Nitschke, Naomi; Atkovska, Kalina; Hub, Jochen S.
2016-09-01
Molecular dynamics simulations are capable of predicting the permeability of lipid membranes for drug-like solutes, but the calculations have remained prohibitively expensive for high-throughput studies. Here, we analyze simple measures for accelerating potential of mean force (PMF) calculations of membrane permeation, namely, (i) using smaller simulation systems, (ii) simulating multiple solutes per system, and (iii) using shorter cutoffs for the Lennard-Jones interactions. We find that PMFs for membrane permeation are remarkably robust against alterations of such parameters, suggesting that accurate PMF calculations are possible at strongly reduced computational cost. In addition, we evaluated the influence of the definition of the membrane center of mass (COM), used to define the transmembrane reaction coordinate. Membrane-COM definitions based on all lipid atoms lead to artifacts due to undulations and, consequently, to PMFs dependent on membrane size. In contrast, COM definitions based on a cylinder around the solute lead to size-independent PMFs, down to systems of only 16 lipids per monolayer. In summary, compared to popular setups that simulate a single solute in a membrane of 128 lipids with a Lennard-Jones cutoff of 1.2 nm, the measures applied here yield a speedup in sampling by factor of ˜40, without reducing the accuracy of the calculated PMF.
Reaction Coordinates and Mechanistic Hypothesis Tests.
Peters, Baron
2016-05-27
Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches.
Reaction Coordinates and Mechanistic Hypothesis Tests
Peters, Baron
2016-05-01
Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches.
Reactivity of bromoalkanes in reactions of coordinated molecular decay
Pokidova, T. S.; Denisov, E. T.
2016-09-01
The results from experiments on reactions of the coordinated molecular decay of RBr bromoalkanes on olefin and HBr are analyzed using the model of intersecting parabolas (MIP). Kinetic parameters within the MIP are calculated from the experimental data, enabling calculation of the activation energies ( E) and rate constants ( k) of such reactions, based on the enthalphy of the reaction and the MIP algorithms. The factors affecting the E of the RBr decay reaction are established: the enthalphy of the reaction, triplet repulsion, the energy of radical R• stabilization, the presence of a π bond adjacent to the reaction center, and the dipole-dipole interaction of polar groups. The energy spectrum of the partial energies of activation is constructed for the reaction of coordinated molecular decay of RBr, and the E and k of inverse addition reactions are evaluated.
How wet should be the reaction coordinate for ligand unbinding?
Tiwary, Pratyush
2016-01-01
We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) (Tiwary and Berne, Proc. Natl. Acad. Sci 2016, 113, 2839 (2016)), to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics, and by comparison through detailed balance with unbiased molecular dynamics estimate of the bindin...
Nonlinear reaction coordinate analysis in the reweighted path ensemble
Lechner, W.; Rogal, J.; Juraszek, J.; Ensing, B.; Bolhuis, P.G.
2010-01-01
We present a flexible nonlinear reaction coordinate analysis method for the transition path ensemble based on the likelihood maximization approach developed by Peters and Trout [J. Chem. Phys. 125, 054108 (2006)] . By parametrizing the reaction coordinate by a string of images in a collective variab
Calculation of turbulent reactive flows in general orthogonal coordinates
Lai, M. K. Y.
1992-02-01
The mathematical and numerical methodology for an extended and enhanced version of the TURCOM computer code, called TURCOM-BFC, is presented. This code solves the conservation equations of multi-component chemically reactive and turbulent flows in general curvilinear orthogonal coordinates. The k-epsilon turbulence submodel is used. Flame chemistry assumes a number of species and chemical reactions. The latter are subdivided into finite-rate reaction steps and a one-step irreversible reaction, whose rate is controlled by a combination of mixing and global kinetics. Both the SIMPLE and PISO algorithms are implemented to solve the system of equations. The capability of TURCOM-BFC is tested and demonstrated by predicting 3-dimensional combustion flow inside a reaction furnace, where both polar-cylindrical and bipolar coordinates are used.
Recent Developments in Methods for Identifying Reaction Coordinates
Li, Wenjin
2015-01-01
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor.
Recent developments in methods for identifying reaction coordinates.
Li, Wenjin; Ma, Ao
2014-01-01
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor.
Density functional calculations on hydrocarbon isodesmic reactions
Fortunelli, Alessandro; Selmi, Massimo
1994-06-01
Hartree—Fock, Hartree—Fock-plus-correlation and self-consistent Kohn—Sham calculations are performed on a set of hydrocarbon isodesmic reactions, i.e. reactions among hydrocarbons in which the number and type of carbon—carbon and carbon—hydrogen bonds is conserved. It is found that neither Hartree—Fock nor Kohn—Sham methods correctly predict standard enthalpies, Δ Hr(298 K), of these reactions, even though — for reactions involving molecules containing strained double bonds — the agreement between the theoretical estimates and the experimental values of Δ Hr seems to be improved by the self-consistent solution of the Kohn—Sham equations. The remaining discrepancies are attributed to intramolecular dispersion effects, that are not described by ordinary exchange—correlation functionals, and are eliminated by introducing corrections based on a simple semi-empirical model.
A benchmark for reaction coordinates in the transition path ensemble.
Li, Wenjin; Ma, Ao
2016-04-01
The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems.
Calculation of the energetics of chemical reactions
Dunning, T.H. Jr.; Harding, L.B.; Shepard, R.L.; Harrison, R.J.
1988-01-01
To calculate the energetics of chemical reactions we must solve the electronic Schroedinger equation for the molecular conformations of importance for the reactive encounter. Substantial changes occur in the electronic structure of a molecular system as the reaction progresses from reactants through the transition state to products. To describe these changes, our approach includes the following three elements: the use of multiconfiguration self-consistent field wave functions to provide a consistent zero-order description of the electronic structure of the reactants, transition state, and products; the use of configuration interaction techniques to describe electron correlation effects needed to provide quantitative predictions of the reaction energetics; and the use of large, optimized basis sets to provide the flexibility needed to describe the variations in the electronic distributions. With this approach we are able to study reactions involving as many as 5--6 atoms with errors of just a few kcal/mol in the predicted reaction energetics. Predictions to chemical accuracy, i.e., to 1 kcal/mol or less, are not yet feasible, although continuing improvements in both the theoretical methodology and computer technology suggest that this will soon be possible, at least for reactions involving small polyatomic species. 4 figs.
The stochastic separatrix and the reaction coordinate for complex systems.
Antoniou, Dimitri; Schwartz, Steven D
2009-04-21
We present a new approach to the identification of degrees of freedom which comprise a reaction coordinate in a complex system. The method begins with the generation of an ensemble of reactive trajectories. Each trajectory is analyzed for its equicommittor position or transition state; then the transition state ensemble is identified as the stochastic separatrix. Numerical analysis of the points along the separatrix for variability of coordinate location correctly identifies the components of the reaction coordinate in a test system of a double well coupled to a promoting vibration and a bath of linearly coupled oscillators.
Rate constant and reaction coordinate of Trp-cage folding in explicit water
Juraszek, J.; Bolhuis, P.G.
2008-01-01
We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the
Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.
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
Awasthi, Neha; Hub, Jochen S
2016-07-12
Transmembrane pores play an important role in various biophysical processes such as membrane permeation, membrane fusion, and antimicrobial peptide activity. In principal, all-atom molecular dynamics (MD) simulations provide an accurate model of pore formation in lipid membranes. However, the free energy landscape of transmembrane pore formation remains poorly understood, partly because potential of mean force (PMF) calculations of pore formation strongly depend on the choice of the reaction coordinate. In this study, we used umbrella sampling to compute PMFs for pore formation using three different reaction coordinates, namely, (i) a coordinate that steers the lipids in the lateral direction away from the pore center, (ii) the distance of a single lipid phosphate group from the membrane center, and (iii) the average water density inside a membrane-spanning cylinder. Our results show that while the three reaction coordinates efficiently form pores in membranes, they suffer from strong hysteresis between pore-opening and pore-closing simulations, suggesting that they do not restrain the systems close to the transition state for pore formation. The two reaction coordinates that act via restraining the lipids lead to more pronounced hysteresis compared with the coordinate acting on the water molecules. By comparing PMFs computed from membranes with different numbers of lipids, we observed significant artifacts from the periodic boundary conditions in small simulation systems. Further analysis suggests that the formation and disruption of a continuous hydrogen-bonding network across the membrane corresponds to the transition state for pore formation. Our study provides molecular insights into the critical steps of transmembrane pore formation, and it may guide the development of efficient reaction coordinates for pore formation.
Accelerating Calculations of Reaction Dissipative Particle Dynamics in LAMMPS
2017-05-17
and generally requires more time to solve per particle . This means that roughly half of the MPI processes will have higher reaction run times, while...ARL-TR-8018 ● MAY 2017 US Army Research Laboratory Accelerating Calculations of Reaction Dissipative Particle Dynamics in LAMMPS...Research Laboratory Accelerating Calculations of Reaction Dissipative Particle Dynamics in LAMMPS by Christopher P Stone Computational
Reaction mechanism and reaction coordinates from the viewpoint of energy flow.
Li, Wenjin; Ma, Ao
2016-03-21
Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.
Microscopic calculations for solar nuclear reactions
Csoto, A; Csoto, Attila; Langanke, Karlheinz
2001-01-01
We have studied the 4He(3He,gamma)7Be, 3He(3He,2p)4He, and 7Be(p,gamma)8B reactions of the solar p-p chain, using microscopic cluster models. Among other results, we showed that the 6Li+p channel has a nontrivial effect on the 7Be-producing reaction, that the existence of a resonance in 6Be close to the 3He+3He threshold is rather unlikely, and that the correlations between some properties of 7Be/8B and the low-energy cross section of 7Be(p,gamma)8B might help one to constrain the value of the S_17(0) astrophysical S-factor.
Sequential Voronoi diagram calculations using simple chemical reactions
Costello, Ben de Lacy; Adamatzky, Andy
2012-01-01
In our recent paper [de Lacy Costello et al. 2010] we described the formation of complex tessellations of the plane arising from the various reactions of metal salts with potassium ferricyanide and ferrocyanide loaded gels. In addition to producing colourful tessellations these reactions are naturally computing generalised Voronoi diagrams of the plane. The reactions reported previously were capable of the calculation of three distinct Voronoi diagrams of the plane. As diffusion coupled with a chemical reaction is responsible for the calculation then this is achieved in parallel. Thus an increase in the complexity of the data input does not utilise additional computational resource. Additional benefits of these chemical reactions is that a permanent record of the Voronoi diagram calculation (in the form of precipitate free bisectors) is achieved, so there is no requirement for further processing to extract the calculation results. Previously it was assumed that the permanence of the results was also a potenti...
Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation
Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J.; Schenter, Gregory K.
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 and 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.
Theoretical Model Calculation for d + 8Li Reaction
HAN Yin-Lu; GUO Hai-Rui; ZHANG Yue; ZHANG Jing-Shang
2008-01-01
Based on the theoretical models for light nuclei, the calculations of reaction cross sections and the angular distributions for d+8Li reaction are performed. Since all of the particle emissions are from the compound nucleus to the discrete levels, the angular momentum coupling effect in pre-equilibrium mechanism is taken into account. The three-body break-up process and the recoil effect are involved. The theoretical calculated results are compared to existing experimental data.
Reaction between radicals and N-alkoxyamines As coordinated cleavage with fragmentation
Denisov, E. T.; Shestakov, A. F.
2015-08-01
Quantum chemical calculations of the enthalpy and activation energy of two reactions with MeO{2/⊙} attacking the CH- and CH2-groups of 2,2,6,6-tetramethylpiperidineoxy-2'-butane are performed. It is shown that the cleavage of hydrogen atoms is accompanied by coordinated breaking of N-O-bonds in the former case and C-O-bonds in the latter. Based on the obtained results, a new scheme is proposed for the cyclic mechanism behind the cleavage of chains on nitroxyl radicals in oxidizing hydrocarbons and polymers that agrees with experimental data. At the center of this cyclic mechanism lies the fast exothermic reaction between peroxyl radicals and N-alkoxyamine with the cleavage of H atoms and the coordinated fragmentation of molecules. Using the model of intersecting parabolas, an algorithm for calculating the enthalpies, activation energies, and rate constants of these reactions with the participation of alkyl, alkoxy, aminyl, peroxyl, phenoxyl, thiyl, and hydroxyl radicals is proposed.
The reaction force: Three key points along an intrinsic reaction coordinate
Peter Politzer; Alejandro Toro-Labbé; Soledad Gutiérrez-Oliva; Bárbara herrera; Pablo Jaque; Monica C Concha; Jane S Murray
2005-09-01
The concept of the reaction force is presented and discussed in detail. For typical processes with energy barriers, it has a universal form which defines three key points along an intrinsic reaction coordinate: the force minimum, zero and maximum. We suggest that the resulting four zones be interpreted as involving preparation of reactants in the first, transition to products in the second and third, and relaxation in the fourth. This general picture is supported by the distinctive patterns of the variations in relevant electronic properties. Two important points that are brought out by the reaction force are that (a) the traditional activation energy comprises two separate contributions, and (b) the transition state corresponds to a balance between the driving and the retarding forces.
Calculation of individual isotope equilibrium constants for geochemical reactions
Thorstenson, D.C.; Parkhurst, D.L.
2004-01-01
Theory is derived from the work of Urey (Urey H. C. [1947] The thermodynamic properties of isotopic substances. J. Chem. Soc. 562-581) to calculate equilibrium constants commonly used in geochemical equilibrium and reaction-transport models for reactions of individual isotopic species. Urey showed that equilibrium constants of isotope exchange reactions for molecules that contain two or more atoms of the same element in equivalent positions are related to isotope fractionation factors by ?? = (Kex)1/n, where n is the number of atoms exchanged. This relation is extended to include species containing multiple isotopes, for example 13C16O18O and 1H2H18O. The equilibrium constants of the isotope exchange reactions can be expressed as ratios of individual isotope equilibrium constants for geochemical reactions. Knowledge of the equilibrium constant for the dominant isotopic species can then be used to calculate the individual isotope equilibrium constants. Individual isotope equilibrium constants are calculated for the reaction CO2g = CO2aq for all species that can be formed from 12C, 13C, 16O, and 18O; for the reaction between 12C18 O2aq and 1H218Ol; and among the various 1H, 2H, 16O, and 18O species of H2O. This is a subset of a larger number of equilibrium constants calculated elsewhere (Thorstenson D. C. and Parkhurst D. L. [2002] Calculation of individual isotope equilibrium constants for implementation in geochemical models. Water-Resources Investigation Report 02-4172. U.S. Geological Survey). Activity coefficients, activity-concentration conventions for the isotopic variants of H2O in the solvent 1H216Ol, and salt effects on isotope fractionation have been included in the derivations. The effects of nonideality are small because of the chemical similarity of different isotopic species of the same molecule or ion. The temperature dependence of the individual isotope equilibrium constants can be calculated from the temperature dependence of the fractionation
Algorithms of Coordinates Scintillations Calculation in the Gamma-Camera Detector
G.A. Polyakov
2010-01-01
Full Text Available The methods and algorithms of scintillation coordinates calculation in gamma-camera position-sensitive detector are considered in the paper. The results of numerical model experiments, which were carried out for clearing-up of relative operating speed of different coordinate calculation methods, are presented. The analysis of obtained results was carried out for determination of perspective for application algorithms and likelihood methods.
Svensson, Fredrik; Engen, Karin; Lundbäck, Thomas; Larhed, Mats; Sköld, Christian
2015-09-28
Transition state and high energy intermediate mimetics have the potential to be very potent enzyme inhibitors. In this study, a model of peptide hydrolysis in the active site of insulin-regulated aminopeptidase (IRAP) was developed using density functional theory calculations and the cluster approach. The 3D structure models of the reaction coordinates were used for virtual screening to obtain new chemical starting points for IRAP inhibitors. This mechanism-based virtual screening process managed to identify several known peptidase inhibitors from a library of over 5 million compounds, and biological testing identified one compound not previously reported as an IRAP inhibitor. This novel methodology for virtual screening is a promising approach to identify new inhibitors mimicking key transition states or intermediates of an enzymatic reaction.
Theoretical calculations and analysis for n + 6Li reaction
Tao, Xi; Wang, Jimin; Chen, Guochang; Shen, Qingbiao
2017-09-01
R-matrix theory is an important methodology for applications on light, medium and heavy mass nuclides nuclear reaction in the resonance energy range. Full R-matrix formalism contains the diagonal elements of the energy levels matrix and it is a rigorous theory. Because of different assumptions and approximations, many kinds of R-matrix derived methods are obtained. The new R-matrix code FDRR is presented and includes 4 kinds of R-matrix applications. It can be used for calculating integral cross sections and angular distributions of 2-bodies reactions. The cross sections and angular distributions of n+ 6Li reaction are calculated and analyzed by FDRR code. The results are in good agreement with experimental data below 20 MeV.
Uncertainty Calculation of Roundness Assessment by Automatic Differentiation in Coordinate Metrology
Jia-chun LIN; Michael Krystek; Zhao-yao SHI
2010-01-01
Recently, Coordinate Measuring Machines (CMMs) are widely used to measure roundness errors. Roundness is calculated from a large number of points collected from the profiles of the parts. According to the Guide to the Expression of Uncertainty in Measurement (GUM), all measurement results must have a stated uncertainty associated the them. However, no CMMs give the uncertainty value of the roundness, because no suitable measurement uncertainty calculation procedure exists. In the case of roundness measurement in coordinate metrology, this paper suggests the algorithms for the calculation of the measurement uncertainty of the roundness deviation based on the two mainly used association criteria, LSC and MZC. The calculation of the sensitivity coefficients for the uncertainty calculation can be done by automatic differentiation, in order to avoid introducing additional errors by the traditional difference quotient approximations. The proposed methods are exact and need input data only as the measured coordinates of the data points and their associated uncertainties.
Excitation function calculations for α + 93Nb nuclear reactions
Yiğit, M.; Tel, E.; Sarpün, İ. H.
2016-10-01
In this study, the excitation functions of alpha-induced reactions on the 93Nb target nucleus were calculated by using ALICE-ASH code. The hybrid model, Weisskopf-Ewing model and geometry dependent hybrid model in this code were used to understand the alpha-niobium interaction. The contribution on the nuclear interaction of compound and pre-compound processes, with variation of the incident alpha particle energy, was presented. Furthermore, the reaction cross sections were calculated by using different level density models such as Superfluid nuclear model, Fermi gas model and Kataria-Ramamurthy Fermi gas model. Obtaining a good agreement between the calculated and the measured cross sections, the exciton numbers and the nuclear level density models were varied. Finally, the proper choice of the exciton numbers and the nuclear level density models was found to be quite important in order to obtain the more realistic cross section values.
Peters, Baron; Bolhuis, Peter G; Mullen, Ryan G; Shea, Joan-Emma
2013-02-01
We propose a method for identifying accurate reaction coordinates among a set of trial coordinates. The method applies to special cases where motion along the reaction coordinate follows a one-dimensional Smoluchowski equation. In these cases the reaction coordinate can predict its own short-time dynamical evolution, i.e., the dynamics projected from multiple dimensions onto the reaction coordinate depend only on the reaction coordinate itself. To test whether this property holds, we project an ensemble of short trajectory swarms onto trial coordinates and compare projections of individual swarms to projections of the ensemble of swarms. The comparison, quantified by the Kullback-Leibler divergence, is numerically performed for each isosurface of each trial coordinate. The ensemble of short dynamical trajectories is generated only once by sampling along an initial order parameter. The initial order parameter should separate the reactants and products with a free energy barrier, and distributions on isosurfaces of the initial parameter should be unimodal. The method is illustrated for three model free energy landscapes with anisotropic diffusion. Where exact coordinates can be obtained from Kramers-Langer-Berezhkovskii-Szabo theory, results from the new method agree with the exact results. We also examine characteristics of systems where the proposed method fails. We show how dynamical self-consistency is related (through the Chapman-Kolmogorov equation) to the earlier isocommittor criterion, which is based on longer paths.
Improved resonance reaction rate calculation for lattice physics subsystem
Finch, D.R.
1974-02-08
The resonance capture calculations of the HAMMER System and HAMBUR System are derived from a consistent statement of the integral slowing down equation and definitions of the resonance integral. The assumptions made in these treatments are explicitly stated, and and an attempt is made to estimate the possible error in the resonance integral arising from these assumptions. This analysis is made to pin-point those parts of the calculation that can be improved and updated. Based on the analysis of existing calculations a method of calculation is derived which avoids most of the problems encountered in HAMMER and HAMBUR. The chief improvements that result are as follows: Careful attention is paid to calculation of the resonance flux as most errors in existing calculations result from consistently overpredicting fluxes in all regions of a lattice cell. The calculation can be modified to produce as crude or detailed a resonance calculation, at the expense of computer time, as required by the user. Resonances that overlap group boundaries contribute the correct contribution to each group's reaction rates. Overlap between resonances of different isotopes is correctly accounted for. Up-to-date resonance formalisms are used including the Adler-Adler multi-level formulations. Provision is made to easily add new formalisms when required. Streaming effects from neutron leaking into a cell may optionally be included in the calculation of resonance reaction rates. A complete description of the physics contained in this new computational module is provided along with additional information on the numerical techniques employed in the module.
Give Me a Hand! Digitizing Images into a Graphing Calculator Using Coordinate Geometry.
Bumbaca, Leonard
This paper describes a classroom, instructor-led activity designed to show how graphic calculators can be used to explore coordinate geometry. The activity involves digitizing an image of a hand and transforming the image through geometrical transformations. Teaching notes and calculator instructions are included as are blackline masters. Also…
Fep1d: a script for the analysis of reaction coordinates.
Banushkina, Polina V; Krivov, Sergei V
2015-05-05
The dynamics of complex systems with many degrees of freedom can be analyzed by projecting it onto one or few coordinates (collective variables). The dynamics is often described then as diffusion on a free energy landscape associated with the coordinates. Fep1d is a script for the analysis of such one-dimensional coordinates. The script allows one to construct conventional and cut-based free energy profiles, to assess the optimality of a reaction coordinate, to inspect whether the dynamics projected on the coordinate is diffusive, to transform (rescale) the reaction coordinate to more convenient ones, and to compute such quantities as the mean first passage time, the transition path times, the coordinate dependent diffusion coefficient, and so forth. Here, we describe the implemented functionality together with the underlying theoretical framework.
A microiterative intrinsic reaction coordinate method for large QM/MM systems.
Polyak, Iakov; Boulanger, Eliot; Sen, Kakali; Thiel, Walter
2013-09-14
Intrinsic reaction coordinate (IRC) computations are a valuable tool in theoretical studies of chemical reactions, but they can usually not be applied in their current form to handle large systems commonly described by quantum mechanics/molecular mechanics (QM/MM) methods. We report on a development that tackles this problem by using a strategy analogous to microiterative transition state optimization. In this approach, the IRC equations only govern the motion of a core region that contains at least the atoms directly involved in the reaction, while the remaining degrees of freedom are relaxed after each IRC step. This strategy can be used together with any existing IRC procedure. The present implementation covers the stabilized Euler, local quadratic approximation, and Hessian predictor-corrector algorithms for IRC calculations. As proof of principle, we perform tests at the QM level on small gas-phase systems and validate the results by comparisons with standard IRC procedures. The broad applicability of the method is demonstrated by IRC computations for two enzymatic reactions using standard QM/MM setups.
Nuclear reaction rates and opacity in massive star evolution calculations
Bahena, D [Astronomical Institute of the Academy of Sciences, BocnI II 1401, 14131 Praha 4 (Czech Republic); Klapp, J [Instituto Nacional de Investigaciones Nucleares, Km. 36.5 Carr. Mexico-Toluca, 52750 Edo. de Mexico (Mexico); Dehnen, H, E-mail: jaime.klapp@inin.gob.m [Universitaet Konstanz, Fachbereich Physik, Fach M568, D-78457 Konstanz (Germany)
2010-07-01
Nuclear reaction rates and opacity are important parameters in stellar evolution. The input physics in a stellar evolution code determines the main theoretical characteristics of the stellar structure, evolution and nucleosynthesis of a star. For different input physics, in this work we calculate stellar evolution models of very massive first stars during the hydrogen and helium burning phases. We have considered 100 and 200M{sub s}un galactic and pregalactic stars with metallicity Z = 10{sup -6} and 10{sup 9}, respectively. The results show important differences from old to new formulations for the opacity and nuclear reaction rates, in particular the evolutionary tracks are significantly affected, that indicates the importance of using up to date and reliable input physics. The triple alpha reaction activates sooner for pregalactic than for galactic stars.
Yang, D; An, L; Chen, L
2001-08-01
In this paper, a simple experimental method for the determination of enthalpy change of coordinating color reaction has been proposed and a relation formula between absorption and temperature has been deduced. Using coordinating color reaction of cobalt(II) thiocyanate in Tween-80 medium, the linear relation of this formula has been validated: r = 0.9957 and delta H = -44.7 kJ.mol-1, which is accordant with the result obtained from Van't Hoff equation.
Present status of coupled-channels calculations for heavy-ion subbarrier fusion reactions
Hagino, K
2015-01-01
The coupled-channels method has been a standard tool in analyzing heavy-ion fusion reactions at energies around the Coulomb barrier. We investigate three simplifications usually adopted in the coupled-channels calculations. These are i) the exclusion of non-collective excitations, ii) the assumption of coordinate independent coupling strengths, and iii) the harmonic oscillator approximation for multi-phonon excitations. In connection to the last point, we propose a novel microscopic method based on the beyond-mean-field approach in order to take into account the anharmonic effects of collective vibrations.
Miliordos, Evangelos; Xantheas, Sotiris S
2013-08-15
We propose a general procedure for the numerical calculation of the harmonic vibrational frequencies that is based on internal coordinates and Wilson's GF methodology via double differentiation of the energy. The internal coordinates are defined as the geometrical parameters of a Z-matrix structure, thus avoiding issues related to their redundancy. Linear arrangements of atoms are described using a dummy atom of infinite mass. The procedure has been automated in FORTRAN90 and its main advantage lies in the nontrivial reduction of the number of single-point energy calculations needed for the construction of the Hessian matrix when compared to the corresponding number using double differentiation in Cartesian coordinates. For molecules of C1 symmetry the computational savings in the energy calculations amount to 36N - 30, where N is the number of atoms, with additional savings when symmetry is present. Typical applications for small and medium size molecules in their minimum and transition state geometries as well as hydrogen bonded clusters (water dimer and trimer) are presented. In all cases the frequencies based on internal coordinates differ on average by coordinates.
Definition and determination of the triplet-triplet energy transfer reaction coordinate
Zapata, Felipe; Marazzi, Marco; Castaño, Obis; Frutos, Luis Manuel, E-mail: luisma.frutos@uah.es [Departamento de Química Física, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid (Spain); Acuña, A. Ulises [Instituto de Química Física “Rocasolano”, C.S.I.C., Serrano 119, 28006 Madrid (Spain)
2014-01-21
A definition of the triplet-triplet energy transfer reaction coordinate within the very weak electronic coupling limit is proposed, and a novel theoretical formalism is developed for its quantitative determination in terms of internal coordinates The present formalism permits (i) the separation of donor and acceptor contributions to the reaction coordinate, (ii) the identification of the intrinsic role of donor and acceptor in the triplet energy transfer process, and (iii) the quantification of the effect of every internal coordinate on the transfer process. This formalism is general and can be applied to classical as well as to nonvertical triplet energy transfer processes. The utility of the novel formalism is demonstrated here by its application to the paradigm of nonvertical triplet-triplet energy transfer involving cis-stilbene as acceptor molecule. In this way the effect of each internal molecular coordinate in promoting the transfer rate, from triplet donors in the low and high-energy limit, could be analyzed in detail.
Hanson-Heine, Magnus W. D., E-mail: magnus.hansonheine@nottingham.ac.uk [School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)
2015-10-28
Carefully choosing a set of optimized coordinates for performing vibrational frequency calculations can significantly reduce the anharmonic correlation energy from the self-consistent field treatment of molecular vibrations. However, moving away from normal coordinates also introduces an additional source of correlation energy arising from mode-coupling at the harmonic level. The impact of this new component of the vibrational energy is examined for a range of molecules, and a method is proposed for correcting the resulting self-consistent field frequencies by adding the full coupling energy from connected pairs of harmonic and pseudoharmonic modes, termed vibrational self-consistent field (harmonic correlation). This approach is found to lift the vibrational degeneracies arising from coordinate optimization and provides better agreement with experimental and benchmark frequencies than uncorrected vibrational self-consistent field theory without relying on traditional correlated methods.
Ab Initio Calculations Of Nuclear Reactions And Exotic Nuclei
Quaglioni, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2014-05-05
Our ultimate goal is to develop a fundamental theory and efficient computational tools to describe dynamic processes between nuclei and to use such tools toward supporting several DOE milestones by: 1) performing predictive calculations of difficult-to-measure landmark reactions for nuclear astrophysics, such as those driving the neutrino signature of our sun; 2) improving our understanding of the structure of nuclei near the neutron drip line, which will be the focus of the DOE’s Facility for Rare Isotope Beams (FRIB) being constructed at Michigan State University; but also 3) helping to reveal the true nature of the nuclear force. Furthermore, these theoretical developments will support plasma diagnostic efforts at facilities dedicated to the development of terrestrial fusion energy.
Solid-state polymerisation via [2+2] cycloaddition reaction involving coordination polymers.
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.
Birkholz, Adam B; Schlegel, H Bernhard
2016-05-14
Reaction path optimization is being used more frequently as an alternative to the standard practice of locating a transition state and following the path downhill. The Variational Reaction Coordinate (VRC) method was proposed as an alternative to chain-of-states methods like nudged elastic band and string method. The VRC method represents the path using a linear expansion of continuous basis functions, allowing the path to be optimized variationally by updating the expansion coefficients to minimize the line integral of the potential energy gradient norm, referred to as the Variational Reaction Energy (VRE) of the path. When constraints are used to control the spacing of basis functions and to couple the minimization of the VRE with the optimization of one or more individual points along the path (representing transition states and intermediates), an approximate path as well as the converged geometries of transition states and intermediates along the path are determined in only a few iterations. This algorithmic efficiency comes at a high per-iteration cost due to numerical integration of the VRE derivatives. In the present work, methods for incorporating redundant internal coordinates and potential energy surface interpolation into the VRC method are described. With these methods, the per-iteration cost, in terms of the number of potential energy surface evaluations, of the VRC method is reduced while the high algorithmic efficiency is maintained.
Hydrothermal reactions: From the synthesis of ligand to new lanthanide 3D-coordination polymers
Silva, Fausthon Fred da; Fernandes de Oliveira, Carlos Alberto; Lago Falcão, Eduardo Henrique [Laboratório de Terras Raras, Departamento de Química Fundamental, Universidade Federal de Pernambuco (DQF-UFPE), 50590-470 Recife, PE (Brazil); Gatto, Claudia Cristina [Laboratório de Síntese Inorgânica e Cristalografia, Instituto de Química, Universidade de Brasília (IQ-UnB), 70904-970 Brasilia, DF (Brazil); Bezerra da Costa, Nivan; Oliveira Freire, Ricardo [Pople Computational Chemistry Laboratory, Departamento de Química, Universidade Federal de Sergipe, São Cristóvão-SE 49100-000 (Brazil); Chojnacki, Jarosław [Department of Inorganic Chemistry, Gdansk University of Technology, 80-233 Gdansk (Poland); Alves Júnior, Severino, E-mail: salvesjr@ufpe.br [Laboratório de Terras Raras, Departamento de Química Fundamental, Universidade Federal de Pernambuco (DQF-UFPE), 50590-470 Recife, PE (Brazil)
2013-11-15
The organic ligand 2,5-piperazinedione-1,4-diacetic acid (H{sub 2}PDA) was synthesized under hydrothermal conditions starting from the iminodiacetic acid and catalyzed by oxalic acid. The X-ray powder diffraction data indicates that the compound crystallizes in the P2{sub 1}/c monoclinic system as reported in the literature. The ligand was also characterized by elemental analysis, magnetic nuclear resonance, infrared spectroscopy and thermogravimetric analysis. Two new coordination networks based on lanthanide ions were obtained with this ligand using hydrothermal reaction. In addition to single-crystal X-ray diffraction, the compounds were characterized by infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy and elemental analysis. Single-crystal XRD showed that the compounds are isostructural, crystallizing in P2{sub 1}/n monoclinic system with chemical formula [Ln(PDA){sub 1.5}(H{sub 2}O)](H{sub 2}O){sub 3} (Ln=Gd{sup 3+}(1) and Eu{sup 3+}(2)).The luminescence properties of both compounds were studied. In the compound (1), a broad emission band was observed at 479 nm, redshifted by 70 nm in comparison of the free ligand. In (2), the typical f–f transition was observed with a maximum peak at 618 nm, related with the red emission of the europium ions. Computational methods were performed to simulate the crystal structure of (2). The theoretical calculations of the intensity parameters are in good agreement with the experimental values. - Graphical abstract: Scheme of obtaining the ligand 2,5-piperazinedione-1,4-diacetic acid (H{sub 2}PDA) and two new isostructural 3D-coordination polymers [Ln(PDA){sub 1.5}(H{sub 2}O)](H{sub 2}O){sub 3} (Ln=Gd{sup 3+} and Eu{sup 3+}) by hydrothermal synthesis. Display Omitted - Highlights: • The ligand 2,5-piperazinedione-1,4-diacetic acid was synthetized using the hydrothermic method and characterized. • Two new 3D-coordination polymers with this ligand containing Gd{sup 3+} and Eu{sup 3+} ions
Wang, Bi-Yao; Li, Ze-Rong; Tan, Ning-Xin; Yao, Qian; Li, Xiang-Yuan
2013-04-25
We present a further interpretation of reaction class transition state theory (RC-TST) proposed by Truong et al. for the accurate calculation of rate coefficients for reactions in a class. It is found that the RC-TST can be interpreted through the isodesmic reaction method, which is usually used to calculate reaction enthalpy or enthalpy of formation for a species, and the theory can also be used for the calculation of the reaction barriers and reaction enthalpies for reactions in a class. A correction scheme based on this theory is proposed for the calculation of the reaction barriers and reaction enthalpies for reactions in a class. To validate the scheme, 16 combinations of various ab initio levels with various basis sets are used as the approximate methods and CCSD(T)/CBS method is used as the benchmarking method in this study to calculate the reaction energies and energy barriers for a representative set of five reactions from the reaction class: R(c)CH(R(b))CR(a)CH2 + OH(•) → R(c)C(•)(R(b))CR(a)CH2 + H2O (R(a), R(b), and R(c) in the reaction formula represent the alkyl or hydrogen). Then the results of the approximate methods are corrected by the theory. The maximum values of the average deviations of the energy barrier and the reaction enthalpy are 99.97 kJ/mol and 70.35 kJ/mol, respectively, before correction and are reduced to 4.02 kJ/mol and 8.19 kJ/mol, respectively, after correction, indicating that after correction the results are not sensitive to the level of the ab initio method and the size of the basis set, as they are in the case before correction. Therefore, reaction energies and energy barriers for reactions in a class can be calculated accurately at a relatively low level of ab initio method using our scheme. It is also shown that the rate coefficients for the five representative reactions calculated at the BHandHLYP/6-31G(d,p) level of theory via our scheme are very close to the values calculated at CCSD(T)/CBS level. Finally, reaction
Fast LiH destruction in reaction with H: quantum calculations and astrophysical consequences
Bovino, S; Gianturco, F A; 10.1088/0004-637X/699/1/383
2009-01-01
We present a quantum-mechanical study of the exothermic 7LiH reaction with H. Accurate reactive probabilities and rate coefficients are obtained by solving the Schrodinger equation for the motion of the three nuclei on a single Born-Oppenheimer potential energy surface (PES) and using a coupled-channel hyperspherical coordinate method. Our new rates indeed confirm earlier, qualitative predictions and some previous theoretical calculations, as discussed in the main text. In the astrophysical domain we find that the depletion process largely dominates for redshift (z) between 400 and 100, a range significant for early Universe models. This new result from first-principle calculations leads us to definitively surmise that LiH should be already destroyed when the survival processes become important. Because of this very rapid depletion reaction, the fractional abundance of LiH is found to be drastically reduced, so that it should be very difficult to manage to observe it as an imprinted species in the cosmic back...
Hydrogen atom in strong magnetic field: a high accurate calculation in spheroidal coordinates
LIU Qiang; KANG Shuai; ZHANG Xian-zhou; SHI Ting-yun
2006-01-01
A B-spline-type basis set method for the calculation of hydrogen atom in strong magnetic fields in the frame of spheroidal coordinates has been introduced.High accurate energy levels of hydrogen in the magnetic field,with strength ranging from 0 to 1000 a.u.,have been obtained.For the ground state,ls0,energies with at least 11 significant digits have been obtained.For the low-lying excited state,2p-1,energies with at least 9 significant digits are obtained.The method has also been applied to the calculation of hydrogen Rydberg states in laboratory magnetic fields.Energy spectra with at least 10 significant digits are presented.A comparison with other results in the literatures has been performed.Our results are comparable to the most accurate one up to date.A possible extension to the cases of parallel and crossed electric and magnetic fields have been discussed.
Separable Potentials for (d,p) Reaction Calculations
Elster, Ch; Eremenko, V; Nunes, F M; Thompson, I J; Arbanas, G; Escher, J E
2015-01-01
An important ingredient for applications of nuclear physics to e.g. astrophysics or nuclear energy are the cross sections for reactions of neutrons with rare isotopes. Since direct measurements are often not possible, indirect methods like $(d,p)$ reactions must be used instead. Those $(d,p)$ reactions may be viewed as effective three-body reactions and described with Faddeev techniques. An additional challenge posed by $(d,p)$ reactions involving heavier nuclei is the treatment of the Coulomb force. To avoid numerical complications in dealing with the screening of the Coulomb force, recently a new approach using the Coulomb distorted basis in momentum space was suggested. In order to implement this suggestion, one needs to derive a separable representation of neutron- and proton-nucleus optical potentials and compute their matrix elements in this basis.
The influence of gymnastics in motor coordination and reaction time in urban public bus drivers
Stela Paula Mezzomo
2014-12-01
Full Text Available This study investigated the influence of labour gymnastics (LG on bus drivers' basic skills such as reaction time and gross motor coordination. Sixty male bus drivers (37.06 ± 7.66 years old from two bus lines in the city of Santa Maria (RS took part of this study. The participants were split into two groups, experimental group (EG and control group (CG. Subjects that were part of the EG took part in a LG intervention program, 2-3 times a week, over a year. Gross motor coordination was assessed by BURPEE Protocol (Johnson & Nelson, 1979, whereas reaction time by software providing a visual stimulus. Data normality was checked through Shapiro-Wilk test, which pointed to normal distribution only for the variables simple reaction time (SRT and choice reaction time (CRT in the EG. Therefore the non-parametric Mann-Whitney U test was selected to compare differences between groups. A statistically significant difference for gross motor coordination was found (z= −2.525, p= 0.012, suggesting the effectiveness of LG to improve motor skills. As regards SRT and CRT, no significant difference was found, in spite of better outcomes having been recorded after the LG program.
Kawai, Shinnosuke; Komatsuzaki, Tamiki
2010-12-21
A framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in a multidimensional Langevin equation is extended to the generalized Langevin equations without a priori assumption of the forms of the potential (in general, nonlinearly coupled systems) and the friction kernel. The equation of motion with memory effect can be transformed into an equation without memory at the cost of an increase in the dimensionality of the system, and hence the theoretical framework developed for the (nonlinear) Langevin formulation can be generalized to the non-Markovian process with colored noise. It is found that the increased dimension can be physically interpreted as effective modes of the fluctuating environment. As an illustrative example, we apply this theory to a multidimensional generalized Langevin equation for motion on the Müller-Brown potential surface with an exponential friction kernel. Numerical simulations find a boundary between the highly reactive region and the less reactive region in the space of initial conditions. The location of the boundary is found to depend significantly on both the memory kernel and the nonlinear couplings. The theory extracts a reaction coordinate whose sign determines the fate of the reaction taking into account thermally fluctuating environments, memory effect, and nonlinearities. It is found that the location of the boundary of reactivity is satisfactorily reproduced as the zero of the statistical average of the new reaction coordinate, which is an analytical functional of both the original position coordinates and velocities of the system, and of the properties of the environment.
Birkholz, Adam B; Schlegel, H Bernhard
2015-12-28
The development of algorithms to optimize reaction pathways between reactants and products is an active area of study. Existing algorithms typically describe the path as a discrete series of images (chain of states) which are moved downhill toward the path, using various reparameterization schemes, constraints, or fictitious forces to maintain a uniform description of the reaction path. The Variational Reaction Coordinate (VRC) method is a novel approach that finds the reaction path by minimizing the variational reaction energy (VRE) of Quapp and Bofill. The VRE is the line integral of the gradient norm along a path between reactants and products and minimization of VRE has been shown to yield the steepest descent reaction path. In the VRC method, we represent the reaction path by a linear expansion in a set of continuous basis functions and find the optimized path by minimizing the VRE with respect to the linear expansion coefficients. Improved convergence is obtained by applying constraints to the spacing of the basis functions and coupling the minimization of the VRE to the minimization of one or more points along the path that correspond to intermediates and transition states. The VRC method is demonstrated by optimizing the reaction path for the Müller-Brown surface and by finding a reaction path passing through 5 transition states and 4 intermediates for a 10 atom Lennard-Jones cluster.
Reaction to Indispensable Manual Calculation Skills in a CAS Environment.
Monaghan, John
2001-01-01
Reacts to an article published in a previous issue of this journal on the effects of graphing calculators and computer algebra systems (CAS) on students' manual calculation and algebraic manipulation skills. Considers the contribution made by Jean-Baptiste Lagrange to thinking about the role of CAS in teaching algebra. (ASK)
Rate Constant Calculation for Thermal Reactions Methods and Applications
DaCosta, Herbert
2011-01-01
Providing an overview of the latest computational approaches to estimate rate constants for thermal reactions, this book addresses the theories behind various first-principle and approximation methods that have emerged in the last twenty years with validation examples. It presents in-depth applications of those theories to a wide range of basic and applied research areas. When doing modeling and simulation of chemical reactions (as in many other cases), one often has to compromise between higher-accuracy/higher-precision approaches (which are usually time-consuming) and approximate/lower-preci
An improved method for calculating self-motion coordinates for redundant manipulators
Reister, D.B.
1997-04-01
For a redundant manipulator, the objective of redundancy resolution is to follow a specified path in Cartesian space and simultaneously perform another task (for example, maximize an objective function or avoid obstacles) at every point along the path. The conventional methods have several drawbacks: a new function must be defined for each task, the extended Jacobian can be singular, closed cycles in Cartesian space may not yield closed cycles in joint space, and the objective is point-wise redundancy resolution (to determine a single point in joint space for each point in Cartesian space). The author divides the redundancy resolution problem into two parts: (1) calculate self-motion coordinates for all possible positions of a manipulator at each point along a Cartesian path and (2) determination of optimal self-motion coordinates that maximize an objective function along the path. This paper will discuss the first part of the problem. The path-wise approach overcomes all of the drawbacks of conventional redundancy resolution methods: no need to define a new function for each task, extended Jacobian cannot be singular, and closed cycles in extended Cartesian space will yield closed cycles in joint space.
Lin, Zhili; Li, Xiaoyan; Zhao, Kuixia; Chen, Xudong; Chen, Mingyu; Pu, Jixiong
2016-06-01
For an inertial confinement fusion (ICF) system, the light intensity distribution in the hohlraum is key to the initial plasma excitation and later laser-plasma interaction process. Based on the concept of coordinate transformation of spatial points and vector, we present a robust method with a detailed procedure that makes the calculation of the three dimensional (3D) light intensity distribution in hohlraum easily. The method is intuitive but powerful enough to solve the complex cases of random number of laser beams with arbitrary polarization states and incidence angles. Its application is exemplified in the Shenguang III Facility (SG-III) that verifies its effectiveness and it is useful for guiding the design of hohlraum structure parameter.
