can be easily adapted in 1D SCTST computation. The resulting 1D SCTST with 1D TES rate constants show good agreement to previous theoretical and experimental works. The effects of the HR on rate constants for different reactions are also investigated.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Author(s).

Product lambda-doublet ratios as an imprint of chemical reaction mechanism

PubMed Central

Jambrina, P. G.; Zanchet, A.; Aldegunde, J.; Brouard, M.; Aoiz, F. J.

2016-01-01

In the last decade, the development of theoretical methods has allowed chemists to reproduce and explain almost all of the experimental data associated with elementary atom plus diatom collisions. However, there are still a few examples where theory cannot account yet for experimental results. This is the case for the preferential population of one of the Λ-doublet states produced by chemical reactions. In particular, recent measurements of the OD(2Π) product of the O(3P)+D2 reaction have shown a clear preference for the Π(A′) Λ-doublet states, in apparent contradiction with ab initio calculations, which predict a larger reactivity on the A′′ potential energy surface. Here we present a method to calculate the Λ-doublet ratio when concurrent potential energy surfaces participate in the reaction. It accounts for the experimental Λ-doublet populations via explicit consideration of the stereodynamics of the process. Furthermore, our results demonstrate that the propensity of the Π(A′) state is a consequence of the different mechanisms of the reaction on the two concurrent potential energy surfaces PMID:27834381

An eight-dimensional quantum dynamics study of the Cl + CH{sub 4}→ HCl + CH{sub 3} reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Na; Yang, Minghui, E-mail: yangmh@wipm.ac.cn

2015-10-07

In this work, the later-barrier reaction Cl + CH{sub 4} → HCl + CH{sub 3} is investigated with an eight-dimensional quantum dynamics method [R. Liu et al., J. Chem. Phys. 137, 174113 (2012)] on the ab initio potential energy surface of Czakó and Bowman [J. Chem. Phys. 136, 044307 (2012)]. The reaction probabilities with CH{sub 4} initially in its ground and vibrationally excited states are calculated with a time-dependent wavepacket method. The theoretical integral cross sections (ICSs) are extensively compared with the available experimental measurements. For the ground state reaction, the theoretical ICSs excellently agree with the experimental ones. Themore » good agreements are also achieved for ratios between ICSs of excited reactions. For ICS ratios between various states, the theoretical values are also consistent with the experimental observations. The rate constants over 200-2000 K are calculated and the non-Arrhenius effect has been observed which is coincident with the previous experimental observations and theoretical calculations.« less

Calculation of astrophysical S-factor in reaction ^{13}C(p,γ )^{14}N for first resonance levels

NASA Astrophysics Data System (ADS)

Moghadasi, A.; Sadeghi, H.; Pourimani, R.

2018-01-01

The ^{13}C(p,γ )^{14}N reaction is one of the important reactions in the CNO cycle, which is a key process in nucleosynthesis. We first calculated wave functions for the bound state of ^{14}N with Faddeev's method. In this method, the considered reaction components are ^{12}C+n+p. Then, by using direct capture cross section and Breit-Wigner formulae, the non-resonant and resonant cross sections were calculated, respectively. In the next step, we calculated the total S-factor and compared it with experimental data, which showed good agreement between them. Next, we extrapolated the S-factor for the transition to the ground state at zero energy and obtained S(0)=5.8 ± 0.7 (keV b) and then calculate reaction rate. These ones are in agreement with previous reported results.

Mean field treatment of heterogeneous steady state kinetics

NASA Astrophysics Data System (ADS)

Geva, Nadav; Vaissier, Valerie; Shepherd, James; Van Voorhis, Troy

2017-10-01

We propose a method to quickly compute steady state populations of species undergoing a set of chemical reactions whose rate constants are heterogeneous. Using an average environment in place of an explicit nearest neighbor configuration, we obtain a set of equations describing a single fluctuating active site in the presence of an averaged bath. We apply this Mean Field Steady State (MFSS) method to a model of H2 production on a disordered surface for which the activation energy for the reaction varies from site to site. The MFSS populations quantitatively reproduce the KMC results across the range of rate parameters considered.

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.

PubMed

Gunner, M R; Baker, N A

2016-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding the underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. © 2016 Elsevier Inc. All rights reserved.

Stochastic simulation of enzyme-catalyzed reactions with disparate timescales.

PubMed

Barik, Debashis; Paul, Mark R; Baumann, William T; Cao, Yang; Tyson, John J

2008-10-01

Many physiological characteristics of living cells are regulated by protein interaction networks. Because the total numbers of these protein species can be small, molecular noise can have significant effects on the dynamical properties of a regulatory network. Computing these stochastic effects is made difficult by the large timescale separations typical of protein interactions (e.g., complex formation may occur in fractions of a second, whereas catalytic conversions may take minutes). Exact stochastic simulation may be very inefficient under these circumstances, and methods for speeding up the simulation without sacrificing accuracy have been widely studied. We show that the "total quasi-steady-state approximation" for enzyme-catalyzed reactions provides a useful framework for efficient and accurate stochastic simulations. The method is applied to three examples: a simple enzyme-catalyzed reaction where enzyme and substrate have comparable abundances, a Goldbeter-Koshland switch, where a kinase and phosphatase regulate the phosphorylation state of a common substrate, and coupled Goldbeter-Koshland switches that exhibit bistability. Simulations based on the total quasi-steady-state approximation accurately capture the steady-state probability distributions of all components of these reaction networks. In many respects, the approximation also faithfully reproduces time-dependent aspects of the fluctuations. The method is accurate even under conditions of poor timescale separation.

How Accurate Are Transition States from Simulations of Enzymatic Reactions?

PubMed Central

2015-01-01

The rate expression of traditional transition state theory (TST) assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium between the ground state and the TS. Currently, it is not well understood to what extent these assumptions influence the nature of the activated complex obtained in traditional TST-based simulations of processes in the condensed phase in general and in enzymes in particular. Here we scrutinize these assumptions by characterizing the TSs for hydride transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches. Specifically, we compare the TSs obtained with common TST-based methods and a dynamics-based method. Using a recently developed accurate hybrid quantum mechanics/molecular mechanics potential, we find that the TST-based and dynamics-based methods give considerably different TS ensembles. This discrepancy, which could be due equilibrium solvation effects and the nature of the reaction coordinate employed and its motion, raises major questions about how to interpret the TSs determined by common simulation methods. We conclude that further investigation is needed to characterize the impact of various TST assumptions on the TS phase-space ensemble and on the reaction kinetics. PMID:24860275

Method of Continuous Variations: Applications of Job Plots to the Study of Molecular Associations in Organometallic Chemistry[**

PubMed Central

Renny, Joseph S.; Tomasevich, Laura L.; Tallmadge, Evan H.; Collum, David B.

2014-01-01

Applications of the method of continuous variations—MCV or the Method of Job—to problems of interest to organometallic chemists are described. MCV provides qualitative and quantitative insights into the stoichiometries underlying association of m molecules of A and n molecules of B to form AmBn. Applications to complex ensembles probe associations that form metal clusters and aggregates. Job plots in which reaction rates are monitored provide relative stoichiometries in rate-limiting transition structures. In a specialized variant, ligand- or solvent-dependent reaction rates are dissected into contributions in both the ground states and transition states, which affords insights into the full reaction coordinate from a single Job plot. Gaps in the literature are identified and critiqued. PMID:24166797

Reduced-Dimensionality Semiclassical Transition State Theory: Application to Hydrogen Atom Abstraction and Exchange Reactions of Hydrocarbons.

PubMed

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

2015-12-17

Quantum mechanical methods for calculating rate constants are often intractable for reactions involving many atoms. Semiclassical transition state theory (SCTST) offers computational advantages over these methods but nonetheless scales exponentially with the number of degrees of freedom (DOFs) of the system. Here we present a method with more favorable scaling, reduced-dimensionality SCTST (RD SCTST), that treats only a subset of DOFs of the system explicitly. We apply it to three H abstraction and exchange reactions for which two-dimensional potential energy surfaces (PESs) have previously been constructed and evaluated using RD quantum scattering calculations. We differentiated these PESs to calculate harmonic frequencies and anharmonic constants, which were then used to calculate cumulative reaction probabilities and rate constants by RD SCTST. This method yielded rate constants in good agreement with quantum scattering results. Notably, it performed well for a heavy-light-heavy reaction, even though it does not explicitly account for corner-cutting effects. Recent extensions to SCTST that improve its treatment of deep tunneling were also evaluated within the reduced-dimensionality framework. The success of RD SCTST in this study suggests its potential applicability to larger systems.

Gas-Phase Reaction Pathways and Rate Coefficients for the Dichlorosilane-Hydrogen and Trichlorosilane-Hydrogen Systems

NASA Technical Reports Server (NTRS)

Dateo, Christopher E.; Walch, Stephen P.

2002-01-01

As part of NASA Ames Research Center's Integrated Process Team on Device/Process Modeling and Nanotechnology our goal is to create/contribute to a gas-phase chemical database for use in modeling microelectronics devices. In particular, we use ab initio methods to determine chemical reaction pathways and to evaluate reaction rate coefficients. Our initial studies concern reactions involved in the dichlorosilane-hydrogen (SiCl2H2--H2) and trichlorosilane-hydrogen (SiCl2H-H2) systems. Reactant, saddle point (transition state), and product geometries and their vibrational harmonic frequencies are determined using the complete-active-space self-consistent-field (CASSCF) electronic structure method with the correlation consistent polarized valence double-zeta basis set (cc-pVDZ). Reaction pathways are constructed by following the imaginary frequency mode of the saddle point to both the reactant and product. Accurate energetics are determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations (CCSD(T)) extrapolated to the complete basis set limit. Using the data from the electronic structure calculations, reaction rate coefficients are obtained using conventional and variational transition state and RRKM theories.

State-to-state mode selectivity in the HD + OH reaction: Perspectives from two product channels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Bin; Guo, Hua, E-mail: hguo@unm.edu; Sun, Zhigang

The state-to-state quantum dynamics (J{sub tot} = 0) of the HD + OH(υ{sub 2} = 0, 1) reaction is studied using a reactant coordinate based method, which allows the analysis of both the H + DOH and D + HOH channels with a single propagation. The stretching vibration of the newly formed bond, namely, the OD bond in DOH and one OH bond in HOH, is excited, thanks to its strong coupling with the reaction coordinate at the transition state. On the other hand, the vibrational energy deposited into the OH reactant (υ{sub 2} = 1) is sequestered during themore » reaction in the spectator OH mode. The combined effect leads to the excitation of both the OD and OH stretching modes in the DOH product, and the dominance of the (002) normal-mode state population in the HOH product, which in the local-mode picture corresponds to the excitation of both OH bonds with one quantum each. The energy flow in this prototypical tetratomic reaction can be understood in terms of the sudden vector projection model.« less

Analytical derivatives of the individual state energies in ensemble density functional theory method. I. General formalism

DOE PAGES

Filatov, Michael; Liu, Fang; Martínez, Todd J.

2017-07-21

The state-averaged (SA) spin restricted ensemble referenced Kohn-Sham (REKS) method and its state interaction (SI) extension, SI-SA-REKS, enable one to describe correctly the shape of the ground and excited potential energy surfaces of molecules undergoing bond breaking/bond formation reactions including features such as conical intersections crucial for theoretical modeling of non-adiabatic reactions. Until recently, application of the SA-REKS and SI-SA-REKS methods to modeling the dynamics of such reactions was obstructed due to the lack of the analytical energy derivatives. Here, the analytical derivatives of the individual SA-REKS and SI-SA-REKS energies are derived. The final analytic gradient expressions are formulated entirelymore » in terms of traces of matrix products and are presented in the form convenient for implementation in the traditional quantum chemical codes employing basis set expansions of the molecular orbitals. Finally, we will describe the implementation and benchmarking of the derived formalism in a subsequent article of this series.« less

Proton threshold states in the Na22(p,γ)Mg23 reaction and astrophysical implications

NASA Astrophysics Data System (ADS)

Comisel, H.; Hategan, C.; Graw, G.; Wolter, H. H.

2007-04-01

Proton threshold states in Mg23 are important for the astrophysically relevant proton capture reaction Na22(p,γ)Mg23. In the indirect determination of the resonance strength of the lowest states, which were not accessible by direct methods, some of the spin-parity-assignments remained experimentally uncertain. We have investigated these states with shell model, Coulomb displacement, and Thomas-Ehrman shift calculations. From the comparison of calculated and observed properties, we relate the lowest relevant resonance state at Ex=7643 keV to an excited 3/2+ state in accordance with a recent experimental determination by Jenkins From this we deduce significantly improved values for the Na22(p,γ)Mg23 reaction rate at stellar temperatures below T9=0.1 K.

Concepts, challenges, and successes in modeling thermodynamics of metabolism.

PubMed

Cannon, William R

2014-01-01

The modeling of the chemical reactions involved in metabolism is a daunting task. Ideally, the modeling of metabolism would use kinetic simulations, but these simulations require knowledge of the thousands of rate constants involved in the reactions. The measurement of rate constants is very labor intensive, and hence rate constants for most enzymatic reactions are not available. Consequently, constraint-based flux modeling has been the method of choice because it does not require the use of the rate constants of the law of mass action. However, this convenience also limits the predictive power of constraint-based approaches in that the law of mass action is used only as a constraint, making it difficult to predict metabolite levels or energy requirements of pathways. An alternative to both of these approaches is to model metabolism using simulations of states rather than simulations of reactions, in which the state is defined as the set of all metabolite counts or concentrations. While kinetic simulations model reactions based on the likelihood of the reaction derived from the law of mass action, states are modeled based on likelihood ratios of mass action. Both approaches provide information on the energy requirements of metabolic reactions and pathways. However, modeling states rather than reactions has the advantage that the parameters needed to model states (chemical potentials) are much easier to determine than the parameters needed to model reactions (rate constants). Herein, we discuss recent results, assumptions, and issues in using simulations of state to model metabolism.

Consistent post-reaction vibrational energy redistribution in DSMC simulations using TCE model

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Alexeenko, Alina

2016-10-01

The direct simulation Monte Carlo (DSMC) method has been widely applied to study shockwaves, hypersonic reentry flows, and other nonequilibrium flow phenomena. Although there is currently active research on high-fidelity models based on ab initio data, the total collision energy (TCE) and Larsen-Borgnakke (LB) models remain the most often used chemistry and relaxation models in DSMC simulations, respectively. The conventional implementation of the discrete LB model, however, may not satisfy detailed balance when recombination and exchange reactions play an important role in the flow energy balance. This issue can become even more critical in reacting mixtures involving polyatomic molecules, such as in combustion. In this work, this important shortcoming is addressed and an empirical approach to consistently specify the post-reaction vibrational states close to thermochemical equilibrium conditions is proposed within the TCE framework. Following Bird's quantum-kinetic (QK) methodology for populating post-reaction states, the new TCE-based approach involves two main steps. The state-specific TCE reaction probabilities for a forward reaction are first pre-computed from equilibrium 0-D simulations. These probabilities are then employed to populate the post-reaction vibrational states of the corresponding reverse reaction. The new approach is illustrated by application to exchange and recombination reactions relevant to H2-O2 combustion processes.

A global reaction route mapping-based kinetic Monte Carlo algorithm

NASA Astrophysics Data System (ADS)

Mitchell, Izaac; Irle, Stephan; Page, Alister J.

2016-07-01

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.

A global reaction route mapping-based kinetic Monte Carlo algorithm.

PubMed

Mitchell, Izaac; Irle, Stephan; Page, Alister J

2016-07-14

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.

Reliable Transition State Searches Integrated with the Growing String Method.

PubMed

Zimmerman, Paul

2013-07-09

The growing string method (GSM) is highly useful for locating reaction paths connecting two molecular intermediates. GSM has often been used in a two-step procedure to locate exact transition states (TS), where GSM creates a quality initial structure for a local TS search. This procedure and others like it, however, do not always converge to the desired transition state because the local search is sensitive to the quality of the initial guess. This article describes an integrated technique for simultaneous reaction path and exact transition state search. This is achieved by implementing an eigenvector following optimization algorithm in internal coordinates with Hessian update techniques. After partial convergence of the string, an exact saddle point search begins under the constraint that the maximized eigenmode of the TS node Hessian has significant overlap with the string tangent near the TS. Subsequent optimization maintains connectivity of the string to the TS as well as locks in the TS direction, all but eliminating the possibility that the local search leads to the wrong TS. To verify the robustness of this approach, reaction paths and TSs are found for a benchmark set of more than 100 elementary reactions.

Direct mapping of the angle-dependent barrier to reaction for Cl + CHD3 using polarized scattering data

NASA Astrophysics Data System (ADS)

Pan, Huilin; Wang, Fengyan; Czakó, Gábor; Liu, Kopin

2017-12-01

The transition state, which gates and modulates reactive flux, serves as the central concept in our understanding of activated reactions. The barrier height of the transition state can be estimated from the activation energy taken from thermal kinetics data or from the energetic threshold in the measured excitation function (the dependence of reaction cross-sections on initial collision energies). However, another critical and equally important property, the angle-dependent barrier to reaction, has not yet been amenable to experimental determination until now. Here, using the benchmark reaction of Cl + CHD3(v1 = 1) as an example, we show how to map this anisotropic property of the transition state as a function of collision energy from the preferred reactant bond alignment of the backward-scattered products—the imprints of small impact-parameter collisions. The deduced bend potential at the transition state agrees with ab initio calculations. We expect that the method should be applicable to many other direct reactions with a collinear barrier.

Propensity approach to nonequilibrium thermodynamics of a chemical reaction network: Controlling single E-coli β-galactosidase enzyme catalysis through the elementary reaction stepsa)

NASA Astrophysics Data System (ADS)

Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam

2013-12-01

In this work, we develop an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the elementary reaction propensities. The method is akin to the microscopic formulation of the dissipation function in terms of the Kullback-Leibler distance of phase space trajectories in Hamiltonian system. The formalism is applied to a single oligomeric enzyme kinetics at chemiostatic condition that leads the reaction system to a nonequilibrium steady state, characterized by a positive total entropy production rate. Analytical expressions are derived, relating the individual reaction contributions towards the total entropy production rate with experimentally measurable reaction velocity. Taking a real case of Escherichia coli β-galactosidase enzyme obeying Michaelis-Menten kinetics, we thoroughly analyze the temporal as well as the steady state behavior of various thermodynamic quantities for each elementary reaction. This gives a useful insight in the relative magnitudes of various energy terms and the dissipated heat to sustain a steady state of the reaction system operating far-from-equilibrium. It is also observed that, the reaction is entropy-driven at low substrate concentration and becomes energy-driven as the substrate concentration rises.

Optimal Sampling of a Reaction Coordinate in Molecular Dynamics

NASA Technical Reports Server (NTRS)

Pohorille, Andrew

2005-01-01

Estimating how free energy changes with the state of a system is a central goal in applications of statistical mechanics to problems of chemical or biological interest. From these free energy changes it is possible, for example, to establish which states of the system are stable, what are their probabilities and how the equilibria between these states are influenced by external conditions. Free energies are also of great utility in determining kinetics of transitions between different states. A variety of methods have been developed to compute free energies of condensed phase systems. Here, I will focus on one class of methods - those that allow for calculating free energy changes along one or several generalized coordinates in the system, often called reaction coordinates or order parameters . Considering that in almost all cases of practical interest a significant computational effort is required to determine free energy changes along such coordinates it is hardly surprising that efficiencies of different methods are of great concern. In most cases, the main difficulty is associated with its shape along the reaction coordinate. If the free energy changes markedly along this coordinate Boltzmann sampling of its different values becomes highly non-uniform. This, in turn, may have considerable, detrimental effect on the performance of many methods for calculating free energies.

State-to-State integral cross section for the H+H2O-->H2+OH abstraction reaction.

PubMed

Zhang, Dong H; Xie, Daiqian; Yang, Minghui; Lee, Soo-Y

2002-12-31

The initial state selected time-dependent wave-packet method was extended to calculate the state-to-state integral cross section for the title reaction with H2O in the ground rovibrational state on the potential energy surface of Yang, Zhang, Collins, and Lee. One OH bond length was fixed in the study, which is justifiable for the abstraction reaction, but the remaining 5 degrees of freedom were treated exactly. It was found that the H2 molecule is produced vibrationally cold for collision energy up to 1.6 eV. The OH rotation takes away about 4% of total available energy in the products, while the fraction of energy going to H2 rotation increases with collision energy to about 20% at 1.6 eV.

Prognosis of the state of health of a person under spaceflight conditions

NASA Technical Reports Server (NTRS)

1977-01-01

Methods of predicting the state of health and human efficiency during space flight are discussed. Diversity of reactions to the same conditions, development of extrapolation methods of prediction, and isolation of informative physiological indexes are among the factors considered.

Rapid Solid-State Metathesis Routes to Nanostructured Silicon-Germainum

NASA Technical Reports Server (NTRS)

Rodriguez, Marc (Inventor); Kaner, Richard B. (Inventor); Bux, Sabah K. (Inventor); Fleurial, Jean-Pierre (Inventor)

2014-01-01

Methods for producing nanostructured silicon and silicon-germanium via solid state metathesis (SSM). The method of forming nanostructured silicon comprises the steps of combining a stoichiometric mixture of silicon tetraiodide (SiI4) and an alkaline earth metal silicide into a homogeneous powder, and initating the reaction between the silicon tetraiodide (SiI4) with the alkaline earth metal silicide. The method of forming nanostructured silicon-germanium comprises the steps of combining a stoichiometric mixture of silicon tetraiodide (SiI4) and a germanium based precursor into a homogeneous powder, and initiating the reaction between the silicon tetraiodide (SiI4) with the germanium based precursors.

Comparison of Enterococcus quantitative polymerase chain reaction analysis results from midwest U.S. river samples using EPA Method 1611 and Method 1609 PCR reagents

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) has provided recommended beach advisory values in its 2012 recreational water quality criteria (RWQC) for states wishing to use quantitative polymerase chain reaction (qPCR) for the monitoring of Enterococcus fecal indicator bacteria...

Kinetics of Hydrogen Abstraction and Addition Reactions of 3-Hexene by ȮH Radicals.

PubMed

Yang, Feiyu; Deng, Fuquan; Pan, Youshun; Zhang, Yingjia; Tang, Chenglong; Huang, Zuohua

2017-03-09

Rate coefficients of H atom abstraction and H atom addition reactions of 3-hexene by the hydroxyl radicals were determined using both conventional transition-state theory and canonical variational transition-state theory, with the potential energy surface (PES) evaluated at the CCSD(T)/CBS//BHandHLYP/6-311G(d,p) level and quantum mechanical effect corrected by the compounded methods including one-dimensional Wigner method, multidimensional zero-curvature tunneling method, and small-curvature tunneling method. Results reveal that accounting for approximate 70% of the overall H atom abstractions occur in the allylic site via both direct and indirect channels. The indirect channel containing two van der Waals prereactive complexes exhibits two times larger rate coefficient relative to the direct one. The OH addition reaction also contains two van der Waals complexes, and its submerged barrier results in a negative temperature coefficient behavior at low temperatures. In contrast, The OH addition pathway dominates only at temperatures below 450 K whereas the H atom abstraction reactions dominate overwhelmingly at temperature over 1000 K. All of the rate coefficients calculated with an uncertainty of a factor of 5 were fitted in a quasi-Arrhenius formula. Analyses on the PES, minimum reaction path and activation free Gibbs energy were also performed in this study.

Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

PubMed

Faheem, Muhammad; Heyden, Andreas

2014-08-12

We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

Pre-Steady-State Kinetic Analysis of Single-Nucleotide Incorporation by DNA Polymerases

PubMed Central

Su, Yan; Guengerich, F. Peter

2016-01-01

Pre-steady-state kinetic analysis is a powerful and widely used method to obtain multiple kinetic parameters. This protocol provides a step-by-step procedure for pre-steady-state kinetic analysis of single-nucleotide incorporation by a DNA polymerase. It describes the experimental details of DNA substrate annealing, reaction mixture preparation, handling of the RQF-3 rapid quench-flow instrument, denaturing polyacrylamide DNA gel preparation, electrophoresis, quantitation, and data analysis. The core and unique part of this protocol is the rationale for preparation of the reaction mixture (the ratio of the polymerase to the DNA substrate) and methods for conducting pre-steady-state assays on an RQF-3 rapid quench-flow instrument, as well as data interpretation after analysis. In addition, the methods for the DNA substrate annealing and DNA polyacrylamide gel preparation, electrophoresis, quantitation and analysis are suitable for use in other studies. PMID:27248785

Mechanistic investigations of the hydrolysis of amides, oxoesters and thioesters via kinetic isotope effects and positional isotope exchange.

PubMed

Robins, Lori I; Fogle, Emily J; Marlier, John F

2015-11-01

The hydrolysis of amides, oxoesters and thioesters is an important reaction in both organic chemistry and biochemistry. Kinetic isotope effects (KIEs) are one of the most important physical organic methods for determining the most likely transition state structure and rate-determining step of these reaction mechanisms. This method induces a very small change in reaction rates, which, in turn, results in a minimum disturbance of the natural mechanism. KIE studies were carried out on both the non-enzymatic and the enzyme-catalyzed reactions in an effort to compare both types of mechanisms. In these studies the amides and esters of formic acid were chosen because this molecular structure allowed development of methodology to determine heavy-atom solvent (nucleophile) KIEs. This type of isotope effect is difficult to measure, but is rich in mechanistic information. Results of these investigations point to transition states with varying degrees of tetrahedral character that fit a classical stepwise mechanism. This article is part of a special issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2014 Elsevier B.V. All rights reserved.

Research on the Relationship between Reaction Ability and Mental State for Online Assessment of Driving Fatigue.

PubMed

Guo, Mengzhu; Li, Shiwu; Wang, Linhong; Chai, Meng; Chen, Facheng; Wei, Yunong

2016-11-24

Background: Driving fatigue affects the reaction ability of a driver. The aim of this research is to analyze the relationship between driving fatigue, physiological signals and driver's reaction time. Methods: Twenty subjects were tested during driving. Data pertaining to reaction time and physiological signals including electroencephalograph (EEG) were collected from twenty simulation experiments. Grey correlation analysis was used to select the input variable of the classification model. A support vector machine was used to divide the mental state into three levels. The penalty factor for the model was optimized using a genetic algorithm. Results: The results show that α/β has the greatest correlation to reaction time. The classification results show an accuracy of 86%, a sensitivity of 87.5% and a specificity of 85.53%. The average increase of reaction time is 16.72% from alert state to fatigued state. Females have a faster decrease in reaction ability than males as driving fatigue accumulates. Elderly drivers have longer reaction times than the young. Conclusions: A grey correlation analysis can be used to improve the classification accuracy of the support vector machine (SVM) model. This paper provides basic research that online detection of fatigue can be performed using only a simple device, which is more comfortable for users.

Research on the Relationship between Reaction Ability and Mental State for Online Assessment of Driving Fatigue

PubMed Central

Guo, Mengzhu; Li, Shiwu; Wang, Linhong; Chai, Meng; Chen, Facheng; Wei, Yunong

2016-01-01

Background: Driving fatigue affects the reaction ability of a driver. The aim of this research is to analyze the relationship between driving fatigue, physiological signals and driver’s reaction time. Methods: Twenty subjects were tested during driving. Data pertaining to reaction time and physiological signals including electroencephalograph (EEG) were collected from twenty simulation experiments. Grey correlation analysis was used to select the input variable of the classification model. A support vector machine was used to divide the mental state into three levels. The penalty factor for the model was optimized using a genetic algorithm. Results: The results show that α/β has the greatest correlation to reaction time. The classification results show an accuracy of 86%, a sensitivity of 87.5% and a specificity of 85.53%. The average increase of reaction time is 16.72% from alert state to fatigued state. Females have a faster decrease in reaction ability than males as driving fatigue accumulates. Elderly drivers have longer reaction times than the young. Conclusions: A grey correlation analysis can be used to improve the classification accuracy of the support vector machine (SVM) model. This paper provides basic research that online detection of fatigue can be performed using only a simple device, which is more comfortable for users. PMID:27886139

Nuclear States with Abnormally Large Radii (size Isomers)

NASA Astrophysics Data System (ADS)

Ogloblin, A. A.; Demyanova, A. S.; Danilov, A. N.; Belyaeva, T. L.; Goncharov, S. A.

2015-06-01

Application of the methods of measuring the radii of the short-lived excited states (Modified diffraction model MDM, Inelastic nuclear rainbow scattering method INRS, Asymptotic normalization coefficients method ANC) to the analysis of some nuclear reactions provide evidence of existing in 9Be, 11B, 12C, 13C the excited states whose radii exceed those of the corresponding ground states by ~ 30%. Two types of structure of these "size isomers" were identified: neutron halo an α-clusters.

γ spectroscopy of states in Cl 32 relevant for the S 31 ( p , γ ) Cl 32 reaction rate

DOE PAGES

Afanasieva, L.; Blackmon, J. C.; Deibel, C. M.; ...

2017-09-01

Background: The 31S(p,gamma) 32Cl reaction becomes important for sulfur production in novae if the P-31(p, alpha)Si-28 reaction rate is somewhat greater than currently accepted. The rate of the S-31(p,gamma) Cl-32 reaction is uncertain, primarily due to the properties of resonances at E-c.m. = 156 and 549 keV. Purpose: We precisely determined the excitation energies of states in Cl-32 through high-resolution. spectroscopy including the two states most important for the S-31(p,gamma) Cl-32 reaction at nova temperatures. Method: Excited states in Cl-32 were populated using the B-10(Mg-24, 2n) Cl-32 reaction with a Mg-24 beam from the ATLAS facility at Argonne National Laboratory.more » The reaction channel of interest was selected using recoils in the Fragment Mass Analyzer, and we determined precise level energies by detecting. rays with Gammasphere. Results: We also observed. rays from the decay of six excited states in Cl-32. The excitation energies for two unbound levels at E-x = 1738.1 (6) keV and 2130.5 (10) keV were determined and found to be in agreement with a previous high-precision measurement of the S-32(He-3, t) Cl-32 reaction [1]. Conclusions: An updated 31S(p,gamma) Cl-32 reaction rate is presented. With the excitation energies of important levels firmly established, the dominant uncertainty in the reaction rate at nova temperatures is due to the strength of the resonance corresponding to the 2131-keV state in Cl-32.« less

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

PubMed

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.

A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

PubMed

Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

2015-01-01

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2. Copyright © 2015 Elsevier Inc. All rights reserved.

Lagrangian descriptors of driven chemical reaction manifolds.

PubMed

Craven, Galen T; Junginger, Andrej; Hernandez, Rigoberto

2017-08-01

The persistence of a transition state structure in systems driven by time-dependent environments allows the application of modern reaction rate theories to solution-phase and nonequilibrium chemical reactions. However, identifying this structure is problematic in driven systems and has been limited by theories built on series expansion about a saddle point. Recently, it has been shown that to obtain formally exact rates for reactions in thermal environments, a transition state trajectory must be constructed. Here, using optimized Lagrangian descriptors [G. T. Craven and R. Hernandez, Phys. Rev. Lett. 115, 148301 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.148301], we obtain this so-called distinguished trajectory and the associated moving reaction manifolds on model energy surfaces subject to various driving and dissipative conditions. In particular, we demonstrate that this is exact for harmonic barriers in one dimension and this verification gives impetus to the application of Lagrangian descriptor-based methods in diverse classes of chemical reactions. The development of these objects is paramount in the theory of reaction dynamics as the transition state structure and its underlying network of manifolds directly dictate reactivity and selectivity.

Proton threshold states in the {sup 22}Na(p,{gamma}){sup 23}Mg reaction and astrophysical implications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Comisel, H.; Hategan, C.; Graw, G.

Proton threshold states in {sup 23}Mg are important for the astrophysically relevant proton capture reaction {sup 22}Na(p,{gamma}){sup 23}Mg. In the indirect determination of the resonance strength of the lowest states, which were not accessible by direct methods, some of the spin-parity-assignments remained experimentally uncertain. We have investigated these states with shell model, Coulomb displacement, and Thomas-Ehrman shift calculations. From the comparison of calculated and observed properties, we relate the lowest relevant resonance state at E{sub x}=7643 keV to an excited 3/2{sup +} state in accordance with a recent experimental determination by Jenkins et al. From this we deduce significantly improvedmore » values for the {sup 22}Na(p,{gamma}){sup 23}Mg reaction rate at stellar temperatures below T{sub 9}=0.1 K.« less

From ab Initio Potential Energy Surfaces to State-Resolved Reactivities: X + H 2O ↔ HX + OH [X = F, Cl, and O( 3P)] Reactions

DOE PAGES

Li, Jun; Jiang, Bin; Song, Hongwei; ...

2015-04-17

Here, we survey the recent advances in theoretical understanding of quantum state resolved dynamics, using the title reactions as examples. It is shown that the progress was made possible by major developments in two areas. First, an accurate analytical representation of many high-level ab initio points over a large configuration space can now be made with high fidelity and the necessary permutation symmetry. The resulting full-dimensional global potential energy surfaces enable dynamical calculations using either quasi-classical trajectory or more importantly quantum mechanical methods. The second advance is the development of accurate and efficient quantum dynamical methods, which are necessary formore » providing a reliable treatment of quantum effects in reaction dynamics such as tunneling, resonances, and zero-point energy. The powerful combination of the two advances has allowed us to achieve a quantitatively accurate characterization of the reaction dynamics, which unveiled rich dynamical features such as steric steering, strong mode specificity, and bond selectivity. The dependence of reactivity on reactant modes can be rationalized by the recently proposed sudden vector projection model, which attributes the mode specificity and bond selectivity to the coupling of reactant modes with the reaction coordinate at the relevant transition state. The deeper insights provided by these theoretical studies have advanced our understanding of reaction dynamics to a new level.« less

Spin-forbidden and spin-allowed cyclopropenone (c-H{sub 2}C{sub 3}O) formation in interstellar medium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmadvand, Seyedsaeid; Zaari, Ryan R.; Varganov, Sergey A., E-mail: svarganov@unr.edu

2014-11-10

Three proposed mechanisms of cyclopropenone (c-H{sub 2}C{sub 3}O) formation from neutral species are studied using high-level electronic structure methods in combination with nonadiabatic transition state and collision theories to deduce the likelihood of each reaction mechanism under interstellar conditions. The spin-forbidden reaction involving the singlet electronic state of cyclopenylidene (c-C{sub 3}H{sub 2}) and the triplet state of atomic oxygen is studied using nonadiabatic transition state theory to predict the rate constant for c-H{sub 2}C{sub 3}O formation. The spin-allowed reactions of c-C{sub 3}H{sub 2} with molecular oxygen and acetylene with carbon monoxide were also investigated. The reaction involving the ground electronicmore » states of acetylene and carbon monoxide has a very large reaction barrier and is unlikely to contribute to c-H{sub 2}C{sub 3}O formation in interstellar medium. The spin-forbidden reaction of c-C{sub 3}H{sub 2} with atomic oxygen, despite the high probability of nonadiabatic transition between the triplet and singlet states, was found to have a very small rate constant due to the presence of a small (3.8 kcal mol{sup –1}) reaction barrier. In contrast, the spin-allowed reaction between c-C{sub 3}H{sub 2} and molecular oxygen is found to be barrierless, and therefore can be an important path to the formation of c-H{sub 2}C{sub 3}O molecule in interstellar environment.« less

Estimation of parameters in rational reaction rates of molecular biological systems via weighted least squares

NASA Astrophysics Data System (ADS)

Wu, Fang-Xiang; Mu, Lei; Shi, Zhong-Ke

2010-01-01

The models of gene regulatory networks are often derived from statistical thermodynamics principle or Michaelis-Menten kinetics equation. As a result, the models contain rational reaction rates which are nonlinear in both parameters and states. It is challenging to estimate parameters nonlinear in a model although there have been many traditional nonlinear parameter estimation methods such as Gauss-Newton iteration method and its variants. In this article, we develop a two-step method to estimate the parameters in rational reaction rates of gene regulatory networks via weighted linear least squares. This method takes the special structure of rational reaction rates into consideration. That is, in the rational reaction rates, the numerator and the denominator are linear in parameters. By designing a special weight matrix for the linear least squares, parameters in the numerator and the denominator can be estimated by solving two linear least squares problems. The main advantage of the developed method is that it can produce the analytical solutions to the estimation of parameters in rational reaction rates which originally is nonlinear parameter estimation problem. The developed method is applied to a couple of gene regulatory networks. The simulation results show the superior performance over Gauss-Newton method.

Growth behavior of LiMn{sub 2}O{sub 4} particles formed by solid-state reactions in air and water vapor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozawa, Takahiro, E-mail: t-kozawa@jwri.osaka-u.ac.jp; Yanagisawa, Kazumichi; Murakami, Takeshi

Morphology control of particles formed during conventional solid-state reactions without any additives is a challenging task. Here, we propose a new strategy to control the morphology of LiMn{sub 2}O{sub 4} particles based on water vapor-induced growth of particles during solid-state reactions. We have investigated the synthesis and microstructural evolution of LiMn{sub 2}O{sub 4} particles in air and water vapor atmospheres as model reactions; LiMn{sub 2}O{sub 4} is used as a low-cost cathode material for lithium-ion batteries. By using spherical MnCO{sub 3} precursor impregnated with LiOH, LiMn{sub 2}O{sub 4} spheres with a hollow structure were obtained in air, while angulated particlesmore » with micrometer sizes were formed in water vapor. The pore structure of the particles synthesized in water vapor was found to be affected at temperatures below 700 °C. We also show that the solid-state reaction in water vapor is a simple and valuable method for the large-scale production of particles, where the shape, size, and microstructure can be controlled. - Graphical abstract: This study has demonstrated a new strategy towards achieving morphology control without the use of additives during conventional solid-state reactions by exploiting water vapor-induced particle growth. - Highlights: • A new strategy to control the morphology of LiMn{sub 2}O{sub 4} particles is proposed. • Water vapor-induced particle growth is exploited in solid-state reactions. • The microstructural evolution of LiMn{sub 2}O{sub 4} particles is investigated. • The shape, size and microstructure can be controlled by solid-state reactions.« less

Computationally efficient characterization of potential energy surfaces based on fingerprint distances

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaefer, Bastian; Goedecker, Stefan, E-mail: stefan.goedecker@unibas.ch

2016-07-21

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 methodmore » 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.« less

Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

PubMed

Huang, Yiran; Zhong, Cheng; Lin, Hai Xiang; Huang, Jing

2016-01-01

Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions) by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.

7Li(15N, 14C)8Be reaction at 81 MeV and 14C + 8Be interaction versus that of 13C + 8Be

NASA Astrophysics Data System (ADS)

Rudchik, A. T.; Rudchik, A. A.; Muravynets, L. M.; Kemper, K. W.; Rusek, K.; Koshchy, E. I.; Piasecki, E.; Trzcinska, A.; Pirnak, Val. M.; Ponkratenko, O. A.; Strojek, I.; Stolarz, A.; Plujko, V. A.; Sakuta, S. B.; Siudak, R.; Ilyin, A. P.; Stepanenko, Yu. M.; Shyrma, Yu. O.; Uleshchenko, V. V.

2018-03-01

Angular distributions of the 7Li(15N, 14C)8Be reaction were measured at the energy Elab(15N) = 81 MeV. Data for transfer to the ground and first two excited states in 8Be were acquired as well as to the 14C ground and excited states. The reaction data were analyzed within the coupled-reaction-channels (CRC) method. The required 15N + 7Li entrance channel potential was taken from the 15N + 7Li elastic scattering. The 14C + 8Be potential was found by fitting Woods-Saxon form potentials to those generated by double folded real and imaginary potentials in the region of interaction. These generated potentials were then used in the CRC calculations. Proton transfer dominants this reaction, including to the excited states of 8Be. The reaction dependence on the exit channel potential was examined by using the 13C + 8Be potential previously deduced from the 9Be(12C, 13C)8Be reaction and 14C + 8Be from the 13C(9Be, 8Be)14C reaction.

Solid catalyzed isoparaffin alkylation at supercritical fluid and near-supercritical fluid conditions

DOEpatents

Ginosar, Daniel M.; Fox, Robert V.; Kong, Peter C.

2000-01-01

This invention relates to an improved method for the alkylation reaction of isoparaffins with olefins over solid catalysts including contacting a mixture of an isoparaffin, an olefin and a phase-modifying material with a solid acid catalyst member under alkylation conversion conditions at either supercritical fluid, or near-supercritical fluid conditions, at a temperature and a pressure relative to the critical temperature(T.sub.c) and the critical pressure(P.sub.c) of the reaction mixture. The phase-modifying phase-modifying material is employed to promote the reaction's achievement of either a supercritical fluid state or a near-supercritical state while simultaneously allowing for decreased reaction temperature and longer catalyst life.

Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

NASA Astrophysics Data System (ADS)

Cannon, William R.; Baker, Scott E.

2017-10-01

Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants. When used to model deterministic systems, the method corresponds to a rescaling of the time dependent reactions in such a way that steady states can be reached on the same time scale but with significantly fewer computational steps. The relationships between reaction affinities, free energy changes and generalized detailed balance are central to the discussion. The significance for applications in systems biology are discussed as is the concept and assumption of maximum entropy production rate as a biological principle that links thermodynamics to natural selection.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afanasieva, L.; Blackmon, J. C.; Deibel, C. M.

Background: The 31S(p,gamma) 32Cl reaction becomes important for sulfur production in novae if the P-31(p, alpha)Si-28 reaction rate is somewhat greater than currently accepted. The rate of the S-31(p,gamma) Cl-32 reaction is uncertain, primarily due to the properties of resonances at E-c.m. = 156 and 549 keV. Purpose: We precisely determined the excitation energies of states in Cl-32 through high-resolution. spectroscopy including the two states most important for the S-31(p,gamma) Cl-32 reaction at nova temperatures. Method: Excited states in Cl-32 were populated using the B-10(Mg-24, 2n) Cl-32 reaction with a Mg-24 beam from the ATLAS facility at Argonne National Laboratory.more » The reaction channel of interest was selected using recoils in the Fragment Mass Analyzer, and we determined precise level energies by detecting. rays with Gammasphere. Results: We also observed. rays from the decay of six excited states in Cl-32. The excitation energies for two unbound levels at E-x = 1738.1 (6) keV and 2130.5 (10) keV were determined and found to be in agreement with a previous high-precision measurement of the S-32(He-3, t) Cl-32 reaction [1]. Conclusions: An updated 31S(p,gamma) Cl-32 reaction rate is presented. With the excitation energies of important levels firmly established, the dominant uncertainty in the reaction rate at nova temperatures is due to the strength of the resonance corresponding to the 2131-keV state in Cl-32.« less

A global reaction route mapping-based kinetic Monte Carlo algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitchell, Izaac; Page, Alister J., E-mail: sirle@chem.nagoya-u.ac.jp, E-mail: alister.page@newcastle.edu.au; Irle, Stephan, E-mail: sirle@chem.nagoya-u.ac.jp, E-mail: alister.page@newcastle.edu.au

2016-07-14

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculatedmore » on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.« less

Methods for Kinetic and Thermodynamic Analysis of Aminoacyl-tRNA Synthetases

PubMed Central

Francklyn, Christopher S.; First, Eric A.; Perona, John J.; Hou, Ya-Ming

2008-01-01

The accuracy of protein synthesis relies on the ability of aminoacyl-tRNA synthetases (aaRSs) to discriminate among true and near cognate substrates. To date, analysis of aaRSs function, including identification of residues of aaRS participating in amino acid and tRNA discrimination, has largely relied on the steady state kinetic pyrophosphate exchange and aminoacylation assays. Pre-steady state kinetic studies investigating a more limited set of aaRS systems have also been undertaken to assess the energetic contributions of individual enzyme-substrate interactions, particularly in the adenylation half reaction. More recently, a renewed interest in the use of rapid kinetics approaches for aaRSs has led to their application to several new aaRS systems, resulting in the identification of mechanistic differences that distinguish the two structurally distinct aaRS classes. Here, we review the techniques for thermodynamic and kinetic analysis of aaRS function. Following a brief survey of methods for the preparation of materials and for steady state kinetic analysis, this review will describe pre-steady state kinetic methods employing rapid quench and stopped-flow fluorescence for analysis of the activation and aminoacyl transfer reactions. Application of these methods to any aaRS system allows the investigator to derive detailed kinetic mechanisms for the activation and aminoacyl transfer reactions, permitting issues of substrate specificity, stereochemical mechanism, and inhibitor interaction to be addressed in a rigorous and quantitative fashion. PMID:18241792

Incorporating extrinsic noise into the stochastic simulation of biochemical reactions: A comparison of approaches

NASA Astrophysics Data System (ADS)

Thanh, Vo Hong; Marchetti, Luca; Reali, Federico; Priami, Corrado

2018-02-01

The stochastic simulation algorithm (SSA) has been widely used for simulating biochemical reaction networks. SSA is able to capture the inherently intrinsic noise of the biological system, which is due to the discreteness of species population and to the randomness of their reciprocal interactions. However, SSA does not consider other sources of heterogeneity in biochemical reaction systems, which are referred to as extrinsic noise. Here, we extend two simulation approaches, namely, the integration-based method and the rejection-based method, to take extrinsic noise into account by allowing the reaction propensities to vary in time and state dependent manner. For both methods, new efficient implementations are introduced and their efficiency and applicability to biological models are investigated. Our numerical results suggest that the rejection-based method performs better than the integration-based method when the extrinsic noise is considered.

Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature

NASA Astrophysics Data System (ADS)

Mitsutake, Ayori; Takano, Hiroshi

2015-09-01

It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component analysis, which extracts modes of large conformational fluctuations around an average structure. We recently applied relaxation mode analysis for protein systems, which approximately estimates the slow relaxation modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation mode analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component analysis and relaxation mode analysis to the system. In the relaxation mode analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new analysis method called Markov state relaxation mode analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation mode analysis. Finally, the relaxation times of the states obtained with a simple Markov state model and the proposed Markov state relaxation mode analysis are compared and discussed.

A Solvent-Free Baeyer-Villiger Lactonization for the Undergraduate Organic Laboratory: Synthesis of Gamma-T-Butyl-Epsilon-Caprolactone

ERIC Educational Resources Information Center

Esteb, John J.; Hohman, Nathan J.; Schlamandinger, Diana E.; Wilson, Anne M.

2005-01-01

The solvent-free or solid-state reaction systems like the Baeyer-Villiger rearrangement have become popular in the synthetic organic community and viable option for undergraduate laboratory series to reduce waste and cost and simplify reaction process. The reaction is an efficient method to transform ketones to esters and lactones.

Method and apparatus for obtaining enhanced production rate of thermal chemical reactions

DOEpatents

Tonkovich, Anna Lee Y.; Wang, Yong; Wegeng, Robert S.; Gao, Yufei

2003-09-09

Reactors and processes are disclosed that can utilize high heat fluxes to obtain fast, steady-state reaction rates. Porous catalysts used in conjunction with microchannel reactors to obtain high rates of heat transfer are also disclosed. Reactors and processes that utilize short contact times, high heat flux and low pressure drop are described. Improved methods of steam reforming are also provided.

Method and apparatus for obtaining enhanced production rate of thermal chemical reactions

DOEpatents

Tonkovich, Anna Lee Y [Pasco, WA; Wang, Yong [Richland, WA; Wegeng, Robert S [Richland, WA; Gao, Yufei [Kennewick, WA

2006-05-16

Reactors and processes are disclosed that can utilize high heat fluxes to obtain fast, steady-state reaction rates. Porous catalysts used in conjunction with microchannel reactors to obtain high rates of heat transfer are also disclosed. Reactors and processes that utilize short contact times, high heat flux and low pressure drop are described. Improved methods of steam reforming are also provided.

Control of diastereoselectivity by solvent effects in the addition of Grignard reagents to enantiopure t-butylsulfinimine: syntheses of the stereoisomers of the hydroxyl derivatives of sibutramine.

PubMed

Lu, Bruce Z; Senanayake, Chris; Li, Nansheng; Han, Zhengxu; Bakale, Roger P; Wald, Stephen A

2005-06-23

[reaction: see text] An efficient method has been developed to prepare all four isomers of the hydroxyl derivatives of sibutramine by addition of Grignard reagents (R)- or (S)-5 to a single enantiomer of sulfinyl imine (R)-1 simply by tuning the reaction solvent. The phenomenon of the reversed diastereoselectivity in CH(2)Cl(2) and THF implied that the reaction may proceed through a chelated cyclic transition state in CH(2)Cl(2) and nonchelated acyclic transition state in THF.

Revisiting and Computing Reaction Coordinates with Directional Milestoning

PubMed Central

Kirmizialtin, Serdal; Elber, Ron

2011-01-01

The method of Directional Milestoning is revisited. We start from an exact and more general expression and state the conditions and validity of the memory-loss approximation. An algorithm to compute a reaction coordinate from Directional Milestoning data is presented. The reaction coordinate is calculated as a set of discrete jumps between Milestones that maximizes the flux between two stable states. As an application we consider a conformational transition in solvated Adenosine. We compare a long molecular dynamic trajectory with Directional Milestoning and discuss the differences between the maximum flux path and minimum energy coordinates. PMID:21500798

Regeneration of aluminum hydride

DOEpatents

Graetz, Jason Allan; Reilly, James J.

2009-04-21

The present invention provides methods and materials for the formation of hydrogen storage alanes, AlH.sub.x, where x is greater than 0 and less than or equal to 6 at reduced H.sub.2 pressures and temperatures. The methods rely upon reduction of the change in free energy of the reaction between aluminum and molecular H.sub.2. The change in free energy is reduced by lowering the entropy change during the reaction by providing aluminum in a state of high entropy, by increasing the magnitude of the change in enthalpy of the reaction or combinations thereof.

Selected specific rates of reactions of transients from water in aqueous solution. III. Hydroxyl radical and perhydroxyl radical and their radical ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ross, F; Ross, A B

1977-01-01

Rates of reactions of OH and HO/sub 2/ with organic and inorganic molecules, ions and transients in aqueous solution have been tabulated, as well as the rates for the corresponding radical ions in aqueous solution (O/sup -/ and O/sub 2//sup -/). Most of the rates have been obtained by radiation chemistry methods, both pulsed and steady-state; data from photochemistry and thermal methods are also included. Rates for over one thousand reactions are listed.

Extracting electron transfer coupling elements from constrained density functional theory

NASA Astrophysics Data System (ADS)

Wu, Qin; Van Voorhis, Troy

2006-10-01

Constrained density functional theory (DFT) is a useful tool for studying electron transfer (ET) reactions. It can straightforwardly construct the charge-localized diabatic states and give a direct measure of the inner-sphere reorganization energy. In this work, a method is presented for calculating the electronic coupling matrix element (Hab) based on constrained DFT. This method completely avoids the use of ground-state DFT energies because they are known to irrationally predict fractional electron transfer in many cases. Instead it makes use of the constrained DFT energies and the Kohn-Sham wave functions for the diabatic states in a careful way. Test calculations on the Zn2+ and the benzene-Cl atom systems show that the new prescription yields reasonable agreement with the standard generalized Mulliken-Hush method. We then proceed to produce the diabatic and adiabatic potential energy curves along the reaction pathway for intervalence ET in the tetrathiafulvalene-diquinone (Q-TTF-Q) anion. While the unconstrained DFT curve has no reaction barrier and gives Hab≈17kcal /mol, which qualitatively disagrees with experimental results, the Hab calculated from constrained DFT is about 3kcal /mol and the generated ground state has a barrier height of 1.70kcal/mol, successfully predicting (Q-TTF-Q)- to be a class II mixed-valence compound.

On the precision of quasi steady state assumptions in stochastic dynamics

NASA Astrophysics Data System (ADS)

Agarwal, Animesh; Adams, Rhys; Castellani, Gastone C.; Shouval, Harel Z.

2012-07-01

Many biochemical networks have complex multidimensional dynamics and there is a long history of methods that have been used for dimensionality reduction for such reaction networks. Usually a deterministic mass action approach is used; however, in small volumes, there are significant fluctuations from the mean which the mass action approach cannot capture. In such cases stochastic simulation methods should be used. In this paper, we evaluate the applicability of one such dimensionality reduction method, the quasi-steady state approximation (QSSA) [L. Menten and M. Michaelis, "Die kinetik der invertinwirkung," Biochem. Z 49, 333369 (1913)] for dimensionality reduction in case of stochastic dynamics. First, the applicability of QSSA approach is evaluated for a canonical system of enzyme reactions. Application of QSSA to such a reaction system in a deterministic setting leads to Michaelis-Menten reduced kinetics which can be used to derive the equilibrium concentrations of the reaction species. In the case of stochastic simulations, however, the steady state is characterized by fluctuations around the mean equilibrium concentration. Our analysis shows that a QSSA based approach for dimensionality reduction captures well the mean of the distribution as obtained from a full dimensional simulation but fails to accurately capture the distribution around that mean. Moreover, the QSSA approximation is not unique. We have then extended the analysis to a simple bistable biochemical network model proposed to account for the stability of synaptic efficacies; the substrate of learning and memory [J. E. Lisman, "A mechanism of memory storage insensitive to molecular turnover: A bistable autophosphorylating kinase," Proc. Natl. Acad. Sci. U.S.A. 82, 3055-3057 (1985)], 10.1073/pnas.82.9.3055. Our analysis shows that a QSSA based dimensionality reduction method results in errors as big as two orders of magnitude in predicting the residence times in the two stable states.

Photochemically Switching Diamidocarbene Spin States Leads to Reversible Büchner Ring Expansions.

PubMed

Perera, Tharushi A; Reinheimer, Eric W; Hudnall, Todd W

2017-10-18

The discovery of thermal and photochemical control by Woodward and Hoffmann revolutionized how we understand chemical reactivity. Similarly, we now describe the first example of a carbene that exhibits differing thermal and photochemical reactivity. When a singlet ground-state N,N'-diamidocarbene 1 was photolyzed at 380 nm, excitation to a triplet state was observed. The triplet-state electronic structure was characteristic of the expected biradical σ 1 p π 1 spin configuration according to a combination of spectroscopic and computational methods. Surprisingly, the triplet state of 1 was found to engage a series of arenes in thermally reversible Büchner ring expansion reactions, marking the first examples where both cyclopropanation and ring expansion of arenes were rendered reversible. Not only are these photochemical reactions different from the known thermal chemistry of 1, but the reversibility enabled us to perform the first examples of photochemically induced arene exchange/expansion reactions at a single carbon center.

Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain.

PubMed

Fekete, Attila; Komáromi, István

2016-12-07

A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.

Nonlinear scalar forcing based on a reaction analogy

NASA Astrophysics Data System (ADS)

Daniel, Don; Livescu, Daniel

2017-11-01

We present a novel reaction analogy (RA) based forcing method for generating stationary passive scalar fields in incompressible turbulence. The new method can produce more general scalar PDFs (e.g. double-delta) than current methods, while ensuring that scalar fields remain bounded, unlike existent forcing methodologies that can potentially violate naturally existing bounds. Such features are useful for generating initial fields in non-premixed combustion or for studying non-Gaussian scalar turbulence. The RA method mathematically models hypothetical chemical reactions that convert reactants in a mixed state back into its pure unmixed components. Various types of chemical reactions are formulated and the corresponding mathematical expressions derived. For large values of the scalar dissipation rate, the method produces statistically steady double-delta scalar PDFs. Gaussian scalar statistics are recovered for small values of the scalar dissipation rate. In contrast, classical forcing methods consistently produce unimodal Gaussian scalar fields. The ability of the new method to produce fully developed scalar fields is discussed using 2563, 5123, and 10243 periodic box simulations.

A barrier-free atomic radical-molecule reaction: N (2D) NO2 (2A1) mechanistic study

NASA Astrophysics Data System (ADS)

Zuo, Ming-Hui; Liu, Hui-Ling; Huang, Xu-Ri; Zhan, Jin-Hui; Sun, Chia-Chung

The reaction of N (2D) radical with NO2 molecule has been studied theoretically using density functional theory and ab initio quantum chemistry method. Singlet electronic state [N2O2] potential energy surfaces (PES) are calculated at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-311+G(d) + ZPE and G3B3 levels of theory. All the involved transition states for generation of (2NO) and (O2 + N2) lie much lower than the reactants. Thus, the novel reaction N + NO2 can proceed effectively even at low temperatures and it is expected to play a role in both combustion and interstellar processes. On the basis of the analysis of the kinetics of all pathways through which the reactions proceed, we expect that the competitive power of reaction pathways may vary with experimental conditions for the title reaction.

Semiquantitative FMO Analysis of Substituent Effect on the Reaction of Permanganate Ion with Unsymmetrical Alkenes.

PubMed

Ogino, Toshio; Watanabe, Toru; Matsuura, Masato; Watanabe, Chikara; Ozaki, Hidetoshi

1998-04-17

The substituent effects on the reactions of permanganate ion with unsymmetrical alkenes are analyzed on the assumption of a concerted (3 + 2) cycloaddition model by using an equation obtained by approximation based on the FMO theory in which development and localization of the frontier molecular orbitals at the reaction sites with progress of the reaction are considered. The Hammett plots are successfully reproduced with the newly obtained rate data for the reactions of trans-chalcone and its derivatives and the data for methyl cinnamates, cinnamate ions, and alkyl vinyl ethers taken from the literature using FMO energies and orbital coefficients calculated by the PM3 method. It was indicated that a factor introduced to the basic equation in order to estimate the extent of localization of the molecular orbitals at the transition state is closely related to the position of the transition state along the reaction path.

Effects of reactant rotation on the dynamics of the OH + CH4 → H2O + CH3 reaction: a six-dimensional study.