Hu, Zeming; Chen, Xuechun; Wu, Yulin
The block-implicit finite-difference method is used to calculate 3D incompressible turbulent flows in the body-fitted coordinate system. In the numerical discretization the hybrid difference scheme is used to treat Reynolds-averaged Navier-Stokes equations. The iterative solution of velocities and pressure on the flow field is obtained by solving simultaneously the Reynolds-averaged N-S equations and continuity equation for each cell. In the iterative process the Gauss-Seidel method is used to solve nonlinear algebraic equations. The turbulent flow is simulated by the k-epsilon turbulence modeling in conjunction with Reynolds equations. The turbulent flow of a curved duct with square cross sections is treated in detail.
Density functional calculation of many-electron systems in cartesian coordinate grid
Roy, Amlan K
2011-01-01
A recently developed density functional method, within Hohenberg-Kohn-Sham framework, is used for faithful description of atoms, molecules in Cartesian coordinate grid, by using an LCAO-MO ansatz. Classical Coulomb potential is obtained by means of a Fourier convolution technique. All two-body potentials (including exchange-correlation (XC)) are constructed directly on real grid, while their corresponding matrix elements are computed from numerical integration. Detailed systematic investigation is made for a representative set of atoms/molecules through a number of properties like total energies, component energies, ionization energies, orbital energies, etc. Two nonlocal XC functionals (FT97 and PBE) are considered for pseudopotential calculation of 35 species while preliminary all-electron results are reported for 6 atoms using the LDA XC density functional. Comparison with literature results, wherever possible, exhibits near-complete agreement. This offers a simple efficient route towards accurate reliable...
Statistical Model Calculations for (n,γ Reactions
Beard Mary
2015-01-01
Full Text Available Hauser-Feshbach (HF cross sections are of enormous importance for a wide range of applications, from waste transmutation and nuclear technologies, to medical applications, and nuclear astrophysics. It is a well-observed result that diﬀerent nuclear input models sensitively aﬀect HF cross section calculations. Less well known however are the eﬀects on calculations originating from model-specific implementation details (such as level density parameter, matching energy, back-shift and giant dipole parameters, as well as eﬀects from non-model aspects, such as experimental data truncation and transmission function energy binning. To investigate the eﬀects or these various aspects, Maxwellian-averaged neutron capture cross sections have been calculated for approximately 340 nuclei. The relative eﬀects of these model details will be discussed.
Implementing the Graphing Calculator in Cincinnati's Precalculus Classes: Teachers' Reactions.
Kaplan, Rose; Herrera, Terese
1995-01-01
Presents data from interviews of (n=15) precalculus teachers required to adopt the technology-intensive Demana/Waits Precalculus Mathematics textbook and to use graphing calculators in their precalculus classes. Results showed that teachers recognized the need for well-organized, extensive workshops. Teacher comments showed a disparity in their…
Capote, R.; Herman, M.; Obložinský, P.; Young, P. G.; Goriely, S.; Belgya, T.; Ignatyuk, A. V.; Koning, A. J.; Hilaire, S.; Plujko, V. A.; Avrigeanu, M.; Bersillon, O.; Chadwick, M. B.; Fukahori, T.; Ge, Zhigang; Han, Yinlu; Kailas, S.; Kopecky, J.; Maslov, V. M.; Reffo, G.; Sin, M.; Soukhovitskii, E. Sh.; Talou, P.
2009-12-01
We describe the physics and data included in the Reference Input Parameter Library, which is devoted to input parameters needed in calculations of nuclear reactions and nuclear data evaluations. Advanced modelling codes require substantial numerical input, therefore the International Atomic Energy Agency (IAEA) has worked extensively since 1993 on a library of validated nuclear-model input parameters, referred to as the Reference Input Parameter Library (RIPL). A final RIPL coordinated research project (RIPL-3) was brought to a successful conclusion in December 2008, after 15 years of challenging work carried out through three consecutive IAEA projects. The RIPL-3 library was released in January 2009, and is available on the Web through http://www-nds.iaea.org/RIPL-3/. This work and the resulting database are extremely important to theoreticians involved in the development and use of nuclear reaction modelling (ALICE, EMPIRE, GNASH, UNF, TALYS) both for theoretical research and nuclear data evaluations. The numerical data and computer codes included in RIPL-3 are arranged in seven segments: MASSES contains ground-state properties of nuclei for about 9000 nuclei, including three theoretical predictions of masses and the evaluated experimental masses of Audi et al. (2003). DISCRETE LEVELS contains 117 datasets (one for each element) with all known level schemes, electromagnetic and γ-ray decay probabilities available from ENSDF in October 2007. NEUTRON RESONANCES contains average resonance parameters prepared on the basis of the evaluations performed by Ignatyuk and Mughabghab. OPTICAL MODEL contains 495 sets of phenomenological optical model parameters defined in a wide energy range. When there are insufficient experimental data, the evaluator has to resort to either global parameterizations or microscopic approaches. Radial density distributions to be used as input for microscopic calculations are stored in the MASSES segment. LEVEL DENSITIES contains
Tu, Renyong; Xie, Yi; Bertoni, Giovanni; Lak, Aidin; Gaspari, Roberto; Rapallo, Arnaldo; Cavalli, Andrea; Trizio, Luca De; Manna, Liberato
2016-06-01
Cu2-xTe nanocubes were used as starting seeds to access metal telluride nanocrystals by cation exchanges at room temperature. The coordination number of the entering cations was found to play an important role in dictating the reaction pathways. The exchanges with tetrahedrally coordinated cations (i.e., with coordination number 4), such as Cd(2+) or Hg(2+), yielded monocrystalline CdTe or HgTe nanocrystals with Cu2-xTe/CdTe or Cu2-xTe/HgTe Janus-like heterostructures as intermediates. The formation of Janus-like architectures was attributed to the high diffusion rate of the relatively small tetrahedrally coordinated cations, which could rapidly diffuse in the Cu2-xTe NCs and nucleate the CdTe (or HgTe) phase in a preferred region of the host structure. Also, with both Cd(2+) and Hg(2+) ions the exchange led to wurtzite CdTe and HgTe phases rather than the more stable zinc-blende ones, indicating that the anion framework of the starting Cu2-xTe particles could be more easily deformed to match the anion framework of the metastable wurtzite structures. As hexagonal HgTe had never been reported to date, this represents another case of metastable new phases that can only be accessed by cation exchange. On the other hand, the exchanges involving octahedrally coordinated ions (i.e., with coordination number 6), such as Pb(2+) or Sn(2+), yielded rock-salt polycrystalline PbTe or SnTe nanocrystals with Cu2-xTe@PbTe or Cu2-xTe@SnTe core@shell architectures at the early stages of the exchange process. In this case, the octahedrally coordinated ions are probably too large to diffuse easily through the Cu2-xTe structure: their limited diffusion rate restricts their initial reaction to the surface of the nanocrystals, where cation exchange is initiated unselectively, leading to core@shell architectures. Interestingly, these heterostructures were found to be metastable as they evolved to stable Janus-like architectures if annealed at 200 °C under vacuum.
Tu, Renyong; Bertoni, Giovanni; Lak, Aidin; Gaspari, Roberto; Rapallo, Arnaldo; Cavalli, Andrea; De Trizio, Luca; Manna, Liberato
2016-01-01
Cu2-xTe nanocubes were used as starting seeds to access metal telluride nanocrystals by cation exchanges at room temperature. The coordination number of the entering cations was found to play an important role in dictating the reaction pathways. The exchanges with tetrahedrally coordinated cations (i.e. with coordination number 4), such as Cd2+ or Hg2+, yielded monocrystalline CdTe or HgTe nanocrystals with Cu2-xTe/CdTe or Cu2-xTe/HgTe Janus-like heterostructures as intermediates. The formation of Janus-like architectures was attributed to the high diffusion rate of the relatively small tetrahedrally coordinated cations, which could rapidly diffuse in the Cu2-xTe NCs and nucleate the CdTe (or HgTe) phase in a preferred region of the host structure. Also, with both Cd2+ and Hg2+ ions the exchange led to wurtzite CdTe and HgTe phases rather than the more stable zinc-blende ones, indicating that the anion framework of the starting Cu2- xTe particles could be more easily deformed to match the anion framework of t...
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Ab initio calculations of reactions of light nuclei
Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr
2017-09-01
An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable as a support tool for accurate evaluations of crucial reaction data for nuclear astrophysics, fusion-energy research, and other applications. We present an efficient many-body approach to nuclear bound and scattering states alike, known as the ab initio no-core shell model with continuum. In this approach, square-integrable energy eigenstates of the A-nucleon system are coupled to (A-A)+A target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges. We show that predictive results for nucleon and deuterium scattering on 4He nuclei can be obtained from the direct solution of the Schröedinger equation with modern nuclear potentials.
Wang, Hsiang-Hsu; Taam, Ronald E
2015-01-01
Investigating the evolution of disk galaxies and the dynamics of proto-stellar disks can involve the use of both a hydrodynamical and a Poisson solver. These systems are usually approximated as infinitesimally thin disks using two- dimensional Cartesian or polar coordinates. In Cartesian coordinates, the calcu- lations of the hydrodynamics and self-gravitational forces are relatively straight- forward for attaining second order accuracy. However, in polar coordinates, a second order calculation of self-gravitational forces is required for matching the second order accuracy of hydrodynamical schemes. We present a direct algorithm for calculating self-gravitational forces with second order accuracy without artifi- cial boundary conditions. The Poisson integral in polar coordinates is expressed in a convolution form and the corresponding numerical complexity is nearly lin- ear using a fast Fourier transform. Examples with analytic solutions are used to verify that the truncated error of this algorithm is of seco...
Kılınç, F.; Karpuz, N.; ćetin, B.
2017-02-01
In medical physics, radionuclides are needed to diagnose functional disorders of organs and to diagnose and treat many diseases. Nuclear reactions are significant for the productions of radionuclides. It is important to analyze the cross sections for much different energy. In this study, reactional cross sections calculations on 13N, 18F radioisotopes are with TALYS 1.6 nuclear reaction simulation code. Cross sections calculated and experimental data taken from EXFOR library were compared
Effect of gamma-strength on nuclear reaction calculations
Kadenko, Igor; Bondar, Borys; Gorbachenko, Oleksandr; Leshchenko, Borys; Solodovnyk, Kateryna; Tkach, Oleksandr; Zheltonozhskyi, Viktor
2016-01-01
The results of the study of gamma-transition description in fast neutron capture and photofission are presented. Recent experimental data were used, namely, the spectrum of prompt gamma-rays in the energy range 2{\\div}18 MeV from 14-MeV neutron capture in natural Ni and isomeric ratios in primary fragments of photofission of the isotopes of U, Np and Pu by bremsstrahlung with end-point energies $E_e$= 10.5, 12 and 18 MeV. The data are compared with the theoretical calculations performed within EMPIRE 3.2 and TALYS 1.6 codes. The mean value of angular momenta and their distributions were determined in the primary fragments $^{84}$Br, $^{97}$Nb, $^{90}$Rb, $^{131,133}$Te, $^{132}$Sb, $^{132,134}$I, $^{135}$Xe of photofissions. An impact of the characteristics of nuclear excited states on the calculation results is studied using different models for photon strength function and nuclear level density.
Hoffmann, Norbert
2012-02-13
Since the time of Giacomo Ciamician at the beginning of the 20th century, photochemical transformations have been recognized as contributing to sustainable chemistry. Electronic excitation significantly changes the reactivity of chemical compounds. Thus, the application of activation reagents is frequently avoided and transformations can be performed under mild conditions. Catalysis plays a central role in sustainable chemistry. Stoichiometric amounts of activation reagents are often avoided. This fact and the milder catalytic reaction conditions diminish the formation of byproducts. In the case of homogeneous catalysis, organometallic compounds are often applied. The combination of both techniques develops synergistic effects in the sense of "Green Chemistry". Herein, metal carbonyl-mediated reactions are reported. These transformations are of considerable interest for the synthesis of complex polyfunctionalized compounds. Copper(I)-catalyzed [2+2] photocycloaddition gives access to a large variety of cyclobutane derivatives. Currently, a large number of publications deal with photochemical electron-transfer-induced reactions with organometallic and coordination compounds, particularly with ruthenium complexes. Several photochemically induced oxidations can easily be performed with air or molecular oxygen when they are catalyzed with organometallic complexes. Photochemical reaction conditions also play a certain role in C-H activation with organometallic catalysts, for instance, with alkanes, although such transformations are conveniently performed with a variety of other photochemical reactions.
Self-consistent collective coordinate for reaction path and inertial mass
Wen, Kai
2016-01-01
We propose a numerical method to determine the optimal collective reaction path for the nucleus-nucleus collision, based on the adiabatic self-consistent collective coordinate (ASCC) method. We use an iterative method combining the imaginary-time evolution and the finite amplitude method, for the solution of the ASCC coupled equations. It is applied to the simplest case, the $\\alpha-\\alpha$ scattering. We determine the collective path, the potential, and the inertial mass. The results are compared with other methods, such as the constrained Hartree-Fock method, the Inglis's cranking formula, and the adiabatic time-dependent Hartree-Fock (ATDHF) method.
Yan, Tianying; Hase, William L.; Doubleday, Charles
2004-05-01
Electronic structure calculations based on multiconfiguration wave functions are used to investigate a set of archetypal reactions relevant to O(3P) processing of hydrocarbon molecules and surfaces. These include O(3P) reactions with methane and ethane to give OH plus methyl or ethyl radicals, O(3P)+ethane to give CH3O+CH3, and secondary reactions of the OH product radical with ethane and the ethyl radical. Geometry optimization is carried out with CASSCF/cc-pVTZ for all reactions, and with CASPT2/cc-pVTZ for O(3P)+methane/ethane. Single-point energy corrections are applied with CASPT2, CASPT3, and MRCI+Q with the cc-pVTZ and cc-pVQZ basis sets, and the energies extrapolated to the complete basis set limit (CBL). Where comparison of computed barriers and energies of reaction with experiment is possible, the agreement is good to excellent. The best agreement (within experimental error) is found for MRCI+Q/CBL applied to O(3P)+methane. For the other reactions, CASPT2/CBL and MRCI+Q/CBL predictions differ from experiment by 1-5 kcal/mol for 0 K enthalpies of reaction, and are within 1 kcal/mol of the best-estimate experimental range of 0 K barriers for O(3P)+ethane and OH+ethane. The accuracy of MRCI+Q/CBL is limited mainly by the quality of the active space. CASPT2/CBL barriers are consistently lower than MRCI+Q/CBL barriers with identical reference spaces.
Neff, Michael; Rauhut, Guntram
2014-02-01
Multidimensional potential energy surfaces obtained from explicitly correlated coupled-cluster calculations and further corrections for high-order correlation contributions, scalar relativistic effects and core-correlation energy contributions were generated in a fully automated fashion for the double-minimum benchmark systems OH3(+) and NH3. The black-box generation of the potentials is based on normal coordinates, which were used in the underlying multimode expansions of the potentials and the μ-tensor within the Watson operator. Normal coordinates are not the optimal choice for describing double-minimum potentials and the question remains if they can be used for accurate calculations at all. However, their unique definition is an appealing feature, which removes remaining errors in truncated potential expansions arising from different choices of curvilinear coordinate systems. Fully automated calculations are presented, which demonstrate, that the proposed scheme allows for the determination of energy levels and tunneling splittings as a routine application.
Moritz, Ralf; Wagner, Manfred; Schollmeyer, Dieter; Baumgarten, Martin; Müllen, Klaus
2015-06-15
Large and rigid tetraarylphosphonium tetrafluoroborate salts have been synthesized representing weakly coordinating cations with diameters of several nanometers. Divergent dendritic growth by means of thermal Diels-Alder cycloaddition was employed for the construction of the hydrophobic polyphenylene framework up to the third generation. X-ray crystal structure analysis of first-generation phosphonium tetrafluoroborate supported the rigidity of the non-collapsible shell around the phosphorus center and gave insight into solid-state packing and cation-anion distances. Copper(I)-catalyzed azide-alkyne ligation served as reliable method for the preparation of a first-generation triazolylphenyl hybrid phosphonium cation under mild reaction conditions. Furthermore, from the synthesis of triarylbenzylphosphonium bromides, Wittig precursors with unprecedented bulky substituents in the α-position were accessible. Employment of these precursors under Wittig conditions by treatment with base and subsequent reaction with aldehydes preferentially provided (Z)-olefins with bulky polyphenylene substituents.
Baumgarte, Thomas W; Cordero-Carrión, Isabel; Müller, Ewald
2012-01-01
In the absence of symmetry assumptions most numerical relativity simulations adopt Cartesian coordinates. While Cartesian coordinates have some desirable properties, spherical polar coordinates appear better suited for certain applications, including gravitational collapse and supernova simulations. Development of numerical relativity codes in spherical polar coordinates has been hampered by the need to handle the coordinate singularities at the origin and on the axis, for example by careful regularization of the appropriate variables. Assuming spherical symmetry and adopting a covariant version of the BSSN equations, Montero and Cordero-Carri\\'on recently demonstrated that such a regularization is not necessary when a partially implicit Runge-Kutta (PIRK) method is used for the time evolution of the gravitational fields. Here we report on an implementation of the BSSN equations in spherical polar coordinates without any symmetry assumptions. Using a PIRK method we obtain stable simulations in three spatial d...
Spectra for the A = 6 reactions calculated from a three-body resonance model
Paris Mark W.
2016-01-01
Full Text Available We develop a resonance model of the transition matrix for three-body breakup reactions of the A = 6 system and present calculations for the nucleon observed spectra, which are important for inertial confinement fusion and Big Bang nucleosynthesis (BBN. The model is motivated by the Faddeev approach where the form of the T matrix is written as a sum of the distinct Jacobi coordinate systems corresponding to particle configurations (α, n-n and (n; n-α to describe the final state. The structure in the spectra comes from the resonances of the two-body subsystems of the three-body final state, namely the singlet (T = 1 nucleon-nucleon (NN anti-bound resonance, and the Nα resonances designated the ground state (Jπ = 3−2${{{3^ - }} \\over 2}$ and first excited state (Jπ = 1−2${{{1^ - }} \\over 2}$ of the A = 5 systems 5He and 5Li. These resonances are described in terms of single-level, single-channel R-matrix parameters that are taken from analyses of NN and Nα scattering data. While the resonance parameters are approximately charge symmetric, external charge-dependent effects are included in the penetrabilities, shifts, and hard-sphere phases, and in the level energies to account for internal Coulomb differences. The shapes of the resonance contributions to the spectrum are fixed by other, two-body data and the only adjustable parameters in the model are the combinatorial amplitudes for the compound system. These are adjusted to reproduce the observed nucleon spectra from measurements at the Omega and NIF facilities. We perform a simultaneous, least-squares fit of the tt neutron spectra and the 3He3He proton spectra. Using these amplitudes we make a prediction of the α spectra for both reactions at low energies. Significant differences in the tt and 3He3He spectra are due to Coulomb effects.
Spectra for the A = 6 reactions calculated from a three-body resonance model
Paris, Mark W.; Hale, Gerald M.
2016-06-01
We develop a resonance model of the transition matrix for three-body breakup reactions of the A = 6 system and present calculations for the nucleon observed spectra, which are important for inertial confinement fusion and Big Bang nucleosynthesis (BBN). The model is motivated by the Faddeev approach where the form of the T matrix is written as a sum of the distinct Jacobi coordinate systems corresponding to particle configurations (α, n-n) and (n; n-α) to describe the final state. The structure in the spectra comes from the resonances of the two-body subsystems of the three-body final state, namely the singlet (T = 1) nucleon-nucleon (NN) anti-bound resonance, and the Nα resonances designated the ground state (Jπ = {{{3^ - }} over 2}) and first excited state (Jπ = {{{1^ - }} over 2}) of the A = 5 systems 5He and 5Li. These resonances are described in terms of single-level, single-channel R-matrix parameters that are taken from analyses of NN and Nα scattering data. While the resonance parameters are approximately charge symmetric, external charge-dependent effects are included in the penetrabilities, shifts, and hard-sphere phases, and in the level energies to account for internal Coulomb differences. The shapes of the resonance contributions to the spectrum are fixed by other, two-body data and the only adjustable parameters in the model are the combinatorial amplitudes for the compound system. These are adjusted to reproduce the observed nucleon spectra from measurements at the Omega and NIF facilities. We perform a simultaneous, least-squares fit of the tt neutron spectra and the 3He3He proton spectra. Using these amplitudes we make a prediction of the α spectra for both reactions at low energies. Significant differences in the tt and 3He3He spectra are due to Coulomb effects.
Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape
Wales, D. J.
2015-04-01
This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of "friction" effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.
Nonadiabatic quantum dynamics calculations for the N + NH --> N(2) + H reaction.
Yang, Huan; Hankel, M; Varandas, Antonio; Han, Keli
2010-09-01
Nonadiabatic quantum dynamics calculations on the two coupled potential energy surfaces (PESs) (1(2)A' and 2(2)A') and also adiabatic quantum calculations on the lowest adiabatic PES are reported for the title reaction. Reaction probabilities for total angular momenta, J, varying from 0 to 160, are calculated to obtain the integral cross section (ICS) for collision energies ranging from 0.05 to 1.0 eV. Calculations using both the close coupling and the Centrifugal Sudden (CS) approximation are carried out to evaluate the role of Coriolis coupling effects for this reaction. The results of the nonadiabatic calculations show that the nonadiabatic effects in the title reaction for the initial state of NH (v = 0, j = 0) could be neglected, at least in the collision energy range considered in this study.
Calculation of reaction energies and adiabatic temperatures for waste tank reactions
Burger, L.L.
1995-10-01
Continual concern has been expressed over potentially hazardous exothermic reactions that might occur in Hanford Site underground waste storage tanks. These tanks contain many different oxidizable compounds covering a wide range of concentrations. The chemical hazards are a function of several interrelated factors, including the amount of energy (heat) produced, how fast it is produced, and the thermal absorption and heat transfer properties of the system. The reaction path(s) will determine the amount of energy produced and kinetics will determine the rate that it is produced. The tanks also contain many inorganic compounds inert to oxidation. These compounds act as diluents and can inhibit exothermic reactions because of their heat capacity and thus, in contrast to the oxidizable compounds, provide mitigation of hazardous reactions. In this report the energy that may be released when various organic and inorganic compounds react is computed as a function of the reaction-mix composition and the temperature. The enthalpy, or integrated heat capacity, of these compounds and various reaction products is presented as a function of temperature; the enthalpy of a given mixture can then be equated to the energy release from various reactions to predict the maximum temperature which may be reached. This is estimated for several different compositions. Alternatively, the amounts of various diluents required to prevent the temperature from reaching a critical value can be estimated. Reactions taking different paths, forming different products such as N{sub 2}O in place of N{sub 2} are also considered, as are reactions where an excess of caustic is present. Oxidants other than nitrate and nitrite are considered briefly.
Alapati, Sudhakar V; Karl Johnson, J; Sholl, David S
2007-03-28
Hydrides of period 2 and 3 elements are promising candidates for hydrogen storage, but typically have heats of reaction that are too high to be of use for fuel cell vehicles. Recent experimental work has focused on destabilizing metal hydrides through mixing metal hydrides with other compounds. A very large number of possible destabilized metal hydride reaction schemes exist, but the thermodynamic data required to assess the enthalpies of these reactions are not available in many cases. We have used density functional theory calculations to predict the reaction enthalpies for more than 300 destabilization reactions that have not previously been reported. The large majority of these reactions are predicted not to be useful for reversible hydrogen storage, having calculated reaction enthalpies that are either too high or too low, and hence these reactions need not be investigated experimentally. Our calculations also identify multiple promising reactions that have large enough hydrogen storage capacities to be useful in practical applications and have reaction thermodynamics that appear to be suitable for use in fuel cell vehicles and are therefore promising candidates for experimental work.
Quantum dynamics calculation of reaction probability for H+Cl2→HCl+Cl
无
2001-01-01
We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + Cl2 based on the GHNS potential energy surface with total angular momentum J = 0. The effects of the translational, vibrational and rotational excitation of Cl2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.
Quantum dynamics calculation of reaction probability for H+Cl2→HC1+Cl
王胜龙; 赵新生
2001-01-01
We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + CI2 based on the GHNS potential energy surface with total angular momentum J= 0. The effects of the translational, vibrational and rotational excitation of CI2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.
Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy
Piccini, GiovanniMaria; Alessio, Maristella
2016-01-01
Abstract The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide‐and‐conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction‐type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre‐exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude). PMID:27008460
Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas; Nørskov, Jens K.
2017-01-01
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 these methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. 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. PMID:28262694
Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas; Nørskov, Jens K.
2017-03-01
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 these methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. 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.
Issack, Bilkiss B; Roy, Pierre-Nicholas
2005-08-22
An approach for the inclusion of geometric constraints in semiclassical initial value representation calculations is introduced. An important aspect of the approach is that Cartesian coordinates are used throughout. We devised an algorithm for the constrained sampling of initial conditions through the use of multivariate Gaussian distribution based on a projected Hessian. We also propose an approach for the constrained evaluation of the so-called Herman-Kluk prefactor in its exact log-derivative form. Sample calculations are performed for free and constrained rare-gas trimers. The results show that the proposed approach provides an accurate evaluation of the reduction in zero-point energy. Exact basis set calculations are used to assess the accuracy of the semiclassical results. Since Cartesian coordinates are used, the approach is general and applicable to a variety of molecular and atomic systems.
Wang, Hsiang-Hsu; Yen, David C. C.; Taam, Ronald E.
2015-11-01
Investigating the evolution of disk galaxies and the dynamics of proto-stellar disks can involve the use of both a hydrodynamical and a Poisson solver. These systems are usually approximated as infinitesimally thin disks using two-dimensional Cartesian or polar coordinates. In Cartesian coordinates, the calculations of the hydrodynamics and self-gravitational forces are relatively straightforward for attaining second-order accuracy. However, in polar coordinates, a second-order calculation of self-gravitational forces is required for matching the second-order accuracy of hydrodynamical schemes. We present a direct algorithm for calculating self-gravitational forces with second-order accuracy without artificial boundary conditions. The Poisson integral in polar coordinates is expressed in a convolution form and the corresponding numerical complexity is nearly linear using a fast Fourier transform. Examples with analytic solutions are used to verify that the truncated error of this algorithm is of second order. The kernel integral around the singularity is applied to modify the particle method. The use of a softening length is avoided and the accuracy of the particle method is significantly improved.
Choi, Woongchul; Yang, Gang; Kim, Suk Lae; Liu, Peng; Sue, Hung-Jue; Yu, Choongho
2016-05-01
Prohibitively expensive precious metal catalysts for oxygen reduction reaction (ORR) have been one of the major hurdles in a wide use of electrochemical cells. Recent significant efforts to develop precious metal free catalysts have resulted in excellent catalytic activities. However, complicated and time-consuming synthesis processes have negated the cost benefit. Moreover, detailed analysis about catalytically active sites and the role of each element in these high-performance catalysts containing nanomaterials for large surface areas are often lacking. Here we report a facile one-step synthesis method of nitrogen-iron coordinated carbon nanotube (CNT) catalysts without precious metals. Our catalysts show excellent long-term stability and onset ORR potential comparable to those of other precious metal free catalysts, and the maximum limiting current density from our catalysts is larger than that of the Pt-based catalysts. We carry out a series of synthesis and characterization experiments with/without iron and nitrogen in CNT, and identify that the coordination of nitrogen and iron in CNT plays a key role in achieving the excellent catalytic performances. We anticipate our one-step process could be used for mass production of precious metal free electrocatalysts for a wide range of electrochemical cells including fuel cells and metal-air batteries.
Duality-based calculations for transition probabilities in stochastic chemical reactions
Ohkubo, Jun
2017-02-01
An idea for evaluating transition probabilities in chemical reaction systems is proposed, which is efficient for repeated calculations with various rate constants. The idea is based on duality relations; instead of direct time evolutions of the original reaction system, the dual process is dealt with. Usually, if one changes rate constants of the original reaction system, the direct time evolutions should be performed again, using the new rate constants. On the other hands, only one solution of an extended dual process can be reused to calculate the transition probabilities for various rate constant cases. The idea is demonstrated in a parameter estimation problem for the Lotka-Volterra system.
Bobbert, Maarten F; Gómez Alvarez, Constanza B; van Weeren, P René; Roepstorff, Lars; Weishaupt, Michael A
2007-06-01
The purpose of this study was to determine whether individual limb forces could be calculated accurately from kinematics of trotting and walking horses. We collected kinematic data and measured vertical ground reaction forces on the individual limbs of seven Warmblood dressage horses, trotting at 3.4 m s(-1) and walking at 1.6 m s(-1) on a treadmill. First, using a segmental model, we calculated from kinematics the total ground reaction force vector and its moment arm relative to each of the hoofs. Second, for phases in which the body was supported by only two limbs, we calculated the individual reaction forces on these limbs. Third, we assumed that the distal limbs operated as linear springs, and determined their force-length relationships using calculated individual limb forces at trot. Finally, we calculated individual limb force-time histories from distal limb lengths. A good correspondence was obtained between calculated and measured individual limb forces. At trot, the average peak vertical reaction force on the forelimb was calculated to be 11.5+/-0.9 N kg(-1) and measured to be 11.7+/-0.9 N kg(-1), and for the hindlimb these values were 9.8+/-0.7 N kg(-1) and 10.0+/-0.6 N kg(-1), respectively. At walk, the average peak vertical reaction force on the forelimb was calculated to be 6.9+/-0.5 N kg(-1) and measured to be 7.1+/-0.3 N kg(-1), and for the hindlimb these values were 4.8+/-0.5 N kg(-1) and 4.7+/-0.3 N kg(-1), respectively. It was concluded that the proposed method of calculating individual limb reaction forces is sufficiently accurate to detect changes in loading reported in the literature for mild to moderate lameness at trot.
Kinetic calculations and mechanism definition for reactions in an ammonium perchlorate flame
Ermolin, N.E.; Fomin, V.M.; Korobeinichev, O.P.; Tereshchenko, A.G.
1982-09-01
This article reports on detailed calculations on the reaction kinetics in APC flames on the basis of a wide set of possible reactions and experimental data on the initial composition of the gas mixture (gasification products from APC). The purpose is to select the most important reactions in this system by comparing the calculations on the kinetics with experimental data on the concentration profiles in APC flames. Discusses kinetic equations; rate constants as the reaction mechanism; results from kinetic calculations; and identification of major stages. A laminar flame such as that provided by ammonium perchlorate is described in general form by a system of differential equations that incorporate the transport of heat and matter in the presence of chemical reactions. APC is a system consisting of 4 elements (N,H,Cl and O). Points out that the scheme enables one to determine which reactions are responsible for producing the final products. Suggests that in the future one will be able to analyze experimental data on the reaction-rate profiles for stable components in order to determine either the atom and radical concentrations or the rate constants of the reactions involving them.
Model Calculation of n + 6Li Reactions Below 20 MeV
ZHANG Jing-Shang; HAN Yin-Lu
2001-01-01
Based on the unified Hauser-Feshbach and exciton model for light nuclei, the calculations of reaction cross sections and the double-differential cross sections for n + 6Li are performed. Since all of the first-particle emissions are from the compound nucleus to the discrete levels, the angular momentum coupling effect in pre-equilibrium mechanism must be taken into account. The fitting of the measured data indicates that the three-body break-up process needs to be involved, and the pre-equilibrium reaction mechanism dominates the reaction processes. In light nucleus reactions the recoil effect must be taken into account.``
Skulason, Egill; Tripkovic, Vladimir; Björketun, Mårten
2010-01-01
Density functional theory calculations have been performed for the three elementary steps―Tafel, Heyrovsky, and Volmer―involved in the hydrogen oxidation reaction (HOR) and its reverse, the hydrogen evolution reaction (HER). For the Pt(111) surface a detailed model consisting of a negatively...... charged Pt(111) slab and solvated protons in up to three water bilayers is considered and reaction energies and activation barriers are determined by using a newly developed computational scheme where the potential can be kept constant during a charge transfer reaction. We determine the rate limiting...
Wilson, J. W.; Khandelwal, G. S.
1976-01-01
Calculational methods for estimation of dose from external proton exposure of arbitrary convex bodies are briefly reviewed. All the necessary information for the estimation of dose in soft tissue is presented. Special emphasis is placed on retaining the effects of nuclear reaction, especially in relation to the dose equivalent. Computer subroutines to evaluate all of the relevant functions are discussed. Nuclear reaction contributions for standard space radiations are in most cases found to be significant. Many of the existing computer programs for estimating dose in which nuclear reaction effects are neglected can be readily converted to include nuclear reaction effects by use of the subroutines described herein.
ZHAO, Yan-Ru(赵艳茹); HOU, An-Xin(侯安新); DONG, Jia-Xin(董家新); ZHAO, Shun-Sheng(赵顺省); LIU, Yi(刘义); QU, Song-Sheng(屈松生)
2004-01-01
Two coordination compounds of rare earth perchlorates with alanine and imidazole, [RE(Ala)n(Im)(H2O)](ClO4)3(s) (RE=La, n=3; RE=Nd, n=2), have been prepared and characterized. The standard molar enthalpies of reaction for the following two reactions, LaCL·7H2O(s)+3Ala(s)+Im(s)+3NaClO4(s)=[La(Ala).(Im)(H2O)]-(ClO4)3(s)+3NaCl(s)+6H2O(I)(1)and NdCl3·6H2O(s)+2Ala(s)+2Ala(s)+Im(s)+3NaClO4(s)=[Nd(Ala)2(Im)(H2O)]-(ClO4)3(s)+3NaCl(s)+5H2O(l) (2), were determined by solution-reaction calorimetry, at T=298.15 K, as 36.168 ±0.642kJ·mol-1 and 48.590±0.934kJ·mol-1 respectively. From the results and other auxiliary quantities, the standard molar enthalpies of formation of [La(Ala)3(Im)(H2O)](ClO4)3(s) and [Nd(Ala)2(Im)(H2O)] (ClO4)3(s) were derived,△fH(-)m｛[La(Ala).(Im)(H2O)](ClO4)3,s｝=(-2984.8±1.0)kJ·mol-1 and △fH(-)m｛[Nd(Ala).(Im)(H2O)]-(ClO4)3,s｝=(-2387.8±0.8)kJ·mol-1, respectively.
Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics
Xu, Zheng; Yasuda, Keiji; Liu, Xiao-Jun
2015-10-01
In order to design a sonochemical reactor with high reaction efficiency, it is important to clarify the size and intensity of the sonochemical reaction field. In this study, the reaction field in a sonochemical reactor is estimated from the distribution of pressure above the threshold for cavitation. The quantitation of hydroxide radical in a sonochemical reactor is obtained from the calculation of bubble dynamics and reaction equations. The distribution of the reaction field of the numerical simulation is consistent with that of the sonochemical luminescence. The sound absorption coefficient of liquid in the sonochemical reactor is much larger than that attributed to classical contributions which are heat conduction and shear viscosity. Under the dual irradiation, the reaction field becomes extensive and intensive because the acoustic pressure amplitude is intensified by the interference of two ultrasonic waves. Project supported by the National Natural Science Foundation of China (Grant Nos. 11404245, 11204129, and 11211140039).
Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics
徐峥; 安田启司; 刘晓峻
2015-01-01
In order to design a sonochemical reactor with high reaction efficiency, it is important to clarify the size and intensity of the sonochemical reaction field. In this study, the reaction field in a sonochemical reactor is estimated from the distribution of pressure above the threshold for cavitation. The quantitation of hydroxide radical in a sonochemical reactor is obtained from the calculation of bubble dynamics and reaction equations. The distribution of the reaction field of the numerical simulation is consistent with that of the sonochemical luminescence. The sound absorption coefficient of liquid in the sonochemical reactor is much larger than that attributed to classical contributions which are heat conduction and shear viscosity. Under the dual irradiation, the reaction field becomes extensive and intensive because the acoustic pressure amplitude is intensified by the interference of two ultrasonic waves.
Chen, Shuli
2013-09-17
Phenylbis(phenylethynyl)phosphane PhP(C≡CPh)2 coordinates regiospecifically to the α-methyl-chiral ortho-platinated and -palladated naphthylamine units at the positions trans to the nitrogen donors. The P→Pt coordination bond is kinetically inert, whereas the P→Pd bond is labile. Upon heating of these phosphane complexes at 70 °C, one of the C≡C bonds in the coordinated PhP(C≡CPh)2 was activated towards an intermolecular Pd-C bond insertion reaction with an external ortho-palladated naphthylamine ring. No intramolecular insertion reaction occurred. In contrast to its palladium analogue, the ortho-platinated ring is not reactive towards coordinated PhP(C≡CPh)2, although it can promote the Pd-C bond insertion reaction. However, despite the high kinetic stability of the P→Pt coordination, the organoplatinum unit is a noticeably weaker activator than its organopalladium counterpart. The chirality of the reacting ortho-metallated naphthylamine ligand exhibited high stereochemical influence on the formation of the new stereogenic phosphorus center during the course of these C-C bond-formation reactions. The coordination chemistry and the absolute stereochemistry of the dimetallic products were determined by single-crystal X-ray crystallographic analysis. The asymmetric monoinsertion of PhP(C≡CPh)2 coordinated to a cyclometallated N,N-dimethyl naphthyl/benzylamine template into the Pd-C bonds of N,N-dimethylnaphthylamine palladacycles has been demonstrated for the synthesis of a variety of new P-stereogenic homo- or heterodimetallic complexes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
A Method of Calculating the 3D Coordinates on a Micro Object in a Virtual Micro-Operation System
无
2001-01-01
A simple method for calculating the 3D coordinates of points on a micro object in a multi-camera system is proposed. It simplifies the algorithms used in traditional computer vision system by eliminating the calculation of the CCD ( charge coupled device)camera parameters and the relative position between cameras, and using solid geometry in the calculation procedures instead of the calculation of the complex matrixes. The algorithm was used in the research of generating a virtual magnified 3D image of a micro object to be operated in a micro operation system, and the satisfactory results were obtained. The application in a virtual tele-operation system for a dexterous mechanical gripper is under test.
Three-body calculation of triple-alpha reaction at low energies
Ishikawa, Souichi
2011-09-01
The reaction rate of the triple-alpha (3α) process at low temperatures, where resonant reaction is not dominant, is calculated through the inverse process, the photodisintegration of a 12C nucleus. For this, Schrödinger equations in a three-alpha (3-α) model of 12C are directly solved by a Faddeev method, which has been successfully applied to three-nucleon problem so far. The nuclear Hamiltonian consists of an α-α potential, which reproduces the 8Be resonance state, together with three-body potentials to reproduce 12C properties. Our results of the 3α reaction rate are about 103 times larger at low temperature (T = 107 K) than a standard rate from the Nuclear Astrophysics Compilation of Reaction Rates (NACRE), which means our results are remarkably smaller than recent results of quantum-mechanical three-body calculations by Ogata et al.
Iftimie, R; Schofield, J P; Iftimie, Radu; Salahub, Dennis; Schofield, Jeremy
2003-01-01
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.
Coordination field calculation for rare earth complexes in dihedral symmetry field
范英芳; 杨频; 潘大丰; 王越奎
1995-01-01
The coordination field perturbation matrix element expressions about D2-field of the terms 2S+1Lf (J=0 - 8 and 7=1/2 - 15/2) with fN (N=1 -13) configuration have been derived The concrete forms of the DSCPCF parameters Akm in the dihedral field (D2, C2v) for various ligand numbers (5 -12) and their reducing behavior in the higher symmetry fields (D4, C4v, D2d, D4d, D2k, D4h and Oh) are discussed with the double sphere coordination point charge field (DSCPCF) model and the irreducible operator tensor method. Besides, the corresponding computational schemes have been developed and the computer program DSF.D has been compiled, which is applicable for the spectral analysis of the rare earth ion complexes with arbitrary ligand numbers in the dihedral, tetragonal and cubical symmetry fields.
Modeling reaction pathways of low energy particle deposition on thiophene via ab initio calculations
Crenshaw, Jasmine D.; Phillpot, Simon R.; Iordanova, Nedialka; Sinnott, Susan B.
2011-07-01
Chemical reactions of thiophene with organic molecules are of interest to modify thermally deposited coatings of conductive polymers. Here, energy barriers for reactions involving thiophene and small hydrocarbon radicals are identified. Enthalpies of formation involving reactants are also calculated using the B3LYP, BMK, and B98 hybrid functionals within the G AUSSIAN03 program. Experimental values, G3, and CBS-QB3 calculations are used as standards, due to their accurate thermochemistry parameters. The BMK functional is found to perform best for the selected organic molecules. These results provide insights into the reactivity of several polymerization and deposition processes.
D. Leontiev
2015-12-01
Full Text Available Based on the analysis of experimental data there was provided a method for determining loading on the rear wheels when the front wheels are raised. By comparing the results of calculations and experiments, it was revealed that the calculation error does not exceed 5 %. A smaller error for the actual weighted vehicles.
D. Leontiev
2015-01-01
Based on the analysis of experimental data there was provided a method for determining loading on the rear wheels when the front wheels are raised. By comparing the results of calculations and experiments, it was revealed that the calculation error does not exceed 5 %. A smaller error for the actual weighted vehicles.
Vagena, E.; Stoulos, S.
2017-01-01
Bremsstrahlung photon beam delivered by a linear electron accelerator has been used to experimentally determine the near threshold photonuclear cross section data of nuclides. For the first time, (γ, n) cross section data was obtained for the astrophysical important nucleus 162Er. Moreover, theoretical calculations have been applied using the TALYS 1.6 code. The effect of the gamma ray strength function on the cross section calculations has been studied. A satisfactorily reproduction of the available experimental data of photonuclear cross section at the energy region below 20 MeV could be achieved. The photon flux was monitored by measuring the photons yield from seven well known (γ, n) reactions from the threshold energy of each reaction up to the end-point energy of the photon beam used. An integrated cross-section 87 ± 14 mb is calculated for the photonuclear reaction 162Er (γ, n) at the energy 9.2-14 MeV. The effective cross section estimated using the TALYS code range between 89 and 96 mb depending on the γ-strength function used. To validate the method for the estimation of the average cross-section data of 162Er (γ, n) reaction, the same procedure has been performed to calculate the average cross-section data of 197Au (γ, n) and 55Mn (γ, n) reactions. In this case, the photons yield from the rest well known (γ, n) reactions was used in order to monitoring the photon flux. The results for 162Er (γ, n), 197Au (γ, n) and 55Mn (γ, n) are found to be in good agreement with the theoretical values obtained by TALYS 1.6. So, the present indirect process could be a valuable tool to estimate the effective cross section of (γ, n) reaction for various isotopes using bremsstrahlung beams.
Cross Sections Calculations of ( d, t) Nuclear Reactions up to 50 MeV
Tel, E.; Yiğit, M.; Tanır, G.
2013-04-01
In nuclear fusion reactions two light atomic nuclei fuse together to form a heavier nucleus. Fusion power is the power generated by nuclear fusion processes. In contrast with fission power, the fusion reaction processes does not produce radioactive nuclides. The fusion will not produce CO2 or SO2. So the fusion energy will not contribute to environmental problems such as particulate pollution and excessive CO2 in the atmosphere. Fusion powered electricity generation was initially believed to be readily achievable, as fission power had been. However, the extreme requirements for continuous reactions and plasma containment led to projections being extended by several decades. In 2010, more than 60 years after the first attempts, commercial power production is still believed to be unlikely before 2050. Although there have been significant research and development studies on the inertial and magnetic fusion reactor technology, there is still a long way to go to penetrate commercial fusion reactors to the energy market. In the fusion reactor, tritium self-sufficiency must be maintained for a commercial power plant. Therefore, for self-sustaining (D-T) fusion driver tritium breeding ratio should be greater than 1.05. Working out the systematics of ( d, t) nuclear reaction cross sections is of great importance for the definition of the excitation function character for the given reaction taking place on various nuclei at different energies. Since the experimental data of charged particle induced reactions are scarce, self-consistent calculation and analyses using nuclear theoretical models are very important. In this study, ( d, t) cross sections for target nuclei 19F, 50Cr, 54Fe, 58Ni, 75As, 89Y, 90Zr, 107Ag, 127I, 197Au and 238U have been investigated up to 50 MeV deuteron energy. The excitation functions for ( d, t) reactions have been calculated by pre-equilibrium reaction mechanism. Calculation results have been also compared with the available measurements in
Zhao, Bin; Sun, Zhigang; Guo, Hua
2016-11-01
A new algorithm is proposed to compute quantum mechanically state-to-state differential cross sections for reactions involving four atoms in full dimensionality. This algorithm, which is based on the propagation of an initial state specific wave packet exclusively in reactant coordinates, extracts the S-matrix elements in the product channel by first interpolating the time-dependent wave packet using a collocation method at selected time intervals on the product coordinate grid and then projecting out the contributions of all final product states. This approach is efficient and accurate, particularly for reactions that are dominated by a product well or long-range interactions. Validation of this approach is demonstrated for the H2 + OH → H + H2O reaction.
The oxygen reduction reaction mechanism on Pt(111) from density functional theory calculations
Tripkovic, Vladimir; Skulason, Egill; Siahrostami, Samira;
2010-01-01
We study the oxygen reduction reaction (ORR) mechanism on a Pt(1 1 1) surface using density functional theory calculations We find that at low overpotentials the surface is covered with a half dissociated water layer We estimate the barrier for proton transfer to this surface and the barrier for ...
Use of pressure insoles to calculate the complete ground reaction forces
Forner Cordero, A.; Koopman, H.F.J.M.; Helm, van der F.C.T.
2004-01-01
A method to calculate the complete ground reaction force (GRF) components from the vertical GRF measured with pressure insoles is presented and validated. With this approach it is possible to measure several consecutive steps without any constraint on foot placement and compute a standard inverse dy
Jensen, L; van Duijnen, PT; Snijders, JG
2003-01-01
A discrete solvent reaction field model for calculating frequency-dependent molecular linear response properties of molecules in solution is presented. The model combines a time-dependent density functional theory (QM) description of the solute molecule with a classical (MM) description of the discr
TIME SCALES OF FUSION-FISSION REACTIONS CALCULATED FROM PRESCISSION NEUTRON MULTIPLICITIES
SIWEKWILCZYNSKA, K; WILCZYNSKI, J; SIEMSSEN, RH; WILSCHUT, HW
1995-01-01
The time scale of fusion-fission reactions was found to be in the range from tau(f) = 5 . 10(-20) to 5 . 10(-19) s. This result was obtained from the analysis of the prescission neutron multiplicities with a new method combining the time-dependent statistical cascade calculations with the nuclear
An equation for calculating the volumetric ratios required in a ligation reaction.
Cranenburgh, R M
2004-08-01
The ligation of two DNA fragments to create a new plasmid DNA molecule is a key reaction in molecular biology. Where the fragment lengths and concentrations are known, existing equations allow the desired relative molar ratio to be calculated, but this must then be related to the required volumes. Further calculations are then necessary if the maximum available volume is to consist of DNA solutions. The equation presented here allows the simple calculation of volumes of DNA solutions required to obtain a desired molar insert-to-vector ratio, and these can comprise all of the available volume in a ligation if required, thus maximising the yield of the recombinant plasmid.
Xie, Hujun; Liu, Chengcheng; Yuan, Ying; Zhou, Tao; Fan, Ting; Lei, Qunfang; Fang, Wenjun
2016-01-21
The mechanisms for the oxidation of phenyl and hydride ligands of bis(pentamethylcyclopentadienyl)hafnium derivatives (Cp* = η(5)-C5Me5) by nitrous oxide via selective oxygen atom transfer reactions have been systematically studied by means of density functional theory (DFT) calculations. On the basis of the calculations, we investigated the original mechanism proposed by Hillhouse and co-workers for the activation of N2O. The calculations showed that the complex with an initial O-coordination of N2O to the coordinatively unsaturated Hf center is not a local minimum. Then we proposed a new reaction mechanism to investigate how N2O is activated and why N2O selectively oxidize phenyl and hydride ligands of . Frontier molecular orbital theory analysis indicates that N2O is activated by nucleophilic attack by the phenyl or hydride ligand. Present calculations provide new insights into the activation of N2O involving the direct oxygen atom transfer from nitrous oxide to metal-ligand bonds instead of the generally observed oxygen abstraction reaction to generate metal-oxo species.
Numerical Calculation of 3—D TUrbulent Flow in Curvilinear Coordinate Systems with Nostaggered Grids
ZhangJingzhou; LiLiguo; 等
1996-01-01
The nonstaggered grids are adopted in this paper for solving the governing equations of flows in the curvilinear coordinate systems.The present paper demonstrates the basic reason and corresponding eliminating method for the pressure oscillation,and deduces the corrected expressions for the curvilinear velocity components in which and additional term representing the difference between the 1-δ and 2-δ difference values for the pressure gradient appears.Thus if an oscillatory pressure filed were arisen,the magnitude of this term would be large and would act to remove the oscillation;whereas for nonoscillatory field the magnitude of this term remains small.As examination for the numerical method 3-D turbulent flow in a square duct with 90° bend and 3-D turbulent mixing low in a lobed-mixer were calculatied respectively.The numerical results are satisfactory.
DCHAIN: A user-friendly computer program for radioactive decay and reaction chain calculations
East, L.V.
1994-05-01
A computer program for calculating the time-dependent daughter populations in radioactive decay and nuclear reaction chains is described. Chain members can have non-zero initial populations and be produced from the preceding chain member as the result of radioactive decay, a nuclear reaction, or both. As presently implemented, chains can contain up to 15 members. Program input can be supplied interactively or read from ASCII data files. Time units for half-lives, etc. can be specified during data entry. Input values are verified and can be modified if necessary, before used in calculations. Output results can be saved in ASCII files in a format suitable for including in reports or other documents. The calculational method, described in some detail, utilizes a generalized form of the Bateman equations. The program is written in the C language in conformance with current ANSI standards and can be used on multiple hardware platforms.
Minyaev, Ruslan M.; Quapp, Wolfgang; Schmidt, Benjamin; Getmanskii, Ilya V.; Koval, Vitaliy V.
2013-11-01
Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.
Zhang, Jiatao
2016-10-01
Abstract: Including the shape and size effect, the controllable doping, hetero-composite and surface/interface are the prerequisite of colloidal nanocrystals for exploring their optoelectronic properties, such as fluorescence, plasmon-exciton coupling, efficient electron/hole separation, and enhanced photocatalysis applications. By controlling soft acid-base coordination reactions between cation molecular complexes and colloidal nanocrystals, we showed that chemical thermodynamics could drive nanoscale monocrystalline growth of the semiconductor shell on metal nano-substrates and the substitutional heterovalent doping in semiconductor nanocrystals. We have demonstrated evolution of relative position of Au and II-VI semiconductor in Au-Semi from symmetric to asymmetric configuration, different phosphines initiated morphology engineering, oriented attachment of quantum dots into micrometer nanosheets with synergistic control of surface/interface and doing, which can further lead to fine tuning of plasmon-exciton coupling. Therefore, different hydrogen photocatalytic performance, Plasmon enhanced photocatalysis properties have been achieved further which lead to the fine tuning of plasmon-exciton coupling. Substitutional heterovalent doping here enables the tailoring of optical, electronic properties and photocatalysis applications of semiconductor nanocrystals because of electronic impurities (p-, n-type doping) control. References: (1) J. Gui, J. Zhang*, et al. Angew. Chem. Int. Ed. 2015, 54, 3683. (2) Q. Zhao, J. Zhang*, etc., Adv. Mater. 2014, 26, 1387. (3) J. Liu, Q. Zhao, S. G. Wang*, J. Zhang*, etc., Adv. Mater. 2015, 27-2753-2761. (4) H. Qian, J. Zhang*, etc., NPG Asia Mater. (2015) 7, e152. (5) M. Ji, M. Xu, etc., J. Zhang*, Adv. Mater. 2016, in proof. (6) S. Yu, J. T. Zhang, Y. Tang, M. Ouyang*, Nano Lett. 2015, 15, 6282-6288. (7) J. Zhang, Y. Tang, K. Lee and M. Ouyang*, Science 2010, 327, 1634. (8) J. Zhang, Y. Tang, K. Lee, M. Ouyang*, Nature 2010, 466
Chandra, Bappaditya; Bhowmik, Debanjan; Maity, Barun Kumar; Mote, Kaustubh R; Dhara, Debabrata; Venkatramani, Ravindra; Maiti, Sudipta; Madhu, Perunthiruthy K
2017-08-22
The structural underpinnings for the higher toxicity of the oligomeric intermediates of amyloidogenic peptides, compared to the mature fibrils, remain unknown at present. The transient nature and heterogeneity of the oligomers make it difficult to follow their structure. Here, using vibrational and solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we show that freely aggregating Aβ40 oligomers in physiological solutions have an intramolecular antiparallel configuration that is distinct from the intermolecular parallel β-sheet structure observed in mature fibrils. The intramolecular hydrogen-bonding network flips nearly 90°, and the two β-strands of each monomeric unit move apart, to give rise to the well-known intermolecular in-register parallel β-sheet structure in the mature fibrils. Solid-state nuclear magnetic resonance distance measurements capture the interstrand separation within monomer units during the transition from the oligomer to the fibril form. We further find that the D23-K28 salt-bridge, a major feature of the Aβ40 fibrils and a focal point of mutations linked to early onset Alzheimer's disease, is not detectable in the small oligomers. Molecular dynamics simulations capture the correlation between changes in the D23-K28 distance and the flipping of the monomer secondary structure between antiparallel and parallel β-sheet architectures. Overall, we propose interstrand separation and salt-bridge formation as key reaction coordinates describing the structural transition of the small Aβ40 oligomers to fibrils. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
MAMEDOV,B.A.
2004-01-01
A closed analytical relation is derived for the two-center nuclear attraction integrals over Slater type orbitals (STOs) in terms of binomial coefficients. This formula can be used in highly accurate calculations of the nuclear attraction integrals. The relationships obtained are valid for arbitrary values of quantum numbers and screening constants of STOs and location of nuclei.
SEXIE 3.0 — an updated computer program for the calculation of coordination shells and geometries
Tabor-Morris, Anne E.; Rupp, Bernhard
1994-08-01
We report a new version of our FORTRAN program SEXIE (ACBV). New features permit interfacing to related programs for EXAFS calculations (FEFF by J.J. Rehr et al.) and structure visualization (SCHAKAL by E. Keller). The code has been refined and the basis transformation matrix from fractional to cartesian coordinates has been corrected and made compatible with IUCr (International Union for Crystallography) standards. We discuss how to determine the correct space group setting and atom position input. New examples for Unix script files are provided.
Han, Jongwoo; Sa, Young Jin; Shim, Yeonjun; Choi, Min; Park, Noejung; Joo, Sang Hoon; Park, Sungjin
2015-10-19
Hybridization of organometallic complexes with graphene-based materials can give rise to enhanced catalytic performance. Understanding the chemical structures within hybrid materials is of primary importance. In this work, archetypical hybrid materials are synthesized by the reaction of an organometallic complex, [Co(II) (acac)2 ] (acac=acetylacetonate), with N-doped graphene-based materials at room temperature. Experimental characterization of the hybrid materials and theoretical calculations reveal that the organometallic cobalt-containing species is coordinated to heterocyclic groups in N-doped graphene as well as to its parental acac ligands. The hybrid material shows high electrocatalytic activity for the oxygen reduction reaction (ORR) in alkaline media, and superior durability and methanol tolerance to a Pt/C catalyst. Based on the chemical structures and ORR experiments, the catalytically active species is identified as a Co-O4 -N structure.
O Scholten; A Usov
2010-08-01
To describe photo- and meson-induced reactions on the nucleon, one is faced with a rather extensive coupled-channel problem. Ignoring the effects of channel coupling, as one would do in describing a certain reaction at the tree level, invariably creates a large inconsistency between the different reactions that are described. In addition, the imaginary parts of the amplitude, which are related through the optical theorem, to total cross-sections, are directly reflected in certain polarization observables. Performing a full coupled-channel calculation thus offers the possibility to implement the maximum number of constraints. The drawback one is faced with is to arrive at a simultaneous fit of a large number of reaction channels. While some of the parameters are common to many reactions, one is still faced with the challenge to optimize a large number of parameters in a highly non-linear calculation. Here we show that such an approach is possible and present some results for photoinduced strangeness production.
Cis/trans Coordination in olefin metathesis by static and molecular dynamic DFT calculations
Poater, Albert
2014-05-25
In regard to [(N-heterocyclic carbene)Ru]-based catalysts, it is still a matter of debate if the substrate binding is preferentially cis or trans to the N-heterocyclic carbene ligand. By means of static and molecular dynamic DFT calculations, a simple olefin, like ethylene, is shown to be prone to the trans binding. Bearing in mind the higher reactivity of trans isomers in olefin metathesis, this insight helps to construct small alkene substrates with increased reactivity. © 2014 Springer Science+Business Media New York.
García-Meseguer, Rafael; Martí, Sergio; Ruiz-Pernía, J. Javier; Moliner, Vicent; Tuñón, Iñaki
2013-07-01
Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We show that the structure of the protein provides an adequate environment for the progress of the reaction, although a certain degree of flexibility is needed to attain the full catalytic effect. However, these motions do not introduce significant dynamical corrections to the rate constant and can be described as equilibrium fluctuations.
Brandán, S. A.; Eroğlu, E.; Ledesma, A. E.; Oltulu, O.; Yalçınkaya, O. B.
2011-05-01
We have studied the 5-acetamido-1,3,4-thiadiazole-2-sulphonamide compound and characterized it by infrared and Raman spectroscopy in the solid phase. The Density Functional Theory (DFT) method together with Pople's basis set show that two stable molecules for the compound have been theoretically determined in the gas phase, and that only the more stable conformation is present in the solid phase, as was experimentally observed. The harmonic vibrational wavenumbers for the optimized geometry were calculated at B3LYP/6-31G ∗ and B3LYP/6-311++G ∗∗ levels at the proximity of the isolated molecule. For a complete assignment of the vibrational spectra in the compound solid, DFT calculations were combined with Pulaýs Scaled Quantum Mechanics Force Field (SQMFF) methodology in order to fit the theoretical wavenumber values to the experimental ones. In this way, a complete assignment of all of the observed bands in the infrared spectrum for the compound was performed. The natural bond orbital (NBO) study reveals the characteristics of the electronic delocalization of the two structures, while the corresponding topological properties of electronic charge density are analysed by employing Bader's Atoms in the Molecules theory (AIM).
Achakovskiy, Oleg; Tselyaev, Victor; Shitov, Mikhail
2015-01-01
The neutron capture cross sections and average radiative widths of neutron resonances for two double-magic nuclei 132Sn and 208Pb have been calculated using the microscopic photon strength functions, which were obtained within the microscopic self-consistent version of the extended theory of finite Fermi systems in the time blocking approximation. For the first time, the microscopic PSFs have been obtained within the fully self-consistent approach with exact accounting for the single particle continuum (for 208Pb). The approach includes phonon coupling effects in addition to the standard RPA approach. The known Skyrme force has been used. The calculations of nuclear reaction characteristics have been performed with the EMPIRE 3.1 nuclear reaction code. Here, three nuclear level density (NLD) models have been used: the so-called phenomenological GSM, the EMPIRE specific (or Enhanced GSM) and the microscopical combinatorial HFB NLD models. For both considered characteristics we found a significant disagreement ...
Weymuth, Thomas; Chen, Peter; Reiher, Markus
2014-01-01
We present the WCCR10 data set of ten ligand dissociation energies of large cationic transition metal complexes for the assessment of approximate exchange--correlation functionals. We analyze nine popular functionals, namely BP86, BP86-D3, B3LYP, B3LYP-D3, B97-D-D2, PBE, TPSS, PBE0, and TPSSh by mutual comparison and by comparison to experimental gas-phase data measured with well-known precision. The comparison of all calculated data reveals a large, system-dependent scattering of results with nonnegligible consequences for computational chemistry studies on transition metal compounds. Considering further the comparison with experiment, the non-empirical functionals PBE and TPSS turn out to be among the best functionals for our reference data set. The deviation can be lowered further by including Hartree--Fock exchange. Accordingly, PBE0 and TPSSh are the two most accurate functionals for our test set, but also these functionals exhibit deviations from experiment by up to 50 kJ/mol for individual reactions. A...
Gardner, D.G.; Gardner, M.A.
1990-12-05
p-Process modeling of some rare but stable proton-rich nuclei requires knowledge of a variety of neutron, charged particle, and photonuclear reaction rates at temperatures of 2 to 3 {times} 10{sup 9} {degrees}K. Detailed balance is usually invoked to obtain the stellar photonuclear rates, in spite of a number of well-known constraints. In this work we attempt to calculate directly the stellar rates for ({gamma},n) and ({gamma},{alpha}) reactions on {sup 151}Eu. These are compared with stellar rates obtained from detailed balance, using the same input parameters for the stellar (n,{gamma}) and ({alpha},{gamma}) reactions on {sup 150}Eu and {sup 147}Pm, respectively. The two methods yielded somewhat different results, which will be discussed along with some sensitivity studies. 16 refs., 7 figs.
Plummer, L.N.; Parkhurst, D.L.; Fleming, G.W.; Dunkle, S.A.
1988-01-01
The program named PHRQPITZ is a computer code capable of making geochemical calculations in brines and other electrolyte solutions to high concentrations using the Pitzer virial-coefficient approach for activity-coefficient corrections. Reaction-modeling capabilities include calculation of (1) aqueous speciation and mineral-saturation index, (2) mineral solubility, (3) mixing and titration of aqueous solutions, (4) irreversible reactions and mineral water mass transfer, and (5) reaction path. The computed results for each aqueous solution include the osmotic coefficient, water activity , mineral saturation indices, mean activity coefficients, total activity coefficients, and scale-dependent values of pH, individual-ion activities and individual-ion activity coeffients , and scale-dependent values of pH, individual-ion activities and individual-ion activity coefficients. A data base of Pitzer interaction parameters is provided at 25 C for the system: Na-K-Mg-Ca-H-Cl-SO4-OH-HCO3-CO3-CO2-H2O, and extended to include largely untested literature data for Fe(II), Mn(II), Sr, Ba, Li, and Br with provision for calculations at temperatures other than 25C. An extensive literature review of published Pitzer interaction parameters for many inorganic salts is given. Also described is an interactive input code for PHRQPITZ called PITZINPT. (USGS)
Afifi, Mahmoud S; Farag, Rabei S; Shaaban, Ibrahim A; Wilson, Lee D; Zoghaib, Wajdi M; Mohamed, Tarek A
2013-07-01
The infrared (4000-200 cm(-1)) spectrum for 4-amino-5-pyrimidinecarbonitrile (APC, C5H4N4) was acquired in the solid phase. In addition, the (1)H and (13)C NMR spectra of APC were obtained in DMSO-d6 along with its mass spectrum. Initially, six isomers were hypothesized and then investigated by means of DFT/B3LYP and MP2(full) quantum mechanical calculations using a 6-31G(d) basis set. Moreover, the (1)H and (13)C NMR chemical shifts were predicted using a GIAO approximation at the 6-311+G(d,p) basis set and the B3LYP method with (and without) solvent effects using PCM method. The correlation coefficients showed good agreement between the experimental/theoretical chemical shift values of amino tautomers (1 and 2) rather than the eliminated imino tautomers (3-6), in agreement with the current quantum mechanical calculations. Structures 3-6 are less stable than the amino tautomers (1 and 2) by about 5206-8673 cm(-1) (62.3-103.7 kJ/mol). The MP2(full)/6-31G(d) computational results favor the amino structure 1 with a pyramidal NH2 moiety and calculated real vibrational frequencies, however; structure 2 is considered a transition state owing to the calculated imaginary frequency. It is worth mentioning that, the calculated structural parameters suggest a strong conjugation between the amino nitrogen and pyrimidine ring. Aided by frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed bands is proposed herein. Finally, NH2 internal rotation barriers for the stable non-planar isomer (1) were carried out using MP2(full)/6-31G(d) optimized structural parameters. Our results are discussed herein and compared to structural parameters for similar molecules whenever appropriate.
YANG,En-Cui(杨恩翠); ZHAO,Xiao-Jun(赵小军); TIAN,Peng(田鹏); HAO,Jin-Ku(郝金库)
2004-01-01
The two possible reaction paths of producing ethane on coupling reaction of methane through plasma were theoretically investigated by B3LYP and MP2 methods with 6-311G* respectively and further compared with the previous results calculated from B3LYP/6-31G*.The new investigated results consistently confirmed the previous conclusion.And the influences of the calculation methods and basis sets on the calculated results were also discussed.
Nagy, Tibor; Vikár, Anna; Lendvay, György, E-mail: lendvay.gyorgy@ttk.mta.hu [Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2., H-1117 Budapest (Hungary)
2016-01-07
The quasiclassical trajectory (QCT) method is an efficient and important tool for studying the dynamics of bimolecular reactions. In this method, the motion of the atoms is simulated classically, and the only quantum effect considered is that the initial vibrational states of reactant molecules are semiclassically quantized. A sensible expectation is that the initial ensemble of classical molecular states generated this way should be stationary, similarly to the quantum state it is supposed to represent. The most widely used method for sampling the vibrational phase space of polyatomic molecules is based on the normal mode approximation. In the present work, it is demonstrated that normal mode sampling provides a nonstationary ensemble even for a simple molecule like methane, because real potential energy surfaces are anharmonic in the reactant domain. The consequences were investigated for reaction CH{sub 4} + H → CH{sub 3} + H{sub 2} and its various isotopologs and were found to be dramatic. Reaction probabilities and cross sections obtained from QCT calculations oscillate periodically as a function of the initial distance of the colliding partners and the excitation functions are erratic. The reason is that in the nonstationary ensemble of initial states, the mean bond length of the breaking C–H bond oscillates in time with the frequency of the symmetric stretch mode. We propose a simple method, one-period averaging, in which reactivity parameters are calculated by averaging over an entire period of the mean C–H bond length oscillation, which removes the observed artifacts and provides the physically most reasonable reaction probabilities and cross sections when the initial conditions for QCT calculations are generated by normal mode sampling.
van Harrevelt, Rob; Honkala, Johanna Karoliina; Nørskov, Jens Kehlet
2005-01-01
Quantum-mechanical calculations of the reaction rate for dissociative adsorption of N-2 on stepped Ru(0001) are presented. Converged six-dimensional quantum calculations for this heavy-atom reaction have been performed using the multiconfiguration time-dependent Hartree method. A potential...
Nguyen, H.D.
1991-11-01
Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a ``glass like`` material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable to other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.
Nguyen, H.D.
1991-11-01
Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a glass like'' material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable to other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.
Li, Xifeng; Cai, Zhongli; Katsumura, Yosuke [Tokyo Univ., Tokai, Ibaraki (Japan). Nuclear Engineering Research Lab
2000-03-01
The interaction of caffeic acid with e{sub aq}{sup -}, (CH{sub 3}){sub 2}(OH) CCH{sub 2}{sup {center_dot}}, CO{sub 2}{sup {center_dot}}{sup -}, H{sup {center_dot}}, {center_dot}OH and N{sub 3}{sup {center_dot}} radicals were studied by {gamma}-, pulse radiolysis and molecular orbital calculation. UV-visible spectra of electron/{center_dot}OH adducts, semi-quinone radicals of caffeic ions, and the stable products from the reactions were derived. The rate constants were determined. The attacked sites and the most favorable structures of the transient radicals were predicted. Reaction mechanisms were proposed. (author)
Calculation for fission decay from heavy ion reactions at intermediate energies
Blaich, T.; Begemann-Blaich, M.; Fowler, M.M.; Wilhelmy, J.B. (Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)); Britt, H.C.; Fields, D.J.; Hansen, L.F.; Namboodiri, M.N.; Sangster, T.C. (Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)); Fraenkel, Z. (Weizmann Institute of Science, 76100 Rehovot (Israel))
1992-02-01
A detailed deexcitation calculation is presented for target residues resulting from intermediate-energy heavy ion reactions. The model involves an intranuclear cascade, subsequent fast nucleon emission, and final decay by statistical evaporation including fission. Results are compared to data from bombardments with Fe and Nb projectiles on targets of Ta, Au, and Th at 100 MeV/nucleon. The majority of observable features are reproduced with this simple approach, making obvious the need for involving new physical phenomena associated with multifragmentation or other collective dissipation mechanisms.
Hofmann, H.M.; Mertelmeier, T. (Erlangen-Nuernberg Univ., Erlangen (Germany, F.R.). Inst. fuer Theoretische Physik); Mello, P.A. (Instituto Nacional de Investigaciones Nucleares, Mexico City. Lab. del Acelerador); Seligman, T.H. (Universidad Nacional Autonoma de Mexico, Mexico City. Inst. de Fisica)
1981-12-14
A comparison is presented between predictions of the entropy approach to statistical nuclear reactions, and numerical calculations performed by generating an ensemble of S-matrices in terms of K-matrices with specified statistical distributions for their parameters. The comparison is done for: (a) the 2nd, 3rd and 4th moments of S in a 4-channel case and (b) the actual distribution of the S-matrix elements in a 2-channel case. In both cases the agreement is found to be very good in the domain of strong absorption.
Darlatt, Erik [BAM - Bundesanstalt fuer Materialforschung und -pruefung, 12200 Berlin (Germany); Traulsen, Christoph H.-H.; Poppenberg, Johannes; Richter, Sebastian [Institut fuer Chemie und Biochemie, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin (Germany); Kuehn, Julius [BAM - Bundesanstalt fuer Materialforschung und -pruefung, 12200 Berlin (Germany); Schalley, Christoph A., E-mail: schalley@chemie.fu-berlin.de [Institut fuer Chemie und Biochemie, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin (Germany); Unger, Wolfgang E.S., E-mail: Wolfgang.Unger@BAM.de [BAM - Bundesanstalt fuer Materialforschung und -pruefung, 12200 Berlin (Germany)
2012-04-15
Highlights: Black-Right-Pointing-Pointer Ethynyl terpyridines were clicked to azide-terminated SAMs on gold. Black-Right-Pointing-Pointer Azides and clicked terpyridines were characterized by N and C K-NEXAFS and N 1s XPS. Black-Right-Pointing-Pointer S 1s + S 2p XPS was used to characterize the buried gold-sulfur interface of the SAM. Black-Right-Pointing-Pointer Higher click reaction temperature leads to an increased amount of terpyridyl groups. Black-Right-Pointing-Pointer Introduced terpyridyl groups are accessible for Pd(II) ion coordination. - Abstract: An ethynylterpyridine was 'clicked' to an azide-terminated self-assembled monolayer on gold and characterized by synchrotron radiation based surface analysis as NEXAFS and XPS. The detection of azide and terpyridine signatures confirmed a partial click reaction at room temperature. The absence of the azides after reaction at 50 Degree-Sign C indicates an almost complete conversion. For the latter case successful Pd(II) coordination has been proven. The Au-S interface of the SAMs has been characterized by S 1s and S 2p XPS.
Analysis of Vibration Mode for H2+F→HF+H Reaction Mechanism: Density functional Theory Calculation
无
2001-01-01
Three density functional theory methods (DFT) have been used to investigate the H2+F?HF+H reaction comparing with the Hartree-Fock method and Moller-Plesset (MP2) perturbation theory method. Through the analysis of the vibrational mode and vibrational frequency in the reaction process, the reaction mechanism has been discussed. The activation energy, the reorganization energy and rate constant of the ET reaction are calculated at semi-quantitative level.
Capote, Roberto; Nichols, Alan L.; Nortier, Francois Meiring; Carlson, Brett V.; Engle, Jonathan W.; Hermanne, Alex; Hussain, Mazhar; Ignatyuk, Anatoly V.; Kellett, Mark A.; Kibédi, Tibor; Kim, Guinyun; Kondev, Filip G.; Lebeda, Ondrej; Luca, Aurelian; Naik, Haladhara; Nagai, Yasuki; Spahn, Ingo; Suryanarayana, Saraswatula V.; Tárkányi, Ferenc T.; Verpelli, Marco
2017-09-01
An IAEA coordinated research project was launched in December 2012 to establish and improve the nuclear data required to characterise charged-particle monitor reactions and extend data for medical radionuclide production. An international team was assembled to undertake work addressing the requirements for more accurate cross-section data over a wide range of targets and projectiles, undertaken in conjunction with a limited number of measurements and more extensive evaluations of the decay data of specific radionuclides. These studies are nearing completion, and are briefly described below.
New reaction rates for improved primordial D /H calculation and the cosmic evolution of deuterium
Coc, Alain; Petitjean, Patrick; Uzan, Jean-Philippe; Vangioni, Elisabeth; Descouvemont, Pierre; Iliadis, Christian; Longland, Richard
2015-12-01
Primordial or big bang nucleosynthesis (BBN) is one of the three historically strong evidences for the big bang model. Standard BBN is now a parameter-free theory, since the baryonic density of the Universe has been deduced with an unprecedented precision from observations of the anisotropies of the cosmic microwave background radiation. There is a good agreement between the primordial abundances of 4He, D, 3He, and 7Li deduced from observations and from primordial nucleosynthesis calculations. However, the 7Li calculated abundance is significantly higher than the one deduced from spectroscopic observations and remains an open problem. In addition, recent deuterium observations have drastically reduced the uncertainty on D /H , to reach a value of 1.6%. It needs to be matched by BBN predictions whose precision is now limited by thermonuclear reaction rate uncertainties. This is especially important as many attempts to reconcile Li observations with models lead to an increased D prediction. Here, we reevaluate the d (p ,γ )3He, d (d ,n ) 3H3, and d (d ,p ) 3H reaction rates that govern deuterium destruction, incorporating new experimental data and carefully accounting for systematic uncertainties. Contrary to previous evaluations, we use theoretical ab initio models for the energy dependence of the S factors. As a result, these rates increase at BBN temperatures, leading to a reduced value of D /H =(2.45 ±0.10 )×10-5 (2 σ ), in agreement with observations.
Refined Calculations of Secondary Nuclear Reactions in Magneto-Inertial Fusion Plasmas
Schmit, Paul; Knapp, Patrick; Hansen, Stephanie; Gomez, Matthew; Hahn, Kelly; Sinars, Daniel; Peterson, Kyle; Slutz, Stephen; Sefkow, Adam; Awe, Thomas; Harding, Eric; Jennings, Christopher
2014-10-01
Diagnosing the degree of magnetic flux compression at stagnation in magneto-inertial fusion (MIF) is critical for charting the performance of any MIF concept. In pure deuterium plasma, the transport of high-energy tritons produced by the aneutronic DD fusion reaction depends strongly on the magnetic field. The tritons probe and occasionally react with the fuel, emitting secondary DT neutrons. We show that the DT/DD neutron yield ratio and the secondary DT neutron spectra can be used to infer the magnetic field-radius product (BR), the critical confinement parameter for MIF. The amount of fuel-pusher mix also can be constrained by secondary reactions. We discuss the sensitivity to plasma inhomogeneities of the calculations and outline methods to relate secondary yields to alpha particle energy deposition in ignition-relevant experiments employing DT fuel. We compare our calculations to recent tests of the Magnetized Liner Inertial Fusion (MagLIF) concept on the Z Pulsed Power Facility. Supported in part by the SNL Truman Fellowship, which is part of the LDRD Program, and sponsored by Sandia Corporation (a wholly owned subsidiary of Lockheed Martin Corporation) as Operator of SNL under its U.S. DoE Contract No. DE-AC04-94AL85000.
Four-body continuum-discretized coupled-channels calculations applied to {sup 6}He reactions
Rodriguez-Gallardo, M. [Consejo Superior de Investigaciones Cientificas (CSIC), Madrid (Spain). Inst. de Estructura de la Materia; Arias, J.M.; Gomez-Camacho, J.M.; Moro, A.M. [Universidad de Sevilla (Spain). Dept. de Fisica Atomica, Molecular y Nuclear; Thompson, I.J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical Science Directorate; Tostevin, J.A. [University of Surrey, Guildford (United Kingdom). Dept. of Physics
2010-07-01
Full text. The scattering of a weakly bound three-body system by a target is discussed. The continuum-discretized coupled-channels (CDCC) framework, recently extended to four-body reactions (three-body projectile plus target), is used for the scattering calculations. Two different methods are used to discretized the three-body continuum of the projectile. In the first case, we make use of a Pseudo-State (PS) method in which the states of the projectile are represented by the eigenstates of its internal Hamiltonian in a truncated basis of square-integrable functions. In particular, we use the transformed harmonic oscillator (THO) method, in which the PS basis is obtained by applying a local scale transformation to the Harmonic Oscillator basis. In the second case, we applied the binning procedure that has just been extended to three-body projectiles. This discretization method requires to calculate first the true continuum of the projectile and then this continuum is discretized making bins or packages of energy. This has been the method used for many years in standard three-body (two-body projectile plus target) CDCC calculations. Its extension to three-body projectiles uses the eigenchannel expansion of the three-body S-matrix. We applied this formalism to several reactions induced by the Borromean nucleus {sup 6}He at different energies, namely {sup 6}He+{sup 9}Be at 16.2 MeV, {sup 6}He+{sup 64}Zn at 13.6 MeV, {sup 6}He+{sup 120}Sn at 17.4 MeV, and {sup 6}He+{sup 208}Pb at 22 MeV. Four-body CDCC calculations for elastic and breakup observables are presented for these reactions comparing both discretization methods, THO and binning. The effect of the mass of the target, which is clearly related to the influence of Coulomb couplings, is investigated. The elastic cross sections are also compared to existing experimental data. (author)
Calculation of Double-Differential Cross Sections of n+7Li Reactions Below 20 MeV
ZHANG Jing-Shang; HAN Ying-Lu
2002-01-01
A new reaction model for light nuclei is proposed to analyze the measured data,especially for analysis of the double-differential cross sections of the outgoing particles.Many channels arc opened in the n + 7Li reaction below En＜ 20 MeV.The reaction mechanism is very complex,beside the sequential emissions there are also three-body breakup processes.Because of a strong recoil effect of light nucleus reactions,the energy balance is strictly taken into account.The comparisons of the calculated results with the double-differential measurements indicate that the model calculations are successful for the total outgoing neutrons.
Salazar-Salinas, Karim; Baldera-Aguayo, Pedro A; Encomendero-Risco, Jimy J; Orihuela, Melvin; Sheen, Patricia; Seminario, Jorge M; Zimic, Mirko
2014-08-28
Mycobacterium tuberculosis pyrazinamidase (PZAse) is a key enzyme to activate the pro-drug pyrazinamide (PZA). PZAse is a metalloenzyme that coordinates in vitro different divalent metal cofactors in the metal coordination site (MCS). Several metals including Co(2+), Mn(2+), and Zn(2+) are able to reactivate the metal-depleted PZAse in vitro. We use quantum mechanical calculations to investigate the Zn(2+), Fe(2+), and Mn(2+) metal cofactor effects on the local MCS structure, metal-ligand or metal-residue binding energy, and charge distribution. Results suggest that the major metal-dependent changes occur in the metal-ligand binding energy and charge distribution. Zn(2+) shows the highest binding energy to the ligands (residues). In addition, Zn(2+) and Mn(2+) within the PZAse MCS highly polarize the O-H bond of coordinated water molecules in comparison with Fe(2+). This suggests that the coordination of Zn(2+) or Mn(2+) to the PZAse protein facilitates the deprotonation of coordinated water to generate a nucleophile for catalysis as in carboxypeptidase A. Because metal ion binding is relevant to enzymatic reaction, identification of the metal binding event is important. The infrared vibrational mode shift of the C═Nε (His) bond from the M. tuberculosis MCS is the best IR probe to metal complexation.
Chen Jianshan; Sheng Tianlu; Hu Shengmin; Xiang Shengchang; Fu Ruibiao; Zhu Qilong [State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002 (China); Wu Xintao, E-mail: wxt@fjirsm.ac.cn [State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002 (China)
2012-08-15
Using aminocarboxylate derivates (S)-N-(4-cyanobenzoic)-glutamic acid (denoted as cbg, 1a) and (S)-N-(4-nitrobenzoic)-glutamic acid (denoted as nbg, 1b) as chiral ligands, five new homochiral coordination polymers formulated as [Cu(cbg)(H{sub 2}O){sub 2}]{sub n} (3), [Cu(cbop){sub 2}(4,4 Prime -bipy)(H{sub 2}O)]{sub n} (4) (cbop=(S)-N-(4-cyanobenzoic)-5-oxoproline, 4,4 Prime -bipy=4,4 Prime -bipyridine), {l_brace}[Cu(nbop){sub 2}(4,4 Prime -bipy)]{center_dot}4H{sub 2}O{r_brace}{sub n} (5) (nbop=(S)-N-(4-nitrobenzoic)-5-oxoproline), {l_brace}[Cd(nbop){sub 2}(4,4 Prime -bipy)]{center_dot}2H{sub 2}O{r_brace}{sub n} (6), and [Ni(nbop){sub 2}(4,4 Prime -bipy)(H{sub 2}O){sub 2}]{sub n} (7) have been hydrothermally synthesized and structurally characterized. Single-crystal X-ray diffraction study reveals that the original chirality of aminocarboxylate derivates is maintained in all these complexes. Complexes 3, 4, and 7 are one-dimensional infinite chain coordination polymers, while complexes 5 and 6 possess two-dimensional network structures. In situ cyclization of 1a and 1b was taken place in the formation of complexes 4-7, which may be due to the competition of 4,4 Prime -bipyridine with chiral ligands during the coordination process. Preliminary optical behavior investigation indicates that ligands 1a, 1b, and complexes 6, 7 are nonlinear optical active. - Graphical abstract: Using aminocarboxylate derivates as chiral ligands, five new homochiral coordination polymers possessing second harmonic generation activities have been hydrothermally synthesized. Highlights: Black-Right-Pointing-Pointer Two new chiral aminocarboxylate derivates were firstly synthesized. Black-Right-Pointing-Pointer Five new homochiral metal organic complexes were obtained hydrothermally based on these ligands. Black-Right-Pointing-Pointer Intramolecular amidation was taken place on the aminocarboxylate derivates during the formation of these complexes. Black-Right-Pointing-Pointer In situ
Semirigid vibrating rotor target calculation for reaction O(3p)+CH4 →CH3+OH
LIU; Xinguo; BAI; Lihua; ZHANG; Qinggang
2004-01-01
The time-dependent quantum dynamics calculation for reaction O(3p)+CH4→ CH3+OH is made, using of the semirigid vibrating rotor target (SVRT) model and the time-dependent wave packet (TDWP) method. The corresponding reaction probabilities of different initial states are provided. From the calculation of initial rovibrational state j= 0,v= 0, 1, we can see that the excitation of the H-CH3 stretching vibration gives significant enhancement of reaction probability and the reaction threshold decreases dramatically with the enhancement of the vibrating excitation, which indicates that the vibrating energy of reagent molecules contributes a lot to the molecular collision. As for the calculation of reaction probability of state v= 0, j= 0,1,2,3, the results show that the reaction probability rises significantly with the enhancement of rotational quantum number j while the reaction threshold has no changes. The spatial steric effect of the title reaction is studied and analyzed too after the calculation of reaction probability of states j= 5, k= 0-2, n= 0 and j=5, k=2, n=0-2 is made.
Vreede, J.; Juraszek, J.; Bolhuis, P.G.
2010-01-01
Understanding the dynamics of large-scale conformational changes in proteins still poses a challenge for molecular simulations. We employ transition path sampling of explicit solvent molecular dynamics trajectories to obtain atomistic insight in the reaction network of the millisecond timescale part
Mielke, Steven L.; Truhlar, Donald G.; Schwenke, David W.
1991-01-01
Improved techniques and well-optimized basis sets are presented for application of the outgoing wave variational principle to calculate converged quantum mechanical reaction probabilities. They are illustrated with calculations for the reactions D + H2 yields HD + H with total angular momentum J = 3 and F + H2 yields HF + H with J = 0 and 3. The optimization involves the choice of distortion potential, the grid for calculating half-integrated Green's functions, the placement, width, and number of primitive distributed Gaussians, and the computationally most efficient partition between dynamically adapted and primitive basis functions. Benchmark calculations with 224-1064 channels are presented.
Kinetic calculation for the reaction of H with Si2H6 using the variational transition state theory
ZHANG; Qingzhu
2001-01-01
［1］Gates, S. M., Kuna, R. R., Greenlief, C. M., Silicon hydride etch products from the reaction of atomic hydrogen with Si(100), Surf. Sci., 1989, 207: 364.［2］Abrefah, J., Olander, D. R., Reaction of atomic hydrogen with crystalline silicon, Surf. Sci., 1989, 209: 291.［3］Kerwin, D. D., Douglas, J. D., Mechanistic insight into gas-phase of H+Si2H6 and hydrogen atom etching of silicon surface, J. Am. Chem. Soc., 1993, 115: 3731.［4］Pollock, T. L., Sandhu, H. S., Jodhan, A. et al., Photochemistry of silicon compounds, IV. Mercury photosensitization of disilane, J. Am. Chem. Soc., 1973, 95: 1017.［5］Austin, E. R., Lampe, F W., Rate constants for the reactions of hydrogen atoms with some silicanes and germanes, J. Phys. Chem., 1977, 81(12): 1134.［6］Fabry, L., Potzinger, P, Reimann, B. et al., Gas-phase homolytic substitution reactions of hydrogen atoms at silicon centers. Organometallics. 1986, 5: 1231.［7］Oberhammer, H., Lobreyer, T., Sundermeyer, W., The Ge-Si bond in silylgermane discrepancy between experiment and theory, J. Mol. Struct., 1994, 323: 125.［8］Durig. J. R., Church, J. S., Vibrational spectra of crystalline disilane and disilane, barrier to internal rotation and some normal coordinate calculations on H3SiSiH3, H3SiNCO, H3SiNCS, J. Chem. Phys., 1980, 73: 4784.［9］Espinosa-Garcia, J., Sanson, J., Corchado, J. C., The SiH4+H→SiH3+H2 reaction: potential energy surface, rate constants, and kinetic isotope effects, J. Chem. Phys., 1998, 109(2): 466.［10］Charles, B. M., Siddharth, D., William, A. G., Hessian biased force field for polysilane polymers, J. Phys. Chem,, 1995, 99:13321.［11］Wu, Y. D., Wong, C. L., Substituion effect on the dissociation energy of the Si-H bond: a density functional study, J. Org. Chem., 1995, 60: 821.［12］Taylor. C. A.. Marshall, P., A discharge-fluoro/chemiluminescence study of the reaction O+SiH at room temperature, Chem. Phys. Lett., 1993, 205(6): 493.［13］Doncaster, A. M., Walsh, R
Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.
2013-11-01
The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.
Kim, Ki Chul; Kulkarni, Anant D; Johnson, J Karl; Sholl, David S
2011-04-21
Systematic thermodynamics calculations based on density functional theory-calculated energies for crystalline solids have been a useful complement to experimental studies of hydrogen storage in metal hydrides. We report the most comprehensive set of thermodynamics calculations for mixtures of light metal hydrides to date by performing grand canonical linear programming screening on a database of 359 compounds, including 147 compounds not previously examined by us. This database is used to categorize the reaction thermodynamics of all mixtures containing any four non-H elements among Al, B, C, Ca, K, Li, Mg, N, Na, Sc, Si, Ti, and V. Reactions are categorized according to the amount of H(2) that is released and the reaction's enthalpy. This approach identifies 74 distinct single step reactions having that a storage capacity >6 wt.% and zero temperature heats of reaction 15 ≤ΔU(0)≤ 75 kJ mol(-1) H(2). Many of these reactions, however, are likely to be problematic experimentally because of the role of refractory compounds, B(12)H(12)-containing compounds, or carbon. The single most promising reaction identified in this way involves LiNH(2)/LiH/KBH(4), storing 7.48 wt.% H(2) and having ΔU(0) = 43.6 kJ mol(-1) H(2). We also examined the complete range of reaction mixtures to identify multi-step reactions with useful properties; this yielded 23 multi-step reactions of potential interest.