PubMed

Song, Hongwei; Li, Jun; Jiang, Bin; Yang, Minghui; Lu, Yunpeng; Guo, Hua

2014-02-28

The dynamics of the hydrogen abstraction reaction between methane and hydroxyl radical is investigated using an initial state selected time-dependent wave packet method within a six-dimensional model. The ab initio calibrated global potential energy surface of Espinosa-García and Corchado was used. Integral cross sections from several low-lying rotational states of both reactants have been obtained using the centrifugal sudden and J-shifting approximations. On the empirical potential energy surface, the rotational excitation of methane has little effect on the reaction cross section, but excited rotational states of OH inhibit the reactivity slightly. These results are rationalized with the newly proposed sudden vector projection model.

Ab initio rate constants from hyperspherical quantum scattering: Application to H+C2H6 and H+CH3OH

NASA Astrophysics Data System (ADS)

Kerkeni, Boutheïna; Clary, David C.

2004-10-01

The dynamics and kinetics of the abstraction reactions of H atoms with ethane and methanol have been studied using a quantum mechanical procedure. Bonds being broken and formed are treated with explicit hyperspherical quantum dynamics. The ab initio potential energy surfaces for these reactions have been developed from a minimal number of grid points (average of 48 points) and are given by analytical functionals. All the degrees of freedom except the breaking and forming bonds are optimized using the second order perturbation theory method with a correlation consistent polarized valence triple zeta basis set. Single point energies are calculated on the optimized geometries with the coupled cluster theory and the same basis set. The reaction of H with C2H6 is endothermic by 1.5 kcal/mol and has a vibrationally adiabatic barrier of 12 kcal/mol. The reaction of H with CH3OH presents two reactive channels: the methoxy and the hydroxymethyl channels. The former is endothermic by 0.24 kcal/mol and has a vibrationally adiabatic barrier of 13.29 kcal/mol, the latter reaction is exothermic by 7.87 kcal/mol and has a vibrationally adiabatic barrier of 8.56 kcal/mol. We report state-to-state and state-selected cross sections together with state-to-state rate constants for the title reactions. Thermal rate constants for these reactions exhibit large quantum tunneling effects when compared to conventional transition state theory results. For H+CH3OH, it is found that the CH2OH product is the dominant channel, and that the CH3O channel contributes just 2% at 500 K. For both reactions, rate constants are in good agreement with some measurements.

Towards a converged barrier height for the entrance channel transition state of the N( 2D) + CH 4 reaction and its implication for the chemistry in Titan's atmosphere

NASA Astrophysics Data System (ADS)

Ouk, Chanda-Malis; Zvereva-Loëte, Natalia; Bussery-Honvault, Béatrice

2011-10-01

The N( 2D) + CH 4 reaction appears to be a key reaction for the chemistry of Titan's atmosphere, opening the door to nitrile formation as recently observed by the Cassini-Huygens mission. Faced to the controversy concerning the existence or not of a potential barrier for this reaction, we have carried out accurate ab initio calculations by means of multi-state multi-reference configuration interaction (MS-MR-SDCI) method. These calculations have been partially corrected for the size-consistency errors (SCE) by Davidson, Pople or AQCC corrections. We suggest a barrier height of 3.86 ± 0.84 kJ/mol, including ZPE, for the entrance transition state, in good agreement with the experimental value. Its implication in Titan's atmopsheric chemistry is discussed.

Theory of the reaction dynamics of small molecules on metal surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Bret

The objective of this project has been to develop realistic theoretical models for gas-surface interactions, with a focus on processes important in heterogeneous catalysis. The dissociative chemisorption of a molecule on a metal is a key step in many catalyzed reactions, and is often the rate-limiting step. We have explored the dissociative chemisorption of H 2, H 2O and CH 4 on a variety of metal surfaces. Most recently, our extensive studies of methane dissociation on Ni and Pt surfaces have fully elucidated its dependence on translational energy, vibrational state and surface temperature, providing the first accurate comparisons with experimentalmore » data. We have explored Eley-Rideal and hot atom reactions of H atoms with H- and C-covered metal surfaces. H atom interactions with graphite have also been explored, including both sticking and Eley-Rideal recombination processes. Again, our methods made it possible to explain several experiments studying these reactions. The sticking of atoms on metal surfaces has also been studied. To help elucidate the experiments that study these processes, we examine how the reaction dynamics depend upon the nature of the molecule-metal interaction, as well as experimental variables such as substrate temperature, beam energy, angle of impact, and the internal states of the molecules. Electronic structure methods based on Density Functional Theory are used to compute each molecule-metal potential energy surface. Both time-dependent quantum scattering techniques and quasi-classical methods are used to examine the reaction or scattering dynamics. Much of our effort has been directed towards developing improved quantum methods that can accurately describe reactions, as well as include the effects of substrate temperature (lattice vibration).« less

Detection of Cysteine Redox States in Mitochondrial Proteins in Intact Mammalian Cells.

PubMed

Habich, Markus; Riemer, Jan

2017-01-01

Import, folding, and activity regulation of mitochondrial proteins are important for mitochondrial function. Cysteine residues play crucial roles in these processes as their thiol groups can undergo (reversible) oxidation reactions. For example, during import of many intermembrane space (IMS) proteins, cysteine oxidation drives protein folding and translocation over the outer membrane. Mature mitochondrial proteins can undergo changes in the redox state of specific cysteine residues, for example, as part of their enzymatic reaction cycle or as adaptations to changes of the local redox environment which might influence their activity. Here we describe methods to study changes in cysteine residue redox states in intact cells. These approaches allow to monitor oxidation-driven protein import as well as changes of cysteine redox states in mature proteins during oxidative stress or during the reaction cycle of thiol-dependent enzymes like oxidoreductases.

The Trojan Horse method for nuclear astrophysics: Recent results for direct reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tumino, A.; Gulino, M.; Spitaleri, C.

2014-05-09

The Trojan Horse method is a powerful indirect technique to determine the astrophysical factor for binary rearrangement processes A+x→b+B at astrophysical energies by measuring the cross section for the Trojan Horse (TH) reaction A+a→B+b+s in quasi free kinematics. The Trojan Horse Method has been successfully applied to many reactions of astrophysical interest, both direct and resonant. In this paper, we will focus on direct sub-processes. The theory of the THM for direct binary reactions will be shortly presented based on a few-body approach that takes into account the off-energy-shell effects and initial and final state interactions. Examples of recent resultsmore » will be presented to demonstrate how THM works experimentally.« less

Electrochemical thermodynamic measurement system

DOEpatents

Reynier, Yvan [Meylan, FR; Yazami, Rachid [Los Angeles, CA; Fultz, Brent T [Pasadena, CA

2009-09-29

The present invention provides systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and electrochemical energy storage and conversion systems. Systems and methods of the present invention are configured for simultaneously collecting a suite of measurements characterizing a plurality of interconnected electrochemical and thermodynamic parameters relating to the electrode reaction state of advancement, voltage and temperature. Enhanced sensitivity provided by the present methods and systems combined with measurement conditions that reflect thermodynamically stabilized electrode conditions allow very accurate measurement of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and electrochemical systems, such as the energy, power density, current rate and the cycle life of an electrochemical cell.

Abstraction kinetics of H-atom by OH radical from pinonaldehyde (C10H16O2): ab initio and transition-state theory calculations.

PubMed

Dash, Manas Ranjan; Rajakumar, B

2012-06-21

The kinetics and abstraction rate coefficients of hydroxyl radical (OH) reaction with pinonaldehyde were computed using G3(MP2) theory and transition-state theory (TST) between 200 and 400 K. Structures of the reactants, reaction complexes (RCs), product complexes (PCs), transition states (TSs), and products were optimized at the MP2(FULL)/6-31G* level of theory. Fifteen transition states were identified for the title reaction and confirmed by intrinsic reaction coordinate (IRC) calculations. The contributions of all the individual hydrogens in the substrate molecule to the total reaction are computed. The quantum mechanical tunneling effect was computed using Wigner's and Eckart's methods (both symmetrical and unsymmetrical methods). The reaction exhibits a negative temperature dependent rate coefficient, k(T) = (1.97 ± 0.34) × 10(-13) exp[(1587 ± 48)/T] cm(3) molecule(-1) s(-1), k(T) = (3.02 ± 0.56) × 10(-13) exp[(1534 ± 52/T] cm(3) molecule(-1) s(-1), and k(T) = (4.71 ± 1.85) × 10(-14) exp[(2042 ± 110)/T] cm(3) molecule(-1) s(-1) with Wigner's, Eckart's symmetrical, and Eckart's unsymmetrical tunneling corrections, respectively. Theoretically calculated rate coefficients are found to be in good agreement with the experimentally measured ones and other theoretical results. It is shown that hydrogen abstraction from -CHO position is the major channel, whereas H-abstraction from -COCH(3) is negligible. The atmospheric lifetime of pinonaldehyde is computed to be few hours and found to be in excellent agreement with the experimentally estimated ones.

Psychophysiological effects of self-regulation method: EEG frequency analysis and contingent negative variations.

PubMed

Ikemi, A

1988-01-01

Experiments were conducted to investigate the psychophysiological effects of self-regulation method (SRM), a newly developed method of self-control, using EEG frequency analysis and contingent negative variations (CNV). The results of the EEG frequency analysis showed that there is a significant increase in the percentage (power) of the theta-band and a significant decrease in the percentage (power) of the beta-band during SRM. Moreover, the results of an identical experiment conducted on subjects in a drowsy state showed that the changes in EEG frequencies during SRM can be differentiated from those of a drowsy state. Furthermore, experiments using CNV showed that there is a significant reduction of CNV amplitude during SRM. Despite the reduced amplitude during SRM, the number of errors in a task to evoke the CNV was reduced significantly without significant delay of reaction time. When an identical experiment was conducted in a drowsy state, CNV amplitude was reduced significantly, but reaction time and errors increased. From these experiments, the state of vigilance during SRM was discussed as a state of 'relaxed alertness'.

Synthesisofc-lifepo4 composite by solid state reaction method

NASA Astrophysics Data System (ADS)

Rahayu, I.; Hidayat, S.; Noviyanti, A. R.; Rakhmawaty, D.; Ernawati, E.

2017-02-01

In this research, the enhancement of LiFePO4 conductivity was conducted by doping method with carbon materials. Carbon-based materials were obtained from the mixture of sucrose, and the precursor of LiH2PO4 and α-Fe2O3 was synthesized by solid state reaction. Sintering temperature was varied at 700°C, 800°C, 900°C and 1,000°C. The result showed that C-LiFePO4 could be synthesized by using solid state reaction method. Based on the XRD and FTIR spectrums, C-LiFePO4 can be identified as the type of crystal, characterized by the appearance of sharp signal on (011), (211) and typical peak of LiFePO4 materials. The result of conductivity measurement from C-LiFePO4 at sintering temperature of 900°C and 1,000°C was 2×10-4 S/cm and 4×10-4S/cm, respectively. The conductivity value at sintering temperature of 700°C and 800°C was very small (<10-6 S/cm), which cannot be measured by the existing equipment.

Diffusion and reactivity of ground-state nitrogen atoms N(4S) between 3 and 15 K: application to the hydrogen abstraction reaction from methane under non-energetic conditions

NASA Astrophysics Data System (ADS)

Nourry, Sendres; Krim, Lahouari

2015-07-01

We have characterized the CH4 + N(4S) reaction in solid phase, at very low temperature, under non-energetic conditions and where the CH4 and N reactants are in their ground states. A microwave-driven atomic source has been used to generate ground-state nitrogen atoms N(4S), and experiments have been carried out at temperatures as low as 3 K to reduce the mobility of the trapped species in solid phase and hence to freeze the first step of the CH4 + N reaction pathway. Leaving the formed solid sample in the dark for a while allows all trapped reactants to relax to the ground state, specifically radicals and excited species streaming from the plasma discharge. Such a method could be the only possibility of proving that the CH4 + N reaction occurs between CH4 and N reactants in their ground states without any additional energy to initiate the chemical process. The appearance of the CH3 reaction product, just by inducing the mobility of N atoms between 3 and 11 K, translates that a hydrogen abstraction reaction from methane, under non-energetic conditions, will start occurring at very low temperature. The formation of methyl radical, under these experimental conditions, is due to recombination processes N(4S)-N(4S) of ground-state nitrogen atoms without any contribution of cosmic ray particles or high-energy photons.

Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch

NASA Astrophysics Data System (ADS)

Morelli, Marco J.; Allen, Rosalind J.; Tǎnase-Nicola, Sorin; ten Wolde, Pieter Rein

2008-01-01

In many stochastic simulations of biochemical reaction networks, it is desirable to "coarse grain" the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network that is particularly sensitive to dynamical fluctuations: a bistable genetic switch. We remove protein-DNA and/or protein-protein association-dissociation reactions from the reaction set using various coarse-graining strategies. We determine the effects on the steady-state probability distribution function and on the rate of fluctuation-driven switch flipping transitions. We find that protein-protein interactions may be safely eliminated from the reaction set, but protein-DNA interactions may not. We also find that it is important to use the chemical master equation rather than macroscopic rate equations to compute effective propensity functions for the coarse-grained reactions.

Computational Analysis of Stereospecificity in the Cope Rearrangement

ERIC Educational Resources Information Center

Glish, Laura; Hanks, Timothy W.

2007-01-01

The Cope rearrangement is a highly stereospecific, concerted reaction of considerable synthetic utility. Experimental product distributions from the reaction of disubstituted 1,5-hexadienes can be readily understood by computer modeling of the various possible transitions states. Semi-empirical methods give relative energies of transition states…

Enhanced Multiferroic Properties of YMnO3 Ceramics Fabricated by Spark Plasma Sintering Along with Low-Temperature Solid-State Reaction

PubMed Central

Wang, Meng; Wang, Ting; Song, Shenhua; Ravi, Muchakayala; Liu, Renchen; Ji, Shishan

2017-01-01

Based on precursor powders with a size of 200–300 nm prepared by the low-temperature solid-state reaction method, phase-pure YMnO3 ceramics are fabricated using spark plasma sintering (SPS). X-ray diffraction (XRD) and scanning electron microscopy (SEM) reveal that the high-purity YMnO3 ceramics can be prepared by SPS at 1000 °C for 5 minutes with annealing at 800 °C for 2 h. The relative density of the sample is as high as 97%, which is much higher than those of the samples sintered by other methods. The present dielectric and magnetic properties are much better than those of the samples fabricated by conventional methods and SPS with ball-milling precursors, and the ferroelectric loops at room temperature can be detected. These findings indicate that the YMnO3 ceramics prepared by the low temperature solid reaction method and SPS possess excellent dielectric lossy ferroelectric properties at room temperature, and magnetic properties at low temperature (10 K), making them suitable for potential multiferroic applications. PMID:28772832

Simulation studies of chemical erosion on carbon based materials at elevated temperatures

NASA Astrophysics Data System (ADS)

Kenmotsu, T.; Kawamura, T.; Li, Zhijie; Ono, T.; Yamamura, Y.

1999-06-01

We simulated the fluence dependence of methane reaction yield in carbon with hydrogen bombardment using the ACAT-DIFFUSE code. The ACAT-DIFFUSE code is a simulation code based on a Monte Carlo method with a binary collision approximation and on solving diffusion equations. The chemical reaction model in carbon was studied by Roth or other researchers. Roth's model is suitable for the steady state methane reaction. But this model cannot estimate the fluence dependence of the methane reaction. Then, we derived an empirical formula based on Roth's model for methane reaction. In this empirical formula, we assumed the reaction region where chemical sputtering due to methane formation takes place. The reaction region corresponds to the peak range of incident hydrogen distribution in the target material. We adopted this empirical formula to the ACAT-DIFFUSE code. The simulation results indicate the similar fluence dependence compared with the experiment result. But, the fluence to achieve the steady state are different between experiment and simulation results.

CN radical reactions with hydrogen cyanide and cyanogen - Comparison of theory and experiment

NASA Technical Reports Server (NTRS)

Yang, D. L.; Yu, T.; Lin, M. C.; Melius, C. F.

1992-01-01

The method of laser photolysis/laser-induced fluorescence is used to obtain absolute rate constants for CN radical reactions with HCN and C2N2. The rate constants were found to be temperature-dependent in the range 300-740 K and pressure independent in the range 100-600 Torr. Rice-Remsperger-Kassel-Marcus theory for both reactions employing the transition state parameters obtained by the BAC-MP4 method are made. These calculations yielded reasonable results for the CN + HCN reaction, predicting both the temperature dependence and pressure independence. No pressure effect was observed in the pressure range 100-1000 Torr at temperatures below 900 K, confirming the experimental results.

Astrophysical reaction rates from a symmetry-informed first-principles perspective

NASA Astrophysics Data System (ADS)

Dreyfuss, Alison; Launey, Kristina; Baker, Robert; Draayer, Jerry; Dytrych, Tomas

2017-01-01

With a view toward a new unified formalism for studying bound and continuum states in nuclei, to understand stellar nucleosynthesis from a fully ab initio perspective, we studied the nature of surface α-clustering in 20Ne by considering the overlap of symplectic states with cluster-like states. We compute the spectroscopic amplitudes and factors, α-decay width, and absolute resonance strength - characterizing major contributions to the astrophysical reaction rate through a low-lying 1- resonant state in 20Ne. As a next step, we consider a fully microscopic treatment for the n+4 He system, based on the successful first-principles No-Core Shell Model/Resonating Group Method (NCSM/RGM) for light nuclei, but with the capability to reach intermediate-mass nuclei. The new model takes advantage of the symmetry-based concept central to the Symmetry-Adapted No-Core Shell Model (SA-NCSM) to reduce computational complexity in physically-informed and methodical way, with sights toward first-principles calculations of rates for important astrophysical reactions, such as the 23 Al(p , γ) 24 Si reaction, believed to have a strong influence on X-ray burst light curves. Supported by the U.S. NSF (OCI-0904874, ACI -1516338) and the U.S. DOE (DE-SC0005248), and benefitted from computing resources provided by Blue Waters and the LSU Center for Computation & Technology.

Time-dependent quantum wave packet calculation for nonadiabatic F(2P3/2,2P1/2)+H2 reaction

NASA Astrophysics Data System (ADS)

Zhang, Yan; Xie, Ting-Xian; Han, Ke-Li; Zhang, John Z. H.

2003-12-01

In this paper we present a time-dependent quantum wave packet calculation for the reaction of F(2P3/2,2P1/2)+H2 on the Alexander-Stark-Werner potential energy surface. The reaction probabilities and the integral cross sections for the reaction of F(2P3/2,2P1/2)+H2 (v=j=0) are computed using time-dependent quantum methods with the centrifugal sudden approximate. The results are compared with recent time-independent quantum calculations. The two-surface reaction probability for the initial ground spin-orbit state of J=0.5 is similar to the time-independent result obtained by Alexander et al. [J. Chem. Phys. 113, 11084 (2000)]. Our calculation also shows that electronic coupling has a relatively minor effect on the reactivity from the 2P3/2 state but a non-negligible one from the 2P1/2 state. By comparison with exact time-independent calculations, it is found that the Coriolis coupling plays a relatively minor role. In addition, most of the reactivity of the excited state of fluorine atom results from the spin-orbit coupling.

Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods.

PubMed

Suleimanov, Yury V; Green, William H

2015-09-08

We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation double- and single-ended transition-state optimization algorithms--the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several single-molecule systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes.

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

PubMed

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.

Cure Schedule for Stycast 2651/Catalyst 9.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kropka, Jamie Michael; McCoy, John D.

2017-11-01

The Emerson & Cuming technical data sheet (TDS) for Stycast 2651/Catalyst 9 lists three alternate cure schedules for the material, each of which would result in a different state of reaction and different material properties. Here, a cure schedule that attains full reaction of the material is defined. The use of this cure schedule will eliminate variance in material properties due to changes in the cure state of the material, and the cure schedule will serve as the method to make material prior to characterizing properties. The following recommendation uses one of the schedules within the TDS and adds amore » “post cure” to obtain full reaction.« less

Low-temperature synthesis of actinide tetraborides by solid-state metathesis reactions

DOEpatents

Lupinetti, Anthony J [Los Alamos, NM; Garcia, Eduardo [Los Alamos, NM; Abney, Kent D [Los Alamos, NM

2004-12-14

The synthesis of actinide tetraborides including uranium tetraboride (UB.sub.4), plutonium tetraboride (PuB.sub.4) and thorium tetraboride (ThB.sub.4) by a solid-state metathesis reaction are demonstrated. The present method significantly lowers the temperature required to .ltoreq.850.degree. C. As an example, when UCl.sub.4 is reacted with an excess of MgB.sub.2, at 850.degree. C., crystalline UB.sub.4 is formed. Powder X-ray diffraction and ICP-AES data support the reduction of UCl.sub.3 as the initial step in the reaction. The UB.sub.4 product is purified by washing water and drying.

Barrierless Reactions with Loose Transition States Govern the Yields and Lifetimes of Organic Nitrates Derived from Isoprene

EPA Science Inventory

The chemical reaction mechanism of NO addition to two β and δ isoprene hydroxy–peroxy radical isomers is examined in detail using density functional theory, coupled cluster methods, and the energy resolved master equation formalism to provide estimates of rate co...

Three-body radiative capture reactions

NASA Astrophysics Data System (ADS)

Casal, J.; Rodríguez-Gallardo, M.; Arias, J. M.; Gómez-Camacho, J.

2018-01-01

Radiative capture reaction rates for 6He, 9Be and 17Ne formation at astrophysical conditions are studied within a three-body model using the analytical transformed harmonic oscillator method to calculate their states. An alternative procedure to estimate these rates from experimental data on low-energy breakup is also discussed.

Physico-Geometrical Kinetics of Solid-State Reactions in an Undergraduate Thermal Analysis Laboratory

ERIC Educational Resources Information Center

Koga, Nobuyoshi; Goshi, Yuri; Yoshikawa, Masahiro; Tatsuoka, Tomoyuki

2014-01-01

An undergraduate kinetic experiment of the thermal decomposition of solids by microscopic observation and thermal analysis was developed by investigating a suitable reaction, applicable techniques of thermal analysis and microscopic observation, and a reliable kinetic calculation method. The thermal decomposition of sodium hydrogen carbonate is…

Regeneration of aluminum hydride

DOEpatents

Graetz, Jason Allan; Reilly, James J; Wegrzyn, James E

2012-09-18

The present invention provides methods and materials for the formation of hydrogen storage alanes, AlH.sub.x, where x is greater than 0 and less than or equal to 6 at reduced H.sub.2 pressures and temperatures. The methods rely upon reduction of the change in free energy of the reaction between aluminum and molecular H.sub.2. The change in free energy is reduced by lowering the entropy change during the reaction by providing aluminum in a state of high entropy, and by increasing the magnitude of the change in enthalpy of the reaction or combinations thereof.

A method to decompose spectral changes in Synechocystis PCC 6803 during light-induced state transitions.

PubMed

Acuña, Alonso M; Kaňa, Radek; Gwizdala, Michal; Snellenburg, Joris J; van Alphen, Pascal; van Oort, Bart; Kirilovsky, Diana; van Grondelle, Rienk; van Stokkum, Ivo H M

2016-12-01

Cyanobacteria have developed responses to maintain the balance between the energy absorbed and the energy used in different pigment-protein complexes. One of the relatively rapid (a few minutes) responses is activated when the cells are exposed to high light intensities. This mechanism thermally dissipates excitation energy at the level of the phycobilisome (PB) antenna before it reaches the reaction center. When exposed to low intensities of light that modify the redox state of the plastoquinone pool, the so-called state transitions redistribute energy between photosystem I and II. Experimental techniques to investigate the underlying mechanisms of these responses, such as pulse-amplitude modulated fluorometry, are based on spectrally integrated signals. Previously, a spectrally resolved fluorometry method has been introduced to preserve spectral information. The analysis method introduced in this work allows to interpret SRF data in terms of species-associated spectra of open/closed reaction centers (RCs), (un)quenched PB and state 1 versus state 2. Thus, spectral differences in the time-dependent fluorescence signature of photosynthetic organisms under varying light conditions can be traced and assigned to functional emitting species leading to a number of interpretations of their molecular origins. In particular, we present evidence that state 1 and state 2 correspond to different states of the PB-PSII-PSI megacomplex.

State space truncation with quantified errors for accurate solutions to discrete Chemical Master Equation

PubMed Central

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-01-01

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEG), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of 1) the birth and death model, 2) the single gene expression model, 3) the genetic toggle switch model, and 4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate out theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks. PMID:27105653

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Youfang; Terebus, Anna; Liang, Jie

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. Wemore » further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks.« less

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

DOE PAGES

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-04-22

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. Wemore » further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks.« less

Reacting gas mixtures in the state-to-state approach: The chemical reaction rates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kustova, Elena V.; Kremer, Gilberto M.

2014-12-09

In this work chemically reacting mixtures of viscous flows are analyzed within the framework of Boltzmann equation. By applying a modified Chapman-Enskog method to the system of Boltzmann equations general expressions for the rates of chemical reactions and vibrational energy transitions are determined as functions of two thermodynamic forces: the velocity divergence and the affinity. As an application chemically reacting mixtures of N{sub 2} across a shock wave are studied, where the first lowest vibrational states are taken into account. Here we consider only the contributions from the first four single quantum vibrational-translational energy transitions. It is shown that themore » contribution to the chemical reaction rate related to the affinity is much larger than that of the velocity divergence.« less

Density function theoretical study on the complex involved in Th atom-activated C-C bond in C2H6

NASA Astrophysics Data System (ADS)

Qing-Qing, Wang; Peng, Li; Tao, Gao; Hong-Yan, Wang; Bing-Yun, Ao

2016-06-01

Density functional theory (DFT) calculations are performed to investigate the reactivity of Th atom toward ethane C-C bond activation. A comprehensive description of the reaction mechanisms leading to two different reaction products is presented. We report a complete exploration of the potential energy surfaces by taking into consideration different spin states. In addition, the intermediate and transition states along the reaction paths are characterized. Total, partial, and overlap population density of state diagrams and analyses are also presented. Furthermore, the natures of the chemical bonding of intermediate and transition states are studied by using topological method combined with electron localization function (ELF) and Mayer bond order. Infrared spectrum (IR) is obtained and further discussed based on the optimized geometries. Project supported by the National Natural Science Foundation of China (Grant Nos. 21371160, 21401173, and 11364023).

Lifetime and g-factor measurements of excited states using Coulomb excitation and alpha transfer reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guevara, Z. E., E-mail: zjguevaram@unal.edu.co; Torres, D. A., E-mail: datorresg@unal.edu.co

2016-07-07

In this contribution the challenges in the use of a setup to simultaneously measure lifetimes and g-factor values will be presented. The simultaneous use of the transient field technique and the Doppler Shift Attenuation Method, to measure magnetic moments and lifetimes respectively, allows to obtain a complete characterization of the currents of nucleons and the deformation in excited states close to the ground state. The technique is at the moment limited to Coulomb excitation and alpha-transfer reactions, what opens an interesting perspective to consider this type of experiments with radioactive beams. The use of deep-inelastic and fusion-evaporation reactions will bemore » discussed. An example of a setup that makes use of a beam of {sup 106}Cd to study excited states of {sup 110}Sn and the beam nuclei itself will be presented.« less

Method and apparatus for waste destruction using supercritical water oxidation

DOEpatents

Haroldsen, Brent Lowell; Wu, Benjamin Chiau-pin

2000-01-01

The invention relates to an improved apparatus and method for initiating and sustaining an oxidation reaction. A hazardous waste, is introduced into a reaction zone within a pressurized containment vessel. An oxidizer, preferably hydrogen peroxide, is mixed with a carrier fluid, preferably water, and the mixture is heated until the fluid achieves supercritical conditions of temperature and pressure. The heating means comprise cartridge heaters placed in closed-end tubes extending into the center region of the pressure vessel along the reactor longitudinal axis. A cooling jacket surrounds the pressure vessel to remove excess heat at the walls. Heating and cooling the fluid mixture in this manner creates a limited reaction zone near the center of the pressure vessel by establishing a steady state density gradient in the fluid mixture which gradually forces the fluid to circulate internally. This circulation allows the fluid mixture to oscillate between supercritical and subcritical states as it is heated and cooled.

Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications.

PubMed

Behn, Andrew; Zimmerman, Paul M; Bell, Alexis T; Head-Gordon, Martin

2011-12-13

The growing string method is a powerful tool in the systematic study of chemical reactions with theoretical methods which allows for the rapid identification of transition states connecting known reactant and product structures. However, the efficiency of this method is heavily influenced by the choice of interpolation scheme when adding new nodes to the string during optimization. In particular, the use of Cartesian coordinates with cubic spline interpolation often produces guess structures which are far from the final reaction path and require many optimization steps (and thus many energy and gradient calculations) to yield a reasonable final structure. In this paper, we present a new method for interpolating and reparameterizing nodes within the growing string method using the linear synchronous transit method of Halgren and Lipscomb. When applied to the alanine dipeptide rearrangement and a simplified cationic alkyl ring condensation reaction, a significant speedup in terms of computational cost is achieved (30-50%).

Extracting electron transfer coupling elements from constrained density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu Qin; Van Voorhis, Troy

2006-10-28

Constrained density functional theory (DFT) is a useful tool for studying electron transfer (ET) reactions. It can straightforwardly construct the charge-localized diabatic states and give a direct measure of the inner-sphere reorganization energy. In this work, a method is presented for calculating the electronic coupling matrix element (H{sub ab}) based on constrained DFT. This method completely avoids the use of ground-state DFT energies because they are known to irrationally predict fractional electron transfer in many cases. Instead it makes use of the constrained DFT energies and the Kohn-Sham wave functions for the diabatic states in a careful way. Test calculationsmore » on the Zn{sub 2}{sup +} and the benzene-Cl atom systems show that the new prescription yields reasonable agreement with the standard generalized Mulliken-Hush method. We then proceed to produce the diabatic and adiabatic potential energy curves along the reaction pathway for intervalence ET in the tetrathiafulvalene-diquinone (Q-TTF-Q) anion. While the unconstrained DFT curve has no reaction barrier and gives H{sub ab}{approx_equal}17 kcal/mol, which qualitatively disagrees with experimental results, the H{sub ab} calculated from constrained DFT is about 3 kcal/mol and the generated ground state has a barrier height of 1.70 kcal/mol, successfully predicting (Q-TTF-Q){sup -} to be a class II mixed-valence compound.« less

A new, double-inversion mechanism of the F- + CH3Cl SN2 reaction in aqueous solution.

PubMed

Liu, Peng; Wang, Dunyou; Xu, Yulong

2016-11-23

Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry. As a novel, double-inversion mechanism has just been found for the F - + CH 3 Cl S N 2 reaction in the gas phase [Nat. Commun., 2015, 6, 5972], here, using multi-level quantum mechanics methods combined with the molecular mechanics method, we discovered a new, double-inversion mechanism for this reaction in aqueous solution. However, the structures of the stationary points along the reaction path show significant differences from those in the gas phase due to the strong influence of solvent and solute interactions, especially due to the hydrogen bonds formed between the solute and the solvent. More importantly, the relationship between the two double-inversion transition states is not clear in the gas phase, but, here we revealed a novel intermediate complex serving as a "connecting link" between the two transition states of the abstraction-induced inversion and the Walden-inversion mechanisms. A detailed reaction path was constructed to show the atomic-level evolution of this novel double reaction mechanism in aqueous solution. The potentials of mean force were calculated and the obtained Walden-inversion barrier height agrees well with the available experimental value.

Measurement of 17F(d ,n )18Ne and the impact on the 17F(p ,γ )18Ne reaction rate for astrophysics

NASA Astrophysics Data System (ADS)

Kuvin, S. A.; Belarge, J.; Baby, L. T.; Baker, J.; Wiedenhöver, I.; Höflich, P.; Volya, A.; Blackmon, J. C.; Deibel, C. M.; Gardiner, H. E.; Lai, J.; Linhardt, L. E.; Macon, K. T.; Rasco, B. C.; Quails, N.; Colbert, K.; Gay, D. L.; Keeley, N.

2017-10-01

Background: The 17F(p ,γ )18Ne reaction is part of the astrophysical "hot CNO" cycles that are important in astrophysical environments like novas. Its thermal reaction rate is low owing to the relatively high energy of the resonances and therefore is dominated by direct, nonresonant capture in stellar environments at temperatures below 0.4 GK. Purpose: An experimental method is established to extract the proton strength to bound and unbound states in experiments with radioactive ion beams and to determine the parameters of direct and resonant capture in the 17F(p ,γ )18Ne reaction. Method: The 17F(d ,n )18Ne reaction is measured in inverse kinematics using a beam of the short-lived isotope 17F and a compact setup of neutron, proton, γ -ray, and heavy-ion detectors called resoneut. Results: The spectroscopic factors for the lowest l =0 proton resonances at Ec .m .=0.60 and 1.17 MeV are determined, yielding results consistent within 1.4 σ of previous proton elastic-scattering measurements. The asymptotic normalization coefficients of the bound 21+ and 22+ states in 18Ne are determined and the resulting direct-capture reaction rates are extracted. Conclusions: The direct-capture component of the 17F(p ,γ )18Ne reaction is determined for the first time from experimental data on 18Ne.

Reaction Paths and Chemical Activation Reactions of 2-Methyl-5-Furanyl Radical with 3O2.

PubMed

Hudzik, Jason M; Bozzelli, Joseph W

2017-10-05

Interest in high-energy substituted furans has been increasing due to their occurrence in biofuel production and their versatility in conversion to other useful products. Methylfurans are the simplest substituted furans and understanding their reaction pathways, thermochemical properties, including intermediate species stability, and chemical kinetics would aid in the study of larger furans. Furan ring C-H bonds have been shown to be extremely strong, approximately 120 kcal mol -1 , due in part to the placement of the oxygen atom and aromatic-like resonance, both within the ring. The thermochemistry and kinetics of the oxidation of 2-methyfuran radical at position 5 of the furan ring, 2-methyl-5-furanyl radical (2MF5j), is analyzed. The resulting chemically activated species, 2MF5OOj radical, has a well depth of 51 kcal mol -1 below the 2MF5j + O 2 reactants; this is 4-5 kcal mol -1 deeper than that of phenyl and vinyl radical plus O 2 , with both of these reactions known to undergo chain branching. Important, low-energy reaction pathways include chain branching dissociations, intramolecular abstractions, group transfers, and radical oxygen additions. Enthalpies of formation, entropies, and heat capacities for the stable molecules, radicals, and transition-state species are analyzed using computational methods. Calculated ΔH ° f 298 values were determined using an isodesmic work reaction from the CBS-QB3 composite method. Elementary rate parameters are from saddle point transition-state structures and compared to variational transition-state analysis for the barrierless reactions. Temperature- and pressure-dependent rate constants which are calculated using QRRK and master equation analysis is used for falloff and stabilization.

Theoretical investigation of the gas-phase reactions of CrO(+) with ethylene.

PubMed

Scupp, Thomas M; Dudley, Timothy J

2010-01-21

The potential energy surfaces associated with the reactions of chromium oxide cation (CrO(+)) with ethylene have been characterized using density functional, coupled-cluster, and multireference methods. Our calculations show that the most probable reaction involves the formation of acetaldehyde and Cr(+) via a hydride transfer involving the metal center. Our calculations support previous experimental hypotheses that a four-membered ring intermediate plays an important role in the reactivity of the system. We have also characterized a number of viable reaction pathways that lead to other products, including ethylene oxide. Due to the experimental observation that CrO(+) can activate carbon-carbon bonds, a reaction pathway involving C-C bond cleavage has also been characterized. Since many of the reactions involve a change in the spin state in going from reactants to products, locations of these spin surface crossings are presented and discussed. The applicability of methods based on Hartree-Fock orbitals is also discussed.

Chemical looping fluidized-bed concentrating solar power system and method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Zhiwen

A concentrated solar power (CSP) plant comprises a receiver configured to contain a chemical substance for a chemical reaction and an array of heliostats. Each heliostat is configured to direct sunlight toward the receiver. The receiver is configured to transfer thermal energy from the sunlight to the chemical substance in a reduction reaction. The CSP plant further comprises a first storage container configured to store solid state particles produced by the reduction reaction and a heat exchanger configured to combine the solid state particles and gas through an oxidation reaction. The heat exchanger is configured to transfer heat produced inmore » the oxidation reaction to a working fluid to heat the working fluid. The CSP plant further comprises a power turbine coupled to the heat exchanger, such that the heated working fluid turns the power turbine, and a generator coupled to and driven by the power turbine to generate electricity.« less

Perspective on the reactions between F- and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels.

PubMed

Ensing, Bernd; Klein, Michael L

2005-05-10

Recently, we computed the 3D free energy surface of the base-induced elimination reaction between F(-) and CH(3)CH(2)F by using a powerful technique within Car-Parrinello molecular dynamics simulation. Here, the set of three order parameters is expanded to six, which allows the study of the competing elimination and substitution reactions simultaneously. The power of the method is exemplified by the exploration of the six-dimensional free energy landscape, sampling, and mapping out the eight stable states as well as the connecting bottlenecks. The free energy profile and barrier along the E2 and S(N)2 reaction channels are refined by using umbrella sampling. The two mechanisms do not share a common "E2C-like" transition state. Comparison with the zero temperature profiles shows a particularly significant entropy contribution to the S(N)2 channel.

Computed potential energy surfaces for chemical reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Levin, Eugene

1993-01-01

A new global potential energy surface (PES) is being generated for O(P-3) + H2 yields OH + H. This surface is being fit using the rotated Morse oscillator method, which was used to fit the previous POL-CI surface. The new surface is expected to be more accurate and also includes a much more complete sampling of bent geometries. A new study has been undertaken of the reaction N + O2 yields NO + O. The new studies have focused on the region of the surface near a possible minimum corresponding to the peroxy form of NOO. A large portion of the PES for this second reaction has been mapped out. Since state to state cross sections for the reaction are important in the chemistry of high temperature air, these studies will probably be extended to permit generation of a new global potential for reaction.

Re-examining the 26Mg(α ,α')26Mg reaction: Probing astrophysically important states in 26Mg

NASA Astrophysics Data System (ADS)

Adsley, P.; Brümmer, J. W.; Li, K. C. W.; Marín-Lámbarri, D. J.; Kheswa, N. Y.; Donaldson, L. M.; Neveling, R.; Papka, P.; Pellegri, L.; Pesudo, V.; Pool, L. C.; Smit, F. D.; van Zyl, J. J.

2017-11-01

Background: The 22Ne(α ,n )25Mg reaction is one of the neutron sources for the s process in massive stars. The properties of levels in 26Mg above the α -particle threshold control the strengths of the 22Ne(α ,n )25Mg and 22Ne(α ,γ )26Mg reactions. The strengths of these reactions as functions of temperature are one of the major uncertainties in the s process. Purpose: Information on the existence, spin, and parity of levels in 26Mg can assist in constraining the strengths of the 22Ne(α ,γ )26Mg and 22Ne(α ,n )25Mg reactions, and therefore in constraining s -process abundances. Methods: Inelastically scattered α particles from a 26Mg target were momentum-analyzed in the K600 magnetic spectrometer at iThemba LABS, South Africa. The differential cross sections of states were deduced from the focal-plane trajectory of the scattered α particles. Based on the differential cross sections, spin and parity assignments to states are made. Results: A newly assigned 0+ state was observed in addition to a number of other states, some of which can be associated with states observed in other experiments. Some of the deduced Jπ values of the states observed in the present study show discrepancies with those assigned in a similar experiment performed at RCNP Osaka. The reassignments and additions of the various states can strongly affect the reaction rate at low temperatures. Conclusion: The number, location, and assignment of levels in 26Mg that may contribute to the 22Ne+α reactions are not clear. Future experimental investigations of 26Mg must have an extremely good energy resolution to separate the contributions from different levels. Coincidence experiments of 26Mg provide a possible route for future investigations.

Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods.

PubMed

Dong, Geng; Ryde, Ulf

2016-06-01

The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SIa, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14-51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein.

Nonadiabatic dynamics of photo-induced proton-coupled electron transfer reactions via ring-polymer surface hopping

NASA Astrophysics Data System (ADS)

Shakib, Farnaz; Huo, Pengfei

Photo-induced proton-coupled electron transfer reactions (PCET) are at the heart of energy conversion reactions in photocatalysis. Here, we apply the recently developed ring-polymer surface-hopping (RPSH) approach to simulate the nonadiabatic dynamics of photo-induced PCET. The RPSH method incorporates ring-polymer (RP) quantization of the proton into the fewest-switches surface-hopping (FSSH) approach. Using two diabatic electronic states, corresponding to the electron donor and acceptor states, we model photo-induced PCET with the proton described by a classical isomorphism RP. From the RPSH method, we obtain numerical results that are comparable to those obtained when the proton is treated quantum mechanically. This accuracy stems from incorporating exact quantum statistics, such as proton tunnelling, into approximate quantum dynamics. Additionally, RPSH offers the numerical accuracy along with the computational efficiency. Namely, compared to the FSSH approach in vibronic representation, there is no need to calculate a massive number of vibronic states explicitly. This approach opens up the possibility to accurately and efficiently simulate photo-induced PCET with multiple transferring protons or electrons.

Methods for thermodynamic evaluation of battery state of health

DOEpatents

Yazami, Rachid; McMenamin, Joseph; Reynier, Yvan; Fultz, Brent T

2013-05-21

Described are systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and battery systems and for characterizing the state of health of electrodes and battery systems. Measurement of physical attributes of electrodes and batteries corresponding to thermodynamically stabilized electrode conditions permit determination of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and battery systems, such as energy, power density, current rate, cycle life and state of health. Also provided are systems and methods for charging a battery according to its state of health.

Methods and systems for thermodynamic evaluation of battery state of health

DOEpatents

Yazami, Rachid; McMenamin, Joseph; Reynier, Yvan; Fultz, Brent T

2014-12-02

Described are systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and battery systems and for characterizing the state of health of electrodes and battery systems. Measurement of physical attributes of electrodes and batteries corresponding to thermodynamically stabilized electrode conditions permit determination of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and battery systems, such as energy, power density, current rate, cycle life and state of health. Also provided are systems and methods for charging a battery according to its state of health.

Numerical Simulation of the Detonation of Condensed Explosives

NASA Astrophysics Data System (ADS)

Wang, Cheng; Ye, Ting; Ning, Jianguo

Detonation process of a condensed explosive was simulated using a finite difference method. Euler equations were applied to describe the detonation flow field, an ignition and growth model for the chemical reaction and Jones-Wilkins-Lee (JWL) equations of state for the state of explosives and detonation products. Based on the simple mixture rule that assumes the reacting explosives to be a mixture of the reactant and product components, 1D and 2D codes were developed to simulate the detonation process of high explosive PBX9404. The numerical results are in good agreement with the experimental results, which demonstrates that the finite difference method, mixture rule and chemical reaction proposed in this paper are adequate and feasible.

Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

PubMed

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mixed quantum-classical simulation of the hydride transfer reaction catalyzed by dihydrofolate reductase based on a mapped system-harmonic bath model

NASA Astrophysics Data System (ADS)

Xu, Yang; Song, Kai; Shi, Qiang

2018-03-01

The hydride transfer reaction catalyzed by dihydrofolate reductase is studied using a recently developed mixed quantum-classical method to investigate the nuclear quantum effects on the reaction. Molecular dynamics simulation is first performed based on a two-state empirical valence bond potential to map the atomistic model to an effective double-well potential coupled to a harmonic bath. In the mixed quantum-classical simulation, the hydride degree of freedom is quantized, and the effective harmonic oscillator modes are treated classically. It is shown that the hydride transfer reaction rate using the mapped effective double-well/harmonic-bath model is dominated by the contribution from the ground vibrational state. Further comparison with the adiabatic reaction rate constant based on the Kramers theory confirms that the reaction is primarily vibrationally adiabatic, which agrees well with the high transmission coefficients found in previous theoretical studies. The calculated kinetic isotope effect is also consistent with the experimental and recent theoretical results.

The use of solid-state reactions with volume loss to engineer stress and porosity into the fiber-matrix interface of a ceramic composite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hay, R.S.

The effect of the 11 vol% losing during reaction of yttrium-aluminas garnet (YAG) and zirconia was observed in zirconia coated single-crystal alumina fiber-YAG matrix composites. The reaction caused plastic deformation in the alumina fibers, and possibly a minor amount of porosity at fiber-matrix interfaces that was usually indistinguishable from matrix porosity. The results were analyzed by models for diffusive cavitation modified to use reaction self-stress. Crack-healing, tensile stress states along the reaction front that approach plane stress, and the small volume of self-stressed material make crack-like pores unlikely at the high temperatures required for reaction. Smaller matrix grains might promotemore » formation of smaller cavities but are also incompatible with high temperature. Both modeling and experiment suggest that sufficient porosity for crack deflection and fiber pullout cannot form unless processing methods that form dense composites at lower temperatures are used.« less

Kinetics and dynamics of the C(3P) + H2O reaction on a full-dimensional accurate triplet state potential energy surface.

PubMed

Li, Jun; Xie, Changjian; Guo, Hua

2017-08-30

A full dimensional accurate potential energy surface (PES) for the C( 3 P) and H 2 O 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.

The size effect to O2- -Ce4+ charge transfer emission and band gap structure of Sr2 CeO4.

PubMed

Wang, Wenjun; Pan, Yu; Zhang, Wenying; Liu, Xiaoguang; Li, Ling

2018-04-24

Sr 2 CeO 4 phosphors with different crystalline sizes were synthesized by the sol-gel method or the solid-state reaction. Their crystalline size, luminescence intensity of O 2- -Ce 4+ charge transfer and energy gaps were obtained through the characterization by X-ray diffraction, photoluminescence spectra, as well as UV-visible diffuse reflectance measurements. An inverse relationship between photoluminescence (PL) spectra and crystalline size was observed when the heating temperature was from 1000°C to 1300°C. In addition, band energy calculated for all samples showed that a reaction temperature of 1200°C for the solid-state method and 1100°C for sol-gel method gave the largest values, which corresponded with the smallest crystalline size. Correlation between PL intensity and crystalline size showed an inverse relationship. Band structure, density of states and partial density of states of the crystal were calculated to analyze the mechanism using the cambrige sequential total energy package (CASTEP) module integrated with Materials Studio software. Copyright © 2018 John Wiley & Sons, Ltd.

State-resolved differential and integral cross sections for the Ne + H{sub 2}{sup +} (v = 0–2, j = 0) → NeH{sup +} + H reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Hui; Yao, Cui-Xia; He, Xiao-Hu

State-to-state quantum dynamic calculations for the proton transfer reaction Ne + H{sub 2}{sup +} (v = 0–2, j = 0) are performed on the most accurate LZHH potential energy surface, with the product Jacobi coordinate based time-dependent wave packet method including the Coriolis coupling. The J = 0 reaction probabilities for the title reaction agree well with previous results in a wide range of collision energy of 0.2-1.2 eV. Total integral cross sections are in reasonable agreement with the available experiment data. Vibrational excitation of the reactant is much more efficient in enhancing the reaction cross sections than translational andmore » rotational excitation. Total differential cross sections are found to be forward-backward peaked with strong oscillations, which is the indication of the complex-forming mechanism. As the collision energy increases, state-resolved differential cross section changes from forward-backward symmetric peaked to forward scattering biased. This forward bias can be attributed to the larger J partial waves, which makes the reaction like an abstraction process. Differential cross sections summed over two different sets of J partial waves for the v = 0 reaction at the collision energy of 1.2 eV are plotted to illustrate the importance of large J partial waves in the forward bias of the differential cross sections.« less

Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.

PubMed

Khavrutskii, Ilja V; Smith, Jason B; Wallqvist, Anders

2013-10-28

Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM∕molecular mechanical (QM∕MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP∕6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP∕6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal∕mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM∕MM studies of reaction mechanisms.

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

PubMed Central

Cao, Youfang; Liang, Jie

2013-01-01

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape. PMID:23862966

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

NASA Astrophysics Data System (ADS)

Cao, Youfang; Liang, Jie

2013-07-01

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape.

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method.

PubMed

Cao, Youfang; Liang, Jie

2013-07-14

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape.

An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis.

PubMed

Varela, J A; Vázquez, S A; Martínez-Núñez, E

2017-05-01

A novel computational method is proposed in this work for use in discovering reaction mechanisms and solving the kinetics of transition metal-catalyzed reactions. The method does not rely on either chemical intuition or assumed a priori mechanisms, and it works in a fully automated fashion. Its core is a procedure, recently developed by one of the authors, that combines accelerated direct dynamics with an efficient geometry-based post-processing algorithm to find transition states (Martinez-Nunez, E., J. Comput. Chem. 2015 , 36 , 222-234). In the present work, several auxiliary tools have been added to deal with the specific features of transition metal catalytic reactions. As a test case, we chose the cobalt-catalyzed hydroformylation of ethylene because of its well-established mechanism, and the fact that it has already been used in previous automated computational studies. Besides the generally accepted mechanism of Heck and Breslow, several side reactions, such as hydrogenation of the alkene, emerged from our calculations. Additionally, the calculated rate law for the hydroformylation reaction agrees reasonably well with those obtained in previous experimental and theoretical studies.

Stochastic surface walking reaction sampling for resolving heterogeneous catalytic reaction network: A revisit to the mechanism of water-gas shift reaction on Cu

NASA Astrophysics Data System (ADS)

Zhang, Xiao-Jie; Shang, Cheng; Liu, Zhi-Pan

2017-10-01

Heterogeneous catalytic reactions on surface and interfaces are renowned for ample intermediate adsorbates and complex reaction networks. The common practice to reveal the reaction mechanism is via theoretical computation, which locates all likely transition states based on the pre-guessed reaction mechanism. Here we develop a new theoretical method, namely, stochastic surface walking (SSW)-Cat method, to resolve the lowest energy reaction pathway of heterogeneous catalytic reactions, which combines our recently developed SSW global structure optimization and SSW reaction sampling. The SSW-Cat is automated and massively parallel, taking a rough reaction pattern as input to guide reaction search. We present the detailed algorithm, discuss the key features, and demonstrate the efficiency in a model catalytic reaction, water-gas shift reaction on Cu(111) (CO + H2O → CO2 + H2). The SSW-Cat simulation shows that water dissociation is the rate-determining step and formic acid (HCOOH) is the kinetically favorable product, instead of the observed final products, CO2 and H2. It implies that CO2 and H2 are secondary products from further decomposition of HCOOH at high temperatures. Being a general purpose tool for reaction prediction, the SSW-Cat may be utilized for rational catalyst design via large-scale computations.

Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

NASA Technical Reports Server (NTRS)

Oie, T.; Loew, G. H.; Burt, S. K.; MacElroy, R. D.

1984-01-01

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.

γ-ray decay from neutron-bound and unbound states in 95Mo and a novel technique for spin determination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiedeking, M.; Krticka, M.; Bernstein, L. A.

2016-02-01

The emission of γ rays from neutron-bound and neutron-unbound states in 95Mo, populated in the 94Mo(d,p) reaction, has been investigated. Charged particles and γ radiation were detected with arrays of annular silicon and Clover-type high-purity Germanium detectors, respectively. Utilizing p-γ and p-γ-γ coincidences, the 95Mo level scheme was greatly enhanced with 102 new transitions and 43 new states. It agrees well with shell model calculations for excitation energies below ≈2 MeV. From p-γ coincidence data, a new method for the determination of spins of discrete levels is proposed. The method exploits the suppression of high-angular momentum neutron emission from levelsmore » with high spins populated in the (d,p) reaction above the neutron separation energy. As a result, spins for almost all 95Mo levels below 2 MeV (and for a few levels above) have been determined with this method.« less

Amorphous and nanocrystalline luminescent Si and Ge obtained via a solid-state chemical metathesis synthesis route

NASA Astrophysics Data System (ADS)

McMillan, Paul F.; Gryko, Jan; Bull, Craig; Arledge, Richard; Kenyon, Anthony J.; Cressey, Barbara A.

2005-03-01

A new solid-state metathesis synthesis route was applied to obtain bulk samples of amorphous or microcrystalline Si and Ge. The method involves reaction of Zintl phases such as NaSi or NaGe, with ammonium or metal (e.g., CuCl, CoBr 2) halides. The driving force for the solid-state reaction is provided by the formation of alkali halides and the transition metals or metal silicides, or gaseous ammonia and hydrogen. The semiconductors were purified by washing to remove other solid products. The amorphous semiconductors were obtained in bulk form from reactions carried out at 200-300 °C. Syntheses at higher temperatures gave rise to microcrystalline semiconductors, or to micro-/nanocrystalline particles contained within the amorphous material. Similar crystalline/amorphous composites were obtained after heat treatment of bulk amorphous materials.

Elementary reaction profile and chemical kinetics study of [C(1D)/(3P) + SiH4] with the CCSD(T) method

NASA Astrophysics Data System (ADS)

Ranka, Karnamohit; Perera, Ajith; Bartlett, Rodney J.

2017-07-01

Carbon and silicon-based molecules are omnipresent in the fields of combustion, atmospheric, semiconductor, and astronomical chemistry, among others. This paper reports the underlying elementary reactions for the [C(1D) + SiH4] and [C(3P) + SiH4] reaction profiles, optimized geometries of the intermediates, transition states (at the CCSD(T) level), RRKM and TST rate constants, and the corresponding branching ratios. Previously unreported van der Waals complex intermediates have been found for both reactions.

Freeze-quench (57)Fe-Mössbauer spectroscopy: trapping reactive intermediates.

PubMed

Krebs, Carsten; Bollinger, J Martin

2009-01-01

(57)Fe-Mössbauer spectroscopy is a method that probes transitions between the nuclear ground state (I=1/2) and the first nuclear excited state (I=3/2). This technique provides detailed information about the chemical environment and electronic structure of iron. Therefore, it has played an important role in studies of the numerous iron-containing proteins and enzymes. In conjunction with the freeze-quench method, (57)Fe-Mössbauer spectroscopy allows for monitoring changes of the iron site(s) during a biochemical reaction. This approach is particularly powerful for detection and characterization of reactive intermediates. Comparison of experimentally determined Mössbauer parameters to those predicted by density functional theory for hypothetical model structures can then provide detailed insight into the structures of reactive intermediates. We have recently used this methodology to study the reactions of various mononuclear non-heme-iron enzymes by trapping and characterizing several Fe(IV)-oxo reaction intermediates. In this article, we summarize these findings and demonstrate the potential of the method. © Springer Science+Business Media B.V. 2009

A comparison of the effects of caffeine following abstinence and normal caffeine use

PubMed Central

Addicott, Merideth A.

2010-01-01

Rationale Caffeine typically produces positive effects on mood and performance. However, tolerance may develop following habitual use, and abrupt cessation can result in withdrawal symptoms, such as fatigue. This study investigated whether caffeine has a greater stimulant effect in a withdrawn state compared to a normal caffeinated state, among moderate daily caffeine consumers. Materials and methods Using a within-subjects design, 17 caffeine consumers (mean±sd=375±101 mg/day) ingested placebo or caffeine (250 mg) following 30-h of caffeine abstention or normal dietary caffeine use on four separate days. Self-reported mood and performance on choice reaction time, selective attention, and memory tasks were measured. Results Caffeine had a greater effect on mood and choice reaction time in the abstained state than in the normal caffeinated state, but caffeine improved selective attention and memory in both states. Conclusions Although improvements in mood and reaction time may best explained as relief from withdrawal symptoms, other performance measures showed no evidence of withdrawal and were equally sensitive to an acute dose of caffeine in the normal caffeinated state. PMID:19777214

Analytical Solution of Steady State Equations for Chemical Reaction Networks with Bilinear Rate Laws

PubMed Central

Halász, Ádám M.; Lai, Hong-Jian; McCabe, Meghan M.; Radhakrishnan, Krishnan; Edwards, Jeremy S.

2014-01-01

True steady states are a rare occurrence in living organisms, yet their knowledge is essential for quasi-steady state approximations, multistability analysis, and other important tools in the investigation of chemical reaction networks (CRN) used to describe molecular processes on the cellular level. Here we present an approach that can provide closed form steady-state solutions to complex systems, resulting from CRN with binary reactions and mass-action rate laws. We map the nonlinear algebraic problem of finding steady states onto a linear problem in a higher dimensional space. We show that the linearized version of the steady state equations obeys the linear conservation laws of the original CRN. We identify two classes of problems for which complete, minimally parameterized solutions may be obtained using only the machinery of linear systems and a judicious choice of the variables used as free parameters. We exemplify our method, providing explicit formulae, on CRN describing signal initiation of two important types of RTK receptor-ligand systems, VEGF and EGF-ErbB1. PMID:24334389

A reaction-diffusion model of the Darien Gap Sterile Insect Release Method

NASA Astrophysics Data System (ADS)

Alford, John G.

2015-05-01

The Sterile Insect Release Method (SIRM) is used as a biological control for invasive insect species. SIRM involves introducing large quantities of sterilized male insects into a wild population of invading insects. A fertile/sterile mating produces offspring that are not viable and the wild insect population will eventually be eradicated. A U.S. government program maintains a permanent sterile fly barrier zone in the Darien Gap between Panama and Columbia to control the screwworm fly (Cochliomyia Hominivorax), an insect that feeds off of living tissue in mammals and has devastating effects on livestock. This barrier zone is maintained by regular releases of massive quantities of sterilized male screwworm flies from aircraft. We analyze a reaction-diffusion model of the Darien Gap barrier zone. Simulations of the model equations yield two types of spatially inhomogeneous steady-state solutions representing a sterile fly barrier that does not prevent invasion and a barrier that does prevent invasion. We investigate steady-state solutions using both phase plane methods and monotone iteration methods and describe how barrier width and the sterile fly release rate affects steady-state behavior.

Feeding of Rh and Ag isomers in fast-neutron-induced reactions

NASA Astrophysics Data System (ADS)

Fotiades, N.; Devlin, M.; Nelson, R. O.; Kawano, T.; Carroll, J. J.

2016-10-01

Background: In (n ,n' ) reactions on stable Ir and Au isotopes in the mass A =190 region, the experimentally established feeding of the isomers relative to the feeding of the corresponding ground states increases with increasing neutron energy, up to the neutron energy where the (n ,2 n ) reaction channel opens up, and then decreases. Purpose: In order to check for similar behavior in the mass A =100 region, the feeding of isomers and ground states in fast-neutron-induced reactions on stable isotopes in this mass region was studied. This is of especial interest for Rh which can be used as a radiochemical detector. Methods: Excited states were studied using the (n ,n'γ ), (n ,2 n γ ), and (n ,3 n γ ) reactions on 103Rh and 109Ag. A germanium detector array for γ -ray detection and the broad-spectrum pulsed neutron source of the Los Alamos Neutron Science Center's Weapons Neutron Research facility were used for the measurement. The energy of the incident neutrons was determined using the time-of-flight technique. Results: Absolute partial γ -ray cross sections were measured for 57 transitions feeding isomers and ground states in 101,102,103Rh and 107,108,109Ag. The feeding of the isomers was found to be very similar in the corresponding reaction channels and it is compared to the feeding determined for the ground states. Conclusions: The opening of reaction channels at higher neutron energies removes angular momentum from the residual nucleus and reduces the population of the higher-spin isomers relative to the feeding of the lower-spin ground states. Similar behavior was observed in the mass A =190 region in the feeding of higher-spin isomers, but the reverse behavior was observed in 176Lu with a lower-spin isomer and a higher-spin ground state.

Theoretical chemical kinetic study of the H-atom abstraction reactions from aldehydes and acids by Ḣ atoms and ȮH, HȮ2, and ĊH3 radicals.

PubMed

Mendes, Jorge; Zhou, Chong-Wen; Curran, Henry J

2014-12-26

We have performed a systematic, theoretical chemical kinetic investigation of H atom abstraction by Ḣ atoms and ȮH, HȮ2, and ĊH3 radicals from aldehydes (methanal, ethanal, propanal, and isobutanal) and acids (methanoic acid, ethanoic acid, propanoic acid, and isobutanoic acid). The geometry optimizations and frequencies of all of the species in the reaction mechanisms of the title reactions were calculated using the MP2 method and the 6-311G(d,p) basis set. The one-dimensional hindered rotor treatment for reactants and transition states and the intrinsic reaction coordinate calculations were also determined at the MP2/6-311G(d,p) level of theory. For the reactions of methanal and methanoic acid with Ḣ atoms and ȮH, HȮ2, and ĊH3 radicals, the calculated relative electronic energies were obtained with the CCSD(T)/cc-pVXZ (where X = D, T, and Q) method and were extrapolated to the complete basis set limit. The electronic energies obtained with the CCSD(T)/cc-pVTZ method were benchmarked against the CCSD(T)/CBS energies and were found to be within 1 kcal mol(-1) of one another. Thus, the energies calculated using the less expensive CCSD(T)/cc-pVTZ method were used in all of the reaction mechanisms and in calculating our high-pressure limit rate constants for the title reactions. Rate constants were calculated using conventional transition state theory with an asymmetric Eckart tunneling correction, as implemented in Variflex. Herein, we report the individual and average rate constants, on a per H atom basis, and total rate constants in the temperature range 500-2000 K. We have compared some of our rate constant results to available experimental and theoretical data, and our results are generally in good agreement.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oshima, Masumi; Kin, Tadahiro; Kimura, Atsushi

Multi-step cascades from the {sup 62}Ni(n{sub cold},{gamma}) {sup 63}Ni reaction were studied via a {gamma}-ray spectroscopy method. With a {gamma}-ray detector array multiple {gamma}-ray coincident events were accumulated. By selecting full cascade events from the capture state to the ground state, we have developed a new computer-based level construction method and it is applied to excited level assignment in {sup 63}Ni.

Using constrained information entropy to detect rare adverse drug reactions from medical forums.

PubMed

Yi Zheng; Chaowang Lan; Hui Peng; Jinyan Li

2016-08-01

Adverse drug reactions (ADRs) detection is critical to avoid malpractices yet challenging due to its uncertainty in pre-marketing review and the underreporting in post-marketing surveillance. To conquer this predicament, social media based ADRs detection methods have been proposed recently. However, existing researches are mostly co-occurrence based methods and face several issues, in particularly, leaving out the rare ADRs and unable to distinguish irrelevant ADRs. In this work, we introduce a constrained information entropy (CIE) method to solve these problems. CIE first recognizes the drug-related adverse reactions using a predefined keyword dictionary and then captures high- and low-frequency (rare) ADRs by information entropy. Extensive experiments on medical forums dataset demonstrate that CIE outperforms the state-of-the-art co-occurrence based methods, especially in rare ADRs detection.

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu, E-mail: okazaki@apchem.nagoya-u.ac.jp

2014-08-28

In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfermore » process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps{sup −1}, which is about 2.5 times faster than that in vacuum, 0.27 ps{sup −1}. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction.« less

Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory.

PubMed

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 for the reactions with a halogen leaving group. This presumably is found because of the bulky (sterically hindered) leaving group in the tosylate reaction. From every prospective, the tosylate reaction is too different from the halogen reactions to be compared.

Nonequilibrium thermodynamics and a fluctuation theorem for individual reaction steps in a chemical reaction network

NASA Astrophysics Data System (ADS)

Pal, Krishnendu; Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam

2015-09-01

We have introduced an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the propensities of the individual elementary reactions and the corresponding reverse reactions. The method is a microscopic formulation of the dissipation function in terms of the relative entropy or Kullback-Leibler distance which is based on the analogy of phase space trajectory with the path of elementary reactions in a network of chemical process. We have introduced here a fluctuation theorem valid for each opposite pair of elementary reactions which is useful in determining the contribution of each sub-reaction on the nonequilibrium thermodynamics of overall reaction. The methodology is applied to an oligomeric enzyme kinetics at a chemiostatic condition that leads the reaction to a nonequilibrium steady state for which we have estimated how each step of the reaction is energy driven or entropy driven to contribute to the overall reaction.

An analytical derivation of MC-SCF vibrational wave functions for the quantum dynamical simulation of multiple proton transfer reactions: Initial application to protonated water chains

NASA Astrophysics Data System (ADS)

Drukker, Karen; Hammes-Schiffer, Sharon

1997-07-01

This paper presents an analytical derivation of a multiconfigurational self-consistent-field (MC-SCF) solution of the time-independent Schrödinger equation for nuclear motion (i.e. vibrational modes). This variational MC-SCF method is designed for the mixed quantum/classical molecular dynamics simulation of multiple proton transfer reactions, where the transferring protons are treated quantum mechanically while the remaining degrees of freedom are treated classically. This paper presents a proof that the Hellmann-Feynman forces on the classical degrees of freedom are identical to the exact forces (i.e. the Pulay corrections vanish) when this MC-SCF method is used with an appropriate choice of basis functions. This new MC-SCF method is applied to multiple proton transfer in a protonated chain of three hydrogen-bonded water molecules. The ground state and the first three excited state energies and the ground state forces agree well with full configuration interaction calculations. Sample trajectories are obtained using adiabatic molecular dynamics methods, and nonadiabatic effects are found to be insignificant for these sample trajectories. The accuracy of the excited states will enable this MC-SCF method to be used in conjunction with nonadiabatic molecular dynamics methods. This application differs from previous work in that it is a real-time quantum dynamical nonequilibrium simulation of multiple proton transfer in a chain of water molecules.

Geometrical Optimization Approach to Isomerization: Models and Limitations.

PubMed

Chang, Bo Y; Shin, Seokmin; Engel, Volker; Sola, Ignacio R

2017-11-02

We study laser-driven isomerization reactions through an excited electronic state using the recently developed Geometrical Optimization procedure. Our goal is to analyze whether an initial wave packet in the ground state, with optimized amplitudes and phases, can be used to enhance the yield of the reaction at faster rates, driven by a single picosecond pulse or a pair of femtosecond pulses resonant with the electronic transition. We show that the symmetry of the system imposes limitations in the optimization procedure, such that the method rediscovers the pump-dump mechanism.

Variational transition state theory: theoretical framework and recent developments.

PubMed

Bao, Junwei Lucas; Truhlar, Donald G

2017-12-11

This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications. The theoretical methods reviewed here include multidimensional quantum mechanical tunneling, multistructural VTST (MS-VTST), multi-path VTST (MP-VTST), both reaction-path VTST (RP-VTST) and variable reaction coordinate VTST (VRC-VTST), system-specific quantum Rice-Ramsperger-Kassel theory (SS-QRRK) for predicting pressure-dependent rate constants, and VTST in the solid phase, liquid phase, and enzymes. We also provide some perspectives regarding the general applicability of VTST.

Surface-mediated nucleation in the solid-state polymorph transformation of terephthalic acid.

PubMed

Beckham, Gregg T; Peters, Baron; Starbuck, Cindy; Variankaval, Narayan; Trout, Bernhardt L

2007-04-18

A molecular mechanism for nucleation for the solid-state polymorph transformation of terephthalic acid is presented. New methods recently developed in our group, aimless shooting and likelihood maximization, are employed to construct a model for the reaction coordinate for the two system sizes studied. The reaction coordinate approximation is validated using the committor probability analysis. The transformation proceeds via a localized, elongated nucleus along the crystal edge formed by fluctuations in the supramolecular synthons, suggesting a nucleation and growth mechanism in the macroscopic system.

Method of realizing catalytic processes under unsteady state conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noskov, A.S.; Lakhmostov, V.S.; Matros, Yu.S.

1988-07-01

The operation of a system with the catalyst bed divided into three parts was investigated theoretically and experimentally. The conditions under which the system will efficiently convert a reaction mixture with a low inlet temperature in an unsteady state regime are determined. Calculations were performed for the industrially typical process of afterburning CO on a copper-chrome catalyst in the form of Raschig rings. A flow sheet of the unit with the catalyst divided into three is shown with temperature profiles along the bed at various moments in time. The method can be used for processing large volumes of gaseous wastesmore » on very active catalysts and for catalytic reactions with optimum temperature profiles close to those presented.« less

Kinetic and mechanisms of methanimine reactions with singlet and triplet molecular oxygen: Substituent and catalyst effects

NASA Astrophysics Data System (ADS)

Asgharzadeh, Somaie; Vahedpour, Morteza

2018-06-01

Methanimine reaction with O2 on singlet and triplet potential energy surfaces are investigated using B3PW91, M06-2X, MP2 and CCSD(T) methods. Thermodynamic and kinetic parameters are calculated at M06-2X method. The most favorable channel involves H-abstraction of CH2NH+O2 to the formation of HCN + H2O2 products via low level energy barrier. The catalytic effect of water molecule on HCN + H2O2 products pathway are investigated. Result shows that contribution of water molecule using complex formation with methanimine can decreases barrier energy of transition state and the reaction rate increases. Also, substituent effect of fluorine atom as deactivating group are investigated on the main reaction pathway.

Human beings' adaptability to extreme environmental changes from medical and physical points of view

NASA Astrophysics Data System (ADS)

Khabarova, Olga; Ragulskaya, Maria; Dimitrova, Svetla; Safaraly-Oghlu Babayev, Elchin; Samsonov, Sergey; Med. Dimitry Markov, Of; Nazarova, Of Med. Olga N.; Rudenchik, Evgeny

The question about features of human reaction on the sharp environmental physical activity (EPA) changes is considered by international group of physicists and physicians on the base of results of monitoring of human health state in different cities spread on latitude and longitude. The typical reaction of human body on the influences, exceeding the organisms' ability to adaptation, is of stress-reaction character. From medical point of view there is no significant difference for human body -what external (EPA) agent shocked an organism (emotional or some physical threats). First attempt of the organism to restore its homeostasis is stress-reaction, being universal for many stress-factors. Its main stages (such as alarm, resistance, and exhaustion) are detectable by different medical equipments, but we tried to find universal, non-traumatic method of daily measurements, enough sensitive and appropriate for observation of people reaction both on weather and space weather (geomagnetic activity) changes. The experiment was based on a method of electrical conductivity measurements of biologically active (acupunctural) points of human skin. The used method (electroacupunctural method by Dr. R.Voll) is very sensitive to current state of an organism and characterize the functional condition of different organs and systems of human body and allows to express so-called "group's health status" in the units, suitable for comparison with meteorological and heliogeophysical parameters. We conduct the parallel investigations as a part of collaborative study in different geographic latitudes-longitudes (Baku:40° 23'43"N -49° 52'56"E, Troitsk (Moscow region): 55° 28'40"N -37° 18'42"E, Yakutsk: 62° 02'00"N -129° 44'00"E). Measurements were carried out on daily basis with permanent group of functionally healthy persons (Moscow -19, Yakutsk -22, CityBaku -12 volunteers). Daily monitoring of nervous, endocrinological, lymphatic systems, blood, lungs, thick and thin intestine, heart and parenhimatic organs, allergy and hypophisis was conducted simultaneously with analyses of space weather (parameters of solar and geomagnetic activities) as well as local meteorological parameters (temperature, atmospheric pressure, humidity, wind speed, etc.). It was proved that it is possible to consider not only weather changes but also geomagnetic field variations as a stressor. It is concluded that : 1. human reaction on the sharp changes of selected external (environmental) physical activity parameters goes like typical stress-reaction; 2. features of stress-reaction depend on history of previous failures of an organism and on state of external background (frequent stresses deplete human organism possibility to adaptation); 3. features of stress-reaction depend on the geographic location (latitude). Possible physi-cal explanation of human organism stress-reaction on changes of geomagnetic oscillatory regime and atmospheric thermobaric variations is discussed.

Study on monostable and bistable reaction-diffusion equations by iteration of travelling wave maps

NASA Astrophysics Data System (ADS)

Yi, Taishan; Chen, Yuming

2017-12-01

In this paper, based on the iterative properties of travelling wave maps, we develop a new method to obtain spreading speeds and asymptotic propagation for monostable and bistable reaction-diffusion equations. Precisely, for Dirichlet problems of monostable reaction-diffusion equations on the half line, by making links between travelling wave maps and integral operators associated with the Dirichlet diffusion kernel (the latter is NOT invariant under translation), we obtain some iteration properties of the Dirichlet diffusion and some a priori estimates on nontrivial solutions of Dirichlet problems under travelling wave transformation. We then provide the asymptotic behavior of nontrivial solutions in the space-time region for Dirichlet problems. These enable us to develop a unified method to obtain results on heterogeneous steady states, travelling waves, spreading speeds, and asymptotic spreading behavior for Dirichlet problem of monostable reaction-diffusion equations on R+ as well as of monostable/bistable reaction-diffusion equations on R.

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method.

PubMed

Nakata, Hiroya; Fedorov, Dmitri G; Nagata, Takeshi; Kitaura, Kazuo; Nakamura, Shinichiro

2015-07-14

The fully analytic first and second derivatives of the energy in the frozen domain formulation of the fragment molecular orbital (FMO) were developed and applied to locate transition states and determine vibrational contributions to free energies. The development is focused on the frozen domain with dimers (FDD) model. The intrinsic reaction coordinate method was interfaced with FMO. Simulations of IR and Raman spectra were enabled using FMO/FDD by developing the calculation of intensities. The accuracy is evaluated for S(N)2 reactions in explicit solvent, and for the free binding energies of a protein-ligand complex of the Trp cage protein (PDB: 1L2Y ). FMO/FDD is applied to study the keto-enol tautomeric reaction of phosphoglycolohydroxamic acid and the triosephosphate isomerase (PDB: 7TIM ), and the role of amino acid residue fragments in the reaction is discussed.

Reaction mechanism studies towards effective fabrication of lithium-rich anti-perovskites Li 3OX (X=Cl, Br)

DOE PAGES

Li, Shuai; Zhu, Jinlong; Wang, Yonggang; ...

2015-12-10

Lithium-rich Anti-perovskite (LiRAP), with general formula Li 3OX (X = Cl, Br, I), and recently reported as superionic conductors with 3-dimensional Li + migrating channels, is emerging as a promising candidate for solid electrolyte of all-solid-state LIBs. But, it is still difficult to fabricate pure LiRAP due to the difficulty of the phase formation and moisture-sensitive nature of the products. In this work, we thoroughly studied the formation mechanism of Li 3OCl and Li 3OBr in various solid state reaction routes. We developed different experimental strategies in order to improve the syntheses, in purposes of improved phase stability and large-scalemore » production of LiRAP. One feasible method is to use strongly reductive agents Li metal or LiH to eliminate OH species. The results show that LiH is more effective than Li metal because of negatively charged H - and uniform reaction. The other well-established method is using Li 2O and LiX mixture as reagents to preventing OH phase at the beginning, and using protected ball milling to make fine powders and hence active the reaction. Finally, IR spectroscopy, thermal analyses and first-principle calculation were performed to give indications on the reaction pathway.« less

Theories of time-dependent and time-independent nearside-farside reactive scattering dynamics

NASA Astrophysics Data System (ADS)

Monks, Phillip David Durrant

The first application of nearside-farside (NF) theory is made to the time-dependent partial wave series (PWS) representation of the scattering amplitude for the reaction H + D[2](v = 0,j = 0, m = 0) → HD(v' = 3,j' = 0, m'= 0) + D. Time-dependent NF angular distributions and time-dependent NF local angular momenta (LAMs) are defined and used to analyse the dynamics in terms of time- direct and time-delayed reaction mechanisms. The concept of a cumulative time-evolving differential cross section (DCS) is introduced and used to provide a new method for visualising the time evolution of a chemical reaction. Time-independent NF DCS and LAM analyses of the H + D[2] reaction are presented, highlighting a distinctive "trench-ridge" feature present in the full and N LAMs. It is used to define a cut line which separates the energy-analogs of the two time- distinct reaction mechanisms. This trench-ridge feature is shown to be an interference between the time-direct (backward-scattered) and time-delayed (forward-scattered) reaction mechanisms. Resummation PWS theory is used to "clean" plots of the NF DCSs and LAMs of unphysical effects. A limitation of the resummation theory is described, whereby unphysical behaviour is sometimes introduced into the N and F subamplitudes. A technique for predicting and avoiding these undesired effects is used to further improve the usefulness of the resummation technique. The fundamental identity for NF local angular momenta is stated and derived by two methods. This identity gives rise to a CLAM plot (where CLAM denotes Cross section x LAM), which provides insight into the empirical obsei'vation that DCS and LAM analyses give consistent, yet complementary, information on the reaction dynamics. Applications are reported for the H + D[2] reaction, as well as for F + H[2](v = 0,j=0, m = 0)→ FH(v' = 3,j' = 3, m' = 0) + H. The angular time-delay for a state-to-state reactive collision often displays complicated behaviour. It is shown for the H + D[2] and F + H[2] reactions that this behaviour is caused by NF interference. The fundamental identity for NF angular time-delays is stated, and CATD (Cross section x Angular Time-Delay) results are reported, which provide further insight into the properties of the angular time-delay.

Can Chlorine Anion Catalyze the Reaction fo HOCl with HCl?

NASA Technical Reports Server (NTRS)

Richardson, S. L.; Francisco, J. S.; Mebel, A. M.; Morokuma, K.

1997-01-01

The reaction of HOCl + HCl -> Cl2 + H20 in the presence of Cl has been studied using ab initio methods. This reaction has been shown to have a high activation barrier of 46.5 kcal/mol. The chlorine anion, Cl- is found to catalyze the reaction, viz. two mechanisms. The first involves Cl- interacting through the concerted four-center transition state of the neutral reaction. The other mechanism involves the formation of a HCl-HOCl-Cl- intermediate which dissociates into Cl2 + Cl- + H20. The steps are found to have no barriers. The overall exothermicity is 15.5 kcal/mol.

Combinatorial pattern discovery approach for the folding trajectory analysis of a beta-hairpin.

PubMed

Parida, Laxmi; Zhou, Ruhong

2005-06-01

The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated) approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters)-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity c in RO((N + nm) log n), where N is the size of the output patterns and (n x m) is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1) The method recovers states previously obtained by visually analyzing free energy surfaces. (2) It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3) The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the choice of reaction coordinates. (An abstract version of this work was presented at the 2005 Asia Pacific Bioinformatics Conference [1].).

Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics.

PubMed

Gani, Terry Z H; Kulik, Heather J

2017-11-14

Accurate predictions of spin-state ordering, reaction energetics, and barrier heights are critical for the computational discovery of open-shell transition-metal (TM) catalysts. Semilocal approximations in density functional theory, such as the generalized gradient approximation (GGA), suffer from delocalization error that causes them to overstabilize strongly bonded states. Descriptions of energetics and bonding are often improved by introducing a fraction of exact exchange (e.g., erroneous low-spin GGA ground states are instead correctly predicted as high-spin with a hybrid functional). The degree of spin-splitting sensitivity to exchange can be understood based on the chemical composition of the complex, but the effect of exchange on reaction energetics within a single spin state is less well-established. Across a number of model iron complexes, we observe strong exchange sensitivities of reaction barriers and energies that are of the same magnitude as those for spin splitting energies. We rationalize trends in both reaction and spin energetics by introducing a measure of delocalization, the bond valence of the metal-ligand bonds in each complex. The bond valence thus represents a simple-to-compute property that unifies understanding of exchange sensitivity for catalytic properties and spin-state ordering in TM complexes. Close agreement of the resulting per-metal-organic-bond sensitivity estimates, together with failure of alternative descriptors demonstrates the utility of the bond valence as a robust descriptor of how differences in metal-ligand delocalization produce differing relative energetics with exchange tuning. Our unified description explains the overall effect of exact exchange tuning on the paradigmatic two-state FeO + /CH 4 reaction that combines challenges of spin-state and reactivity predictions. This new descriptor-sensitivity relationship provides a path to quantifying how predictions in transition-metal complex screening are sensitive to the method used.

The 1,5-H-shift in 1-butoxy: A case study in the rigorous implementation of transition state theory for a multirotamer system

NASA Astrophysics Data System (ADS)

Vereecken, Luc; Peeters, Jozef

2003-09-01

The rigorous implementation of transition state theory (TST) for a reaction system with multiple reactant rotamers and multiple transition state conformers is discussed by way of a statistical rate analysis of the 1,5-H-shift in 1-butoxy radicals, a prototype reaction for the important class of H-shift reactions in atmospheric chemistry. Several approaches for deriving a multirotamer TST expression are treated: oscillator versus (hindered) internal rotor models; distinguishable versus indistinguishable atoms; and direct count methods versus degeneracy factors calculated by (simplified) direct count methods or from symmetry numbers and number of enantiomers, where applicable. It is shown that the various treatments are fully consistent, even if the TST expressions themselves appear different. The 1-butoxy H-shift reaction is characterized quantum chemically using B3LYP-DFT; the performance of this level of theory is compared to other methods. Rigorous application of the multirotamer TST methodology in an harmonic oscillator approximation based on this data yields a rate coefficient of k(298 K,1 atm)=1.4×105 s-1, and an Arrhenius expression k(T,1 atm)=1.43×1011 exp(-8.17 kcal mol-1/RT) s-1, which both closely match the experimental recommendations in the literature. The T-dependence is substantially influenced by the multirotamer treatment, as well as by the tunneling and fall-off corrections. The present results are compared to those of simplified TST calculations based solely on the properties of the lowest energy 1-butoxy rotamer.

Association rate constants for reactions between resonance-stabilized radicals: C 3H 3 + C 3H 3, C 3H 3 + C 3H 5, and C 3H 5 + C 3H 5

DOE PAGES

Georgievskii, Yuri; Miller, James A.; Klippenstein, Stephen J.

2007-05-18

Reactions between resonance-stabilized radicals play an important role in combustion chemistry. The theoretical prediction of rate coefficients and product distributions for such reactions is complicated by the fact that the initial complex-formation steps and some dissociation steps are barrierless. In this work, direct variable reaction coordinate transition state theory (VRC-TST) is used to predict accurately the association rate constants for the self and cross reactions of propargyl and allyl radicals. For each reaction, a set of multifaceted dividing surfaces is used to account for the multiple possible addition channels. Because of their resonant nature the geometric relaxation of the radicalsmore » is important. Here, the effect of this relaxation is explicitly calculated with the UB3LYP/cc-pvdz method for each mutual orientation encountered in the configurational integrals over the transition state dividing surfaces. The final energies are obtained from CASPT2/cc-pvdz calculations with all π-orbitals in the active space. Evaluations along the minimum energy path suggest that basis set corrections are negligible. The VRC-TST approach was also used to calculate the association rate constant and the corresponding number of states for the C 6H 5 + H → C 6H 6 exit channel of the C 3H 3 + C 3H 3 reaction, which is also barrierless. For this reaction, the interaction energies were evaluated with the CASPT2(2e,2o)/cc-pvdz method and a 1-D correction is included on the basis of CAS+1+2+QC/aug-cc-pvtz calculations for the CH 3 + H reference system. For the C 3H 3 + C 3H 3 reaction, the VRC-TST results for the energy and angular momentum resolved numbers of states in the entrance channels and in the C 6H 5 + H exit channel are incorporated in a master equation simulation to determine the temperature and pressure dependence of the phenomenological rate coefficients. The rate constants for the C 3H 3 + C 3H 3 and C 3H 5 + C 3H 5 self-reactions compare favorably with the available experimental data. Finally, to our knowledge there are no experimental rate data for the C 3H 3 + C 3H 5 reaction.« less

Test of the combined method for extracting spectroscopic factors in N =50 nuclei

NASA Astrophysics Data System (ADS)

Walter, David; Cizewski, J. A.; Baugher, T.; Ratkiewicz, A.; Pain, S. D.; Nunes, F. M.; Ahn, S.; Cerizza, G.; Jones, K. L.; Manning, B.; Thornsberry, C.

2017-09-01

The single-particle properties of nuclei near shell closures and r-process waiting points can be observed using single-nucleon transfer reactions with beams of rare isotopes. However, approximations have to be made about the final bound state to extract spectroscopic information. An approach to constrain the bound state potential has been proposed by Mukhamedzhanov and Nunes. At peripheral reaction energies ( 5 MeV/u), the ANC for the nucleus can be extracted, and is combined with the same reaction at higher energies ( 40 MeV/u). These combined measurements can constrain the shape of the bound state potential, and the spectroscopic factor can be reliably extracted. To test this method, the 86Kr(d , p) reaction was performed in inverse kinematics with a 35 MeV/u beam at the National Superconducting Cyclotron Laboratory (NSCL) with the ORRUBA and SIDAR arrays of silicon strip detectors coupled to the S800 spectrometer. Successful results supported the measurement of a radioactive ion beam of 84Se at 45 MeV/u at the NSCL to be measured at the end of 2017. Results from the 86Kr(d , p) measurement will be presented as well as preparations for the upcoming 84Se(d , p) measurement. This work is supported in part by the National Science Foundation and U.S. D.O.E.

Theoretical and kinetic study of the hydrogen atom abstraction reactions of esters with H(O.)2 radicals.

PubMed

Mendes, Jorge; Zhou, Chong-Wen; Curran, Henry J

2013-12-27

This work details an ab initio and chemical kinetic study of the hydrogen atom abstraction reactions by the hydroperoxyl radical (HȮ2) on the following esters: methyl ethanoate, methyl propanoate, methyl butanoate, methyl pentanoate, methyl isobutyrate, ethyl ethanoate, propyl ethanoate, and isopropyl ethanoate. Geometry optimizations and frequency calculations of all of the species involved, as well as the hindrance potential descriptions for reactants and transition states, have been performed with the Møller-Plesset (MP2) method using the 6-311G(d,p) basis set. A validation of all of the connections between transition states and local minima was performed by intrinsic reaction coordinate calculations. Electronic energies for all of the species are reported at the CCSD(T)/cc-pVTZ level of theory in kcal mol(-1) with the zero-point energy corrections. The CCSD(T)/CBS (extrapolated from CCSD(T)/cc-pVXZ, in which X = D, T, Q) was used for the reactions of methyl ethanoate + HȮ2 radicals as a benchmark in the electronic energy calculations. High-pressure limit rate constants, in the temperature range 500-2000 K, have been calculated for all of the reaction channels using conventional transition state theory with asymmetric Eckart tunneling corrections. The 1-D hindered rotor approximation has been used for the low frequency torsional modes in both reactants and transition states. The calculated individual and total rate constants are reported for all of the reaction channels in each reaction system. A branching ratio analysis for each reaction site has also been investigated for all of the esters studied in this work.

Amorphous and nanocrystalline luminescent Si and Ge obtained via a solid-state chemical metathesis synthesis route

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMillan, Paul F.; Gryko, Jan; Bull, Craig

A new solid-state metathesis synthesis route was applied to obtain bulk samples of amorphous or microcrystalline Si and Ge. The method involves reaction of Zintl phases such as NaSi or NaGe, with ammonium or metal (e.g., CuCl, CoBr{sub 2}) halides. The driving force for the solid-state reaction is provided by the formation of alkali halides and the transition metals or metal silicides, or gaseous ammonia and hydrogen. The semiconductors were purified by washing to remove other solid products. The amorphous semiconductors were obtained in bulk form from reactions carried out at 200-300{sup o}C. Syntheses at higher temperatures gave rise tomore » microcrystalline semiconductors, or to micro-/nanocrystalline particles contained within the amorphous material. Similar crystalline/amorphous composites were obtained after heat treatment of bulk amorphous materials.« less

The H2 + + He proton transfer reaction: quantum reactive differential cross sections to be linked with future velocity mapping experiments

NASA Astrophysics Data System (ADS)

Hernández Vera, Mario; Wester, Roland; Gianturco, Francesco Antonio

2018-01-01

We construct the velocity map images of the proton transfer reaction between helium and molecular hydrogen ion {{{H}}}2+. We perform simulations of imaging experiments at one representative total collision energy taking into account the inherent aberrations of the velocity mapping in order to explore the feasibility of direct comparisons between theory and future experiments planned in our laboratory. The asymptotic angular distributions of the fragments in a 3D velocity space is determined from the quantum state-to-state differential reactive cross sections and reaction probabilities which are computed by using the time-independent coupled channel hyperspherical coordinate method. The calculations employ an earlier ab initio potential energy surface computed at the FCI/cc-pVQZ level of theory. The present simulations indicate that the planned experiments would be selective enough to differentiate between product distributions resulting from different initial internal states of the reactants.

Accuracy and Calibration of High Explosive Thermodynamic Equations of State

NASA Astrophysics Data System (ADS)

Baker, Ernest L.; Capellos, Christos; Stiel, Leonard I.; Pincay, Jack

2010-10-01

The Jones-Wilkins-Lee-Baker (JWLB) equation of state (EOS) was developed to more accurately describe overdriven detonation while maintaining an accurate description of high explosive products expansion work output. The increased mathematical complexity of the JWLB high explosive equations of state provides increased accuracy for practical problems of interest. Increased numbers of parameters are often justified based on improved physics descriptions but can also mean increased calibration complexity. A generalized extent of aluminum reaction Jones-Wilkins-Lee (JWL)-based EOS was developed in order to more accurately describe the observed behavior of aluminized explosives detonation products expansion. A calibration method was developed to describe the unreacted, partially reacted, and completely reacted explosive using nonlinear optimization. A reasonable calibration of a generalized extent of aluminum reaction JWLB EOS as a function of aluminum reaction fraction has not yet been achieved due to the increased mathematical complexity of the JWLB form.

7Li(d,p)8Li transfer reaction in the NCSM/RGM approach

NASA Astrophysics Data System (ADS)

Raimondi, F.; Hupin, G.; Navrátil, P.; Quaglioni, S.

2018-03-01

Recently, we applied an ab initio method, the no-core shell model combined with the resonating group method, to the transfer reactions with light p-shell nuclei as targets and deuteron as the projectile. In particular, we studied the elastic scattering of deuterium on 7Li and the 7Li(d,p)8Li transfer reaction starting from a realistic two-nucleon interaction. In this contribution, we review of our main results on the 7Li(d,p)8Li transfer reaction, and we extend the study of the relevant reaction channels, by showing the dominant resonant phase shifts of the scattering matrix. We assess also the impact of the polarization effects of the deuteron below the breakup on the positive-parity resonant states in the reaction. For this purpose, we perform an analysis of the convergence trend of the phase and eigenphase shifts, with respect to the number of deuteron pseudostates included in the model space.

Determination of thermodynamics and kinetics of RNA reactions by force

PubMed Central

Tinoco, Ignacio; Li, Pan T. X.; Bustamante, Carlos

2008-01-01

Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force. PMID:17040613

Pre-recombination quenching of the radiation induced fluorescence as the approach to study kinetics of ion-molecular reactions

NASA Astrophysics Data System (ADS)

Borovkov, V. I.; Ivanishko, I. S.

2011-04-01

This study deals with the geminate ion recombination in the presence of bulk scavengers, that is the so-called scavenger problem, as well as with the effect of the scavenging reaction on the radiation-induced recombination fluorescence. Borovkov and Velizhanin (2004) have proposed a method to determine the rate constant of the bulk reaction between neutral scavengers and one of the geminate ions if the ion-molecular reaction prevented the formation of electronically excited states upon recombination involving a newly formed ion. If such pre-recombination quenching of the radiation-induced fluorescence took place, it manifested itself as a progressive decrease in the decay of the fluorescence intensity. The relative change in the fluorescence decay as caused by the scavengers was believed to be closely related to the kinetics of the scavenging reaction. The goal of the present study is to support this method, both computationally and experimentally because there are two factors, which cast doubt on the intuitively obvious approach to the scavenger problem: spatial correlations between the particles involved and the drift of the charged reagent in the electric field of its geminate partner. Computer simulation of geminate ions recombination with an explicit modeling of the motion trajectories of scavengers has been performed for media of low dielectric permittivity, i.e. for the maximal Coulomb interaction between the ions. The simulation has shown that upon continuous diffusion of the particles involved, the joint effect of the two above factors can be considered as insignificant with a high accuracy. Besides, it is concluded then that the method of pre-recombination quenching could be applied to study parallel and consecutive reactions where the yields of excited states in the reaction pathways are different with the use of very simple analytical relations of the formal chemical kinetics. The conclusion has been confirmed experimentally by the example of the reactions of electron transfer from the diphenylacetylene radical anion to dibromoethane and hexafluorobenzene in n-dodecane solutions.

Perspective on the reactions between F– and CH3CH2F: The free energy landscape of the E2 and SN2 reaction channels

PubMed Central

Ensing, Bernd; Klein, Michael L.

2005-01-01

Recently, we computed the 3D free energy surface of the base-induced elimination reaction between F– and CH3CH2F by using a powerful technique within Car–Parrinello molecular dynamics simulation. Here, the set of three order parameters is expanded to six, which allows the study of the competing elimination and substitution reactions simultaneously. The power of the method is exemplified by the exploration of the six-dimensional free energy landscape, sampling, and mapping out the eight stable states as well as the connecting bottlenecks. The free energy profile and barrier along the E2 and SN2 reaction channels are refined by using umbrella sampling. The two mechanisms do not share a common “E2C-like” transition state. Comparison with the zero temperature profiles shows a particularly significant entropy contribution to the SN2 channel. PMID:15863622

Coupling of kinetic Monte Carlo simulations of surface reactions to transport in a fluid for heterogeneous catalytic reactor modeling.

PubMed

Schaefer, C; Jansen, A P J

2013-02-07

We have developed a method to couple kinetic Monte Carlo simulations of surface reactions at a molecular scale to transport equations at a macroscopic scale. This method is applicable to steady state reactors. We use a finite difference upwinding scheme and a gap-tooth scheme to efficiently use a limited amount of kinetic Monte Carlo simulations. In general the stochastic kinetic Monte Carlo results do not obey mass conservation so that unphysical accumulation of mass could occur in the reactor. We have developed a method to perform mass balance corrections that is based on a stoichiometry matrix and a least-squares problem that is reduced to a non-singular set of linear equations that is applicable to any surface catalyzed reaction. The implementation of these methods is validated by comparing numerical results of a reactor simulation with a unimolecular reaction to an analytical solution. Furthermore, the method is applied to two reaction mechanisms. The first is the ZGB model for CO oxidation in which inevitable poisoning of the catalyst limits the performance of the reactor. The second is a model for the oxidation of NO on a Pt(111) surface, which becomes active due to lateral interaction at high coverages of oxygen. This reaction model is based on ab initio density functional theory calculations from literature.

Temperature field calculation with allowance for heat of chemical reactions under electroexplosion nickel plating of aluminum

NASA Astrophysics Data System (ADS)

Romanov, Denis A.; Semina, Olga A.; Stepikov, Maksim A.; Gromov, Victor E.

2017-01-01

The analysis of stress-strained state at the boundary «faced surface layer - substrate» is performed by methods of elasticity theory of inhomogeneous media, on exposure to the load distributed in a circle. The fundamental aspects of Kelvin - Helmholtz and Richtmayer - Meshkov instabilities are considered. The following methods are used for the research. The analytical method of solution is used for finding the temperature distribution of substrate and coating material as well as distribution of speed of material motion in deposition of the coating. Finite element method is required in accounting for the parameters of convective mixing. For the analysis of the proposed thickness and dispersion of the coating the concepts of hydrodynamic Kelvin - Helmholtz and Richtmayer - Meshkov instabilities are used. Using the mass, energy and momentum conservation laws, with allowance for the possible exothermal reactions, the system of equations of the mathematical model of electroexplosion synthesis on the basis of thermoreacting components of Ni-Al system is formulated. The degree of effect of model's parameters on dispersion and thickness of the coating is determined. The comparison of the modeling and experimental data is carried out. It is established that the due regard to the thermal effect of chemical reaction increases considerably the time of existence of the reacting elements in the liquid state and it facilitates the participation of the entire nickel in the reaction. The increased time of heat effect enables the other processes to occur more completely.

A quantum informational approach for dissecting chemical reactions

NASA Astrophysics Data System (ADS)

Duperrouzel, Corinne; Tecmer, Paweł; Boguslawski, Katharina; Barcza, Gergely; Legeza, Örs; Ayers, Paul W.

2015-02-01

We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected, which allows us to monitor the interplay of back-bonding and π-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods, revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

Capture approximations beyond a statistical quantum mechanical method for atom-diatom reactions

NASA Astrophysics Data System (ADS)

Barrios, Lizandra; Rubayo-Soneira, Jesús; González-Lezana, Tomás

2016-03-01

Statistical techniques constitute useful approaches to investigate atom-diatom reactions mediated by insertion dynamics which involves complex-forming mechanisms. Different capture schemes based on energy considerations regarding the specific diatom rovibrational states are suggested to evaluate the corresponding probabilities of formation of such collision species between reactants and products in an attempt to test reliable alternatives for computationally demanding processes. These approximations are tested in combination with a statistical quantum mechanical method for the S + H2(v = 0 ,j = 1) → SH + H and Si + O2(v = 0 ,j = 1) → SiO + O reactions, where this dynamical mechanism plays a significant role, in order to probe their validity.

Repercussion of Solid state vs. Liquid state synthesized p-n heterojunction RGO-copper phosphate on proton reduction potential in water.

PubMed

Samal, Alaka; Das, Dipti P; Madras, Giridhar

2018-02-13

The same copper phosphate catalysts were synthesized by obtaining the methods involving solid state as well as liquid state reactions in this work. And then the optimised p-n hybrid junction photocatalysts have been synthesized following the same solid/liquid reaction pathways. The synthesized copper phosphate photocatalyst has unique rod, flower, caramel-treat-like morphology. The Mott-Schottky behavior is in accordance with the expected behavior of n-type semiconductor and the carrier concentration was calculated using the M-S analysis for the photocatalyst. And for the p-n hybrid junction of 8RGO-Cu 3 (PO 4 ) 2 -PA (PA abbreviated for photoassisted synthesis method), 8RGO-Cu 3 (PO 4 ) 2 -EG(EG abbreviated for Ethylene Glycol based synthesis method), 8RGO-Cu 3 (PO 4 ) 2 -PEG (PEG abbreviated for Poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol based synthesis method)the amount of H 2 synthesized was 7500, 6500 and 4500 µmol/h/g, respectively. The excited electrons resulting after the irradiation of visible light on the CB of p-type reduced graphene oxide (RGO) migrate easily to n-type Cu 3 (PO 4 ) 2 via. the p-n junction interfaces and hence great charge carrier separation was achieved.

Taking the plunge: chemical reaction dynamics in liquids.

PubMed

Orr-Ewing, Andrew J

2017-12-11

The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.

Stabilization strategies of a general nonlinear car-following model with varying reaction-time delay of the drivers.

PubMed

Li, Shukai; Yang, Lixing; Gao, Ziyou; Li, Keping

2014-11-01

In this paper, the stabilization strategies of a general nonlinear car-following model with reaction-time delay of the drivers are investigated. The reaction-time delay of the driver is time varying and bounded. By using the Lyapunov stability theory, the sufficient condition for the existence of the state feedback control strategy for the stability of the car-following model is given in the form of linear matrix inequality, under which the traffic jam can be well suppressed with respect to the varying reaction-time delay. Moreover, by considering the external disturbance for the running cars, the robust state feedback control strategy is designed, which ensures robust stability and a smaller prescribed H∞ disturbance attenuation level for the traffic flow. Numerical examples are given to illustrate the effectiveness of the proposed methods. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

A Luenberger observer for reaction-diffusion models with front position data

NASA Astrophysics Data System (ADS)

Collin, Annabelle; Chapelle, Dominique; Moireau, Philippe

2015-11-01

We propose a Luenberger observer for reaction-diffusion models with propagating front features, and for data associated with the location of the front over time. Such models are considered in various application fields, such as electrophysiology, wild-land fire propagation and tumor growth modeling. Drawing our inspiration from image processing methods, we start by proposing an observer for the eikonal-curvature equation that can be derived from the reaction-diffusion model by an asymptotic expansion. We then carry over this observer to the underlying reaction-diffusion equation by an ;inverse asymptotic analysis;, and we show that the associated correction in the dynamics has a stabilizing effect for the linearized estimation error. We also discuss the extension to joint state-parameter estimation by using the earlier-proposed ROUKF strategy. We then illustrate and assess our proposed observer method with test problems pertaining to electrophysiology modeling, including with a realistic model of cardiac atria. Our numerical trials show that state estimation is directly very effective with the proposed Luenberger observer, while specific strategies are needed to accurately perform parameter estimation - as is usual with Kalman filtering used in a nonlinear setting - and we demonstrate two such successful strategies.

Calculation of electronic coupling matrix elements for ground and excited state electron transfer reactions: Comparison of the generalized Mulliken-Hush and block diagonalization methods

NASA Astrophysics Data System (ADS)

Cave, Robert J.; Newton, Marshall D.

1997-06-01

Two independent methods are presented for the nonperturbative calculation of the electronic coupling matrix element (Hab) for electron transfer reactions using ab initio electronic structure theory. The first is based on the generalized Mulliken-Hush (GMH) model, a multistate generalization of the Mulliken Hush formalism for the electronic coupling. The second is based on the block diagonalization (BD) approach of Cederbaum, Domcke, and co-workers. Detailed quantitative comparisons of the two methods are carried out based on results for (a) several states of the system Zn2OH2+ and (b) the low-lying states of the benzene-Cl atom complex and its contact ion pair. Generally good agreement between the two methods is obtained over a range of geometries. Either method can be applied at an arbitrary nuclear geometry and, as a result, may be used to test the validity of the Condon approximation. Examples of nonmonotonic behavior of the electronic coupling as a function of nuclear coordinates are observed for Zn2OH2+. Both methods also yield a natural definition of the effective distance (rDA) between donor (D) and acceptor (A) sites, in contrast to earlier approaches which required independent estimates of rDA, generally based on molecular structure data.

A Method for Decomposition of the Basic Reaction of Biological Macromolecules into Exponential Components

NASA Astrophysics Data System (ADS)

Barabash, Yu. M.; Lyamets, A. K.

2016-12-01

The structural and dynamical properties of biological macromolecules under non-equilibrium conditions determine the kinetics of their basic reaction to external stimuli. This kinetics is multiexponential in nature. This is due to the operation of various subsystems in the structure of macromolecules, as well as the effect of the basic reaction on the structure of macromolecules. The situation can be interpreted as a manifestation of the stationary states of macromolecules, which are represented by monoexponential components of the basic reaction (Monod-Wyman-Changeux model) Monod et al. (J Mol Cell Biol 12:88-118, 1965). The representation of multiexponential kinetics of the basic reaction in the form of a sum of exponential functions (A(t)={sum}_{i=1}^n{a}_i{e}^{-{k}_it}) is a multidimensional optimization problem. To solve this problem, a gradient method of optimization with software determination of the amount of exponents and reasonable calculation time is developed. This method is used to analyze the kinetics of photoinduced electron transport in the reaction centers (RC) of purple bacteria and the fluorescence induction in the granum thylakoid membranes which share a common function of converting light energy.

Extraction of the ANC from the 10Be(d, p)11Be transfer reaction using the ADWA method

NASA Astrophysics Data System (ADS)

Yang, J.; Capel, P.

2018-05-01

A halo nucleus is built from a core and at least one weakly bound neutron or proton. To understand this unique cluster structure, lots of efforts have been undertaken. During the past decades, the (d, p) reaction has been widely used in experiments and has become an important tool for extracting single-particle properties of nuclei. In this work, our goal is to obtain the Asymptotic Normalization Coefficient (ANC) of the halo nuclei 11Be using the ADWA method. We perform the analysis for the 10Be(d, p)11Be stripping reaction at Ed =21.4, 18, 15, and 12MeV for the ground state and first excited state of the composite nucleus 11Be. The experimental measurement was carried out at Oak Ridge National Laboratory by Schmitt et al. [1] The sensitivity of the calculations to the optical potential choice is also checked. Overall, the transfer process becomes more peripheral at lower energies and forward angles. Investigation in this area is the best way to extract a reliable ANC from the experimental data. For the ground state of 11Be, the ANC obtained using our method (C={0.785}-0.030+0.026{\\text{fm}}-1/2) shows perfect agreement with the one obtained by Ab initio calculations (C Ab=0.786 fm‑1/2) [2].

LSENS, The NASA Lewis Kinetics and Sensitivity Analysis Code

NASA Technical Reports Server (NTRS)

Radhakrishnan, K.

2000-01-01

A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS (the NASA Lewis kinetics and sensitivity analysis code), are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include: static system; steady, one-dimensional, inviscid flow; incident-shock initiated reaction in a shock tube; and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method (LSODE, the Livermore Solver for Ordinary Differential Equations), which works efficiently for the extremes of very fast and very slow reactions, is used to solve the "stiff" ordinary differential equation systems that arise in chemical kinetics. For static reactions, the code uses the decoupled direct method to calculate sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters. Solution methods for the equilibrium and post-shock conditions and for perfectly stirred reactor problems are either adapted from or based on the procedures built into the NASA code CEA (Chemical Equilibrium and Applications).

Application of inorganic oxidants to the spectrophotometric determination of ribavirin in bulk and capsules.

PubMed

Darwish, Ibrahim A; Khedr, Alaa S; Askal, Hassan F; Mohamed, Ramadan M

2006-01-01

Eight spectrophotometric methods for determination of ribavirin have been developed and validated. These methods were based on the oxidation of the drug by different inorganic oxidants: ceric ammonium sulfate, potassium permanganate, ammonium molybdate, ammonium metavanidate, chromium trioxide, potassium dichromate, potassium iodate, and potassium periodate. The oxidation reactions were performed in perchloric acid medium for ceric ammonium sulfate and in sulfuric acid medium for the other reagents. With ceric ammonium sulfate and potassium permanganate, the concentration of ribavirin in its samples was determined by measuring the decrease in the absorption intensity of the colored reagents at 315 and 525 nm, respectively. With the other reagents, the concentration of ribavirin was determined by measuring the intensity of the developed colored reaction products at the wavelengths of maximum absorbance: 675, 780, 595, 595, 475, and 475 nm for reactions with ammonium molybdate, ammonium metavanidate, chromium trioxide, potassium dichromate, potassium iodate, and potassium periodate, respectively. Different variables affecting the reaction conditions were carefully studied and optimized. Under the optimum conditions, linear relationships with good correlation coefficients (0.9984-0.9998) were found between the absorbance readings and the concentrations of ribavirin in the range of 4-1400 microg/mL. The molar absorptivities were correlated with the oxidation potential of the oxidants used. The precision of the methods were satisfactory; the values of relative standard deviation did not exceed 1.64%. The proposed methods were successfully applied to the analysis of ribavirin in pure drug material and capsules with good accuracy and precision; the recovery values were 99.2-101.2 +/- 0.48-1.30%. The results obtained using the proposed spectrophotometric methods were comparable with those obtained with the official method stated in the United States Pharmacopeia.

Insights into reaction mechanisms in heterogeneous catalysis revealed by in situ NMR spectroscopy.

PubMed

Blasco, Teresa

2010-12-01

This tutorial review intends to show the possibilities of in situ solid state NMR spectroscopy in the elucidation of reaction mechanisms and the nature of the active sites in heterogeneous catalysis. After a brief overview of the more usual experimental devices used for in situ solid state NMR spectroscopy measurements, some examples of applications taken from the recent literature will be presented. It will be shown that in situ NMR spectroscopy allows: (i) the identification of stable intermediates and transient species using indirect methods, (ii) to prove shape selectivity in zeolites, (iii) the study of reaction kinetics, and (iv) the determination of the nature and the role played by the active sites in a catalytic reaction. The approaches and methodology used to get this information will be illustrated here summarizing the most relevant contributions on the investigation of the mechanisms of a series of reactions of industrial interest: aromatization of alkanes on bifunctional catalysts, carbonylation reaction of methanol with carbon monoxide, ethylbenzene disproportionation, and the Beckmann rearrangement reaction. Special attention is paid to the research carried out on the role played by carbenium ions and alkoxy as intermediate species in the transformation of hydrocarbon molecules on solid acid catalysts.

Manifestation of α clustering in 10Be via α -knockout reaction

NASA Astrophysics Data System (ADS)

Lyu, Mengjiao; Yoshida, Kazuki; Kanada-En'yo, Yoshiko; Ogata, Kazuyuki

2018-04-01

Background: Proton-induced α -knockout reactions may allow direct experimental observation of α clustering in nuclei. This is obtained by relating the theoretical descriptions of clustering states to the experimental reaction observables. It is desired to introduce microscopic structure models into the theoretical frameworks for α -knockout reactions. Purpose: Our goal is to probe the α clustering in the 10Be nucleus by proton-induced α -knockout reaction observables. Method: We adopt an extended version of the Tohsaki-Horiuchi-Schuck-Röpke wave function of 10Be and integrate it with the distorted-wave impulse approximation framework for the calculation of (p ,p α ) -knockout reactions. Results: We make the first calculation for the 10Be(p ,p α )6He reaction at 250 MeV by implementing a microscopic α -cluster wave function, and we predict the triple-differential cross section (TDX). Furthermore, by constructing artificial states of the target nucleus 10Be with compact or dilute spatial distributions, the TDX is found to be highly sensitive to the extent of clustering in the target nuclei. Conclusions: These results provide reliable manifestation of α clustering in 10Be.

Dynamic target ionization using an ultrashort pulse of a laser field

NASA Astrophysics Data System (ADS)

Makarov, D. N.; Matveev, V. I.; Makarova, K. A.

2014-09-01

Ionization processes under the interaction of an ultrashort pulse of an electromagnetic field with atoms in nonstationary states are considered. As an example, the ionization probability of the hydrogen-like atom upon the decay of quasi-stationary state is calculated. The method developed can be applied to complex systems, including targets in collisional states and various chemical reactions.

DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less

DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

DOE PAGES

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

2017-01-16

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less

State-specific catalytic recombination boundary condition for DSMC methods in aerospace applications

NASA Astrophysics Data System (ADS)

Bariselli, F.; Torres, E.; Magin, T. E.

2016-11-01

Accurate characterization of the hypersonic flow around a vehicle during its atmospheric entry is important for a precise quantification of heat flux margins. In some cases, exothermic reactions promoted by the catalytic properties of the surface material can significantly contribute to the overall heat flux. In this work, the effect of catalytic recombination of atomic nitrogen is examined within the framework of a state-specific DSMC implementation. State-to-state reaction cross sections are derived from a detailed quantum-chemical database for the N2(v, J) + N system. A coarse-grain model is used to reduce the number of internal states and state-specific reactions to a manageable level. The catalytic boundary condition is based on an phenomenological approach and the state-specific surface recombination probabilities can be imposed by the user. This can represent an important aspect in modelling catalysis, since experiments and molecular dynamics suggest that only part of the chemical energy is absorbed by the wall, with the formed molecules leaving the surface in an excited state. The implementation is verified in a simplified geometrical configuration by comparing the numerical results with an analytical solution, developed for a 1D diffusion problem in a binary mixture. Then, the effect of catalysis in a hypersonic flow along the stagnation line of a blunt body is studied.

Role of intramolecular hydrogen bonding in the excited-state intramolecular double proton transfer (ESIDPT) of calix[4]arene: A TDDFT study

NASA Astrophysics Data System (ADS)

Wang, Se; Wang, Zhuang; Hao, Ce

2016-01-01

The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state intramolecular double proton transfer (ESIDPT) reaction of calix[4] arene (C4A) and the role of the intramolecular hydrogen bonds in the ESIDPT process. The geometries of C4A in the ground state and excited states (S1, S2 and T1) were optimized. Four intramolecular hydrogen bonds formed in the C4A are strengthened or weakened in the S2 and T1 states compared to those in the ground state. Interestingly, upon excitation to the S1 state of C4A, two protons H1 and H2 transfer along the two intramolecular hydrogen bonds O1-H1···O2 and O2-H2···O3, while the other two protons do not transfer. The ESIDPT reaction breaks the primary symmetry of C4A in the ground state. The potential energy curves of proton transfer demonstrate that the ESIDPT process follows the stepwise mechanism but not the concerted mechanism. Findings indicate that intramolecular hydrogen bonding is critical to the ESIDPT reactions in intramolecular hydrogen-bonded systems.

Carbon monoxide oxidation over three different states of copper: Development of a model metal oxide catalyst

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jernigan, Glenn Geoffrey

1994-10-01

Carbon monoxide oxidation was performed over the three different oxidation states of copper -- metallic (Cu), copper (I) oxide (Cu 2O), and copper (II) oxide (CuO) as a test case for developing a model metal oxide catalyst amenable to study by the methods of modern surface science and catalysis. Copper was deposited and oxidized on oxidized supports of aluminum, silicon, molybdenum, tantalum, stainless steel, and iron as well as on graphite. The catalytic activity was found to decrease with increasing oxidation state (Cu > Cu 2O > CuO) and the activation energy increased with increasing oxidation state (Cu, 9 kcal/molmore » < Cu 2O, 14 kcal/mol < CuO, 17 kcal/mol). Reaction mechanisms were determined for the different oxidation states. Lastly, NO reduction by CO was studied. A Cu and CuO catalyst were exposed to an equal mixture of CO and NO at 300--350 C to observe the production of N 2 and CO 2. At the end of each reaction, the catalyst was found to be Cu 2O. There is a need to study the kinetics of this reaction over the different oxidation states of copper.« less

Cluster states and container picture in light nuclei, and triple-alpha reaction rate

NASA Astrophysics Data System (ADS)

Funaki, Yasuro

2015-04-01

The excited states in 12C are investigated by using an extended version of the so- called Tohsaki-Horiuchi-Schuck-Röpke (THSR) wave function, where both the 3α condensate and 8Be + α cluster asymptotic configurations are included. We focus on the structures of the “Hoyle band” states, 2+2, and 4+2 states, which are recently observed above the Hoyle state, and of the 0+3 and 0+4 states, which are also quite recently identified in experiment. We show that the Hoyle band is not simply considered to be the 8Be(0+) + α rotation as suggested by previous cluster model calculations, nor to be a rotation of a rigid-body triangle-shaped object composed of the 3α particles. We also discuss the rate of the triple-alpha radiative capture reaction, applyng the imaginary-time method. Results of the triple-alpha reaction rate are consistent with NACRE rate for both high (≈ 109K) and low (≈ 107 K) temperatures. We show that the rate of the imaginary-time calculation in coupled-channels approach has a large enhancement for low temperatures if we truncate the number of channels.

Exploring the full catalytic cycle of rhodium(i)–BINAP-catalysed isomerisation of allylic amines: a graph theory approach for path optimisation† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00401j Click here for additional data file.

PubMed Central

Yoshimura, Takayoshi; Taketsugu, Tetsuya; Sawamura, Masaya

2017-01-01

We explored the reaction mechanism of the cationic rhodium(i)–BINAP complex catalysed isomerisation of allylic amines using the artificial force induced reaction method with the global reaction route mapping strategy, which enabled us to search for various reaction paths without assumption of transition states. The entire reaction network was reproduced in the form of a graph, and reasonable paths were selected from the complicated network using Prim’s algorithm. As a result, a new dissociative reaction mechanism was proposed. Our comprehensive reaction path search provided rationales for the E/Z and S/R selectivities of the stereoselective reaction. PMID:28970877

Electronic excitation spectra of molecules in solution calculated using the symmetry-adapted cluster-configuration interaction method in the polarizable continuum model with perturbative approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukuda, Ryoichi, E-mail: fukuda@ims.ac.jp; Ehara, Masahiro; Elements Strategy Initiative for Catalysts and Batteries

A perturbative approximation of the state specific polarizable continuum model (PCM) symmetry-adapted cluster-configuration interaction (SAC-CI) method is proposed for efficient calculations of the electronic excitations and absorption spectra of molecules in solutions. This first-order PCM SAC-CI method considers the solvent effects on the energies of excited states up to the first-order with using the zeroth-order wavefunctions. This method can avoid the costly iterative procedure of the self-consistent reaction field calculations. The first-order PCM SAC-CI calculations well reproduce the results obtained by the iterative method for various types of excitations of molecules in polar and nonpolar solvents. The first-order contribution ismore » significant for the excitation energies. The results obtained by the zeroth-order PCM SAC-CI, which considers the fixed ground-state reaction field for the excited-state calculations, are deviated from the results by the iterative method about 0.1 eV, and the zeroth-order PCM SAC-CI cannot predict even the direction of solvent shifts in n-hexane for many cases. The first-order PCM SAC-CI is applied to studying the solvatochromisms of (2,2{sup ′}-bipyridine)tetracarbonyltungsten [W(CO){sub 4}(bpy), bpy = 2,2{sup ′}-bipyridine] and bis(pentacarbonyltungsten)pyrazine [(OC){sub 5}W(pyz)W(CO){sub 5}, pyz = pyrazine]. The SAC-CI calculations reveal the detailed character of the excited states and the mechanisms of solvent shifts. The energies of metal to ligand charge transfer states are significantly sensitive to solvents. The first-order PCM SAC-CI well reproduces the observed absorption spectra of the tungsten carbonyl complexes in several solvents.« less

Ergonomics research methods

NASA Technical Reports Server (NTRS)

Uspenskiy, S. I.; Yermakova, S. V.; Chaynova, L. D.; Mitkin, A. A.; Gushcheva, T. M.; Strelkov, Y. K.; Tsvetkova, N. F.