Dhara, Barun; Sappati, Subrahmanyam; Singh, Santosh K; Kurungot, Sreekumar; Ghosh, Prasenjit; Ballav, Nirmalya
2016-04-28
Fe and Al belong to different groups in the periodic table, one from the p-block and the other from the d-block. In spite of their different groups, they have the similarity of exhibiting a stable 3+ oxidation state. Here we have prepared Fe(iii) and Al(iii) based coordination polymers in the form of metal-organic gels with the 4,4',4''-tricarboxyltriphenylamine (TCA) ligand, namely Fe-TCA and Al-TCA, and evaluated some important physicochemical properties. Specifically, the electrical conductivity, redox-activity, porosity, and electrocatalytic activity (oxygen evolution reaction) of the Fe-TCA system were noted to be remarkably higher than those of the Al-TCA system. As for the photophysical properties, almost complete quenching of the fluorescence originating from TCA was observed in case of the Fe-TCA system, whereas for the Al-TCA system a significant retention of fluorescence with red-shifted emission was observed. Quantum mechanical calculations based on density functional theory (DFT) were performed to unravel the origin of such discriminative behaviour of these coordination polymer systems.
Calculation of A x for the Proton-Deuteron Breakup Reaction at 135 MeV
Eslami-Kalantari, M.; Mehmandoost-Khajeh-Dad, A. A.; Shafaei, M. A.; Amir-Ahmadi, H. R.; Biegun, A.; Gašparic, I.; Joulaeizadeh, L.; Kalantar-Nayestanaki, N.; Kistryn, St.; Kozela, A.; Mardanpour, H.; Messchendorp, J. G.; Moeini, H.; Ramazani-Moghaddam-Arani, A.; Shende, S. V.; Stephan, E.; Sworst, R.
2013-08-01
Observables in proton-deuteron scattering are sensitive probes of the nucleon-nucleon interaction and three-nucleon force effects (3NF). Several facilities in the world, including Kernfysisch Versneller Instituut (KVI), allow a detailed study a few-nucleon interaction below the pion-production threshold exploiting polarized proton and deuteron beams. In this contribution we explored 3NF effects in the break-up scattering process by performing a measurement of differential cross section and the analyzing power, especially the x component of the analyzing power, using a 135 MeV polarized-proton beam impinging on a liquid-deuteron target. The proton-deuteron breakup reaction leads to a final state with three free particles and a rich phase space that allows us to study observables for continuous set of kinematical configurations of the outgoing nucleons. The results are interpreted with the help of state-of-the-art Faddeev calculations.
Calculations of three-nucleon reactions with N3LO chiral forces: achievements and challenges
Witala, Henryk; Skibinski, Roman; Topolnicki, Kacper
2013-01-01
We discuss the application of the chiral N3LO forces to three-nucleon reactions and point to the challenges which will have to be addressed. Present approaches to solve three-nucleon Faddeev equations are based on a partial-wave decomposition. A rapid increase of the number of terms contributing to the chiral three-nucleon force when increasing the order of the chiral expansion from N2LO to N3LO forced us to develop a fast and effective method of automatized partial wave decomposition. At low energies of the incoming nucleon below about 20MeV, where only a limited number of partial waves is required, this method allowed us to perform calculations of reactions in the three-nucleon continuum using N3LO two- and three-nucleon forces. It turns out that inclusion of consistent chiral interactions, with relativistic 1/m corrections and short-range 2pi-contact term omitted in the N3LO three-nucleon force, does not explain the long standing low energy Ay-puzzle. We discuss problems arising when chiral forces are appl...
Balasekaran, Samundeeswari Mariappan; Spandl, Johann; Hagenbach, Adelheid; Köhler, Klaus; Drees, Markus; Abram, Ulrich
2014-05-19
A mixture of [Tc(NO)F5](2-) and [Tc(NO)(NH3)4F](+) is formed during the reaction of pertechnetate with acetohydroxamic acid (Haha) in aqueous HF. The blue pentafluoridonitrosyltechnetate(II) has been isolated in crystalline form as potassium and rubidium salts, while the orange-red ammine complex crystallizes as bifluoride or PF6(-) salts. Reactions of [Tc(NO)F5](2-) salts with HCl give the corresponding [Tc(NO)Cl4/5](-/2-) complexes, while reflux in neat pyridine (py) results in the formation of the technetium(I) cation [Tc(NO)(py)4F](+), which can be crystallized as hexafluoridophosphate. The same compound can be synthesized directly from pertechnetate, Haha, HF, and py or by a ligand-exchange procedure starting from [Tc(NO)(NH3)4F](HF2). The technetium(I) cation [Tc(NO)(NH3)4F](+) can be oxidized electrochemically or by the reaction with Ce(SO4)2 to give the corresponding Tc(II) compound [Tc(NO)(NH3)4F](2+). The fluorido ligand in [Tc(NO)(NH3)4F](+) can be replaced by CF3COO(-), leaving the "[Tc(NO)(NH3)4](2+) core" untouched. The experimental results are confirmed by density functional theory calculations on [Tc(NO)F5](2-), [Tc(NO)(py)4F](+), [Tc(NO)(NH3)4F](+), and [Tc(NO)(NH3)4F](2+).
New reaction rates for improved primordial D/H calculation and the cosmic evolution of deuterium
Coc, Alain; Uzan, Jean-Philippe; Vangioni, Elisabeth; Descouvemont, Pierre; Illiadis, Christian; Longland, Richard
2015-01-01
Primordial or big bang nucleosynthesis (BBN) is one of the three historical strong evidences for the big bang model. Standard BBN is now a parameter free theory, since the baryonic density of the Universe has been deduced with an unprecedented precision from observations of the anisotropies of the cosmic microwave background (CMB) radiation. There is a good agreement between the primordial abundances of 4He, D, 3He and 7Li deduced from observations and from primordial nucleosynthesis calculations. However, the 7Li calculated abundance is significantly higher than the one deduced from spectroscopic observations and remains an open problem. In addition, recent deuterium observations have drastically reduced the uncertainty on D/H, to reach a value of 1.6%. It needs to be matched by BBN predictions whose precision is now limited by thermonuclear reaction rate uncertainties. This is especially important as many attempts to reconcile Li observations with models lead to an increased D prediction. Here, we re-evalua...
Jensen, Lasse; van Duijnen, Piet Th.; Snijders, Jaap G.
2003-12-01
We present a discrete solvent reaction field (DRF) model for the calculation of frequency-dependent hyperpolarizabilities of molecules in solution. In this model the solute is described using density functional theory (DFT) and the discrete solvent molecules are described with a classical polarizable model. The first hyperpolarizability is obtained in an efficient way using time-dependent DFT and the (2n+1) rule. The method was tested for liquid water using a model in which a water molecule is embedded in a cluster of 127 classical water molecules. The frequency-dependent first and second hyperpolarizabilities related to the electric field induced second harmonic generation (EFISH) experiment, were calculated both in the gas phase and in the liquid phase. For water in the gas phase, results are obtained in good agreement with correlated wave function methods and experiments by using the so-called shape-corrected exchange correlation (xc)-potentials. In the liquid phase the effect of using asymptotically correct functionals is discussed. The model reproduced the experimentally observed sign change in the first hyperpolarizaibility when going from the gas phase to the liquid phase. Furthermore, it is shown that the first hyperpolarizability is more sensitive to damping of the solvent-solute interactions at short range than the second hyperpolarizability.
Calculation of radiation reaction effect on orbital parameters in Kerr spacetime
Sago, Norichika
2015-01-01
We calculate the secular changes of the orbital parameters of a point particle orbiting a Kerr black hole, due to the gravitational radiation reaction. For this purpose, we use the post-Newtonian (PN) approximation in the first order black hole perturbation theory, with the expansion with respect to the orbital eccentricity. In this work, the calculation is done up to the fourth post-Newtonian (4PN) order and to the sixth order of the eccentricity, including the effect of the absorption of gravitational waves by the black hole. We confirm that, in the Kerr case, the effect of the absorption appears at the 2.5PN order beyond the leading order in the secular change of the particle's energy and may induce a superradiance, as known previously for circular orbits. In addition, we find that the superradiance may be suppressed when the orbital plane inclines with respect to the equatorial plane of the central black hole. We also investigate the accuracy of the 4PN formulae by comparing to numerical results. If we re...
Ghosh, Sandip; Sahoo, Tapas; Adhikari, Satrajit; Sharma, Rahul; Varandas, António J C
2015-12-17
We implement a coupled three-dimensional (3D) time-dependent wave packet formalism for the 4D reactive scattering problem in hyperspherical coordinates on the accurate double many body expansion (DMBE) potential energy surface (PES) for the ground and first two singlet states (1(1)A', 2(1)A', and 3(1)A') to account for nonadiabatic processes in the D(+) + H2 reaction for both zero and nonzero values of the total angular momentum (J). As the long-range interactions in D(+) + H2 contribute significantly due to nonadiabatic effects, the convergence profiles of reaction probabilities for the reactive noncharge transfer (RNCT), nonreactive charge transfer (NRCT), and reactive charge transfer (RCT) processes are shown for different collisional energies with respect to the helicity (K) and total angular momentum (J) quantum numbers. The total and state-to-state cross sections are presented as a function of the collision energy for the initial rovibrational state v = 0, j = 0 of the diatom, and the calculated cross sections compared with other theoretical and experimental results.
Sato, Yoichiro; Yamada, Norimasa
2017-05-01
Although it was reported that ground reaction forces (GRFs) are generated simultaneously by the leading and trailing limbs during the double stance phase, the finding was not examined by temporal analyses. Therefore, the purpose of the present study is to clarify how GRFs can act to propel the body in a forward direction during the double stance phase. GRFs were recorded during the double stance phase in eleven healthy volunteers. We calculated the instantaneous phase of the GRFs for vertical and anterior-posterior (AP) components, and then calculated the relative phase between the leading and trailing limbs for each component. The relative phase of the vertical component was approximately 180° (i.e., anti-phase), indicating that the lower limb transfers weight smoothly from the trailing limb to the leading limb. The relative phase of the AP component ranged from 40 to 55°, indicating that the AP component of the forces do not occur simultaneously, but instead has a lag. This finding suggests that the forces exerted by the leading and trailing limbs would temporally coordinate to propel the body in the forward direction. Copyright © 2017 Elsevier B.V. All rights reserved.
Jensen, Lasse; van Duijnen, Piet Th.; Snijders, Jaap G.
2003-08-01
A discrete solvent reaction field model for calculating frequency-dependent molecular linear response properties of molecules in solution is presented. The model combines a time-dependent density functional theory (QM) description of the solute molecule with a classical (MM) description of the discrete solvent molecules. The classical solvent molecules are represented using distributed atomic charges and polarizabilities. All the atomic parameters have been chosen so as to describe molecular gas phase properties of the solvent molecule, i.e., the atomic charges reproduce the molecular dipole moment and the atomic polarizabilities reproduce the molecular polarizability tensor using a modified dipole interaction model. The QM/MM interactions are introduced into the Kohn-Sham equations and all interactions are solved self-consistently, thereby allowing for the solute to be polarized by the solvent. Furthermore, the inclusion of polarizabilities in the MM part allows for the solvent molecules to be polarized by the solute and by interactions with other solvent molecules. Initial applications of the model to calculate the vertical electronic excitation energies and frequency-dependent molecular polarizability of a water molecule in a cluster of 127 classical water molecules are presented. The effect of using different exchange correlation (xc)-potentials is investigated and the results are compared with results from wave function methods combined with a similar solvent model both at the correlated and uncorrelated level of theory. It is shown that accurate results in agreement with correlated wave function results can be obtained using xc-potentials with the correct asymptotic behavior.
Yalcin, C; Rauscher, T; Kiss, G G; Özkan, N; Güray, R T; Halász, Z; Szücs, T; Fülöp, Zs; Korkulu, Z; Somorjai, E
2015-01-01
Astrophysical reaction rates, which are mostly derived from theoretical cross sections, are necessary input to nuclear reaction network simulations for studying the origin of $p$ nuclei. Past experiments have found a considerable difference between theoretical and experimental cross sections in some cases, especially for ($\\alpha$,$\\gamma$) reactions at low energy. Therefore, it is important to experimentally test theoretical cross section predictions at low, astrophysically relevant energies. The aim is to measure reaction cross sections of $^{107}$Ag($\\alpha$,$\\gamma$)$^{111}$In and $^{107}$Ag($\\alpha$,n)$^{110}$In at low energies in order to extend the experimental database for astrophysical reactions involving $\\alpha$ particles towards lower mass numbers. Reaction rate predictions are very sensitive to the optical model parameters and this introduces a large uncertainty into theoretical rates involving $\\alpha$ particles at low energy. We have also used Hauser-Feshbach statistical model calculations to s...
Three-Body Model Calculation of Spin Distribution in Two-Nucleon Transfer Reaction
Ogata, Kazuyuki; Chiba, Satoshi
2011-01-01
The differential cross sections of two-nucleon transfer reactions 238U(18O,16O)240U around 10 MeV per nucleon are calculated by one-step Born-approximation with a 16O+2n+238U three-body model. The three-body wave function in the initial channel is obtained with the continuum-discretized coupled-channels method, and that in the final channel is evaluated with adiabatic approximation. The resulting cross sections have a peak around the grazing angle, and the spin distribution, i.e., the cross section at the peak as a function of the transferred spin, is investigated. The shape of the spin distribution is found not sensitive to the incident energies, optical potentials, and treatment of the breakup channels both in the initial and final states, while it depends on the excitation energy of the residual nucleus 240U. The peak of the spin distribution moves to the large-spin direction as the excitation energy increases. To fulfill the condition that the peak position should not exceeds 10 hbar, which is necessary f...
Farberow, Carrie A.; Dumesic, James A.; Mavrikakis, Manos
2014-10-03
Reaction pathways are explored for low temperature (e.g., 400 K) reduction of nitric oxide by hydrogen on Pt(111). First-principles electronic structure calculations based on periodic, self-consistent density functional theory(DFT-GGA, PW91) are employed to obtain thermodynamic and kinetic parameters for proposed reaction schemes on Pt(111). The surface of Pt(111) during NO reduction by H₂ at low temperatures is predicted to operate at a high NO coverage, and this environment is explicitly taken into account in the DFT calculations. Maximum rate analyses are performed to assess the most likely reaction mechanisms leading to formation of N₂O, the major product observed experimentally at low temperatures. The results of these analyses suggest that the reaction most likely proceeds via the addition of at least two H atoms to adsorbed NO, followed by cleavage of the N-O bond.
Yalçin, C.
2017-02-01
The theoretical cross section calculations for the astrophysical p process are very crucial due to the most of the related reactions are technically very difficult to measure at the laboratory. On the other hand, the theoretical cross sections are not in agreement with the experimental results, especially for the (α,γ) reactions. One of the main reason of the difference between theoretical and experimental cross section is description of the α+nucleus optical model potential. In order to understand current situation and improvement of the theoretical calculations, the 112Sn(α,γ)116Te reaction were investigated for different global optical model potentials at the astrophysically interested energies. Astrophysical S factors were also calculated and compared with experimental data available at EXFOR database.
Liu, Zhe; Lin, Lei; Xie, Lian; Gao, Huiwang
2016-10-01
To improve the efficiency of the terrain-following σ-coordinate non-hydrostatic ocean model, a partially implicit finite difference (PIFD) scheme is proposed. By using explicit terms instead of implicit terms to discretize the parts of the vertical dynamic pressure gradient derived from the σ-coordinate transformation, the coefficient matrix of the discrete Poisson equation that the dynamic pressure satisfies can be simplified from 15 diagonals to 7 diagonals. The PIFD scheme is shown to run stably when it is applied to simulate five benchmark cases, namely, a standing wave in a basin, a surface solitary wave, a lock-exchange problem, a periodic wave over a bar and a tidally induced internal wave. Compared with the conventional fully implicit finite difference (FIFD) scheme, the PIFD scheme produces simulation results of equivalent accuracy at only 40-60% of the computational cost. The PIFD scheme demonstrates strong applicability and can be easily implemented in σ-coordinate ocean models.
Minomo, Kosho
2016-01-01
We analyze the $\\alpha$-$^{12}$C inelastic scattering to the $0^+_2$ state of $^{12}$C, the Hoyle state, in a fully microscopic framework. With no free adjustable parameter, the inelastic cross sections at forward angles are well reproduced by the microscopic reaction calculation using the transition density of $^{12}$C obtained by the resonating group method and the nucleon-nucleon $g$ matrix interaction developed by the Melbourne group. It is thus shown that the monopole transition strength obtained by the structural calculation is consistent with that extracted from the reaction observable, suggesting no missing monopole strength of the Hoyle state.
Guillaume eViejo
2015-08-01
Full Text Available Current learning theory provides a comprehensive description of how we and other animalslearn, and places behavioral flexibility and automaticity at heart of adaptive behaviors. However, the computations supporting the interactions between goal-directed and habitual decision-making systems are still poorly understood. Previous functional magnetic resonance imaging(fMRI results suggest that the brain hosts complementary computations that may differentiallysupport goal-directed and habitual processes in the form of a dynamical interplay rather than aserial recruitment of strategies. To better elucidate the computations underlying flexible behavior, we develop a dual-system computational model which can predict both performance (i.e.,participants’ choices and modulations in reaction times during learning of a stimulus-response association task. The habitual system is modelled with a simple Q-learning algorithm (QL.For the goal-directed system, we propose a new Bayesian Working Memory (BWM modelwhich searches for information in the history of previous trials in order to minimize Shannonentropy. We propose a model for QL and BWM coordination such that the expensive memorymanipulation is under control of, among others, the level of convergence of the habitual learning.We test the ability of QL or BWM alone to explain human behavior, and compare them with theperformance of model combinations, to highlight the need for such combinations to explainbehavior. Two of the tested combination models are derived from the literature, the latter beingour new proposal. In conclusion, all subjects were better explained by model combinations, andthe majority of them by our new coordination proposal.
Jonathan S. Merritt
2008-01-01
Full Text Available The equine distal forelimb is a common location of injuries related to mechanical overload. In this study, a two-dimensional model of the musculoskeletal system of the region was developed and applied to kinematic and kinetic data from walking and trotting horses. The forces in major tendons and joint reaction forces were calculated. The components of the joint reaction forces caused by wrapping of tendons around sesamoid bones were found to be of similar magnitude to the reaction forces between the long bones at each joint. This finding highlighted the importance of taking into account muscle-tendon wrapping when evaluating joint loading in the equine distal forelimb.
Polkowski, Marcin
2016-04-01
Seismic wave travel time calculation is the most common numerical operation in seismology. The most efficient is travel time calculation in 1D velocity model - for given source, receiver depths and angular distance time is calculated within fraction of a second. Unfortunately, in most cases 1D is not enough to encounter differentiating local and regional structures. Whenever possible travel time through 3D velocity model has to be calculated. It can be achieved using ray calculation or time propagation in space. While single ray path calculation is quick it is complicated to find the ray path that connects source with the receiver. Time propagation in space using Fast Marching Method seems more efficient in most cases, especially when there are multiple receivers. In this presentation a Python module pySeismicFMM is presented - simple and very efficient tool for calculating travel time from sources to receivers. Calculation requires regular 2D or 3D velocity grid either in Cartesian or geographic coordinates. On desktop class computer calculation speed is 200k grid cells per second. Calculation has to be performed once for every source location and provides travel time to all receivers. pySeismicFMM is free and open source. Development of this tool is a part of authors PhD thesis. National Science Centre Poland provided financial support for this work via NCN grant DEC-2011/02/A/ST10/00284.
Naumov, Sergej; von Sonntag, Clemens
2011-11-01
Free radicals are common intermediates in the chemistry of ozone in aqueous solution. Their reactions with ozone have been probed by calculating the standard Gibbs free energies of such reactions using density functional theory (Jaguar 7.6 program). O(2) reacts fast and irreversibly only with simple carbon-centered radicals. In contrast, ozone also reacts irreversibly with conjugated carbon-centered radicals such as bisallylic (hydroxycylohexadienyl) radicals, with conjugated carbon/oxygen-centered radicals such as phenoxyl radicals, and even with nitrogen- oxygen-, sulfur-, and halogen-centered radicals. In these reactions, further ozone-reactive radicals are generated. Chain reactions may destroy ozone without giving rise to products other than O(2). This may be of importance when ozonation is used in pollution control, and reactions of free radicals with ozone have to be taken into account in modeling such processes.
Josip Sertić
2014-01-01
Full Text Available The values of reaction forces in the boiler supports are the basis for the dimensioning of bearing steel structure of steam boiler. In this paper, the application of the method of equivalent stiffness of membrane wall is proposed for the calculation of reaction forces. The method of equalizing displacement, as the method of homogenization of membrane wall stiffness, was applied. On the example of “Milano” boiler, using the finite element method, the calculation of reactions in the supports for the real geometry discretized by the shell finite element was made. The second calculation was performed with the assumption of ideal stiffness of membrane walls and the third using the method of equivalent stiffness of membrane wall. In the third case, the membrane walls are approximated by the equivalent orthotropic plate. The approximation of membrane wall stiffness is achieved using the elasticity matrix of equivalent orthotropic plate at the level of finite element. The obtained results were compared, and the advantages of using the method of equivalent stiffness of membrane wall for the calculation of reactions in the boiler supports were emphasized.
Sertić, Josip; Kozak, Dražan; Samardžić, Ivan
2014-01-01
The values of reaction forces in the boiler supports are the basis for the dimensioning of bearing steel structure of steam boiler. In this paper, the application of the method of equivalent stiffness of membrane wall is proposed for the calculation of reaction forces. The method of equalizing displacement, as the method of homogenization of membrane wall stiffness, was applied. On the example of "Milano" boiler, using the finite element method, the calculation of reactions in the supports for the real geometry discretized by the shell finite element was made. The second calculation was performed with the assumption of ideal stiffness of membrane walls and the third using the method of equivalent stiffness of membrane wall. In the third case, the membrane walls are approximated by the equivalent orthotropic plate. The approximation of membrane wall stiffness is achieved using the elasticity matrix of equivalent orthotropic plate at the level of finite element. The obtained results were compared, and the advantages of using the method of equivalent stiffness of membrane wall for the calculation of reactions in the boiler supports were emphasized.
Zhang, Guojie; Müller, Marcus
2017-08-14
Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i.e., its subsequent rupture that completes the fission process does not occur spontaneously but requires additional, external effects, e.g., dynamin's (unknown) conformational changes or membrane tension. Using simulations of a coarse-grained, implicit-solvent model of lipid membranes, we investigate the molecular mechanism of rupturing the hemi-fission intermediate, such as its pathway, the concomitant transition states, and barriers, as well as the role of membrane tension. The membrane tension is controlled by the chemical potential of the lipids, and the free-energy landscape as a function of two reaction coordinates is obtained by grand canonical Wang-Landau sampling. Our results show that, in the course of rupturing, the hemi-fission intermediate undergoes a "thinning → local pinching → rupture/fission" pathway, with a bottle-neck-shaped cylindrical micelle as a transition state. Although an increase of membrane tension facilitates the fission process by reducing the corresponding free-energy barrier, for biologically relevant tensions, the free-energy barriers still significantly exceed the thermal energy scale kBT.
Strasberg, Philipp; Schaller, Gernot; Lambert, Neill; Brandes, Tobias
2016-07-01
We propose a method to study the thermodynamic behaviour of small systems beyond the weak coupling and Markovian approximation, which is different in spirit from conventional approaches. The idea is to redefine the system and environment such that the effective, redefined system is again coupled weakly to Markovian residual baths and thus, allows to derive a consistent thermodynamic framework for this new system-environment partition. To achieve this goal we make use of the reaction coordinate (RC) mapping, which is a general method in the sense that it can be applied to an arbitrary (quantum or classical and even time-dependent) system coupled linearly to an arbitrary number of harmonic oscillator reservoirs. The core of the method relies on an appropriate identification of a part of the environment (the RC), which is subsequently included as a part of the system. We demonstrate the power of this concept by showing that non-Markovian effects can significantly enhance the steady state efficiency of a three-level-maser heat engine, even in the regime of weak system-bath coupling. Furthermore, we show for a single electron transistor coupled to vibrations that our method allows one to justify master equations derived in a polaron transformed reference frame.
Sekizawa, Kazuyuki
2016-01-01
Background: Multinucleon transfer (MNT) and quasifission (QF) processes are dominant processes in low-energy collisions of two heavy nuclei. They are expected to be useful to produce neutron-rich unstable nuclei. Nuclear dynamics leading to these processes depends sensitively on nuclear properties such as deformation and shell structure. Purpose: We elucidate reaction mechanisms of MNT and QF processes involving heavy deformed nuclei, making detailed comparisons between microscopic TDHF calculations and measurements for $^{64}$Ni+$^{238}$U reaction. Methods: Three-dimensional Skyrme-TDHF calculations are performed. Particle-number projection method is used to evaluate MNT cross sections from the TDHF wave function after collision. Results: Fragment masses, total kinetic energy (TKE), scattering angle, contact time, and MNT cross sections are investigated for $^{64}$Ni+$^{238}$U reaction. They show reasonable agreements with measurements. At small impact parameters, collision dynamics depends sensitively on th...
Variational RRKM calculation of thermal rate constant for C–H bond fission reaction of nitro methane
Afshin Taghva Manesh
2017-02-01
Full Text Available The present work provides quantitative results for the rate constants of unimolecular C–H bond fission reactions in the nitro methane at elevated temperatures up to 2000 K. In fact, there are three different hydrogen atoms in the nitro methane. The potential energy surface for each C–H bond fission reaction of nitro methane was investigated by ab initio calculations. The geometry and vibrational frequencies of the species involved in this process were optimized at the MP2 level of theory, using the cc-pvdz basis set. Since C–H bond fission channel is a barrierless reaction, we have used variational RRKM theory to predict rate coefficients. By means of calculated rate coefficients at different temperatures, the Arrhenius expression of the channel over the temperature range of 100–2000 K is k(T = 5.9E19∗exp(−56274.6/T.
Calculation and analysis of cross-sections for p+184W reactions up to 200 MeV
Sun, Jian-Ping; Zhang, Zheng-Jun; Han, Yin-Lu
2015-08-01
A set of optimal proton optical potential parameters for p+ 184W reactions are obtained at incident proton energy up to 250 MeV. Based on these parameters, the reaction cross-sections, elastic scattering angular distributions, energy spectra and double differential cross sections of proton-induced reactions on 184W are calculated and analyzed by using theoretical models which integrate the optical model, distorted Born wave approximation theory, intra-nuclear cascade model, exciton model, Hauser-Feshbach theory and evaporation model. The calculated results are compared with existing experimental data and good agreement is achieved. Supported by National Basic Research Program of China, Technology Research of Accelerator Driven Sub-critical System for Nuclear Waste Transmutation (2007CB209903) and Strategic Priority Research Program of Chinese Academy of Sciences, Thorium Molten Salt Reactor Nuclear Energy System (XDA02010100)
Tao Haiqiao; Long Jun; Zhou Han; Xie Chaogang; Dai Zhenyu; Wei Xiaoli
2009-01-01
The structure and energy of the carbonium ions formed upon protonation of butane were studied by the DFT methods. Four stable structures are identified for the protonated form of n-butane, the energy increases in the following order: C2HC3C1HC2>C2HH>C1HH. The stability of the penta-enordinated carbonium ions may be explained by the electron distribution in the three-center-two-electron bonds. The delocalization of the penta-eoordinated carbonium ion CHC with three-center-two-electron bonds on positive charges was stronger than that of the penta-coordinated carbonium ion CHH with three-center-two-electron bonds and its stability was higher than that of the penta-coordinated earbonium ion CHH with three-center-two-electron bonds.
Calculation of excitation functions of the 54,56,57,58Fe(, ) reaction from threshold to 30 MeV
Damewan Suchiang; J Joseph Jeremiah; B M Jyrwa
2014-10-01
The cross-sections for the formation of 54,56,57,58Co in the 54,56,57,58Fe(, ) reaction from threshold to 30 MeV protons have been theoretically calculated using the TALYS-1.4 nuclear model code, whereby we have studied major nuclear reaction mechanisms, including direct, preequilibrium and compound nuclear reaction. Subsequently, the level density and shell damping parameters have been adjusted and at the same time, the odd–even effects are well comprehended. The excitation functions have been compared with experimental nuclear data. It is observed that the theoretical cross-sections match fairly well. Proton-induced reaction cross-sections provide clues to understand the nuclear structure and offers a good testing ground for ideas about nuclear forces. In addition, complete information in this field is very much required for application in accelerator-driven subcritical system.
Ichikawa, Kazuhide; Fukushima, Akinori; Ishihara, Yoshio; Isaki, Ryuichiro; Takeguchi, Toshio; Tachibana, Akitomo; 10.1016/j.theochem.2009.08.026
2009-01-01
We investigate a reaction of boron trichloride (BCl3) with iron(III) hydroxide (Fe(OH)3) by ab initio quantum chemical calculation as a simple model for a reaction of iron impurities in BCl3 gas. We also examine a reaction with water. We find that compounds such as Fe(Cl)(OBCl2)2(OHBCl2) and Fe(Cl)2(OBCl2)(OHBCl2) are formed while producing HCl and reaction paths to them are revealed. We also analyze the stabilization mechanism of these paths using newly-developed interaction energy density derived from electronic stress tensor in the framework of the Regional DFT (Density Functional Theory) and Rigged QED (Quantum ElectroDynamics).
Theoretical Calculations and Analysis for n+59Co Reaction up to 20 MeV
2008-01-01
<正>All cross-sections of neutron-induced reactions, angular distributions, double differential cross sections, and energy spectra for neutron, proton, deuteron, triton, helium and alpha-particle emissions are
Muthu, S; Elamuruguporchelvi, E; Varghese, Anitha
2015-03-05
The solid phase FTIR and FT-Raman spectra of 2-[(5-nitro-1,3-thiazol-2-yl)carbamoyl]phenyl acetate (25N2LCPA) have been recorded 450-4000cm(-1) and 100-4000cm(-1) respectively. The normal coordinate analysis was carried out to confirm the precision of the assignments. DFT calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies and IR intensities. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31+G(d,p) basis set. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The Vibrational frequencies are calculated in the above method and are compared with experimental frequencies which yield good agreement between observed and calculated frequencies. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. In addition, Frontiers molecular orbital and molecular electrostatic potential were computed by using Density Functional Theory (DFT) B3LYP/6-31+G(d,p) basis set. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule.
Meija, Juris; Pagliano, Enea; Mester, Zoltán
2014-09-02
Uncertainty of the result from the method of standard addition is often underestimated due to neglect of the covariance between the intercept and the slope. In order to simplify the data analysis from standard addition experiments, we propose x-y coordinate swapping in conventional linear regression. Unlike the ratio of the intercept and slope, which is the result of the traditional method of standard addition, the result of the inverse standard addition is obtained directly from the intercept of the swapped calibration line. Consequently, the uncertainty evaluation becomes markedly simpler. The method is also applicable to nonlinear curves, such as the quadratic model, without incurring any additional complexity.
Kaplan Abdullah
2015-01-01
Full Text Available Implementation of projects of new generation nuclear power plants requires the solving of material science and technological issues in developing of reactor materials. Melts of heavy metals (Pb, Bi and Pb-Bi due to their nuclear and thermophysical properties, are the candidate coolants for fast reactors and accelerator-driven systems (ADS. In this study, α, γ, p, n and 3He induced fission cross section calculations for 209Bi target nucleus at high-energy regions for (α,f, (γ,f, (p,f, (n,f and (3He,f reactions have been investigated using different fission reaction models. Mamdouh Table, Sierk, Rotating Liquid Drop and Fission Path models of theoretical fission barriers of TALYS 1.6 code have been used for the fission cross section calculations. The calculated results have been compared with the experimental data taken from the EXFOR database. TALYS 1.6 Sierk model calculations exhibit generally good agreement with the experimental measurements for all reactions used in this study.
Nuclear model calculations of (n,p) and (n,n'p) reactions on molybdenum isotopes
Ivascu, M.; Avrigeanu, M.; Avrigeanu, V.
1983-06-01
Cross sections for the (n,p) and (n,n'p) reactions on stable molybdenum isotopes have been calculated in the energy range from threshold up to 20 MeV. The calculations have involved the optical model (SCAT2 code), the statistical model (Kauser-Feshbach STAPRE code) and the preequilibrium decay exciton and hybrid models (incorporated in STAPRE). The input model parameters have been determined or checked analyzing against the available experimental data the calculated neutron strength functions, potential scattering radius, total, differential shape elastic and inelastic scattering cross sections (SPRT method), the excitation function of the reaction /sup 93/Nb(p,n)/sup 93/Mo, neutron resonance data and discrete levels at low excitation energies, neutron radiative capture cross sections on /sup 93/Nb and /sup 98,100/Mo target nuclei, the excitation function of the reaction /sup 92/Mo(n,2n)/sup 91/Mo cross section and isomer ratio, and the proton - emission spectrum for 15 MeV neutron incident energy on /sup 92/Mo target. The calculation of nuclear level density for excitation energies higher than approx.23 MeV are more reliable done by means of the liquid drop model predictions for the back - shifted Fermi gas model parameters. That enables also to use in a unified way the average level density parameter anti a = A/8 MeV/sup -1/ in both statistical and exciton models. The calculated (n,p) and (n,n'p) reaction cross sections are compared with the available experimental data and their sensitivity to the input parameter variations are discussed. 132 refs., 25 figs., 11 tabs.
Wiebe, Heather; Prachnau, Melissa; Weinberg, Noham
2013-01-01
Two-dimensional potential energy and free energy surfaces are obtained using quantum mechanical and molecular dynamics calculations for four hydrogen transfer reactions in n-hexane solvent: the methyl–methane, n-propyl–n-propane, n-pentyl...
Dorofeeva, Olga V; Ryzhova, Oxana N
2014-05-15
Accurate gas-phase enthalpies of formation (ΔfH298°) of 20 common α-amino acids, seven uncommon amino acids, and three small peptides were calculated by combining G4 theory calculations with an isodesmic reaction approach. The internal consistency over a set of ΔfH298°(g) values was achieved by sequential adjustment of their values through the isodesmic reactions. Four amino acids, alanine, β-alanine, sarcosine, and glycine, with reliable internally self-consistent experimental data, were chosen as the key reference compounds. These amino acids together with about 100 compounds with reliable experimental data (their accuracy was supported by G4 calculations) were used to estimate the enthalpies of formation of remaining amino acids. All of the amino acids with the previously established enthalpies of formation were later used as the reference species in the isodesmic reactions for the other amino acids. A systematic comparison was made of 14 experimentally determined enthalpies of formation with the results of calculations. The experimental enthalpies of formation for 10 amino acids were reproduced with good accuracy, but the experimental and calculated values for 4 compounds differed by 11–21 kJ/mol. For these species, the theoretical ΔfH298°(g) values were suggested as more reliable than the experimental values. On the basis of theoretical results, the recommended values for the gas-phase enthalpies of formation were also provided for amino acids for which the experimental ΔfH298°(g) were not available. The enthalpies of sublimation were evaluated for all compounds by taking into account the literature data on the solid-phase enthalpies of formation and the ΔfH298°(g) values recommended in our work. A special attention was paid to the accurate prediction of enthalpies of formation of amino acids from the atomization reactions. The problems associated with conformational flexibility of these compounds and harmonic treatment of low frequency torsional
Calculation method of quantum efficiency to TiO2 nanocrystal photocatalysis reaction
无
2002-01-01
The quantum yield is an important factor to evaluate the efficiency of photoreactor. This article gives an overall calculation method of the quantum efficiency(ф) and the apparent quantum efficiency(ф2) to the TiO2/UV photocatalysis system. Furthermore, for the immobility system (IS), the formulation of the faction of light absorbed by the TiO2 thin film is proposed so as to calculate the quantum efficiency by using the measured value and theoretic calculated value of transmissivity (T). For the suspension system(SS), due to the difficulty to obtain the absorption coefficient (α) of TiO2 particulates, the quantum efficiency is calculated by means of the relative photonic efficiency (ξr) and the standard quantum yield (фstandard).
McCourt, M.; Shibata, M.; McIver, J. W.; Rein, R.
1988-01-01
Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.
Heshmat, Mojgan; Privalov, Timofei
2017-09-01
Using Born-Oppenheimer molecular dynamics (BOMD), we explore the nature of interactions between H2 and the activated carbonyl carbon, C(carbonyl), of the acetone-B(C6F5)3 adduct surrounded by an explicit solvent (1,4-dioxane). BOMD simulations at finite (non-zero) temperature with an explicit solvent produced long-lasting instances of significant vibrational perturbation of the H—H bond and H2-polarization at C(carbonyl). As far as the characteristics of H2 are concerned, the dynamical transient state approximates the transition-state of the heterolytic H2-cleavage. The culprit is the concerted interactions of H2 with C(carbonyl) and a number of Lewis basic solvent molecules—i.e., the concerted C(carbonyl)⋯H2⋯solvent interactions. On one hand, the results presented herein complement the mechanistic insight gained from our recent transition-state calculations, reported separately from this article. But on the other hand, we now indicate that an idea of the sufficiency of just one simple reaction coordinate in solution-phase reactions can be too simplistic and misleading. This article goes in the footsteps of the rapidly strengthening approach of investigating molecular interactions in large molecular systems via "computational experimentation" employing, primarily, ab initio molecular dynamics describing reactants-interaction without constraints of the preordained reaction coordinate and/or foreknowledge of the sampling order parameters.
钟晨; 蔡翔舟; 沈文庆; 张虎勇; 魏义彬; 陈金根; 马余刚; 郭威; 方德清
2003-01-01
The Boltzmann-Uehling-Uhlenbeck (BUU) model, which includes the Fermi motion, the mean field, individual nucleon-nucleon (N-N) interactions and the Pauli blocking effect, etc., is used to calculate the total reaction cross section σR induced by α-particles on different targets in the incident energy range from 17.4 to 48.1 MeV/u. The calculation result can well reproduce the experimental data. The nucleus-nucleus interaction radius parameterγ0 was extracted from experimental σR. It is found that γ0 becomes constant with the increasing mass number of target.
Veli ÇAPALI
2016-05-01
Full Text Available BeO is one of the most common moderator material for neutron moderation; due to its high density, neutron capture cross section and physical-chemical properties that provides usage at elevated temperatures. As it’s known, for various applications in the field of reactor design and neutron capture, reaction cross–section data are required. The cross–sections of (n,α, (n,2n, (n,t, (n,EL and (n,TOT reactions for 9Be and 16O nuclei have been calculated by using TALYS 1.6 Two Component Exciton model and EMPIRE 3.2 Exciton model in this study. Hadronic interactions of low energetic neutrons and generated isotopes–particles have been investigated for a situation in which BeO was used as a neutron moderator by using GEANT4, which is a powerful simulation software. In addition, energy deposition along BeO material has been obtained. Results from performed calculations were compared with the experimental nuclear reaction data exist in EXFOR.
Should Thermostatted Ring Polymer Molecular Dynamics be used to calculate reaction rates?
Hele, Timothy J H
2015-01-01
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to rigorous Quantum Transition-State Theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H+H$_2$, D+MuH and F+H$_2$, and the prototypical polyatomic reaction H+CH$_4$. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is less accurate than Ring Polymer Molecular Dynamics (RPMD) for symmetric reactions, and in certain asymmetric systems closer to the q...
Moreira, Cátia; Ramos, Maria J; Fernandes, Pedro Alexandrino
2016-06-27
This paper is devoted to the understanding of the reaction mechanism of mycobacterium tuberculosis glutamine synthetase (mtGS) with atomic detail, using computational quantum mechanics/molecular mechanics (QM/MM) methods at the ONIOM M06-D3/6-311++G(2d,2p):ff99SB//B3LYP/6-31G(d):ff99SB level of theory. The complete reaction undergoes a three-step mechanism: the spontaneous transfer of phosphate from ATP to glutamate upon ammonium binding (ammonium quickly loses a proton to Asp54), the attack of ammonia on phosphorylated glutamate (yielding protonated glutamine), and the deprotonation of glutamine by the leaving phosphate. This exothermic reaction has an activation free energy of 21.5 kcal mol(-1) , which is consistent with that described for Escherichia coli glutamine synthetase (15-17 kcal mol(-1) ). The participating active site residues have been identified and their role and energy contributions clarified. This study provides an insightful atomic description of the biosynthetic reaction that takes place in this enzyme, opening doors for more accurate studies for developing new anti-tuberculosis therapies.
Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?
Hele, Timothy J. H., E-mail: tjhh2@cam.ac.uk [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Suleimanov, Yury V. [Computation-based Science and Technology Research Center, Cyprus Institute, 20 Kavafi St., Nicosia 2121 (Cyprus); Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139 (United States)
2015-08-21
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H{sub 2}, D + MuH, and F + H{sub 2}, and the prototypical polyatomic reaction H + CH{sub 4}. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method.
Ballester, L.; Perpinan, M. F.
1988-01-01
Described is an undergraduate coordination chemistry experiment that enables students to relate concepts developed in class about the stereochemistry and coordination numbers to the interpretation of the electronic and infrared spectra and their magnetic behavior. Indicates that thermal decomposition and x-ray diffraction studies can also be…
Wan, Liang; Zhang, Yuexing; Qi, Dongdong; Jiang, Jianzhuang
2010-06-01
On the basis of the density functional theory (DFT) calculation of ZnPc (1), Zn[Pc(alpha-OC(5)H(11))(4)] (2), Ni[Pc(alpha-OC(5)H(11))(4)] (3), and Zn[Pc(alpha-OC(5)H(11))(4)]xH(2)O (4), the effects of non-peripheral substitution, different transition metals, and axial water coordination on the molecular structure, molecular orbital, atomic charge, infrared (IR) spectrum, and electronic absorption spectrum were investigated. The calculation results reveal that bulky 3-pentyloxy groups at the non-peripheral positions of the phthalocyanine ring evince great changes in structure and properties: they deflect the isoindole units, lift the frontier molecular orbitals, alter the atomic charge distribution, shift the bands of IR and electronic absorption spectra, etc. Though the central metal can shorten or lengthen the bond length, its effect on the electronic structure and properties of the phthalocyanine complex is very limited. Axial coordination significantly enhances the non-planarity of the phthalocyanine ring and, thus, alters the electronic structure, which is important for the formation of novel dimeric supramolecular structures through intermolecular hydrogen bonds. In addition, the calculated structures of 3 as well as the simulated IR and electronic absorption spectra of 4 were compared with the experimental data and showed good agreement.
BUU calculations for {sup 12}C+{sup 26}Mg reaction at 6-11 MeV/u
Kicinska-Habior, M. [Warsaw Univ., Inst. of Experimental Physics, Nuclear Physics Div., Warsaw (Poland)]|[Washington Univ., Nuclear Physics Lab., Seattle, WA (United States); Trznadel, Z. [Warsaw Univ., Inst. of Experimental Physics, Nuclear Physics Div., Warsaw (Poland); Snover, K.A.; Kelly, M.P. [Washington Univ., Nuclear Physics Lab., Seattle, WA (United States); Maj, A. [Washington Univ., Nuclear Physics Lab., Seattle, WA (United States)]|[Inst. of Nuclear Physics, Cracow (Poland)
1997-12-31
High energy gamma spectra measured in the {sup 12}C +{sup 26}Mg reaction at energies of 5, 8.5 and 11 MeV/u have been analysed using the BUU computer code (cascade model). In the calculation the statistical and nonstatistical gamma-ray emission as well as the Bremsstrahlung have been taken into account. The parameters of the Giant Dipole Resonance have been extracted. 4 refs, 1 fig., 2 tabs.
Bassem Elshahat; Akhtar Naqvi; Nabil Maalej
2015-01-01
Purpose: Boron neutron capture therapy (BNCT) is a promising technique for the treatment of malignant disease targeting organs of the human body. Monte Carlo simulations were carried out to calculate optimum design parameters of an accelerator based beam shaping assembly (BSA) for BNCT of brain cancer setup.Methods: Epithermal beam of neutrons were obtained through moderation of fast neutrons from 3H(p,n) reaction in a high density polyethylene moderator and a graphite reflector. The dimensio...