1973-01-01

Various factors used in ergonomic research are given. They are: (1) anthrometric measurement, (2) polyeffector method of assessing the functional state of man, (3) galvanic skin reaction, (4) pneumography, (5) electromyography, (6) electrooculography, and (7) tachestoscopy. A brief summary is given of each factor and includes instrumentation and results.

Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryo-EM

PubMed Central

Chen, Bo; Kaledhonkar, Sandip; Sun, Ming; Shen, Bingxin; Lu, Zonghuan; Barnard, David; Lu, Toh-Ming; Gonzalez, Ruben L.; Frank, Joachim

2015-01-01

Ribosomal subunit association is a key checkpoint in translation initiation, but its structural dynamics are poorly understood. Here, we used a recently developed mixing-spraying, time-resolved, cryogenic electron microscopy (cryo-EM) method to study ribosomal subunit association in the sub-second time range. We have improved this method and increased the cryo-EM data yield by tenfold. Pre-equilibrium states of the association reaction were captured by reacting the mixture of ribosomal subunits for 60 ms and 140 ms. We also identified three distinct ribosome conformations in the associated ribosomes. The observed proportions of these conformations are the same in these two time points, suggesting that ribosomes equilibrate among the three conformations within less than 60 ms upon formation. Our results demonstrate that the mixing-spraying method can capture multiple states of macromolecules during a sub-second reaction. Other fast processes, such as translation initiation, decoding and ribosome recycling, are amenable to study with this method. PMID:26004440

New analytical methodology for analysing S(IV) species at low pH solutions by one stage titration method (bichromatometry) with a clear colour change. Could potentially replace the state-of-art-method iodometry at low pH analysis due higher accuracy

PubMed Central

Galfi, Istvan; Virtanen, Jorma; Gasik, Michael M.

2017-01-01

A new, faster and more reliable analytical methodology for S(IV) species analysis at low pH solutions by bichromatometry is proposed. For decades the state of the art methodology has been iodometry that is still well justified method for neutral solutions, thus at low pH media possess various side reactions increasing inaccuracy. In contrast, the new methodology has no side reactions at low pH media, requires only one titration step and provides a clear color change if S(IV) species are present in the solution. The method is validated using model solutions with known concentrations and applied to analyses of gaseous SO2 from purged solution in low pH media samples. The results indicate that bichromatometry can accurately analyze SO2 from liquid samples having pH even below 0 relevant to metallurgical industrial processes. PMID:29145479

Space-time least-squares finite element method for convection-reaction system with transformed variables

PubMed Central

Nam, Jaewook

2011-01-01

We present a method to solve a convection-reaction system based on a least-squares finite element method (LSFEM). For steady-state computations, issues related to recirculation flow are stated and demonstrated with a simple example. The method can compute concentration profiles in open flow even when the generation term is small. This is the case for estimating hemolysis in blood. Time-dependent flows are computed with the space-time LSFEM discretization. We observe that the computed hemoglobin concentration can become negative in certain regions of the flow; it is a physically unacceptable result. To prevent this, we propose a quadratic transformation of variables. The transformed governing equation can be solved in a straightforward way by LSFEM with no sign of unphysical behavior. The effect of localized high shear on blood damage is shown in a circular Couette-flow-with-blade configuration, and a physiological condition is tested in an arterial graft flow. PMID:21709752

Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction.

PubMed

Sadowski, Peter; Fooshee, David; Subrahmanya, Niranjan; Baldi, Pierre

2016-11-28

Machine learning (ML) and quantum mechanical (QM) methods can be used in two-way synergy to build chemical reaction expert systems. The proposed ML approach identifies electron sources and sinks among reactants and then ranks all source-sink pairs. This addresses a bottleneck of QM calculations by providing a prioritized list of mechanistic reaction steps. QM modeling can then be used to compute the transition states and activation energies of the top-ranked reactions, providing additional or improved examples of ranked source-sink pairs. Retraining the ML model closes the loop, producing more accurate predictions from a larger training set. The approach is demonstrated in detail using a small set of organic radical reactions.

Full-dimensional quantum dynamics study of the H{sub 2} + C{sub 2}H → H + C{sub 2}H{sub 2} reaction on an ab initio potential energy surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Liuyang; University of Chinese Academy of Sciences, Beijing 100049; Shao, Kejie

2016-05-21

This work performs a time-dependent wavepacket study of the H{sub 2} + C{sub 2}H → H + C{sub 2}H{sub 2} reaction on a new ab initio potential energy surface (PES). The PES is constructed using neural network method based on 68 478 geometries with energies calculated at UCCSD(T)-F12a/aug-cc-pVTZ level and covers H{sub 2} + C{sub 2}H↔H + C{sub 2}H{sub 2}, H + C{sub 2}H{sub 2} → HCCH{sub 2}, and HCCH{sub 2} radial isomerization reaction regions. The reaction dynamics of H{sub 2} + C{sub 2}H → H + C{sub 2}H{sub 2} are investigated using full-dimensional quantum dynamics method. The initial-state selected reactionmore » probabilities are calculated for reactants in eight vibrational states. The calculated results showed that the H{sub 2} vibrational excitation predominantly enhances the reactivity while the excitation of bending mode of C{sub 2}H slightly inhibits the reaction. The excitations of two stretching modes of C{sub 2}H molecule have negligible effect on the reactivity. The integral cross section is calculated with J-shift approximation and the mode selectivity in this reaction is discussed. The rate constants over 200-2000 K are calculated and agree well with the experimental measured values.« less

A variational approach to parameter estimation in ordinary differential equations.

PubMed

Kaschek, Daniel; Timmer, Jens

2012-08-14

Ordinary differential equations are widely-used in the field of systems biology and chemical engineering to model chemical reaction networks. Numerous techniques have been developed to estimate parameters like rate constants, initial conditions or steady state concentrations from time-resolved data. In contrast to this countable set of parameters, the estimation of entire courses of network components corresponds to an innumerable set of parameters. The approach presented in this work is able to deal with course estimation for extrinsic system inputs or intrinsic reactants, both not being constrained by the reaction network itself. Our method is based on variational calculus which is carried out analytically to derive an augmented system of differential equations including the unconstrained components as ordinary state variables. Finally, conventional parameter estimation is applied to the augmented system resulting in a combined estimation of courses and parameters. The combined estimation approach takes the uncertainty in input courses correctly into account. This leads to precise parameter estimates and correct confidence intervals. In particular this implies that small motifs of large reaction networks can be analysed independently of the rest. By the use of variational methods, elements from control theory and statistics are combined allowing for future transfer of methods between the two fields.

Exact dynamic properties of molecular motors

NASA Astrophysics Data System (ADS)

Boon, N. J.; Hoyle, R. B.

2012-08-01

Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.

Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory.

PubMed

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.

Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

NASA Astrophysics Data System (ADS)

Lu, Xiu Hui; Yu, Hai Bin; Wu, Wei Rong; Xu, Yue Hua

Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second-order Møller-Plesset (MP2)/6-31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero-point energy (ZPE) and CCSD(T)/6-31G* single-point calculations. From the PES obtained with the CCSD(T)//MP2/6-31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four-membered ring intermediate, INT2, which is a barrier-free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four-membered product P2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier-free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier-free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P3 via a transition state TS3 with an energy barrier of 25.8 kJ/mol.

Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

PubMed

Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu

2008-01-01

A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

Synthesis and Characterization of AlCl3 Impregnated Molybdenum Oxide as Heterogeneous Nano-Catalyst for the Friedel-Crafts Acylation Reaction in Ambient Condition.

PubMed

Jadhav, Arvind H; Chinnappan, Amutha; Hiremath, Vishwanath; Seo, Jeong Gil

2015-10-01

Aluminum trichloride (AlCl3) impregnated molybdenum oxide heterogeneous nano-catalyst was prepared by using simple impregnation method. The prepared heterogeneous catalyst was characterized by powder X-ray diffraction, FT-IR spectroscopy, solid-state NMR spectroscopy, SEM imaging, and EDX mapping. The catalytic activity of this protocol was evaluated as heterogeneous catalyst for the Friedel-Crafts acylation reaction at room temperature. The impregnated MoO4(AlCl2)2 catalyst showed tremendous catalytic activity in Friedel-Crafts acylation reaction under solvent-free and mild reaction condition. As a result, 84.0% yield of acyl product with 100% consumption of reactants in 18 h reaction time at room temperature was achieved. The effects of different solvents system with MoO4(AlCl2)2 catalyst in acylation reaction was also investigated. By using optimized reaction condition various acylated derivatives were prepared. In addition, the catalyst was separated by simple filtration process after the reaction and reused several times. Therefore, heterogeneous MoO4(AlCl2)2 catalyst was found environmentally benign catalyst, very convenient, high yielding, and clean method for the Friedel-Crafts acylation reaction under solvent-free and ambient reaction condition.

From metadynamics to dynamics.

PubMed

Tiwary, Pratyush; Parrinello, Michele

2013-12-06

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased molecular dynamics runs.

From Metadynamics to Dynamics

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush; Parrinello, Michele

2013-12-01

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased molecular dynamics runs.

Transition state-finding strategies for use with the growing string method.

PubMed

Goodrow, Anthony; Bell, Alexis T; Head-Gordon, Martin

2009-06-28

Efficient identification of transition states is important for understanding reaction mechanisms. Most transition state search algorithms require long computational times and a good estimate of the transition state structure in order to converge, particularly for complex reaction systems. The growing string method (GSM) [B. Peters et al., J. Chem. Phys. 120, 7877 (2004)] does not require an initial guess of the transition state; however, the calculation is still computationally intensive due to repeated calls to the quantum mechanics code. Recent modifications to the GSM [A. Goodrow et al., J. Chem. Phys. 129, 174109 (2008)] have reduced the total computational time for converging to a transition state by a factor of 2 to 3. In this work, three transition state-finding strategies have been developed to complement the speedup of the modified-GSM: (1) a hybrid strategy, (2) an energy-weighted strategy, and (3) a substring strategy. The hybrid strategy initiates the string calculation at a low level of theory (HF/STO-3G), which is then refined at a higher level of theory (B3LYP/6-31G(*)). The energy-weighted strategy spaces points along the reaction pathway based on the energy at those points, leading to a higher density of points where the energy is highest and finer resolution of the transition state. The substring strategy is similar to the hybrid strategy, but only a portion of the low-level string is refined using a higher level of theory. These three strategies have been used with the modified-GSM and are compared in three reactions: alanine dipeptide isomerization, H-abstraction in methanol oxidation on VO(x)/SiO(2) catalysts, and C-H bond activation in the oxidative carbonylation of toluene to p-toluic acid on Rh(CO)(2)(TFA)(3) catalysts. In each of these examples, the substring strategy was proved most effective by obtaining a better estimate of the transition state structure and reducing the total computational time by a factor of 2 to 3 compared to the modified-GSM. The applicability of the substring strategy has been extended to three additional examples: cyclopropane rearrangement to propylene, isomerization of methylcyclopropane to four different stereoisomers, and the bimolecular Diels-Alder condensation of 1,3-butadiene and ethylene to cyclohexene. Thus, the substring strategy used in combination with the modified-GSM has been demonstrated to be an efficient transition state-finding strategy for a wide range of types of reactions.

Enhancing chemical reactions

DOEpatents

Morrey, John R.

1978-01-01

Methods of enhancing selected chemical reactions. The population of a selected high vibrational energy state of a reactant molecule is increased substantially above its population at thermal equilibrium by directing onto the molecule a beam of radiant energy from a laser having a combination of frequency and intensity selected to pump the selected energy state, and the reaction is carried out with the temperature, pressure, and concentrations of reactants maintained at a combination of values selected to optimize the reaction in preference to thermal degradation by transforming the absorbed energy into translational motion. The reaction temperature is selected to optimize the reaction. Typically a laser and a frequency doubler emit radiant energy at frequencies of .nu. and 2.nu. into an optical dye within an optical cavity capable of being tuned to a wanted frequency .delta. or a parametric oscillator comprising a non-centrosymmetric crystal having two indices of refraction, to emit radiant energy at the frequencies of .nu., 2.nu., and .delta. (and, with a parametric oscillator, also at 2.nu.-.delta.). Each unwanted frequency is filtered out, and each desired frequency is focused to the desired radiation flux within a reaction chamber and is reflected repeatedly through the chamber while reactants are fed into the chamber and reaction products are removed therefrom.

Long-range versus short-range correlations in the two-neutron transfer reaction 64Ni(18O,16O)66Ni

NASA Astrophysics Data System (ADS)

Paes, B.; Santagati, G.; Vsevolodovna, R. Magana; Cappuzzello, F.; Carbone, D.; Cardozo, E. N.; Cavallaro, M.; García-Tecocoatzi, H.; Gargano, A.; Ferreira, J. L.; Lenzi, S. M.; Linares, R.; Santopinto, E.; Vitturi, A.; Lubian, J.

2017-10-01

Recently, various two-neutron transfer studies using the (18O,16O) reaction were performed with a large success. This was achieved because of a combined use of the microscopic quantum description of the reaction mechanism and of the nuclear structure. In the present work we use this methodology to study the two-neutron transfer reaction of the 18O+64Ni system at 84 MeV incident energy, to the ground and first 2+ excited state of the residual 66Ni nucleus. All the experimental data were measured by the large acceptance MAGNEX spectrometer at the Instituto Nazionale di Fisica Nucleare -Laboratori Nazionali del Sud (Italy). We have performed exact finite range cross section calculations using the coupled channel Born approximation (CCBA) and coupled reaction channel (CRC) method for the sequential and direct two-neutron transfers, respectively. Moreover, this is the first time that the formalism of the microscopic interaction boson model (IBM-2) was applied to a two-neutron transfer reaction. From our results we conclude that for two-neutron transfer to the ground state of 66Ni, the direct transfer is the dominant reaction mechanism, whereas for the transfer to the first excited state of 66Ni, the sequential process dominates. A competition between long-range and short-range correlations is discussed, in particular, how the use of two different models (Shell model and IBM's) help to disentangle long- and short-range correlations.

Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization.

PubMed

Tachikawa, Hiroto

2017-06-30

Reactions of water dimer cation (H2O)2+ following ionization have been investigated by means of a direct ab initio molecular dynamics method. In particular, the effects of zero point vibration and zero point energy (ZPE) on the reaction mechanism were considered in this work. Trajectories were run on two electronic potential energy surfaces (PESs) of (H2O)2+: ground state ( 2 A″-like state) and the first excited state ( 2 A'-like state). All trajectories on the ground-state PES lead to the proton-transferred product: H 2 O + (Wd)-H 2 O(Wa) → OH(Wd)-H 3 O + (Wa), where Wd and Wa refer to the proton donor and acceptor water molecules, respectively. Time of proton transfer (PT) varied widely from 15 to 40 fs (average time of PT = 30.9 fs). The trajectories on the excited-state PES gave two products: an intermediate complex with a face-to-face structure (H 2 O-OH 2 ) + and a PT product. However, the proton was transferred to the opposite direction, and the reverse PT was found on the excited-state PES: H 2 O(Wd)-H 2 O + (Wa) → H 3 O + (Wd)-OH(Wa). This difference occurred because the ionizing water molecule in the dimer switched between the ground and excited states. The reaction mechanism of (H2O)2+ and the effects of ZPE are discussed on the basis of the results. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A theoretical study of the reaction of Ti+ with ethane

NASA Astrophysics Data System (ADS)

Moc, Jerzy; Fedorov, Dmitri G.; Gordon, Mark S.

2000-06-01

The doublet and quartet potential energy surfaces for the Ti++C2H6→TiC2H4++H2 and Ti++C2H6→TiCH2++CH4 reactions are studied using density functional theory (DFT) with the B3LYP functional and ab initio coupled cluster CCSD(T) methods with high quality basis sets. Structures have been optimized at the DFT level and the minima connected to each transition state (TS) by following the intrinsic reaction coordinate (IRC). Relative energies are calculated both at the DFT and coupled-cluster levels of theory. The relevant parts of the potential energy surface, especially key transition states, are also studied using multireference wave functions with the final energetics obtained with multireference second-order perturbation theory.

RAPID COMMUNICATION: Formation of MgB2 at ambient temperature with an electrochemical process: a plausible mechanism

NASA Astrophysics Data System (ADS)

Jadhav, A. B.; Subhedar, K. M.; Hyam, R. S.; Talaptra, A.; Sen, Pintu; Bandyopadhyay, S. K.; Pawar, S. H.

2005-06-01

The binary intermetallic MgB2 superconductor has been synthesized by many research groups. However, the mechanism of its formation is not clearly understood. In this communication, a comprehensive mechanism of the formation of MgB2 from Le Chatelier's principle of equilibrium reaction has been explained both for solid-state reaction and electrodeposition methods.

Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

PubMed

Gruden, Maja; Andjeklović, Ljubica; Jissy, Akkarapattiakal Kuriappan; Stepanović, Stepan; Zlatar, Matija; Cui, Qiang; Elstner, Marcus

2017-09-30

Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A RAPID DNA EXTRACTION METHOD FOR PCR IDENTIFICATION OF FUNGAL INDOOR AIR CONTAMINANTS

EPA Science Inventory

Following air sampling, fungal DNA needs to be extracted and purified to a state suitable for laboratory use. Our laboratory has developed a simple method of extraction and purification of fungal DNA appropriate for enzymatic manipulation and polymerase chain reaction (PCR) appli...

Setting the Record Straight: Bottom-Up Carbon Nanostructures via Solid-State Reactions

NASA Astrophysics Data System (ADS)

Jordan, Robert Stanley

Chapter 1 describes the development and spectroscopic investigation of a novel synthetic route to N = 8 armchair graphene nanoribbons from polydiacetylene polymers. Four distinct diphenyl polydiacetylene polymers are produced from the crystal-phase topochemical polymerization of their corresponding diphenyl-1,4-butadiynes. These polydiacetylene polymers are transformed into spectroscopically indistinguishable N = 8 armchair graphene nanoribbons via simple heating in the bulk, solid-state. The stepwise transformation of polydiacetylenes to graphene nanoribbons is examined in detail by the use of complementary spectroscopic methods, namely solid-state nuclear magnetic resonance, infrared, Raman and X-ray photoelectron spectroscopy. The final morphology and width of the nanoribbons is established through the use of high-resolution transmission electron microscopy. Chapter 2 chronicles the implementation of a similar approach to N = 12 armchair graphene nanoribbons from a dinaphthyl substituted polydiacetylene polymer. The mild nature of the process and pristine structure of the nanoribbons is again confirmed with the use of spectroscopic and microscopic methods. The chapter concludes with preliminary electrical measurements of the nanoribbons confirming that they are indeed conductive. Chapter 3 details the development of a synthetic route to diaryl trans-enediynes as structural models of individual reactive units within a polydiacetylene polymer. The trans-enediynes described are found to undergo three distinct annulation reactions depending on reaction conditions. Finally, the synthetic routes developed are utilized to access diethynyl [5]helicenes and phenanthrenes which fueled studies on the mechanism of the Bergman polymerization reaction.

Determination of the in vivo NAD:NADH ratio in Saccharomyces cerevisiae under anaerobic conditions, using alcohol dehydrogenase as sensor reaction.

PubMed

Bekers, K M; Heijnen, J J; van Gulik, W M

2015-08-01

With the current quantitative metabolomics techniques, only whole-cell concentrations of NAD and NADH can be quantified. These measurements cannot provide information on the in vivo redox state of the cells, which is determined by the ratio of the free forms only. In this work we quantified free NAD:NADH ratios in yeast under anaerobic conditions, using alcohol dehydrogenase (ADH) and the lumped reaction of glyceraldehyde-3-phosphate dehydrogenase and 3-phosphoglycerate kinase as sensor reactions. We showed that, with an alternative accurate acetaldehyde determination method, based on rapid sampling, instantaneous derivatization with 2,4 diaminophenol hydrazine (DNPH) and quantification with HPLC, the ADH-catalysed oxidation of ethanol to acetaldehyde can be applied as a relatively fast and simple sensor reaction to quantify the free NAD:NADH ratio under anaerobic conditions. We evaluated the applicability of ADH as a sensor reaction in the yeast Saccharomyces cerevisiae, grown in anaerobic glucose-limited chemostats under steady-state and dynamic conditions. The results found in this study showed that the cytosolic redox status (NAD:NADH ratio) of yeast is at least one order of magnitude lower, and is thus much more reduced, under anaerobic conditions compared to aerobic glucose-limited steady-state conditions. The more reduced state of the cytosol under anaerobic conditions has major implications for (central) metabolism. Accurate determination of the free NAD:NADH ratio is therefore of importance for the unravelling of in vivo enzyme kinetics and to judge accurately the thermodynamic reversibility of each redox reaction. Copyright © 2015 John Wiley & Sons, Ltd.

Double shock experiments and reactive flow modeling on LX-17 to understand the reacted equation of state

NASA Astrophysics Data System (ADS)

Vandersall, Kevin S.; Garcia, Frank; Fried, Laurence E.; Tarver, Craig M.

2014-05-01

Experimental data from measurements of the reacted state of an energetic material are desired to incorporate reacted states in modeling by computer codes. In a case such as LX-17 (92.5% TATB and 7.5% Kel-F by weight), where the time dependent kinetics of reaction is still not fully understood and the reacted state may evolve over time, this information becomes even more vital. Experiments were performed to measure the reacted state of LX-17 using a double shock method involving the use of two flyer materials (with known properties) mounted on the projectile that send an initial shock through the material close to or above the Chapman-Jouguet (CJ) state followed by a second shock at a higher magnitude into the detonated material. By measuring the parameters of the first and second shock waves, information on the reacted state can be obtained. The LX-17 detonation reaction zone profiles plus the arrival times and amplitudes of reflected shocks in LX-17 detonation reaction products were measured using Photonic Doppler Velocimetry (PDV) probes and an aluminum foil coated LiF window. A discussion of this work will include the experimental parameters, velocimetry profiles, data interpretation, reactive CHEETAH and Ignition and Growth modeling, as well as detail on possible future experiments.

Generic HPLC platform for automated enzyme reaction monitoring: Advancing the assay toolbox for transaminases and other PLP-dependent enzymes.

PubMed

Börner, Tim; Grey, Carl; Adlercreutz, Patrick

2016-08-01

Methods for rapid and direct quantification of enzyme kinetics independent of the substrate stand in high demand for both fundamental research and bioprocess development. This study addresses the need for a generic method by developing an automated, standardizable HPLC platform monitoring reaction progress in near real-time. The method was applied to amine transaminase (ATA) catalyzed reactions intensifying process development for chiral amine synthesis. Autosampler-assisted pipetting facilitates integrated mixing and sampling under controlled temperature. Crude enzyme formulations in high and low substrate concentrations can be employed. Sequential, small (1 µL) sample injections and immediate detection after separation permits fast reaction monitoring with excellent sensitivity, accuracy and reproducibility. Due to its modular design, different chromatographic techniques, e.g. reverse phase and size exclusion chromatography (SEC) can be employed. A novel assay for pyridoxal 5'-phosphate-dependent enzymes is presented using SEC for direct monitoring of enzyme-bound and free reaction intermediates. Time-resolved changes of the different cofactor states, e.g. pyridoxal 5'-phosphate, pyridoxamine 5'-phosphate and the internal aldimine were traced in both half reactions. The combination of the automated HPLC platform with SEC offers a method for substrate-independent screening, which renders a missing piece in the assay and screening toolbox for ATAs and other PLP-dependent enzymes. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oxidation and Reduction Reactions in Organic Chemistry

ERIC Educational Resources Information Center

Shibley, Ivan A., Jr.; Amaral, Katie E.; Aurentz, David J.; McCaully, Ronald J.

2010-01-01

A variety of approaches to the concept of oxidation and reduction appear in organic textbooks. The method proposed here is different than most published approaches. The oxidation state is calculated by totaling the number of heterogeneous atoms, [pi]-bonds, and rings. A comparison of the oxidation states of reactant and product determine what type…

A theoretical study of concentration of profiles of primary cytochemical-enzyme reaction products in membrane-bound cell organelles and its application to lysosomal acid phosphatase.

PubMed

Cornelisse, C J; Hermens, W T; Joe, M T; Duijndam, W A; van Duijn, P

1976-11-01

A numerical method was developed for computing the steady-state concentration gradient of a diffusible enzyme reaction product in a membrane-limited compartment of a simplified theoretical cell model. In cytochemical enzyme reactions proceeding according to the metal-capture principle, the local concentration of the primary reaction product is an important factor in the onset of the precipitation process and in the distribution of the final reaction product. The following variables were incorporated into the model: enzyme activity, substrate concentration, Km, diffusion coefficient of substrate and product, particle radius and cell radius. The method was applied to lysosomal acid phosphatase. Numerical values for the variables were estimated from experimental data in the literature. The results show that the calculated phosphate concentrations inside lysosomes are several orders of magnitude lower than the critical concentrations for efficient phosphate capture found in a previous experimental model study. Reasons for this apparent discrepancy are discussed.

An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin.

PubMed

Stewart, James J P

2017-05-01

The catalytic cycle for the serine protease α-chymotrypsin was investigated in an attempt to determine the suitability of using the semiempirical method PM7 in the program MOPAC for investigating enzyme-catalyzed reactions. All six classical intermediates were modeled using standard methods, and were characterized as stable minima on the potential energy surface. Using a modified saddle point optimization method, five transition states were located and verified both by vibrational and by intrinsic reaction coordinate analysis. Some individual features, such as the hydrogen bonds in the oxyanion hole, the nature of various electrostatic interactions, and the role of Met192, were examined. This involved designing and running computational experiments to model mutations that would allow features of interest, in particular the energies involved, to be isolated. Three features within the enzyme were examined in detail: the reaction site itself, where covalent bonds were made and broken, the electrostatic effects of the buried aspartate anion, a passive but essential component of the catalytic triad, and the oxyanion hole, where hydrogen bonds help stabilize charged intermediates. With one minor exception, all phenomena investigated agreed with previously-reported descriptions. This result, along with the fact that all the techniques used were relatively straightforward, leads to the recommendation that PM7 and related methods, such as PM6-D3H4, are appropriate for modeling similar enzyme-catalyzed reactions. Graphical abstract Fifth of six transition states, showing water splitting into hydroxyl anion and a proton, to form the second tetrahedral intermediate and histidinium ion. Atoms of the water molecule involved in the hydrolysis are indicated by halos.

Polynomial-time quantum algorithm for the simulation of chemical dynamics

PubMed Central

Kassal, Ivan; Jordan, Stephen P.; Love, Peter J.; Mohseni, Masoud; Aspuru-Guzik, Alán

2008-01-01

The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can be applied only to small systems. By contrast, we demonstrate that quantum computers could exactly simulate chemical reactions in polynomial time. Our algorithm uses the split-operator approach and explicitly simulates all electron-nuclear and interelectronic interactions in quadratic time. Surprisingly, this treatment is not only more accurate than the Born–Oppenheimer approximation but faster and more efficient as well, for all reactions with more than about four atoms. This is the case even though the entire electronic wave function is propagated on a grid with appropriately short time steps. Although the preparation and measurement of arbitrary states on a quantum computer is inefficient, here we demonstrate how to prepare states of chemical interest efficiently. We also show how to efficiently obtain chemically relevant observables, such as state-to-state transition probabilities and thermal reaction rates. Quantum computers using these techniques could outperform current classical computers with 100 qubits. PMID:19033207

Investigation of singlet oxygen generation in Vit C-Cu2+ -LDL system by chemiluminescence method

NASA Astrophysics Data System (ADS)

Wang, Juan; Xing, Da; Tan, Shici; Tang, Yonghong; He, Yonghong

2002-04-01

In this study, by chemiluminescence method using a Cypridina luciferin analog, 2-methyl-6-(p-methoxyphenyl)-3,7- dihydroimidazo[1,2-a]pyrazin-3-one (MCLA), as a selective and sensitive chemiluminescence probe, singlet oxygen (1O2) formation was observed in the vit C- LDL-Cu2+ reaction system. Another experimental evidence for the generation of 1O2 was the quenching effect of sodium azide (NaN3) on vit C-induced chemiluminescence in the reaction mixture of LDL- Cu2+-MCLA. Analysis based on the experimental results indicated the plausible reaction mechanism is that vit C converts Cu2+ to its reduced state and vit C becomes vit C radical itself, thereby stimulating the formation of peroxyl radicals, and bimolecular reaction of peroxyl radicals results in 1O2 production in the above systems.

Advancing the Theory of Nuclear Reactions with Rare Isotopes. From the Laboratory to the Cosmos

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nunes, Filomena

2015-06-01

The mission of the Topical Collaboration on the Theory of Reactions for Unstable iSotopes (TORUS) was to develop new methods to advance nuclear reaction theory for unstable isotopes—particularly the (d,p) reaction in which a deuteron, composed of a proton and a neutron, transfers its neutron to an unstable nucleus. After benchmarking the state-of-the-art theories, the TORUS collaboration found that there were no exact methods to study (d,p) reactions involving heavy targets; the difficulty arising from the long-range nature of the well known, yet subtle, Coulomb force. To overcome this challenge, the TORUS collaboration developed a new theory where the complexitymore » of treating the long-range Coulomb interaction is shifted to the calculation of so-called form-factors. An efficient implementation for the computation of these form factors was a major achievement of the TORUS collaboration. All the new machinery developed are essential ingredients to analyse (d,p) reactions involving heavy nuclei relevant for astrophysics, energy production, and stockpile stewardship.« less

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm.

PubMed

Roh, Min K; Gillespie, Dan T; Petzold, Linda R

2010-11-07

The weighted stochastic simulation algorithm (wSSA) was developed by Kuwahara and Mura [J. Chem. Phys. 129, 165101 (2008)] to efficiently estimate the probabilities of rare events in discrete stochastic systems. The wSSA uses importance sampling to enhance the statistical accuracy in the estimation of the probability of the rare event. The original algorithm biases the reaction selection step with a fixed importance sampling parameter. In this paper, we introduce a novel method where the biasing parameter is state-dependent. The new method features improved accuracy, efficiency, and robustness.

Efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems

PubMed Central

Yang, Jin; Hlavacek, William S.

2011-01-01

Rule-based models, which are typically formulated to represent cell signaling systems, can now be simulated via various network-free simulation methods. In a network-free method, reaction rates are calculated for rules that characterize molecular interactions, and these rule rates, which each correspond to the cumulative rate of all reactions implied by a rule, are used to perform a stochastic simulation of reaction kinetics. Network-free methods, which can be viewed as generalizations of Gillespie’s method, are so named because these methods do not require that a list of individual reactions implied by a set of rules be explicitly generated, which is a requirement of other methods for simulating rule-based models. This requirement is impractical for rule sets that imply large reaction networks (i.e., long lists of individual reactions), as reaction network generation is expensive. Here, we compare the network-free simulation methods implemented in RuleMonkey and NFsim, general-purpose software tools for simulating rule-based models encoded in the BioNetGen language. The method implemented in NFsim uses rejection sampling to correct overestimates of rule rates, which introduces null events (i.e., time steps that do not change the state of the system being simulated). The method implemented in RuleMonkey uses iterative updates to track rule rates exactly, which avoids null events. To ensure a fair comparison of the two methods, we developed implementations of the rejection and rejection-free methods specific to a particular class of kinetic models for multivalent ligand-receptor interactions. These implementations were written with the intention of making them as much alike as possible, minimizing the contribution of irrelevant coding differences to efficiency differences. Simulation results show that performance of the rejection method is equal to or better than that of the rejection-free method over wide parameter ranges. However, when parameter values are such that ligand-induced aggregation of receptors yields a large connected receptor cluster, the rejection-free method is more efficient. PMID:21832806

High-resolution study of levels in the astrophysically important nucleus 26Mg and resulting updated level assignments

NASA Astrophysics Data System (ADS)

Adsley, P.; Brümmer, J. W.; Faestermann, T.; Fox, S. P.; Hammache, F.; Hertenberger, R.; Meyer, A.; Neveling, R.; Seiler, D.; de Séréville, N.; Wirth, H.-F.

2018-04-01

Background: The 22Ne(α ,n )25Mg reaction is an important source of neutrons for the s -process. Direct measurement of this reaction and the competing 22Ne(α ,γ )26Mg reaction are challenging due to the gaseous nature of both reactants, the low cross section and the experimental challenges of detecting neutrons and high-energy γ rays. Detailed knowledge of the resonance properties enables the rates to be constrained for s -process models. Purpose: Previous experimental studies have demonstrated a lack of agreement in both the number and excitation energy of levels in 26Mg. To try to resolve the disagreement between different experiments, proton and deuteron inelastic scattering from 26Mg have been used to identify excited states. Method: Proton and deuteron beams from the tandem accelerator at the Maier-Leibnitz Laboratorium at Garching, Munich, were incident upon enriched 26MgO targets. Scattered particles were momentum-analyzed in the Q3D magnetic spectrograph and detected at the focal plane. Results: Reassignments of states around Ex=10.8 -10.83 MeV in 26Mg suggested in previous works have been confirmed. In addition, new states in 26Mg have been observed, two below and two above the neutron threshold. Up to six additional states above the neutron threshold may have been observed compared to experimental studies of neutron reactions on 25Mg, but some or all of these states may be due to 24Mg contamination in the target. Finally, inconsistencies between measured resonance strengths and some previously accepted Jπ assignments of excited 26Mg states have been noted. Conclusion: There are still a large number of nuclear properties in 26Mg that have yet to be determined and levels that are, at present, not included in calculations of the reaction rates. In addition, some inconsistencies between existing nuclear data exist that must be resolved in order for the reaction rates to be properly calculated.

Investigation of the reaction 74Ge(p,γ)75As using the in-beam method to improve reaction network predictions for p nuclei

NASA Astrophysics Data System (ADS)

Sauerwein, A.; Endres, J.; Netterdon, L.; Zilges, A.; Foteinou, V.; Provatas, G.; Konstantinopoulos, T.; Axiotis, M.; Ashley, S. F.; Harissopulos, S.; Rauscher, T.

2012-09-01

Background: Astrophysical models studying the origin of the neutron-deficient p nuclides require knowledge of proton capture cross sections at low energy. The production site of the p nuclei is still under discussion but a firm basis of nuclear reaction rates is required to address the astrophysical uncertainties. Data at astrophysically relevant interaction energies are scarce. Problems with the prediction of charged particle capture cross sections at low energy were found in the comparisons between previous data and calculations in the Hauser-Feshbach statistical model of compound reactions.Purpose: A measurement of 74Ge(p,γ)75As at low proton energies, inside the astrophysically relevant energy region, is important in several respects. The reaction is directly important because it is a bottleneck in the reaction flow which produces the lightest p nucleus 74Se. It is also an important addition to the data set required to test reaction-rate predictions and to allow an improvement in the global p+nucleus optical potential required in such calculations.Method: An in-beam experiment was performed, making it possible to measure in the range 2.1≤Ep≤3.7MeV, which is for the most part inside the astrophysically relevant energy window. Angular distributions of the γ-ray transitions were measured with high-purity germanium detectors at eight angles relative to the beam axis. In addition to the total cross sections, partial cross sections for the direct population of 12 levels were determined.Results: The resulting cross sections were compared to Hauser-Feshbach calculations using the code smaragd. Only a constant renormalization factor of the calculated proton widths allowed a good reproduction of both total and partial cross sections. The accuracy of the calculation made it possible to check the spin assignment of some states in 75As. In the case of the 1075-keV state, a double state with spins and parities of 3/2- and 5/2- is needed to explain the experimental partial cross sections. A change in parity from 5/2+ to 5/2- is required for the state at 401 keV. Furthermore, in the case of 74Ge, studying the combination of total and partial cross sections made it possible to test the γ width, which is essential in the calculation of the astrophysical 74As(n,γ)75As rate.Conclusions: Between data and statistical model prediction a factor of about two was found. Nevertheless, the improved astrophysical reaction rate of 74Ge(p,γ) (and its reverse reaction) is only 28% larger than the previous standard rate. The prediction of the 74As(n,γ)75As rate (and its reverse) was confirmed, the newly calculated rate differs only by a few percent from the previous prediction. The in-beam method with high-efficiency detectors proved to be a powerful tool for studies in nuclear astrophysics and nuclear structure.

Enhanced photoluminescence of SrWO{sub 4}:Eu{sup 3+} red phosphor synthesized by mechanochemically assisted solid state metathesis reaction method at room temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peter, Anthuvan John, E-mail: quantajohn@gmail.com; Banu, I. B. Shameem

2015-06-24

Optically efficient europium activated alkaline earth metal tungstate nano phosphor (SrWO{sub 4}) with different doping concentrations have been synthesized by mechanochemically assisted solid state metathesis reaction at room temperature for the first time. The XRD and Raman spectra results indicated that the prepared powders exhibit a scheelite-type tetragonal structure. FTIR spectra exhibited a high absorption band situated at around 854 cm{sup −1}, which was ascribed to the W–O antisymmetric stretching vibrations into the [WO{sub 4}]{sup 2−} tetrahedron groups. Analysis of the emission spectra with different Eu{sup 3+} concentrations revealed that the optimum dopant concentration for SrWO{sub 4}: x Eu{sup 3+} phosphormore » is about 8 mol% of Eu{sup 3+}.The red emission intensity of the SSM prepared SrWO{sub 4}: 0.08Eu{sup 3+} phosphors are 2 times greater than that of the commercial Y{sub 2}O{sub 2}S: Eu{sup 3+} red phosphor prepared by the conventional solid state reaction method. All the results indicate that the phosphor is a promising red phosphor pumped by NUV InGaN chip for fabricating WLED.« less

New chemical sources of energy: A theoretical study

NASA Astrophysics Data System (ADS)

Chaban, Galina

The research presented in this dissertation employs methods of quantum chemistry for the search of highly energetic chemical compounds that can have applications as possible energy sources. The areas of research include: (1) improvement of orbital optimization methods for different types of wavefunctions which leads to substantial savings of computer time and memory; (2) predicting new high energy isomers for singlet and triplet states of Nsb3F and their kinetic stability with respect to isomerisation and dissociation reactions; (3) estimation of minimum energy reaction paths for dissociation reactions of high energy isomers of Nsb2Osb2 including potential energy barriers and minimum energy crossing points between the closest singlet and triplet states; (4) investigation of thermodynamic and kinetic stability of Van der Waals complexes M-Hsb2 (M = Li, Be, B, C, Na, Mg, Al, Si) that can play an important role in improvement of energetic properties of hydrogen based rocket fuels; (5) mapping of the potential energy surface for AlHsb2 compound in the region of crossing between sp2Bsb2 and sp2Asb1 electronic states and predicting the kinetic stability of Al complex, which suggests that Al may be among the promising candidates for inclusion into solid hydrogen for the purpose of energy storage.

Free energies from dynamic weighted histogram analysis using unbiased Markov state model.

PubMed

Rosta, Edina; Hummer, Gerhard

2015-01-13

The weighted histogram analysis method (WHAM) is widely used to obtain accurate free energies from biased molecular simulations. However, WHAM free energies can exhibit significant errors if some of the biasing windows are not fully equilibrated. To account for the lack of full equilibration, we develop the dynamic histogram analysis method (DHAM). DHAM uses a global Markov state model to obtain the free energy along the reaction coordinate. A maximum likelihood estimate of the Markov transition matrix is constructed by joint unbiasing of the transition counts from multiple umbrella-sampling simulations along discretized reaction coordinates. The free energy profile is the stationary distribution of the resulting Markov matrix. For this matrix, we derive an explicit approximation that does not require the usual iterative solution of WHAM. We apply DHAM to model systems, a chemical reaction in water treated using quantum-mechanics/molecular-mechanics (QM/MM) simulations, and the Na(+) ion passage through the membrane-embedded ion channel GLIC. We find that DHAM gives accurate free energies even in cases where WHAM fails. In addition, DHAM provides kinetic information, which we here use to assess the extent of convergence in each of the simulation windows. DHAM may also prove useful in the construction of Markov state models from biased simulations in phase-space regions with otherwise low population.

Theoretical determination of chemical rate constants using novel time-dependent methods

NASA Technical Reports Server (NTRS)

Dateo, Christopher E.

1994-01-01

The work completed within the grant period 10/1/91 through 12/31/93 falls primarily in the area of reaction dynamics using both quantum and classical mechanical methodologies. Essentially four projects have been completed and have been or are in preparation of being published. The majority of time was spent in the determination of reaction rate coefficients in the area of hydrocarbon fuel combustion reactions which are relevant to NASA's High Speed Research Program (HSRP). These reaction coefficients are important in the design of novel jet engines with low NOx emissions, which through a series of catalytic reactions contribute to the deterioration of the earth's ozone layer. A second area of research studied concerned the control of chemical reactivity using ultrashort (femtosecond) laser pulses. Recent advances in pulsed-laser technologies have opened up a vast new field to be investigated both experimentally and theoretically. The photodissociation of molecules adsorbed on surfaces using novel time-independent quantum mechanical methods was a third project. And finally, using state-of-the-art, high level ab initio electronic structure methods in conjunction with accurate quantum dynamical methods, the rovibrational energy levels of a triatomic molecule with two nonhydrogen atoms (HCN) were calculated to unprecedented levels of agreement between theory and experiment.

State-to-state reaction dynamics of 18O+32O2 studied by a time-dependent quantum wavepacket method

NASA Astrophysics Data System (ADS)

Xie, Wenbo; Liu, Lan; Sun, Zhigang; Guo, Hua; Dawes, Richard

2015-02-01

The title isotope exchange reaction was studied by converged time-dependent wave packet calculations, where an efficient 4th order split operator was applied to propagate the initial wave packet. State-to-state differential and integral cross sections up to the collision energy of 0.35 eV were obtained with 32O2 in the hypothetical j0 = 0 state. It is discovered that the differential cross sections are largely forward biased in the studied collision energy range, due to the fact that there is a considerable part of the reaction occurring with large impact parameter and short lifetime relative to the rotational period of the intermediate complex. The oscillations of the forward scattering amplitude as a function of collision energy, which result from coherent contribution of adjacent resonances, may be a sensitive probe for examining the quality of the underlying potential energy surface. A good agreement between the theoretical and recent experimental integral and differential cross sections at collision energy of 7.3 kcal/mol is obtained. However, the theoretical results predict slightly too much forward scattering and colder rotational distributions than the experimental observations at collision energy of 5.7 kcal/mol.

Solid-State Reaction Between Fe-Al-Ca Alloy and Al2O3-CaO-FeO Oxide During Heat Treatment at 1473 K (1200 °C)

NASA Astrophysics Data System (ADS)

Liu, Chengsong; Yang, Shufeng; Li, Jingshe; Ni, Hongwei; Zhang, Xueliang

2017-04-01

The aim of this study was to control the physicochemical characteristics of inclusions in steel through appropriate heat treatment. Using a confocal scanning laser microscope (CSLM) and pipe furnace, the solid-state reactions between Fe-Al-Ca alloy and Al2O3-CaO-FeO oxide during heat treatment at 1473 K (1200 °C) and the influence of these reactions on the compositions of and phases in the alloy and oxide were investigated by the diffusion couple method. Suitable pretreatment of the oxide using a CSLM and production of the diffusion couple of Fe-Al-Ca alloy and Al2O3-CaO-FeO oxide gave good contact between the alloy and oxide. The diffusion couple was then sealed in a quartz tube with a piece of Ti foil to lower oxygen partial pressure and a block of Fe-Al-Ca alloy was introduced to conduct heat treatment experiments. Solid-state reactions between the alloy and oxide during heat treatment at 1473 K (1200 °C) were analyzed and discussed. A dynamic model to calculate the width of the particle precipitation zone based on the Wagner model of internal oxidation of metal was proposed. This model was helpful to understand the solid-state reaction mechanism between Fe-Al-Ca alloy and Al2O3-CaO-FeO oxide.

Development of a high-throughput liquid state assay for lipase activity using natural substrates and rhodamine B.

PubMed

Zottig, Ximena; Meddeb-Mouelhi, Fatma; Beauregard, Marc

2016-03-01

A fluorescence-based assay for the determination of lipase activity using rhodamine B as an indicator, and natural substrates such as olive oil, is described. It is based on the use of a rhodamine B-natural substrate emulsion in liquid state, which is advantageous over agar plate assays. This high-throughput method is simple and rapid and can be automated, making it suitable for screening and metagenomics application. Reaction conditions such as pH and temperature can be varied and controlled. Using triolein or olive oil as a natural substrate allows monitoring of lipase activity in reaction conditions that are closer to those used in industrial settings. The described method is sensitive over a wide range of product concentrations and offers good reproducibility. Copyright © 2015 Elsevier Inc. All rights reserved.

Studies of ARO-Relevant Fuels using Shock Tube/Laser Absorption Methods

DTIC Science & Technology

2017-08-19

elementary reaction rate constants. These experimental methods are the mainstay of this ARO research program at Stanford. The primary scientific... methods and able to pursue careers as leaders in science and engineering in the United States. Results Dissemination: Descriptions of the research have...constants. These experimental methods are the mainstay of this ARO research program at Stanford. The primary scientific problem that this research

A Century of Enzyme Kinetic Analysis, 1913 to 2013

PubMed Central

Johnson, Kenneth A.

2013-01-01

This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function. PMID:23850893

Comprehensive mechanism and structure-sensitivity of ethanol oxidation on platinum: new transition-state searching method for resolving the complex reaction network.

PubMed

Wang, Hui-Fang; Liu, Zhi-Pan

2008-08-20

Ethanol oxidation on Pt is a typical multistep and multiselectivity heterogeneous catalytic process. A comprehensive understanding of this fundamental reaction would greatly benefit design of catalysts for use in direct ethanol fuel cells and the degradation of biomass-derived oxygenates. In this work, the reaction network of ethanol oxidation on different Pt surfaces, including close-packed Pt{111}, stepped Pt{211}, and open Pt{100}, is explored thoroughly with an efficient reaction path searching method, which integrates our new transition-state searching technique with periodic density functional theory calculations. Our new technique enables the location of the transition state and saddle points for most surface reactions simply and efficiently by optimization of local minima. We show that the selectivity of ethanol oxidation on Pt depends markedly on the surface structure, which can be attributed to the structure-sensitivity of two key reaction steps: (i) the initial dehydrogenation of ethanol and (ii) the oxidation of acetyl (CH3CO). On open surface sites, ethanol prefers C-C bond cleavage via strongly adsorbed intermediates (CH2CO or CHCO), which leads to complete oxidation to CO2. However, only partial oxidizations to CH3CHO and CH3COOH occur on Pt{111}. Our mechanism points out that the open surface Pt{100} is the best facet to fully oxidize ethanol at low coverages, which sheds light on the origin of the remarkable catalytic performance of Pt tetrahexahedra nanocrystals found recently. The physical origin of the structure-selectivity is rationalized in terms of both thermodynamics and kinetics. Two fundamental quantities that dictate the selectivity of ethanol oxidation are identified: (i) the ability of surface metal atoms to bond with unsaturated C-containing fragments and (ii) the relative stability of hydroxyl at surface atop sites with respect to other sites.

OH{sup +} in astrophysical media: state-to-state formation rates, Einstein coefficients and inelastic collision rates with He

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gómez-Carrasco, Susana; Godard, Benjamin; Lique, François

The rate constants required to model the OH{sup +} observations in different regions of the interstellar medium have been determined using state of the art quantum methods. First, state-to-state rate constants for the H{sub 2}(v = 0, J = 0, 1) + O{sup +}({sup 4} S) → H + OH{sup +}(X {sup 3}Σ{sup –}, v', N) reaction have been obtained using a quantum wave packet method. The calculations have been compared with time-independent results to assess the accuracy of reaction probabilities at collision energies of about 1 meV. The good agreement between the simulations and the existing experimental cross sectionsmore » in the 0.01-1 eV energy range shows the quality of the results. The calculated state-to-state rate constants have been fitted to an analytical form. Second, the Einstein coefficients of OH{sup +} have been obtained for all astronomically significant rovibrational bands involving the X {sup 3}Σ{sup –} and/or A {sup 3}Π electronic states. For this purpose, the potential energy curves and electric dipole transition moments for seven electronic states of OH{sup +} are calculated with ab initio methods at the highest level, including spin-orbit terms, and the rovibrational levels have been calculated including the empirical spin-rotation and spin-spin terms. Third, the state-to-state rate constants for inelastic collisions between He and OH{sup +}(X {sup 3}Σ{sup –}) have been calculated using a time-independent close coupling method on a new potential energy surface. All these rates have been implemented in detailed chemical and radiative transfer models. Applications of these models to various astronomical sources show that inelastic collisions dominate the excitation of the rotational levels of OH{sup +}. In the models considered, the excitation resulting from the chemical formation of OH{sup +} increases the line fluxes by about 10% or less depending on the density of the gas.« less

Accurate study on the quantum dynamics of the He + HeH(+) (X1Σ+) reaction on a new ab initio potential energy surface for the lowest 1(1)A' electronic singlet state.

PubMed

Xu, Wenwu; Zhang, Peiyu

2013-02-21

A time-dependent quantum wave packet method is used to investigate the dynamics of the He + HeH(+)(X(1)Σ(+)) reaction based on a new potential energy surface [Liang et al., J. Chem. Phys.2012, 136, 094307]. The coupled channel (CC) and centrifugal-sudden (CS) reaction probabilities as well as the total integral cross sections are calculated. A comparison of the results with and without Coriolis coupling revealed that the number of K states N(K) (K is the projection of the total angular momentum J on the body-fixed z axis) significantly influences the reaction threshold. The effective potential energy profiles of each N(K) for the He + HeH(+) reaction in a collinear geometry indicate that the barrier height gradually decreased with increased N(K). The calculated time evolution of CC and CS probability density distribution over the collision energy of 0.27-0.36 eV at total angular momentum J = 50 clearly suggests a lower reaction threshold of CC probabilities. The CC cross sections are larger than the CS results within the entire energy range, demonstrating that the Coriolis coupling effect can effectively promote the He + HeH(+) reaction.

Nanodusty plasma chemistry: a mechanistic and variational transition state theory study of the initial steps of silyl anion-silane and silylene anion-silane polymerization reactions.

PubMed

Bao, Junwei Lucas; Seal, Prasenjit; Truhlar, Donald G

2015-06-28

The growth of nanodusty particles, which is critical in plasma chemistry, physics, and engineering. The aim of the present work is to understand the detailed reaction mechanisms of early steps in this growth. The polymerization of neutral silane with the silylene or silyl anion, which eliminates molecular hydrogen with the formation of their higher homologues, governs the silicon hydride clustering in nanodusty plasma chemistry. The detailed mechanisms of these important polymerization reactions in terms of elementary reactions have not been proposed yet. In the present work, we investigated the initial steps of these polymerization reactions, i.e., the SiH4 + Si2H4(-)/Si2H5(-) reactions, and we propose a three-step mechanism, which is also applicable to the following polymerization steps. CM5 charges of all the silicon-containing species were computed in order to analyze the character of the species in the proposed reaction mechanisms. We also calculated thermal rate constant of each step using multi-structural canonical variational transition state theory (MS-CVT) with the small-curvature tunneling (SCT) approximation, based on the minimum energy path computed using M08-HX/MG3S electronic structure method.

Analysis of transformations of the ultrafast electron transfer photoreaction mechanism in liquid solutions by the rate distribution approach.

PubMed

Kuzmin, Michael G; Soboleva, Irina V

2014-05-01

Representation of the experimental reaction kinetics in the form of rate distribution is shown to be an effective method for the analysis of the mechanisms of these reactions and for comparisons of the kinetics with QC calculations, as well as with the experimental data on the medium mobility. The rate constant distribution function P(k) can be obtained directly from the experimental kinetics N(t) by an inverse Laplace transform. The application of this approach to kinetic data for several excited-state electron transfer reactions reveals the transformations of their rate control factors in the time domain of 1-1000 ps. In neat electron donating solvents two components are observed. The fastest component (k > 1 ps(-1)) was found to be controlled by the fluctuations of the overall electronic coupling matrix element, involving all the reactant molecules, located inside the interior of the solvent shell, rather than for specific pairs of reactant molecules. The slower component (1 > k > 0.1 ps(-1)) is controlled by the medium reorganization (longitudinal relaxation times, τL). A substantial contribution from the non-stationary diffusion controlled reaction is observed in diluted solutions ([Q] < 1 M). No contribution from the long-distance electron transfer (electron tunneling) proposed earlier for the excited-state electron transfer between perylene and tetracyanoethylene in acetonitrile is observed. The rate distribution approach provides a simple and efficient method for the quantitative analysis of the reaction mechanism and transformation of the rate control factors in the course of the reactions.

Advanced methodology to determine plant stresses using in-situ spectral data

NASA Astrophysics Data System (ADS)

Polinova, Maria; Brook, Anna; Housh, Mashor

2017-04-01

Fluorescence method in remote sensing has long been a traditional method estimating plant state. Vegetation indices (VIs) are tool for assessment plants' state based on its spectral characteristics. During the last half-century, in this domain were developed many vegetation indices and even more modifications of these indices. Nowadays, visible range across electromagnetic waves allows assessing plants' health and calculating its physical parameters. One of the VI's capabilities is detecting stress in plants. This approach has application in different areas. For discerning external environment (unnatural) stress from features of plant's development most of VIs have border values for greenness and health. This is the reason for these methods to be superficial and insufficient detecting and estimating stresses on the early stages. This limits plays especial importance in agriculture. Late stress detection leads to irreversible damage in crops and yield loss. We propose new principle of VI analysis for determination unnatural stress on early stages. Novelty of this method is common consideration several VIs related to plant's pigmentation: chlorophyll, carotenoids and anthocyanins. We have tasted this method on two agriculture fields: tomatoes and cotton. The goal of study was to determinate water crop stress at its beginning. A single VI shows reactions on emergence growth stage, fruit producing and ripening phase. It was hard to isolate crops' reaction on water from reaction on growth changes. Nevertheless, we have noted that there is correlation between chlorophyll VIs and carotenoid VIs. The correlation strength was depended on stress type. Based on common VIs analysis we were able to identify dryness and over irrigation stress. In addition, we have determine reaction on fertilizers input. Common VIs analysis can improve existing fluorescence method of remote sensing monitoring. It can find application in areas where the early plant's stress detection is very impotent (e.g. agriculture). Another advantage of this method is identifying stress type. It can increase the role of spectral data for design making.

A kinetic and thermochemical database for organic sulfur and oxygen compounds.

PubMed

Class, Caleb A; Aguilera-Iparraguirre, Jorge; Green, William H

2015-05-28

Potential energy surfaces and reaction kinetics were calculated for 40 reactions involving sulfur and oxygen. This includes 11 H2O addition, 8 H2S addition, 11 hydrogen abstraction, 7 beta scission, and 3 elementary tautomerization reactions, which are potentially relevant in the combustion and desulfurization of sulfur compounds found in various fuel sources. Geometry optimizations and frequencies were calculated for reactants and transition states using B3LYP/CBSB7, and potential energies were calculated using CBS-QB3 and CCSD(T)-F12a/VTZ-F12. Rate coefficients were calculated using conventional transition state theory, with corrections for internal rotations and tunneling. Additionally, thermochemical parameters were calculated for each of the compounds involved in these reactions. With few exceptions, rate parameters calculated using the two potential energy methods agreed reasonably, with calculated activation energies differing by less than 5 kJ mol(-1). The computed rate coefficients and thermochemical parameters are expected to be useful for kinetic modeling.

Combinatorial synthesis of phosphors using arc-imaging furnace

PubMed Central

Ishigaki, Tadashi; Toda, Kenji; Yoshimura, Masahiro; Uematsu, Kazuyoshi; Sato, Mineo

2011-01-01

We have applied a novel ‘melt synthesis technique’ rather than a conventional solid-state reaction to rapidly synthesize phosphor materials. During a synthesis, the mixture of oxides or their precursors is melted by light pulses (10–60 s) in an arc-imaging furnace on a water-cooled copper hearth to form a globule of 1–5 mm diameter, which is then rapidly cooled by turning off the light. Using this method, we synthesized several phosphor compounds including Y3Al5O12:Ce(YAG) and SrAl2O4:Eu,Dy. Complex phosphor oxides are difficult to produce by conventional solid-state reaction techniques because of the slow reaction rates among solid oxides; as a result, the oxides form homogeneous compounds or solid solutions. On the other hand, melt reactions are very fast (10–60 s) and result in homogeneous compounds owing to rapid diffusion and mixing in the liquid phase. Therefore, melt synthesis techniques are suitable for preparing multi component homogeneous compounds and solid solutions. PMID:27877432

Combinatorial synthesis of phosphors using arc-imaging furnace

NASA Astrophysics Data System (ADS)

Ishigaki, Tadashi; Toda, Kenji; Yoshimura, Masahiro; Uematsu, Kazuyoshi; Sato, Mineo

2011-10-01

We have applied a novel 'melt synthesis technique' rather than a conventional solid-state reaction to rapidly synthesize phosphor materials. During a synthesis, the mixture of oxides or their precursors is melted by light pulses (10-60 s) in an arc-imaging furnace on a water-cooled copper hearth to form a globule of 1-5 mm diameter, which is then rapidly cooled by turning off the light. Using this method, we synthesized several phosphor compounds including Y3Al5O12:Ce(YAG) and SrAl2O4:Eu,Dy. Complex phosphor oxides are difficult to produce by conventional solid-state reaction techniques because of the slow reaction rates among solid oxides; as a result, the oxides form homogeneous compounds or solid solutions. On the other hand, melt reactions are very fast (10-60 s) and result in homogeneous compounds owing to rapid diffusion and mixing in the liquid phase. Therefore, melt synthesis techniques are suitable for preparing multi component homogeneous compounds and solid solutions.

Kinetic analysis of non-isothermal solid-state reactions: multi-stage modeling without assumptions in the reaction mechanism.

PubMed

Pomerantsev, Alexey L; Kutsenova, Alla V; Rodionova, Oxana Ye

2017-02-01

A novel non-linear regression method for modeling non-isothermal thermogravimetric data is proposed. Experiments for several heating rates are analyzed simultaneously. The method is applicable to complex multi-stage processes when the number of stages is unknown. Prior knowledge of the type of kinetics is not required. The main idea is a consequent estimation of parameters when the overall model is successively changed from one level of modeling to another. At the first level, the Avrami-Erofeev functions are used. At the second level, the Sestak-Berggren functions are employed with the goal to broaden the overall model. The method is tested using both simulated and real-world data. A comparison of the proposed method with a recently published 'model-free' deconvolution method is presented.

Temporal mapping of photochemical reactions and molecular excited states with carbon specificity

NASA Astrophysics Data System (ADS)

Wang, K.; Murahari, P.; Yokoyama, K.; Lord, J. S.; Pratt, F. L.; He, J.; Schulz, L.; Willis, M.; Anthony, J. E.; Morley, N. A.; Nuccio, L.; Misquitta, A.; Dunstan, D. J.; Shimomura, K.; Watanabe, I.; Zhang, S.; Heathcote, P.; Drew, A. J.

2017-04-01

Photochemical reactions are essential to a large number of important industrial and biological processes. A method for monitoring photochemical reaction kinetics and the dynamics of molecular excitations with spatial resolution within the active molecule would allow a rigorous exploration of the pathway and mechanism of photophysical and photochemical processes. Here we demonstrate that laser-excited muon pump-probe spin spectroscopy (photo-μSR) can temporally and spatially map these processes with a spatial resolution at the single-carbon level in a molecule with a pentacene backbone. The observed time-dependent light-induced changes of an avoided level crossing resonance demonstrate that the photochemical reactivity of a specific carbon atom is modified as a result of the presence of the excited state wavefunction. This demonstrates the sensitivity and potential of this technique in probing molecular excitations and photochemistry.

Solid-state polymerisation via [2+2] cycloaddition reaction involving coordination polymers.

PubMed

Medishetty, Raghavender; Park, In-Hyeok; Lee, Shim Sung; Vittal, Jagadese J

2016-03-14

Highly crystalline metal ions containing organic polymers are potentially useful to manipulate the magnetic and optical properties to make advanced multifunctional materials. However, it is challenging to synthesise monocrystalline metal complexes of organic polymers and single-phase hybrid materials made up of both coordination and organic polymers by traditional solution crystallisation. This requires an entirely different approach in the solid-state by thermal or photo polymerisation of the ligands. Among the photochemical methods available, [2+2] cycloaddition reaction has been recently employed to generate cyclobutane based coordination polymers from the metal complexes. Cyclobutane polymers have also been integrated into coordination polymers in this way. Recent advancements in the construction of polymeric chains of cyclobutane rings through photo-dimerisation reaction in the monocrystalline solids containing metal complexes, coordination polymers and metal-organic framework structures are discussed here.

Lithium vanadium oxides (Li1+xV3O8) as cathode materials in lithium-ion batteries for soldier portable power systems

NASA Astrophysics Data System (ADS)

Wang, Gaojun; Chen, Linfeng; Mathur, Gyanesh N.; Varadan, Vijay K.

2011-04-01

Improving soldier portable power systems is very important for saving soldiers' lives and having a strategic advantage in a war. This paper reports our work on synthesizing lithium vanadium oxides (Li1+xV3O8) and developing their applications as the cathode (positive) materials in lithium-ion batteries for soldier portable power systems. Two synthesizing methods, solid-state reaction method and sol-gel method, are used in synthesizing lithium vanadium oxides, and the chemical reaction conditions are determined mainly based on thermogravimetric and differential thermogravimetric (TG-DTG) analysis. The synthesized lithium vanadium oxides are used as the active positive materials in the cathodes of prototype lithium-ion batteries. By using the new solid-state reaction technique proposed in this paper, lithium vanadium oxides can be synthesized at a lower temperature and in a shorter time, and the synthesized lithium vanadium oxide powders exhibit good crystal structures and good electrochemical properties. In the sol-gel method, different lithium source materials are used, and it is found that lithium nitrate (LiNO3) is better than lithium carbonate (Li2CO3) and lithium hydroxide (LiOH). The lithium vanadium oxides synthesized in this work have high specific charge and discharge capacities, which are helpful for reducing the sizes and weights, or increasing the power capacities, of soldier portable power systems.

Ab Initio Theoretical Studies on the Kinetics of Hydrogen Abstraction Type Reactions of Hydroxyl Radicals with CH3CCl2F and CH3CClF2

NASA Astrophysics Data System (ADS)

Saheb, Vahid; Maleki, Samira

2018-03-01

The hydrogen abstraction reactions from CH3Cl2F (R-141b) and CH3CClF2 (R-142b) by OH radicals are studied theoretically by semi-classical transition state theory. The stationary points for the reactions are located by using KMLYP density functional method along with 6-311++G(2 d,2 p) basis set and MP2 method along with 6-311+G( d, p) basis set. Single-point energy calculations are performed by the CBS-Q and G4 combination methods on the geometries optimized at the KMLYP/6-311++G(2 d,2 p) level of theory. Vibrational anharmonicity coefficients, x ij , which are needed for semi-classical transition state theory calculations, are computed at the KMLYP/6-311++G(2 d,2 p) and MP2/6-311+G( d, p) levels of theory. The computed barrier heights are slightly sensitive to the quantum-chemical method. Thermal rate coefficients are computed over the temperature range from 200 to 2000 K and they are shown to be in accordance with available experimental data. On the basis of the computed rate coefficients, the tropospheric lifetime of the CH3CCl2F and CH3CClF2 are estimated to be about 6.5 and 12.0 years, respectively.

Solid-state reaction synthesis for mixed-phase Eu3+-doped bismuth molybdate and its luminescence properties

NASA Astrophysics Data System (ADS)

Liang, Danyang; Ding, Yu; Wang, Nan; Cai, Xiaomeng; Li, Jia; Han, Linyu; Wang, Shiqi; Han, Yuanyuan; Jia, Guang; Wang, Liyong

2017-09-01

A method for mixed-phase bismuth molybdate doped with Eu3+ ions was developed by solid-state reaction assisting with polyvinyl alcohol (PVA). The results of powder X-ray diffraction showed a mixed-phase structure and the microscopical characterization technology revealed the formation process with the addition of PVA. As a structure inducer, the PVA molecules played a vital role in the formation of phase structure. The as-obtained Eu3+-doped bismuth molybdates were also characterized by using different spectroscopic techniques including FTIR and photoluminescence (PL). The results show that doping concentration, PVA addition and calcination temperature affect photoluminescence properties remarkably.

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

NASA Astrophysics Data System (ADS)

Kim, Changho; Nonaka, Andy; Bell, John B.; Garcia, Alejandro L.; Donev, Aleksandar

2017-03-01

We develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules, to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. By comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

DOE PAGES

Kim, Changho; Nonaka, Andy; Bell, John B.; ...

2017-03-24

Here, we develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules,more » to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. Furthermore, by comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.« less

Low Frequencies of Interference to EPA Quantitative Polymerase Chain Reaction (qPCR) Methods for Microbial Water Quality Monitoring in U.S. Rivers and Streams and Coastal Waters

EPA Science Inventory

In collaboration with U.S States and Tribes, the United States Environmental Protection Agency (EPA) conducts periodic and rotating, statistically based surveys of U.S. rivers and streams (National Rivers and Streams Assessment, NRSA), estuarine and Great Lakes nearshore coastal ...

Preparation of LaB{sub 3}O{sub 6}:Eu{sup 3+} phosphors by a facile precursor method and their luminescent properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xia; Liang, Pan; Huang, Hong-Sheng

2014-04-01

Graphical abstract: LaB{sub 3}O{sub 6}:Eu{sup 3+} phosphor was obtained by calcining the precursor which was synthesized by boric acid melting method. It (a) exhibits much stronger PL intensity than that (b) prepared by conventional solid state reaction method. - Highlights: • A calcining precursor method was used for preparation of LaB{sub 3}O{sub 6}:Eu{sup 3+} phosphor. • Precursor was prepared by boric acid melting method. • The luminescence intensity of LaB{sub 3}O{sub 6}:Eu{sup 3+} was enhanced by the present method. - Abstract: The LaB{sub 3}O{sub 6}:Eu{sup 3+} phosphors were prepared by calcining the precursors which were synthesized by boric acid meltingmore » method using rare earth oxide and boric acid as raw materials, and they were characterized by EDS, XRD, IR, SEM and PL. The influences of reaction temperature for the preparation of precursor and subsequent calcination temperature and time of precursor on the luminescence properties of LaB{sub 3}O{sub 6}:Eu{sup 3+} phosphor were investigated. The results showed that the LaB{sub 3}O{sub 6}:Eu{sup 3+} phosphors with maximum luminescent intensity were obtained by calcining precursor at 1000 °C for 6 h, in which the precursor was prepared at 200 °C for 72 h. Compared with the conventional high temperature solid-state reaction method, the pure LaB{sub 3}O{sub 6}:Eu{sup 3+} phosphor can be obtained at relatively lower calcination temperature by the precursor method and exhibits much stronger emission intensity.« less

Effects of the Physical Characteristics of Cerium Oxide on Plasma-Enhanced Tetraethylorthosiliate Removal Rate of Chemical Mechanical Polishing for Shallow Trench Isolation

NASA Astrophysics Data System (ADS)

Kim, Sang-Kyun; Paik, Ungyu; Oh, Seong-Geun; Park, Yong-Kook; Katoh, Takeo; Park, Jea-Gun

2003-03-01

Ceria powders were synthesized by two different methods, solid-state displacement reaction and wet chemical precipitation, and the influence of the physical characteristics of cerium oxide on the removal rate of plasma-enhanced tetraethylorthosilicate (PETEOS) and chemical vapor deposition (CVD) nitride films in chemical mechanical planarization (CMP) was investigated. The fundamental physicochemical property and electrokinetic behavior of ceria particles in aqueous suspending media were investigated to identify the correlation between the colloidal property of ceria and the CMP performance. The surface potentials of two different ceria particles are found to have different isoelectric point (pHiep) values and differences in physical properties of ceria particles such as porosity and density were found to be the key parameters in CMP of PETEOS films. Ceria powders synthesized by the solid-state displacement reaction method yielded a higher removal rate of PETEOS and higher selectivity than powders synthesized by the wet chemical precipitation method.

Mixed quantum-classical studies of energy partitioning in unimolecular chemical reactions

NASA Astrophysics Data System (ADS)

Bladow, Landon Lowell

A mixed quantum-classical reaction path Hamiltonian method is utilized to study the dynamics of unimolecular reactions. The method treats motion along the reaction path classically and treats the transverse vibrations quantum mechanically. The theory leads to equations that predict the disposai of the exit-channel potential energy to product translation and vibration. In addition, vibrational state distributions are obtained for the product normal modes. Vibrational excitation results from the curvature of the minimum energy reaction path. The method is applied to six unimolecular reactions: HF elimination from fluoroethane, 1,1-difluoroethane, 1,1-difluoroethene, and trifluoromethane; and HCl elimination from chloroethane and acetyl chloride. The minimum energy paths were calculated at either the MP2 or B3LYP level of theory. In all cases, the majority of the vibrational excitation of the products occurs in the HX fragment. The results are compared to experimental data and other theoretical results, where available. The best agreement between the experimental and calculated HX vibrational distributions is found for the halogenated ethanes, and the experimental deduction that the majority of the HX vibrational excitation arises from the potential energy release is supported. It is believed that the excess energy provided in experiments contributes to the poorer agreement between experiment and theory observed for HF elimination from 1,1-difluoroethene and trifluoromethane. An attempt is described to incorporate a treatment of the excess energy into the present method. However, the sign of the curvature coupling elements is then found to affect the dynamics. Overall, the method appears to be an efficient dynamical tool for modeling the disposal of the exit-channel potential energy in unimolecular reactions.

Ab initio and RRKM study of the reaction of ClO with HOCO radicals.

PubMed

Yu, Hua-Gen; Francisco, Joseph S

2009-11-19

The reaction pathways for the ClO + HOCO reaction have been explored using the coupled-cluster method to locate and optimize the critical points on the ground-state potential-energy surface. Results show that the ClO + HOCO reaction can produce Cl + HOC(O)O, HOCl + CO(2), HCl + CO(3), and HClO + CO(2) via an addition or a direct hydrogen abstraction reaction mechanism. The reaction kinetics has been studied using the variational RRKM theory. It is found that the ClO + HOCO reaction is fast and has a negative temperature dependence at low temperatures. At room temperature, the thermal rate coefficient is obtained as 4.26 x 10(-12) cm(3) molecules(-1) s(-1) with product branching fractions of Cl (0.518), HOCl (0.469), HCl (0.01), and HClO (0.003) at zero pressure. The Cl + HOC(O)O products are major, compared to the HOCl + CO(2) products, because of the loose transition state along the dissociation pathway to eliminate Cl. In addition, the RRKM/master equation simulations indicate that the stabilization of the HOC(O)OCl intermediates is noticeable at moderate pressures as its thermal rate constants reach about 6.0 x 10(-13) cm(3) molecules(-1) s(-1). In contrast, the other product branching ratios for the ClO + HOCO reaction are weakly dependent on pressure.

Theoretical study on the mechanism of the reaction of FOX-7 with OH and NO2 radicals: bimolecular reactions with low barrier during the decomposition of FOX-7

NASA Astrophysics Data System (ADS)

Zhang, Ji-Dong; Zhang, Li-Li

2017-12-01

The decomposition of 1,1-diamino-2,2-dinitroethene (FOX-7) attracts great interests, while the studies on bimolecular reactions during the decomposition of FOX-7 are scarce. This study for the first time investigated the bimolecular reactions of OH and NO2 radicals, which are pyrolysis products of ammonium perchlorate (an efficient oxidant usually used in solid propellant), with FOX-7 by computational chemistry methods. The molecular geometries and energies were calculated using the (U)B3LYP/6-31++G(d,p) method. The rate constants of the reactions were calculated by canonical variational transition state theory. We found three mechanisms (H-abstraction, OH addition to C and N atom) for the reaction of OH + FOX-7 and two mechanisms (O abstraction and H abstraction) for the reaction of NO2 + FOX-7. OH radical can abstract H atom or add to C atom of FOX-7 with barriers near to zero, which means OH radical can effectively degrade FOX-7. The O abstraction channel of the reaction of NO2 + FOX-7 results in the formation of NO3 radical, which has never been detected experimentally during the decomposition of FOX-7.

Synthesis and Characterization of a Perovskite Barium Zirconate (BaZrO[subscript 3]): An Experiment for an Advanced Inorganic Chemistry Laboratory

ERIC Educational Resources Information Center

Thananatthanachon, Todsapon

2016-01-01

In this experiment, the students explore the synthesis of a crystalline solid-state material, barium zirconate (BaZrO3) by two different synthetic methods: (a) the wet chemical method using BaCl[subscript 2]·2H[subscript 2]O and ZrOCl[subscript 2]·8H[subscript 2]O as the precursors, and (b) the solid-state reaction from BaCO[subscript 3] and…

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

PubMed Central

Kaltenbacher, Barbara; Hasenauer, Jan

2017-01-01

Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large- and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics. PMID:28114351

Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G.

Here, 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 statemore » 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.« less

An Analytical Framework for Studying Small-Number Effects in Catalytic Reaction Networks: A Probability Generating Function Approach to Chemical Master Equations

PubMed Central

Nakagawa, Masaki; Togashi, Yuichi

2016-01-01

Cell activities primarily depend on chemical reactions, especially those mediated by enzymes, and this has led to these activities being modeled as catalytic reaction networks. Although deterministic ordinary differential equations of concentrations (rate equations) have been widely used for modeling purposes in the field of systems biology, it has been pointed out that these catalytic reaction networks may behave in a way that is qualitatively different from such deterministic representation when the number of molecules for certain chemical species in the system is small. Apart from this, representing these phenomena by simple binary (on/off) systems that omit the quantities would also not be feasible. As recent experiments have revealed the existence of rare chemical species in cells, the importance of being able to model potential small-number phenomena is being recognized. However, most preceding studies were based on numerical simulations, and theoretical frameworks to analyze these phenomena have not been sufficiently developed. Motivated by the small-number issue, this work aimed to develop an analytical framework for the chemical master equation describing the distributional behavior of catalytic reaction networks. For simplicity, we considered networks consisting of two-body catalytic reactions. We used the probability generating function method to obtain the steady-state solutions of the chemical master equation without specifying the parameters. We obtained the time evolution equations of the first- and second-order moments of concentrations, and the steady-state analytical solution of the chemical master equation under certain conditions. These results led to the rank conservation law, the connecting state to the winner-takes-all state, and analysis of 2-molecules M-species systems. A possible interpretation of the theoretical conclusion for actual biochemical pathways is also discussed. PMID:27047384

Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory

DOE PAGES

Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G.

2016-02-03

Here, 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 statemore » 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.« less

Quantum scattering studies of spin-orbit effects in the Cl({sup 2}P) + HCl {yields} ClH + Cl({sup 2}P) reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schatz, G.C.; McCabe, P.; Connor, J.N.L.

1998-07-01

The authors present quantum scattering calculations for the Cl + HCl {yields} ClH + Cl reaction in which they include the three electronic states that correlate asymptotically to the ground state of Cl({sup 2}P) + HCl(X{sup 1}{Sigma}{sup +}). The potential surfaces and couplings are taken from the recent work of C.S. Maierle, G.C. Schatz, M.S. Gordon, P. McCabe and J.N.L. Connor, J. Chem. Soc. Farad. Trans. (1997). They are based on extensive ab initio calculations for geometries in the vicinity of the lowest energy saddle point, and on an electrostatic expansion (plus empirical dispersion and repulsion) for long range geometriesmore » including the van der Waals wells. Spin-orbit coupling has been included using a spin-orbit coupling parameter {lambda} that is assumed to be independent of nuclear geometry, and Coriolis interactions are incorporated accurately. The scattering calculations use a hyperspherical coordinate coupled channel method in full dimensionality. AJ-shifting approximation is employed to convert cumulative reaction probabilities for total angular momentum quantum number J = 1/2 into state selected and thermal rate coefficients. Two issues have been studied: (a) the influence of the magnitude of {lambda} on the fine-structure resolved cumulative probabilities and rate coefficients (the authors consider {lambda}`s that vary from 0 to {+-}100% of the true Cl value), and (b) the transition state resonance spectrum, and its variation with {lambda} and with other parameters in the calculations. Cl + HCl is a simple hydrogen transfer reaction which serves as a canonical model both for heavy-light-heavy atom reactions, and for the reactions of halogen atoms with closed shell molecules.« less

Advancing the frontiers in nanocatalysis, biointerfaces, and renewable energy conversion by innovations of surface techniques.

PubMed

Somorjai, Gabor A; Frei, Heinz; Park, Jeong Y

2009-11-25

The challenge of chemistry in the 21st century is to achieve 100% selectivity of the desired product molecule in multipath reactions ("green chemistry") and develop renewable energy based processes. Surface chemistry and catalysis play key roles in this enterprise. Development of in situ surface techniques such as high-pressure scanning tunneling microscopy, sum frequency generation (SFG) vibrational spectroscopy, time-resolved Fourier transform infrared methods, and ambient pressure X-ray photoelectron spectroscopy enabled the rapid advancement of three fields: nanocatalysts, biointerfaces, and renewable energy conversion chemistry. In materials nanoscience, synthetic methods have been developed to produce monodisperse metal and oxide nanoparticles (NPs) in the 0.8-10 nm range with controlled shape, oxidation states, and composition; these NPs can be used as selective catalysts since chemical selectivity appears to be dependent on all of these experimental parameters. New spectroscopic and microscopic techniques have been developed that operate under reaction conditions and reveal the dynamic change of molecular structure of catalysts and adsorbed molecules as the reactions proceed with changes in reaction intermediates, catalyst composition, and oxidation states. SFG vibrational spectroscopy detects amino acids, peptides, and proteins adsorbed at hydrophobic and hydrophilic interfaces and monitors the change of surface structure and interactions with coadsorbed water. Exothermic reactions and photons generate hot electrons in metal NPs that may be utilized in chemical energy conversion. The photosplitting of water and carbon dioxide, an important research direction in renewable energy conversion, is discussed.

Nudged elastic band method and density functional theory calculation for finding a local minimum energy pathway of p-benzoquinone and phenol fragmentation in mass spectrometry.

PubMed

Sugimura, Natsuhiko; Igarashi, Yoko; Aoyama, Reiko; Shibue, Toshimichi

2017-02-01

Analysis of the fragmentation pathways of molecules in mass spectrometry gives a fundamental insight into gas-phase ion chemistry. However, the conventional intrinsic reaction coordinates method requires knowledge of the transition states of ion structures in the fragmentation pathways. Herein, we use the nudged elastic band method, using only the initial and final state ion structures in the fragmentation pathways, and report the advantages and limitations of the method. We found a minimum energy path of p-benzoquinone ion fragmentation with two saddle points and one intermediate structure. The primary energy barrier, which corresponded to the cleavage of the C-C bond adjacent to the CO group, was calculated to be 1.50 eV. An additional energy barrier, which corresponded to the cleavage of the CO group, was calculated to be 0.68 eV. We also found an energy barrier of 3.00 eV, which was the rate determining step of the keto-enol tautomerization in CO elimination from the molecular ion of phenol. The nudged elastic band method allowed the determination of a minimum energy path using only the initial and final state ion structures in the fragmentation pathways, and it provided faster than the conventional intrinsic reaction coordinates method. In addition, this method was found to be effective in the analysis of the charge structures of the molecules during the fragmentation in mass spectrometry.

Test of the Brink-Axel Hypothesis for the Pygmy Dipole Resonance

NASA Astrophysics Data System (ADS)

Martin, D.; von Neumann-Cosel, P.; Tamii, A.; Aoi, N.; Bassauer, S.; Bertulani, C. A.; Carter, J.; Donaldson, L.; Fujita, H.; Fujita, Y.; Hashimoto, T.; Hatanaka, K.; Ito, T.; Krugmann, A.; Liu, B.; Maeda, Y.; Miki, K.; Neveling, R.; Pietralla, N.; Poltoratska, I.; Ponomarev, V. Yu.; Richter, A.; Shima, T.; Yamamoto, T.; Zweidinger, M.

2017-11-01

The gamma strength function and level density of 1- states in 96Mo have been extracted from a high-resolution study of the (p → , p→ ' ) reaction at 295 MeV and extreme forward angles. By comparison with compound nucleus γ decay experiments, this allows a test of the generalized Brink-Axel hypothesis in the energy region of the pygmy dipole resonance. The Brink-Axel hypothesis is commonly assumed in astrophysical reaction network calculations and states that the gamma strength function in nuclei is independent of the structure of the initial and final state. The present results validate the Brink-Axel hypothesis for 96Mo and provide independent confirmation of the methods used to separate gamma strength function and level density in γ decay experiments.

Preface: Special Topic on Reaction Pathways

NASA Astrophysics Data System (ADS)

Clementi, Cecilia; Henkelman, Graeme

2017-10-01

This Special Topic Issue on Reaction Pathways collects original research articles illustrating the state of the art in the development and application of methods to describe complex chemical systems in terms of relatively simple mechanisms and collective coordinates. A broad range of applications is presented, spanning the sub-fields of biophysics and material science, in an attempt to showcase the similarities in the formulation of the approaches and highlight the different needs of the different application domains.

Native Chemical Ligation Strategy to Overcome Side Reactions during Fmoc-Based Synthesis of C-Terminal Cysteine-Containing Peptides.

PubMed

Lelièvre, Dominique; Terrier, Victor P; Delmas, Agnès F; Aucagne, Vincent

2016-03-04

The Fmoc-based solid phase synthesis of C-terminal cysteine-containing peptides is problematic, due to side reactions provoked by the pronounced acidity of the Cα proton of cysteine esters. We herein describe a general strategy consisting of the postsynthetic introduction of the C-terminal Cys through a key chemoselective native chemical ligation reaction with N-Hnb-Cys peptide crypto-thioesters. This method was successfully applied to the demanding peptide sequences of two natural products of biological interest, giving remarkably high overall yields compared to that of a state of the art strategy.

Non-invasive estimation of dissipation from non-equilibrium fluctuations in chemical reactions.

PubMed

Muy, S; Kundu, A; Lacoste, D

2013-09-28

We show how to extract an estimate of the entropy production from a sufficiently long time series of stationary fluctuations of chemical reactions. This method, which is based on recent work on fluctuation theorems, is direct, non-invasive, does not require any knowledge about the underlying dynamics and is applicable even when only partial information is available. We apply it to simple stochastic models of chemical reactions involving a finite number of states, and for this case, we study how the estimate of dissipation is affected by the degree of coarse-graining present in the input data.

Efficient Application of Continuous Fractional Component Monte Carlo in the Reaction Ensemble

PubMed Central

2017-01-01

A new formulation of the Reaction Ensemble Monte Carlo technique (RxMC) combined with the Continuous Fractional Component Monte Carlo method is presented. This method is denoted by serial Rx/CFC. The key ingredient is that fractional molecules of either reactants or reaction products are present and that chemical reactions always involve fractional molecules. Serial Rx/CFC has the following advantages compared to other approaches: (1) One directly obtains chemical potentials of all reactants and reaction products. Obtained chemical potentials can be used directly as an independent check to ensure that chemical equilibrium is achieved. (2) Independent biasing is applied to the fractional molecules of reactants and reaction products. Therefore, the efficiency of the algorithm is significantly increased, compared to the other approaches. (3) Changes in the maximum scaling parameter of intermolecular interactions can be chosen differently for reactants and reaction products. (4) The number of fractional molecules is reduced. As a proof of principle, our method is tested for Lennard-Jones systems at various pressures and for various chemical reactions. Excellent agreement was found both for average densities and equilibrium mixture compositions computed using serial Rx/CFC, RxMC/CFCMC previously introduced by Rosch and Maginn (Journal of Chemical Theory and Computation, 2011, 7, 269–279), and the conventional RxMC approach. The serial Rx/CFC approach is also tested for the reaction of ammonia synthesis at various temperatures and pressures. Excellent agreement was found between results obtained from serial Rx/CFC, experimental results from literature, and thermodynamic modeling using the Peng–Robinson equation of state. The efficiency of reaction trial moves is improved by a factor of 2 to 3 (depending on the system) compared to the RxMC/CFCMC formulation by Rosch and Maginn. PMID:28737933

Effects of Morning Caffeine’ Ingestion on Mood States, Simple Reaction Time, and Short-Term Maximal Performance on Elite Judoists

PubMed Central

Souissi, Makram; Abedelmalek, Salma; Chtourou, Hamdi; Atheymen, Rim; Hakim, Ahmed; Sahnoun, Zouhair

2012-01-01

Purpose The purpose of the present study was to evaluate the ergogenic effect of caffeine ingestion on mood state, simple reaction time, and muscle power during the Wingate test recorded in the morning on elite Judoists. Methods Twelve elite judoists (age: 21.08 ± 1.16 years, body mass: 83.75 ± 20.2 kg, height: 1.76 ±6.57 m) participated in this study. Mood states, simple reaction time, and muscle power during the Wingate test were measured during two test sessions at 07:00 h and after placebo or caffeine ingestion (i.e. 5 mg/kg). Plasma concentrations of caffeine were measured before (T0) and 1-h after caffeine’ ingestion (T1) and after the Wingate test (T3). Results Our results revealed an increase of the anxiety and the vigor (P<0.01), a reduction of the simple reaction time (P<0.001) and an improvement of the peak and mean powers during the Wingate test. However, the fatigue index during this test was unaffected by the caffeine ingestion. In addition, plasma concentration of caffeine was significantly higher at T1 in comparison with T0. Conclusions In conclusion, the results of this study suggest that morning caffeine ingestion has ergogenic properties with the potential to benefit performance, increase anxiety and vigor, and decrease the simple reaction time. PMID:23012635

Steady-state kinetic mechanism of the NADP+- and NAD+-dependent reactions catalysed by betaine aldehyde dehydrogenase from Pseudomonas aeruginosa.

PubMed Central

Velasco-García, R; González-Segura, L; Muñoz-Clares, R A

2000-01-01

Betaine aldehyde dehydrogenase (BADH) catalyses the irreversible oxidation of betaine aldehyde to glycine betaine with the concomitant reduction of NAD(P)(+) to NADP(H). In Pseudomonas aeruginosa this reaction is a compulsory step in the assimilation of carbon and nitrogen when bacteria are growing in choline or choline precursors. The kinetic mechanisms of the NAD(+)- and NADP(+)-dependent reactions were examined by steady-state kinetic methods and by dinucleotide binding experiments. The double-reciprocal patterns obtained for initial velocity with NAD(P)(+) and for product and dead-end inhibition establish that both mechanisms are steady-state random. However, quantitative analysis of the inhibitions, and comparison with binding data, suggest a preferred route of addition of substrates and release of products in which NAD(P)(+) binds first and NAD(P)H leaves last, particularly in the NADP(+)-dependent reaction. Abortive binding of the dinucleotides, or their analogue ADP, in the betaine aldehyde site was inferred from total substrate inhibition by the dinucleotides, and parabolic inhibition by NADH and ADP. A weak partial uncompetitive substrate inhibition by the aldehyde was observed only in the NADP(+)-dependent reaction. The kinetics of P. aeruginosa BADH is very similar to that of glucose-6-phosphate dehydrogenase, suggesting that both enzymes fulfil a similar amphibolic metabolic role when the bacteria grow in choline and when they grow in glucose. PMID:11104673

Final Report for''Numerical Methods and Studies of High-Speed Reactive and Non-Reactive Flows''

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwendeman, D W

2002-11-20

The work carried out under this subcontract involved the development and use of an adaptive numerical method for the accurate calculation of high-speed reactive flows on overlapping grids. The flow is modeled by the reactive Euler equations with an assumed equation of state and with various reaction rate models. A numerical method has been developed to solve the nonlinear hyperbolic partial differential equations in the model. The method uses an unsplit, shock-capturing scheme, and uses a Godunov-type scheme to compute fluxes and a Runge-Kutta error control scheme to compute the source term modeling the chemical reactions. An adaptive mesh refinementmore » (AMR) scheme has been implemented in order to locally increase grid resolution. The numerical method uses composite overlapping grids to handle complex flow geometries. The code is part of the ''Overture-OverBlown'' framework of object-oriented codes [1, 2], and the development has occurred in close collaboration with Bill Henshaw and David Brown, and other members of the Overture team within CASC. During the period of this subcontract, a number of tasks were accomplished, including: (1) an extension of the numerical method to handle ''ignition and grow'' reaction models and a JWL equations of state; (2) an improvement in the efficiency of the AMR scheme and the error estimator; (3) an addition of a scheme of numerical dissipation designed to suppress numerical oscillations/instabilities near expanding detonations and along grid overlaps; and (4) an exploration of the evolution to detonation in an annulus and of detonation failure in an expanding channel.« less

Coherent diffractive imaging of solid state reactions in zinc oxide crystals

NASA Astrophysics Data System (ADS)

Leake, Steven J.; Harder, Ross; Robinson, Ian K.

2011-11-01

We investigated the doping of zinc oxide (ZnO) microcrystals with iron and nickel via in situ coherent x-ray diffractive imaging (CXDI) in vacuum. Evaporated thin metal films were deposited onto the ZnO microcrystals. A single crystal was selected and tracked through annealing cycles. A solid state reaction was observed in both iron and nickel experiments using CXDI. A combination of the shrink wrap and guided hybrid-input-output phasing methods were applied to retrieve the electron density. The resolution was 33 nm (half order) determined via the phase retrieval transfer function. The resulting images are nevertheless sensitive to sub-angstrom displacements. The exterior of the microcrystal was found to degrade dramatically. The annealing of ZnO microcrystals coated with metal thin films proved an unsuitable doping method. In addition the observed defect structure of one crystal was attributed to the presence of an array of defects and was found to change upon annealing.

Theoretical study of photoinduced epoxidation of olefins catalyzed by ruthenium porphyrin.

PubMed

Ishikawa, Atsushi; Sakaki, Shigeyoshi

2011-05-12

Epoxidation of olefin by [Ru(TMP)(CO)(O)](-) (TMP = tetramesitylporphine), which is a key step of the photocatalyzed epoxidation of olefin by [Ru(TMP)(CO)], is studied mainly with the density functional theory (DFT) method, where [Ru(Por)(CO)] is employed as a model complex (Por = unsubstituted porphyrin). The CASSCF method was also used to investigate the electronic structure of important species in the catalytic cycle. In all of the ruthenium porphyrin species involved in the catalytic cycle, the weight of the main configuration of the CASSCF wave function is larger than 85%, suggesting that the static correlation is not very large. Also, unrestricted-DFT-calculated natural orbitals are essentially the same as CASSCF-calculated ones, here. On the basis of these results, we employed the DFT method in this work. Present computational results show characteristic features of this reaction, as follows: (i) The epoxidation reaction occurs via carboradical-type transition state. Neither carbocation-type nor concerted oxene-insertion-type character is observed in the transition state. (ii) Electron and spin populations transfer from the olefin moiety to the porphyrin ring in the step of the C-O bond formation. (iii) Electron and spin populations of the olefin and porphyrin moieties considerably change around the transition state. (iv) The atomic and spin populations of Ru change little in the reaction, indicating that the Ru center keeps the +II oxidation state in the whole catalytic cycle. (v) The stability of the olefin adduct [Ru(Por)(CO)(O)(olefin)](-) considerably depends on the kind of olefin, such as ethylene, n-hexene, and styrene. In particular, styrene forms a stable olefin adduct. And, (vi) interestingly, the difference in the activation barrier among these olefins is small in the quantitative level (within 5 kcal/mol), indicating that this catalyst can be applied to various substrates. This is because the stabilities and electronic structures of both the olefin adduct and the transition state are similarly influenced by the substituent of olefin.

Search for excited states in 25O

NASA Astrophysics Data System (ADS)

Jones, M. D.; Fossez, K.; Baumann, T.; DeYoung, P. A.; Finck, J. E.; Frank, N.; Kuchera, A. N.; Michel, N.; Nazarewicz, W.; Rotureau, J.; Smith, J. K.; Stephenson, S. L.; Stiefel, K.; Thoennessen, M.; Zegers, R. G. T.

2017-11-01

Background: Theoretical calculations suggest the presence of low-lying excited states in 25O. Previous experimental searches by means of proton knockout on 26F produced no evidence for such excitations. Purpose: We search for excited states in 25O using the 24O(d ,p ) 25O reaction. The theoretical analysis of excited states in unbound O,2725 is based on the configuration interaction approach that accounts for couplings to the scattering continuum. Method: We use invariant-mass spectroscopy to measure neutron-unbound states in 25O. For the theoretical approach, we use the complex-energy Gamow Shell Model and Density Matrix Renormalization Group method with a finite-range two-body interaction optimized to the bound states and resonances of O-2623, assuming a core of 22O. We predict energies, decay widths, and asymptotic normalization coefficients. Results: Our calculations in a large s p d f space predict several low-lying excited states in 25O of positive and negative parity, and we obtain an experimental limit on the relative cross section of a possible Jπ=1/2 + state with respect to the ground state of 25O at σ1 /2 +/σg .s .=0 .25-0.25+1.0 . We also discuss how the observation of negative parity states in 25O could guide the search for the low-lying negative parity states in 27O. Conclusion: Previous experiments based on the proton knockout of 26F suffered from the low cross sections for the population of excited states in 25O because of low spectroscopic factors. In this respect, neutron transfer reactions carry more promise.

Computational Study of Field Initiated Surface Reactions for Synthesis of Diamond and Silicon

NASA Technical Reports Server (NTRS)

Musgrave, Charles Bruce

1999-01-01

This project involves using quantum chemistry to simulate surface chemical reactions in the presence of an electric field for nanofabrication of diamond and silicon. A field delivered by a scanning tunneling microscope (STM) to a nanometer scale region of a surface affects chemical reaction potential energy surfaces (PES) to direct atomic scale surface modification to fabricate sub-nanometer structures. Our original hypothesis is that the applied voltage polarizes the charge distribution of the valence electrons and that these distorted molecular orbitals can be manipulated with the STM so as to change the relative stabilities of the electronic configurations over the reaction coordinates and thus the topology of the PES and reaction kinetics. Our objective is to investigate the effect of applied bias on surface reactions and the extent to which STM delivered fields can be used to direct surface chemical reactions on an atomic scale on diamond and silicon. To analyze the fundamentals of field induced chemistry and to investigate the application of this technique for the fabrication of nanostructures, we have employed methods capable of accurately describing molecular electronic structure. The methods we employ are density functional theory (DFT) quantum chemical (QC) methods. To determine the effect of applied bias on surface reactions we have calculated the QC PESs in various applied external fields for various reaction steps for depositing or etching diamond and silicon. We have chosen reactions which are thought to play a role in etching and the chemical vapor deposition growth of Si and diamond. The PESs of the elementary reaction steps involved are then calculated under the applied fields, which we vary in magnitude and configuration. We pay special attention to the change in the reaction barriers, and transition state locations, and search for low energy reaction channels which were inaccessible without the applied bias.

Interplay between inhibited transport and reaction in nanoporous materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ackerman, David Michael

2013-01-01

This work presents a detailed formulation of reaction and diffusion dynamics of molecules in confined pores such as mesoporous silica and zeolites. A general reaction-diffusion model and discrete Monte Carlo simulations are presented. Both transient and steady state behavior is covered. Failure of previous mean-field models for these systems is explained and discussed. A coarse-grained, generalized hydrodynamic model is developed that accurately captures the interplay between reaction and restricted transport in these systems. This method incorporates the non-uniform chemical diffusion behavior present in finite pores with multi-component diffusion. Two methods of calculating these diffusion values are developed: a random walkmore » based approach and a driven diffusion model based on an extension of Fick's law. The effects of reaction, diffusion, pore length, and catalytic site distribution are investigated. In addition to strictly single file motion, quasi-single file diffusion is incorporated into the model to match a range of experimental systems. The connection between these experimental systems and model parameters is made through Langevin dynamics modeling of particles in confined pores.« less

Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

2002-01-01

The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

Processes of ionization of atoms in nonstationary states by the field of an attosecond pulse

NASA Astrophysics Data System (ADS)

Makarov, D. N.; Matveev, V. I.

2015-02-01

Processes of ionization at the interaction of attosecond pulses of an electromagnetic field with atoms in nonstationary states have been considered. The probabilities and ionization cross section at the radiative relaxation of an excited state of a single-electron atom and at the Auger decay of the autoionization state of a two-electron atom have been calculated. The developed method allows the expansion to the case of more complex targets, including those in the collision state, and to various chemical reactions.

Nucleon resonance structure in the finite volume of lattice QCD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Jia -Jun; Kamano, H.; Lee, T. -S. H.

An approach for relating the nucleon resonances extracted from πN reaction data to lattice QCD calculations has been developed by using the finite-volume Hamiltonian method. Within models of πN reactions, bare states are introduced to parametrize the intrinsic excitations of the nucleon. We show that the resonance can be related to the probability P N*(E) of finding the bare state, N*, in the πN scattering states in infinite volume. We further demonstrate that the probability P V N*(E) of finding the same bare states in the eigenfunctions of the underlying Hamiltonian in finite volume approaches P N*(E) as the volumemore » increases. Our findings suggest that the comparison of P N*(E) and P V N*(E) can be used to examine whether the nucleon resonances extracted from the πN reaction data within the dynamical models are consistent with lattice QCD calculation. We also discuss the measurement of P V N*(E) directly from lattice QCD. Furthermore, the practical differences between our approach and the approach using the Lüscher formalism to relate LQCD calculations to the nucleon resonance poles embedded in the data are also discussed.« less

Nucleon resonance structure in the finite volume of lattice QCD

DOE PAGES

Wu, Jia -Jun; Kamano, H.; Lee, T. -S. H.; ...

2017-06-19

An approach for relating the nucleon resonances extracted from πN reaction data to lattice QCD calculations has been developed by using the finite-volume Hamiltonian method. Within models of πN reactions, bare states are introduced to parametrize the intrinsic excitations of the nucleon. We show that the resonance can be related to the probability P N*(E) of finding the bare state, N*, in the πN scattering states in infinite volume. We further demonstrate that the probability P V N*(E) of finding the same bare states in the eigenfunctions of the underlying Hamiltonian in finite volume approaches P N*(E) as the volumemore » increases. Our findings suggest that the comparison of P N*(E) and P V N*(E) can be used to examine whether the nucleon resonances extracted from the πN reaction data within the dynamical models are consistent with lattice QCD calculation. We also discuss the measurement of P V N*(E) directly from lattice QCD. Furthermore, the practical differences between our approach and the approach using the Lüscher formalism to relate LQCD calculations to the nucleon resonance poles embedded in the data are also discussed.« less

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

PubMed

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 electrostatic stabilization for the transition state through the amidinium group as well as a synergism of transition state recognition and metal ion catalysis. The result was an excellent catalyst for carbonate hydrolysis. These enzyme mimics represent the most active catalysts ever prepared through the molecular imprinting strategy. Their catalytic activity, catalytic efficiency, and catalytic proficiency clearly surpass those of the corresponding catalytic antibodies. The active structures in natural enzymes evolve within soluble proteins, typically by the refining of the folding of one polypeptide chain. To incorporate these characteristics into synthetic polymers, we used the concept of transition state stabilization to develop soluble, nanosized carboxypeptidase A models using a new polymerization method we term the "post-dilution polymerization method". With this methodology, we were able to prepare soluble, highly cross-linked, single-molecule nanoparticles. These particles have controlled molecular weights (39 kDa, for example) and, on average, one catalytically active site per particle. Our strategies have made it possible to obtain efficient new enzyme models and further advance the structural and functional analogy with natural enzymes. Moreover, this bioinspired design based on molecular imprinting in synthetic polymers offers further support for the concept of transition state stabilization in catalysis.

Cure Schedule for Stycast 2651/Catalyst 11.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kropka, Jamie Michael; McCoy, John D.

2017-11-01

The Henkel technical data sheet (TDS) for Stycast 2651/Catalyst 11 lists three alternate cure schedules for the material, each of which would result in a different state of reaction and different material properties. Here, a cure schedule that attains full reaction of the material is defined. The use of this cure schedule will eliminate variance in material properties due to changes in the cure state of the material, and the cure schedule will serve as the method to make material prior to characterizing properties. The following recommendation was motivated by (1) a desire to cure at a single temperature formore » ease of manufacture and (2) a desire to keep the cure temperature low (to minimize residual stress build-up associated with the cooldown from the cure temperature to room temperature) without excessively limiting the cure reaction due to vitrification (i.e., material glass transition temperature, T g, exceeding cure temperature).« less

Accurate rates of the complex mechanisms for growth and dissolu-tion of minerals using a combination of rare event theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stack, Andrew G; Raiten, Paolo; Gale, Julian D.

2012-01-01

Mineral growth and dissolution are often treated as occurring via a single, reversible process that governs the rate of reaction. We show that multiple, distinct intermediate states can occur during both growth and dissolution. Specifically, we have used metadynamics, a method to efficiently explore the free energy landscape of a system, coupled to umbrella sampling and reactive flux calculations, to examine the mechanism and rates of attachment and detachment of a barium ion onto a stepped, barite (BaSO4) surface. The activation energies calculated for the rate limiting reactions, which are different for attachment and detachment, precisely match those measured experimentallymore » during both growth and dissolution. These results can potentially explain anomalous, non-steady state mineral reaction rates observed experimentally, and will enable the design of more efficient growth inhibitors and facilitate an understanding of the effect of impurities.« less

Photochemistry and Transmission Pump-Probe Spectroscopy of 2-Azidobiphenyls in Aqueous Nanocrystalline Suspensions: Simplified Kinetics in Crystalline Solids.

PubMed

Chung, Tim S; Ayitou, Anoklase J-L; Park, Jin H; Breslin, Vanessa M; Garcia-Garibay, Miguel A

2017-04-20

Aqueous nanocrystalline suspensions provide a simple and efficient medium for performing transmission spectroscopy measurements in the solid state. In this Letter we describe the use of laser flash photolysis methods to analyze the photochemistry of 2-azidobiphenyl and several aryl-substituted derivatives. We show that all the crystalline compounds analyzed in this study transform quantitatively into carbazole products via a crystal-to-crystal reconstructive phase transition. While the initial steps of the reaction cannot be followed within the time resolution of our instrument (ca. 8 ns), we detected the primary isocarbazole photoproducts and analyzed the kinetics of their formal 1,5-H shift reactions, which take place in time scales that range from a few nanoseconds to several microseconds. It is worth noting that the high reaction selectivity observed in the crystalline state translates into a clean and simple kinetic process compared to that in solution.

State-to-state reaction dynamics of {sup 18}O+{sup 32}O{sub 2} studied by a time-dependent quantum wavepacket method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Wenbo; Liu, Lan; Sun, Zhigang, E-mail: zsun@dicp.ac.cn

2015-02-14

The title isotope exchange reaction was studied by converged time-dependent wave packet calculations, where an efficient 4th order split operator was applied to propagate the initial wave packet. State-to-state differential and integral cross sections up to the collision energy of 0.35 eV were obtained with {sup 32}O{sub 2} in the hypothetical j{sub 0} = 0 state. It is discovered that the differential cross sections are largely forward biased in the studied collision energy range, due to the fact that there is a considerable part of the reaction occurring with large impact parameter and short lifetime relative to the rotational periodmore » of the intermediate complex. The oscillations of the forward scattering amplitude as a function of collision energy, which result from coherent contribution of adjacent resonances, may be a sensitive probe for examining the quality of the underlying potential energy surface. A good agreement between the theoretical and recent experimental integral and differential cross sections at collision energy of 7.3 kcal/mol is obtained. However, the theoretical results predict slightly too much forward scattering and colder rotational distributions than the experimental observations at collision energy of 5.7 kcal/mol.« less

Molten salt synthesis of nanocrystalline phase of high dielectric constant material CaCu3Ti4O12.

PubMed

Prakash, B Shri; Varma, K B R

2008-11-01

Nanocrystalline powders of giant dielectric constant material, CaCu3Ti4O12 (CCTO), have been prepared successfully by the molten salt synthesis (MSS) using KCl at 750 degrees C/10 h, which is significantly lower than the calcination temperature (approximately 1000 degrees C) that is employed to obtain phase pure CCTO in the conventional solid-state reaction route. The water washed molten salt synthesized powder, characterized by X-ray powder diffraction (XRD), Scanning electron microscopy (SEM), and Transmission electron microscopy (TEM) confirmed to be a phase pure CCTO associated with approximately 150 nm sized crystallites of nearly spherical shape. The decrease in the formation temperature/duration of CCTO in MSS method was attributed to an increase in the diffusion rate or a decrease in the diffusion length of reacting ions in the molten salt medium. As a consequence of liquid phase sintering, pellets of as-synthesized KCl containing CCTO powder exhibited higher sinterability and grain size than that of KCl free CCTO samples prepared by both MSS method and conventional solid-state reaction route. The grain size and the dielectric constant of KCl containing CCTO ceramics increased with increasing sintering temperature (900 degrees C-1050 degrees C). Indeed the dielectric constants of these ceramics were higher than that of KCl free CCTO samples prepared by both MSS method and those obtained via the solid-state reaction route and sintered at the same temperature. Internal barrier layer capacitance (IBLC) model was invoked to correlate the observed dielectric constant with the grain size in these samples.

Analysis of reaction schemes using maximum rates of constituent steps

PubMed Central

Motagamwala, Ali Hussain; Dumesic, James A.

2016-01-01

We show that the steady-state kinetics of a chemical reaction can be analyzed analytically in terms of proposed reaction schemes composed of series of steps with stoichiometric numbers equal to unity by calculating the maximum rates of the constituent steps, rmax,i, assuming that all of the remaining steps are quasi-equilibrated. Analytical expressions can be derived in terms of rmax,i to calculate degrees of rate control for each step to determine the extent to which each step controls the rate of the overall stoichiometric reaction. The values of rmax,i can be used to predict the rate of the overall stoichiometric reaction, making it possible to estimate the observed reaction kinetics. This approach can be used for catalytic reactions to identify transition states and adsorbed species that are important in controlling catalyst performance, such that detailed calculations using electronic structure calculations (e.g., density functional theory) can be carried out for these species, whereas more approximate methods (e.g., scaling relations) are used for the remaining species. This approach to assess the feasibility of proposed reaction schemes is exact for reaction schemes where the stoichiometric coefficients of the constituent steps are equal to unity and the most abundant adsorbed species are in quasi-equilibrium with the gas phase and can be used in an approximate manner to probe the performance of more general reaction schemes, followed by more detailed analyses using full microkinetic models to determine the surface coverages by adsorbed species and the degrees of rate control of the elementary steps. PMID:27162366

Analysis of reaction schemes using maximum rates of constituent steps

DOE PAGES

Motagamwala, Ali Hussain; Dumesic, James A.

2016-05-09

In this paper, we show that the steady-state kinetics of a chemical reaction can be analyzed analytically in terms of proposed reaction schemes composed of series of steps with stoichiometric numbers equal to unity by calculating the maximum rates of the constituent steps, r max,i, assuming that all of the remaining steps are quasi-equilibrated. Analytical expressions can be derived in terms of r max,i to calculate degrees of rate control for each step to determine the extent to which each step controls the rate of the overall stoichiometric reaction. The values of r max,i can be used to predict themore » rate of the overall stoichiometric reaction, making it possible to estimate the observed reaction kinetics. This approach can be used for catalytic reactions to identify transition states and adsorbed species that are important in controlling catalyst performance, such that detailed calculations using electronic structure calculations (e.g., density functional theory) can be carried out for these species, whereas more approximate methods (e.g., scaling relations) are used for the remaining species. Finally, this approach to assess the feasibility of proposed reaction schemes is exact for reaction schemes where the stoichiometric coefficients of the constituent steps are equal to unity and the most abundant adsorbed species are in quasi-equilibrium with the gas phase and can be used in an approximate manner to probe the performance of more general reaction schemes, followed by more detailed analyses using full microkinetic models to determine the surface coverages by adsorbed species and the degrees of rate control of the elementary steps.« less

Calculation of electronic coupling matrix elements for ground and excited state electron transfer reactions: Comparison of the generalized Mulliken{endash}Hush and block diagonalization methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cave, R.J.; Newton, M.D.

1997-06-01

Two independent methods are presented for the nonperturbative calculation of the electronic coupling matrix element (H{sub ab}) for electron transfer reactions using {ital ab initio} electronic structure theory. The first is based on the generalized Mulliken{endash}Hush (GMH) model, a multistate generalization of the Mulliken Hush formalism for the electronic coupling. The second is based on the block diagonalization (BD) approach of Cederbaum, Domcke, and co-workers. Detailed quantitative comparisons of the two methods are carried out based on results for (a) several states of the system Zn{sub 2}OH{sub 2}{sup +} and (b) the low-lying states of the benzene{endash}Cl atom complex andmore » its contact ion pair. Generally good agreement between the two methods is obtained over a range of geometries. Either method can be applied at an arbitrary nuclear geometry and, as a result, may be used to test the validity of the Condon approximation. Examples of nonmonotonic behavior of the electronic coupling as a function of nuclear coordinates are observed for Zn{sub 2}OH{sub 2}{sup +}. Both methods also yield a natural definition of the effective distance (r{sub DA}) between donor (D) and acceptor (A) sites, in contrast to earlier approaches which required independent estimates of r{sub DA}, generally based on molecular structure data. {copyright} {ital 1997 American Institute of Physics.}« less

Comparison between histopathologic features of leprosy in reaction lesions in HIV coinfected and non-coinfected patients*

PubMed Central

Pires, Carla Andréa Avelar; de Miranda, Mario Fernando Ribeiro; Bittencourt, Maraya de Jesus Semblano; de Brito, Arival Cardoso; Xavier, Marília Brasil

2015-01-01

BACKGROUND Leprosy and HIV are diseases that have a major impact on public health in Brazil. Patients coinfected with both diseases, appear to be at higher risk to develop leprosy reactions. OBJECTIVE The aim of this study is to describe the histopathological aspects of cutaneous lesions during reactional states in a group of patients with HIV-leprosy coinfection, compared to patients with leprosy, without coinfection. METHODS Two groups were established: group 1 comprised of 40 patients coinfected with HIV-leprosy; group 2, comprised of 107 patients with leprosy only. Patients presenting reactional states of leprosy had their lesions biopsied and comparatively evaluated. RESULTS Reversal reaction was the most frequent feature in both groups, with dermis edema as the most common histopathological finding. Giant cells were seen in all group 1 histopathological examinations. Dermis edema was the most common finding in patients with erythema nodosum leprosum. CONCLUSION Few histopathological differences were found in both groups, with reversal reaction as the most significant one, although this fact should be analyzed considering the predominant BT clinical form in the coinfected group and BB form in the group without HIV. Larger prospective studies in patients with HIV-leprosy coinfection are needed to confirm and broaden these results. PMID:25672296

Photooxidation of 3-substituted pyrroles:  a postcolumn reaction detection system for singlet molecular oxygen in HPLC.

PubMed

Denham, K; Milofsky, R E

1998-10-01

A postcolumn photochemical reaction detection scheme, based on the reaction of 3-substituted pyrroles with singlet molecular oxygen ((1)O(2)), has been developed. The method is selective and sensitive for the determination of a class of organic compounds called (1)O(2)-sensitizers and is readily coupled to HPLC. Following separation by HPLC, analytes ((1)O(2)-sensitizers) are excited by a Hg pen-ray lamp. Analytes that are efficient (1)O(2)-sensitizers promote ground-state O(2) ((3)Σ(g)(-)) to an excited state ((1)Σ(g)(+) or (1)Δ(g)), which reacts rapidly with tert-butyl-3,4,5-trimethylpyrrolecarboxylate (BTMPC) or N-benzyl-3-methoxypyrrole-2-tert-carboxylate (BMPC), which is added to the mobile phase. Detection is based on the loss of pyrrole (BTMPC or BMPC). The reaction is catalytic in nature since one analyte molecule may absorb light many times, producing large amounts of (1)O(2). Detection limits for several (1)O(2)-sensitizers were improved by 1-2 orders of magnitude over optimized UV-absorbance detection. This paper discusses the optimization of the reaction conditions for this photochemical reaction detection scheme and its application to the detection of PCBs, nitrogen heterocycles, nitro and chloro aromatics, and other substituted aromatic compounds.

Kinetic Analysis for the Multistep Profiles of Organic Reactions: Significance of the Conformational Entropy on the Rate Constants of the Claisen Rearrangement.

PubMed

Sumiya, Yosuke; Nagahata, Yutaka; Komatsuzaki, Tamiki; Taketsugu, Tetsuya; Maeda, Satoshi

2015-12-03

The significance of kinetic analysis as a tool for understanding the reactivity and selectivity of organic reactions has recently been recognized. However, conventional simulation approaches that solve rate equations numerically are not amenable to multistep reaction profiles consisting of fast and slow elementary steps. Herein, we present an efficient and robust approach for evaluating the overall rate constants of multistep reactions via the recursive contraction of the rate equations to give the overall rate constants for the products and byproducts. This new method was applied to the Claisen rearrangement of allyl vinyl ether, as well as a substituted allyl vinyl ether. Notably, the profiles of these reactions contained 23 and 84 local minima, and 66 and 278 transition states, respectively. The overall rate constant for the Claisen rearrangement of allyl vinyl ether was consistent with the experimental value. The selectivity of the Claisen rearrangement reaction has also been assessed using a substituted allyl vinyl ether. The results of this study showed that the conformational entropy in these flexible chain molecules had a substantial impact on the overall rate constants. This new method could therefore be used to estimate the overall rate constants of various other organic reactions involving flexible molecules.

LSENS, a general chemical kinetics and sensitivity analysis code for gas-phase reactions: User's guide

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; Bittker, David A.

1993-01-01

A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS, are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include static system, steady, one-dimensional, inviscid flow, shock initiated reaction, and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method, which works efficiently for the extremes of very fast and very slow reaction, is used for solving the 'stiff' differential equation systems that arise in chemical kinetics. For static reactions, sensitivity coefficients of all dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters can be computed. This paper presents descriptions of the code and its usage, and includes several illustrative example problems.

Exact PDF equations and closure approximations for advective-reactive transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Venturi, D.; Tartakovsky, Daniel M.; Tartakovsky, Alexandre M.