Deltuva, A
2016-01-01
Angular-momentum or parity-dependent nonlocal optical potentials for nucleon-${}^{16}\\mathrm{O}$ scattering able to fit differential cross section data over the whole angular regime are developed and applied to the description of deuteron-${}^{16}\\mathrm{O}$ scattering in the framework of three-body Faddeev-type equations for transition operators. Differential cross sections and deuteron analyzing powers for elastic scattering and ${}^{16}\\mathrm{O}(d,p){}^{17}\\mathrm{O}$ transfer reactions are calculated using a number of local and nonlocal optical potentials and compared with experimental data. Angular-momentum or parity-dependence of the optical potential turns out to be quite irrelevant in the considered three-body reactions while nonlocality is essential for a successful description of the differential cross section data, especially in transfer reactions.
Zhao, Zhiqiang; Chen, Jun; Zhang, Zhaojun; Zhang, Dong H.; Lauvergnat, David; Gatti, Fabien
2016-05-01
Full quantum mechanical calculations of vibrational energies of methane and fluoromethane are carried out using a polyspherical description combining Radau and Jacobi coordinates. The Hamiltonian is built in a potential-optimized discrete variable representation, and vibrational energies are solved using an iterative eigensolver. This new approach can be applied to a large variety of molecules. In particular, we show that it is able to accurately and efficiently compute eigenstates for four different molecules : CH4, CHD3, CH2D2, and CH3F. Very good agreement is obtained with the results reported previously in the literature with different approaches and with experimental data.
Quantum three-body calculation of the nonresonant triple-\\alpha reaction rate at low temperatures
Ogata, Kazuyuki; Kamimura, Masayasu
2009-01-01
The triple-\\alpha reaction rate is re-evaluated by directly solving the three-body Schroedinger equation. The resonant and nonresonant processes are treated on the same footing using the continuum-discretized coupled-channels method for three-body scattering. Accurate description of the \\alpha-\\alpha nonresonant states significantly quenches the Coulomb barrier between the two-\\alpha's and the third \\alpha particle. Consequently, the \\alpha-\\alpha nonresonant continuum states below the resonance at 92.04 keV, i.e., the ground state of 8Be, give markedly larger contribution at low temperatures than in foregoing studies. We find about 20 orders-of-magnitude enhancement of the triple-\\alpha reaction rate around 10^7 K compared to the rate of the NACRE compilation.
Lifshitz, Assa; Tamburu, Carmen; Dubnikova, Faina
2009-10-01
The reactions of 1-naphthyl radicals with acetylene were studied behind reflected shock waves in a single-pulse shock tube, covering the temperature range 950-1200 K at overall densities behind the reflected shocks of approximately 2.5 x 10(-5) mol/cm3. 1-Iodonaphthalene served as the source for 1-naphthyl radicals. The [acetylene]/[1-iodonaphthalene] ratio in all of the experiments was approximately 100 to channel the free radicals into reactions with acetylene rather than iodonaphthalene. Only two major products resulting from the reactions of 1-naphthyl radicals with acetylene and with hydrogen atoms were found in the post shock samples. They were acenaphthylene and naphthalene. Some low molecular weight aliphatic products at rather low concentrations, resulting from an attack of various free radicals on acetylene, were also found in the shocked samples. In view of the relatively low temperatures employed in the present experiments, the unimolecular decomposition rate of acetylene is negligible. One potential energy surface describes the production of acenaphthylene and 1-naphthyl acetylene, although the latter was not found experimentally due to the high barrier (calculated) required for its production. Using quantum chemical methods, the rate constants for three unimolecular elementary steps on the surface were calculated using transition state theory. A kinetics scheme containing 16 elementary steps was constructed, and computer modeling was performed. An excellent agreement between the experimental yields of the two major products and the calculated yields was obtained. Differences and similarities in the potential energy surfaces of 1-naphthyl radical + acetylene and those of ethylene are presented, and the kinetics mechanisms are discussed.
Saritas, Kayahan; Grossman, Jeffrey C.
2015-03-01
Molecules that undergo pericyclic isomerization reactions find interesting optical and energy storage applications, because of their usually high quantum yields, large spectral shifts and small structural changes upon light absorption. These reactions induce a drastic change in the conjugated structure such that substituents that become a part of the conjugated system upon isomerization can play an important role in determining properties such as enthalpy of isomerization and HOMO-LUMO gap. Therefore, theoretical investigations dealing with such systems should be capable of accurately capturing the interplay between electron correlation and exchange effects. In this work, we examine the dihydroazulene isomerization as an example conjugated system. We employ the highly accurate quantum Monte Carlo (QMC) method to predict thermochemical properties and to benchmark results from density functional theory (DFT) methods. Although DFT provides sufficient accuracy for similar systems, in this particular system, DFT predictions of ground state and reaction paths are inconsistent and non-systematic errors arise. We present a comparison between QMC and DFT results for enthalpy of isomerization, HOMO-LUMO gap and charge densities with a range of DFT functionals.
Lifshitz, Assa; Tamburu, Carmen; Dubnikova, Faina
2008-02-07
The reactions of 1-naphthyl radicals with ethylene were studied behind reflected shock waves in a single pulse shock tube, covering the temperature range 950-1200 K at overall densities behind the reflected shocks of approximately 2.5 x 10(-5) mol/cm3. 1-Iodonaphthalene served as the source for 1-naphthyl radicals as its C-I bond dissociation energy is relatively small. It is only approximately 65 kcal/mol as compared to the C-H bond strength in naphthalene which is approximately 112 kcal/mol and can thus produce naphthyl radicals at rather low reflected shock temperatures. The [ethylene]/[1-iodo-naphthalene] ratio in all of the experiments was approximately 100 in order to channel the free radicals into reactions with ethylene rather than iodonaphthalene. Four products resulting from the reactions of 1-naphthyl radicals with ethylene were found in the post shock samples. They were vinyl naphthalene, acenaphthene, acenaphthylene, and naphthalene. Some low molecular weight aliphatic products at rather low concentrations, resulting from the attack of various free radicals on ethylene were also found in the shocked samples. In view of the relatively low temperatures employed in the present experiments, the unimolecular decomposition rate of ethylene is negligible. Three potential energy surfaces describing the production of vinyl naphthalene, acenaphthene, and acenaphthylene were calculated using quantum chemical methods and rate constants for the elementary steps on the surfaces were calculated using transition state theory. Naphthalene is not part of the reactions on the surfaces. Acenaphthylene is obtained only from acenaphthene. A kinetics scheme containing 27 elementary steps most of which were obtained from the potential energy surfaces was constructed and computer modeling was performed. An excellent agreement between the experimental yields of the four major products and the calculated yields was obtained.
Isaacson, A.D.
1978-08-01
Using an approximate evaluation of Miller's golden rule formula to calculate autoionization widths which allows for the consideration only of L/sup 2/ functions, the positions and lifetimes of the lowest /sup 1/,/sup 3/P autoionizing states of He have been obtained to reasonable accuracy. This method has been extended to molecular problems, and the ab initio configuration interaction potential energy and width surfaces for the He(2/sup 3/S) + H/sub 2/ system have been obtained. Quantum mechanical close-coupling calculations of ionization cross sections using the complex V* - (i/2) GAMMA-potential have yielded rate constants in good agreement with the experimental results of Lindinger, et al. The potential energy surface of the He(2/sup 1/S) + H/sub 2/ system has also been obtained and exhibits not only a high degree of anisotropy, but also contains a relative maximum for a perpendicular (C/sub 2//sub v/) approach which appears to arise from s-p hybridization of the outer He orbital. However, similar ab initio calculations on the He(2/sup 1/S) + Ar system do not show such anomalous structure. In addition, the complex poles of the S-matrix (Siegert eigenvalues) were calculated for several autoionizing states of He and H/sup -/, with encouraging results even for quite modest basis sets. This method was extended to molecular problems, and results obtained for the He(2/sup 3/S) + H and He(2/sup 1/S) + H systems. 75 references.
Shizgal, Bernie D.
2016-08-01
Nonclassical quadratures based on a new set of half-range polynomials, Tn(x) , orthogonal with respect to w(x) =e - x - b /√{ x } for x ∈ [ 0 , ∞) are employed in the efficient calculation of the nuclear fusion reaction rate coefficients from cross section data. The parameter b = B /√{kB T } in the weight function is temperature dependent and B is the Gamow factor. The polynomials Tn(x) satisfy a three term recurrence relation defined by two sets of recurrence coefficients, αn and βn. These recurrence coefficients define in turn the tridiagonal Jacobi matrix whose eigenvalues are the quadrature points and the weights are calculated from the first components of the eigenfunctions. For nonresonant nuclear reactions for which the astrophysical function can be expressed as a lower order polynomial in the relative energy, the convergence of the thermal average of the reactive cross section with this nonclassical quadrature is extremely rapid requiring in many cases 2-4 quadrature points. The results are compared with other libraries of nuclear reaction rate coefficient data reported in the literature.
Wefstaedt Patrick
2009-11-01
Full Text Available Abstract Background Among other causes the long-term result of hip prostheses in dogs is determined by aseptic loosening. A prevention of prosthesis complications can be achieved by an optimization of the tribological system which finally results in improved implant duration. In this context a computerized model for the calculation of hip joint loadings during different motions would be of benefit. In a first step in the development of such an inverse dynamic multi-body simulation (MBS- model we here present the setup of a canine hind limb model applicable for the calculation of ground reaction forces. Methods The anatomical geometries of the MBS-model have been established using computer tomography- (CT- and magnetic resonance imaging- (MRI- data. The CT-data were collected from the pelvis, femora, tibiae and pads of a mixed-breed adult dog. Geometric information about 22 muscles of the pelvic extremity of 4 mixed-breed adult dogs was determined using MRI. Kinematic and kinetic data obtained by motion analysis of a clinically healthy dog during a gait cycle (1 m/s on an instrumented treadmill were used to drive the model in the multi-body simulation. Results and Discussion As a result the vertical ground reaction forces (z-direction calculated by the MBS-system show a maximum deviation of 1.75%BW for the left and 4.65%BW for the right hind limb from the treadmill measurements. The calculated peak ground reaction forces in z- and y-direction were found to be comparable to the treadmill measurements, whereas the curve characteristics of the forces in y-direction were not in complete alignment. Conclusion In conclusion, it could be demonstrated that the developed MBS-model is suitable for simulating ground reaction forces of dogs during walking. In forthcoming investigations the model will be developed further for the calculation of forces and moments acting on the hip joint during different movements, which can be of help in context with the in
郑娜; 钟春来; 樊铁栓
2012-01-01
An attempt is made to improve the evaluation of the prompt fission neutron emis- sion from 233U(n, f) reaction for incident neutron energies below 6 MeV. The multi-modal fission approach is applied to the improved version of Los Alamos model and the point by point model. The prompt fission neutron spectra and the prompt fission neutron as a function of fragment mass (usually named "sawtooth" data) v(A) are calculated independently for the three most dominant fission modes (standard I, standard II and superlong), and the total spectra and v(A) are syn- thesized. The multi-modal parameters are determined on the basis of experimental data of fission fragment mass distributions. The present calculation results can describe the experimental data very well, and the proposed treatment is thus a useful tool for prompt fission neutron emission prediction.
Quantum Tunneling Rates of Gas-Phase Reactions from On-the-Fly Instanton Calculations.
Beyer, Adrian N; Richardson, Jeremy O; Knowles, Peter J; Rommel, Judith; Althorpe, Stuart C
2016-11-03
The instanton method obtains approximate tunneling rates from the minimum-action path (known as the instanton) linking reactants to the products at a given temperature. An efficient way to find the instanton is to search for saddle-points on the ring-polymer potential surface, which is obtained by expressing the quantum Boltzmann operator as a discrete path-integral. Here we report a practical implementation of this ring-polymer form of instanton theory into the Molpro electronic-structure package, which allows the rates to be computed on-the-fly, without the need for a fitted analytic potential-energy surface. As a test case, we compute tunneling rates for the benchmark H + CH4 reaction, showing how the efficiency of the instanton method allows the user systematically to converge the tunneling rate with respect to the level of electronic-structure theory.
Astrophysical S factor of the 12C(α ,γ )6O reaction calculated with reduced R -matrix theory
An, Zhen-Dong; Chen, Zhen-Peng; Ma, Yu-Gang; Yu, Jian-Kai; Sun, Ye-Ying; Fan, Gong-Tao; Li, Yong-Jiang; Xu, Hang-Hua; Huang, Bo-Song; Wang, Kan
2015-10-01
Determination of the accurate astrophysical S factor of 12C(α ,γ )16O reaction has been regarded as the holy grail of nuclear astrophysics for decades. In current stellar models, a knowledge of that value to better than 10% is desirable. Due to the practical issues, tremendous experimental and theoretical efforts over nearly 50 years are not able to reach this goal, and the published values contradicted with each other strongly and their uncertainties are two times larger than the required precision. To this end we have developed a reduced R -matrix theory based on the classical R -matrix theory of Lane and Thomas, which treats primary transitions to the ground state and four bound states as the independent reaction channels in the channel spin representation. With the coordination of covariance statistics and error-propagation theory, a global fitting for almost all available experimental data of 16O system has been multi-iteratively analyzed by our powerful code. A reliable, accurate, and self-consistent astrophysical S factor of 12C(α ,γ )16O was obtained with a recommended value Stot(0.3 MeV ) =162.7 ±7.3 keV b (4.5%) which could meet the required precision.
Zhang, Chao-Zhi; Li, Shi-Juan; Cao, Hui; Song, Ming-Xia; Kong, Qing-Gang
2015-05-01
A convenient method was reported to synthesize 3-(4‧-nitrophenyl)iminocoumarin by a cyclization reaction following a Knoevenagel reaction of 2-hydroxybenzaldehyde with 4-nitrophenylacenitrile in an ethanol solution. Piperidine or piperazine was employed respectively as catalyst. Crystal structure of 3-(4‧-nitrophenyl)iminocoumarin shows that the molecules are H-aggregation due to π-π stacking and hydrogen bonds between adjacent molecules, as a result, electrons would transfer easily from a molecule to an adjacent molecule. Based on theoretical calculations of the electronic structures and thermodynamic parameters of the reactive intermediates in these cyclization reactions, the reaction mechanisms were postulated. Data of single crystal and spectrum of UV-vis absorption show that 3-(4‧-nitrophenyl)iminocoumarin is good π-conjugated compound and would be potentially employed as donor-acceptor polymer units for developing bulk heterojunction solar cell. This paper suggests a convenient and effective method for synthesizing ring-locked D-A copolymer units for developing solar cell materials.
Liu, Peng; Li, Chen; Wang, Dunyou
2017-09-25
The Cl(-) + CH3I → CH3Cl + I(-) reaction in water was studied using combined multi-level quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculations with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 kcal/mol and 19.0 kcal/mol respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.
Zhao, Bin; Sun, Zhigang; Guo, Hua
2015-06-28
Quantum state-to-state dynamics of a prototypical four-atom reaction, namely, Cl + H2O → HCl + OH, is investigated for the first time in full dimensionality using a transition-state wave packet method. The state-to-state reactivity and its dependence on the reactant internal excitations are analyzed and found to share many similarities both energetically and dynamically with the H + H2O → H2 + OH reaction. The strong enhancement of reactivity by the H2O stretching vibrational excitations in both reactions is attributed to the favorable energy flow into the reaction coordinate near the transition state. On the other hand, the insensitivity of the product state distributions with regard to reactant internal excitation stems apparently from the transition-state control of product energy disposal.
Kanai, Y; Takeuchi, N
2009-10-14
We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.
Morzyk-Ociepa, Barbara; Szmigiel, Ksenia; Petrus, Rafał; Turowska-Tyrk, Ilona; Michalska, Danuta
2017-09-01
A novel two-dimensional coordination polymer, catena-poly[(μ2-7-azaindole-3-carboxylato-O:N)-di-aqua-sodium], [Na(7AI3CAH)(H2O)2]n has been synthesized and investigated by a single crystal X-ray diffraction, vibrational spectroscopy and DFT calculations. The sodium complex crystallizes in the triclinic system, space group Pī with a = 7.2226 (4), b = 7.4342 (7), c = 8.8428 (8) Å, α = 103.568 (8), β = 93.425 (6), γ = 91.233 (6)°, V = 460.42 (7) A3 and Z = 2. The asymmetric unit contains two crystallographically independent, half occupied sodium cations surrounded by one 7AI3CAH anion and two water molecules. The O-deprotonated 7-azaindole-3-carboxylate ligand (7AI3CAH) bridges the adjacent Na ions via one oxygen atom of the carboxylate group and via the pyridine nitrogen atom of the 7-azaindole group, which is quite unusual. The sodium cations are six-coordinated in a distorted octahedral geometry, where two apical positions are occupied by two water molecules. Extensive intermolecular Nsbnd H⋯O and Osbnd H⋯O hydrogen bonds stabilize the crystal structure of the complex. The infrared and Raman spectra of [Na(7AI3CAH)(H2O)2]n were recorded in the solid state. The theoretical wavenumbers, infrared intensities, Raman scattering activities and Raman intensities were calculated at the B3LYP/6-311++G(d,p) level for a theoretical model of the title compound including an inter ligand Nsbnd H⋯O(aqua) interaction. A detailed vibrational assignment has been made on the basis of the calculated potential energy distribution.
Monge-Palacios, M; Yang, M; Espinosa-García, J
2012-04-14
A detailed dynamics study, using both quasi-classical trajectory (QCT) and reduced-dimensional quantum mechanical (QM) calculations, was carried out to understand the reactivity and mechanism of the Cl((2)P) + NH(3)→ HCl + NH(2) gas-phase reaction, which evolves through deep wells in the entry and exit channels. The calculations were performed on an analytical potential energy surface recently developed by our group, PES-2010 [M. Monge-Palacios, C. Rangel, J. C. Corchado and J. Espinosa-Garcia, Int. J. Quantum. Chem., 2011], together with a simplified model surface, mod-PES, in which the reactant well is removed to analyze its influence. The main finding was that the QCT and QM methods show a change of the reaction probability with collision energy, suggesting a change of the atomic-level mechanism of reaction with energy. This change disappeared when the mod-PES was used, showing that the behaviour at low energies is a direct consequence of the existence of the reactant well. Analysis of the trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (E(coll) > 5 kcal mol(-1)) practically all trajectories are direct, at low energies (E(coll) cross section results reinforce this change of mechanism, showing also the influence of the reactant well on this reaction. Thus, the PES-2010 surface yields a forward-backward symmetry in the scattering, while when the reactant well is removed with the mod-PES the shape is more isotropic.
Yang, Huan; Han, Keli; Schatz, George C; Smith, Sean C; Hankel, Marlies
2010-10-21
We present exact quantum differential cross sections and exact and estimated integral cross sections and branching ratios for the title reaction. We employ a time-dependent wavepacket method as implemented in the DIFFREALWAVE code including all Coriolis couplings and also an adapted DIFFREALWAVE code where the helicity quantum number and with this the Coriolis couplings have been truncated. Our exact differential cross sections at 0.453 eV total energy, one of the experimental energies, show good agreement with the experimental results for one of the product channels. While the truncated calculation present a significant reduction in the computational effort needed they overestimate the exact integral cross sections.
Brons, S; Elsässer, T; Ferrari, A; Gadioli, E; Mairani, A; Parodi, K; Sala, P; Scholz, M; Sommerer, F
2010-01-01
Monte Carlo codes are rapidly spreading among hadron therapy community due to their sophisticated nuclear/electromagnetic models which allow an improved description of the complex mixed radiation field produced by nuclear reactions in therapeutic irradiation. In this contribution results obtained with the Monte Carlo code FLUKA are presented focusing on the production of secondary fragments in carbon ion interaction with water and on CT-based calculations of absorbed and biological effective dose for typical clinical situations. The results of the simulations are compared with the available experimental data and with the predictions of the GSI analytical treatment planning code TRiP.
Dreij, Kristian; Chaudhry, Qasim Ali; Jernström, Bengt; Morgenstern, Ralf; Hanke, Michael
2011-01-01
A general description of effects of toxic compounds in mammalian cells is facing several problems. Firstly, most toxic compounds are hydrophobic and partition phenomena strongly influence their behaviour. Secondly, cells display considerable heterogeneity regarding the presence, activity and distribution of enzymes participating in the metabolism of foreign compounds i.e. bioactivation/biotransformation. Thirdly, cellular architecture varies greatly. Taken together, complexity at several levels has to be addressed to arrive at efficient in silico modelling based on physicochemical properties, metabolic preferences and cell characteristics. In order to understand the cellular behaviour of toxic foreign compounds we have developed a mathematical model that addresses these issues. In order to make the system numerically treatable, methods motivated by homogenization techniques have been applied. These tools reduce the complexity of mathematical models of cell dynamics considerably thus allowing to solve efficiently the partial differential equations in the model numerically on a personal computer. Compared to a compartment model with well-stirred compartments, our model affords a more realistic representation. Numerical results concerning metabolism and chemical solvolysis of a polycyclic aromatic hydrocarbon carcinogen show good agreement with results from measurements in V79 cell culture. The model can easily be extended and refined to include more reactants, and/or more complex reaction chains, enzyme distribution etc, and is therefore suitable for modelling cellular metabolism involving membrane partitioning also at higher levels of complexity.
Kristian Dreij
Full Text Available A general description of effects of toxic compounds in mammalian cells is facing several problems. Firstly, most toxic compounds are hydrophobic and partition phenomena strongly influence their behaviour. Secondly, cells display considerable heterogeneity regarding the presence, activity and distribution of enzymes participating in the metabolism of foreign compounds i.e. bioactivation/biotransformation. Thirdly, cellular architecture varies greatly. Taken together, complexity at several levels has to be addressed to arrive at efficient in silico modelling based on physicochemical properties, metabolic preferences and cell characteristics. In order to understand the cellular behaviour of toxic foreign compounds we have developed a mathematical model that addresses these issues. In order to make the system numerically treatable, methods motivated by homogenization techniques have been applied. These tools reduce the complexity of mathematical models of cell dynamics considerably thus allowing to solve efficiently the partial differential equations in the model numerically on a personal computer. Compared to a compartment model with well-stirred compartments, our model affords a more realistic representation. Numerical results concerning metabolism and chemical solvolysis of a polycyclic aromatic hydrocarbon carcinogen show good agreement with results from measurements in V79 cell culture. The model can easily be extended and refined to include more reactants, and/or more complex reaction chains, enzyme distribution etc, and is therefore suitable for modelling cellular metabolism involving membrane partitioning also at higher levels of complexity.
Adsorption and Reaction of CO on (100) Surface of SrTiO3 by Density Function Theory Calculation
YUN Jiang-Ni; ZHANG Zhi-Yong; ZHANG Fu-Chun
2008-01-01
Adsorption and reaction of CO on two possible terminations of SrTi03 (100) surface are investigated by the first-principles calculation of plane wave ultrasoft pseudopotential based on the density function theory. The adsorption energy, Mulliken population analysis, density of states (DOS) and electronic density difference of CO on SrTi03 (100) surface, which have never been investigated before as far as we know are performed. The calculated results reveal that the Ti-CO orientation is the most stable configuration and the adsorption energy (0.449eV) is quite small. CO molecules adsorb weakly on the SrTiO3 (100) surface, there is predominantly electrostatic attraction between CO and the surface rather than a chemical bonding mechanism.
Al-abyad, Mogahed; Mohamed, Gehan Y. [Atomic Energy Authority, Cairo (Egypt). Experimental Nuclear Physics Dept.
2017-08-01
Neutron capture cross section (σ{sub 0}) and resonance integral (I{sub 0}) of the reaction {sup 186}W(n,γ){sup 187}W were measured experimentally using the research reactor (ETRR-2) and an Am-Be neutron source, also calculated using TALYS-1.6 code. The present results of σ{sub 0} are (39.08±2.6, 38.75±0.98 and 38.33 barn) and I{sub 0} are (418.5±74, 439.3±36 and 445.5 barn) by using the reactor, neutron source and TALYS-1.6, respectively. The present results are in acceptable agreement with most of the previous experimental and evaluated data as well as the theoretical calculations.
Zheng, Yao
2017-02-21
Organometallic complexes with metal-nitrogen/carbon (M-N/C) coordination are the most important alternatives to precious metal catalysts for oxygen reduction and evolution reactions (ORR and OER) in energy conversion devices. Here, we designed and developed a range of molecule-level graphitic carbon nitride (g-C3N4) coordinated transition metals (M-C3N4) as a new generation of M-N/C catalysts for these oxygen electrode reactions. As a proof-of-concept example, we conducted theoretical evaluation and experimental validation on a cobalt-C3N4 catalyst with a desired molecular configuration, which possesses comparable electrocatalytic activity to that of precious metal benchmarks for the ORR and OER in alkaline media. The correlation of experimental and computational results confirms that this high activity originates from the precise M-N2 coordination in the g-C3N4 matrix. Moreover, the reversible ORR/OER activity trend for a wide variety of M-C3N4 complexes has been constructed to provide guidance for the molecular design of this promising class of catalysts.
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.
Bahgat, Khaled; EL-Emary, Talaat
2013-02-01
FT Raman and IR spectra of the crystallized biologically active molecule, 5-Amino-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (5-APHC, C11H11N3O) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of 5-APHC have been investigated with the help of B3LYP density functional theory (DFT) method with 6-31G(d) and 6-311+G(d,p) as basis set. The calculated molecular geometry has been compared with the experimental data. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field (SQM) technique. The optimized geometry shows the co-planarity of the aldehyde group with pyrazole ring. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G(d,p) basis set. The red shifting of NH2 stretching wavenumber indicates the formation of N-H⋯O hydrogen bonding. 1H and 13C NMR spectra were recorded and 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-Vis spectrum of the compound was recorded in the region 200-400 nm and the electronic properties HOMO and LUMO energies were calculated by time-dependent TD-DFT approach. Mulliken charges of the 5-APHC molecule was also calculated and interpreted.
Siddik, Tarik
2013-01-01
Fusion serves an inexhaustible energy for humankind. Although there have been significant research and development studies on the inertial and magnetic fusion reactor technology, Furthermore, there are not radioactive nuclear waste problems in the fusion reactors. In this study, (n, p) reactions for some structural fusion materials such as 27Al, 51V, 52Cr, 55Mn and 56Fe have been investigated. The new calculations on the excitation functions of 27 Al(n,p) 27 Mg, 51 V(n,p) 51 Ti, 52 Cr(n,p) 52 V, 55 Mn(n,p) 55 Cr and 56 Fe(n,p) 56 Mn reactions have been carried out up to 30 MeV incident neutron energy. Statistical model calculations, based on the Hauser-Feshbach formalism, have been carried out using the TALYS-1.0 and were compared with available experimental data in the literature and with ENDF/B-VII, T=300k; JENDL-3.3, T=300k and JEFF3.1, T=300k evaluated libraries .
Krapf, Sebastian; Koslowski, Thorsten; Steinbrecher, Thomas
2010-08-28
DNA Photolyases are light sensitive oxidoreductases present in many organisms that participate in the repair of photodamaged DNA. They are capable of electron transfer between a bound cofactor and a chain of tryptophan amino acid residues. Due to their unique mechanism and important function, photolyases have been subject to intense study in recent times, with both experimental and computational efforts. In this work, we present a novel application of classical molecular dynamics based free energy calculations, combined with quantum mechanical computations, to biomolecular charge transfer. Our approach allows for the determination of all reaction parameters in Marcus' theory of charge transport. We were able to calculate the free energy profile for the movement of a positive charge along protein sidechains involved in the biomolecule's function as well as charge-transfer rates that are in good agreement with experimental results. Our approach to simulate charge-transfer reactions explicitly includes the influence of protein flexibility and solvent dynamics on charge-transfer energetics. As applied here to a biomolecular system of considerable scientific interest, we believe the method to be easily adaptable to the study of charge-transfer phenomena in biochemistry and other fields.
Beyeh, Ngong Kodiah; Puttreddy, Rakesh
2015-06-07
Pyridine and 2-picolinic acid N-oxides form 2 : 2 and 2 : 1 ligand : metal (L : M) discrete L2M2 and polymeric complexes with CuCl2 and Cu(NO3)2, respectively, with copper(ii) salts. The N-oxides also form 1 : 1 host-guest complexes with methylresorcinarene. In combination, the three components form a unique 2 : 2 : 1 host-ligand-metal complex. The methylresorcinarene acts as a reaction vessel/protecting group to control the coordination of copper(ii) from cis-see-saw to trans-square planar, and from octahedral to square planar coordination geometry. These processes were studied in solution and in the solid state via(1)H NMR spectroscopy and single crystal X-ray diffraction.
Zhang, Y. C.; Zhang, J. Z. H.; Kouri, D. J.; Haug, K.; Schwenke, D. W.
1988-01-01
Numerically exact, fully three-dimensional quantum mechanicl reactive scattering calculations are reported for the H2Br system. Both the exchange (H + H-prime Br to H-prime + HBr) and abstraction (H + HBR to H2 + Br) reaction channels are included in the calculations. The present results are the first completely converged three-dimensional quantum calculations for a system involving a highly exoergic reaction channel (the abstraction process). It is found that the production of vibrationally hot H2 in the abstraction reaction, and hence the extent of population inversion in the products, is a sensitive function of initial HBr rotational state and collision energy.
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
Wang, Haoyang; Xu, Chu; Zhang, Li; Tang, Qinghong; Guo, Yinlong; Lu, Long
2011-01-01
The CH(3)OH solutions of pyrimidinyloxy-N-arylbenzylamines (1-5) in the presence of Mg(II)X(2) salts (X = Cl or ClO(4)) were investigated by electrospray ionization mass spectrometry and tandem mass spectrometry (MS/MS) subsequently, showing that the cationic Mg(II) complexes 1-5·MgX(+) were important active complexes or intermediates for initiating interesting Smiles rearrangement reactions in both the gas and solution phases. By using different MgX(2) salts and selecting a set of reactants with different substitutes, the role of the counter-ion (X(-)) and the structure effect of the reactants on the Mg(II) catalyzed Smiles rearrangement reactions were studied. Moreover, the solvent effect on Mg(II) catalyzed Smiles rearrangement reactions was revealed by studying the CH(3)OH adduct complexes of 1-5·MgCl(+), which showed that the coordination of CH(3)OH to the Mg(II) center in the complexes decreased the reaction tendency. The mechanisms involved in the gas-phase Mg(II) catalyzed Smiles rearrangement reactions were proposed on the basis of MS/MS experiments and theoretical computations, showing some unique chemistries initiated by introducing Mg(II) into the template molecules.
Bisson, Claudine; Britton, K. Linda; Sedelnikova, Svetlana E.; Rodgers, H. Fiona; Eadsforth, Thomas C.; Viner, Russell C.; Hawkes, Tim R.; Baker, Patrick J.; Rice, David W.
2015-01-01
Summary Imidazoleglycerol-phosphate dehydratase (IGPD) catalyzes the Mn(II)-dependent dehydration of imidazoleglycerol phosphate (IGP) to 3-(1H-imidazol-4-yl)-2-oxopropyl dihydrogen phosphate during biosynthesis of histidine. As part of a program of herbicide design, we have determined a series of high-resolution crystal structures of an inactive mutant of IGPD2 from Arabidopsis thaliana in complex with IGP. The structures represent snapshots of the enzyme trapped at different stages of the catalytic cycle and show how substrate binding triggers a switch in the coordination state of an active site Mn(II) between six- and five-coordinate species. This switch is critical to prime the active site for catalysis, by facilitating the formation of a high-energy imidazolate intermediate. This work not only provides evidence for the molecular processes that dominate catalysis in IGPD, but also describes how the manipulation of metal coordination can be linked to discrete steps in catalysis, demonstrating one way that metalloenzymes exploit the unique properties of metal ions to diversify their chemistry. PMID:26095028
Bassem Elshahat
2015-09-01
Full Text Available Purpose: Boron neutron capture therapy (BNCT is a promising technique for the treatment of malignant disease targeting organs of the human body. Monte Carlo simulations were carried out to calculate optimum design parameters of an accelerator based beam shaping assembly (BSA for BNCT of brain cancer setup.Methods: Epithermal beam of neutrons were obtained through moderation of fast neutrons from 3H(p,n reaction in a high density polyethylene moderator and a graphite reflector. The dimensions of the moderator and the reflector were optimized through optimization of epithermal / fast neutron intensity ratio as a function of geometric parameters of the setup. Results: The results of our calculation showed the capability of our setup to treat the tumor within 4 cm of the head surface. The calculated peak therapeutic ratio for the setup was found to be 2.15. Conclusion: With further improvement in the polyethylene moderator design and brain phantom irradiation arrangement, the setup capabilities can be improved to reach further deep-seated tumor.
Skorpa, Ragnhild; Simon, Jean-Marc; Bedeaux, Dick; Kjelstrup, Signe
2014-09-28
We show how we can find the enthalpy of a chemical reaction under non-ideal conditions using the Small System Method to sample molecular dynamics simulation data for fluctuating variables. This method, created with Hill's thermodynamic analysis, is used to find properties in the thermodynamic limit, such as thermodynamic correction factors, partial enthalpies, volumes, heat capacities and compressibility. The values in the thermodynamic limit at (T,V, μj) are then easily transformed into other ensembles, (T,V,Nj) and (T,P,Nj), where the last ensemble gives the partial molar properties which are of interest to chemists. The dissociation of hydrogen from molecules to atoms was used as a convenient model system. Molecular dynamics simulations were performed with three densities; ρ = 0.0052 g cm(-3) (gas), ρ = 0.0191 g cm(-3) (compressed gas) and ρ = 0.0695 g cm(-3) (liquid), and temperatures in the range; T = 3640-20,800 K. The enthalpy of reaction was observed to follow a quadratic trend as a function of temperature for all densities. The enthalpy of reaction was observed to only have a small pressure dependence. With a reference point close to an ideal state (T = 3640 K and ρ = 0.0052 g cm(-3)), we were able to calculate the thermodynamic equilibrium constant, and thus the deviation from ideal conditions for the lowest density. We found the thermodynamic equilibrium constant to increase with increasing temperature, and to have a negligible pressure dependence. Taking the enthalpy variation into account in the calculation of the thermodynamic equilibrium constant, we found the ratio of activity coefficients to be in the order of 0.7-1.0 for the lowest density, indicating repulsive forces between H and H2. This study shows that the compressed gas- and liquid density values at higher temperatures are far from those calculated under ideal conditions. It is important to have a method that can give access to partial molar properties, independent of the ideality of
Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.
2013-01-01
In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.
Tamiya, K.; Tamagaki, R.
1981-10-01
Results obtained by applying a formulation based on the reaction matrix theory developed in I are given. Calculations by making use of a modified realistic potential, the Reid soft-core potential with the OPEP-part enhanced due to the isobar (Δ)-mixing, show that the transition to the [ALS] phase of quasi-neutrons corresponding to a typical π0 condensation occurs in the region of (2 ˜ 3) times the nuclear density. The most important ingredients responsible for this transition are the growth of the attractive 3P2 + 3F2 contribution mainly from the spin-parallel pairs in the same leyers and the reduction of the repulsive 3P1 contribution mainly from the spin-antiparallel pairs in the nearest layers; these mainfest themselves as the [ALS]-type localization develops. Properties of the matter under the new phase thus obtained such as the shape of the Fermi surface and the effective mass are discussed.
Theoretical calculation of the 1CCl2+O2 reaction mechanism%1CCl2+O2反应机理的理论研究
石从云; 伊双莉
2011-01-01
在B3LYP/6-311+ +G(d,p)水平上研究了二氯卡宾1CCl2与O2在单重态势能面上的微观反应机理.优化了中间体、过渡态和产物的构型,并得到了相应的能量值.研究发现1CCl2+O2反应有4种产物通道:CO2+Cl2、CO2+2Cl、ClCO+ClO和CO+Cl2O,且前两种是主要通道.%The dissolution enthalpies of the[Tb(Gly)3·6H2O(s)+3 Gly (s)] and Tb(Gly)3Cl3· 3H2O(s) in 2 mol·L-1 HC1 solution have been measured at 298.2 K by isoperibol calorimeter.The standard molar reaction enthalpy of the coordination reaction of terbium chloride with glycine has been determined by a thermochemical cycle, △rHmθ(298.15 K) = -6.247±0.060 kJ·mol-1.According to the results, the standard molar enthalpy of formation of Tb(Gly)3Cl3·3H2O(s) has been calculated to be △rHmθ(298.15 K) =-3631.9±2.9 kJ·mol-1, and the molar dissolution enthalpy of Tb(Gly)3Cl3 ·3H2O(s) in water has been measured by isopribel calorimeter, the standard molar enthalpy of formation of Tb(Gly)33+(aq) has been calculated at 298.15 K to be △rHmθ[Tb(Gly)33+ ,aq,298.15 K] = -2 260.6+2.9 kJ·mol-1.
Criscenti, Louise J; Kubicki, James D; Brantley, Susan L
2006-01-12
Molecular orbital energy minimizations were performed with the B3LYP/6-31G(d) method on a [((OH)3SiO)3SiOH-(H3O+).4(H2O)] cluster to follow the reaction path for hydrolysis of an Si-O-Si linkage via proton catalysis in a partially solvated system. The Q3 molecule was chosen (rather than Q2 or Q1) to estimate the maximum activation energy for a fully relaxed cluster representing the surface of an Al-depleted acid-etched alkali feldspar. Water molecules were included in the cluster to investigate the influence of explicit solvation on proton-transfer reactions and on the energy associated with hydroxylating the bridging oxygen atom (Obr). Single-point energy calculations were performed with the B3LYP/6-311+G(d,p) method. Proton transfer from the hydronium cation to an Obr requires sufficient energy to suggest that the Si-(OH)-Si species will occur only in trace quantities on a silica surface. Protonation of the Obr lengthens the Si-Obr bond and allows for the formation of a pentacoordinate Si intermediate ([5]Si). The energy required to form this species is the dominant component of the activation energy barrier to hydrolysis. After formation of the pentacoordinate intermediate, hydrolysis occurs via breaking the [5]Si-(OH)-Si linkage with a minimal activation energy barrier. A concerted mechanism involving stretching of the [5]Si-(OH) bond, proton transfer from the Si-(OH2)+ back to form H3O+, and a reversion of [5]Si to tetrahedral coordination was predicted. The activation energy for Q3Si hydrolysis calculated here was found to be less than that reported for Q3Si using a constrained cluster in the literature but significantly greater than the measured activation energies for the hydrolysis of Si-Obr bonds in silicate minerals. These results suggest that the rate-limiting step in silicate dissolution is not the hydrolysis of Q3Si-Obr bonds but rather the breakage of Q2 or Q1Si-Obr bonds.
Holm-Jørgensen, Jacob R; Jensen, Mikael; Bjerrum, Morten J
2011-12-19
To enable utilization of the broad potential of copper isotopes in nuclear medicine, rapid and robust chelation of the copper is required. Bowl adamanzanes (bicyclic tetraaza ligands) can form kinetically stable copper complexes, but they are usually formed at low rates unless high pH values and high temperatures are applied. We have investigated the effects of the variation in the pH, different anions, and UV irradiation on the chelation rate. UV spectra of mixtures of Cu(2+) and [2(4).3(1)]adz in water show the existence of a long-lived two-coordinated copper(II) intermediate (only counting coordinated amine groups) at pH above 6. These findings are supported by pH titrations of mixtures of Cu(2+) and [2(4).3(1)]adz in water. Irradiation of this complex in the ligand-to-metal charge-transfer (LMCT) band by a diode-array spectrophotometer leads to photodeprotonation and subsequently to formation of the four-coordinated copper(II) complex at a rate up to 7800-fold higher at 25 °C than in the dark. Anions in the solution were found to have three major effects: competitive inhibition due to Cu(II) binding anions, inhibition of the photoinduced transchelation from UV-absorbing anions, and photoredox inhibition from acido ligands capable of acting as electron donors in LMCT reactions. Dissolved O(2) was also found to result in photoredox inhibition.
MATLAB在反应工程计算中的应用%Application of MATLAB in Reaction Engineering Calculation
宋颖韬; 党明岩
2012-01-01
反应工程计算复杂,常需采用数值方法求解。文中以MATLAB为编程语言,将计算机辅助计算应用于反应工程问题求解,并列举典型实例。实践表明,基于MATLAB的计算机辅助计算引入课程的教学中可为学生理解课程内容和解答习题提供方便,并有助于调动学生的学习兴趣,提高其计算机应用能力。%Numerical method was often used to deal with the complex problems in reaction engineering.Several application examples in actual reaction engineering were presented and solved with the compute program complier by MATLAB.The practice showed that the introduction of computer-aided calculating based on MATLAB could facilitate effectively the understanding and answering to exercises for students.The learning interest and computer application capability were also improved dramatically.
Daschakraborty, Snehasis; Kiefer, Philip M; Miller, Yifat; Motro, Yair; Pines, Dina; Pines, Ehud; Hynes, James T
2016-03-10
The protonation of methylamine base CH3NH2 by carbonic acid H2CO3 within a hydrogen (H)-bonded complex in aqueous solution was studied via Car-Parrinello dynamics in the preceding paper (Daschakraborty, S.; Kiefer, P. M.; Miller, Y.; Motro, Y.; Pines, D.; Pines, E.; Hynes, J. T. J. Phys. Chem. B 2016, DOI: 10.1021/acs.jpcb.5b12742). Here some important further details of the reaction path are presented, with specific emphasis on the water solvent's role. The overall reaction is barrierless and very rapid, on an ∼100 fs time scale, with the proton transfer (PT) event itself being very sudden (water solvent changes little until the actual PT occurrence; this results from the very strong driving force for the reaction, as indicated by the very favorable acid-protonated base ΔpKa difference. Further solvent rearrangement follows immediately the sudden PT's production of an incipient contact ion pair, stabilizing it by establishment of equilibrium solvation. The solvent water's short time scale ∼120 fs response to the incipient ion pair formation is primarily associated with librational modes and H-bond compression of water molecules around the carboxylate anion and the protonated base. This is consistent with this stabilization involving significant increase in H-bonding of hydration shell waters to the negatively charged carboxylate group oxygens' (especially the former H2CO3 donor oxygen) and the nitrogen of the positively charged protonated base's NH3(+).
Welsch, Ralph, E-mail: rwelsch@uni-bielefeld.de; Manthe, Uwe, E-mail: uwe.manthe@uni-bielefeld.de [Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld (Germany)
2015-02-14
Initial state-selected reaction probabilities of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction are calculated in full and reduced dimensionality on a recent neural network potential [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. The quantum dynamics calculation employs the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach and rigorously studies the reaction for vanishing total angular momentum (J = 0). The calculations investigate the accuracy of the neutral network potential and study the effect resulting from a reduced-dimensional treatment. Very good agreement is found between the present results obtained on the neural network potential and previous results obtained on a Shepard interpolated potential energy surface. The reduced-dimensional calculations only consider motion in eight degrees of freedom and retain the C{sub 3v} symmetry of the methyl fragment. Considering reaction starting from the vibrational ground state of methane, the reaction probabilities calculated in reduced dimensionality are moderately shifted in energy compared to the full-dimensional ones but otherwise agree rather well. Similar agreement is also found if reaction probabilities averaged over similar types of vibrational excitation of the methane reactant are considered. In contrast, significant differences between reduced and full-dimensional results are found for reaction probabilities starting specifically from symmetric stretching, asymmetric (f{sub 2}-symmetric) stretching, or e-symmetric bending excited states of methane.