2013-06-01

Mathematical models of advection–reaction phenomena rely on advective flow velocity and (bio) chemical reaction rates that are notoriously random. By using functional integral methods, we derive exact evolution equations for the probability density function (PDF) of the state variables of the advection–reaction system in the presence of random transport velocity and random reaction rates with rather arbitrary distributions. These PDF equations are solved analytically for transport with deterministic flow velocity and a linear reaction rate represented mathematically by a heterog eneous and strongly-correlated random field. Our analytical solution is then used to investigate the accuracy and robustness of the recentlymore » proposed large-eddy diffusivity (LED) closure approximation [1]. We find that the solution to the LED-based PDF equation, which is exact for uncorrelated reaction rates, is accurate even in the presence of strong correlations and it provides an upper bound of predictive uncertainty.« less

Analyses of bifurcation of reaction pathways on a global reaction route map: A case study of gold cluster Au5

NASA Astrophysics Data System (ADS)

Harabuchi, Yu; Ono, Yuriko; Maeda, Satoshi; Taketsugu, Tetsuya

2015-07-01

A global reaction route map is generated for Au5 by the anharmonic downward distortion following method in which 5 minima and 14 transition states (TSs) are located. Through vibrational analyses in the 3N - 7 (N = 5) dimensional space orthogonal to the intrinsic reaction coordinate (IRC), along all the IRCs, four IRCs are found to have valley-ridge transition (VRT) points on the way where a potential curvature changes its sign from positive to negative in a direction orthogonal to the IRC. The detailed mechanisms of bifurcations related to the VRTs are discussed by surveying a landscape of the global reaction route map, and the connectivity of VRT points and minima is clarified. Branching of the products through bifurcations is confirmed by ab initio molecular dynamics simulations starting from the TSs. A new feature of the reaction pathways, unification, is found and discussed.

Synthesis and characterization of iron based superconductor Nd-1111

NASA Astrophysics Data System (ADS)

Alborzi, Z.; Daadmehr, V.

2018-06-01

Polycrystalline sample of NdFeAsO0.8F0.2 was prepared by one-step solid-state reaction method. The structural and electrical properties of sample were characterized through XRD pattern and the 4-probe method. The critical temperature was obtained at 56 K. The crystal structure was tetragonal with P4/nmm:2 symmetry group.

A four-body model for the breakup of Borromean nucleus 22C

NASA Astrophysics Data System (ADS)

Miyamoto, Tomokazu

A Borromean system is a bound 3-body system where no 2-body subsystems are bound. In nuclear physics, a nucleus that can be modelled as a Borromean system is called a Borromean nucleus; 6 He and 11 Li are good examples of this. Recent research suggests that this Borromean nature should also be exhibited by 22 C, the heaviest-known carbon isotope. In this PhD thesis, a schematic approach is taken to study reactions involving Borromean nuclei. Hyperspherical formalism (HH) and coordinate space Faddeev (CSF) method are used for creating their 3-body bound state wave functions. We formulate the reactions of a Borromean nucleus with a stable target at incident energies ranging from tens of (MeV) to a few hundred (MeV); we adopt a 4-body reaction model to deepen our understanding of the reaction mechanism involving Borromean nuclei. The Glauber-WKB framework is used to describe these reactions, which is well-suited for these incident energies. Introducing Watson-Migdal final state interaction, we calculate the E1 strengths for Borromean nuclei so as to elucidate their breakup mechanism and we explore the possibility of the existence of a soft dipole mode. We also calculate the differential breakup cross sections to see how the post-collision interaction can have an impact on the cross sections. As far as 22 C is concerned, it is found that the reactions are mainly focused on the forward angle region, and the contributions from the higher order terms are not significant. This implies that the non-eikonal trajectories do not play a crucial role in the reaction mechanism. Also, both E1 distributions and breakup cross sections seem to sensitive to the 2n-separation energies of the bound state wave functions, but the E1 distributions and the cross sections to 1- continuum state seem not to be sensitive to the FSIs; cross sections to 0+ and 2+ continuum states seem to be sensitive to the FSIs. Our findings does not support the view that, if an soft dipole mode exists, it is induced by the FSIs.

Reactive collisions for NO(2Π) + N(4S) at temperatures relevant to the hypersonic flight regime.

PubMed

Denis-Alpizar, Otoniel; Bemish, Raymond J; Meuwly, Markus

2017-01-18

The NO(X 2 Π) + N( 4 S) reaction which occurs entirely in the triplet manifold of N 2 O is investigated using quasiclassical trajectories and quantum simulations. Fully-dimensional potential energy surfaces for the 3 A' and 3 A'' states are computed at the MRCI+Q level of theory and are represented using a reproducing kernel Hilbert space. The N-exchange and N 2 -formation channels are followed by using the multi-state adiabatic reactive molecular dynamics method. Up to 5000 K these reactions occur predominantly on the N 2 O 3 A'' surface. However, for higher temperatures the contributions of the 3 A' and 3 A'' states are comparable and the final state distributions are far from thermal equilibrium. From the trajectory simulations a new set of thermal rate coefficients of up to 20 000 K is determined. Comparison of the quasiclassical trajectory and quantum simulations shows that a classical description is a good approximation as determined from the final state analysis.

Low-lying electromagnetic transition strengths in 180Pt

NASA Astrophysics Data System (ADS)

Müller-Gatermann, C.; Dewald, A.; Fransen, C.; Braunroth, T.; Jolie, J.; Litzinger, J.; Régis, J. M.; von Spee, F.; Warr, N.; Zell, K. O.; Grahn, T.; Greenlees, P. T.; Hauschild, K.; Jakobsson, U.; Julin, R.; Juutinen, S.; Ketelhut, S.; Nieminen, P.; Nyman, M.; Peura, P.; Rahkila, P.; Ruotsalainen, P.; Sandzelius, M.; Sarén, J.; Scholey, C.; Sorri, J.; Stolze, S.; Uusitalo, J.; Petkov, P.

2018-02-01

Lifetime measurements have been performed using the 98Mo(86Kr,4 n )180Pt reaction at a beam energy of 380 MeV, and the recoil distance Doppler-shift method. In a second experiment the 168Yb(16O,4 n )180Pt reaction at a beam energy of 88 MeV using the Ge-gated γ -γ fast timing technique was used to determine lifetimes. Lifetimes of the four lowest yrast states of 180Pt have been determined. The experimental data are compared to calculations within the framework of the interacting boson model and the general collective model. Both models predict a deformed ground state and are consistent with all the remaining experimental results.

Scientific Transactions No. 11 of the Institute of Mechanics, Moscow State University. [supersonic and hypersonic gas flow and the movement of gas with exothermic reactions

NASA Technical Reports Server (NTRS)

Gonor, A. L. (Editor)

1982-01-01

The results of flow around wings, the determination of the optimal form, and the interaction of the wake with the accompanying flow at supersonic and hypersonic speeds of the free-stream flow are given. Methods of numerical and analytical calculation of one dimensional unsteady and two dimensional steady motions of fuel-gas mixtures with exothermic reactions are also considered.

An experience in the clinical use of specific immunoglobulin from horse blood serum for prophylaxis of Ebola haemorrhagic fever.

PubMed

Borisevich, I V; Chemikova, Natalya K; Markov, V I; Krasnianskiy, V P; Borisevich, S V; Rozhdestvenskiy, E V

The aim of this work was to estimate the efficacy and safety of single intramuscular introduction of specific heterologous immunoglobulin as prophylactic drug against Ebola hemorrhagic fever. Materials and methods. The specific heterologous immunoglobulin was introduced as a special prophylactic drug to 28 patients in epidemic situations, after skin hurt with infectious materials or contact with infectious blood. Clinico-laboratory observation was performed in 24 subjects after single intramuscular introduction of heterologous immunoglobulin Ebola. The samples of blood serum were investigated for immunoglobulin Ebola and antibodies to horse gamma-globulin on the 30th and 60th days after prophylaxis. Results. None of the subjects of the study contracted Ebola fever. There were no anaphylactic reactions after special prophylaxis with specific heterologous immunoglobulin. Among the subjects with normal allergic state 31% responded with local reactions; 13%, with a general reaction (mild case of the serum disease). Almost no reaction was observed in patients with unfavorable allergic state subjected to desensitizing therapy; in the absence of desensitizing therapy, 50% of patients with unfavorable allergic state exhibited local reactions; 17%, mild cases of the serum disease; 33%, moderate cases of the serum disease. In summary, if the tactics of immunoglobulin application was right, the quantity of local allergic reactions was 28%; of wide spread reactions, 6%. Weak serum disease was observed in 11% of the subjects. The prognostic period of resistance to Ebola fever was less than 30 days. Conclusion. The prophylactic use of specific immunoglobulin from horse blood serum against hemorrhagic Ebola fever is effective and relatively safe in patients subjected to desensitizing therapy.

Non-Born-Oppenheimer molecular dynamics of the spin-forbidden reaction O(3P) + CO(X 1Σ+) → CO2(tilde X{}^1Σ _g^ +)

NASA Astrophysics Data System (ADS)

Jasper, Ahren W.; Dawes, Richard

2013-10-01

The lowest-energy singlet (1 1A') and two lowest-energy triplet (1 3A' and 1 3A″) electronic states of CO2 are characterized using dynamically weighted multireference configuration interaction (dw-MRCI+Q) electronic structure theory calculations extrapolated to the complete basis set (CBS) limit. Global analytic representations of the dw-MRCI+Q/CBS singlet and triplet surfaces and of their CASSCF/aug-cc-pVQZ spin-orbit coupling surfaces are obtained via the interpolated moving least squares (IMLS) semiautomated surface fitting method. The spin-forbidden kinetics of the title reaction is calculated using the coupled IMLS surfaces and coherent switches with decay of mixing non-Born-Oppenheimer molecular dynamics. The calculated spin-forbidden association rate coefficient (corresponding to the high pressure limit of the rate coefficient) is 7-35 times larger at 1000-5000 K than the rate coefficient used in many detailed chemical models of combustion. A dynamical analysis of the multistate trajectories is presented. The trajectory calculations reveal direct (nonstatistical) and indirect (statistical) spin-forbidden reaction mechanisms and may be used to test the suitability of transition-state-theory-like statistical methods for spin-forbidden kinetics. Specifically, we consider the appropriateness of the "double passage" approximation, of assuming statistical distributions of seam crossings, and of applications of the unified statistical model for spin-forbidden reactions.

Method of fabricating free-form, high-aspect ratio components for high-current, high-speed microelectrics

DOEpatents

Maxwell, James L; Rose, Chris R; Black, Marcie R; Springer, Robert W

2014-03-11

Microelectronic structures and devices, and method of fabricating a three-dimensional microelectronic structure is provided, comprising passing a first precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures to enhance formation of a first portion of said three-dimensional microelectronic structure; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said first portion of a selected three-dimensional microelectronic structure is formed from said first precursor material; positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs; passing a second precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures whereby a second portion of said three-dimensional microelectronic structure formation is enhanced; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said second portion of a selected three-dimensional microelectronic structure is formed from said second precursor material; and, positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs.

Reactive flow model development for PBXW-126 using modern nonlinear optimization methods

NASA Astrophysics Data System (ADS)

Murphy, M. J.; Simpson, R. L.; Urtiew, P. A.; Souers, P. C.; Garcia, F.; Garza, R. G.

1996-05-01

The initiation and detonation behavior of PBXW-126 has been characterized and is described. PBXW-126 is a composite explosive consisting of approximately equal amounts of RDX, AP, AL, and NTO with a polyurethane binder. The three term ignition and growth of reaction model parameters (ignition+two growth terms) have been found using nonlinear optimization methods to determine the "best" set of model parameters. The ignition term treats the initiation of up to 0.5% of the RDX. The first growth term in the model treats the RDX growth of reaction up to 20% reacted. The second growth term treats the subsequent growth of reaction of the remaining AP/AL/NTO. The unreacted equation of state (EOS) was determined from the wave profiles of embedded gauge tests while the JWL product EOS was determined from cylinder expansion test results. The nonlinear optimization code, NLQPEB/GLO, was used to determine the "best" set of coefficients for the three term Lee-Tarver ignition and growth of reaction model.

One-neutron stripping processes to excited states of *90Y in the 89Y(6Li,5Li )*90Y reaction

NASA Astrophysics Data System (ADS)

Zhang, G. L.; Zhang, G. X.; Hu, S. P.; Yao, Y. J.; Xiang, J. B.; Zhang, H. Q.; Lubian, J.; Ferreira, J. L.; Paes, B.; Cardozo, E. N.; Sun, H. B.; Valiente-Dobón, J. J.; Testov, D.; Goasduff, A.; John, P. R.; Siciliano, M.; Galtarossa, F.; Francesco, R.; Mengoni, D.; Bazzacco, D.; Li, E. T.; Hao, X.; Qu, W. W.

2018-01-01

The measurement of one-neutron stripping cross sections for the 89Y(6Li,5Li )*90Y reaction at 22 MeV and 34 MeV is reported, using both in-beam and off-beam γ -ray spectroscopy methods. Characteristic γ lines of 90Y are clearly identified by both the γ -γ and proton-γ coincidence methods. The obtained cross section of one-neutron stripping at 34 MeV is found to be much smaller than that at 22 MeV. The one-neutron stripping cross sections measured for this system have the same order of magnitude as the one measured for the same reaction for the 6Li+96Zr system at energies around the Coulomb barrier. Parameter-free coupled reaction channel calculations agree quite well with the experimental data. Theoretical study of the effect of the one-neutron transfer on the elastic total fusion cross section is performed.

Effect of wall-mediated hydrodynamic fluctuations on the kinetics of a Brownian nanoparticle

NASA Astrophysics Data System (ADS)

Yu, Hsiu-Yu; Eckmann, David M.; Ayyaswamy, Portonovo S.; Radhakrishnan, Ravi

2016-12-01

The reactive flux formalism (Chandler 1978 J. Chem. Phys. 68, 2959-2970. (doi:10.1063/1.436049)) and the subsequent development of methods such as transition path sampling have laid the foundation for explicitly quantifying the rate process in terms of microscopic simulations. However, explicit methods to account for how the hydrodynamic correlations impact the transient reaction rate are missing in the colloidal literature. We show that the composite generalized Langevin equation (Yu et al. 2015 Phys. Rev. E 91, 052303. (doi:10.1103/PhysRevE.91.052303)) makes a significant step towards solving the coupled processes of molecular reactions and hydrodynamic relaxation by examining how the wall-mediated hydrodynamic memory impacts the two-stage temporal relaxation of the reaction rate for a nanoparticle transition between two bound states in the bulk, near-wall and lubrication regimes.

Combined gradient projection/single component artificial force induced reaction (GP/SC-AFIR) method for an efficient search of minimum energy conical intersection (MECI) geometries

NASA Astrophysics Data System (ADS)

Harabuchi, Yu; Taketsugu, Tetsuya; Maeda, Satoshi

2017-04-01

We report a new approach to search for structures of minimum energy conical intersection (MECIs) automatically. Gradient projection (GP) method and single component artificial force induced reaction (SC-AFIR) method were combined in the present approach. As case studies, MECIs of benzene and naphthalene between their ground and first excited singlet electronic states (S0/S1-MECIs) were explored. All S0/S1-MECIs reported previously were obtained automatically. Furthermore, the number of force calculations was reduced compared to the one required in the previous search. Improved convergence in a step in which various geometrical displacements are induced by SC-AFIR would contribute to the cost reduction.

Exploration of cellular reaction systems.

PubMed

Kirkilionis, Markus

2010-01-01

We discuss and review different ways to map cellular components and their temporal interaction with other such components to different non-spatially explicit mathematical models. The essential choices made in the literature are between discrete and continuous state spaces, between rule and event-based state updates and between deterministic and stochastic series of such updates. The temporal modelling of cellular regulatory networks (dynamic network theory) is compared with static network approaches in two first introductory sections on general network modelling. We concentrate next on deterministic rate-based dynamic regulatory networks and their derivation. In the derivation, we include methods from multiscale analysis and also look at structured large particles, here called macromolecular machines. It is clear that mass-action systems and their derivatives, i.e. networks based on enzyme kinetics, play the most dominant role in the literature. The tools to analyse cellular reaction networks are without doubt most complete for mass-action systems. We devote a long section at the end of the review to make a comprehensive review of related tools and mathematical methods. The emphasis is to show how cellular reaction networks can be analysed with the help of different associated graphs and the dissection into modules, i.e. sub-networks.

A transformation theory of stochastic evolution in Red Moon methodology to time evolution of chemical reaction process in the full atomistic system.

PubMed

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H 2 + I 2  ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H 2 and I 2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H 2 ] eq and equilibrium constants K eq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H 2 ] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

Model studies of hydrogen atom addition and abstraction processes involving ortho-, meta-, and para-benzynes.

PubMed

Clark, A E; Davidson, E R

2001-10-31

H-atom addition and abstraction processes involving ortho-, meta-, and para-benzyne have been investigated by multiconfigurational self-consistent field methods. The H(A) + H(B)...H(C) reaction (where r(BC) is adjusted to mimic the appropriate singlet-triplet energy gap) is shown to effectively model H-atom addition to benzyne. The doublet multiconfiguration wave functions are shown to mix the "singlet" and "triplet" valence bond structures of H(B)...H(C) along the reaction coordinate; however, the extent of mixing is dependent on the singlet-triplet energy gap (DeltaE(ST)) of the H(B)...H(C) diradical. Early in the reaction, the ground-state wave function is essentially the "singlet" VB function, yet it gains significant "triplet" VB character along the reaction coordinate that allows H(A)-H(B) bond formation. Conversely, the wave function of the first excited state is predominantly the "triplet" VB configuration early in the reaction coordinate, but gains "singlet" VB character when the H-atom is close to a radical center. As a result, the potential energy surface (PES) for H-atom addition to triplet H(B)...H(C) diradical is repulsive! The H3 model predicts, in agreement with the actual calculations on benzyne, that the singlet diradical electrons are not coupled strongly enough to give rise to an activation barrier associated with C-H bond formation. Moreover, this model predicts that the PES for H-atom addition to triplet benzyne will be characterized by a repulsive curve early in the reaction coordinate, followed by a potential avoided crossing with the (pi)1(sigma*)1 state of the phenyl radical. In contrast to H-atom addition, large activation barriers characterize the abstraction process in both the singlet ground state and first triplet state. In the ground state, this barrier results from the weakly avoided crossing of the dominant VB configurations in the ground-state singlet (S0) and first excited singlet (S1) because of the large energy gap between S0 and S1 early in the reaction coordinate. Because the S1 state is best described as the combination of the triplet X-H bond and the triplet H(B)...H(C) spin couplings, the activation barrier along the S0 abstraction PES will have much less dependence on the DeltaE(ST) of H(B)...H(C) than previously speculated. For similar reasons, the T1 potential surface is quite comparable to the S0 PES.

Cluster formation in precompound nuclei in the time-dependent framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schuetrumpf, B.; Nazarewicz, W.

Background: Modern applications of nuclear time-dependent density functional theory (TDDFT) are often capable of providing quantitative description of heavy ion reactions. However, the structures of precompound (preequilibrium, prefission) states produced in heavy ion reactions are difficult to assess theoretically in TDDFT as the single-particle density alone is a weak indicator of shell structure and cluster states. Purpose: We employ the time-dependent nucleon localization function (NLF) to reveal the structure of precompound states in nuclear reactions involving light and medium-mass ions. We primarily focus on spin saturated systems with N = Z . Furthermore, we study reactions with oxygen and carbonmore » ions, for which some experimental evidence for α clustering in precompound states exists. Method: We utilize the symmetry-free TDDFT approach with the Skyrme energy density functional UNEDF1 and compute the time-dependent NLFs to describe 16O + 16O, 40Ca + 16O, 40Ca + 40Ca , and 16,18O + 12C collisions at energies above the Coulomb barrier. Results: We show that NLFs reveal a variety of time-dependent modes involving cluster structures. For instance, the 16O + 16O collision results in a vibrational mode of a quasimolecular α - 12 C - 12 C- α state. For heavier ions, a variety of cluster configurations are predicted. For the collision of 16,18O + 12C, we showed that the precompound system has a tendency to form α clusters. This result supports the experimental findings that the presence of cluster structures in the projectile and target nuclei gives rise to strong entrance channel effects and enhanced α emission. Conclusion: The time-dependent nucleon localization measure is a very good indicator of cluster structures in complex precompound states formed in heavy-ion fusion reactions. Finally, the localization reveals the presence of collective vibrations involving cluster structures, which dominate the initial dynamics of the fusing system.« less

Cluster formation in precompound nuclei in the time-dependent framework

DOE PAGES

Schuetrumpf, B.; Nazarewicz, W.

2017-12-15

Background: Modern applications of nuclear time-dependent density functional theory (TDDFT) are often capable of providing quantitative description of heavy ion reactions. However, the structures of precompound (preequilibrium, prefission) states produced in heavy ion reactions are difficult to assess theoretically in TDDFT as the single-particle density alone is a weak indicator of shell structure and cluster states. Purpose: We employ the time-dependent nucleon localization function (NLF) to reveal the structure of precompound states in nuclear reactions involving light and medium-mass ions. We primarily focus on spin saturated systems with N = Z . Furthermore, we study reactions with oxygen and carbonmore » ions, for which some experimental evidence for α clustering in precompound states exists. Method: We utilize the symmetry-free TDDFT approach with the Skyrme energy density functional UNEDF1 and compute the time-dependent NLFs to describe 16O + 16O, 40Ca + 16O, 40Ca + 40Ca , and 16,18O + 12C collisions at energies above the Coulomb barrier. Results: We show that NLFs reveal a variety of time-dependent modes involving cluster structures. For instance, the 16O + 16O collision results in a vibrational mode of a quasimolecular α - 12 C - 12 C- α state. For heavier ions, a variety of cluster configurations are predicted. For the collision of 16,18O + 12C, we showed that the precompound system has a tendency to form α clusters. This result supports the experimental findings that the presence of cluster structures in the projectile and target nuclei gives rise to strong entrance channel effects and enhanced α emission. Conclusion: The time-dependent nucleon localization measure is a very good indicator of cluster structures in complex precompound states formed in heavy-ion fusion reactions. Finally, the localization reveals the presence of collective vibrations involving cluster structures, which dominate the initial dynamics of the fusing system.« less

Cluster formation in precompound nuclei in the time-dependent framework

NASA Astrophysics Data System (ADS)

Schuetrumpf, B.; Nazarewicz, W.

2017-12-01

Background: Modern applications of nuclear time-dependent density functional theory (TDDFT) are often capable of providing quantitative description of heavy ion reactions. However, the structures of precompound (preequilibrium, prefission) states produced in heavy ion reactions are difficult to assess theoretically in TDDFT as the single-particle density alone is a weak indicator of shell structure and cluster states. Purpose: We employ the time-dependent nucleon localization function (NLF) to reveal the structure of precompound states in nuclear reactions involving light and medium-mass ions. We primarily focus on spin saturated systems with N =Z . Furthermore, we study reactions with oxygen and carbon ions, for which some experimental evidence for α clustering in precompound states exists. Method: We utilize the symmetry-free TDDFT approach with the Skyrme energy density functional UNEDF1 and compute the time-dependent NLFs to describe 16O + 16O,40Ca + 16O, 40Ca + 40Ca, and O,1816 + 12C collisions at energies above the Coulomb barrier. Results: We show that NLFs reveal a variety of time-dependent modes involving cluster structures. For instance, the 16O + 16O collision results in a vibrational mode of a quasimolecular α - 12C - 12C-α state. For heavier ions, a variety of cluster configurations are predicted. For the collision of O,1816 + 12C, we showed that the precompound system has a tendency to form α clusters. This result supports the experimental findings that the presence of cluster structures in the projectile and target nuclei gives rise to strong entrance channel effects and enhanced α emission. Conclusion: The time-dependent nucleon localization measure is a very good indicator of cluster structures in complex precompound states formed in heavy-ion fusion reactions. The localization reveals the presence of collective vibrations involving cluster structures, which dominate the initial dynamics of the fusing system.

Part-2: Analytical Expressions of Concentrations of Glucose, Oxygen, and Gluconic Acid in a Composite Membrane for Closed-Loop Insulin Delivery for the Non-steady State Conditions.

PubMed

Mehala, N; Rajendran, L; Meena, V

2017-02-01

A mathematical model developed by Abdekhodaie and Wu (J Membr Sci 335:21-31, 2009), which describes a dynamic process involving an enzymatic reaction and diffusion of reactants and product inside glucose-sensitive composite membrane has been discussed. This theoretical model depicts a system of non-linear non-steady state reaction diffusion equations. These equations have been solved using new approach of homotopy perturbation method and analytical solutions pertaining to the concentrations of glucose, oxygen, and gluconic acid are derived. These analytical results are compared with the numerical results, and limiting case results for steady state conditions and a good agreement is observed. The influence of various kinetic parameters involved in the model has been presented graphically. Theoretical evaluation of the kinetic parameters like the maximal reaction velocity (V max ) and Michaelis-Menten constants for glucose and oxygen (K g and K ox ) is also reported. This predicted model is very much useful for designing the glucose-responsive composite membranes for closed-loop insulin delivery.

Quantum and quasi-classical calculations for the S+ + H2(v, j) →SH+(v′, j′)+H reactive collisions

PubMed Central

Zanchet, Alexandre; Roncero, Octavio; Bulut, Niyazi

2016-01-01

State-to-state cross sections for the S+ + H2(v, j) → SH+ (v′, j′) + H endothermic reaction are obtained with quantum wave packet(WP) and quasi-classical (QCT) methods for different initial rovibrational H2(v, j) over a wide range of translation energies. Final state distribution as a function of the initial quantum number is obtained and discussed. Additionally, the effect of the internal excitation of H2 on the reactivity is carefully studied. It appears that energy transfer among modes is very inefficient, that vibrational energy is the most favorable for reaction and rotational excitation significantly enhance reactivity when vibrational energy is sufficient to reach the product. Special attention is also paid on an unusual discrepancy between classical and quantum dynamics for low rotational levels while agreement improves with rotational excitation of H2, An interesting resonant behaviour found in WP calculations is also discussed and is associated to the existence of roaming classical trajectories that enhance the reactivity of the title reaction. Finally, a comparison with the experimental results of Stowe et al.[1] for S+ + HD and S+ +D2 reactions, finding a reasonably good agreement with those results. PMID:27055725

Quantum and quasi-classical calculations for the S⁺ + H₂(v,j) → SH⁺(v',j') + H reactive collisions.

PubMed

Zanchet, Alexandre; Roncero, Octavio; Bulut, Niyazi

2016-04-28

State-to-state cross-sections for the S(+) + H2(v,j) → SH(+)(v',j') + H endothermic reaction are obtained using quantum wave packet (WP) and quasi-classical (QCT) methods for different initial ro-vibrational H2(v,j) over a wide range of translation energies. The final state distribution as a function of the initial quantum number is obtained and discussed. Additionally, the effect of the internal excitation of H2 on the reactivity is carefully studied. It appears that energy transfer among modes is very inefficient that vibrational energy is the most favorable for the reaction, and rotational excitation significantly enhances the reactivity when vibrational energy is sufficient to reach the product. Special attention is also paid to an unusual discrepancy between classical and quantum dynamics for low rotational levels while agreement improves with rotational excitation of H2. An interesting resonant behaviour found in WP calculations is also discussed and associated with the existence of roaming classical trajectories that enhance the reactivity of the title reaction. Finally, a comparison with the experimental results of Stowe et al. for S(+) + HD and S(+) + D2 reactions exhibits a reasonably good agreement with those results.

Reducing Ambiguities in Spectroscopic Factors with Combined Measurements and the 86Kr(d,p) Reaction at 35MeV/u

NASA Astrophysics Data System (ADS)

Walter, D.; Cizewski, J. A.; Baugher, T.; Ratkiewicz, A.; Manning, B.; Lonsdale, S. J.; Burcher, S.; Pain, S. D.; Chipps, K. A.; Nunes, F. M.; Ahn, S.; Baumann, T.; Bazin, D.; Pereira, J.; Williams, S.; Thompson, P.; Cerizza, G.; Thornsberry, C.; Jones, K. L.; Bardayan, D. W.; O'Malley, P. D.; Kozub, R. L.; Ota, S.

2015-10-01

Spectroscopic information for low-lying states above shell closures depends on the shape of the bound-state potential, which greatly affects the extracted spectroscopic factors. To mitigate this uncertainty, Mukhamedzhanov and Nunes have proposed a combined method; the external portion is fixed with a peripheral reaction, and is combined with a higher energy measurement with a larger contribution from the interior. This will constrain the single-particle ANC, and should enable spectroscopic factors to be deduced with uncertainties dominated by cross-section measurements rather than the bound-state potential. Published measurements of 86Kr(d,p) at 5.5 MeV/u were used for the external contribution of this reaction. An ANC analysis shows that the reaction is peripheral at this energy and the ANC has been extracted. At less-peripheral energies, 86Kr(d,p) at 35 MeV/u has been measured in inverse kinematics at the NSCL using the ORRUBA and SIDAR arrays of silicon strip detectors. Results of the ANC analysis and preliminary results from 86Kr(d,p) at 35 MeV/u will be presented. This work is supported in part by the NSF and the U.S. DOE.

Triplet state dissolved organic matter in aquatic photochemistry: reaction mechanisms, substrate scope, and photophysical properties.

PubMed

McNeill, Kristopher; Canonica, Silvio

2016-11-09

Excited triplet states of chromophoric dissolved organic matter ( 3 CDOM*) play a major role among the reactive intermediates produced upon absorption of sunlight by surface waters. After more than two decades of research on the aquatic photochemistry of 3 CDOM*, the need for improving the knowledge about the photophysical and photochemical properties of these elusive reactive species remains considerable. This critical review examines the efforts to date to characterize 3 CDOM*. Information on 3 CDOM* relies mainly on the use of probe compounds because of the difficulties associated with directly observing 3 CDOM* using transient spectroscopic methods. Singlet molecular oxygen ( 1 O 2 ), which is a product of the reaction between 3 CDOM* and dissolved oxygen, is probably the simplest indicator that can be used to estimate steady-state concentrations of 3 CDOM*. There are two major modes of reaction of 3 CDOM* with substrates, namely triplet energy transfer or oxidation (via electron transfer, proton-coupled electron transfer or related mechanisms). Organic molecules, including several environmental contaminants, that are susceptible to degradation by these two different reaction modes are reviewed. It is proposed that through the use of appropriate sets of probe compounds and model photosensitizers an improved estimation of the distribution of triplet energies and one-electron reduction potentials of 3 CDOM* can be achieved.

Spectral theory of extreme statistics in birth-death systems

NASA Astrophysics Data System (ADS)

Meerson, Baruch

2008-03-01

Statistics of rare events, or large deviations, in chemical reactions and systems of birth-death type have attracted a great deal of interest in many areas of science including cell biochemistry, astrochemistry, epidemiology, population biology, etc. Large deviations become of vital importance when discrete (non-continuum) nature of a population of ``particles'' (molecules, bacteria, cells, animals or even humans) and stochastic character of interactions can drive the population to extinction. I will briefly review the novel spectral method [1-3] for calculating the extreme statistics of a broad class of birth-death processes and reactions involving a single species. The spectral method combines the probability generating function formalism with the Sturm-Liouville theory of linear differential operators. It involves a controlled perturbative treatment based on a natural large parameter of the problem: the average number of particles/individuals in a stationary or metastable state. For extinction (the first passage) problems the method yields accurate results for the extinction statistics and for the quasi-stationary probability distribution, including the tails, of metastable states. I will demonstrate the power of the method on the example of a branching and annihilation reaction, A ->-2.8mm2mm2A,,A ->-2.8mm2mm , representative of a rather general class of processes. *M. Assaf and B. Meerson, Phys. Rev. Lett. 97, 200602 (2006). *M. Assaf and B. Meerson, Phys. Rev. E 74, 041115 (2006). *M. Assaf and B. Meerson, Phys. Rev. E 75, 031122 (2007).

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

PubMed

Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R

2014-10-14

The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a small subset of atoms within the system.

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

PubMed Central

2015-01-01

The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a small subset of atoms within the system. PMID:25328492

Adaptive hybrid simulations for multiscale stochastic reaction networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa

2015-01-21

The probability distribution describing the state of a Stochastic Reaction Network (SRN) evolves according to the Chemical Master Equation (CME). It is common to estimate its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases, these simulations can take an impractical amount of computational time. Therefore, many methods have been developed that approximate sample paths of the underlying stochastic process and estimate the solution of the CME. A prominent class of these methods include hybrid methods that partition the set of species and the set of reactions into discrete and continuous subsets. Such amore » partition separates the dynamics into a discrete and a continuous part. Simulating such a stochastic process can be computationally much easier than simulating the exact discrete stochastic process with SSA. Moreover, the quasi-stationary assumption to approximate the dynamics of fast subnetworks can be applied for certain classes of networks. However, as the dynamics of a SRN evolves, these partitions may have to be adapted during the simulation. We develop a hybrid method that approximates the solution of a CME by automatically partitioning the reactions and species sets into discrete and continuous components and applying the quasi-stationary assumption on identifiable fast subnetworks. Our method does not require any user intervention and it adapts to exploit the changing timescale separation between reactions and/or changing magnitudes of copy-numbers of constituent species. We demonstrate the efficiency of the proposed method by considering examples from systems biology and showing that very good approximations to the exact probability distributions can be achieved in significantly less computational time. This is especially the case for systems with oscillatory dynamics, where the system dynamics change considerably throughout the time-period of interest.« less

Adaptive hybrid simulations for multiscale stochastic reaction networks.

PubMed

Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa

2015-01-21

The probability distribution describing the state of a Stochastic Reaction Network (SRN) evolves according to the Chemical Master Equation (CME). It is common to estimate its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases, these simulations can take an impractical amount of computational time. Therefore, many methods have been developed that approximate sample paths of the underlying stochastic process and estimate the solution of the CME. A prominent class of these methods include hybrid methods that partition the set of species and the set of reactions into discrete and continuous subsets. Such a partition separates the dynamics into a discrete and a continuous part. Simulating such a stochastic process can be computationally much easier than simulating the exact discrete stochastic process with SSA. Moreover, the quasi-stationary assumption to approximate the dynamics of fast subnetworks can be applied for certain classes of networks. However, as the dynamics of a SRN evolves, these partitions may have to be adapted during the simulation. We develop a hybrid method that approximates the solution of a CME by automatically partitioning the reactions and species sets into discrete and continuous components and applying the quasi-stationary assumption on identifiable fast subnetworks. Our method does not require any user intervention and it adapts to exploit the changing timescale separation between reactions and/or changing magnitudes of copy-numbers of constituent species. We demonstrate the efficiency of the proposed method by considering examples from systems biology and showing that very good approximations to the exact probability distributions can be achieved in significantly less computational time. This is especially the case for systems with oscillatory dynamics, where the system dynamics change considerably throughout the time-period of interest.

Ab Initio Study of Chemical Reactions of Cold SrF and CaF Molecules with Alkali-Metal and Alkaline-Earth-Metal Atoms: The Implications for Sympathetic Cooling.

PubMed

Kosicki, Maciej Bartosz; Kędziera, Dariusz; Żuchowski, Piotr Szymon

2017-06-01

We investigate the energetics of the atom exchange reaction in the SrF + alkali-metal atom and CaF + alkali-metal atom systems. Such reactions are possible only for collisions of SrF and CaF with the lithium atoms, while they are energetically forbidden for other alkali-metal atoms. Specifically, we focus on SrF interacting with Li, Rb, and Sr atoms and use ab initio methods to demonstrate that the SrF + Li and SrF + Sr reactions are barrierless. We present potential energy surfaces for the interaction of the SrF molecule with the Li, Rb, and Sr atoms in their energetically lowest-lying electronic spin states. The obtained potential energy surfaces are deep and exhibit profound interaction anisotropies. We predict that the collisions of SrF molecules in the rotational or Zeeman excited states most likely have a strong inelastic character. We discuss the prospects for the sympathetic cooling of SrF and CaF molecules using ultracold alkali-metal atoms.

Transition state theory for activated systems with driven anharmonic barriers.

PubMed

Revuelta, F; Craven, Galen T; Bartsch, Thomas; Borondo, F; Benito, R M; Hernandez, Rigoberto

2017-08-21

Classical transition state theory has been extended to address chemical reactions across barriers that are driven and anharmonic. This resolves a challenge to the naive theory that necessarily leads to recrossings and approximate rates because it relies on a fixed dividing surface. We develop both perturbative and numerical methods for the computation of a time-dependent recrossing-free dividing surface for a model anharmonic system in a solvated environment that interacts strongly with an oscillatory external field. We extend our previous work, which relied either on a harmonic approximation or on periodic force driving. We demonstrate that the reaction rate, expressed as the long-time flux of reactive trajectories, can be extracted directly from the stability exponents, namely, Lyapunov exponents, of the moving dividing surface. Comparison to numerical results demonstrates the accuracy and robustness of this approach for the computation of optimal (recrossing-free) dividing surfaces and reaction rates in systems with Markovian solvation forces. The resulting reaction rates are in strong agreement with those determined from the long-time flux of reactive trajectories.

Coprocessing of plastics with coal and petroleum resid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joo, H.; Curtis, C.W.

1995-12-31

Waste plastics have become an increasing problem in the United States since land filling is no longer considered a feasible disposal method. Since plastics are petroleum-derived materials, coprocessing then with coal to produce transportation fuels is a feasible alternative. In this study, catalytic coprocessing reactions were performed using Blind Canyon bituminous coal, Manji petroleum resid, and waste plastics. Model polymers including polystyrene, low density polyethylene (LDPE) and polyethylene tereplithalare (PET) were selected because they represent a substantial portion of the waste plastics generated in the United States. Coprocessing reactions of coal, resid, and polymer as well as reactions of individualmore » components and combinations of two components were performed at 430{degrees}C for one hour with an initial H{sub 2} pressure of 8.5 MPa introduced at ambient temperature with presulfided NiMo/Al{sub 2}O{sub 3} as catalyst. Coprocessing all three materials resulted in a substantial improvement in the total conversion compared to the coal plus polymer reaction and slightly less conversion than the resid plus polymer combinations.« less

On the Maillard reaction of meteoritic amino acids

NASA Astrophysics Data System (ADS)

Kolb, Vera M.; Bajagic, Milica; Liesch, Patrick J.; Philip, Ajish; Cody, George D.

2006-08-01

We have performed the Maillard reaction of a series of meteoritic amino acids with sugar ribose under simulated prebiotic conditions, in the solid state at 65°C and at the room temperature. Many meteoritic amino acids are highly reactive with ribose, even at the room temperature. We have isolated high molecular weight products that are insoluble in water, and have studied their structure by the IR (infrared) and solid-state C-13 NMR (nuclear magnetic resonance) spectroscopic methods. The functional groups and their distribution were similar among these products, and were comparable to the previously isolated insoluble organic materials from the Maillard reaction of the common amino acids with ribose. In addition, there were some similarities with the insoluble organic material that is found on Murchison. Our results suggest that the Maillard products may contribute to the composition of the part of the insoluble organic material that is found on Murchison. We have also studied the reaction of sodium silicate solution with the Maillard mixtures, to elucidate the process by which the organic compounds are preserved under prebiotic conditions.

A moment-convergence method for stochastic analysis of biochemical reaction networks.

PubMed

Zhang, Jiajun; Nie, Qing; Zhou, Tianshou

2016-05-21

Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

Establishing a theory for deuteron-induced surrogate reactions

NASA Astrophysics Data System (ADS)

Potel, G.; Nunes, F. M.; Thompson, I. J.

2015-09-01

Background: Deuteron-induced reactions serve as surrogates for neutron capture into compound states. Although these reactions are of great applicability, no theoretical efforts have been invested in this direction over the last decade. Purpose: The goal of this work is to establish on firm grounds a theory for deuteron-induced neutron-capture reactions. This includes formulating elastic and inelastic breakup in a consistent manner. Method: We describe this process both in post- and prior-form distorted wave Born approximation following previous works and discuss the differences in the formulation. While the convergence issues arising in the post formulation can be overcome in the prior formulation, in this case one still needs to take into account additional terms due to nonorthogonality. Results: We apply our method to the 93Nb(d ,p )X at Ed=15 and 25 MeV and are able to obtain a good description of the data. We look at the various partial wave contributions, as well as elastic versus inelastic contributions. We also connect our formulation with transfer to neutron bound states. Conclusions: Our calculations demonstrate that the nonorthogonality term arising in the prior formulation is significant and is at the heart of the long-standing controversy between the post and the prior formulations of the theory. We also show that the cross sections for these reactions are angular-momentum dependent and therefore the commonly used Weisskopf limit is inadequate. Finally, we make important predictions for the relative contributions of elastic breakup and nonelastic breakup and call for elastic-breakup measurements to further constrain our model.

Establishing a theory for deuteron induced surrogate reactions

DOE PAGES

Potel, G.; Nunes, F. M.; Thompson, I. J.

2015-09-18

Background: Deuteron-induced reactions serve as surrogates for neutron capture into compound states. Although these reactions are of great applicability, no theoretical efforts have been invested in this direction over the last decade. Purpose: The goal of this work is to establish on firm grounds a theory for deuteron-induced neutron-capture reactions. This includes formulating elastic and inelastic breakup in a consistent manner. Method: We describe this process both in post- and prior-form distorted wave Born approximation following previous works and discuss the differences in the formulation. While the convergence issues arising in the post formulation can be overcome in the priormore » formulation, in this case one still needs to take into account additional terms due to nonorthogonality. Results: We apply our method to the Nb93(d,p)X at Ed=15 and 25 MeV and are able to obtain a good description of the data. We then look at the various partial wave contributions, as well as elastic versus inelastic contributions. We also connect our formulation with transfer to neutron bound states.Conclusions: Our calculations demonstrate that the nonorthogonality term arising in the prior formulation is significant and is at the heart of the long-standing controversy between the post and the prior formulations of the theory. We also show that the cross sections for these reactions are angular-momentum dependent and therefore the commonly used Weisskopf limit is inadequate. We finally make important predictions for the relative contributions of elastic breakup and nonelastic breakup and call for elastic-breakup measurements to further constrain our model.« less

A GC-MS method for the detection of toluene and ethylbenzene in volatile substance abuse.

PubMed

El-Haj, B M; Al-Amri, A M; Hassan, M H; Bin-Khadem, R K; Al-Hadi, A A

2000-09-01

The interference of some substances with the gas chromatography-flame ionization detection and gas chromatography-Fourier transform infrared detection of toluene and ethylbenzene in volatile substance abuse poses problems. A gas chromatography-mass spectrometry (GC-MS) method that will overcome such interference has been developed for the detection of toluene and/or ethylbenzene in the headspace of preparations and products containing these substances and in the headspace of blood samples in the cases of volatile substance abuse. The method is based on converting toluene to benzoic acid via the formation of benzotrichloride. The latter compound was obtained upon the reaction of toluene with chlorine gas under direct sunlight conditions. In the presence of water, benzotrichloride was converted to benzoic acid. Ethylbenzene was converted to benzoic acid and two phenylethanols via the formation of side chain chloro-substituted phenylethanes followed by reaction with water. The chloro-substituted phenylethanes were obtained by the reaction of ethylbenzene with chlorine under direct sunlight conditions. The benzoic acid resulting from toluene and/or ethylbenzene and the two phenylethanols resulting from ethylbenzene were detected by GC-MS as their trimethylsilyl (TMS) derivatives. For the method to be viable for the detection of volatile substance abuse, the chlorination reactions were effected in the gaseous state.

Intermediate mass fragment emission and iso-scaling in dissipative Ca+Sn reactions at 45 AMeV

NASA Astrophysics Data System (ADS)

Singh, H.; Quinlan, M. J.; Tõke, J.; Pawelczak, I.; Henry, E.; Schröder, W. U.; Amorini, F.; Anzalone, A.; Maiolino, C.; Auditore, L.; Loria, D.; Trifiro, A.; Trimarchi, M.; Cardella, G.; De Filippo, E.; Pagano, A.; Chatterjee, M. B.; Cavallaro, S.; Geraci, E.; Papa, M.; Pirrone, S.; Verde, G.; Grzeszczuk, A.; Guazzoni, P.; Zetta, L.; La Guidara, E.; Lanzalone, G.; Lo Nigro, S.; Politi, G.; Loria, D.; Porto, F.; Rizzo, F.; Russotto, P.; Vigilante, M.

2013-04-01

The production mechanism of intermediate-mass fragments (IMFs) with atomic numbers Z = 3 - 7 is explored in the intermediate energy regime, studying dissipative 48Ca+112Sn and 48Ca+124Sn reactions at E/A = 45MeV. Various aspects of IMF emission patterns point to an inelastic break-up type production mechanism involving excited projectile-like fragment from dissipative interactions. Isotopic yield ratios of identical IMFs from the above two dissipative reactions have been analysed using the "isoscaling" method. Observed trends are correlated with ground-state binding energy systematics and their relevance for an evaluation of the symmetry energy is discussed.

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Masunov, Artëm E.; Wait, Elizabeth E.; Atlanov, Arseniy A.

In oxy-fuel combustion, the pure oxygen (O 2), diluted with CO 2 is used as oxidant instead air. Hence, the combustion products (CO 2 and H 2O) are free from pollution by nitrogen oxides. Moreover, high pressures results in the near-liquid density of CO 2 at supercritical state (sCO 2). Unfortunately, the effects of sCO 2 on the combustion kinetics are far from being understood. In order to assist in this understanding, in this work we are using quantum chemistry methods. Here we investigate potential energy surfaces of important combustion reactions in the presence of carbon dioxide melocule. All transitionmore » states, reactant and product complexes are reported for three reactions: H 2CO+HO 2→HCO+H 2O 2 (R1), 2HO 2→H 2O 2+O 2 (R2), and CO+OH→CO 2+H (R3). In the reaction R3, covalent binding of CO 2 to OH radical and then CO molecule opens a new pathway, including hydrogen transfer from oxygen to carbon atoms followed by CH bond dissociation. Compared to bimolecular OH+CO mechanism, this pathway reduces the activation barrier by 5 kcal/mol, and is expected to accelerate the reaction. This is the first report of autocatalytic effect in combustion. In case of hydroperoxyl self-reaction 2HO 2→H 2O 2+O 2 the intermediates, containing covalent bonds to CO 2 were found not to be competitive. However, the spectator CO 2 molecule is able to stabilize the cyclic transition state and lower the barrier by 3 kcal/mol. Formation of covalent intermediates was also discovered in H 2CO+HO 2→HCO+H 2O 2 reaction, but these specie lead to substantially higher activation barriers which makes them unlikely to play role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide also stabilized transition state and reduces reaction barrier. Lastly, these results indicate that CO 2 environment is likely to have catalytic effect on combustion reactions, which needs to be included in kinetic combustion mechanisms in supercritical CO 2.« less

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics

DOE PAGES

Masunov, Artëm E.; Wait, Elizabeth E.; Atlanov, Arseniy A.; ...

2017-05-03

In oxy-fuel combustion, the pure oxygen (O 2), diluted with CO 2 is used as oxidant instead air. Hence, the combustion products (CO 2 and H 2O) are free from pollution by nitrogen oxides. Moreover, high pressures results in the near-liquid density of CO 2 at supercritical state (sCO 2). Unfortunately, the effects of sCO 2 on the combustion kinetics are far from being understood. In order to assist in this understanding, in this work we are using quantum chemistry methods. Here we investigate potential energy surfaces of important combustion reactions in the presence of carbon dioxide melocule. All transitionmore » states, reactant and product complexes are reported for three reactions: H 2CO+HO 2→HCO+H 2O 2 (R1), 2HO 2→H 2O 2+O 2 (R2), and CO+OH→CO 2+H (R3). In the reaction R3, covalent binding of CO 2 to OH radical and then CO molecule opens a new pathway, including hydrogen transfer from oxygen to carbon atoms followed by CH bond dissociation. Compared to bimolecular OH+CO mechanism, this pathway reduces the activation barrier by 5 kcal/mol, and is expected to accelerate the reaction. This is the first report of autocatalytic effect in combustion. In case of hydroperoxyl self-reaction 2HO 2→H 2O 2+O 2 the intermediates, containing covalent bonds to CO 2 were found not to be competitive. However, the spectator CO 2 molecule is able to stabilize the cyclic transition state and lower the barrier by 3 kcal/mol. Formation of covalent intermediates was also discovered in H 2CO+HO 2→HCO+H 2O 2 reaction, but these specie lead to substantially higher activation barriers which makes them unlikely to play role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide also stabilized transition state and reduces reaction barrier. Lastly, these results indicate that CO 2 environment is likely to have catalytic effect on combustion reactions, which needs to be included in kinetic combustion mechanisms in supercritical CO 2.« less

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics.

PubMed

Masunov, Artëm E; Wait, Elizabeth E; Atlanov, Arseniy A; Vasu, Subith S

2017-05-18

In oxy-fuel combustion, the pure oxygen (O 2 ), diluted with CO 2 is used as oxidant instead air. Hence, the combustion products (CO 2 and H 2 O) are free from pollution by nitrogen oxides. Moreover, high pressures result in the near-liquid density of CO 2 at supercritical state (sCO 2 ). Unfortunately, the effects of sCO 2 on the combustion kinetics are far from being understood. To assist in this understanding, in this work we are using quantum chemistry methods. Here we investigate potential energy surfaces of important combustion reactions in the presence of the carbon dioxide molecule. All transition states and reactant and product complexes are reported for three reactions: H 2 CO + HO 2 → HCO + H 2 O 2 (R1), 2HO 2 → H 2 O 2 + O 2 (R2), and CO + OH → CO 2 + H (R3). In reaction R3, covalent binding of CO 2 to the OH radical and then the CO molecule opens a new pathway, including hydrogen transfer from oxygen to carbon atoms followed by CH bond dissociation. Compared to the bimolecular OH + CO mechanism, this pathway reduces the activation barrier by 5 kcal/mol and is expected to accelerate the reaction. In the case of hydroperoxyl self-reaction 2HO 2 → H 2 O 2 + O 2 the intermediates, containing covalent bonds to CO 2 are found not to be competitive. However, the spectator CO 2 molecule can stabilize the cyclic transition state and lower the barrier by 3 kcal/mol. Formation of covalent intermediates is also discovered in the H 2 CO + HO 2 → HCO + H 2 O 2 reaction, but these species lead to substantially higher activation barriers, which makes them unlikely to play a role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide also stabilizes the transition state and reduces the reaction barrier. These results indicate that the CO 2 environment is likely to have a catalytic effect on combustion reactions, which needs to be included in kinetic combustion mechanisms in supercritical CO 2 .

Nonenzymatic and enzymatic hydrolysis of alkyl halides: A theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides

PubMed Central

Maulitz, Andreas H.; Lightstone, Felice C.; Zheng, Ya-Jun; Bruice, Thomas C.

1997-01-01

The SN2 displacements of chloride ion from CH3Cl, C2H5Cl, and C2H4Cl2 by acetate and hydroxide ions have been investigated, using ab initio molecular orbital theory at the HF/6–31+G(d), MP2/6–31+G(d), and MP4/6–31+G(d) levels of theory. The central barriers (calculated from the initial ion–molecule complex) of the reactions, the differences of the overall reaction energies, and the geometries of the transition states are compared. Essential stereochemical changes before and after the displacement reactions are described for selected cases. The gas phase reactions of hydroxide with CH3Cl, C2H5Cl, and C2H4Cl2 have no overall barrier, but there is a small overall barrier for the reactions of acetate with CH3Cl, C2H5Cl, and C2H4Cl2. A self-consistent reaction field solvation model was used to examine the SN2 reactions between methyl chloride and hydroxide ion and between 1,2-dichloroethane and acetate in solution. As expected, the reactions in polar solvent have a large barrier. However, the transition state structures determined by ab initio calculations change only slightly in the presence of a highly polar solvent as compared with the gas phase. We also calibrated the PM3 method for future study of an enzymatic SN2 displacement of halogen. PMID:9192609

Implementation of steady state approximation for modelling of reaction kinetic of UV catalysed hydrogen peroxide oxidation of starch

NASA Astrophysics Data System (ADS)

Kumoro, Andri Cahyo; Retnowati, Diah Susetyo; Ratnawati, Budiyati, Catarina Sri

2015-12-01

With regard to its low viscosity, high stability, clarity, film forming and binding properties, oxidised starch has been widely used in various applications specifically in the food, paper, textile, laundry finishing and binding materials industries. A number of methods have been used to produce oxidised starch through reactions with various oxidizing agents, such as hydrogen peroxide, air oxygen, ozone, bromine, chromic acid, permanganate, nitrogen dioxide and hypochlorite. Unfortunately, most of previous works reported in the literatures were focused on the study of reaction mechanism and physicochemical properties characterization of the oxidised starches produced without investigation of the reaction kinetics of the oxidation process. This work aimed to develop a simple kinetic model for UV catalysed hydrogen peroxide oxidation of starch through implementation of steady state approximation for the radical reaction rates. The model was then verified using experimental data available in the literature. The model verification revealed that the proposed model shows its good agreement with the experimental data as indicated by an average absolute relative error of only 2.45%. The model also confirmed that carboxyl groups are oxidised further by hydroxyl radical. The carbonyl production rate was found to follow first order reaction with respect to carbonyl concentration. Similarly, carboxyl production rate also followed first order reaction with respect to carbonyl concentration. The apparent reaction rate constant for carbonyl formation and oxidation were 6.24 × 104 s-1 and 1.01 × 104 M-1.s-1, respectively. While apparent reaction rate constant for carboxyl oxidation was 4.86 × 104 M-1.s-1.

Proton transfer reactions and dynamics in CH(3)OH-H(3)O(+)-H(2)O complexes.

PubMed

Sagarik, Kritsana; Chaiwongwattana, Sermsiri; Vchirawongkwin, Viwat; Prueksaaroon, Supakit

2010-01-28

Proton transfer reactions and dynamics in hydrated complexes formed from CH(3)OH, H(3)O(+) and H(2)O were studied using theoretical methods. The investigations began with searching for equilibrium structures at low hydration levels using the DFT method, from which active H-bonds in the gas phase and continuum aqueous solution were characterized and analyzed. Based on the asymmetric stretching coordinates (Deltad(DA)), four H-bond complexes were identified as potential transition states, in which the most active unit is represented by an excess proton nearly equally shared between CH(3)OH and H(2)O. These cannot be definitive due to the lack of asymmetric O-H stretching frequencies (nu(OH)) which are spectral signatures of transferring protons. Born-Oppenheimer molecular dynamics (BOMD) simulations revealed that, when the thermal energy fluctuations and dynamics were included in the model calculations, the spectral signatures at nu(OH) approximately 1000 cm(-1) appeared. In continuum aqueous solution, the H-bond complex with incomplete water coordination at charged species turned out to be the only active transition state. Based on the assumption that the thermal energy fluctuations and dynamics could temporarily break the H-bonds linking the transition state complex and water molecules in the second hydration shell, elementary reactions of proton transfer were proposed. The present study showed that, due to the coupling among various vibrational modes, the discussions on proton transfer reactions cannot be made based solely on static proton transfer potentials. Inclusion of thermal energy fluctuations and dynamics in the model calculations, as in the case of BOMD simulations, together with systematic IR spectral analyses, have been proved to be the most appropriate theoretical approaches.

Double Shock Experiments and Reactive Flow Modeling on LX-17 to Understand the Reacted Equation of State

NASA Astrophysics Data System (ADS)

Vandersall, Kevin; Garcia, Frank; Fried, Laurence; Tarver, Craig

2013-06-01

Experimental data from measurements of the reacted state of an energetic material are desired to incorporate reacted states in modeling by computer codes. In a case such as LX-17 (92.5% TATB and 7.5% Kel-F by weight), where the time dependent kinetics of reaction is still not fully understood and the reacted state may evolve over time, this information becomes even more vital. Experiments were performed to measure the reacted state of LX-17 using a double shock method involving the use of two flyer materials (with known properties) mounted on the projectile that send an initial shock through the material close to or above the Chapman-Jouguet (CJ) state followed by a second shock at a higher magnitude into the detonated material. By measuring the parameters of the first and second shock waves, information on the reacted state can be obtained. The LX-17 detonation reaction zone profiles plus the arrival times and amplitudes of reflected shocks in LX-17 detonation reaction products were measured using Photonic Doppler Velocimetry (PDV) probes and an aluminum foil coated LiF window. A discussion of this work will include the experimental parameters, velocimetry profiles, data interpretation, reactive CHEETAH and Ignition and Growth modeling, as well as possible future experiments. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

To address surface reaction network complexity using scaling relations machine learning and DFT calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas

Surface reaction networks involving hydrocarbons exhibit enormous complexity with thousands of species and reactions for all but the very simplest of chemistries. We present a framework for optimization under uncertainty for heterogeneous catalysis reaction networks using surrogate models that are trained on the fly. The surrogate model is constructed by teaching a Gaussian process adsorption energies based on group additivity fingerprints, combined with transition-state scaling relations and a simple classifier for determining the rate-limiting step. The surrogate model is iteratively used to predict the most important reaction step to be calculated explicitly with computationally demanding electronic structure theory. Applying thesemore » methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. Lastly, propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations.« less

To address surface reaction network complexity using scaling relations machine learning and DFT calculations

DOE PAGES

Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas; ...

2017-03-06

Surface reaction networks involving hydrocarbons exhibit enormous complexity with thousands of species and reactions for all but the very simplest of chemistries. We present a framework for optimization under uncertainty for heterogeneous catalysis reaction networks using surrogate models that are trained on the fly. The surrogate model is constructed by teaching a Gaussian process adsorption energies based on group additivity fingerprints, combined with transition-state scaling relations and a simple classifier for determining the rate-limiting step. The surrogate model is iteratively used to predict the most important reaction step to be calculated explicitly with computationally demanding electronic structure theory. Applying thesemore » methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. Lastly, propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations.« less

Semi-Supervised Recurrent Neural Network for Adverse Drug Reaction mention extraction.

PubMed

Gupta, Shashank; Pawar, Sachin; Ramrakhiyani, Nitin; Palshikar, Girish Keshav; Varma, Vasudeva

2018-06-13

Social media is a useful platform to share health-related information due to its vast reach. This makes it a good candidate for public-health monitoring tasks, specifically for pharmacovigilance. We study the problem of extraction of Adverse-Drug-Reaction (ADR) mentions from social media, particularly from Twitter. Medical information extraction from social media is challenging, mainly due to short and highly informal nature of text, as compared to more technical and formal medical reports. Current methods in ADR mention extraction rely on supervised learning methods, which suffer from labeled data scarcity problem. The state-of-the-art method uses deep neural networks, specifically a class of Recurrent Neural Network (RNN) which is Long-Short-Term-Memory network (LSTM). Deep neural networks, due to their large number of free parameters rely heavily on large annotated corpora for learning the end task. But in the real-world, it is hard to get large labeled data, mainly due to the heavy cost associated with the manual annotation. To this end, we propose a novel semi-supervised learning based RNN model, which can leverage unlabeled data also present in abundance on social media. Through experiments we demonstrate the effectiveness of our method, achieving state-of-the-art performance in ADR mention extraction. In this study, we tackle the problem of labeled data scarcity for Adverse Drug Reaction mention extraction from social media and propose a novel semi-supervised learning based method which can leverage large unlabeled corpus available in abundance on the web. Through empirical study, we demonstrate that our proposed method outperforms fully supervised learning based baseline which relies on large manually annotated corpus for a good performance.

Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoang, Tuan L.; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, CA 94550; Marian, Jaime, E-mail: jmarian@ucla.edu

2015-11-01

An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a proceduremore » for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe{sup 3+}, He{sup +} and H{sup +}) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.« less

Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials

NASA Astrophysics Data System (ADS)

Hoang, Tuan L.; Marian, Jaime; Bulatov, Vasily V.; Hosemann, Peter

2015-11-01

An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a procedure for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe3+, He+ and H+) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.

Noncovalent Organocatalysis Based on Hydrogen Bonding: Elucidation of Reaction Paths by Computational Methods

NASA Astrophysics Data System (ADS)

Etzenbach-Effers, Kerstin; Berkessel, Albrecht

In this article, the functions of hydrogen bonds in organocatalytic reactions are discussed on atomic level by presenting DFT studies of selected examples. Theoretical investigation provides a detailed insight in the mechanism of substrate activation and orientation, and the stabilization of transition states and intermediates by hydrogen bonding (e.g. oxyanion hole). The examples selected comprise stereoselective catalysis by bifunctional thioureas, solvent catalysis by fluorinated alcohols in epoxidation by hydrogen peroxide, and intramolecular cooperative hydrogen bonding in TADDOL-type catalysts.

The Trojan Horse Method application on the 10B(p,α0)7Be reaction cross section measurements

NASA Astrophysics Data System (ADS)

Cvetinović, A.; Spitaleri, C.; Spartá, R.; Rapisarda, G. G.; Puglia, S. M.; La Cognata, M.; Cherubini, S.; Guardo, G. L.; Gulino, M.; Lamia, L.; Pizzone, R. G.; Romano, S.; Sergi, M. L.

2018-01-01

The 10B(p,α0)7Be reaction cross section has been measured in an wide energy range from 2.2 MeV down to 3 keV in a single experiment applying THM. Optimized experimental set-up ensured good energy resolution leading to a good separation of α0 and α1 contributions to the cross section coming from the 7Be ground and first excited state, respectively.

A framework for discrete stochastic simulation on 3D moving boundary domains

DOE PAGES

Drawert, Brian; Hellander, Stefan; Trogdon, Michael; ...

2016-11-14

We have developed a method for modeling spatial stochastic biochemical reactions in complex, three-dimensional, and time-dependent domains using the reaction-diffusion master equation formalism. In particular, we look to address the fully coupled problems that arise in systems biology where the shape and mechanical properties of a cell are determined by the state of the biochemistry and vice versa. To validate our method and characterize the error involved, we compare our results for a carefully constructed test problem to those of a microscale implementation. Finally, we demonstrate the effectiveness of our method by simulating a model of polarization and shmoo formationmore » during the mating of yeast. The method is generally applicable to problems in systems biology where biochemistry and mechanics are coupled, and spatial stochastic effects are critical.« less

A century of enzyme kinetic analysis, 1913 to 2013.

PubMed

Johnson, Kenneth A

2013-09-02

This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Ultrafast Adiabatic Photodehydration of 2-Hydroxymethylphenol and the Formation of Quinone Methide.

PubMed

Škalamera, Đani; Antol, Ivana; Mlinarić-Majerski, Kata; Vančik, Hrvoj; Phillips, David Lee; Ma, Jiani; Basarić, Nikola

2018-04-20

The photochemical reactivity of 2-hydroxymethylphenol (1) was investigated experimentally by photochemistry under cryogenic conditions, by detecting reactive intermediates by IR spectroscopy, and by using nanosecond and femtosecond transient absorption spectroscopic methods in solution at room temperature. In addition, theoretical studies were performed to facilitate the interpretation of the experimental results and also to simulate the reaction pathway to obtain a better understanding of the reaction mechanism. The main finding of this work is that photodehydration of 1 takes place in an ultrafast adiabatic photochemical reaction without any clear intermediate, delivering quinone methide (QM) in the excited state. Upon photoexcitation to a higher vibrational level of the singlet excited state, 1 undergoes vibrational relaxation leading to two photochemical pathways, one by which synchronous elimination of H 2 O gives QM 2 in its S 1 state and the other by which homolytic cleavage of the phenolic O-H bond produces a phenoxyl radical (S 0 ). Both are ultrafast processes that occur within a picosecond. The excited state of QM 2 (S 1 ) probably deactivates to S 0 through a conical intersection to give QM 2 (S 0 ), which subsequently delivers benzoxete 4. Elucidation of the reaction mechanisms for the photodehydration of phenols by which QMs are formed is important to tune the reactivity of QMs with DNA and proteins for the potential application of QMs in medicine as therapeutic agents. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Myocardial electrical conduction blockade time dominated by irradiance on photodynamic reaction: in vitro and in silico study

NASA Astrophysics Data System (ADS)

Ogawa, Emiyu; Arai, Tsunenori

2018-02-01

The time for electrical conduction blockade induced by a photodynamic reaction was studied on a myocardial cell wire in vitro and an in silico simulation model was constructed to understand the necessary time for electrical conduction blockade for the wire. Vulnerable state of the cells on a laser interaction would be an unstable and undesirable state since the cells might progress to completely damaged or repaired to change significantly therapeutic effect. So that in silico model, which can calculate the vulnerable cell state, is needed. Understanding an immediate electrical conduction blockade is needed for our proposed new methodology for tachyarrhythmia catheter ablation applying a photodynamic reaction. We studied the electrical conduction blockade occurrence on the electrical conduction wire made of cultured myocardial cells in a line shape and constructed in silico model based on this experimental data. The intracellular Ca2+ ion concentrations were obtained using Fluo-4 AM dye under a confocal laser microscope. A cross-correlation function was used for the electrical conduction blockade judgment. The photodynamic reaction was performed under the confocal microscopy with 3-120 mW/cm2 in irradiance by the diode laser with 663 nm in wavelength. We obtained that the time for the electrical conduction blockade decreased with the irradiance increasing. We constructed a simulation model composed of three states; living cells, vulnerable cells, and blocked cells, using the obtained experimental data and we found the rate constant by an optimization using a conjugate gradient method.

Systematic R -matrix analysis of the 13C(p ,γ )14N capture reaction

NASA Astrophysics Data System (ADS)

Chakraborty, Suprita; deBoer, Richard; Mukherjee, Avijit; Roy, Subinit

2015-04-01

Background: The proton capture reaction 13C(p ,γ )14N is an important reaction in the CNO cycle during hydrogen burning in stars with mass greater than the mass of the Sun. It also occurs in astrophysical sites such as red giant stars: the asymptotic giant branch (AGB) stars. The low energy astrophysical S factor of this reaction is dominated by a resonance state at an excitation energy of around 8.06 MeV (Jπ=1-,T =1 ) in 14N. The other significant contributions come from the low energy tail of the broad resonance with Jπ=0-,T =1 at an excitation of 8.78 MeV and the direct capture process. Purpose: Measurements of the low energy astrophysical S factor of the radiative capture reaction 13C(p ,γ )14N reported extrapolated values of S (0 ) that differ by about 30 % . Subsequent R -matrix analysis and potential model calculations also yielded significantly different values for S (0 ) . The present work intends to look into the discrepancy through a detailed R -matrix analysis with emphasis on the associated uncertainties. Method: A systematic reanalysis of the available decay data following the capture to the Jπ=1-,T =1 resonance state of 14N around 8.06 MeV excitation had been performed within the framework of the R -matrix method. A simultaneous analysis of the 13C(p ,p0 ) data, measured over a similar energy range, was carried out with the capture data. The data for the ground state decay of the broad resonance state (Jπ=0-,T =1 ) around 8.78 MeV excitations was included as well. The external capture model along with the background poles to simulate the internal capture contribution were used to estimate the direct capture contribution. The asymptotic normalization constants (ANCs) for all states were extracted from the capture data. The multichannel, multilevel R -matrix code azure2 was used for the calculation. Results: The values of the astrophysical S factor at zero relative energy, resulting from the present analysis, are found to be consistent within the error bars for the two sets of capture data used. However, it is found from the fits to the elastic scattering data that the position of the Jπ=1-,T =1 resonance state is uncertain by about 0.6 keV, preferring an excitation energy value of 8.062 MeV. Also the extracted ANC values for the states of 14N corroborate the values from the transfer reaction studies. The reaction rates from the present calculation are about 10 -15 % lower than the values of the NACRE II compilation but compare well with those from NACRE I. Conclusion: The precise energy of the Jπ=1-,T =1 resonance level around 8.06 MeV in 14N must be determined. Further measurements around and below 100 keV with precision are necessary to reduce the uncertainty in the S -factor value at zero relative energy.

Quantum mechanical reaction probability of triplet ketene at the multireference second-order perturbation level of theory.

PubMed

Ogihara, Yusuke; Yamamoto, Takeshi; Kato, Shigeki

2010-09-23

Triplet ketene exhibits a steplike structure in the experimentally observed dissociation rates, but its mechanism is still unknown despite many theoretical efforts in the past decades. In this paper we revisit this problem by quantum mechanically calculating the reaction probability with multireference-based electronic structure theory. Specifically, we first construct an analytical potential energy surface of triplet state by fitting it to about 6000 ab initio energies computed at the multireference second-order Mller-Plesset perturbation (MRMP2) level. We then evaluate the cumulative reaction probability by using the transition state wave packet method together with an adiabatically constrained Hamiltonian. The result shows that the imaginary barrier frequency on the triplet surface is 328i cm-1, which is close to the CCSD(T) result (321i cm-1) but is likely too large for reproducing the experimentally observed steps. Indeed, our calculated reaction probability exhibits no signature of steps, reflecting too strong tunneling effect along the reaction coordinate. Nevertheless, it is emphasized that the flatness of the potential profile in the transition-state region (which governs the degree of tunneling) depends strongly on the level of electronic structure calculation, thus leaving some possibility that the use of more accurate theories might lead to the observed steps. We also demonstrate that the triplet potential surface differs significantly between the CASSCF and MRMP2 results, particularly in the transition-state region. This fact seems to require more attention when studying the "nonadiabatic" scenario for the steps, in which the crossing seam between S0 and T1 surfaces is assumed to play a central role.

Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J.

2016-04-14

Understanding reaction mechanisms in many chemical and biological processes require application of rare event theories. In these theories, an effective choice of a reaction coordinate to describe a reaction pathway is essential. To this end, we study ion solvation in water using molecular dynamics simulations and explore the utility of coordination number (n = number of water molecules in the first solvation shell) as the reaction coordinate. Here we compute the potential of mean force (W(n)) using umbrella sampling, predicting multiple metastable n-states for both cations and anions. We find with increasing ionic size, these states become more stable andmore » structured for cations when compared to anions. We have extended transition state theory (TST) to calculate transition rates between n-states. TST overestimates the rate constant due to solvent-induced barrier recrossings that are not accounted for. We correct the TST rates by calculating transmission coefficients using the reactive flux method. This approach enables a new way of understanding rare events involving coordination complexes. We gratefully acknowledge Liem Dang and Panos Stinis for useful discussion. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. SR, CJM, and GKS were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.

PubMed

Du, Bin; Zhang, Zhen; Grubner, Sharon; Yurkovich, James T; Palsson, Bernhard O; Zielinski, Daniel C

2018-06-05

Reaction-equilibrium constants determine the metabolite concentrations necessary to drive flux through metabolic pathways. Group-contribution methods offer a way to estimate reaction-equilibrium constants at wide coverage across the metabolic network. Here, we present an updated group-contribution method with 1) additional curated thermodynamic data used in fitting and 2) capabilities to calculate equilibrium constants as a function of temperature. We first collected and curated aqueous thermodynamic data, including reaction-equilibrium constants, enthalpies of reaction, Gibbs free energies of formation, enthalpies of formation, entropy changes of formation of compounds, and proton- and metal-ion-binding constants. Next, we formulated the calculation of equilibrium constants as a function of temperature and calculated the standard entropy change of formation (Δ f S ∘ ) using a model based on molecular properties. The median absolute error in estimating Δ f S ∘ was 0.013 kJ/K/mol. We also estimated magnesium binding constants for 618 compounds using a linear regression model validated against measured data. We demonstrate the improved performance of the current method (8.17 kJ/mol in median absolute residual) over the current state-of-the-art method (11.47 kJ/mol) in estimating the 185 new reactions added in this work. The efforts here fill in gaps for thermodynamic calculations under various conditions, specifically different temperatures and metal-ion concentrations. These, to our knowledge, new capabilities empower the study of thermodynamic driving forces underlying the metabolic function of organisms living under diverse conditions. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Rovibrational transitions of H2 by collision with H+ at high temperature

NASA Astrophysics Data System (ADS)

González-Lezana, T.; Honvault, P.

2017-05-01

The H+ + H2 reaction is studied by means of both exact and statistical quantum methods. Integral cross-sections for processes initiated with rotationally excited H2(v, j = 1) to produce molecular hydrogen in its rotational ground state are reported up to a value of the collision energy of 3 eV. Rate constants for state-to-state transitions between different H2 rovibrational states are calculated up to 3000 K. Special emphasis is made on ortho/para conversion processes in which the parity j of the H2(j) states changes.

Toward efficiency in heterogeneous multispecies reactive transport modeling: A particle-tracking solution for first-order network reactions

NASA Astrophysics Data System (ADS)

Henri, Christopher; Fernàndez-Garcia, Daniel

2015-04-01

Modeling multi-species reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterwards. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the effect of biochemical reactions.

Toward efficiency in heterogeneous multispecies reactive transport modeling: A particle-tracking solution for first-order network reactions

NASA Astrophysics Data System (ADS)

Henri, Christopher V.; Fernàndez-Garcia, Daniel

2014-09-01

Modeling multispecies reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterward. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the effect of biochemical reactions.

Marginal states in a cubic autocatalytic reaction

NASA Astrophysics Data System (ADS)

Das, Debojyoti; Ghosh, Pushpita; Ray, Deb Shankar

2011-09-01

Marginal steady state belongs to a special class of states in nonlinear dynamics. To realize this state we consider a cubic autocatalytic reaction A + 2B → 3B in a continuous-stirred-tank-reactor, where the flow rate of the reactant A can be controlled to manipulate the dynamical behavior of the open system. We demonstrate that when the flow rate is weakly noisy the autocatalytic reaction admits of a steady state which is marginal in nature and is surrounded by infinite number of periodic trajectories. When the uncatalyzed reaction A → B is included in the reaction scheme, there exists a marginal steady state which is a critical state corresponding to the point of transition between the flow branch and the equilibrium branch, similar to gas-liquid critical point of transition. This state loses its stability in the weak noise limit.

Measuring explosive non-ideality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Souers, P C

1999-02-17

The sonic reaction zone length may be measured by four methods: (1) size effect, (2) detonation front curvature, (3) crystal interface velocity and (4) in-situ gauges. The amount of data decreases exponentially from (1) to (4) with there being almost no gauge data for prompt detonation at steady state. The ease and clarity of obtaining the reaction zone length increases from (1) to (4). The method of getting the reaction zone length, , is described for the four methods. A measure of non-ideality is proposed: the reaction zone length divided by the cylinder radius. N = /R{sub o}.more » N = 0 for true ideality. It also decreases with increasing radius as it should. For N < 0.10, an equilibrium EOS like the JWL may be used. For N > 0.10, a time-dependent description is essential. The crystal experiment, which measures the particle velocity of an explosive-transparent material interface, is presently rising in importance. We examine the data from three experiments and apply: (1) an impedance correction that transfers the explosive C-J particle velocity to the corresponding value for the interface, and (2) multiplies the interface time by 3/4 to simulate the explosive speed of sound. The result is a reaction zone length comparable to those obtained by other means. A few explosives have reaction zones so small that the change of slope in the particle velocity is easily seen.« less

Transfer reaction code with nonlocal interactions

DOE PAGES

Titus, L. J.; Ross, A.; Nunes, F. M.

2016-07-14

We present a suite of codes (NLAT for nonlocal adiabatic transfer) to calculate the transfer cross section for single-nucleon transfer reactions, (d,N)(d,N) or (N,d)(N,d), including nonlocal nucleon–target interactions, within the adiabatic distorted wave approximation. For this purpose, we implement an iterative method for solving the second order nonlocal differential equation, for both scattering and bound states. The final observables that can be obtained with NLAT are differential angular distributions for the cross sections of A(d,N)BA(d,N)B or B(N,d)AB(N,d)A. Details on the implementation of the TT-matrix to obtain the final cross sections within the adiabatic distorted wave approximation method are also provided.more » This code is suitable to be applied for deuteron induced reactions in the range of View the MathML sourceEd=10–70MeV, and provides cross sections with 4% accuracy.« less

Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks.

PubMed

Rathinam, Muruhan; Sheppard, Patrick W; Khammash, Mustafa

2010-01-21

Parametric sensitivity of biochemical networks is an indispensable tool for studying system robustness properties, estimating network parameters, and identifying targets for drug therapy. For discrete stochastic representations of biochemical networks where Monte Carlo methods are commonly used, sensitivity analysis can be particularly challenging, as accurate finite difference computations of sensitivity require a large number of simulations for both nominal and perturbed values of the parameters. In this paper we introduce the common random number (CRN) method in conjunction with Gillespie's stochastic simulation algorithm, which exploits positive correlations obtained by using CRNs for nominal and perturbed parameters. We also propose a new method called the common reaction path (CRP) method, which uses CRNs together with the random time change representation of discrete state Markov processes due to Kurtz to estimate the sensitivity via a finite difference approximation applied to coupled reaction paths that emerge naturally in this representation. While both methods reduce the variance of the estimator significantly compared to independent random number finite difference implementations, numerical evidence suggests that the CRP method achieves a greater variance reduction. We also provide some theoretical basis for the superior performance of CRP. The improved accuracy of these methods allows for much more efficient sensitivity estimation. In two example systems reported in this work, speedup factors greater than 300 and 10,000 are demonstrated.

Unimolecular reaction of acetone oxide and its reaction with water in the atmosphere.

PubMed

Long, Bo; Bao, Junwei Lucas; Truhlar, Donald G

2018-05-29

Criegee intermediates (i.e., carbonyl oxides with two radical sites) are known to be important atmospheric reagents; however, our knowledge of their reaction kinetics is still limited. Although experimental methods have been developed to directly measure the reaction rate constants of stabilized Criegee intermediates, the experimental results cover limited temperature ranges and do not completely agree well with one another. Here we investigate the unimolecular reaction of acetone oxide [(CH 3 ) 2 COO] and its bimolecular reaction with H 2 O to obtain rate constants with quantitative accuracy comparable to experimental accuracy. We do this by using CCSDT(Q)/CBS//CCSD(T)-F12a/DZ-F12 benchmark results to select and validate exchange-correlation functionals, which are then used for direct dynamics calculations by variational transition state theory with small-curvature tunneling and torsional and high-frequency anharmonicity. We find that tunneling is very significant in the unimolecular reaction of (CH 3 ) 2 COO and its bimolecular reaction with H 2 O. We show that the atmospheric lifetimes of (CH 3 ) 2 COO depend on temperature and that the unimolecular reaction of (CH 3 ) 2 COO is the dominant decay mode above 240 K, while the (CH 3 ) 2 COO + SO 2 reaction can compete with the corresponding unimolecular reaction below 240 K when the SO 2 concentration is 9 × 10 10 molecules per cubic centimeter. We also find that experimental results may not be sufficiently accurate for the unimolecular reaction of (CH 3 ) 2 COO above 310 K. Not only does the present investigation provide insights into the decay of (CH 3 ) 2 COO in the atmosphere, but it also provides an illustration of how to use theoretical methods to predict quantitative rate constants of medium-sized Criegee intermediates.

Knockout beyond the dripline

NASA Astrophysics Data System (ADS)

Bonaccorso, A.; Charity, R. J.; Kumar, R.; Salvioni, G.

2015-02-01

In this contribution, we will describe neutron and proton removal from 9C and 7Be which are two particularly interesting nuclei entering the nucleo-synthesis pp-chain [1, 2]. Neutron and proton removal reactions have been used in the past twenty years to probe the single-particle structure of exotic nuclei. The core parallel-momentum distribution can give information on the angular momentum and spin of the nucleon initial state while the total removal cross section is sensitive to the asymptotic part of the initial wave function and also to the reaction mechanism. Because knockout is a peripheral reaction from which the Asymptotic Normalization Constant (ANC) of the single-particle wave function can be extracted, it has been used as an indirect method to obtain the rate of reactions like 8B ( p ,γ)9C or 7Be ( p ,γ)8B . Nucleon removal has recently been applied by the HiRA collaboration [3] to situations in which the remaining "core" is beyond the drip line, such as 8C and 6Be , unbound by one or more protons, and whose excitation-energy spectrum can be obtained by the invariant-mass method. By gating on the ground-state peak, "core" parallel-momentum distributions and total knockout cross sections have been obtained similar to previous studies with well-bound "cores". In addition for each projectile, knock out to final bound states has also been obtained in several cases. We will report on the theoretical description and comparison to this experimental data for a few cases for which advances in the accuracy of the transfer-to-the continuum model [4, 5] have been made [6]. These include the use, when available, of "ab-initio" overlaps for the initial state [7] and in particular their ANC values [8]. Also, the construction of a nucleus-target folding potential for the treatment of the core-target S-matrix [9] using for the cores "ab-initio" densities [10] and state-of-the-art n-9Be optical potentials [11]. Preliminary results and open problems will be discussed.

RuleMonkey: software for stochastic simulation of rule-based models

PubMed Central

2010-01-01

Background The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen language (BNGL). A set of rules implicitly defines a (bio)chemical reaction network. The reaction network implied by a set of rules is often very large, and as a result, generation of the network implied by rules tends to be computationally expensive. Moreover, the cost of many commonly used methods for simulating network dynamics is a function of network size. Together these factors have limited application of the rule-based modeling approach. Recently, several methods for simulating rule-based models have been developed that avoid the expensive step of network generation. The cost of these "network-free" simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is now needed for the simulation and analysis of rule-based models of biochemical systems. Results Here, we present a software tool called RuleMonkey, which implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including models with rules that have global application conditions, such as rules for intramolecular association reactions. In addition, the method is rejection free, unlike other network-free methods that introduce null events, i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant tool for network-free simulation of rule-based models. We also compare RuleMonkey against problem-specific codes implementing network-free simulation methods. Conclusions RuleMonkey enables the simulation of rule-based models for which the underlying reaction networks are large. It is typically faster than DYNSTOC for benchmark problems that we have examined. RuleMonkey is freely available as a stand-alone application http://public.tgen.org/rulemonkey. It is also available as a simulation engine within GetBonNie, a web-based environment for building, analyzing and sharing rule-based models. PMID:20673321

Exploring reaction pathways for O-GlcNAc transferase catalysis. A string method study.

PubMed

Kumari, Manju; Kozmon, Stanislav; Kulhánek, Petr; Štepán, Jakub; Tvaroška, Igor; Koča, Jaroslav

2015-03-26

The inverting O-GlcNAc glycosyltransferase (OGT) is an important post-translation enzyme, which catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine (UDP-GlcNAc) to the hydroxyl group of the Ser/Thr of cytoplasmic, nuclear, and mitochondrial proteins. In the past, three different catalytic bases were proposed for the reaction: His498, α-phosphate, and Asp554. In this study, we used hybrid quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello molecular dynamics to investigate reaction paths using α-phosphate and Asp554 as the catalytic bases. The string method was used to calculate the free-energy reaction profiles of the tested mechanisms. During the investigations, an additional mechanism was observed. In this mechanism, a proton is transferred to α-phosphate via a water molecule. Our calculations show that the mechanism with α-phosphate acting as the base is favorable. This reaction has a rate-limiting free-energy barrier of 23.5 kcal/mol, whereas reactions utilizing Asp554 and water-assisted α-phosphate have barriers of 41.7 and 40.9 kcal/mol, respectively. Our simulations provide a new insight into the catalysis of OGT and may thus guide rational drug design of transition-state analogue inhibitors with potential therapeutic use.

Spin-isospin excitation of 3He with three-proton final state

NASA Astrophysics Data System (ADS)

Ishikawa, Souichi

2018-01-01

Spin-isospin excitation of the {}^3He nucleus by a proton-induced charge exchange reaction, {}^3He(p,n)ppp, at forward neutron scattering angle is studied in a plane wave impulse approximation (PWIA). In PWIA, cross sections of the reaction are written in terms of proton-neutron scattering amplitudes and response functions of the transition from {}3He to the three-proton state by spin-isospin transition operators. The response functions are calculated with realistic nucleon-nucleon potential models using a Faddeev three-body method. Calculated cross sections agree with available experimental data in substance. Possible effects arising from the uncertainty of proton-neutron amplitudes and three-nucleon interactions in the three-proton system are examined.

Fabrication, characterization and applications of iron selenide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hussain, Raja Azadar, E-mail: hussainazadar@yahoo.com; Badshah, Amin; Lal, Bhajan

This review article presents fabrication of FeSe by solid state reactions, solution chemistry routes, chemical vapor deposition, spray pyrolysis and chemical vapor transport. Different properties and applications such as crystal structure and phase transition, band structure, spectroscopy, superconductivity, photocatalytic activity, electrochemical sensing, and fuel cell activity of FeSe have been discussed. - Graphical abstract: Iron selenide can be synthesized by solid state reactions, chemical vapor deposition, solution chemistry routes, chemical vapor transport and spray pyrolysis. - Highlights: • Different fabrication methods of iron selenide (FeSe) have been reviewed. • Crystal structure, band structure and spectroscopy of FeSe have been discussed.more » • Superconducting, catalytic and fuel cell application of FeSe have been presented.« less

Multinucleon transfer reactions – a pathway to new heavy and superheavy nuclei?

NASA Astrophysics Data System (ADS)

Heinz, Sophie

2018-05-01

Recently, we reported the observation of several new neutron-deficient isotopes with proton numbers Z ≥ 92 in collisions of 48Ca + 248Cm at the Coulomb barrier. The peculiarity is that these nuclei were produced in deep inelastic multinucleon transfer reactions, a method which is presently discussed as a possible new pathway to enter so far unknown regions in the upper part of the Chart of Nuclides. Of particular interest are multinucleon transfer reactions as a possible means to produce neutron-rich superheavy nuclei and nuclei along the magic neutron shell N = 126. Based on present-day physical and technical state-of-the art, we will discuss the question how big are our chances to enter these regions by applying multinucleon transfer reactions.

The manifestation of vibrational excitation effect in reactions C + SH(v = 0-20, j = 0) \\rightarrow H + CS, S + CH

NASA Astrophysics Data System (ADS)

Zhang, Lulu; Gao, Shoubao; Song, Yuzhi; Meng, Qingtian

2018-03-01

The dependence of the cross section for the C + SH \\to H + CS, S + CH reactions on the vibrational excitation of SH(v = 0-20, j = 0) is analyzed in detail at the collision energies of 0.3 and 0.8 eV by using the quasi-classical trajectory method and the new potential energy surface (Song et al 2016 Sci. Rep. 6 37734) of the {{HCS}}({{X}}{}2{{A}}\\prime ). The efficiency of vibrational excitation to promote the reaction is investigated through the analysis of the cross section and its v dependence in terms of the reaction probability, maximum impact parameter, and the features of the potential energy surface. The differential cross sections obtained show that at higher vibrational levels, the products (CS, CH) are mainly forward scattered, and the sideward and backward scatterings are quite weak. In addition to the scalar properties, the stereodynamical attributes, such as angle distribution functions P(θ r ), P(ϕ r ) and P(θ r , ϕ r ) at different vibrational levels are explored in detail. Furthermore, through the investigation of the state-to-state dynamics for the titled reaction, it is clear that the vibrational excitation of the product for C + SH \\to H + CS reaction is quite strong, with the most probable population appearing at high vibration numbers.

New astrophysical S factor for the {sup 15}N(p,{gamma}){sup 16}O reaction via the asymptotic normalization coefficient (ANC) method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukhamedzhanov, A. M.; Gagliardi, C. A.; Goldberg, V. Z.

2008-07-15

The {sup 15}N(p,{gamma}){sup 16}O reaction provides a path from the CN cycle to the CNO bi-cycle and CNO tri-cycle. The measured astrophysical factor for this reaction is dominated by resonant capture through two strong J{sup {pi}}=1{sup -} resonances at E{sub R}=312 and 962 keV and direct capture to the ground state. Asymptotic normalization coefficients (ANCs) for the ground and seven excited states in {sup 16}O were extracted from the comparison of experimental differential cross sections for the {sup 15}N({sup 3}He,d){sup 16}O reaction with distorted-wave Born approximation calculations. Using these ANCs and proton and {alpha} resonance widths determined from an R-matrixmore » fit to the data from the {sup 15}N(p,{alpha}){sup 12}C reaction, we carried out an R-matrix calculation to obtain the astrophysical factor for the {sup 15}N(p,{gamma}){sup 16}O reaction. The results indicate that the direct capture contribution was previously overestimated. We find the astrophysical factor to be S(0)=36.0{+-}6.0 keV b, which is about a factor of 2 lower than the presently accepted value. We conclude that for every 2200{+-}300 cycles of the main CN cycle one CN catalyst is lost due to this reaction.« less

Analyzing the dependence of oxygen incorporation current density on overpotential and oxygen partial pressure in mixed conducting oxide electrodes.

PubMed

Guan, Zixuan; Chen, Di; Chueh, William C

2017-08-30

The oxygen incorporation reaction, which involves the transformation of an oxygen gas molecule to two lattice oxygen ions in a mixed ionic and electronic conducting solid, is a ubiquitous and fundamental reaction in solid-state electrochemistry. To understand the reaction pathway and to identify the rate-determining step, near-equilibrium measurements have been employed to quantify the exchange coefficients as a function of oxygen partial pressure and temperature. However, because the exchange coefficient contains contributions from both forward and reverse reaction rate constants and depends on both oxygen partial pressure and oxygen fugacity in the solid, unique and definitive mechanistic assessment has been challenging. In this work, we derive a current density equation as a function of both oxygen partial pressure and overpotential, and consider both near and far from equilibrium limits. Rather than considering specific reaction pathways, we generalize the multi-step oxygen incorporation reaction into the rate-determining step, preceding and following quasi-equilibrium steps, and consider the number of oxygen ions and electrons involved in each. By evaluating the dependence of current density on oxygen partial pressure and overpotential separately, one obtains the reaction orders for oxygen gas molecules and for solid-state species in the electrode. We simulated the oxygen incorporation current density-overpotential curves for praseodymium-doped ceria for various candidate rate-determining steps. This work highlights a promising method for studying the exchange kinetics far away from equilibrium.

Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease.

PubMed

Kóna, Juraj

2008-01-21

Two possible mechanisms of the irreversible inhibition of HIV-1 protease by epoxide inhibitors are investigated on an enzymatic model using ab initio (MP2) and density functional theory (DFT) methods (B3LYP, MPW1K and M05-2X). The calculations predict the inhibition as a general acid-catalyzed nucleophilic substitution reaction proceeding by a concerted SN2 mechanism with a reaction barrier of ca. 15-21 kcal mol(-1). The irreversible nature of the inhibition is characterized by a large negative reaction energy of ca. -17-(-24) kcal mol(-1). A mechanism with a direct proton transfer from an aspartic acid residue of the active site onto the epoxide ring has been shown to be preferred compared to one with the proton transfer from the acid catalyst facilitated by a bridging catalytic water molecule. Based on the geometry of the transition state, structural data important for the design of irreversible epoxide inhibitors of HIV-1 protease were defined. Here we also briefly discuss differences between the epoxide ring-opening reaction in HIV-1 protease and epoxide hydrolase, and the accuracy of the DFT method used.

End-Member Formulation of Solid Solutions and Reactive Transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lichtner, Peter C.

2015-09-01

A model for incorporating solid solutions into reactive transport equations is presented based on an end-member representation. Reactive transport equations are solved directly for the composition and bulk concentration of the solid solution. Reactions of a solid solution with an aqueous solution are formulated in terms of an overall stoichiometric reaction corresponding to a time-varying composition and exchange reactions, equivalent to reaction end-members. Reaction rates are treated kinetically using a transition state rate law for the overall reaction and a pseudo-kinetic rate law for exchange reactions. The composition of the solid solution at the onset of precipitation is assumed tomore » correspond to the least soluble composition, equivalent to the composition at equilibrium. The stoichiometric saturation determines if the solid solution is super-saturated with respect to the aqueous solution. The method is implemented for a simple prototype batch reactor using Mathematica for a binary solid solution. Finally, the sensitivity of the results on the kinetic rate constant for a binary solid solution is investigated for reaction of an initially stoichiometric solid phase with an undersaturated aqueous solution.« less

Lifetime measurement of high spin states in (75) Kr

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheikh, Javid; Trivedi, T.; Maurya, K.

2010-01-01

The lifetimes of high spin states of {sup 75}Kr have been determined via {sup 50}Cr ({sup 28}Si, 2pn) {sup 75}Kr reaction in positive parity band using the Doppler-shift attenuation method. The transition quadrupole moments Q deduced from lifetime measurements have been compared with {sup 75}Br. Experimental results obtained from lifetime measurement are interpreted in the framework of projected shell model.

Nanowire membrane-based nanothermite: towards processable and tunable interfacial diffusion for solid state reactions.

PubMed

Yang, Yong; Wang, Peng-peng; Zhang, Zhi-cheng; Liu, Hui-ling; Zhang, Jingchao; Zhuang, Jing; Wang, Xun

2013-01-01

Interfacial diffusion is of great importance in determining the performance of solid-state reactions. For nanometer sized particles, some solid-state reactions can be triggered accidently by mechanical stress owing to their large surface-to-volume ratio compared with the bulk ones. Therefore, a great challenge is the control of interfacial diffusion for solid state reactions, especially for energetic materials. Here we demonstrate, through the example of nanowire-based thermite membrane, that the thermite solid-state reaction can be easily tuned via the introduction of low-surface-energy coating layer. Moreover, this silicon-coated thermite membrane exhibit controlled wetting behavior ranging from superhydrophilic to superhydrophobic and, simultaneously, to significantly reduce the friction sensitivity of thermite membrane. This effect enables to increase interfacial resistance by increasing the amount of coating material. Indeed, our results described here make it possible to tune the solid-state reactions through the manipulation of interfacial diffusion between the reactants.

Nanowire Membrane-based Nanothermite: towards Processable and Tunable Interfacial Diffusion for Solid State Reactions

NASA Astrophysics Data System (ADS)

Yang, Yong; Wang, Peng-Peng; Zhang, Zhi-Cheng; Liu, Hui-Ling; Zhang, Jingchao; Zhuang, Jing; Wang, Xun

2013-04-01

Interfacial diffusion is of great importance in determining the performance of solid-state reactions. For nanometer sized particles, some solid-state reactions can be triggered accidently by mechanical stress owing to their large surface-to-volume ratio compared with the bulk ones. Therefore, a great challenge is the control of interfacial diffusion for solid state reactions, especially for energetic materials. Here we demonstrate, through the example of nanowire-based thermite membrane, that the thermite solid-state reaction can be easily tuned via the introduction of low-surface-energy coating layer. Moreover, this silicon-coated thermite membrane exhibit controlled wetting behavior ranging from superhydrophilic to superhydrophobic and, simultaneously, to significantly reduce the friction sensitivity of thermite membrane. This effect enables to increase interfacial resistance by increasing the amount of coating material. Indeed, our results described here make it possible to tune the solid-state reactions through the manipulation of interfacial diffusion between the reactants.

RAINIER: A simulation tool for distributions of excited nuclear states and cascade fluctuations

NASA Astrophysics Data System (ADS)

Kirsch, L. E.; Bernstein, L. A.

2018-06-01

A new code has been developed named RAINIER that simulates the γ-ray decay of discrete and quasi-continuum nuclear levels for a user-specified range of energy, angular momentum, and parity including a realistic treatment of level spacing and transition width fluctuations. A similar program, DICEBOX, uses the Monte Carlo method to simulate level and width fluctuations but is restricted in its initial level population algorithm. On the other hand, modern reaction codes such as TALYS and EMPIRE populate a wide range of states in the residual nucleus prior to γ-ray decay, but do not go beyond the use of deterministic functions and therefore neglect cascade fluctuations. This combination of capabilities allows RAINIER to be used to determine quasi-continuum properties through comparison with experimental data. Several examples are given that demonstrate how cascade fluctuations influence experimental high-resolution γ-ray spectra from reactions that populate a wide range of initial states.

Slow Photoelectron Velocity-Map Imaging of Cryogenically Cooled Anions

NASA Astrophysics Data System (ADS)

Weichman, Marissa L.; Neumark, Daniel M.

2018-04-01

Slow photoelectron velocity-map imaging spectroscopy of cryogenically cooled anions (cryo-SEVI) is a powerful technique for elucidating the vibrational and electronic structure of neutral radicals, clusters, and reaction transition states. SEVI is a high-resolution variant of anion photoelectron spectroscopy based on photoelectron imaging that yields spectra with energy resolution as high as 1-2 cm‑1. The preparation of cryogenically cold anions largely eliminates hot bands and dramatically narrows the rotational envelopes of spectral features, enabling the acquisition of well-resolved photoelectron spectra for complex and spectroscopically challenging species. We review the basis and history of the SEVI method, including recent experimental developments that have improved its resolution and versatility. We then survey recent SEVI studies to demonstrate the utility of this technique in the spectroscopy of aromatic radicals, metal and metal oxide clusters, nonadiabatic interactions between excited states of small molecules, and transition states of benchmark bimolecular reactions.

Simplification of reversible Markov chains by removal of states with low equilibrium occupancy.

PubMed

Ullah, Ghanim; Bruno, William J; Pearson, John E

2012-10-21

We present a practical method for simplifying Markov chains on a potentially large state space when detailed balance holds. A simple and transparent technique is introduced to remove states with low equilibrium occupancy. The resulting system has fewer parameters. The resulting effective rates between the remaining nodes give dynamics identical to the original system's except on very fast timescales. This procedure amounts to using separation of timescales to neglect small capacitance nodes in a network of resistors and capacitors. We illustrate the technique by simplifying various reaction networks, including transforming an acyclic four-node network to a three-node cyclic network. For a reaction step in which a ligand binds, the law of mass action implies a forward rate proportional to ligand concentration. The effective rates in the simplified network are found to be rational functions of ligand concentration. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dual neutral particle induced transmutation in CINDER2008

NASA Astrophysics Data System (ADS)

Martin, W. J.; de Oliveira, C. R. E.; Hecht, A. A.

2014-12-01

Although nuclear transmutation methods for fission have existed for decades, the focus has been on neutron-induced reactions. Recent novel concepts have sought to use both neutrons and photons for purposes such as active interrogation of cargo to detect the smuggling of highly enriched uranium, a concept that would require modeling the transmutation caused by both incident particles. As photonuclear transmutation has yet to be modeled alongside neutron-induced transmutation in a production code, new methods need to be developed. The CINDER2008 nuclear transmutation code from Los Alamos National Laboratory is extended from neutron applications to dual neutral particle applications, allowing both neutron- and photon-induced reactions for this modeling with a focus on fission. Following standard reaction modeling, the induced fission reaction is understood as a two-part reaction, with an entrance channel to the excited compound nucleus, and an exit channel from the excited compound nucleus to the fission fragmentation. Because photofission yield data-the exit channel from the compound nucleus-are sparse, neutron fission yield data are used in this work. With a different compound nucleus and excitation, the translation to the excited compound state is modified, as appropriate. A verification and validation of these methods and data has been performed. This has shown that the translation of neutron-induced fission product yield sets, and their use in photonuclear applications, is appropriate, and that the code has been extended correctly.

Review of computer simulations of isotope effects on biochemical reactions: From the Bigeleisen equation to Feynman's path integral.

PubMed

Wong, Kin-Yiu; Xu, Yuqing; Xu, Liang

2015-11-01

Enzymatic reactions are integral components in many biological functions and malfunctions. The iconic structure of each reaction path for elucidating the reaction mechanism in details is the molecular structure of the rate-limiting transition state (RLTS). But RLTS is very hard to get caught or to get visualized by experimentalists. In spite of the lack of explicit molecular structure of the RLTS in experiment, we still can trace out the RLTS unique "fingerprints" by measuring the isotope effects on the reaction rate. This set of "fingerprints" is considered as a most direct probe of RLTS. By contrast, for computer simulations, oftentimes molecular structures of a number of TS can be precisely visualized on computer screen, however, theoreticians are not sure which TS is the actual rate-limiting one. As a result, this is an excellent stage setting for a perfect "marriage" between experiment and theory for determining the structure of RLTS, along with the reaction mechanism, i.e., experimentalists are responsible for "fingerprinting", whereas theoreticians are responsible for providing candidates that match the "fingerprints". In this Review, the origin of isotope effects on a chemical reaction is discussed from the perspectives of classical and quantum worlds, respectively (e.g., the origins of the inverse kinetic isotope effects and all the equilibrium isotope effects are purely from quantum). The conventional Bigeleisen equation for isotope effect calculations, as well as its refined version in the framework of Feynman's path integral and Kleinert's variational perturbation (KP) theory for systematically incorporating anharmonicity and (non-parabolic) quantum tunneling, are also presented. In addition, the outstanding interplay between theory and experiment for successfully deducing the RLTS structures and the reaction mechanisms is demonstrated by applications on biochemical reactions, namely models of bacterial squalene-to-hopene polycyclization and RNA 2'-O-transphosphorylation. For all these applications, we used our recently-developed path-integral method based on the KP theory, called automated integration-free path-integral (AIF-PI) method, to perform ab initio path-integral calculations of isotope effects. As opposed to the conventional path-integral molecular dynamics (PIMD) and Monte Carlo (PIMC) simulations, values calculated from our AIF-PI path-integral method can be as precise as (not as accurate as) the numerical precision of the computing machine. Lastly, comments are made on the general challenges in theoretical modeling of candidates matching the experimental "fingerprints" of RLTS. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2015 Elsevier B.V. All rights reserved.

The quantum dynamics of electronically nonadiabatic chemical reactions

NASA Technical Reports Server (NTRS)

Truhlar, Donald G.

1993-01-01

Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally adiabatic functions in various quantum scattering algorithms.

Dual-level direct dynamics studies for the hydrogen abstraction reaction of 1,1-difluoroethane with O( 3P)

NASA Astrophysics Data System (ADS)

Liu, Jing-yao; Li, Ze-sheng; Dai, Zhen-wen; Zhang, Gang; Sun, Chia-chung

2004-01-01

We present dual-level direct dynamics calculations for the CH 3CHF 2 + O( 3P) hydrogen abstraction reaction in a wide temperature range, based on canonical variational transition-state theory including small curvature tunneling corrections. For this reaction, three distinct transition states, one for α-abstraction and two for β-abstraction, have been located. The potential energy surface information is obtained at the MP2(full)/6-311G(d,p) level of theory, and higher-level single-point calculations for the stationary points are preformed at several levels, namely QCISD(T)/6-311+G(3df,3pd), G2, and G3 using the MP2 geometries, as well as at the G3//MP4SDQ/6-311G(d,p) level. The energy profiles are further refined with the interpolated single-point energies method at the G3//MP2(full)/6-311G(d,p) level. The total rate constants match the experimental data reasonable well in the measured temperature range 1110-1340 K. It is shown that at low temperature α-abstraction may be the major reaction channel, while β-abstraction will have more contribution to the whole reaction rate as the temperature increases.

Exploring mechanisms of a tropospheric archetype: CH{sub 3}O{sub 2} + NO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Launder, Andrew M.; Agarwal, Jay; Schaefer, Henry F., E-mail: ccq@uga.edu

Methylperoxy radical (CH{sub 3}O{sub 2}) and nitric oxide (NO) contribute to the propagation of photochemical smog in the troposphere via the production of methoxy radical (CH{sub 3}O) and nitrogen dioxide (NO{sub 2}). This reaction system also furnishes trace quantities of methyl nitrate (CH{sub 3}ONO{sub 2}), a sink for reactive NO{sub x} species. Here, the CH{sub 3}O{sub 2} + NO reaction is examined with highly reliable coupled-cluster methods. Specifically, equilibrium geometries for the reactants, products, intermediates, and transition states of the ground-state potential energy surface are characterized. Relative reaction enthalpies at 0 K (ΔH{sub 0K}) are reported; these values are comprisedmore » of electronic energies extrapolated to the complete basis set limit of CCSDT(Q) and zero-point vibrational energies computed at CCSD(T)/cc-pVTZ. A two-part mechanism involving CH{sub 3}O and NO{sub 2} production followed by radical recombination to CH{sub 3}ONO{sub 2} is determined to be the primary channel for formation of CH{sub 3}ONO{sub 2} under tropospheric conditions. Constrained optimizations of the reaction paths at CCSD(T)/cc-pVTZ suggest that the homolytic bond dissociations involved in this reaction path are barrierless.« less

Chemical reactions in reverse micelle systems

DOEpatents

Matson, Dean W.; Fulton, John L.; Smith, Richard D.; Consani, Keith A.

1993-08-24

This invention is directed to conducting chemical reactions in reverse micelle or microemulsion systems comprising a substantially discontinuous phase including a polar fluid, typically an aqueous fluid, and a microemulsion promoter, typically a surfactant, for facilitating the formation of reverse micelles in the system. The system further includes a substantially continuous phase including a non-polar or low-polarity fluid material which is a gas under standard temperature and pressure and has a critical density, and which is generally a water-insoluble fluid in a near critical or supercritical state. Thus, the microemulsion system is maintained at a pressure and temperature such that the density of the non-polar or low-polarity fluid exceeds the critical density thereof. The method of carrying out chemical reactions generally comprises forming a first reverse micelle system including an aqueous fluid including reverse micelles in a water-insoluble fluid in the supercritical state. Then, a first reactant is introduced into the first reverse micelle system, and a chemical reaction is carried out with the first reactant to form a reaction product. In general, the first reactant can be incorporated into, and the product formed in, the reverse micelles. A second reactant can also be incorporated in the first reverse micelle system which is capable of reacting with the first reactant to form a product.

Catalysis of Photochemical Reactions.

ERIC Educational Resources Information Center

Albini, A.

1986-01-01

Offers a classification system of catalytic effects in photochemical reactions, contrasting characteristic properties of photochemical and thermal reactions. Discusses catalysis and sensitization, examples of catalyzed reactions of excepted states, complexing ground state substrates, and catalysis of primary photoproducts. (JM)

Modeling the optimal central carbon metabolic pathways under feedback inhibition using flux balance analysis.

PubMed

De, Rajat K; Tomar, Namrata

2012-12-01

Metabolism is a complex process for energy production for cellular activity. It consists of a cascade of reactions that form a highly branched network in which the product of one reaction is the reactant of the next reaction. Metabolic pathways efficiently produce maximal amount of biomass while maintaining a steady-state behavior. The steady-state activity of such biochemical pathways necessarily incorporates feedback inhibition of the enzymes. This observation motivates us to incorporate feedback inhibition for modeling the optimal activity of metabolic pathways using flux balance analysis (FBA). We demonstrate the effectiveness of the methodology on a synthetic pathway with and without feedback inhibition. Similarly, for the first time, the Central Carbon Metabolic (CCM) pathways of Saccharomyces cerevisiae and Homo sapiens have been modeled and compared based on the above understanding. The optimal pathway, which maximizes the amount of the target product(s), is selected from all those obtained by the proposed method. For this, we have observed the concentration of the product inhibited enzymes of CCM pathway and its influence on its corresponding metabolite/substrate. We have also studied the concentration of the enzymes which are responsible for the synthesis of target products. We further hypothesize that an optimal pathway would opt for higher flux rate reactions. In light of these observations, we can say that an optimal pathway should have lower enzyme concentration and higher flux rates. Finally, we demonstrate the superiority of the proposed method by comparing it with the extreme pathway analysis.

Origin of Capacity Fading in Nano-Sized Co3O4 Electrodes: Electrochemical Impedance Spectroscopy Study

NASA Astrophysics Data System (ADS)

Kang, Jin-Gu; Ko, Young-Dae; Park, Jae-Gwan; Kim, Dong-Wan

2008-10-01

Transition metal oxides have been suggested as innovative, high-energy electrode materials for lithium-ion batteries because their electrochemical conversion reactions can transfer two to six electrons. However, nano-sized transition metal oxides, especially Co3O4, exhibit drastic capacity decay during discharge/charge cycling, which hinders their practical use in lithium-ion batteries. Herein, we prepared nano-sized Co3O4 with high crystallinity using a simple citrate-gel method and used electrochemical impedance spectroscopy method to examine the origin for the drastic capacity fading observed in the nano-sized Co3O4 anode system. During cycling, AC impedance responses were collected at the first discharged state and at every subsequent tenth discharged state until the 100th cycle. By examining the separable relaxation time of each electrochemical reaction and the goodness-of-fit results, a direct relation between the charge transfer process and cycling performance was clearly observed.

Thermoelectric Properties of the Perovskite-Type Oxide SrTi1-xNbxO3 Synthesized by Solid-State Reaction Method

NASA Astrophysics Data System (ADS)

Khan, Tamal Tahsin; Ur, Soon-Chul

2018-05-01

The perovskite-type oxide materials SrTi1-xNbxO3 (X = .02, 0.03, 0.04, 0.05 and 0.06) were synthesized by the conventional solid-state reaction method and the thermoelectric properties in terms of Nb doping at the B-site in the oxides were investigated in this study. The formation of single phase cubic perovskite structure was confirmed by the powder X-ray diffraction analysis. Negative conduction is shown in this materials system. The absolute value of Seebeck coefficient increased with increasing temperature over the measured temperature. The electrical conductivity decreased monotonically with increasing temperature, showing degenerating conduction behavior. The thermal conductivity, k, generally decreased with increasing temperature. The power factor increased with increasing Nb-doping level up to 5.0 mol% and hence the dimensionless figure of merit ZT, increased up to 5.0 mol%. The maximum ZT value was observed for SrTi0.95Nb0.05O3 at 873 K.

Theoretical study of the thermodynamics and kinetics of hydrogen abstractions from hydrocarbons.

PubMed

Vandeputte, Aäron G; Sabbe, Maarten K; Reyniers, Marie-Françoise; Van Speybroeck, Veronique; Waroquier, Michel; Marin, Guy B

2007-11-22

Thermochemical and kinetic data were calculated at four cost-effective levels of theory for a set consisting of five hydrogen abstraction reactions between hydrocarbons for which experimental data are available. The selection of a reliable, yet cost-effective method to study this type of reactions for a broad range of applications was done on the basis of comparison with experimental data or with results obtained from computationally demanding high level of theory calculations. For this benchmark study two composite methods (CBS-QB3 and G3B3) and two density functional theory (DFT) methods, MPW1PW91/6-311G(2d,d,p) and BMK/6-311G(2d,d,p), were selected. All four methods succeeded well in describing the thermochemical properties of the five studied hydrogen abstraction reactions. High-level Weizmann-1 (W1) calculations indicated that CBS-QB3 succeeds in predicting the most accurate reaction barrier for the hydrogen abstraction of methane by methyl but tends to underestimate the reaction barriers for reactions where spin contamination is observed in the transition state. Experimental rate coefficients were most accurately predicted with CBS-QB3. Therefore, CBS-QB3 was selected to investigate the influence of both the 1D hindered internal rotor treatment about the forming bond (1D-HR) and tunneling on the rate coefficients for a set of 21 hydrogen abstraction reactions. Three zero curvature tunneling (ZCT) methods were evaluated (Wigner, Skodje & Truhlar, Eckart). As the computationally more demanding centrifugal dominant small curvature semiclassical (CD-SCS) tunneling method did not yield significantly better agreement with experiment compared to the ZCT methods, CD-SCS tunneling contributions were only assessed for the hydrogen abstractions by methyl from methane and ethane. The best agreement with experimental rate coefficients was found when Eckart tunneling and 1D-HR corrections were applied. A mean deviation of a factor 6 on the rate coefficients is found for the complete set of 21 reactions at temperatures ranging from 298 to 1000 K. Tunneling corrections play a critical role in obtaining accurate rate coefficients, especially at lower temperatures, whereas the hindered rotor treatment only improves the agreement with experiment in the high-temperature range.

Studies of X-ray burst reactions with radioactive ion beams from RESOLUT

NASA Astrophysics Data System (ADS)

Blackmon, J. C.; Wiedenhöver, I.; Belarge, J.; Kuvin, S. A.; Anastasiou, M.; Baby, L. T.; Baker, J.; Colbert, K.; Deibel, C. M.; de Lucio, O.; Gardiner, H. E.; Gay, D. L.; Good, E.; Höflich, P.; Hood, A. A. D.; Keely, N.; Lai, J.; Laminack, A.; Linhardt, L. E.; Lighthall, J.; Macon, K. T.; Need, E.; Quails, N.; Rasco, B. C.; Rijal, N.; Volya, A.

2018-01-01

Reactions on certain proton-rich, radioactive nuclei have been shown to have a significant influence on X-ray bursts. We provide an overview of two recent measurements of important X-ray burst reactions using in-flight radioactive ion beams from the RESOLUT facility at the J. D. Fox Superconducting Accelerator Laboratory at Florida State University. The 17F(d,n)18Ne reaction was measured, and Asymptotic Normalization Coefficients were extracted for bound states in 18Ne that determine the direct-capture cross section dominating the 17F(p,γ)18Ne reaction rate for T≲ 0.45 GK. Unbound resonant states were also studied, and the single-particle strength for the 4.523-MeV (3+) state was found to be consistent with previous results. The 19Ne(d,n)20Na proton transfer reaction was used to study resonances in the 19Ne(p,γ)20Na reaction. The most important 2.65-MeV state in 20Na was observed to decay by proton emission to both the ground and first-excited states in 19Ne, providing strong evidence for a 3+ spin assignment and indicating that proton capture on the thermally-populated first-excited state in 19Ne is an important contributor to the 19Ne(p,γ)20Na reaction rate.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, L. X.; Zhang, X.; Lockard, J. V.

Transient molecular structures along chemical reaction pathways are important for predicting molecular reactivity, understanding reaction mechanisms, as well as controlling reaction pathways. During the past decade, X-ray transient absorption spectroscopy (XTA, or LITR-XAS, laser-initiated X-ray absorption spectroscopy), analogous to the commonly used optical transient absorption spectroscopy, has been developed. XTA uses a laser pulse to trigger a fundamental chemical process, and an X-ray pulse(s) to probe transient structures as a function of the time delay between the pump and probe pulses. Using X-ray pulses with high photon flux from synchrotron sources, transient electronic and molecular structures of metal complexes havemore » been studied in disordered media from homogeneous solutions to heterogeneous solution-solid interfaces. Several examples from the studies at the Advanced Photon Source in Argonne National Laboratory are summarized, including excited-state metalloporphyrins, metal-to-ligand charge transfer (MLCT) states of transition metal complexes, and charge transfer states of metal complexes at the interface with semiconductor nanoparticles. Recent developments of the method are briefly described followed by a future prospective of XTA. It is envisioned that concurrent developments in X-ray free-electron lasers and synchrotron X-ray facilities as well as other table-top laser-driven femtosecond X-ray sources will make many breakthroughs and realise dreams of visualizing molecular movies and snapshots, which ultimately enable chemical reaction pathways to be controlled.« less

Scattering study of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction on an ab initio based analytical potential energy surface

NASA Astrophysics Data System (ADS)

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N.

2016-01-01

Initial state selected dynamics of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]+ structure lying 0.72 eV below the Ne + NeH+ asymptote is found to be the most stable geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.

Deciphering Selectivity in Organic Reactions: A Multifaceted Problem.