Welsch, Ralph; Manthe, Uwe
2015-02-14
Initial state-selected reaction probabilities of the H + CH4 → H2 + CH3 reaction are calculated in full and reduced dimensionality on a recent neural network potential [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. The quantum dynamics calculation employs the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach and rigorously studies the reaction for vanishing total angular momentum (J = 0). The calculations investigate the accuracy of the neutral network potential and study the effect resulting from a reduced-dimensional treatment. Very good agreement is found between the present results obtained on the neural network potential and previous results obtained on a Shepard interpolated potential energy surface. The reduced-dimensional calculations only consider motion in eight degrees of freedom and retain the C3v symmetry of the methyl fragment. Considering reaction starting from the vibrational ground state of methane, the reaction probabilities calculated in reduced dimensionality are moderately shifted in energy compared to the full-dimensional ones but otherwise agree rather well. Similar agreement is also found if reaction probabilities averaged over similar types of vibrational excitation of the methane reactant are considered. In contrast, significant differences between reduced and full-dimensional results are found for reaction probabilities starting specifically from symmetric stretching, asymmetric (f2-symmetric) stretching, or e-symmetric bending excited states of methane.
Welsch, Ralph; Manthe, Uwe
2015-02-01
Initial state-selected reaction probabilities of the H + CH4 → H2 + CH3 reaction are calculated in full and reduced dimensionality on a recent neural network potential [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. The quantum dynamics calculation employs the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach and rigorously studies the reaction for vanishing total angular momentum (J = 0). The calculations investigate the accuracy of the neutral network potential and study the effect resulting from a reduced-dimensional treatment. Very good agreement is found between the present results obtained on the neural network potential and previous results obtained on a Shepard interpolated potential energy surface. The reduced-dimensional calculations only consider motion in eight degrees of freedom and retain the C3v symmetry of the methyl fragment. Considering reaction starting from the vibrational ground state of methane, the reaction probabilities calculated in reduced dimensionality are moderately shifted in energy compared to the full-dimensional ones but otherwise agree rather well. Similar agreement is also found if reaction probabilities averaged over similar types of vibrational excitation of the methane reactant are considered. In contrast, significant differences between reduced and full-dimensional results are found for reaction probabilities starting specifically from symmetric stretching, asymmetric (f2-symmetric) stretching, or e-symmetric bending excited states of methane.
Moore-Russo, Deborah A.; Cortes-Figueroa, Jose E.; Schuman, Michael J.
2006-01-01
The use of Calculator-Based Laboratory (CBL) technology, the graphing calculator, and the cooling and heating of water to model the behavior of consecutive first-order reactions is presented, where B is the reactant, I is the intermediate, and P is the product for an in-class demonstration. The activity demonstrates the spontaneous and consecutive…
Ab initio many-body calculations of the (3)H(d,n)(4)He and (3)He(d,p)(4)He fusion reactions.
Navrátil, Petr; Quaglioni, Sofia
2012-01-27
We apply the ab initio no-core shell model combined with the resonating-group method approach to calculate the cross sections of the (3)H(d,n)(4)He and (3)He(d,p)(4)He fusion reactions. These are important reactions for the big bang nucleosynthesis and the future of energy generation on Earth. Starting from a selected similarity-transformed chiral nucleon-nucleon interaction that accurately describes two-nucleon data, we performed many-body calculations that predict the S factor of both reactions. Virtual three-body breakup effects are obtained by including excited pseudostates of the deuteron in the calculation. Our results are in satisfactory agreement with experimental data and pave the way for microscopic investigations of polarization and electron-screening effects, of the (3)H(d,γn)(4)He bremsstrahlung and other reactions relevant to fusion research.
Mohamed, Tarek A.; Hassan, Ali M.; Soliman, Usama A.; Zoghaib, Wajdi M.; Husband, John; Abdelall, Mahmoud M.
2011-01-01
The Raman and infrared spectra of solid 5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbothioamide (AMPC, C 6H 7N 5S 2) were measured in the spectral range of 3700-100 cm -1 and 4000-200 cm -1 with a resolution of 4 and 0.5 cm -1, respectively. Aided by normal coordinate analysis and potential energy distributions, a confident vibrational assignment of all fundamentals is proposed herein. As a result of internal rotation around C sbnd N and/or C sbnd S bonds, 32 rotational isomers are suggested for AMPC (C s symmetry). RHF and DFT/B3LYP quantum mechanical calculations including polarization and diffusion functions up to 6-311++G(d,p) basis sets, predict that after complete relaxation of the 32 possible isomers, four structures lie within 1500 cm -1 of the lowest energy conformer. However, vibrational analysis reveals the lowest energy conformer to be the only structure giving all real frequencies. Thus, the only stable conformer of AMPC is shown to have a fully planar skeleton with the NH 2 groups trans to one another. The recorded IR and Raman spectral measurements favor the calculated structural parameters which are further supported by spectral simulation. Additional support is given by 1H and 13C NMR spectra recorded with the sample dissolved in DMSO-d 6 and by predicted chemical shifts at the B3LYP/6-311+G(2d,p) level obtained using the Gauge-Invariant Atomic Orbitals (GIAO) method with and without inclusion of solvent using the Polarizable Continuum Model (PCM). Finally, CH 3, CH 3S, and NH 2 torsional barriers to internal rotation have been investigated using the optimized structural parameters from the B3LYP method with the 6-31G(d) basis set. The results are discussed herein and compared with similar molecules whenever appropriate.
Han, You; Sun, Mengxia; Li, Wei; Zhang, Jinli
2015-03-28
The catalytic mechanism of Ru-based catalysts in the acetylene hydrochlorination reaction has been investigated via the density functional theory (DFT) method. To study the effect of the chlorine coordination number on the catalytic mechanism, Ru3Cl9, Ru3Cl7, Ru5Cl7, Ru3Cl3 and Ru3 clusters were chosen as the catalytic models. Our results show that the energy barrier for acetylene hydrochlorination on Ru3Cl9 was as high as 1.51 eV at 458 K. When the chlorine coordination number decreased, the energy barriers on Ru3Cl7, Ru5Cl7, Ru3Cl3 and Ru3 were 1.29, 0.89, 1.01 and 1.42 eV, respectively. On Ru3Cl9, the H and Cl atoms of HCl were simultaneously added to C2H2 to form C2H3Cl, while the reaction was divided into two steps on Ru3Cl7, Ru3Cl3 and Ru3 clusters. The first step was the addition of H atom of HCl to C2H2 to form C2H3˙, and the second step was the addition of Cl atom to C2H3˙ to form C2H3Cl. The step involving the addition of Cl was the rate-controlling step during the whole reaction. On Ru5Cl7 cluster, there was an additional step before the steps involving the addition of H and Cl: the transfer of H atom from HCl to Ru atom. This step was the rate-controlling step during the reaction of acetylene hydrochlorination on Ru5Cl7 and its energy barrier was the lowest among all the above-mentioned catalytic models. Therefore, the Ru5Cl7 cluster played the most predominant role in acetylene hydrochlorination with the largest reaction rate constant kTST of 10(3).
Kurtikyan, Tigran S; Hovhannisyan, Astghik A; Hakobyan, Manya E; Patterson, James C; Iretskii, Alexei; Ford, Peter C
2007-03-28
Detailed experimental studies are described for reactions of several nitrogen oxides with iron porphyrin models for heme/NxOy systems. It is shown by FTIR and optical spectroscopy and by isotope labeling experiments that reaction of small increments of NO2 with sublimed thin layers of the iron(II) complex Fe(Por) (Por = meso-tetraphenylporphyrinato dianion, TPP, or meso-tetra-p-tolylporphyrinato dianion, TTP) leads to formation of the 5-coordinate nitrito complexes Fe(Por)(eta1-ONO) (1), which are fairly stable but very slowly decompose under vacuum giving mostly the corresponding nitrosyl complexes Fe(Por)(NO). Further reaction of 1 with new NO2 increments leads to formation of the nitrato complex Fe(Por)(eta2-O2NO) (2). The interaction of NO with 1 at low temperature involves ligand addition to give the nitrito-nitrosyl complexes Fe(Por)(eta1-ONO)(NO) (3); however, these isomerize to the nitro-nitrosyl analogs Fe(Por)(eta1-NO2)(NO) (4) upon warming. Experiments with labeled nitrogen oxides argue for an intramolecular isomerization ("flipping") mechanism rather than one involving dissociation and rebinding of NO2. The Fe(III) centers in the 6-coordinate species 3 and 4 are low spin in contrast to 1, which appears to be high-spin, although DFT computations of the porphinato models Fe(P)(nitrite) suggest that the doublet nitro species and the quartet and sextet nitrito complexes are all relatively close in energy. The nitro-nitrosyl complex 4 is stable under an NO atmosphere but decomposes under intense pumping to give a mixture of the ferrous nitrosyl complex Fe(Por)(NO) and the ferric nitrito complex Fe(Por)(eta1-ONO) indicating the competitive dissociation of NO and NO2. Hence, loss of NO from 4 is accompanied with nitro --> nitrito isomerization consistent with 1 being the more stable of the 5-coordinate NO2 complexes of iron porphyrins.
Cong, Jingkun; Li, Changqing; Zhao, Tao; Wu, Jin; Zhang, Rui; Ren, Wenjing; Wang, Shunli; Gao, Junkuo; Liu, Yi; Yao, Juming
2017-09-01
In this paper, we reported the fabrication of Co-embedded nitrogen-doped carbon nanotube (Co-NCNT) by using Co-melamine coordination polymer (CP) as precursor. The sample was well characterized via SEM, TEM, XRD, XPS and BET methods. The Co-NCNT shows excellent and stable catalytic performance for OER. The overpotential of Co-NCNT at 10 mA cm-2 is 370 mV (vs RHE). The current density of Co-NCNT could reach 100 mA cm-2 at overpotential of 520 mV, which showed much better performance than RuO2, while the largest current density of RuO2 could reach is only 44 mA cm-2. The Tafel slope of Co-NCNT is 56 mV dec-1, which is smaller than that of commercial RuO2 (58 mV dec-1). The results indicate that metal-melamine based CPs or MOFs can be promising precursors for the preparation of efficient metal-embedded nitrogen-doped carbon materials for electrocatalysis.
周传佩; 陈文生; 刘义; 屈松生
2001-01-01
The reaction enthalpy of solid-solid coordination reaction of L-Leucine with copper acetate is determined by solution calorimetry in an isoperibel reaction calorimeter. The calorimetric solvent is the solution of hydrochloric acid(4 mol/L), a new thermochemical cycle is designed. The values of △fHθm=1S. 64 kJ/mol, △fHθm(trans-Cu(L-Leu)2,s)=-1194. 7 kJ/mol are evalcated.
Bulut, Niyazi; Kłos, Jacek; Roncero, Octavio
2015-06-07
We present accurate state-to-state quantum wave packet calculations of integral cross sections and rate constants for the title reaction. Calculations are carried out on the best available ground 1(2)A' global adiabatic potential energy surface of Deskevich et al. [J. Chem. Phys. 124, 224303 (2006)]. Converged state-to-state reaction cross sections have been calculated for collision energies up to 0.5 eV and different initial rotational and vibrational excitations, DCl(v = 0, j = 0 - 1; v = 1, j = 0). Also, initial-state resolved rate constants of the title reaction have been calculated in a temperature range of 100-400 K. It is found that the initial rotational excitation of the DCl molecule does not enhance reactivity, in contract to the reaction with the isotopologue HCl in which initial rotational excitation produces an important enhancement. These differences between the isotopologue reactions are analyzed in detail and attributed to the presence of resonances for HCl(v = 0, j), absent in the case of DCl(v = 0, j). For vibrational excited DCl(v = 1, j), however, the reaction cross section increases noticeably, what is also explained by another resonance.
Koner, Debasish; Panda, Aditya N., E-mail: adi07@iitg.ernet.in [Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039 (India); Barrios, Lizandra; González-Lezana, Tomás, E-mail: t.gonzalez.lezana@csic.es [Instituto de Física Fundamental, C.S.I.C., Serrano 123, Madrid 28006 (Spain)
2014-09-21
A real wave packet based time-dependent method and a statistical quantum method have been used to study the He + NeH{sup +} (v, j) reaction with the reactant in various ro-vibrational states, on a recently calculated ab initio ground state potential energy surface. Both the wave packet and statistical quantum calculations were carried out within the centrifugal sudden approximation as well as using the exact Hamiltonian. Quantum reaction probabilities exhibit dense oscillatory pattern for smaller total angular momentum values, which is a signature of resonances in a complex forming mechanism for the title reaction. Significant differences, found between exact and approximate quantum reaction cross sections, highlight the importance of inclusion of Coriolis coupling in the calculations. Statistical results are in fairly good agreement with the exact quantum results, for ground ro-vibrational states of the reactant. Vibrational excitation greatly enhances the reaction cross sections, whereas rotational excitation has relatively small effect on the reaction. The nature of the reaction cross section curves is dependent on the initial vibrational state of the reactant and is typical of a late barrier type potential energy profile.
Ara, Irene; Forniés, Juan; García, Ana; Gómez, Julio; Lalinde, Elena; Moreno, M Teresa
2002-08-16
The reactions between cis-[M(C(6)F(5))(2)(PPh(2)CtriplebondCR)(2)] (M=Pt, Pd; R=Ph, tBu, Tol 2, 3) or cis-[Pt(C(6)F(5))(2)(PPh(2)CtriplebondCR)(PPh(2)CtriplebondCtBu)] (R=Ph 4, Tol 5) and cis-[Pt(C(6)F(5))(2)(thf)(2)] 1 have been investigated. Whereas [M](PPh(2)CtriplebondCtBu)(2) ([M]=cis-M(C(6)F(5))(2)) is inert towards 1, the analogous reactions starting from [M](PPh(2)CtriplebondCR)(2) or [Pt](PPh(2)CtriplebondCR)(PPh(2)CtriplebondCtBu) (R=Ph, Tol) afford unusual binuclear species [Pt(C(6)F(5))(S)mu-[C(R')dbondC(PPh(2))C(PPh(2))doublebondC(R)(C(6)F(5))]M(C(6)F(5))(2)] (R=R'=Ph, Tol, M=Pt 6 a,c, M=Pd 7 a,c; M=Pt, R'=tBu, R=Ph 8, Tol 9) containing a bis(diphenylphosphanyl)butadienyl bridging ligand formed by an unprecedented sequential insertion reaction of two P-coordinated PPh(2)CtriplebondCR ligands into a PtbondC(6)F(5) bond. Although in solution the presence of coordinated solvent S (S=(thf)(x)(H(2)O)(y)) in 6, 7 is suggested by NMR spectroscopy, X-ray diffraction analyses of different crystals of the mixed complex [Pt(C(6)F(5))mu-[C(tBu)doublebondC(PPh(2))C(PPh(2))doublebondC(Tol)(C(6)F(5))]Pt(C(6)F(5))(2)] 9 unequivocally establish that in the solid state the steric crowding of the new diphenylbutadienyl ligand formed stabilizes an unusual coordinatively unsaturated T-shaped 3-coordinated platinum(II) center. Structure determinations of the mononuclear precursors cis-[Pt(C(6)F(5))(2)(PPh(2)CtriplebondCR)(2)] (R=Ph, tBu, Tol) have been carried out to evaluate the factors affecting the insertion processes. The reactions of the platinum complexes 6 towards neutral ligands (L=CO, py, PPh(2)H, CNtBu) in a 1:1 molar ratio afford related diplatinum derivatives 10-13, whereas treatment with CNtBu (1:2 molar ratio) or 2,2'-bipy (1:1 molar ratio) results in the opening of the chelating ring to give cis,cis-[Pt(C(6)F(5))(L)(2)mu-[1-kappaC(1):2-kappaPP'-C(R)doublebondC(PPh(2))C(PPh(2))doublebondC(R)(C(6)F(5))]Pt(C(6)F(5))(2)] (14, 15). The unsaturated or solvento
Tamiya, K.; Tamagaki, R.
1981-09-01
Based on the viewpoint that a typical π0 condensation is realized with the [ALS] (Alternating-Layer-Spin) structure of nucleon system, a framework to calculate the energy of neutron matter under such a new phase is presented in the reaction matrix theory. This enables us to treat both effects on equal footing; the long-range effect dominated by the OPEP tensor component with the enhancement due to the mixing of Δ(1236MeV) and the sort-range effect much influenced by repulsive core and spin-orbit force. Starting with the [ALS] model wave function constructed on the Bloch basis which assures to take the limit of no localization, we have the expressions for energy quantities expressed by the partial-wave contributions. This scheme provides a way to understand the mechanism of energy gain in the new phase, by making use of the notions of the ordinary unclear matter theory such as the potential picture and the partial waves. Some numerical examples are shown.
Borgia, Alessandro; Wensley, Beth G; Soranno, Andrea; Nettels, Daniel; Borgia, Madeleine B; Hoffmann, Armin; Pfeil, Shawn H; Lipman, Everett A; Clarke, Jane; Schuler, Benjamin
2012-01-01
Theory, simulations and experimental results have suggested an important role of internal friction in the kinetics of protein folding. Recent experiments on spectrin domains provided the first evidence for a pronounced contribution of internal friction in proteins that fold on the millisecond timescale. However, it has remained unclear how this contribution is distributed along the reaction and what influence it has on the folding dynamics. Here we use a combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, microfluidic mixing and denaturant- and viscosity-dependent protein-folding kinetics to probe internal friction in the unfolded state and at the early and late transition states of slow- and fast-folding spectrin domains. We find that the internal friction affecting the folding rates of spectrin domains is highly localized to the early transition state, suggesting an important role of rather specific interactions in the rate-limiting conformational changes.
Schatz, George C.; Amaee, B.; Connor, J. N. L.
1987-10-01
We describe a method for calculating cross sections for atom plus diatom reactive collisions based on the centrifugal sudden distorted wave (CSDW) approximation. This method is nearly exact at low energies where reactive cross sections are small. Representative CPU times are given for applications of the CSDW method to the Cl + HCl → ClH + Cl reaction using CDC 7600, Cyber 176, Cyber 205, Cray X-MP and Cray-2 computers. We also present differential cross sections for the Cl + HCl reaction and apply a simple semiclassical model which relates these cross sections to the partial wave reaction probabilities, and to the energy dependence of the reaction probabilities for zero total angular momentum. This model explains why the differential cross sections are backward peaked, and why the oscillatory cross sections seen in earlier, more approximate infinite order sudden calculations are not found in the present results at low energy.
Valiev, Marat; Garrett, Bruce C.; Tsai, Ming-Kang; Kowalski, Karol; Kathmann, Shawn M.; Schenter, Gregory K.; Dupuis, Michel
2007-08-01
We present an approach to calculate the free energy profile along a condensed-phase reaction path based on high-level electronic structure methods for the reactive region. The bulk of statistical averaging is shifted toward less expensive descriptions by using a hierarchy of representations that includes molecular mechanics, density functional theory, and coupled cluster theories. As an application of this approach we study the reaction of CHCl3 with OH- in aqueous solution.
Wang, Jin-Hua; Zhang, E.; Tang, Gui-Mei; Wang, Yong-Tao; Cui, Yue-Zhi; Ng, Seik Weng
2016-09-01
Three new metal coordination complexes, namely, [Co(BPO)2(H2O)4](BS)2(H2O)2 (1), [Co(BPO)2(H2O)4](ABS)2(H2O)2 (2), [Co(BPO)2(H2O)4](MBS)2(H2O)2 (3) [BPO=2,5-di(pyridin-4-yl)-1,3,4-oxadiazole, BS=benzenesulphonate, ABS=4-aminobenzenesulphonate, MBS=4-methylbenzenesulphonate] were obtained under hydrothermal conditions. Complexes 1-3 were structurally characterized by single-crystal X-ray diffraction, powder X-ray diffraction, IR and thermogravimetric analyses (TGA). All of them display a zero-dimensional motif, in which strong intermolecular hydrogen bonding interactions (O-H···O/N) and packing interactions (C-H···π and π···π) make them achieve a three-dimensional supramolecular architecture. The primary catalytic results of these three complexes show that high efficiency for the green synthesis of a variety of 3,4-dihydropyrimidin-2(1H)-ones was observed under solvent free conditions through Biginelli reactions. The present catalytic protocols exhibit advantages such as excellent yield, easy isolation, eco-friendly conditions, and short reaction time.
Bender, Jason D; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G; Schwartzentruber, Thomas; Candler, Graham V
2015-08-01
Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30,000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature T(v). The rate constant depends more strongly on T when T(v) is low, and it depends more strongly on T(v) when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = T(v) and a nonequilibrium test set in which T(v) test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as T(v) decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability's dependence on v weakens. In
Bender, Jason D.; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G.; Schwartzentruber, Thomas; Candler, Graham V.
2015-08-01
Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30 000 K were considered for each of the two temperatures. Over 2.4 × 109 trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature Tv. The rate constant depends more strongly on T when Tv is low, and it depends more strongly on Tv when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = Tv and a nonequilibrium test set in which Tv rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as Tv decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability's dependence on v weakens. In this way, as Tv decreases, rotational energy appears to compensate for the decline in average vibrational energy in
Solvent effect in the Walden inversion reactions
Jaume, J.; Lluch, J. M.; Oliva, A.; Bertrán, J.
1984-04-01
The solvent effect on the fluoride exchange reaction has been studied by means of ab initio calculations using the 3-21G basis set. It is shown that the motion of the solvent molecules is an important part of the reaction coordinate.
C. Yalcin; Gyürky, Gy.; Rauscher, T.; Kiss, G G; Özkan, N.; Güray, R T; Z. Halász; Szücs, T.; Fülöp, Zs.; Z. Korkulu; Somorjai, E.
2015-01-01
Astrophysical reaction rates, which are mostly derived from theoretical cross sections, are necessary input to nuclear reaction network simulations for studying the origin of $p$ nuclei. Past experiments have found a considerable difference between theoretical and experimental cross sections in some cases, especially for ($\\alpha$,$\\gamma$) reactions at low energy. Therefore, it is important to experimentally test theoretical cross section predictions at low, astrophysically relevant energies...
Lo, Warrick K C; Cavigliasso, Germán; Stranger, Robert; Crowley, James D; Blackman, Allan G
2014-04-07
The reaction of [Pt(N-N)2](2+) [N-N = 2,2'-bipyridine (bpy) or 4,4'-dimethyl-2,2'-bipyridine (4,4'-Me2bpy)] with phosphine ligands [PPh3 or PPh(PhSO3)2(2-)] in aqueous or methanolic solutions was studied by multinuclear ((1)H, (13)C, (31)P, and (195)Pt) NMR spectroscopy, X-ray crystallography, UV-visible spectroscopy, and high-resolution mass spectrometry. NMR spectra of solutions containing equimolar amounts of [Pt(N-N)2](2+) and phosphine ligand give evidence for rapid formation of long-lived, 5-coordinate [Pt(II)(N-N)2(phosphine)](n+) complexes. In the presence of excess phosphine ligand, these intermediates undergo much slower entry of a second phosphine ligand and loss of a bpy ligand to give [Pt(II)(N-N)(phosphine)2](n+) as the final product. The coordination of a phosphine ligand to the Pt(II) ion in the intermediate [Pt(N-N)2(phosphine)](n+) complexes is supported by the observation of (31)P-(195)Pt coupling in the (31)P NMR spectra. The 5-coordinate nature of [Pt(bpy)2{PPh(PhSO3)2}] is confirmed by X-ray crystallography. X-ray crystal structural analysis shows that the Pt(II) ion in [Pt(bpy)2{PPh(PhSO3)2}]·5.5H2O displays a distorted square pyramidal geometry, with one bpy ligand bound asymmetrically. These results provide strong support for the widely accepted associative ligand substitution mechanism for square planar Pt(II) complexes. X-ray structural characterization of the distorted square planar complex [Pt(bpy)(PPh3)2](ClO4)2 confirms this as the final product of the reaction of [Pt(bpy)2](2+) with PPh3 in CD3OD. The results of density functional calculations on [Pt(bpy)2](2+), [Pt(bpy)2(phosphine)](n+), and [Pt(bpy)(phosphine)2](n+) indicate that the bonding energy follows the trend of [Pt(bpy)(phosphine)2](n+) > [Pt(bpy)2(phosphine)](n+) > [Pt(bpy)2](2+) for stability and that the formation reactions of [Pt(bpy)2(phosphine)](n+) from [Pt(bpy)2](2+) and [Pt(bpy)(phosphine)2](n+) from [Pt(bpy)2(phosphine)](n+) are energetically favorable. These
Artun, Ozan, E-mail: ozanartun@yahoo.com; Aytekin, Hüseyin, E-mail: huseyinaytekin@gmail.com
2015-02-15
In this work, the excitation functions for production of medical radioisotopes {sup 122–125}I with proton, alpha, and deuteron induced reactions were calculated by two different level density models. For the nuclear model calculations, the Talys 1.6 code were used, which is the latest version of Talys code series. Calculations of excitation functions for production of the {sup 122–125}I isotopes were carried out by using the generalized superfluid model (GSM) and Fermi-gas model (FGM). The results have shown that generalized superfluid model is more successful than Fermi-gas model in explaining the experimental results.
Xu, Yi; Luo, Wen; Balabanski, Dimiter; Goriely, Stephane; Matei, Catalin; Tesileanu, Ovidiu
2017-09-01
The astrophysical p-process is an important way of nucleosynthesis to produce the stable and proton-rich nuclei beyond Fe which can not be reached by the s- and r-processes. In the present study, the astrophysical reaction rates of (γ,n), (γ,p), and (γ,α) reactions are computed within the modern reaction code TALYS for about 3000 stable and proton-rich nuclei with 12 reaction rates are very sensitive to the nuclear potential, and the better determination of nuclear potential would be important to reduce the uncertainties of reaction rates. Meanwhile, the Extreme Light Infrastructure-Nuclear Physics (ELI-NP) facility is being developed, which will provide the great opportunity to experimentally study the photonuclear reactions in p-process. Simulations of the experimental setup for the measurements of the photonuclear reactions 96Ru(γ,p) and 96Ru(γ,α) are performed. It is shown that the experiments of photonuclear reactions in p-process based on ELI-NP are quite promising.
Excel VBA 在 GPS 坐标转换计算中的应用%Application of Excel VBA For GPS Coordinate Transformation Calculation
吴伟军; 孟凡超
2013-01-01
为了使G PS 的观测成果在实际中得到更好的应用，必须把 G PS 观测得到的WGS-84坐标转换成实际需要的国家大地坐标或地方独立坐标。本文利用 Excel软件的宏程序VBA进行编程，实现不同坐标系之间坐标的相互转换。并且例举了坐标转换的算例，实验表明：所编程序可以快捷、准确、可靠地解决不同坐标间的转换问题，能够满足实际工作的需要。%In order to make better use of GPS in engineering ,WGS-84 coordinates ob-tained from GPS observations must be converted to the actual needs of the national geodetic coordinates or local independent coordinates .ExcellVBA macro software for programming is realized conversion between different coordinate system ,and examples are given .The pro-gram can be fast ,accurate and reliable to solution for conversion between different coordi-nate systems .
Chu, Tian-Shu; Han, Ke-Li; Hankel, Marlies; Balint-Kurti, Gabriel G
2007-06-01
The quantum wavepacket parallel computational code DIFFREALWAVE is used to calculate state-to-state integral and differential cross sections for the title reaction on the BKMP2 surface in the total energy range of 0.4-1.2 eV with D2 initially in its ground vibrational-rotational state. The role of Coriolis couplings in the state-to-state quantum calculations is examined in detail. Comparison of the results from calculations including the full Coriolis coupling and those using the centrifugal sudden approximation demonstrates that both the energy dependence and the angular dependence of the calculated cross sections are extremely sensitive to the Coriolis coupling, thus emphasizing the importance of including it correctly in an accurate state-to-state calculation.
Osz, Katalin
2008-12-01
A new calculation method to determine microscopic protonation processes from CD spectra measured at different pH and Cu(II):ligand ratios was developed and used to give the relative binding strengths for the three histidines of hsPrP(84-114), a 31-mer polypeptide modeling the N-terminal copper(II) binding region of human (homo sapiens) prion protein. Mutants of hsPrP(84-114) with two or one histidyl residues have also been synthesized and their copper(II) complexes studied by CD spectroscopy. The 1-His models were analyzed first, and the molar CD spectra for the different coordination modes on the different histidines were calculated using the general computational program PSEQUAD. These spectra were deconvoluted into the sum of Gaussian curves and used as a first parameter set to calculate the molar spectra for the different coordination modes (3N and 4N coordination) and coordination positions (His85, His96 and His111) of the 2-His peptides. The calculation method therefore does not require the direct use of CD spectra measured in the smaller peptide models. This is a significant improvement over earlier calculation methods. In the same runs, the stepwise deprotonation pK(mic) values were refined and the pH-dependent distribution of copper(II) between the two histidines was determined. The results revealed the high, but different copper(II) binding affinities of the three separate histidines in the following order: His85 copper(II) binding preferences are transferable from the 2-His peptides to the 3-His hsPrP(84-114).
Shi, Jiaqi; Qu, Ruijuan; Feng, Mingbao; Wang, Xinghao; Wang, Liansheng; Yang, Shaogui; Wang, Zunyao
2015-04-07
This study found that decabromodiphenyl ether (BDE 209) could be oxidized effectively by potassium permanganate (KMnO4) in sulfuric acid medium. A total of 15 intermediate oxidative products were detected. The reaction pathways were proposed, which primarily included cleavage of the ether bond to form pentabromophenol. Direct oxidation on the benzene ring also played an important role because hydroxylated polybrominated diphenyl ethers (PBDEs) were produced during the oxidation process. The degradation occurred dramatically in the first few minutes and fitted pseudo-first-order kinetics. Increasing the water content decelerated the reaction rate, whereas increasing the temperature facilitated the reaction. In addition, density functional theory (DFT) was employed to determine the frontier molecular orbital (FMO) and frontier electron density (FED) of BDE 209 and the oxidative products. The theoretical calculation results confirmed the proposed reaction pathways.
Liu, Jinyong; Han, Mengwei; Wu, Dimao; Chen, Xi; Choe, Jong Kwon; Werth, Charles J; Strathmann, Timothy J
2016-06-01
Rapid reduction of aqueous ClO4(-) to Cl(-) by H2 has been realized by a heterogeneous Re(hoz)2-Pd/C catalyst integrating Re(O)(hoz)2Cl complex (hoz = oxazolinyl-phenolato bidentate ligand) and Pd nanoparticles on carbon support, but ClOx(-) intermediates formed during reactions with concentrated ClO4(-) promote irreversible Re complex decomposition and catalyst deactivation. The original catalyst design mimics the microbial ClO4(-) reductase, which integrates Mo(MGD)2 complex (MGD = molybdopterin guanine dinucleotide) for oxygen atom transfer (OAT). Perchlorate-reducing microorganisms employ a separate enzyme, chlorite dismutase, to prevent accumulation of the destructive ClO2(-) intermediate. The structural intricacy of MGD ligand and the two-enzyme mechanism for microbial ClO4(-) reduction inspired us to improve catalyst stability by rationally tuning Re ligand structure and adding a ClOx(-) scavenger. Two new Re complexes, Re(O)(htz)2Cl and Re(O)(hoz)(htz)Cl (htz = thiazolinyl-phenolato bidentate ligand), significantly mitigate Re complex decomposition by slightly lowering the OAT activity when immobilized in Pd/C. Further stability enhancement is then obtained by switching the nanoparticles from Pd to Rh, which exhibits high reactivity with ClOx(-) intermediates and thus prevents their deactivating reaction with the Re complex. Compared to Re(hoz)2-Pd/C, the new Re(hoz)(htz)-Rh/C catalyst exhibits similar ClO4(-) reduction activity but superior stability, evidenced by a decrease of Re leaching from 37% to 0.25% and stability of surface Re speciation following the treatment of a concentrated "challenge" solution containing 1000 ppm of ClO4(-). This work demonstrates the pivotal roles of coordination chemistry control and tuning of individual catalyst components for achieving both high activity and stability in environmental catalyst applications.
Zhao, Bin [Center for Theoretical and Computational Chemistry, and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Sun, Zhigang, E-mail: zsun@dicp.ac.cn, E-mail: hguo@unm.edu [Center for Theoretical and Computational Chemistry, and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Guo, Hua, E-mail: zsun@dicp.ac.cn, E-mail: hguo@unm.edu [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States)
2014-06-21
A recently proposed transition-state wave packet method [R. Welsch, F. Huarte-Larrañaga, and U. Manthe, J. Chem. Phys. 136, 064117 (2012)] provides an efficient and intuitive framework to study reactive quantum scattering at the state-to-state level. It propagates a few transition-state wave packets, defined by the eigenfunctions of the low-rank thermal flux operator located near the transition state, into the asymptotic regions of the reactant and product arrangement channels separately using the corresponding Jacobi coordinates. The entire S-matrix can then be assembled from the corresponding flux-flux cross-correlation functions for all arrangement channels. Since the transition-state wave packets can be defined in a relatively small region, its transformation into either the reactant or product Jacobi coordinates is accurate and efficient. Furthermore, the grid/basis for the propagation, including the maximum helicity quantum number K, is much smaller than that required in conventional wave packet treatments of state-to-state reactive scattering. This approach is implemented for atom-diatom reactions using a time-dependent wave packet method and applied to the H + D{sub 2} reaction with all partial waves. Excellent agreement with benchmark integral and differential cross sections is achieved.
Zhao, Bin; Sun, Zhigang; Guo, Hua
2014-06-01
A recently proposed transition-state wave packet method [R. Welsch, F. Huarte-Larrañaga, and U. Manthe, J. Chem. Phys. 136, 064117 (2012)] provides an efficient and intuitive framework to study reactive quantum scattering at the state-to-state level. It propagates a few transition-state wave packets, defined by the eigenfunctions of the low-rank thermal flux operator located near the transition state, into the asymptotic regions of the reactant and product arrangement channels separately using the corresponding Jacobi coordinates. The entire S-matrix can then be assembled from the corresponding flux-flux cross-correlation functions for all arrangement channels. Since the transition-state wave packets can be defined in a relatively small region, its transformation into either the reactant or product Jacobi coordinates is accurate and efficient. Furthermore, the grid/basis for the propagation, including the maximum helicity quantum number K, is much smaller than that required in conventional wave packet treatments of state-to-state reactive scattering. This approach is implemented for atom-diatom reactions using a time-dependent wave packet method and applied to the H + D2 reaction with all partial waves. Excellent agreement with benchmark integral and differential cross sections is achieved.
Dodsworth, Jeremy A; McDonald, Austin I; Hedlund, Brian P
2012-08-01
To inform hypotheses regarding the relative importance of chemolithotrophic metabolisms in geothermal environments, we calculated free energy yields of 26 chemical reactions potentially supporting chemolithotrophy in two US Great Basin hot springs, taking into account the effects of changing reactant and product activities on the Gibbs free energy as each reaction progressed. Results ranged from 1.2 × 10(-5) to 3.6 J kg(-1) spring water, or 3.7 × 10(-5) to 11.5 J s(-1) based on measured flow rates, with aerobic oxidation of CH(4) or NH4 + giving the highest average yields. Energy yields calculated without constraining pH were similar to those at constant pH except for reactions where H(+) was consumed, which often had significantly lower yields when pH was unconstrained. In contrast to the commonly used normalization of reaction chemical affinities per mole of electrons transferred, reaction energy yields for a given oxidant varied by several orders of magnitude and were more sensitive to differences in the activities of products and reactants. The high energy yield of aerobic ammonia oxidation is consistent with previous observations of significant ammonia oxidation rates and abundant ammonia-oxidizing archaea in sediments of these springs. This approach offers an additional lens through which to view the thermodynamic landscape of geothermal springs.
周传佩; 陈文生; 刘义; 李林尉; 屈松生
2000-01-01
The reaction enthalpy of coordination reaction of lanthanum chloride with Glycine is determined by solution calorimetry in an isoperibel reaction calorimeter. The calormetric solvent is the solution of hydrochloric acid (2 mol·L- 1), a new thermochemical cycle is designed. According to the results, the following date:()(298.2 K)=- 4.310 kJ·mol- 1()(La(Gly)3Cl3· 5H2O, s, 298.2 K)=- 4222.93 kJ·mol- 1 were obtained.
温德才; 刘义; 胡立新; 李昕; 屈松生
1999-01-01
The reaction enthalpy of solid-solid coordination reaction of 8-hoxine with zinc acetate is determined by solution calorimetry in an isoperibel reaction calorimeter. The calorimetric solvent is the solution of hydrochloric acid (4 mol·L-1). According to the results, the value ΔrH(-○m)=-1.002 kJ·mol-1ΔfH(-○m)(Zn(oxin)2·H2O)=-582.123 kJ·mol-1 are recommended.
Dermenci, Alpay; Whittaker, Rachel E.; Gao, Yang; Cruz, Faben A.; Yu, Zhi-Xiang; Dong, Guangbin
2015-01-01
In this full article, detailed development of a catalytic decarbonylation of conjugated monoynones to synthesize disubstituted alkynes is described. The reaction scope and limitation has been thoroughly investigated, and a broad range of functional groups including heterocycles were compatible under the catalytic conditions. Mechanistic exploration via DFT calculations has also been executed. Through the computational study, a proposed catalytic mechanism has been carefully evaluated. These efforts are expected to serve as an important exploratory study for developing catalytic alkyne-transfer reactions via carbon−alkyne bond activation. PMID:26229587
Calculations of (n,2n reaction cross sections for 74,76,78,80,82Se up to 20 MeV
Şahan Halide
2016-01-01
Full Text Available In the present work, the excitation functions of (n,2n reactions for five isotopes of selenium (74,76,78,80,82Se are calculated using ALICE/ASH, EMPIRE-3.2.2, PCROSS, and TALYS 1.6 computer codes based on statistical model up to 20 MeV. The theoretical calculations provide information of the (n,2n excitation functions with the increasing target neutron number of selenium element. The calculated cross-sections were compared with experimental data from EXFOR and also with the crosssections estimated with semi empirical formula developed by Tet et al. (2008 [18]. Results show a reasonably good agreement between the calculations and the experimental data from literature.
Uitdehaag, Joost C.M.; Veen, Bart A. van der; Dijkhuizen, Lubbert; Elber, Ron; Dijkstra, Bauke W.
2001-01-01
Cyclodextrin glycosyltransferase (CGTase) is an enzyme belonging to the ol-amylase family that forms cyclodextrins (circularly linked oligosaccharides) from starch. X-ray work has indicated that this cyclization reaction of CGTase involves a 23-Angstrom movement of the nonreducing end of a linear ma
Tamao, Kohei
2008-01-01
Some synthetically useful transformations of organosilicon compounds have been developed since the mid 1970s, based on the new concept that the silicon-carbon bonds are activated toward electrophilic cleavage via the formation of penta- and hexa-coordinate species. This review mainly consists of the following aspects: (1) a general concept for the activation of the silicon-carbon bond via penta- and hexa-coordinate species, (2) synthetic application of hexa-coordinate organopentafluorosilicat...
Wei, Donghui; Fang, Lei; Tang, Mingsheng; Zhan, Chang-Guo
2013-10-31
Proteasome is the major component of the crucial non-lysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-O(γ). The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-O(γ), followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-N(z). Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-N(z) to Thr1-O(γ). According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3(b)) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally derived activation free energy of ∼18.3-19.4 kcal/mol, suggesting that the computational results are reasonable.
Juanes-Marcos, Juan Carlos; Althorpe, Stuart C
2005-05-22
We report quantum wave-packet calculations on the H+H(2) reaction, aimed at resolving the controversy over whether geometric phase (GP) effects can be observed in this reaction. Two sets of calculations are reported of the state-to-state reaction probabilities, and integral and differential cross sections (ICSs and DCSs). One set includes the GP using the vector potential approach of Mead and Truhlar; the other set neglects the phase. We obtain unequivocal agreement with recent results of Kendrick [J. Phys. Chem. A 107, 6739 (2003)], predicting GP effects in the state-to-state reaction probabilities, which cancel exactly on summing the partial waves to yield the ICS. Our results therefore contradict those of Kuppermann and Wu [Chem. Phys. Lett. 349 537 (2001)], which predicted pronounced GP effects in the cross sections. We also agree with Kendrick in predicting that there are no significant GP effects in the full DCS at energies below 1.8 eV, and in the partial (0
Choi, Sungjun; Sang, Byoung-In; Hong, Jongsup; Yoon, Kyung Joong; Son, Ji-Won; Lee, Jong-Ho; Kim, Byung-Kook; Kim, Hyoungchul
2017-01-01
High-temperature chemical reactions are ubiquitous in (electro) chemical applications designed to meet the growing demands of environmental and energy protection. However, the fundamental understanding and optimization of such reactions are great challenges because they are hampered by the spontaneous, dynamic, and high-temperature conditions. Here, we investigated the roles of metal catalysts (Pd, Ni, Cu, and Ag) in the high-temperature reverse water-gas shift (RWGS) reaction using in-situ surface analyses and density functional theory (DFT) calculations. Catalysts were prepared by the deposition-precipitation method with urea hydrolysis and freeze-drying. Most metals show a maximum catalytic activity during the RWGS reaction (reaching the thermodynamic conversion limit) with formate groups as an intermediate adsorbed species, while Ag metal has limited activity with the carbonate species on its surface. According to DFT calculations, such carbonate groups result from the suppressed dissociation and adsorption of hydrogen on the Ag surface, which is in good agreement with the experimental RWGS results.
Fasano, C.G.; Locher, M.P. (Paul Scherrer Inst., Villigen (Switzerland). Theory Group)
1991-02-01
We present a fully relativistic calculation for anti pd {yields} 5 {pi}p and anti pd {yields} 3 {pi}p that includes angular momentum and spin dynamics. We calculate the inclusive proton distributions from two diagrams: the leading 'tree' diagram, and the diagram for pion rescattering. Pion-nucleon rescattering proceeds through the {Delta} , in the Rarita-Swinger formalism, thus preserving the correct angular dependence. We use realistic parameterizations of the deuteron, keeping both the S and D states. The loop integrations for the rescattering amplitude and the phase space integrations have been done numerically. We find that the combined effects of a correct treatment of the rescattered pion and relativity are small in comparison with a simple non-relativistic calculation. (orig.).
Qi, Xiaotian; Liu, Song; Zhang, Tao; Long, Rong; Huang, Jun; Gong, Jianxian; Yang, Zhen; Lan, Yu
2016-09-16
Theoretical calculation was performed to study the chirality transfer in a newly reported intramolecular [3+2] cycloaddition of enal and alleno rhodium species, generated in situ from an enynol precursor. [3.3.0] bicyclic system which contains two bridgehead quaternary carbons that can be achieved, the chirality of which are controlled by those of the starting material, and the product stereoselectivity is only determined by the α-position of the acetylene moiety. Density functional theory calculations predicted that only the cis [3.3.0] bicyclic product could be generated, regardless of either erythro or threo substrate, which was also confirmed by experimental observations.
Wu Xing-Ju; Chen Xiang-Jun; Shan Xu; Chen Li-Qing; Xu Ke-Zun
2004-01-01
The triple differential cross section for the low-energy electron impact ionization of inner-valence 3s orbital of argon has been calculated using the modified distorted wave Born approximation in coplanar symmetric energy-sharing geometry. Satisfactory agreement between theory and experiment is achieved when the polarization and post-collisional interaction (PCI) are included in the calculations. It is shown that the polarization and PCI effects play a very important role in the case of argon at low incident energies.
Wiberg, Kenneth B
2014-11-21
The properties and reactions of compounds in which the O of dimethyl ether or acetone has been replaced by NH, PH, or AsH have been studied computationally using CBS-QB3, CBS-APNO, G4, and W1BD. The properties include the bond dissociation energies and ionization potentials, and the reactions include those with with protons, methyl cations, and lithium cations. The effect on keto-enol equilibria also was examined. In all cases there was good agreement with the available experimental data. The agreement between these methods suggests that the least computationally costly model (CBS-QB3) should be of general use in studying organic compounds. The double-bond dissociation enthalpies of CH2═XHn were linearly related to those of the corresponding CH3-XHn+1 single bonds with a slope of 2.5. With the exception of C-C, the order corresponded to the electronegativity of X, suggesting that the differences are largely determined by internal Coulombic interactions. The differences in the electronegativities of the heteroatoms are largely responsible for the differences in the properties and reactions. Oxygen has a significantly higher electronegativity than the others, and as a result, the oxygen-substituted compounds are often different than the others.
Ng, Maggie; Mok, Daniel K W; Lee, Edmond P F; Dyke, John M
2015-03-21
The reaction between atomic chlorine (Cl) and methyl nitrate (CH3ONO2) is significant in the atmosphere, as Cl is a key oxidant, especially in the marine boundary layer, and alkyl nitrates are important nitrogen-containing organic compounds, which are temporary reservoirs of the reactive nitrogen oxides NO, NO2 and NO3 (NOx). Four reaction channels HCl + CH2ONO2, CH3OCl + NO2, CH3Cl + NO3 and CH3O + ClNO2 were considered. The major channel is found to be the H abstraction channel, to give the products HCl + CH2ONO2. For all channels, geometry optimization and frequency calculations were carried out at the M06-2X/6-31+G** level, while relative electronic energies were improved to the UCCSD(T*)-F12/CBS level. The reaction barrier (ΔE(‡)0K) and reaction enthalpy (ΔH(RX)298K) of the H abstraction channel were computed to be 0.61 and -2.30 kcal mol(-1), respectively, at the UCCSD(T*)-F12/CBS//M06-2X/6-31+G** level. Reaction barriers (ΔE(‡)0K) for the other channels are more positive and these pathways do not contribute to the overall reaction rate coefficient in the temperature range considered (200-400 K). Rate coefficients were calculated for the H-abstraction channel at various levels of variational transition state theory (VTST) including tunnelling. Recommended ICVT/SCT rate coefficients in the temperature range 200-400 K are presented for the first time for this reaction. The values obtained in the 200-300 K region are particularly important as they will be valuable for atmospheric modelling calculations involving reactions with methyl nitrate. The implications of the results to atmospheric chemistry are discussed. Also, the enthalpies of formation, ΔHf,298K, of CH3ONO2 and CH2ONO2 were computed to be -29.7 and 19.3 kcal mol(-1), respectively, at the UCCSD(T*)-F12/CBS level.
Calculation of Prompt Fission Neutron Spectrum for 233U（n, f） Reaction by Semi-empirical Method
CHEN; Yong-jing; LIU; Ting-jin; SHU; Neng-chuan
2013-01-01
The prompt fission neutron spectra for neutron-induced fission of 233U for low energy neutron(below 6 MeV)are calculated using the nuclear evaporation theory with a semi-empirical method,in which the partition of the total excitation energy between the fission fragments for the nth+233U fission
Shankar, Bhaskaran; Elumalai, Palani; Shanmugam, Ramasamy; Singh, Virender; Masram, Dhanraj T; Sathiyendiran, Malaichamy
2013-09-16
A one-pot, multicomponent, coordination-driven self-assembly approach was used to synthesize the first examples of neutral bridging phosphine oxide donor-based supramolecular coordination complexes. The complexes were self-assembled from a fac-Re(CO)3 acceptor, an anionic bridging O donor, and a neutral soft phosphine or hard phosphine oxide donor.
Calculation of (p,γ and (p,α nuclear reaction cross sections in stars up to 10 MeV
Tel Eyyup
2016-01-01
Full Text Available In Knowledge of the proton-proton (p-p chain and CNO cycle are required for the evolution of main sequence stars during the early formation of the universe. In this study, we summarized the excitation functions of (p,γ and (p,α reactions for 7Be(p,γ8B, 12C(p,γ13N, 13C(p,γ14N, 14N(p,γ15O and 15N(p,α15O in p-p chain and CNO cycle using EMPIRE and TALYS computer up to 10 MeV. The calculated data on nuclear fusion cross sections in hydrogen-burning stars were compared with theoretical TENDL-2014 and ENDF/B-VII data from EXFOR. The calculation results show closed agreement between the calculations and the data from literature.
Calculation of (p,γ) and (p,α) nuclear reaction cross sections in stars up to 10 MeV
Tel, Eyyup; Sahan, Muhittin; Sarpun, Ismail Hakki; Okur, Sureyya Gulistan
2016-11-01
In Knowledge of the proton-proton (p-p) chain and CNO cycle are required for the evolution of main sequence stars during the early formation of the universe. In this study, we summarized the excitation functions of (p,γ) and (p,α) reactions for 7Be(p,γ)8B, 12C(p,γ)13N, 13C(p,γ)14N, 14N(p,γ)15O and 15N(p,α)15O in p-p chain and CNO cycle using EMPIRE and TALYS computer up to 10 MeV. The calculated data on nuclear fusion cross sections in hydrogen-burning stars were compared with theoretical TENDL-2014 and ENDF/B-VII data from EXFOR. The calculation results show closed agreement between the calculations and the data from literature.
Benstead J.
2016-01-01
Full Text Available The surrogate reaction method may be used to determine the cross section for neutron induced reactions not accessible through standard experimental techniques. This is achieved by creating the same compound nucleus as would be expected in the desired reaction, but through a different incident channel, generally a direct transfer reaction. So far, the surrogate technique has been applied with reasonable success to determine the fission cross section for a number of actinides, but has been less successful when applied to other reactions, e.g. neutron capture, due to a ‘spin-parity mismatch’. This mismatch, between the spin and parity distributions of the excited levels of the compound nucleus populated in the desired and surrogate channels, leads to differing decay probabilities and hence reduces the validity of using the surrogate method to infer the cross section in the desired channel. A greater theoretical understanding of the expected distribution of levels excited in both the desired and surrogate channels is therefore required in order to attempt to address this mismatch and allow the method to be utilised with greater confidence. Two neutron transfer reactions, e.g. (p,t, which allow the technique to be utilised for isotopes further removed from the line of stability, are the subject of this study. Results are presented for the calculated distribution of compound nucleus states populated in 90Zr, via the 90Zr(p,t90Zr reaction, and are compared against measured data at an incident proton energy of 28.56 MeV.
An end-on-coordinated As4 tetrahedron.
Schwarzmaier, Christoph; Timoshkin, Alexey Y; Scheer, Manfred
2013-07-15
One time only: The reaction of [Cp*Ru(dppe)Cl] with the potent As4 transfer reagent [Ag(η(2)-As4)2](+)[pftb](-) leads to [Cp*Ru(dppe)(η(1)-As4)](+)[pftb](-) with an unprecedented end-on-coordinated As4 tetrahedron. Reaction with a second cationic ruthenium complex fragment does not lead to a second end-on coordination but to the cleavage of one basal As-As bond. This behavior, which differs from its phosphorus analogues, is rationalized by DFT calculations.
Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun
2011-05-14
We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.
Schmidt, M.W.
1982-12-01
The Full Optimized Reaction Space (FORS) model is used for the theoretical calculation of molecular potential energy surfaces involved in chemical reactions. The FORS model is applied to two polyatomic reactions: the dihydrogen exchange between ethane and etylene, and the formation and dissolution of dioxirane and dioxymethane. The former reaction is found to possess a high barrier, in spite of its symmetry allowed nature. The latter reaction involves significant configuration mixing as methylene and oxygen react to form, successively, dioxirane, dioxymethane, and hydrogen and carbon dioxide. Finally, FORS wavefunctions can be expressed in terms of a basis of antisymmetrized products of atomic state functions, using the predominantly atomic projected localized orbitals. The atoms in molecules analysis permits the incorporation of data from atomic spectra into the molecular Hamiltonian to achieve the IntraAtomic Correlation Correction (IACC). The IACC scheme is illustrated for a few small diatomics (H/sub 2/, NH, F/sub 2/), and is shown to yield more accurate results than the uncorrected FORS wavefunctions.
Kiselev, Vitaly G; Gritsan, Nina P
2014-09-11
The primary thermolysis reactions of a promising insensitive explosive 1,1-diamino-2,2-dinitroethylene (DADNE, FOX-7) have been studied in the gas phase at a high level of theory (CCSD(T)-F12/aVTZ). Our calculations revealed that none of the conventional reactions (C-NO2 bond fission, nitro-nitrite and nitro-aci-nitro rearrangements) dominate thermolysis of FOX-7. On the contrary, two new decomposition pathways specific for this particular species that commenced with enamino-imino isomerization and intramolecular cyclization were found instead to be more feasible energetically. The activation barriers of these primary isomerization reactions were calculated to be 48.4 and 28.8 kcal/mol, while the activation energies of the overall decomposition pathways are predicted to be ∼49 and ∼56 kcal/mol, respectively. The new pathways can also be relevant for a wide series of unsaturated hydrocarbons substituted with both nitro- and amino-groups (e.g., triaminotrinitrobenzene, TATB).
环己烯催化环氧化反应体系热力学参数计算%Cyclohexene epoxidation reaction calculated thermodynamic parameters
徐燏; 蒋登高
2013-01-01
The thermodynamics property of this catalytic epoxidation reaction system was analysed in this paper. Thermodynamic basic datas (the heat capacity at constant pressure, formation heat and gibbs free energy) of components in the reaction system were calculated by using Joback genetic contribution method. In the same time, Chemical reaction equilibrium constants were calculated. These are the important basic datas for the industrialized production process design.% 本文对所研究的催化环氧化反应体系进行了热力学性质的有关分析，采用 Joback 基因贡献法估算了反应体系中相关组分的恒压热容、生成热和吉布斯自由能等热力学基础数据，并计算了相关反应的平衡常数，为其工业化生产过程的设计提供了相关基础数据。
Adamescu, Adrian; Hamilton, Ian P; Al-Abadleh, Hind A
2014-07-31
Aromatic organoarsenicals, such as p-arsanilic acid (pAsA), are still used today as feed additives in the poultry and swine industries in developing countries. Through the application of contaminated litter as a fertilizer, these compounds enter the environment and interact with reactive soil components such as iron and aluminum oxides. Little is known about these surface interactions at the molecular level. We report density functional theory (DFT) calculations on the energies, optimal geometries, and vibrational frequencies for hydrated pAsA/iron oxide complexes, as well as changes in Gibbs free energy, enthalpy, and entropy for various types of ligand exchange reactions leading to both inner- and outer-sphere complexes. Similar calculations using arsenate are also shown for comparison, along with activation barriers and transition state geometries between inner-sphere complexes. Minimum energy calculations show that the formation of inner- and outer-sphere pAsA/iron oxide complexes is thermodynamically favorable, with the monodentate mononuclear complexes being the most favorable. Interatomic As-Fe distances are calculated to be between 3.3 and 3.5 Å for inner-sphere complexes and between 5.2 and 5.6 Å for outer-sphere complexes. In addition, transition state calculations show that activation energies greater than 23 kJ/mol are required to form the bidentate binuclear pAsA/iron oxide complexes, and that formation of arsenate bidentate binuclear complexes is thermodynamically -rather than kinetically- driven. Desorption thermodynamics using phosphate ions show that reactions are most favorable using HPO4(2-) species. The significance of our results for the overall surface complexation mechanism of pAsA and arsenate is discussed.
Zhang, Ju-Wen; Kan, Xiao-Min; Liu, Bin-Qiu; Liu, Guo-Cheng; Tian, Ai-Xiang; Wang, Xiu-Li
2015-11-02
Three series of copper-lanthanide/lanthanide coordination polymers (CPs) Ln(III) Cu(II) Cu(I) (bct)3 (H2 O)2 [Ln=La (1), Ce (2), Pr (3), Nd (4), Sm (5), Eu (6), Gd (7), Tb (8), Dy (9), Er (10), Yb (11), and Lu (12), H2 bct=2,5-bis(carboxymethylmercapto)-1,3,4-thiadiazole acid], Ln(III) Cu(I) (bct)2 [Ln=Ce (2 a), Pr (3 a), Nd (4 a), Sm (5 a), Eu (6 a), Gd (7 a), Tb (8 a), Dy (9 a), Er (10 a), Yb (11 a), and Lu (12 a)], and Ln(III) 2 (bct)3 (H2 O)5 [Ln=La (1 b), Ce (2 b), Pr (3 b), Nd (4 b), Sm (5 b), Eu (6 b), Gd (7 b), Tb (8 b), and Dy (9 b)] have been successfully constructed under hydrothermal conditions by modulating the reaction time. Structural characterization has revealed that CPs 1-12 possess a unique one-dimensional (1D) strip-shaped structure containing two types of double-helical chains and a double-helical channel. CPs 2 a-12 a show a three-dimensional (3D) framework formed by Cu(I) linking two types of homochiral layers with double-helical channels. CPs 1 b-9 b exhibit a 3D framework with single-helical channels. CPs 6 b and 8 b display visible red and green luminescence of the Eu(III) and Tb(III) ions, respectively, sensitized by the bct ligand, and microsecond-level lifetimes. CP 8 b shows a rare magnetic transition between short-range ferromagnetic ordering at 110 K and long-range ferromagnetic ordering below 10 K. CPs 9 a and 9 b display field-induced single-chain magnet (SCM) and/or single-molecule magnet (SMM) behaviors, with Ueff values of 51.7 and 36.5 K, respectively.
Thakur Meenu
2015-01-01
Full Text Available The reaction mechanism of 19F + 232Th and 28Si + 232Th systems populating the near-super-heavy compound nuclei 251Es and 260Rf respectively are investigated using neutron multiplicity as a probe. The prescission neutron multiplicities of these compound nuclei are calculated at different excitation energies using a statistical model code. These calculations are performed using the Bohr-Wheeler transition state fission width as well as the dissipative dynamical fission width based on the Kramers’ prescription. For 19F + 232Th system, the measured yield of pre-scission is compared with the statistical model calculations for the decay of a compound nucleus in the excitation energy range of 54-90 MeV. The comparison between the measured and the calculated values indicates that the Bohr-Wheeler fission width underestimates the pre-scission neutron yield and a large amount of dissipation strength is required to reproduce the experimental pre-scission neutron multiplicities. The excitation energy dependence of the fitted values of the dissipation coefficient is also discussed. In addition, exploratory statistical model calculations of pre-scission neutron multiplicity for the 28Si + 232Th system are presented in the above range of excitation energy.
Kaplan, A., E-mail: abdullahkaplan@sdu.edu.tr [Süleyman Demirel Univesity, Faculty of Arts and Sciences, Department of Physics (Turkey); Sarpün, İ. H. [Afyon Kocatepe University, Faculty of Arts and Sciences, Department of Physics (Turkey); Aydın, A. [Kırıkkale University, Faculty of Arts and Sciences, Department of Physics (Turkey); Tel, E. [Osmaniye Korkut Ata University, Faculty of Arts and Sciences, Department of Physics (Turkey); Çapalı, V.; Özdoǧan, H. [Süleyman Demirel Univesity, Faculty of Arts and Sciences, Department of Physics (Turkey)
2015-01-15
There are several level density models that can be used to predict photo-neutron cross sections. Some of them are Constant Temperature + Fermi Gas Model (CTFGM), Back-Shifted Fermi Gas Model (BSFM), Generalized Superfluid Model (GSM), Hartree-Fock-Bogoliubov microscopic Model (HFBM). In this study, the theoretical photo-neutron cross sections produced by (γ, 2n) reactions for several eveneven lanthanide nuclei such as {sup 140,142}Ce, {sup 142,144,146,148,150}Nd, {sup 144,148,150,152,154}Sm, and {sup 160}Gd have been calculated on the different level density models as mentioned above by using TALYS 1.6 and EMPIRE 3.1 computer codes for incident photon energies up to 30 MeV. The obtained results have been compared with each other and available experimental data existing in the EXFOR database. Generally, at least one level density model cross-section calculations are in agreement with the experimental results for all reactions except {sup 144}Sm(γ, 2n){sup 142}Sm along the incident photon energy, TALYS 1.6 BSFM option for the level density model cross-section calculations can be chosen if the experimental data are not available or are improbable to be produced due to the experimental difficulty.
无
2001-01-01
Taking the CNC machining for the spatial barrel-cam with rectilinear translating and a conical roller follower as an example, the calculation method and the law of the profile error △n influenced by the tool error AR is given.
Orbital Energy-Based Reaction Analysis of SN2 Reactions
Takao Tsuneda
2016-07-01
Full Text Available An orbital energy-based reaction analysis theory is presented as an extension of the orbital-based conceptual density functional theory. In the orbital energy-based theory, the orbitals contributing to reactions are interpreted to be valence orbitals giving the largest orbital energy variation from reactants to products. Reactions are taken to be electron transfer-driven when they provide small variations for the gaps between the contributing occupied and unoccupied orbital energies on the intrinsic reaction coordinates in the initial processes. The orbital energy-based theory is then applied to the calculations of several S N2 reactions. Using a reaction path search method, the Cl− + CH3I → ClCH3 + I− reaction, for which another reaction path called “roundabout path” is proposed, is found to have a precursor process similar to the roundabout path just before this SN2 reaction process. The orbital energy-based theory indicates that this precursor process is obviously driven by structural change, while the successor SN2 reaction proceeds through electron transfer between the contributing orbitals. Comparing the calculated results of the SN2 reactions in gas phase and in aqueous solution shows that the contributing orbitals significantly depend on solvent effects and these orbitals can be correctly determined by this theory.
Lan, Yu; Zou, Lufeng; Cao, Yang; Houk, K N
2011-12-01
Theoretical calculations were performed on the 1,3-dipolar cycloaddition reactions of 24 1,3-dipoles with ethylene and acetylene. The 24 1,3-dipoles are of the formula X≡Y(+)-Z(-) (where X is HC or N, Y is N, and Z is CH(2), NH, or O) or X═Y(+)-Z(-) (where X and Z are CH(2), NH, or O and Y is NH, O, or S). The high-accuracy G3B3 method was employed as the reference. CBS-QB3, CCSD(T)//B3LYP, SCS-MP2//B3LYP, B3LYP, M06-2X, and B97-D methods were benchmarked to assess their accuracies and to determine an accurate method that is practical for large systems. Several basis sets were also evaluated. Compared to the G3B3 method, CBS-QB3 and CCSD(T)/maug-cc-pV(T+d)Z//B3LYP methods give similar results for both activation and reaction enthalpies (mean average deviation, MAD, < 1.5 kcal/mol). SCS-MP2//B3LYP and M06-2X give small errors for the activation enthalpies (MAD < 1.5 kcal/mol), while B3LYP has MAD = 2.3 kcal/mol. SCS-MP2//B3LYP and B3LYP give the reasonable reaction enthalpies (MAD < 5.0 kcal/mol). The B3LYP functional also gives good results for most 1,3-dipoles (MAD = 1.9 kcal/mol for 17 common 1,3-dipoles), but the activation and reaction enthalpies for ozone and sulfur dioxide are difficult to calculate by any of the density functional methods.
Fahr, Askar; Halpern, Joshua B.; Tardy, Dwight C.
2007-01-01
Pressure-dependent product yields have been experimentally determined for the cross-radical reaction C2H5 + C2H3. These results have been extended by calculations. It is shown that the chemically activated combination adduct, 1-C4H8*, is either stabilized by bimolecular collisions or subject to a variety of unimolecular reactions including cyclizations and decompositions. Therefore the "apparent" combination/disproportionation ratio exhibits a complex pressure dependence. The experimental studies were performed at 298 K and at selected pressures between about 4 Torr (0.5 kPa) and 760 Torr (101 kPa). Ethyl and vinyl radicals were simultaneously produced by 193 nm excimer laser photolysis of C2H5COC2H3 or photolysis of C2H3Br and C2H5COC2H5. Gas chromatograph/mass spectrometry/flame ionization detection (GC/MS/FID) were used to identify and quantify the final reaction products. The major combination reactions at pressures between 500 (66.5 kPa) and 760 Torr are (1c) C2H5 + C2H3 yields 1-butene, (2c) C2H5 + C2H5 yields n-butane, and (3c) C2H3 + C2H3 yields 1,3-butadiene. The major products of the disproportionation reactions are ethane, ethylene, and acetylene. At moderate and lower pressures, secondary products, including propene, propane, isobutene, 2-butene (cis and trans), 1-pentene, 1,4-pentadiene, and 1,5-hexadiene are also observed. Two isomers of C4H6, cyclobutene and/or 1,2-butadiene, were also among the likely products. The pressure-dependent yield of the cross-combination product, 1-butene, was compared to the yield of n-butane, the combination product of reaction (2c), which was found to be independent of pressure over the range of this study. The [ 1-C4H8]/[C4H10] ratio was reduced from approx.1.2 at 760 Torr (101 kPa) to approx.0.5 at 100 Torr (13.3 kPa) and approx.0.1 at pressures lower than about 5 Torr (approx.0.7 kPa). Electronic structure and RRKM calculations were used to simulate both unimolecular and bimolecular processes. The relative importance
Ptushenko, Vasily V; Cherepanov, Dmitry A; Krishtalik, Lev I
2015-12-01
Continuum electrostatic calculation of the transfer energies of anions from water into aprotic solvents gives the figures erroneous by order of magnitude. This is due to the hydrogen bond disruption that suggests the necessity to reconsider the traditional approach of the purely electrostatic calculation of the transfer energy from water into protein. In this paper, the method combining the experimental estimates of the transfer energies from water into aprotic solvent and the electrostatic calculation of the transfer energies from aprotic solvent into protein is proposed. Hydrogen bonds between aprotic solvent and solute are taken into account by introducing an imaginary aprotic medium incapable to form hydrogen bonds with the solute. Besides, a new treatment of the heterogeneous intraprotein dielectric permittivity based on the microscopic protein structure and electrometric measurements is elaborated. The method accounts semi-quantitatively for the electrostatic effect of diverse charged amino acid substitutions in the donor and acceptor parts of the photosynthetic bacterial reaction center from Rhodobacter sphaeroides. Analysis of the volatile secondary acceptor site QB revealed that in the conformation with a minimal distance between quinone QB and Glu L 212 the proton uptake upon the reduction of QB is prompted by Glu L 212 in alkaline and by Asp L 213 in slightly acidic regions. This agrees with the pH dependences of protonation degrees and the proton uptake. The method of pK calculation was applied successfully also for dissociation of Asp 26 in bacterial thioredoxin.
Papajak, Ewa; Truhlar, Donald G
2011-01-11
We present sets of convergent, partially augmented basis set levels corresponding to subsets of the augmented "aug-cc-pV(n+d)Z" basis sets of Dunning and co-workers. We show that for many molecular properties a basis set fully augmented with diffuse functions is computationally expensive and almost always unnecessary. On the other hand, unaugmented cc-pV(n+d)Z basis sets are insufficient for many properties that require diffuse functions. Therefore, we propose using intermediate basis sets. We developed an efficient strategy for partial augmentation, and in this article, we test it and validate it. Sequentially deleting diffuse basis functions from the "aug" basis sets yields the "jul", "jun", "may", "apr", etc. basis sets. Tests of these basis sets for Møller-Plesset second-order perturbation theory (MP2) show the advantages of using these partially augmented basis sets and allow us to recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large systems. Similar truncations in the diffuse space can be performed for the aug-cc-pVxZ, aug-cc-pCVxZ, etc. basis sets.
张灵翠; 阮永丰; 王丹丽; 邱春霞
2011-01-01
A novel method named “coordination reaction method” was developed to fabricate zinc oxide (ZnO) nanowire arrays. The ZnO nanowires in the holes of the porous anodic alumina (PAA) template were synthesized with ammonia as a coordination agent and zinc- amino complex as a precursor by the coordination reaction method. The growth mechanism of ZnO nanowires and the conditions of the coordination reaction were also discussed. The microstructures and morphology of PAA/ZnO assembly were characterized by X-ray diffractometer, scanning electron microscope and transmission electron microscope. The results show that the ZnO nanowires prepared are a polycrystalline structure, and the nanowire arrays possess a periodic array of structure with the same morphological characteristics of PAA template.%研究了一种新型的制备氧化锌(ZnO)纳米线的配位反应法.以氨水为配位剂、氨水与可溶性的锌盐反应配制的锌氨配合物溶液为前驱液,在多孔阳极氧化铝(porous anodic alumina,PAA)模板中沉积了ZnO纳米线.研究了ZnO纳米线的生长机理和配位反应条件.用X射线衍射仪、扫描电子显微镜和透射电子显微镜对PAA/ZnO组装体的组成和形貌进行了表征.结果表明:所制备的ZnO纳米线为多晶结构,纳米线阵列具有周期排列结构,与多孔氧化铝模板形态特征一致.
Cao, Jun
2015-06-01
In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π* transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π* excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S1(1ππ*) and S2(1nNπ*) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.
Thimm, Wulf; Gradert, Christian; Broda, Henning; Wennmohs, Frank; Neese, Frank; Tuczek, Felix
2015-10-05
A series of density functional theory (DFT) calculations on the full [Mo(HIPT)N3N] catalyst are performed to obtain an energy profile of the Schrock cycle. This is a continuation of our earlier investigation of this cycle in which the bulky hexaisopropyterphenyl (HIPT) substituents of the ligand were replaced by hydrogen atoms (Angew. Chem., Int. Ed. 2005, 44, 5639). In an effort to provide a treatment that is as converged as possible from a quantum-chemical point of view, the present study now fully takes the HIPT moieties into account. Moreover, structures and energies are calculated with a near-saturated basis set, leading to models with 280 atoms and 4850 basis functions. Solvent and scalar relativistic effects have been treated using the conductor-like screening model and zeroth-order regular approximation, respectively. Free reaction enthalpies are evaluated using the PBE and B3LYP functionals. A comparison to the available experimental data reveals much better agreement with the experiment than preceding DFT treatments of the Schrock cycle. In particular, free reaction enthalpies of reduction steps and NH3/N2 exchange are now excellently reproduced.
Rodríguez-Kessler, P. L., E-mail: peter.rodriguez@ipicyt.edu.mx [Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí 78216 (Mexico); Rodríguez-Domínguez, A. R. [Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78000 (Mexico)
2015-11-14
Size and structure effects on the oxygen reduction reaction on Pt{sub N} clusters with N = 12–13 atoms have been investigated using periodic density functional theory calculations with the generalized gradient approximation. To describe the catalytic activity, we calculated the O and OH adsorption energies on the cluster surface. The oxygen binding on the 3-fold hollow sites on stable Pt{sub 12−13} cluster models resulted more favorable for the reaction with O, compared with the Pt{sub 13}(I{sub h}) and Pt{sub 55}(I{sub h}) icosahedral particles, in which O binds strongly. However, the rate-limiting step resulted in the removal of the OH species due to strong adsorptions on the vertex sites, reducing the utility of the catalyst surface. On the other hand, the active sites of Pt{sub 12−13} clusters have been localized on the edge sites. In particular, the OH adsorption on a bilayer Pt{sub 12} cluster is the closest to the optimal target; with 0.0-0.2 eV weaker than the Pt(111) surface. However, more progress is necessary to activate the vertex sites of the clusters. The d-band center of Pt{sub N} clusters shows that the structural dependence plays a decisive factor in the cluster reactivity.
Cao, Jun, E-mail: caojunbnu@mail.bnu.edu.cn [Guizhou Provincial Key Laboratory of Computational Nano-Material Sciences, Guizhou Normal College, Guiyang, Guizhou 550018, China and Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China)
2015-06-28
In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π{sup *} transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π{sup *} excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S{sub 1}({sup 1}ππ{sup *}) and S{sub 2}({sup 1}n{sub N}π{sup *}) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.
陈东平; 孔超; 韩彦霞; 侯丽杰; 仵博万; 王永成
2013-01-01
The reaction mechanism between Co+in ground state and excited state with CO and N 2O has been studied using the den-sity functional theory(DFT )at UB3LYP/6-311+G(2d)level.The geometries for reactant,the transition states and the products were completely optimized.All the transition states were verified by the vibration analysis and the intrinsic reaction coordinate calcula -tions.For each stationary point,single-point energy calculations were carried out by UB 3LYP/6-311++G(3df,3pd)method.The po-tential energy curve-crossing diagrams were investigated for state correlation between triplet and quintuplet state in the reaction of Co+with CO and N2 O.The results showed that the reaction is a two-step reaction and the reaction mechanism was an insertion-elimi-nation mechanism.Every step occurs spin-forbidden between the triplet and quintuplet potential energy surfaces ( PESs).There is two crossing points(CP)between the triplet and quintuplet potential energy surfaces ,which would play a significant role in this cata-lytic reaction.The minimum energy crossing points(MECP)that obtained by the mathematical algorithm proposed by Harvey et al . has been also employed .The values of the SOC constants at MECP indicate that the spin crossing process in this reaction can occur efficiently due to the large SOC involved .%采用密度泛函UB3LYP/6-311＋G（2d）方法计算研究了Co ＋在基态和激发态下与N 2O的反应机理，全参数优化了反应势能面上各驻点的几何构型，用频率分析方法和内禀反应坐标（ IRC）方法对过渡态进行了验证，并用UB3LYP/6-311＋＋G（3df，3pd）、单点垂直激发、Harvey 等人的方法分别进行各驻点单点能校正，三重态和五重态反应势能面两个交叉点 CP确定，最低能量交叉点（ MECP ）的优化及MECP处相应的自旋-轨道耦合常数（ SOC）计算，计算结果表明，该反应为两步反应，较大的SOC值说明了在势能面上的翻转能够有
Algorithm for calculating the coordinates of unsymmetrical easement curve%非对称缓和曲线坐标计算方法
闵世平; 林宗坚
2011-01-01
本文重点阐述高等级公路非标准缓和曲线的施工放样测量.缓和曲线是设置在直线和圆曲线之间的一种线型,起缓和过渡作用,其目的在于保证车辆由直线进入圆曲线(或由圆曲线进入直线)时的横向稳定,缓和曲线的曲率半径随曲线长度的增加而均匀连续地变小,本文综合了各种情况下的曲线计算,给出了直接计算和间接计算两种计算方法,并用C编写了计算程序,给出了计算算例.%This text focused on the construction and lofting of unsymmetrical easement curve for high standard highway. Easement curve is a kind of linetypes between circle curve and line, the purpose is to transfer alleviation and ensure lateral stability when the car drives from line to circle curve. Its Curve Radius will be uniform continuity lessening as its length increases. Through research for all kinds of curves, two kinds of new calculation methods were found as direct method and indirect method. At the same time, the paper developed the software for the calculation methods and showed example by C.
Lipschutz, Michael I; Tilley, T Don
2014-07-01
Recently, the development of more sustainable catalytic systems based on abundant first-row metals, especially nickel, for cross-coupling reactions has attracted significant interest. One of the key intermediates invoked in these reactions is a Ni(III) -alkyl species, but no such species that is part of a competent catalytic cycle has yet been isolated. Herein, we report a carbon-carbon cross-coupling system based on a two-coordinate Ni(II) -bis(amido) complex in which a Ni(III) -alkyl species can be isolated and fully characterized. This study details compelling experimental evidence of the role played by this Ni(III) -alkyl species as well as those of other key Ni(I) and Ni(II) intermediates. The catalytic cycle described herein is also one of the first examples of a two-coordinate complex that competently catalyzes an organic transformation, potentially leading to a new class of catalysts based on the unique ability of first-row transition metals to accommodate two-coordinate complexes.
Parkhurst, David L.; Appelo, C.A.J.
2013-01-01
PHREEQC version 3 is a computer program written in the C and C++ programming languages that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC implements several types of aqueous models: two ion-association aqueous models (the Lawrence Livermore National Laboratory model and WATEQ4F), a Pitzer specific-ion-interaction aqueous model, and the SIT (Specific ion Interaction Theory) aqueous model. Using any of these aqueous models, PHREEQC has capabilities for (1) speciation and saturation-index calculations; (2) batch-reaction and one-dimensional (1D) transport calculations with reversible and irreversible reactions, which include aqueous, mineral, gas, solid-solution, surface-complexation, and ion-exchange equilibria, and specified mole transfers of reactants, kinetically controlled reactions, mixing of solutions, and pressure and temperature changes; and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for differences in composition between waters within specified compositional uncertainty limits. Many new modeling features were added to PHREEQC version 3 relative to version 2. The Pitzer aqueous model (pitzer.dat database, with keyword PITZER) can be used for high-salinity waters that are beyond the range of application for the Debye-Hückel theory. The Peng-Robinson equation of state has been implemented for calculating the solubility of gases at high pressure. Specific volumes of aqueous species are calculated as a function of the dielectric properties of water and the ionic strength of the solution, which allows calculation of pressure effects on chemical reactions and the density of a solution. The specific conductance and the density of a solution are calculated and printed in the output file. In addition to Runge-Kutta integration, a stiff ordinary differential equation solver (CVODE) has been included for kinetic calculations with multiple rates that occur at widely different time scales
Shi, Qicun; Meroueh, Samy O; Fisher, Jed F; Mobashery, Shahriar
2008-07-23
Penicillin-binding protein 5 (PBP 5) of Escherichia coli hydrolyzes the terminal D-Ala-D-Ala peptide bond of the stem peptides of the cell wall peptidoglycan. The mechanism of PBP 5 catalysis of amide bond hydrolysis is initial acylation of an active site serine by the peptide substrate, followed by hydrolytic deacylation of this acyl-enzyme intermediate to complete the turnover. The microscopic events of both the acylation and deacylation half-reactions have not been studied. This absence is addressed here by the use of explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations. The potential-energy surface for the acylation reaction, based on MP2/6-31+G(d) calculations, reveals that Lys47 acts as the general base for proton abstraction from Ser44 in the serine acylation step. A discrete potential-energy minimum for the tetrahedral species is not found. The absence of such a minimum implies a conformational change in the transition state, concomitant with serine addition to the amide carbonyl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for progression to the acyl-enzyme intermediate. Molecular dynamics simulations indicate that transiently protonated Lys47 is the proton donor in tetrahedral intermediate collapse to the acyl-enzyme species. Two pathways for this proton transfer are observed. One is the direct migration of a proton from Lys47. The second pathway is proton transfer via an intermediary water molecule. Although the energy barriers for the two pathways are similar, more conformers sample the latter pathway. The same water molecule that mediates the Lys47 proton transfer to the nitrogen of the departing D-Ala is well positioned, with respect to the Lys47 amine, to act as the hydrolytic water in the deacylation step. Deacylation occurs with the formation of a tetrahedral intermediate over a 24 kcal x mol(-1) barrier. This barrier is approximately 2
Iyer, C G; Languillon, J; Ramanujam, K; Tarabini-Castellani, G; De las Aguas, J T; Bechelli, L M; Uemura, K; Martinez Dominguez, V; Sundaresan, T
1971-01-01
The treatment of lepra reactions constitutes one of the most serious problems in leprosy. For this reason, the first reports in 1965 of the favourable results obtained with thalidomide aroused considerable interest and led WHO, in 1967, to carry out a trial with the co-operation of four centres. A short-term double-blind trial was designed to study the effect of thalidomide, in comparison with acetylsalicylic acid, in the treatment of acute lepra reactions in male lepromatous patients. Acetylsalicylic acid was used instead of a placebo because of its antipyretic and analgesic activity. Because of the severe adverse reactions that may be caused by thalidomide, mainly the teratogenic effects, only males were included in the trial.The results of this short-term study seem to confirm previous reports of the efficacy of thalidomide and indicate that acetylsalicylic acid also seems to be helpful in the management of certain symptoms of lepra reactions.
Wang, Shengkai; Dames, Enoch E; Davidson, David F; Hanson, Ronald K
2014-11-06
The rate constant of the H-abstraction reaction of formaldehyde (CH2O) by hydrogen atoms (H), CH2O + H = H2 + HCO, has been studied behind reflected shock waves with use of a sensitive mid-IR laser absorption diagnostic for CO, over temperatures of 1304-2006 K and at pressures near 1 atm. C2H5I was used as an H atom precursor and 1,3,5-trioxane as the CH2O precursor, to generate a well-controlled CH2O/H reacting system. By designing the experiments to maintain relatively constant H atom concentrations, the current study significantly boosted the measurement sensitivity of the target reaction and suppressed the influence of interfering reactions. The measured CH2O + H rate constant can be expressed in modified Arrhenius from as kCH2O+H(1304-2006 K, 1 atm) = 1.97 × 10(11)(T/K)(1.06) exp(-3818 K/T) cm(3) mol(-1)s(-1), with uncertainty limits estimated to be +18%/-26%. A transition-state-theory (TST) calculation, using the CCSD(T)-F12/VTZ-F12 level of theory, is in good agreement with the shock tube measurement and extended the temperature range of the current study to 200-3000 K, over which a modified Arrhenius fit of the rate constant can be expressed as kCH2O+H(200-3000 K) = 5.86 × 10(3)(T/K)(3.13) exp(-762 K/T) cm(3) mol(-1)s(-1).
Minyaev, Ruslan M., E-mail: minyaev@ipoc.sfedu.ru [Institute of Physical and Organic Chemistry, Southern Federal University, 194/2 Stachka Ave., Rostov-on-Don 344090 (Russian Federation); Quapp, Wolfgang; Schmidt, Benjamin [Leipzig University, Mathematical Institute, Augustusplatz, D-04109 Leipzig (Germany); Getmanskii, Ilya V.; Koval, Vitaliy V. [Institute of Physical and Organic Chemistry, Southern Federal University, 194/2 Stachka Ave., Rostov-on-Don 344090 (Russian Federation)
2013-11-08
Highlights: • High level quantum chemical calculations are performed for two S{sub N}2 reactions. • The calculated gradient reaction pathways for reactions have an unusual behavior. • An unusual saddle point of index two lies on the gradient reaction path. • VRI points have been detected by using Newton trajectories for the reaction path. • An infinite flow of gradient lines emanates at three equivalent product minima. - Abstract: Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the S{sub N}2 nucleophile substitution reactions CH{sub 4} + H{sup −} → CH{sub 4} + H{sup −} and CH{sub 4} + F{sup −} → CH{sub 3}F + H{sup −}. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.
The Convex Coordinates of the Symmedian Point
Boyd, J. N.; Raychowdhury, P. N.
2006-01-01
In this note, we recall the convex (or barycentric) coordinates of the points of a closed triangular region. We relate the convex and trilinear coordinates of the interior points of the triangular region. We use the relationship between convex and trilinear coordinates to calculate the convex coordinates of the symmedian point of the triangular…
Li, Xian-Ying; Hu, Shi-Min
2013-02-01
Harmonic functions are the critical points of a Dirichlet energy functional, the linear projections of conformal maps. They play an important role in computer graphics, particularly for gradient-domain image processing and shape-preserving geometric computation. We propose Poisson coordinates, a novel transfinite interpolation scheme based on the Poisson integral formula, as a rapid way to estimate a harmonic function on a certain domain with desired boundary values. Poisson coordinates are an extension of the Mean Value coordinates (MVCs) which inherit their linear precision, smoothness, and kernel positivity. We give explicit formulas for Poisson coordinates in both continuous and 2D discrete forms. Superior to MVCs, Poisson coordinates are proved to be pseudoharmonic (i.e., they reproduce harmonic functions on n-dimensional balls). Our experimental results show that Poisson coordinates have lower Dirichlet energies than MVCs on a number of typical 2D domains (particularly convex domains). As well as presenting a formula, our approach provides useful insights for further studies on coordinates-based interpolation and fast estimation of harmonic functions.
Bonnet, L; Corchado, J
2015-01-01
Ten years ago, Liu and co-workers measured pair-correlated product speed and angular distributions for the OH+CH4/CD4 reactions at the collision energy of ~ 10 kcal/mol [B. Zhang, W. Shiu, J. J. Lin and K. Liu, J. Chem. Phys 122, 131102 (2005); B. Zhang, W. Shiu and K. Liu, J. Phys. Chem. A 2005, 109, 8989]. Recently, two of us could semi-quantitatively reproduce these measurements by performing full-dimensional classical trajectory calculations in a quantum spirit on an ab-initio potential energy surface of their own [J. Espinosa-Garcia and J. C. Corchado, Theor Chem Acc, 2015, 134, 6 ; J. Phys. Chem. B, Article ASAP, DOI: 10.1021/acs.jpcb.5b04290]. The goal of the present work is to show that these calculations can be significantly improved by adding a few more constraints to better comply with the experimental conditions. Overall, the level of agreement between theory and experiment is remarkable considering the large dimensionality of the processes under scrutiny.
Laundal, K M
2016-01-01
Geospace phenomena such as the aurora, plasma motion, ionospheric currents and associated magnetic field disturbances are highly organized by Earth's main magnetic field. This is due to the fact that the charged particles that comprise space plasma can move almost freely along magnetic field lines, but not across them. For this reason it is sensible to present such phenomena relative to Earth's magnetic field. A large variety of magnetic coordinate systems exist, designed for different purposes and regions, ranging from the magnetopause to the ionosphere. In this paper we review the most common magnetic coordinate systems and describe how they are defined, where they are used, and how to convert between them. The definitions are presented based on the spherical harmonic expansion coefficients of the International Geomagnetic Reference Field (IGRF) and, in some of the coordinate systems, the position of the Sun which we show how to calculate from the time and date. The most detailed coordinate systems take the...
Schrenk, Claudio; Gerke, Birgit; Pöttgen, Rainer; Clayborne, Andre; Schnepf, Andreas
2015-05-26
Chemistry that uses metalloid tin clusters as a starting material is of fundamental interest towards understanding the reactivity of such compounds. Since we identified {Sn10[Si(SiMe3)3]4}(2-) 7 as an ideal candidate for such reactions, we present a further step in the understanding of metalloid tin cluster chemistry. In contrast to germanium chemistry, ligand elimination seems to be a major reaction channel, which leads to the more open metalloid cluster {Sn10[Si(SiMe3)3]3}(-) 9, in which the Sn core is only shielded by three Si(SiMe3)3 ligands. Compound 9 is obtained through different routes and is crystallised together with two different countercations. Besides the structural characterisation of this novel metalloid tin cluster, the electronic structure is analysed by (119)Sn Mössbauer spectroscopy. Additionally, possible reaction pathways are discussed. The presented first step into the chemistry of metalloid tin clusters thus indicates that, with respect to metalloid germanium clusters, more reaction channels are accessible, thereby leading to a more complex reaction system.
Holm-Jørgensen, Jacob Rørdam; Jensen, Mikael; Bjerrum, Morten
2011-01-01
To enable utilization of the broad potential of copper isotopes in nuclear medicine, rapid and robust chelation of the copper is required. Bowl adamanzanes (bicyclic tetraaza ligands) can form kinetically stable copper complexes, but they are usually formed at low rates unless high pH values...... and high temperatures are applied. We have investigated the effects of the variation in the pH, different anions, and UV irradiation on the chelation rate. UV spectra of mixtures of Cu2+ and [24.31]adz in water show the existence of a longlived two-coordinated copper(II) intermediate (only counting...
Fu, Yuwei; Rong, Mingzhe; Yang, Kang; Yang, Aijun; Wang, Xiaohua; Gao, Qingqing; Liu, Dingxin; Murphy, Anthony B.
2016-04-01
SF6 is widely used in electrical equipment as an insulating gas. In the presence of an electric arc, partial discharge (PD) or spark, SF6 dissociation products (such as SF2, SF3 and SF4) react with the unavoidable gas impurities (such as water vapor and oxygen), electrodes and surrounding solid insulation materials, forming several toxic and corrosive byproducts. The main stable decomposition products are SO2F, SO2F2 and SOF2, which have been confirmed experimentally to have a direct relationship with discharge faults, and are thus expected to be useful in the fault diagnosis of power equipment. Various studies have been performed of the main SF6 decomposition species and their concentrations under different types of faults. However, most of the experiments focused on the qualitative analysis of the relationship between the stable products and discharge faults. Although some theoretical research on the formation of main SF6 derivatives have been carried out using chemical kinetics models, the basic data (chemical reactions and their rate constants) adopted in the model are inaccurate and incomplete. The complex chemical reactions of SF6 with the impurities are ignored in most cases. The rate constants of some reactions obtained at ambient temperature or in a narrow temperature range are adopted in the models over a far greater range, for example up to 12 000 K, due to the difficulty in the experimental measurement and theoretical estimation of rate coefficients, particularly at high temperatures. Therefore, improved theoretical models require not only the consideration of additional SF6 decomposition reactions in the presence of impurities but also on improved values of rate constants. This paper is devoted to determining the rate constants of the chemical reactions relating to the main byproducts of SF6 decomposition in SF6 gas-insulated power equipment: SO2F, SOF2 and SO2F2. Quantum chemistry calculations with density functional theory, conventional
Coordinate an Attack Using the Calculator
Kranz, Sharie R.; Amato, Carlo A.; Freudenthal, Eric A.