PubMed

Balcells, David; Clot, Eric; Eisenstein, Odile; Nova, Ainara; Perrin, Lionel

2016-05-17

Computational chemistry has made a sustained contribution to the understanding of chemical reactions. In earlier times, half a century ago, the goal was to distinguish allowed from forbidden reactions (e.g., Woodward-Hoffmann rules), that is, reactions with low or high to very high activation barriers. A great achievement of computational chemistry was also to contribute to the determination of structures with the bonus of proposing a rationalization (e.g., anomeric effect, isolobal analogy, Gillespie valence shell pair electron repulsion rules and counter examples, Wade-Mingos rules for molecular clusters). With the development of new methods and the constant increase in computing power, computational chemists move to more challenging problems, close to the daily concerns of the experimental chemists, in determining the factors that make a reaction both efficient and selective: a key issue in organic synthesis. For this purpose, experimental chemists use advanced synthetic and analytical techniques to which computational chemists added other ways of determining reaction pathways. The transition states and intermediates contributing to the transformation of reactants into the desired and undesired products can now be determined, including their geometries, energies, charges, spin densities, spectroscopy properties, etc. Such studies remain challenging due to the large number of chemical species commonly present in the reactive media whose role may have to be determined. Calculating chemical systems as they are in the experiment is not always possible, bringing its own share of complexity through the large number of atoms and the associated large number of conformers to consider. Modeling the chemical species with smaller systems is an alternative that historically led to artifacts. Another important topic is the choice of the computational method. While DFT is widely used, the vast diversity of functionals available is both an opportunity and a challenge. Though chemical knowledge helps, the relevant computational method is best chosen in conjunction with the nature of the experimental systems and many studies have been concerned with this topic. We will not address this aspect but give references in the text. Usually, a computational study starts with the validation of the method by means of benchmark calculations vs accurate experimental data or state-of-the-art calculations. Finally, computational chemists can bring more than the sole determination of the reaction pathways through the analysis of the electronic structure. In our case, we have privileged the NBO analysis, which has the advantage of describing interactions on the basis of terms and concepts that are shared within the chemical community. In this Account, we have chosen to select representative reactions from our own work to highlight the diversity of situations than can be addressed nowadays. These include selective activation of C(sp(3))-H bonds, selective reactions with low energy barriers, involving closed shell or radical species, the role of noncovalent interactions, and the importance of considering side reactions.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins.

PubMed

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-05

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

A Specific Nucleophilic Ring-Opening Reaction of Aziridines as a Unique Platform for the Construction of Hydrogen Polysulfides Sensors

DOE PAGES

Chen, Wei; Rosser, Ethan W.; Zhang, Di; ...

2015-05-11

Hydrogen polysulfides (H 2S n, n>1) have been recently suggested to be the actual signalling molecules that involved in sulfur-related redox biology. However the exact mechanisms of H 2S n are still poorly understood and a major hurdle in this field is the lack of reliable and convenient methods for H 2S n detection. In this work we report a unique ring-opening reaction of N-sulfonylaziridine by Na 2S 2 under mild conditions. Based on this reaction a novel H 2S n-specific fluorescent probe (AP) was developed. The probe showed high sensitivity and selectivity for H 2S n. Notably, the fluorescentmore » turn-on product, i.e. compound 1, exhibited excellent two-photon photophysical properties and a large Stokes shift. Moreover, the high solid state luminescent efficiency of compound 1 makes it a potential candidate for organic emitters and solid-state lighting devices.« less

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

NASA Astrophysics Data System (ADS)

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-11-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance.

Theoretical studies on atmospheric chemistry of HFE-245mc and perfluoro-ethyl formate: Reaction with OH radicals, atmospheric fate of alkoxy radical and global warming potential

NASA Astrophysics Data System (ADS)

Lily, Makroni; Baidya, Bidisha; Chandra, Asit K.

2017-02-01

Theoretical studies have been performed on the kinetics, mechanism and thermochemistry of the hydrogen abstraction reactions of CF3CF2OCH3 (HFE-245mc) and CF3CF2OCHO with OH radical using DFT based M06-2X method. IRC calculation shows that both hydrogen abstraction reactions proceed via weakly bound hydrogen-bonded complex preceding to the formation of transition state. The rate coefficients calculated by canonical transition state theory along with Eckart's tunnelling correction at 298 K: k1(CF3CF2OCH3 + OH) = 1.09 × 10-14 and k2(CF3CF2OCHO + OH) = 1.03 × 10-14 cm3 molecule-1 s-1 are in very good agreement with the experimental values. The atmospheric implications of CF3CF2OCH3 and CF3CF2OCHO are also discussed.

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice–Ramsperger–Kassel theory

PubMed Central

Bao, Junwei Lucas; Zhang, Xin

2016-01-01

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. PMID:27834727

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice-Ramsperger-Kassel theory.

PubMed

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 (C 2 F 4 ), 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.

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

PubMed Central

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-01-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance. PMID:27901129

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins

NASA Astrophysics Data System (ADS)

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-01

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

Fabrication of Ni-silicide/Si heterostructured nanowire arrays by glancing angle deposition and solid state reaction.

PubMed

Hsu, Hsun-Feng; Huang, Wan-Ru; Chen, Ting-Hsuan; Wu, Hwang-Yuan; Chen, Chun-An

2013-05-10

This work develops a method for growing Ni-silicide/Si heterostructured nanowire arrays by glancing angle Ni deposition and solid state reaction on ordered Si nanowire arrays. Samples of ordered Si nanowire arrays were fabricated by nanosphere lithography and metal-induced catalytic etching. Glancing angle Ni deposition deposited Ni only on the top of Si nanowires. When the annealing temperature was 500°C, a Ni3Si2 phase was formed at the apex of the nanowires. The phase of silicide at the Ni-silicide/Si interface depended on the diameter of the Si nanowires, such that epitaxial NiSi2 with a {111} facet was formed at the Ni-silicide/Si interface in Si nanowires with large diameter, and NiSi was formed in Si nanowires with small diameter. A mechanism that is based on flux divergence and a nucleation-limited reaction is proposed to explain this phenomenon of size-dependent phase formation.

Fabrication of Ni-silicide/Si heterostructured nanowire arrays by glancing angle deposition and solid state reaction

PubMed Central

2013-01-01

This work develops a method for growing Ni-silicide/Si heterostructured nanowire arrays by glancing angle Ni deposition and solid state reaction on ordered Si nanowire arrays. Samples of ordered Si nanowire arrays were fabricated by nanosphere lithography and metal-induced catalytic etching. Glancing angle Ni deposition deposited Ni only on the top of Si nanowires. When the annealing temperature was 500°C, a Ni3Si2 phase was formed at the apex of the nanowires. The phase of silicide at the Ni-silicide/Si interface depended on the diameter of the Si nanowires, such that epitaxial NiSi2 with a {111} facet was formed at the Ni-silicide/Si interface in Si nanowires with large diameter, and NiSi was formed in Si nanowires with small diameter. A mechanism that is based on flux divergence and a nucleation-limited reaction is proposed to explain this phenomenon of size-dependent phase formation. PMID:23663726

Role of deformation in odd-even staggering in reaction cross sections for 30,31,32Ne and 36,37,38Mg isotopes

NASA Astrophysics Data System (ADS)

Urata, Y.; Hagino, K.; Sagawa, H.

2017-12-01

We discuss the role of pairing antihalo effect in the observed odd-even staggering in reaction cross sections for 30,31,32Ne and 36,37,38Mg isotopes by taking into account the ground-state deformation of these nuclei. To this end, we construct the ground-state density for the Ne,3130 and Mg,3736 nuclei based on a deformed Woods-Saxon potential, while for the 32Ne and 38Mg nuclei we also take into account the pairing correlation using the Hartree-Fock-Bogoliubov method. We demonstrate that, when the one-neutron separation energy is small for the odd-mass nuclei, a significant odd-even staggering still appears even with finite deformation, although the degree of staggering is somewhat reduced compared to the spherical case. This implies that the pairing antihalo effect in general plays an important role in generating the odd-even staggering in reaction cross sections for weakly bound nuclei.

Triplet photosensitizers: from molecular design to applications.

PubMed

Zhao, Jianzhang; Wu, Wanhua; Sun, Jifu; Guo, Song

2013-06-21

Triplet photosensitizers (PSs) are compounds that can be efficiently excited to the triplet excited state which subsequently act as catalysts in photochemical reactions. The name is originally derived from compounds that were used to transfer the triplet energy to other compounds that have only a small intrinsic triplet state yield. Triplet PSs are not only used for triplet energy transfer, but also for photocatalytic organic reactions, photodynamic therapy (PDT), photoinduced hydrogen production from water and triplet-triplet annihilation (TTA) upconversion. A good PS should exhibit strong absorption of the excitation light, a high yield of intersystem crossing (ISC) for efficient production of the triplet state, and a long triplet lifetime to allow for the reaction with a reactant molecule. Most transition metal complexes show efficient ISC, but small molar absorption coefficients in the visible spectral region and short-lived triplet excited states, which make them unsuitable as triplet PSs. One obstacle to the development of new triplet PSs is the difficulty in predicting the ISC of chromophores, especially of organic compounds without any heavy atoms. This review article summarizes some molecular design rationales for triplet PSs, based on the molecular structural factors that facilitate ISC. The design of transition metal complexes with large molar absorption coefficients in the visible spectral region and long-lived triplet excited states is presented. A new method of using a spin converter to construct heavy atom-free organic triplet PSs is discussed, with which ISC becomes predictable, C60 being an example. To enhance the performance of triplet PSs, energy funneling based triplet PSs are proposed, which show broadband absorption in the visible region. Applications of triplet PSs in photocatalytic organic reactions, hydrogen production, triplet-triplet annihilation upconversion and luminescent oxygen sensing are briefly introduced.

The photodimerisation of the α- and β-forms of trans-cinnamic acid: a study of single crystals by vibrational microspectroscopy

NASA Astrophysics Data System (ADS)

Atkinson, Samantha D. M.; Almond, Matthew J.; Hollins, Peter; Jenkins, Samantha L.

2003-02-01

Infrared and Raman microspectroscopy have been used to follow the photodimerisation reactions of single crystals, the α- and β-forms of trans-cinnamic acid. This approach allows the starting materials and products—α-truxillic acid that has Ci symmetry and β-truxinic acid, which has Cs symmetry—to be identified. It also allows the topotactic nature of the reaction to be confirmed. Attempts to produce the poorly-defined unreactive γ-form of trans-cinnamic acid resulted only in a mixture of the α- and β-forms. The findings suggest a wide role for these spectroscopic methods in monitoring solid-state organic reactions.

Hybrid method for numerical modelling of LWR coolant chemistry

NASA Astrophysics Data System (ADS)

Swiatla-Wojcik, Dorota

2016-10-01

A comprehensive approach is proposed to model radiation chemistry of the cooling water under exposure to neutron and gamma radiation at 300 °C. It covers diffusion-kinetic processes in radiation tracks and secondary reactions in the bulk coolant. Steady-state concentrations of the radiolytic products have been assessed based on the simulated time dependent concentration profiles. The principal reactions contributing to the formation of H2, O2 and H2O2 were indicated. Simulation was carried out depending on the amount of extra hydrogen dissolved in the coolant to reduce concentration of corrosive agents. High sensitivity to the rate of reaction H+H2O=OH+H2 is shown and discussed.

The relationship between stochastic and deterministic quasi-steady state approximations.

PubMed

Kim, Jae Kyoung; Josić, Krešimir; Bennett, Matthew R

2015-11-23

The quasi steady-state approximation (QSSA) is frequently used to reduce deterministic models of biochemical networks. The resulting equations provide a simplified description of the network in terms of non-elementary reaction functions (e.g. Hill functions). Such deterministic reductions are frequently a basis for heuristic stochastic models in which non-elementary reaction functions are used to define reaction propensities. Despite their popularity, it remains unclear when such stochastic reductions are valid. It is frequently assumed that the stochastic reduction can be trusted whenever its deterministic counterpart is accurate. However, a number of recent examples show that this is not necessarily the case. Here we explain the origin of these discrepancies, and demonstrate a clear relationship between the accuracy of the deterministic and the stochastic QSSA for examples widely used in biological systems. With an analysis of a two-state promoter model, and numerical simulations for a variety of other models, we find that the stochastic QSSA is accurate whenever its deterministic counterpart provides an accurate approximation over a range of initial conditions which cover the likely fluctuations from the quasi steady-state (QSS). We conjecture that this relationship provides a simple and computationally inexpensive way to test the accuracy of reduced stochastic models using deterministic simulations. The stochastic QSSA is one of the most popular multi-scale stochastic simulation methods. While the use of QSSA, and the resulting non-elementary functions has been justified in the deterministic case, it is not clear when their stochastic counterparts are accurate. In this study, we show how the accuracy of the stochastic QSSA can be tested using their deterministic counterparts providing a concrete method to test when non-elementary rate functions can be used in stochastic simulations.

Computational methods for reactive transport modeling: An extended law of mass-action, xLMA, method for multiphase equilibrium calculations

NASA Astrophysics Data System (ADS)

Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg; Saar, Martin O.

2016-10-01

We present an extended law of mass-action (xLMA) method for multiphase equilibrium calculations and apply it in the context of reactive transport modeling. This extended LMA formulation differs from its conventional counterpart in that (i) it is directly derived from the Gibbs energy minimization (GEM) problem (i.e., the fundamental problem that describes the state of equilibrium of a chemical system under constant temperature and pressure); and (ii) it extends the conventional mass-action equations with Lagrange multipliers from the Gibbs energy minimization problem, which can be interpreted as stability indices of the chemical species. Accounting for these multipliers enables the method to determine all stable phases without presuming their types (e.g., aqueous, gaseous) or their presence in the equilibrium state. Therefore, the here proposed xLMA method inherits traits of Gibbs energy minimization algorithms that allow it to naturally detect the phases present in equilibrium, which can be single-component phases (e.g., pure solids or liquids) or non-ideal multi-component phases (e.g., aqueous, melts, gaseous, solid solutions, adsorption, or ion exchange). Moreover, our xLMA method requires no technique that tentatively adds or removes reactions based on phase stability indices (e.g., saturation indices for minerals), since the extended mass-action equations are valid even when their corresponding reactions involve unstable species. We successfully apply the proposed method to a reactive transport modeling problem in which we use PHREEQC and GEMS as alternative backends for the calculation of thermodynamic properties such as equilibrium constants of reactions, standard chemical potentials of species, and activity coefficients. Our tests show that our algorithm is efficient and robust for demanding applications, such as reactive transport modeling, where it converges within 1-3 iterations in most cases. The proposed xLMA method is implemented in Reaktoro, a unified open-source framework for modeling chemically reactive systems.

Simultaneous Detection of Electronic Structure Changes from Two Elements of a Bifunctional Catalyst Using Wavelength-Dispersive X-ray Emission Spectroscopy and in situ Electrochemistry

PubMed Central

Gul, Sheraz; Desmond Ng, Jia Wei; Alonso-Mori, Roberto; Kern, Jan; Sokaras, Dimosthenis; Anzenberg, Eitan; Lassalle-Kaiser, Benedikt; Gorlin, Yelena; Weng, Tsu-Chien; Zwart, Petrus H.; Zhang, Jin Z.; Bergmann, Uwe; Yachandra, Vittal K.; Jaramillo, Thomas F.; Yano, Junko

2015-01-01

Multielectron catalytic reactions, such as water oxidation, nitrogen reduction, or hydrogen production in enzymes and inorganic catalysts often involve multimetallic clusters. In these systems, the reaction takes place between metals or metals and ligands to facilitate charge transfer, bond formation/breaking, substrate binding, and release of products. In this study, we present a method to detect X-ray emission signals from multiple elements simultaneously, which allows for the study of charge transfer and the sequential chemistry occurring between elements. Kβ X-ray emission spectroscopy (XES) probes charge and spin states of metals as well as their ligand environment. A wavelength-dispersive spectrometer based on the von Hamos geometry was used to disperse Kβ signals of multiple elements onto a position detector, enabling an XES spectrum to be measured in a single-shot mode. This overcomes the scanning needs of the scanning spectrometers, providing data free from temporal and normalization errors and therefore ideal to follow sequential chemistry at multiple sites. We have applied this method to study MnOx-based bifunctional electrocatalysts for the oxygen evolution reaction (OER) and the oxygen reduction reaction (ORR). In particular, we investigated the effects of adding a secondary element, Ni, to form MnNiOx and its impact on the chemical states and catalytic activity, by tracking the redox characteristics of each element upon sweeping the electrode potential. The detection scheme we describe here is general and can be applied to time-resolved studies of materials consisting of multiple elements, to follow the dynamics of catalytic and electron transfer reactions. PMID:25747045

Simultaneous detection of electronic structure changes from two elements of a bifunctional catalyst using wavelength-dispersive X-ray emission spectroscopy and in situ electrochemistry.

PubMed

Gul, Sheraz; Ng, Jia Wei Desmond; Alonso-Mori, Roberto; Kern, Jan; Sokaras, Dimosthenis; Anzenberg, Eitan; Lassalle-Kaiser, Benedikt; Gorlin, Yelena; Weng, Tsu-Chien; Zwart, Petrus H; Zhang, Jin Z; Bergmann, Uwe; Yachandra, Vittal K; Jaramillo, Thomas F; Yano, Junko

2015-04-14

Multielectron catalytic reactions, such as water oxidation, nitrogen reduction, or hydrogen production in enzymes and inorganic catalysts often involve multimetallic clusters. In these systems, the reaction takes place between metals or metals and ligands to facilitate charge transfer, bond formation/breaking, substrate binding, and release of products. In this study, we present a method to detect X-ray emission signals from multiple elements simultaneously, which allows for the study of charge transfer and the sequential chemistry occurring between elements. Kβ X-ray emission spectroscopy (XES) probes charge and spin states of metals as well as their ligand environment. A wavelength-dispersive spectrometer based on the von Hamos geometry was used to disperse Kβ signals of multiple elements onto a position detector, enabling an XES spectrum to be measured in a single-shot mode. This overcomes the scanning needs of the scanning spectrometers, providing data free from temporal and normalization errors and therefore ideal to follow sequential chemistry at multiple sites. We have applied this method to study MnOx-based bifunctional electrocatalysts for the oxygen evolution reaction (OER) and the oxygen reduction reaction (ORR). In particular, we investigated the effects of adding a secondary element, Ni, to form MnNiOx and its impact on the chemical states and catalytic activity, by tracking the redox characteristics of each element upon sweeping the electrode potential. The detection scheme we describe here is general and can be applied to time-resolved studies of materials consisting of multiple elements, to follow the dynamics of catalytic and electron transfer reactions.

Simultaneous detection of electronic structure changes from two elements of a bifunctional catalyst using wavelength-dispersive X-ray emission spectroscopy and in situ electrochemistry

DOE PAGES

Gul, Sheraz; Ng, Jia Wei Desmond; Alonso-Mori, Roberto; ...

2015-02-25

Multielectron catalytic reactions, such as water oxidation, nitrogen reduction, or hydrogen production in enzymes and inorganic catalysts often involve multimetallic clusters. In these systems, the reaction takes place between metals or metals and ligands to facilitate charge transfer, bond formation/breaking, substrate binding, and release of products. In this study, we present a method to detect X-ray emission signals from multiple elements simultaneously, which allows for the study of charge transfer and the sequential chemistry occurring between elements. Kβ X-ray emission spectroscopy (XES) probes charge and spin states of metals as well as their ligand environment. A wavelength-dispersive spectrometer based onmore » the von Hamos geometry was used to disperse Kβ signals of multiple elements onto a position detector, enabling an XES spectrum to be measured in a single-shot mode. This overcomes the scanning needs of the scanning spectrometers, providing data free from temporal and normalization errors and therefore ideal to follow sequential chemistry at multiple sites. We have applied this method to study MnOx-based bifunctional electrocatalysts for the oxygen evolution reaction (OER) and the oxygen reduction reaction (ORR). In particular, we investigated the effects of adding a secondary element, Ni, to form MnNiOx and its impact on the chemical states and catalytic activity, by tracking the redox characteristics of each element upon sweeping the electrode potential. In conclusion, the detection scheme we describe here is general and can be applied to time-resolved studies of materials consisting of multiple elements, to follow the dynamics of catalytic and electron transfer reactions.« less

Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling

NASA Astrophysics Data System (ADS)

Núñez, M.; Robie, T.; Vlachos, D. G.

2017-10-01

Kinetic Monte Carlo (KMC) simulation provides insights into catalytic reactions unobtainable with either experiments or mean-field microkinetic models. Sensitivity analysis of KMC models assesses the robustness of the predictions to parametric perturbations and identifies rate determining steps in a chemical reaction network. Stiffness in the chemical reaction network, a ubiquitous feature, demands lengthy run times for KMC models and renders efficient sensitivity analysis based on the likelihood ratio method unusable. We address the challenge of efficiently conducting KMC simulations and performing accurate sensitivity analysis in systems with unknown time scales by employing two acceleration techniques: rate constant rescaling and parallel processing. We develop statistical criteria that ensure sufficient sampling of non-equilibrium steady state conditions. Our approach provides the twofold benefit of accelerating the simulation itself and enabling likelihood ratio sensitivity analysis, which provides further speedup relative to finite difference sensitivity analysis. As a result, the likelihood ratio method can be applied to real chemistry. We apply our methodology to the water-gas shift reaction on Pt(111).

Unravelling the mysteries of sub-second biochemical processes using time-resolved mass spectrometry.

PubMed

Lento, Cristina; Wilson, Derek J

2017-05-21

Many important chemical and biochemical phenomena proceed on sub-second time scales before entering equilibrium. In this mini-review, we explore the history and recent advancements of time-resolved mass spectrometry (TRMS) for the characterization of millisecond time-scale chemical reactions and biochemical processes. TRMS allows for the simultaneous tracking of multiple reactants, intermediates and products with no chromophoric species required, high sensitivity and temporal resolution. The method has most recently been used for the characterization of several short-lived reaction intermediates in rapid chemical reactions. Most of the reactions that occur in living organisms are accelerated by enzymes, with pre-steady state kinetics only attainable using time-resolved methods. TRMS has been increasingly used to monitor the conversion of substrates to products and the resulting changes to the enzyme during catalytic turnover. Early events in protein folding systems have also been elucidated, along with the characterization of dynamics and transient secondary structures in intrinsically disordered proteins. In this review, we will highlight representative examples where TRMS has been applied to study these phenomena.

Reactive flow model development for PBXW-126 using modern nonlinear optimization methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murphy, M.J.; Simpson, R.L.; Urtiew, P.A.

1995-08-01

The initiation and detonation behavior of PBXW-126 has been characterized and is described. PBXW-126 is a composite explosive consisting of approximately equal amounts of RDX, AP, AL, and NTO with a polyurethane binder. The three term ignition and growth of reaction model parameters (ignition + two growth terms) have been found using nonlinear optimization methods to determine the {open_quotes}best{close_quotes} set of model parameters. The ignition term treats the initiation of up to 0.5% of the RDX The first growth term in the model treats the RDX growth of reaction up to 20% reacted. The second growth term treats the subsequentmore » growth of reaction of the remaining AP/AL/NTO. The unreacted equation of state (EOS) was determined from the wave profiles of embedded gauge tests while the JWL product EOS was determined from cylinder expansion test results. The nonlinear optimization code, NLQPEB/GLO, was used to determine the {open_quotes}best{close_quotes} set of coefficients for the three term Lee-Tarver ignition and growth of reaction model.« less

Determination of 20Ne(p ,γ )21Na cross sections from Ep=500 -2000 keV

NASA Astrophysics Data System (ADS)

Lyons, S.; Görres, J.; deBoer, R. J.; Stech, E.; Chen, Y.; Gilardy, G.; Liu, Q.; Long, A. M.; Moran, M.; Robertson, D.; Seymour, C.; Vande Kolk, B.; Wiescher, M.; Best, A.

2018-06-01

Background: The reaction 20Ne(p ,γ )21Na influences the nucleosynthesis of Ne, Na, and Mg isotopes while contributing to hydrogen burning in several stellar sites, such as red giants, asymptotic giant branch (AGB) stars, massive stars, and oxygen-neon (ONe) novae. In the relevant temperature range for these environments (T = 0.05-0.5 GK), the main contributions to this reaction rate are from the direct capture process as well as the high-energy tail of a subthreshold resonance in the ground-state transition at Ex = 2425 keV in the 21Na compound nucleus. Purpose: The previous measurement of this reaction reports cross sections with large uncertainties for the ground-state transition. At higher energies, where the subthreshold resonance makes a smaller contribution to the total cross section, only upper limits are provided. This work aims to reduce the uncertainty in the cross section where direct capture dominates, as well as provide cross-section data in previously unmeasured regions. Method: The 20Ne(p ,γ )21Na reaction was measured over a wide proton energy range (Ep = 0.5-2.0 MeV) at θlab = 90∘. Transitions to the ground state and to the 332 and 2425 keV excited states were observed. The primary transitions to these three bound states were utilized in an R -matrix analysis to determine the contributions of the direct capture and the subthreshold resonance to the total cross section. Results: The cross sections of the present measurements have been found to be in good agreement with the previous data at low energy. Significantly improved cross-section measurements have been obtained over the Ep = 1300-1900 keV region. The narrow resonance at Ec.m. = 1113 keV (Ex = 3544.3 keV) has also been remeasured and its strength has been found to be in good agreement with previous measurements. Conclusions: An extrapolation of the S factor of 20Ne(p ,γ )21Na has been made to low energies using the R -matrix fit. The reaction rate from the subthreshold resonance was found to be the main contributor to the reaction rate at temperatures below about 0.1 GK. The present rate is lower in the temperature range of interest than those presented in current reaction rate libraries by up to 20%.

Bifurcation analysis of a delay reaction-diffusion malware propagation model with feedback control

NASA Astrophysics Data System (ADS)

Zhu, Linhe; Zhao, Hongyong; Wang, Xiaoming

2015-05-01

With the rapid development of network information technology, information networks security has become a very critical issue in our work and daily life. This paper attempts to develop a delay reaction-diffusion model with a state feedback controller to describe the process of malware propagation in mobile wireless sensor networks (MWSNs). By analyzing the stability and Hopf bifurcation, we show that the state feedback method can successfully be used to control unstable steady states or periodic oscillations. Moreover, formulas for determining the properties of the bifurcating periodic oscillations are derived by applying the normal form method and center manifold theorem. Finally, we conduct extensive simulations on large-scale MWSNs to evaluate the proposed model. Numerical evidences show that the linear term of the controller is enough to delay the onset of the Hopf bifurcation and the properties of the bifurcation can be regulated to achieve some desirable behaviors by choosing the appropriate higher terms of the controller. Furthermore, we obtain that the spatial-temporal dynamic characteristics of malware propagation are closely related to the rate constant for nodes leaving the infective class for recovered class and the mobile behavior of nodes.

Breast Cancer Redox Heterogeneity Detectable with Chemical Exchange Satruation Transfer (CEST) MRI

PubMed Central

Cai, Kejia; Xu, He N.; Singh, Anup; Moon, Lily; Haris, Mohammad; Reddy, Ravinder; Li, Lin

2014-01-01

Purpose Tissue redox state is an important mediator of various biological processes in health and diseases such as cancer. Previously, we discovered that the mitochondrial redox state of ex vivo tissues detected by redox scanning (an optical imaging method) revealed interesting tumor redox state heterogeneity that could differentiate tumor aggressiveness. Because the noninvasive chemical exchange saturation transfer (CEST) MRI can probe the proton transfer and generate contrasts from endogenous metabolites, we aim to investigate if the in vivo CEST contrast is sensitive to proton transfer of the redox reactions so as to reveal the tissue redox states in breast cancer animal models. Procedures CEST MRI has been employed to characterize tumor metabolic heterogeneity and correlated with the redox states measured by the redox scanning in two human breast cancer mouse xenograft models, MDA-MB-231 and MCF-7. The possible biological mechanism on the correlation between the two imaging modalities was further investigated by phantom studies where the reductants and the oxidants of the representative redox reactions were measured. Results The CEST contrast is found linearly correlated with NADH concentration and the NADH redox ratio with high statistical significance, where NADH is the reduced form of nicotinamide adenine dinucleotide. The phantom studies showed that the reductants of the redox reactions have more CEST contrast than the corresponding oxidants, indicating that higher CEST effect corresponds to the more reduced redox state. Conclusions This preliminary study suggests that CEST MRI, once calibrated, might provide a novel noninvasive imaging surrogate for the tissue redox state and a possible diagnostic biomarker for breast cancer in the clinic. PMID:24811957

Breast cancer redox heterogeneity detectable with chemical exchange saturation transfer (CEST) MRI.

PubMed

Cai, Kejia; Xu, He N; Singh, Anup; Moon, Lily; Haris, Mohammad; Reddy, Ravinder; Li, Lin Z

2014-10-01

Tissue redox state is an important mediator of various biological processes in health and diseases such as cancer. Previously, we discovered that the mitochondrial redox state of ex vivo tissues detected by redox scanning (an optical imaging method) revealed interesting tumor redox state heterogeneity that could differentiate tumor aggressiveness. Because the noninvasive chemical exchange saturation transfer (CEST) MRI can probe the proton transfer and generate contrasts from endogenous metabolites, we aim to investigate if the in vivo CEST contrast is sensitive to proton transfer of the redox reactions so as to reveal the tissue redox states in breast cancer animal models. CEST MRI has been employed to characterize tumor metabolic heterogeneity and correlated with the redox states measured by the redox scanning in two human breast cancer mouse xenograft models, MDA-MB-231 and MCF-7. The possible biological mechanism on the correlation between the two imaging modalities was further investigated by phantom studies where the reductants and the oxidants of the representative redox reactions were measured. The CEST contrast is found linearly correlated with NADH concentration and the NADH redox ratio with high statistical significance, where NADH is the reduced form of nicotinamide adenine dinucleotide. The phantom studies showed that the reductants of the redox reactions have more CEST contrast than the corresponding oxidants, indicating that higher CEST effect corresponds to the more reduced redox state. This preliminary study suggests that CEST MRI, once calibrated, might provide a novel noninvasive imaging surrogate for the tissue redox state and a possible diagnostic biomarker for breast cancer in the clinic.

Effect of Electronic Excitation on Hydrogen Atom Transfer (Tautomerization) Reactions for the DNA Base Adenine

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Salter, Latasha M.; Kwak, Dochan (Technical Monitor)

2002-01-01

Geometrical structures and energetic properties for four different tautomers of adenine are calculated in this study, using multi-configurational wave functions. Both the ground and the lowest single excited state potential energy surface are studied. The energetic order of the tautomers on the ground state potential surface is 9H less than 7H less than 3H less than 1H, while on the excited state surface this order is found to be different: 3H less than 1H less than 9H less than 7H. Minimum energy reaction paths are obtained for hydrogen atom transfer (9 yields 3 tautomerization) reactions in the ground and the lowest excited electronic state. It is found that the barrier heights and the shapes of the reaction paths are different for the ground and the excited electronic state, suggesting that the probability of such tautomerization reaction is higher on the excited state potential energy surface. The barrier for this reaction in the excited state may become very low in the presence of water or other polar solvent molecules, and therefore such tautomerization reaction may play an important role in the solution phase photochemistry of adenine.

S-matrix decomposition, natural reaction channels, and the quantum transition state approach to reactive scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manthe, Uwe, E-mail: uwe.manthe@uni-bielefeld.de; Ellerbrock, Roman, E-mail: roman.ellerbrock@uni-bielefeld.de

2016-05-28

A new approach for the quantum-state resolved analysis of polyatomic reactions is introduced. Based on the singular value decomposition of the S-matrix, energy-dependent natural reaction channels and natural reaction probabilities are defined. It is shown that the natural reaction probabilities are equal to the eigenvalues of the reaction probability operator [U. Manthe and W. H. Miller, J. Chem. Phys. 99, 3411 (1993)]. Consequently, the natural reaction channels can be interpreted as uniquely defined pathways through the transition state of the reaction. The analysis can efficiently be combined with reactive scattering calculations based on the propagation of thermal flux eigenstates. Inmore » contrast to a decomposition based straightforwardly on thermal flux eigenstates, it does not depend on the choice of the dividing surface separating reactants from products. The new approach is illustrated studying a prototypical example, the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction. The natural reaction probabilities and the contributions of the different vibrational states of the methyl product to the natural reaction channels are calculated and discussed. The relation between the thermal flux eigenstates and the natural reaction channels is studied in detail.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greene, Samuel M., E-mail: samuel.greene@chem.ox.ac.uk; Shan, Xiao, E-mail: xiao.shan@chem.ox.ac.uk; Clary, David C., E-mail: david.clary@chem.ox.ac.u

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 aremore » 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.« less

Bifurcations on Potential Energy Surfaces of Organic Reactions

PubMed Central

Ess, Daniel H.; Wheeler, Steven E.; Iafe, Robert G.; Xu, Lai; Çelebi-Ölçüm, Nihan; Houk, K. N.

2009-01-01

A single transition state may lead to multiple intermediates or products if there is a post-transition state reaction path bifurcation. These bifurcations arise when there are sequential transition states with no intervening energy minimum. For such systems, the shape of the potential energy surface and dynamic effects control selectivity rather than transition state energetics. This minireview covers recent investigations of organic reactions exhibiting reaction pathway bifurcations. Such phenomena are surprisingly general and affect experimental observables such as kinetic isotope effects and product distributions. PMID:18767086

MICROBIAL TRANSFORMATION OF SELECTED ORGANIC CHEMICALS IN NATURAL AQUATIC SYSTEMS

EPA Science Inventory

A method for describing the microbial degradation of xenobiotics through the use of a second-order reaction equation was tested in several water bodies in the United States and Russia. he experiment was aimed at studying the microbial transformation of a herbicide widely used in ...

A moment-convergence method for stochastic analysis of biochemical reaction networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Jiajun; Nie, Qing; Zhou, Tianshou, E-mail: mcszhtsh@mail.sysu.edu.cn

Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in termsmore » of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.« less

Fabrication and microstructure of cerium doped lutetium aluminum garnet (Ce:LuAG) transparent ceramics by solid-state reaction method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Junlang, E-mail: lijunlangx@163.com; Xu, Jian, E-mail: xu.jian.57z@st.kyoto-u.ac.jp; Graduate School of Human and Environmental Studies, Division of Materials Function, Kyoto University, Kyoto 606-8501

2014-07-01

Highlights: • We fabricate Ce doped lutetium aluminum garnet ceramics by solid-state method. • The raw materials include Lu{sub 2}O{sub 3} nanopowders synthesized by co-precipitation method. • The density of the transparent ceramics reach 99.7% of the theoretical value. • The optical transmittance of the bulk ceramic at 550 nm was 57.48%. • Some scattering centers decrease the optical characteristic of the ceramic. - Abstract: Polycrystalline Ce{sup 3+} doped lutetium aluminum garnet (Ce:LuAG) transparent ceramics fabricated by one step solid-state reaction method using synthetic nano-sized Lu{sub 2}O{sub 3}, commercial α-Al{sub 2}O{sub 3} and CeO{sub 2} powders were investigated in thismore » paper. The green compacts shaped by the mixed powders were successfully densified into Ce:LuAG transparent ceramics after vacuum sintering at 1750 °C for 10 h. The in-line optical transmittance of the Ce:LuAG ceramic made by home-made Lu{sub 2}O{sub 3} powders could reach 57.48% at 550 nm, which was higher than that of the ceramic made by commercial Lu{sub 2}O{sub 3} powders (22.96%). The microstructure observation showed that light scattering centers caused by micro-pores, aluminum segregation and refraction index inhomogeneities induced the decrease of optical transparency of the Ce:LuAG ceramics, which should be removed and optimized in the future work.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Jiayue; Zhang, Dong; Chen, Zhen

The vibrationally excited reaction of F + CHD{sub 3}(ν{sub 1} = 1) → DF + CHD{sub 2} at a collision energy of 9.0 kcal/mol is investigated using the crossed-beams and time-sliced velocity map imaging techniques. Detailed and quantitative information of the CH stretching excitation effects on the reactivity and dynamics of the title reaction is extracted with the help of an accurate determination of the fraction of the excited CHD{sub 3} reagent in the crossed-beam region. It is found that all vibrational states of the CHD{sub 2} products observed in the ground-state reaction, which mainly involve the excitation of themore » umbrella mode of the CHD{sub 2} products, are severely suppressed by the CH stretching excitation. However, there are four additional vibrational states of the CHD{sub 2} products appearing in the excited-state reaction which are not presented in the ground-state reaction. These vibrational states either have the CH stretching excitation retained or involve one quantum excitation in the CH stretching and the excitation of the umbrella mode. Including all observed vibrational states, the overall cross section of the excited-state reaction is estimated to be 66.6% of that of the ground-state one. Experimental results also show that when the energy of CH stretching excitation is released during the reaction, it is deposited almost exclusively as the rovibrational energy of the DF products, with little portion in the translational degree of freedom. For vibrational states of the CHD{sub 2} products observed in both ground- and excited-state reactions, the CH stretching excitation greatly suppresses the forward scattered products, causing a noticeable change in the product angular distributions.« less

Stochastic flux analysis of chemical reaction networks

PubMed Central

2013-01-01

Background Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. Results We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. Conclusions We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network. PMID:24314153

Systematic derivation of reaction-diffusion equations with distributed delays and relations to fractional reaction-diffusion equations and hyperbolic transport equations: application to the theory of Neolithic transition.

PubMed

Vlad, Marcel Ovidiu; Ross, John

2002-12-01

We introduce a general method for the systematic derivation of nonlinear reaction-diffusion equations with distributed delays. We study the interactions among different types of moving individuals (atoms, molecules, quasiparticles, biological organisms, etc). The motion of each species is described by the continuous time random walk theory, analyzed in the literature for transport problems, whereas the interactions among the species are described by a set of transformation rates, which are nonlinear functions of the local concentrations of the different types of individuals. We use the time interval between two jumps (the transition time) as an additional state variable and obtain a set of evolution equations, which are local in time. In order to make a connection with the transport models used in the literature, we make transformations which eliminate the transition time and derive a set of nonlocal equations which are nonlinear generalizations of the so-called generalized master equations. The method leads under different specified conditions to various types of nonlocal transport equations including a nonlinear generalization of fractional diffusion equations, hyperbolic reaction-diffusion equations, and delay-differential reaction-diffusion equations. Thus in the analysis of a given problem we can fit to the data the type of reaction-diffusion equation and the corresponding physical and kinetic parameters. The method is illustrated, as a test case, by the study of the neolithic transition. We introduce a set of assumptions which makes it possible to describe the transition from hunting and gathering to agriculture economics by a differential delay reaction-diffusion equation for the population density. We derive a delay evolution equation for the rate of advance of agriculture, which illustrates an application of our analysis.

Stochastic flux analysis of chemical reaction networks.

PubMed

Kahramanoğulları, Ozan; Lynch, James F

2013-12-07

Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network.

Redox chemistry and natural organic matter (NOM): Geochemists' dream, analytical chemists' nightmare

USGS Publications Warehouse

Macalady, Donald L.; Walton-Day, Katherine

2011-01-01

Natural organic matter (NOM) is an inherently complex mixture of polyfunctional organic molecules. Because of their universality and chemical reversibility, oxidation/reductions (redox) reactions of NOM have an especially interesting and important role in geochemistry. Variabilities in NOM composition and chemistry make studies of its redox chemistry particularly challenging, and details of NOM-mediated redox reactions are only partially understood. This is in large part due to the analytical difficulties associated with NOM characterization and the wide range of reagents and experimental systems used to study NOM redox reactions. This chapter provides a summary of the ongoing efforts to provide a coherent comprehension of aqueous redox chemistry involving NOM and of techniques for chemical characterization of NOM. It also describes some attempts to confirm the roles of different structural moieties in redox reactions. In addition, we discuss some of the operational parameters used to describe NOM redox capacities and redox states, and describe nomenclature of NOM redox chemistry. Several relatively facile experimental methods applicable to predictions of the NOM redox activity and redox states of NOM samples are discussed, with special attention to the proposed use of fluorescence spectroscopy to predict relevant redox characteristics of NOM samples.

Measurement of 240Pu Angular Momentum Dependent Fission Probabilities Using the (α ,α') Reaction

NASA Astrophysics Data System (ADS)

Koglin, Johnathon; Burke, Jason; Fisher, Scott; Jovanovic, Igor

2017-09-01

The surrogate reaction method often lacks the theoretical framework and necessary experimental data to constrain models especially when rectifying differences between angular momentum state differences between the desired and surrogate reaction. In this work, dual arrays of silicon telescope particle identification detectors and photovoltaic (solar) cell fission fragment detectors have been used to measure the fission probability of the 240Pu(α ,α' f) reaction - a surrogate for the 239Pu(n , f) - and fission fragment angular distributions. Fission probability measurements were performed at a beam energy of 35.9(2) MeV at eleven scattering angles from 40° to 140°e in 10° intervals and at nuclear excitation energies up to 16 MeV. Fission fragment angular distributions were measured in six bins from 4.5 MeV to 8.0 MeV and fit to expected distributions dependent on the vibrational and rotational excitations at the saddle point. In this way, the contributions to the total fission probability from specific states of K angular momentum projection on the symmetry axis are extracted. A sizable data collection is presented to be considered when constraining microscopic cross section calculations.

Theoretical investigation on the potential energy surface for the reactions of B, Al and Ga with NO

NASA Astrophysics Data System (ADS)

Zhang, Luning; Zhou, Mingfei

2000-06-01

The structures, binding energies and vibrational frequencies of various MNO structural isomers (M=B, Al and Ga) in their ground triplet states have been determined using the density functional (B3LYP, BP86 and B3PW91) and MP2 methods. The potential energy surfaces of the M+NO reactions have been developed at the B3LYP/6-311+G(d) level of theory, and transition states on the isomerization potential energy surfaces have been characterized. Our calculation results show that four BNO isomers, namely, nitrosyl BNO, isonitrosyl BON, side-bonded B- η2-NO and the inserted NBO molecules are stationary points, while for Al and Ga, only the MNO (nitrosyl), MON (isonitrosyl) and the OMN (insertion) molecules are local minimum. The B+NO reaction products are more strongly bonded compared to the Al and Ga+NO systems due to strong covalent bonding. The interactions of B, Al and Ga atoms with NO to generate nitrosyl and isonitrosyl addition molecules are barrierless, but subsequent isomerization reactions to form the side-bonded molecules and the inserted products require activation energy.

The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions

PubMed Central

2012-01-01

Background It is well known that the deterministic dynamics of biochemical reaction networks can be more easily studied if timescale separation conditions are invoked (the quasi-steady-state assumption). In this case the deterministic dynamics of a large network of elementary reactions are well described by the dynamics of a smaller network of effective reactions. Each of the latter represents a group of elementary reactions in the large network and has associated with it an effective macroscopic rate law. A popular method to achieve model reduction in the presence of intrinsic noise consists of using the effective macroscopic rate laws to heuristically deduce effective probabilities for the effective reactions which then enables simulation via the stochastic simulation algorithm (SSA). The validity of this heuristic SSA method is a priori doubtful because the reaction probabilities for the SSA have only been rigorously derived from microscopic physics arguments for elementary reactions. Results We here obtain, by rigorous means and in closed-form, a reduced linear Langevin equation description of the stochastic dynamics of monostable biochemical networks in conditions characterized by small intrinsic noise and timescale separation. The slow-scale linear noise approximation (ssLNA), as the new method is called, is used to calculate the intrinsic noise statistics of enzyme and gene networks. The results agree very well with SSA simulations of the non-reduced network of elementary reactions. In contrast the conventional heuristic SSA is shown to overestimate the size of noise for Michaelis-Menten kinetics, considerably under-estimate the size of noise for Hill-type kinetics and in some cases even miss the prediction of noise-induced oscillations. Conclusions A new general method, the ssLNA, is derived and shown to correctly describe the statistics of intrinsic noise about the macroscopic concentrations under timescale separation conditions. The ssLNA provides a simple and accurate means of performing stochastic model reduction and hence it is expected to be of widespread utility in studying the dynamics of large noisy reaction networks, as is common in computational and systems biology. PMID:22583770

Gradient-based multiconfiguration Shepard interpolation for generating potential energy surfaces for polyatomic reactions.

PubMed

Tishchenko, Oksana; Truhlar, Donald G

2010-02-28

This paper describes and illustrates a way to construct multidimensional representations of reactive potential energy surfaces (PESs) by a multiconfiguration Shepard interpolation (MCSI) method based only on gradient information, that is, without using any Hessian information from electronic structure calculations. MCSI, which is called multiconfiguration molecular mechanics (MCMM) in previous articles, is a semiautomated method designed for constructing full-dimensional PESs for subsequent dynamics calculations (classical trajectories, full quantum dynamics, or variational transition state theory with multidimensional tunneling). The MCSI method is based on Shepard interpolation of Taylor series expansions of the coupling term of a 2 x 2 electronically diabatic Hamiltonian matrix with the diagonal elements representing nonreactive analytical PESs for reactants and products. In contrast to the previously developed method, these expansions are truncated in the present version at the first order, and, therefore, no input of electronic structure Hessians is required. The accuracy of the interpolated energies is evaluated for two test reactions, namely, the reaction OH+H(2)-->H(2)O+H and the hydrogen atom abstraction from a model of alpha-tocopherol by methyl radical. The latter reaction involves 38 atoms and a 108-dimensional PES. The mean unsigned errors averaged over a wide range of representative nuclear configurations (corresponding to an energy range of 19.5 kcal/mol in the former case and 32 kcal/mol in the latter) are found to be within 1 kcal/mol for both reactions, based on 13 gradients in one case and 11 in the other. The gradient-based MCMM method can be applied for efficient representations of multidimensional PESs in cases where analytical electronic structure Hessians are too expensive or unavailable, and it provides new opportunities to employ high-level electronic structure calculations for dynamics at an affordable cost.

Prediction of Stereochemistry using Q2MM

PubMed Central

2016-01-01

Conspectus The standard method of screening ligands for selectivity in asymmetric, transition metal-catalyzed reactions requires experimental testing of hundreds of ligands from ligand libraries. This “trial and error” process is costly in terms of time as well as resources and, in general, is scientifically and intellectually unsatisfying as it reveals little about the underlying mechanism behind the selectivity. The accurate computational prediction of stereoselectivity in enantioselective catalysis requires adequate conformational sampling of the selectivity-determining transition state but has to be fast enough to compete with experimental screening techniques to be useful for the synthetic chemist. Although electronic structure calculations are accurate and general, they are too slow to allow for sampling or fast screening of ligand libraries. The combined requirements can be fulfilled by using appropriately fitted transition state force fields (TSFFs) that represent the transition state as a minimum and allow fast conformational sampling using Monte Carlo. Quantum-guided molecular mechanics (Q2MM) is an automated force field parametrization method that generates accurate, reaction-specific TSFFs by fitting the functional form of an arbitrary force field using only electronic structure calculations by minimization of an objective function. A key feature that distinguishes the Q2MM method from many other automated parametrization procedures is the use of the Hessian matrix in addition to geometric parameters and relative energies. This alleviates the known problems of overfitting of TSFFs. After validation of the TSFF by comparison to electronic structure results for a test set and available experimental data, the stereoselectivity of a reaction can be calculated by summation over the Boltzman-averaged relative energies of the conformations leading to the different stereoisomers. The Q2MM method has been applied successfully to perform virtual ligand screens on a range of transition metal-catalyzed reactions that are important from both an industrial and an academic perspective. In this Account, we provide an overview of the continued improvement of the prediction of stereochemistry using Q2MM-derived TSFFs using four examples from different stages of development: (i) Pd-catalyzed allylation, (ii) OsO4-catalyzed asymmetric dihydroxylation (AD) of alkenes, (iii) Rh-catalyzed hydrogenation of enamides, and (iv) Ru-catalyzed hydrogenation of ketones. In the current form, correlation coefficients of 0.8–0.9 between calculated and experimental ee values are typical for a wide range of substrate–ligand combinations, and suitable ligands can be predicted for a given substrate with ∼80% accuracy. Although the generation of a TSFF requires an initial effort and will therefore be most useful for widely used reactions that require frequent screening campaigns, the method allows for a rapid virtual screen of large ligand libraries to focus experimental efforts on the most promising substrate–ligand combinations. PMID:27064579

Charge-dependent non-bonded interaction methods for use in quantum mechanical modeling of condensed phase reactions

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.

Molecular modeling and computer simulation techniques can provide detailed insight into biochemical phenomena. This dissertation describes the development, implementation and parameterization of two methods for the accurate modeling of chemical reactions in aqueous environments, with a concerted scientific effort towards the inclusion of charge-dependent non-bonded non-electrostatic interactions into currently used computational frameworks. The first of these models, QXD, modifies interactions in a hybrid quantum mechanical/molecular (QM/MM) mechanical framework to overcome the current limitations of 'atom typing' QM atoms; an inaccurate and non-intuitive practice for chemically active species as these static atom types are dictated by the local bonding and electrostatic environment of the atoms they represent, which will change over the course of the simulation. The efficacy QXD model is demonstrated using a specific reaction parameterization (SRP) of the Austin Model 1 (AM1) Hamiltonian by simultaneously capturing the reaction barrier for chloride ion attack on methylchloride in solution and the solvation free energies of a series of compounds including the reagents of the reaction. The second, VRSCOSMO, is an implicit solvation model for use with the DFTB3/3OB Hamiltonian for biochemical reactions; allowing for accurate modeling of ionic compound solvation properties while overcoming the discontinuous nature of conventional PCM models when chemical reaction coordinates. The VRSCOSMO model is shown to accurately model the solvation properties of over 200 chemical compounds while also providing smooth, continuous reaction surfaces for a series of biologically motivated phosphoryl transesterification reactions. Both of these methods incorporate charge-dependent behavior into the non-bonded interactions variationally, allowing the 'size' of atoms to change in meaningful ways with respect to changes in local charge state, as to provide an accurate, predictive and transferable models for the interactions between the quantum mechanical system and their solvated surroundings.

Method of detecting sulfur dioxide

DOEpatents

Spicer, Leonard D.; Bennett, Dennis W.; Davis, Jon F.

1985-01-01

(CH.sub.3).sub.3 SiNSO is produced by the reaction of ((CH.sub.3).sub.3 Si).sub.2 NH with SO.sub.2. Also produced in the reaction are ((CH.sub.3).sub.3 Si).sub.2 O and a new solid compound [NH.sub.4 ][(CH.sub.3).sub.3 SiOSO.sub.2 ]. Both (CH.sub.3).sub.3 SiNSO and [NH.sub.4 ][(CH.sub.3).sub.3 SiOSO.sub.2 ] have fluorescent properties. The reaction of the subject invention is used in a method of measuring the concentration of SO.sub.2 pollutants in gases. By the method, a sample of gas is bubbled through a solution of ((CH.sub.3).sub.3 Si).sub.2 NH, whereby any SO.sub.2 present in the gas will react to produce the two fluorescent products. The measured fluorescence of these products can then be used to calculate the concentration of SO.sub.2 in the original gas sample. The solid product [NH.sub.4][(CH.sub.3).sub.3 SiOSO.sub.2 ] may be used as a standard in solid state NMR spectroscopy.

Nanowire Membrane-based Nanothermite: towards Processable and Tunable Interfacial Diffusion for Solid State Reactions

PubMed Central

Yang, Yong; Wang, Peng-peng; Zhang, Zhi-cheng; Liu, Hui-ling; Zhang, Jingchao; Zhuang, Jing; Wang, Xun

2013-01-01

Interfacial diffusion is of great importance in determining the performance of solid-state reactions. For nanometer sized particles, some solid-state reactions can be triggered accidently by mechanical stress owing to their large surface-to-volume ratio compared with the bulk ones. Therefore, a great challenge is the control of interfacial diffusion for solid state reactions, especially for energetic materials. Here we demonstrate, through the example of nanowire-based thermite membrane, that the thermite solid-state reaction can be easily tuned via the introduction of low-surface-energy coating layer. Moreover, this silicon-coated thermite membrane exhibit controlled wetting behavior ranging from superhydrophilic to superhydrophobic and, simultaneously, to significantly reduce the friction sensitivity of thermite membrane. This effect enables to increase interfacial resistance by increasing the amount of coating material. Indeed, our results described here make it possible to tune the solid-state reactions through the manipulation of interfacial diffusion between the reactants. PMID:23603809

Semi-analytical solutions of the Schnakenberg model of a reaction-diffusion cell with feedback

NASA Astrophysics Data System (ADS)

Al Noufaey, K. S.

2018-06-01

This paper considers the application of a semi-analytical method to the Schnakenberg model of a reaction-diffusion cell. The semi-analytical method is based on the Galerkin method which approximates the original governing partial differential equations as a system of ordinary differential equations. Steady-state curves, bifurcation diagrams and the region of parameter space in which Hopf bifurcations occur are presented for semi-analytical solutions and the numerical solution. The effect of feedback control, via altering various concentrations in the boundary reservoirs in response to concentrations in the cell centre, is examined. It is shown that increasing the magnitude of feedback leads to destabilization of the system, whereas decreasing this parameter to negative values of large magnitude stabilizes the system. The semi-analytical solutions agree well with numerical solutions of the governing equations.

Approaches to the Treatment of Equilibrium Perturbations

NASA Astrophysics Data System (ADS)

Canagaratna, Sebastian G.

2003-10-01

Perturbations from equilibrium are treated in the textbooks by a combination of Le Châtelier's principle, the comparison of the equilibrium constant K with the reaction quotient Q,and the kinetic approach. Each of these methods is briefly reviewed. This is followed by derivations of the variation of the equilibrium value of the extent of reaction, ξeq, with various parameters on which it depends. Near equilibrium this relationship can be represented by a straight line. The equilibrium system can be regarded as moving on this line as the parameter is varied. The slope of the line depends on quantities like enthalpy of reaction, volume of reaction and so forth. The derivation shows that these quantities pertain to the equilibrium system, not the standard state. Also, the derivation makes clear what kind of assumptions underlie our conclusions. The derivation of these relations involves knowledge of thermodynamics that is well within the grasp of junior level physical chemistry students. The conclusions that follow from the derived relations are given as subsidiary rules in the form of the slope of ξeq, with T, p, et cetera. The rules are used to develop a visual way of predicting the direction of shift of a perturbed system. This method can be used to supplement one of the other methods even at the introductory level.

Convergence to equilibrium of renormalised solutions to nonlinear chemical reaction–diffusion systems

NASA Astrophysics Data System (ADS)

Fellner, Klemens; Tang, Bao Quoc

2018-06-01

The convergence to equilibrium for renormalised solutions to nonlinear reaction-diffusion systems is studied. The considered reaction-diffusion systems arise from chemical reaction networks with mass action kinetics and satisfy the complex balanced condition. By applying the so-called entropy method, we show that if the system does not have boundary equilibria, i.e. equilibrium states lying on the boundary of R_+^N, then any renormalised solution converges exponentially to the complex balanced equilibrium with a rate, which can be computed explicitly up to a finite-dimensional inequality. This inequality is proven via a contradiction argument and thus not explicitly. An explicit method of proof, however, is provided for a specific application modelling a reversible enzyme reaction by exploiting the specific structure of the conservation laws. Our approach is also useful to study the trend to equilibrium for systems possessing boundary equilibria. More precisely, to show the convergence to equilibrium for systems with boundary equilibria, we establish a sufficient condition in terms of a modified finite-dimensional inequality along trajectories of the system. By assuming this condition, which roughly means that the system produces too much entropy to stay close to a boundary equilibrium for infinite time, the entropy method shows exponential convergence to equilibrium for renormalised solutions to complex balanced systems with boundary equilibria.

γ-Particle coincidence technique for the study of nuclear reactions

NASA Astrophysics Data System (ADS)

Zagatto, V. A. B.; Oliveira, J. R. B.; Allegro, P. R. P.; Chamon, L. C.; Cybulska, E. W.; Medina, N. H.; Ribas, R. V.; Seale, W. A.; Silva, C. P.; Gasques, L. R.; Zahn, G. S.; Genezini, F. A.; Shorto, J. M. B.; Lubian, J.; Linares, R.; Toufen, D. L.; Silveira, M. A. G.; Rossi, E. S.; Nobre, G. P.

2014-06-01

The Saci-Perere γ ray spectrometer (located at the Pelletron AcceleratorLaboratory - IFUSP) was employed to implement the γ-particle coincidence technique for the study of nuclear reaction mechanisms. For this, the 18O+110Pd reaction has been studied in the beam energy range of 45-54 MeV. Several corrections to the data due to various effects (energy and angle integrations, beam spot size, γ detector finite size and the vacuum de-alignment) are small and well controlled. The aim of this work was to establish a proper method to analyze the data and identify the reaction mechanisms involved. To achieve this goal the inelastic scattering to the first excited state of 110Pd has been extracted and compared to coupled channel calculations using the São Paulo Potential (PSP), being reasonably well described by it.

Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism.

PubMed

Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori

2016-10-11

The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an S N 1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

Synchronization criteria for generalized reaction-diffusion neural networks via periodically intermittent control.

PubMed

Gan, Qintao; Lv, Tianshi; Fu, Zhenhua

2016-04-01

In this paper, the synchronization problem for a class of generalized neural networks with time-varying delays and reaction-diffusion terms is investigated concerning Neumann boundary conditions in terms of p-norm. The proposed generalized neural networks model includes reaction-diffusion local field neural networks and reaction-diffusion static neural networks as its special cases. By establishing a new inequality, some simple and useful conditions are obtained analytically to guarantee the global exponential synchronization of the addressed neural networks under the periodically intermittent control. According to the theoretical results, the influences of diffusion coefficients, diffusion space, and control rate on synchronization are analyzed. Finally, the feasibility and effectiveness of the proposed methods are shown by simulation examples, and by choosing different diffusion coefficients, diffusion spaces, and control rates, different controlled synchronization states can be obtained.

Simulation methods with extended stability for stiff biochemical Kinetics.

PubMed

Rué, Pau; Villà-Freixa, Jordi; Burrage, Kevin

2010-08-11

With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (bio)chemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA). The key quantity is the step size, or waiting time, tau, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where tau can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called tau-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as tau grows. In this paper we extend Poisson tau-leap methods to a general class of Runge-Kutta (RK) tau-leap methods. We show that with the proper selection of the coefficients, the variance of the extended tau-leap can be well-behaved, leading to significantly larger step sizes. The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original tau-leap method. The approach paves the way to explore new multiscale methods to simulate (bio)chemical systems.