2013-01-01
In this culture of instantaneous technology, students are familiar with immediate feedback. To maintain student engagement, it is vital for teachers to create similarly interactive experiences. Student-centered instruction is important in connecting students to key mathematical concepts. If the connection is not obvious, they may be unaware of…
Gudowska, I; Brahme, A; Andreo, P; Gudowski, W; Kierkegaard, J
1999-09-01
The absorbed dose due to photonuclear reactions in soft tissue, lung, breast, adipose tissue and cortical bone has been evaluated for a scanned bremsstrahlung beam of end point 50 MeV from a racetrack accelerator. The Monte Carlo code MCNP4B was used to determine the photon source spectrum from the bremsstrahlung target and to simulate the transport of photons through the treatment head and the patient. Photonuclear particle production in tissue was calculated numerically using the energy distributions of photons derived from the Monte Carlo simulations. The transport of photoneutrons in the patient and the photoneutron absorbed dose to tissue were determined using MCNP4B; the absorbed dose due to charged photonuclear particles was calculated numerically assuming total energy absorption in tissue voxels of 1 cm3. The photonuclear absorbed dose to soft tissue, lung, breast and adipose tissue is about (0.11-0.12)+/-0.05% of the maximum photon dose at a depth of 5.5 cm. The absorbed dose to cortical bone is about 45% larger than that to soft tissue. If the contributions from all photoparticles (n, p, 3He and 4He particles and recoils of the residual nuclei) produced in the soft tissue and the accelerator, and from positron radiation and gammas due to induced radioactivity and excited states of the nuclei, are taken into account the total photonuclear absorbed dose delivered to soft tissue is about 0.15+/-0.08% of the maximum photon dose. It has been estimated that the RBE of the photon beam of 50 MV acceleration potential is approximately 2% higher than that of conventional 60Co radiation.
Laundal, K. M.; Richmond, A. D.
2017-03-01
Geospace phenomena such as the aurora, plasma motion, ionospheric currents and associated magnetic field disturbances are highly organized by Earth's main magnetic field. This is due to the fact that the charged particles that comprise space plasma can move almost freely along magnetic field lines, but not across them. For this reason it is sensible to present such phenomena relative to Earth's magnetic field. A large variety of magnetic coordinate systems exist, designed for different purposes and regions, ranging from the magnetopause to the ionosphere. In this paper we review the most common magnetic coordinate systems and describe how they are defined, where they are used, and how to convert between them. The definitions are presented based on the spherical harmonic expansion coefficients of the International Geomagnetic Reference Field (IGRF) and, in some of the coordinate systems, the position of the Sun which we show how to calculate from the time and date. The most detailed coordinate systems take the full IGRF into account and define magnetic latitude and longitude such that they are constant along field lines. These coordinate systems, which are useful at ionospheric altitudes, are non-orthogonal. We show how to handle vectors and vector calculus in such coordinates, and discuss how systematic errors may appear if this is not done correctly.
Chemical potential and reaction electronic flux in symmetry controlled reactions.
Vogt-Geisse, Stefan; Toro-Labbé, Alejandro
2016-07-15
In symmetry controlled reactions, orbital degeneracies among orbitals of different symmetries can occur along a reaction coordinate. In such case Koopmans' theorem and the finite difference approximation provide a chemical potential profile with nondifferentiable points. This results in an ill-defined reaction electronic flux (REF) profile, since it is defined as the derivative of the chemical potential with respect to the reaction coordinate. To overcome this deficiency, we propose a new way for the calculation of the chemical potential based on a many orbital approach, suitable for reactions in which symmetry is preserved. This new approach gives rise to a new descriptor: symmetry adapted chemical potential (SA-CP), which is the chemical potential corresponding to a given irreducible representation of a symmetry group. A corresponding symmetry adapted reaction electronic flux (SA-REF) is also obtained. Using this approach smooth chemical potential profiles and well defined REFs are achieved. An application of SA-CP and SA-REF is presented by studying the Cs enol-keto tautomerization of thioformic acid. Two SA-REFs are obtained, JA'(ξ) and JA'' (ξ). It is found that the tautomerization proceeds via an in-plane delocalized 3-center 4-electron O-H-S hypervalent bond which is predicted to exist only in the transition state (TS) region. © 2016 Wiley Periodicals, Inc.
Tan, Rui Shan; Yan, Wei; Lin, Shi Ying
2017-01-01
A computational study for the title reaction is carried out employing recent ab initio potential energy surface. J = 0 reaction probability is obtained using both quasiclassical trajectory (QCT) and wave packet methods. The total and state resolved integral as well as differential cross sections are also obtained by means of QCT method. Dynamics of the title reaction shows qualitative similarity with its isotopic counterpart, the H + CaCl reaction, but quantitatively, reactivity is significantly enhanced in the title reaction. In addition, the effect of initial rotational state excitation on H + CaCl reaction is investigated.
Knutz, B. C.; Berg, R. W.; Hjuler, H. A.; Bjerrum, N. J.
1993-12-01
The battery systems: Al/NaCl-AlCl3-Al2 X3/Ni-felt (X = S, Se, Te) and the corresponding system without chalcogen have been studied experimentally at 175 C. Charge/discharge experiments, performed on cells with NaCl saturated melts, show that advantages with regard to rate capability and cyclability can be obtained with systems containing dissolved chalcogen compared with the chalcogen-free system. Exchange of chalcogen between cathode and electrolyte during cycling was confirmed by performing gravimetric analysis and Raman spectroscopy of the electrolytes. Cathode reactions were studied by coulometric titrations (performed on cells with slightly acidic NaCl-AlCl3 melts and small amounts of chalcogen) and compared with model calculations. Cells containing chalcogen revealed at least three voltage plateaus during cycling. The lowest plateau is associated with formation/decomposition of essentially Ni(y)S(z) an d Ni(y)Se(z) in the sulfide and selenide system, respectively. Cells containing selenide revealed extra capacity below the Ni(y) Se(z)-plateau, most probably associated with a Al(v)Ni(y)Se(z) compound. On the second plateau of sulfide systems NiCl2 or a Ni(y)S(z) Cl(2y - 2z) compound with y greater than (4.4 +/- 0.2), z is formed during charging. Reduction of the formed compound to Ni takes place via consumption of sodium chloride.
Efficient calculation of rate constants: Downhill versus uphill sampling
Klenin, Konstantin V.
2014-08-01
The classical transition state theory (TST), together with the notion of transmission coefficient, provides a useful tool for calculation of rate constants for rare events. However, in complex biomolecular reactions, such as protein folding, it is difficult to find a good reaction coordinate, so the transition state is ill-defined. In this case, other approaches are more popular, such as the transition interface sampling (TIS) and the forward flux sampling (FFS). Here, we show that the algorithms developed in the frames of TIS and FFS can be successfully applied, after a modification, for calculation of the transmission coefficient. The new procedure (which we call "downhill sampling") is more efficient in comparison with the traditional TIS and FFS ("uphill sampling") even if the reaction coordinate is bad. We also propose a new computational scheme that combines the advantages of TST, TIS, and FFS.
Nyiri, Agnes
2005-07-01
-relativistic heavy ion reactions is an important hadronic observable sensitive to the early stages of system evolution. The flow analysis involves the particles, which have already been frozen out. Therefore, to perform realistic flow computations from the Multi Module Model we need a complete freeze out description and a well identified freeze out surface. However, the freeze out module is still not ready. Although we have not yet been able to evaluate collective flow using the Multi Module Model, the method and code for the calculation of flow components has been worked out in an independent module. This module is completed and can be coupled to the previous modules when those are ready for use. In order to test the code, we have calculated directed and elliptic flow from a tilted, ellipsoidally expanding source using a simple, blast wave type of model. This model was developed directly for this aim based on Buda-Lund hydro models. Although, this oversimplified blast wave model is not suitable to reproduce the experimental data--which will be an important task in the future to check our Multi Module Model--it has provided us with important information. We have found that the directed flow, is very sensitive to the correct identification of the reaction plane included the determination of the impact parameter vector, and can be misinterpreted by some experimental methods. We have shown that misidentification of the reaction plane may even set the directed flow to zero by construction. We have presented results of the rapidity dependence of the directed flow, v1, and elliptic flow, v2, furthermore, the transverse momentum dependence of v2. We have also investigated the dependence of the flow pattern on the initial geometry of the fireball by calculating flow components from two ellipsoidal sources with the same thermodynamical properties but different shape. The code determining the freeze out hypersurface should still be improved in order to avoid inaccuracies in the further
Nyiri, Agnes
2005-07-01
-relativistic heavy ion reactions is an important hadronic observable sensitive to the early stages of system evolution. The flow analysis involves the particles, which have already been frozen out. Therefore, to perform realistic flow computations from the Multi Module Model we need a complete freeze out description and a well identified freeze out surface. However, the freeze out module is still not ready. Although we have not yet been able to evaluate collective flow using the Multi Module Model, the method and code for the calculation of flow components has been worked out in an independent module. This module is completed and can be coupled to the previous modules when those are ready for use. In order to test the code, we have calculated directed and elliptic flow from a tilted, ellipsoidally expanding source using a simple, blast wave type of model. This model was developed directly for this aim based on Buda-Lund hydro models. Although, this oversimplified blast wave model is not suitable to reproduce the experimental data--which will be an important task in the future to check our Multi Module Model--it has provided us with important information. We have found that the directed flow, is very sensitive to the correct identification of the reaction plane included the determination of the impact parameter vector, and can be misinterpreted by some experimental methods. We have shown that misidentification of the reaction plane may even set the directed flow to zero by construction. We have presented results of the rapidity dependence of the directed flow, v1, and elliptic flow, v2, furthermore, the transverse momentum dependence of v2. We have also investigated the dependence of the flow pattern on the initial geometry of the fireball by calculating flow components from two ellipsoidal sources with the same thermodynamical properties but different shape. The code determining the freeze out hypersurface should still be improved in order to avoid inaccuracies in the further
Meana-Pañeda, Rubén; Truhlar, Donald G; Fernández-Ramos, Antonio
2011-03-07
We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH(3)OH+H→CH(2)OH+H(2) (R1) reaction and the CH(3)OH+H→CH(3)O+H(2) (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298≤T (K)≤2500 and that anharmonic effects on the torsional mode about the C-O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions.
R Baldik; H Aytekin; E Tel
2013-02-01
In this study, the pre-equilibrium and equilibrium calculations of cross-sections of 89Y(, ), 90Zr$(p, xn)$ and 94Mo(, ) reactions, which were used for the production of 89Zr, 90Nb and 94Tc positron-emitting radioisotopes, have been investigated. Pre-equilibrium calculations have been performed at different proton incident energies by using the hybrid, geometry-dependent-hybrid and full exciton models. The Weisskopf–Ewing model is used for calculating the equilibrium effects at the same incident energies. The calculated results have been discussed and compared with the experimental results.
A semiclassical theory of electron transfer reactions in Condon approximation and beyond
Kuznetsov, A. M.; Sokolov, V. V.; Ulstrup, Jens
2001-01-01
The effect of the modulation of the electronic wave functions by configurational fluctuations of the molecular environment on the kinetic parameters of electron transfer reactions is discussed. A self-consistent algorithm for the calculation of the potential profile along the reaction coordinate...
屈稳太; 应蓓华; 董凤莲
2014-01-01
Calculation of large rigid body pose and its high precision control was studied herein .Ai‐ming at the 6-DOF large rigid body pose alignment system ,a fast calculation approach to the pose and a high precision multi-axis coordinating control system was presented .Firstly ,mathematic models of large rigid body pose calculation were established respectively on a global frame which was found on the basic platform and a body-fixed frame system which was found on the center of the large rigid body .By detecting the initial positions and the final positions of four marks on the large rigid body ,the displacement increments of three coordinates of the four supports could be easily calculated .Then ,a compensation of synchronization error integration technology was proposed for the large rigid body pose alignment system .By the technology ,the precision and speed of large rigid pose alignment could be improved significantly .The simulation results show that the proposed approach is rapid and effec‐tive ,the control algorithm has guiding significance for engineering applications of large rigid body pose alignment .%大刚体的姿态计算及其高精度控制是飞机、舰船等大型机器总装生产线的关键技术。针对一种六自由度的大刚体的姿态控制系统提出一种快速的姿态计算方法和高精度的多轴协调控制方法。以基础平台建立固定坐标系，以大刚体的中心建立连体坐标系，在此基础上建立大刚体姿态计算数学模型，通过测量大刚体上4个靶标的初始位置和目标位置，就可计算出大刚体4个支撑柱的三坐标的位移增量；在多轴同步控制技术中，引入同步误差积分补偿方法（CSEI），通过同步误差在相反方向的控制作用，可显著提高大刚体姿态调整的速度和精度。仿真表明，所提出的姿态计算方法和 CSEI 控制方法快速有效，对工程应用具有指导意义。
白宁
2011-01-01
针对深水管道铺设中滚轮支撑坐标难以确定的问题,开发了一种能够建立精细的托管架模型及自动获得最优化的托管架形状和滚轮高度的计算程序.应用结果表明,本文方法能够有效弥补传统管道铺设设计方法的缺陷,大大提高设计效率和可靠性.%In deep water pipeline laying analysis, exact roller support coordinates are often required but difficult to obtain. A calculation program which can build the precise stinger model and obtain automatically the optimized stinger profile and roller support heights has been developed. The program application result shows that the method in this paper can improve the traditional design procedure effectively and increase design efficiency and reliability obviously.
Chen, Chi-Shian; Yeh, Wen-Yann
2010-05-14
[(2,6-(Ph(2)P(o-C(6)H(4))CH=N)(2)C(5)H(3)N)(2)Cu(2)](BF(4))(2) (2) has been prepared by treating 2,6-(Ph(2)P(o-C(6)H(4))CH=N)(2)C(5)H(3)N (1) with [Cu(NCMe)(4)]BF(4). Reaction of 2 and [Ph(3)PNPPh(3)]NO(2) produces (2,6-(Ph(2)P(o-C(6)H(4))CH=N)(2)C(5)H(3)N)Cu(NO(2)) (3), with the nitrite ligand in a unique eta(2)-O,O coordination mode. Protonation of 3 releases NO gas, which mimics the reactivity of the Type 2 Cu-NiRs.
REN,Yi-Xia; CHEN,San-Ping; GAO,Sheng-Li
2007-01-01
A new three-dimensional coordination polymer, [Ho(5-nip)(phen)(NO3)(DMF)] (5-nip=5-nitroisophthalic acid and phen=1,10-phenanthroline), was prepared and characterized by single crystal X-ray diffraction, elemental analysis, IR spectrum and DTG-DSC techniques. The results show that the title complex crystallizes in space group P2/m with a= 1.0906(3) nm, b=1.2804 (3) nm, c= 1.6987(4) nm,β=91.400(5)°, Z=4, Dc= 1.931 Mg/m3, F(000)=1352. Each Ho(Ⅲ) ion is nine-coordinated by one chelating bidentate and two monodentate bridging carboxylate groups, one chelating bidentate NO3- anion, one DMF molecule and one 1,10-phenanthroline molecule. The complex is constructed with one-dimensional ribbons featuring dinuclear units and the one-dimensional ribbons are further assembled into two-dimensional networks by strong π-π stacking interactions with the distance of 0.327 nm,then the networks are arranged into three-dimensional structure according to ABAB fashion. The complex exhibits high stability up to 600 ℃. Its enthalpy change of formation of the reaction in liquid-phase in solvent DMF was measured using an RD496-Ⅲ type microcalorimeter with a value of (-11.016±0.184) kJ·mol-1.
Lu Zl, Zhong-lin; Duan Cy, Chun-ying; Tian Yp, Yu-peng; You Xz, Xiao-zeng; Huang Xy, Xiao-ying
1996-04-10
The titled compound, (tris(2-aminoethyl)amine)(4,5-diazafluoren-9-one) copper(II) perchlorate, [Cu(C(6)H(18)N(4))(C(11)H(6)N(2)O)(ClO(4))(2)], 1, has been designed, synthesized, and characterized. The electronic and ESR spectra are very different from those of [Cu(tren)L](2+) complexes where L is monodentate ligand. The X-ray analysis revealed that the complex crystallizes in the monoclinic space group P2(1)/c, with a = 10.726(6) Å, b = 14.921(7) Å, c = 14.649(4) Å, beta = 95.13(3) degrees, and Z = 4. The copper(II) ion is coordinated by four nitrogen atoms from tris(2-aminoethyl)amine (tren) and two nitrogen atoms from 4,5-diazafluoren-9-one (dzf) to form an unusual six-coordinate (4 + 1 + 1') geometry. The structure is very rare, and to our knowledge, it is the first example of an asymmetric bidentate phenanthroline derivative metal complex. The structure could be used as a model of the associative complex in the ligand-exchange and ligand-substitution reactions of [Cu(tren)L](2+) and the catalytic mechanisms of enzymes involving copper sites. From the electronic and variable-temperature ESR spectra in solution, the possible mechanism of these reactions has also been proposed. As a comparison, the complex [Cu(tren)(ImH)(ClO(4))(2)], 2, was also synthesized and characterized, where ImH is imidazole.
2017-01-01
A critical step toward the rational design of new catalysts that achieve selective and efficient reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed reaction mechanism including kinetics and product selectivity as a function of pH and applied potential for known systems. To accomplish this, we apply ab initio molecular metadynamics simulations (AIMμD) for the water/Cu(100) system with five layers of the explicit solvent under a potential of −0.59 V [reversible hydrogen electrode (RHE)] at pH 7 and compare with experiment. From these free-energy calculations, we determined the kinetics and pathways for major products (ethylene and methane) and minor products (ethanol, glyoxal, glycolaldehyde, ethylene glycol, acetaldehyde, ethane, and methanol). For an applied potential (U) greater than −0.6 V (RHE) ethylene, the major product, is produced via the Eley–Rideal (ER) mechanism using H2O + e–. The rate-determining step (RDS) is C–C coupling of two CO, with ΔG‡ = 0.69 eV. For an applied potential less than −0.60 V (RHE), the rate of ethylene formation decreases, mainly due to the loss of CO surface sites, which are replaced by H*. The reappearance of C2H4 along with CH4 at U less than −0.85 V arises from *CHO formation produced via an ER process of H* with nonadsorbed CO (a unique result). This *CHO is the common intermediate for the formation of both CH4 and C2H4. These results suggest that, to obtain hydrocarbon products selectively and efficiency at pH 7, we need to increase the CO concentration by changing the solvent or alloying the surface. PMID:28167767
A. Ball
Overview From a technical perspective, CMS has been in “beam operation” state since 6th November. The detector is fully closed with all components operational and the magnetic field is normally at the nominal 3.8T. The UXC cavern is normally closed with the radiation veto set. Access to UXC is now only possible during downtimes of LHC. Such accesses must be carefully planned, documented and carried out in agreement with CMS Technical Coordination, Experimental Area Management, LHC programme coordination and the CCC. Material flow in and out of UXC is now strictly controlled. Access to USC remains possible at any time, although, for safety reasons, it is necessary to register with the shift crew in the control room before going down.It is obligatory for all material leaving UXC to pass through the underground buffer zone for RP scanning, database entry and appropriate labeling for traceability. Technical coordination (notably Stephane Bally and Christoph Schaefer), the shift crew and run ...
Quitterer, Felix
2015-04-11
IspG is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. Its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. Using a moderate reducing agent as well as an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the IspG catalyzed conversion of 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate (MEcPP) to (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate (HMBPP). In addition, the enzyme’s structure was determined in complex with several inhibitors. These results, combined with recent electron paramagnetic resonance data, allowed us to deduce a detailed and complete IspG catalytic mechanism which describes all stages from initial ring opening to formation of HMBPP via discrete radical and carbanion intermediates. The data presented in this article provide a guide for the design of selective drugs against many pro- and eukaryotic pathogens to which the non-mevalonate pathway is essential for survival and virulence.
Li, Yang; Xiao, Jie; Shubina, Tatyana E; Chen, Min; Shi, Ziliang; Schmid, Martin; Steinrück, Hans-Peter; Gottfried, J Michael; Lin, Nian
2012-04-11
We investigated the coordination self-assembly and metalation reaction of Cu with 5,10,15,20-tetra(4-pyridyl)porphyrin (2HTPyP) on a Au(111) surface by means of scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory calculations. 2HTPyP was found to interact with Cu through both the peripheral pyridyl groups and the porphyrin core. Pairs of pyridyl groups from neighboring molecules coordinate Cu(0) atoms, which leads to the formation of a supramolecular metal-organic coordination network. The network formation occurs at room temperature; annealing at 450 K enhances the process. The interaction of Cu with the porphyrin core is more complex. At room temperature, formation of an initial complex Cu(0)-2HTPyP is observed. Annealing at 450 K activates an intramolecular redox reaction, by which the coordinated Cu(0) is oxidized to Cu(II) and the complex Cu(II)TPyP is formed. The coordination network consists then of Cu(II) complexes linked by Cu(0) atoms; that is, it represents a mixed-valence two-dimensional coordination network consisting of an ordered array of Cu(II) and Cu(0) centers. Above 520 K, the network degrades and the Cu atoms in the linking positions diffuse into the substrate, while the Cu(II)TPyP complexes form a close-packed structure that is stabilized by weak intermolecular interactions. Density functional theory investigations show that the reaction with Cu(0) proceeds via formation of an initial complex between metal atom and porphyrin followed by formation of Cu(II) porphyrin within the course of the reaction. The activation barrier of the rate limiting step was found to be 24-37 kcal mol(-1) depending on the method used. In addition, linear coordination of a Cu atom by two CuTPyP molecules is favorable according to gas-phase calculations. © 2012 American Chemical Society
Kumar, Pawan; Siddiqui, Mujahuddin M; Reddi, Yerrnaidu; Mague, Joel T; Sunoj, Raghavan B; Balakrishna, Maravanji S
2013-08-28
The bisphosphomide, 1,3-{Ph2PC(O)}2C6H4 (1), was prepared by the reaction of isophthaloyl chloride with diphenylphosphine in the presence of triethylamine. The corresponding bromo-derivative, 2-Br-1,3-{Ph2PC(O)}2C6H3 (2), was obtained by the reaction of 2-bromoisophthaloyl chloride with diphenylphosphine. The reaction of 1 with elemental sulfur or selenium yielded the bis(chalcogenides), 1,3-{Ph2P(S)C(O)}2C6H4 (3) and {1,3-Ph2P(Se)C(O)}2C6H4 (4). The reaction between 1 and [Ru(η(6)-p-cymene)Cl2]2 and [Pd(η(3)-C3H5)Cl]2 in 1 : 1 stoichiometry yielded the corresponding binuclear complexes, [Ru2(η(6)-p-cymene)2Cl4{1,3-{Ph2PC(O)}2(C6H4)}] (5) and [Pd2(η(3)-C3H5)2Cl2{1,3-{Ph2PC(O)}2(C6H4)}] (6). The reaction of 1 with AgClO4 followed by the addition of [Pd(COD)Cl2] at room temperature resulted in the formation of a pincer complex [PdCl{2,6-{Ph2PC(O)}2(C6H3)}] (9), via transmetallation. Pincer complex formation through C-H activation requires drastic conditions and yields are generally moderate. The oxidative addition reaction between 2 and [Ni(COD)2] gave a pincer complex [NiBr{2,6-{Ph2PC(O)}2(C6H3)}] (8), whereas the 2:1 reaction of 2 with [Pd2(dba)3] yielded the palladium analogue [PdBr{2,6-{Ph2PC(O)}2(C6H3)}] (9) in quantitative yield. The reaction between 1 and CuX in a 1:1 molar ratio produced binuclear complexes, [Cu2(μ-X)2{1,3-{Ph2PC(O)}2(C6H4)}2] (10, X = Cl; 11, X = Br; 12, X = I), whereas the reaction between 1 and [Cu(NCCH3)4]BF4 led to the isolation of a spirocyclic complex, [Cu(CH3CN)2{1,3-{Ph2PC(O)}2(C6H4)}]BF4 (13). The silver complexes [Ag2(μ-ClO4)2{1,3-{Ph2PC(O)}2(C6H4)}2] (14), [Ag2(μ-OTf)2{1,3-{Ph2PC(O)}2(C6H4)}2] (15) and [Ag2X2{1,3-{Ph2PC(O)}2(C6H4)}] (16, X = ClO4; 17, X = OTf) were obtained by treating 1 with AgClO4 or AgOTf in 1:1 or 1:2 molar ratios. The reactions of 1 with [AuCl(SMe2)] in 1 : 1 and 1 : 2 molar ratios afforded mono- and binuclear complexes, [AuCl{1,3-{Ph2PC(O)}2(C6H4)}2] (18) and [Au2Cl2{1,3-{Ph2PC(O)}2(C6H4
Baesjou, PJ; Driessen, WL; Challa, G; Reedijk, J
1997-01-01
Ab initio unrestricted Hartree-Fock calculations with a 6-31G* basis set were performed on 2, 6-dimethylphenol (DMP or monomer) and 4-(2, 6-dimethylphenoxy)-2, 6-dimethylphenol (dimer) to gain more insight into the mechanism of the copper-catalyzed oxidative phenol coupling reaction. Atomic charges
Weishaupt, M A; Wiestner, T; von Peinen, K; Waldern, N; Roepstorff, L; van Weeren, R; Meyer, H; Johnston, C
2006-08-01
Little is known in quantitative terms about the influence of different head-neck positions (HNPs) on the loading pattern of the locomotor apparatus. Therefore it is difficult to predict whether a specific riding technique is beneficial for the horse or if it may increase the risk for injury. To improve the understanding of forelimb-hindlimb balance and its underlying temporal changes in relation to different head and neck positions. Vertical ground reaction force and time parameters of each limb were measured in 7 high level dressage horses while being ridden at walk and trot on an instrumented treadmill in 6 predetermined HNPs: HNP1 - free, unrestrained with loose reins; HNP2 - neck raised, bridge of the nose in front of the vertical; HNP3 - neck raised, bridge of the nose behind the vertical; HNP4 - neck lowered and flexed, bridge of the nose considerably behind the vertical; HNP5 - neck extremely elevated and bridge of the nose considerably in front of the vertical; HNP6 - neck and head extended forward and downward. Positions were judged by a qualified dressage judge. HNPs were assessed by comparing the data to a velocity-matched reference HNP (HNP2). Differences were tested using paired t test or Wilcoxon signed rank test (Pwalk, stride duration and overreach distance increased in HNP1, but decreased in HNP3 and HNP5. Stride impulse was shifted to the forehand in HNP1 and HNP6, but shifted to the hindquarters in HNP5. At the trot, stride duration increased in HNP4 and HNP5. Overreach distance was shorter in HNP4. Stride impulse shifted to the hindquarters in HNP5. In HNP1 peak forces decreased in the forelimbs; in HNP5 peak forces increased in fore- and hindlimbs. HNP5 had the biggest impact on limb timing and load distribution and behaved inversely to HNP1 and HNP6. Shortening of forelimb stance duration in HNP5 increased peak forces although the percentage of stride impulse carried by the forelimbs decreased. An extremely high HNP affects functionality much
Roy, Subhadip; Oyarzabal, Itziar; Vallejo, Julia; Cano, Joan; Colacio, Enrique; Bauza, Antonio; Frontera, Antonio; Kirillov, Alexander M; Drew, Michael G B; Das, Subrata
2016-09-06
A mononuclear cobalt(II) complex [Co(3,5-dnb)2(py)2(H2O)2] {3,5-Hdnb = 3,5-dinitrobenzoic acid; py = pyridine} was isolated in two polymorphs, in space groups C2/c (1) and P21/c (2). Single-crystal X-ray diffraction analyses reveal that 1 and 2 are not isostructural in spite of having equal formulas and ligand connectivity. In both structures, the Co(II) centers adopt octahedral {CoN2O4} geometries filled by pairs of mutually trans terminal 3,5-dnb, py, and water ligands. However, the structures of 1 and 2 disclose distinct packing patterns driven by strong intermolecular O-H···O hydrogen bonds, leading to their 0D→2D (1) or 0D→1D (2) extension. The resulting two-dimensional layers and one-dimensional chains were topologically classified as the sql and 2C1 underlying nets, respectively. By means of DFT theoretical calculations, the energy variations between the polymorphs were estimated, and the binding energies associated with the noncovalent interactions observed in the crystal structures were also evaluated. The study of the direct-current magnetic properties, as well as ab initio calculations, reveal that both 1 and 2 present a strong easy-plane magnetic anisotropy (D > 0), which is larger for the latter polymorph (D is found to exhibit values between +58 and 117 cm(-1) depending on the method). Alternating current dynamic susceptibility measurements show that these polymorphs exhibit field-induced slow relaxation of the magnetization with Ueff values of 19.5 and 21.1 cm(-1) for 1 and 2, respectively. The analysis of the whole magnetic data allows the conclusion that the magnetization relaxation in these polymorphs mainly takes place through a virtual excited state (Raman process). It is worth noting that despite the notable difference between the supramolecular networks of 1 and 2, they exhibit almost identical magnetization dynamics. This fact suggests that the relaxation process is intramolecular in nature and that the virtual state involved in the
Felix S. Olise
2016-04-01
Full Text Available The Feshbach–Kerman–Koonin (FKK multi-step direct (MSD theory of pre-equilibrium reactions has been used to compute the single-step cross-sections for some (p,α reactions using the knock-on and pick-up reaction mechanisms at two incident proton energies. For the knock-on mechanism, the reaction was assumed to have taken place by the direct ejection of a preformed alpha cluster in a shell-model state of the target. But the reaction was assumed to have taken place by the pick-up of a preformed triton cluster (also bound in a shell-model state of the target core by the incident proton for the pick-up mechanism. The Yukawa forms of potential were used for the proton-alpha (for the knock-on process and proton-triton (for the pick-up process interaction and several parameter sets for the proton and alpha-particle optical potentials. The calculated cross-sections for both mechanisms gave satisfactory fits to the experimental data. Furthermore, it has been shown that some combinations of the calculated distorted wave Born approximation cross-sections for the two reaction mechanisms in the FKK MSD theory are able to give better fits to the experimental data, especially in terms of range of agreement. In addition, the theory has been observed to be valid over a wider range of energy.
Olise, Felix S.; Ajala, Afis; Olamiyl, Hezekiah B. [Dept. of Physics and Engineering Physics, Obafemi Awolowo University, Ile-Ife (Nigeria)
2016-04-15
The Feshbach-Kerman-Koonin (FKK) multi-step direct (MSD) theory of pre-equilibrium reactions has been used to compute the single-step cross-sections for some (p,α) reactions using the knock-on and pick-up reaction mechanisms at two incident proton energies. For the knock-on mechanism, the reaction was assumed to have taken place by the direct ejection of a preformed alpha cluster in a shell-model state of the target. But the reaction was assumed to have taken place by the pick-up of a preformed triton cluster (also bound in a shell-model state of the target core) by the incident proton for the pick-up mechanism. The Yukawa forms of potential were used for the proton-alpha (for the knock-on process) and proton-triton (for the pick-up process) interaction and several parameter sets for the proton and alpha-particle optical potentials. The calculated cross-sections for both mechanisms gave satisfactory fits to the experimental data. Furthermore, it has been shown that some combinations of the calculated distorted wave Born approximation cross-sections for the two reaction mechanisms in the FKK MSD theory are able to give better fits to the experimental data, especially in terms of range of agreement. In addition, the theory has been observed to be valid over a wider range of energy.
李清; 黄竹青; 王运民; 李亮; 张伦柱
2012-01-01
The calculation of enthalpy drop and reaction degree is an important content and basis of the calculation for governing stage in off-design condition. The calculation method of the steam turbine governing stage enthalpy drop and reaction degree in off-design condition is introduced in this paper, and a instance calculating of a power plant - N600 - 16.67 -538 / 538 -1 steam turbine in Hunan province is simulated by MATLAB software. Finally,the changing curves of governing stage enthalpy drop and reaction degree is drawn according to the calculation results. The results from the research have an important value in theory and application.%调节级焓降和反动度的计算是调节级变工况计算的基础和重要内容.介绍了汽轮机调节级变工况时焓降和反动度的计算方法,并以湖南某电厂N600-16.67 -538/538 -Ⅰ型汽轮机为例,应用MATLAB语言编制计算软件进行了实例计算,根据计算结果绘制了调节级焓降和反动度的变化曲线.研究成果具有重要的理论意义和应用价值.
A. Ball
2010-01-01
Operational Experience At the end of the first full-year running period of LHC, CMS is established as a reliable, robust and mature experiment. In particular common systems and infrastructure faults accounted for <0.6 % CMS downtime during LHC pp physics. Technical operation throughout the entire year was rather smooth, the main faults requiring UXC access being sub-detector power systems and rack-cooling turbines. All such problems were corrected during scheduled technical stops, in the shadow of tunnel access needed by the LHC, or in negotiated accesses or access extensions. Nevertheless, the number of necessary accesses to the UXC averaged more than one per week and the technical stops were inevitably packed with work packages, typically 30 being executed within a few days, placing a high load on the coordination and area management teams. It is an appropriate moment for CMS Technical Coordination to thank all those in many CERN departments and in the Collaboration, who were involved in CMS techni...
Andrés, J. L.; Lledós, A.; Duran, M.; Bertrán, J.
1988-12-01
Ab initio SCF calculations have been carried out on the fluoride exchange reaction F -+CH 3F→FCH 3+F -. An external uniform electric field along the FCF axis has been incorporated by proper changes in the one-electron part of the Fock matrix. The reaction profile has been found to be dramatically modified with increase in strength of the applied field. The electric field is found to be essential to describe the potential energy hypersurface so that it intervenes in the reaction coordinate. It is concluded that strong electric fields open a new way to catalyze reactions.
唐乾; 张越; 曹洪玉; 史珊珊; 郑学仿
2015-01-01
As we all known ,the instantaneous reaction between protein and ligands are very important to adjust the normal pla‐ying of biological function .And nitric oxide interactions with iron are the most important biological reactions in which NO partic‐ipates .Unlike carbon monoxide or oxygen ,NO can also bind reversibly to ferric iron .In this paper ,UV‐Vis absorption and CD spectra were used to study coordination reaction process between horse heart metMb and NO ,to demonstrate the coordination reaction mechanism and to explore the influencing factors of metMb with NO .The experimental results showed that metMb could react with NO ,and obtained three new peaks at 420 nm ,534 and 568 nm ,respectively ,which implied metMb and NO have reacted and generated a new complex‐nitrosylmetmyoglobin (metMbNO) .Then as time went on ,NO concentration de‐creased in the solution ,and the Fe‐N bond fractured under the attack of H2O ,then NO leaves slowly from metMbNO ,and met‐Mb was regenerated .In this experiment ,we also found that external conditions such as buffer medium ,ionic strength ,pH , temperature ,etc ,had an important influence on the coordination reaction between metMb and NO .It was favorable for the coor‐dination reaction ,when the 0.01 mol・L -1 phosphate buffer solution is near neutral condition ,the temperature is 280 K ,the co‐ordination reaction could reach equilibrium at a fastest speed .In addition ,the CD date show that NO only reacts with Fe atom in the center of heme and has less effect on the secondary structuers of protein .The research of metMb and NO played an important role to further study the function of NO .Especially the establish of equilibrium reaction mechanism between NO and heme pro‐tein has an important research value on maintaining the balance of NO in vivo and keeping the normal function in the body ’s cells .%蛋白质与配体作用的瞬时性对调节生物功能的正常发挥至关重要。采用紫外‐可见
Tachimori, Shoichi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Kitamura, Tatsuaki
1996-10-01
A computer code REACT-Mod which simulates various chemical reactions in an aqueous nitric acid solution involving uranium, plutonium, neptunium, technetium etc. e.g., redox, radiolytic and disproportionation reactions of 68, was developed based on the kinetics model. The numerical solution method adopted in the code are two, a kinetics model totally based on the rate law of which differential equations are solved by the modified Porsing method, and a two-step model based on both the rate law and equilibrium law. Only the former treats 27 radiolytic reactions. The latter is beneficially used to have a quick and approximate result by economical computation. The present report aims not only to explain the concept, chemical reactions treated and characteristics of the model but also to provide details of the program for users of the REACT-Mod code. (author)
Reaction mechanism of -acylhydroxamate with cysteine proteases
R Shankar; P Kolandaivel
2007-09-01
The gas-phase reaction mechanism of -acylhydroxamate with cysteine proteases has been investigated using ab initio and density functional theory. On the irreversible process, after breakdown of tetrahedral intermediate (INT1), small 1-2 anionotropic has been formed and rearranged to give stable by-products sulfenamide (P1) and thiocarbamate (P2) with considerable energy loss. While, on the reversible part of this reaction mechanism, intermediate (INT2) breaks down on oxidation, to form a stable product (P3). Topological and AIM analyses have been performed for hydrogen bonded complex in this reaction profile. Intrinsic reaction coordinates [IRC, minimum-energy path (MEP)] calculation connects the transition state between R-INT1, INT1-P1 and INT1-P2. The products P1, P2 and P3 are energetically more stable than the reactant and hence the reaction enthalpy is found to be exothermic.
Banks, Simon T; Tautermann, Christofer S; Remmert, Sarah M; Clary, David C
2009-07-28
A method for projecting chemical reaction surface coordinates from a Hessian in curvilinear internal coordinates has recently been developed. Here we introduce a modification to this approach which allows for analytical evaluation of the necessary coordinate derivatives, thus reducing the number of ab initio calculations required. We apply this method to the determination of spectator mode frequencies and zero-point energies for the series of hydrogen abstraction reactions X + CH(4) --> XH + CH(3), X = muonium (mu), H, D, CH(3). Comparison of these frequencies with those obtained using rectilinear coordinates allows us to examine how the mass of X affects the coordinate sensitivity of the spectator modes. We carry out two-dimensional quantum reactive scattering calculations for these reactions to highlight instances where the choice of coordinates may have a significant impact on the evaluated thermal rate constants.
Cuff, Paul; Cover, Thomas
2009-01-01
We develop elements of a theory of cooperation and coordination in networks. Rather than considering a communication network as a means of distributing information, or of reconstructing random processes at remote nodes, we ask what dependence can be established among the nodes given the communication constraints. Specifically, in a network with communication rates between the nodes, we ask what is the set of all achievable joint distributions p(x1, ..., xm) of actions at the nodes on the network. Several networks are solved, including arbitrarily large cascade networks. Distributed cooperation can be the solution to many problems such as distributed games, distributed control, and establishing mutual information bounds on the influence of one part of a physical system on another.
Stone, N. J., E-mail: n.stone@physics.ox.ac.uk; Stone, J. R. [University of Oxford (United Kingdom); Jonsson, P. [Malmo University (Sweden)
2010-04-15
Calculations of hyperfine interaction strength and life-times of states in highly ionized atoms, using the GRASP atomic structure package, are reported. The calculations aim at providing calibration for Recoil-in-Vacuum nuclear excited state g-factor measurements. The method is outlined and results compared with experiment. Inclusion of decay of higher electronic states is discussed.
左国平; 唐壁玉; 韩克利
2005-01-01
An exact three-dimensional time-dependent quantum wave packet was employed to calculate the O(3P) +HBr(DBr) reaction using a generalized London-Ering-Polanyi-Sato(LEPS) potential energy surface. The results showed that vibrational excitation is effective for the reaction, and rotational excitation has an orientational effect in definite energy range. The rate constants and the reaction cross sections for the title reactions have been computed, the calculated rate constants ko+HBr agreed well with experimental data. By comparing with relevant results, it can be found that the kinetic isotopic effects of the reaction are relatively obvious.%基于LEPS势能面,用三维含时量子波包法对O(3P)+HBr(DBr)反应进行了准确的动力学计算.计算的结果表明,振动激发对这个反应是有效的,而转动激发在某一能量范围内具有方位效应.计算得到了该反应的速率常数和反应截面,速率常数kO+HBr的计算值同实验值符合得很好.通过对相应结果的对比,可以发现这个反应具有比较明显的同位素效应.
Yang, Huan; Han, Ke-Li; Nanbu, Shinkoh; Nakamura, Hiroki; Balint-Kurti, Gabriel G; Zhang, Hong; Smith, Sean C; Hankel, Marlies
2008-08-28
OCl/OH product branching ratios are calculated as a function of total energy for the O( (1) D) + HCl reaction using quantum wavepacket methods. The calculations take account of reaction on all the three electronic state potential energy surfaces which correlate with both reactants and products. Our results show that reaction on the excited electronic state surfaces has a large effect on the branching ratio at higher energies and that these surfaces must therefore be fully taken into account. The calculations use the potential energy surfaces of Nanbu and co-workers. Product vibrational and rotational quantum state distributions are also calculated as a function of energy for both product channels. Inclusion of the excited electronic state potential energy surfaces improves the agreement of the predicted product vibrational quantum state distributions with experiment for the OH product channel. For OCl agreement between theory and experiment is retained for the vibrational quantum state distributions when the excited electronic state potential energy surfaces are included in the analysis. For the rotational state distributions good agreement between theory and experiment is maintained for energies at which experimental results are available. At higher energies, above 0.7 eV of total energy, the OCl rotational state distributions predicted using all three electronic state potential energy surfaces shift to markedly smaller rotational quantum numbers.
Stephens, Susanna L.; Zaleski, Daniel P.; Walker, Nicholas R., E-mail: nick.walker@newcastle.ac.uk, E-mail: a.c.legon@bristol.ac.uk [School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE1 7RU (United Kingdom); Mizukami, Wataru; Tew, David P.; Legon, Anthony C., E-mail: nick.walker@newcastle.ac.uk, E-mail: a.c.legon@bristol.ac.uk [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom)
2014-03-28
The rotational spectra of six isotopologues of a complex of ethyne and silver acetylide, C{sub 2}H{sub 2}⋅⋅⋅AgCCH, are measured by both chirped-pulse and Fabry-Perot cavity versions of Fourier-transform microwave spectroscopy. The complex is generated through laser ablation of a silver target in the presence of a gas sample containing 1% C{sub 2}H{sub 2}, 1% SF{sub 6}, and 98% Ar undergoing supersonic expansion. Rotational, A{sub 0}, B{sub 0}, C{sub 0}, and centrifugal distortion Δ{sub J} and Δ{sub JK} constants are determined for all isotopologues of C{sub 2}H{sub 2}⋅⋅⋅AgCCH studied. The geometry is planar, C{sub 2v} and T-shaped in which the C{sub 2}H{sub 2} sub-unit comprises the bar of the “T” and binds to the metal atom through its π electrons. In the r{sub 0} geometry, the distance of the Ag atom from the centre of the triple bond in C{sub 2}H{sub 2} is 2.2104(10) Å. The r(HC≡CH) parameter representing the bond distance separating the two carbon atoms and the angle, ∠(CCH), each defined within the C{sub 2}H{sub 2} sub-unit, are determined to be 1.2200(24) Å and 186.0(5)°, respectively. This distortion of the linear geometry of C{sub 2}H{sub 2} involves the hydrogen atoms moving away from the silver atom within the complex. The results thus reveal that the geometry of C{sub 2}H{sub 2} changes measurably on coordination to AgCCH. A value of 59(4) N m{sup −1} is determined for the intermolecular force constant, k{sub σ}, confirming that the complex is significantly more strongly bound than hydrogen and halogen-bonded analogues. Ab initio calculations of the r{sub e} geometry at the CCSD(T)(F12{sup *})/ACVTZ level of theory are consistent with the experimental results. The spectra of the {sup 107}Ag{sup 13}C{sup 13}CH and {sup 109}Ag{sup 13}C{sup 13}CH isotopologues of free silver acetylide are also measured for the first time allowing the geometry of the AgCCH monomer to be examined in greater detail than previously.
C. Delaere
2013-01-01
Since the LHC ceased operations in February, a lot has been going on at Point 5, and Run Coordination continues to monitor closely the advance of maintenance and upgrade activities. In the last months, the Pixel detector was extracted and is now stored in the pixel lab in SX5; the beam pipe has been removed and ME1/1 removal has started. We regained access to the vactank and some work on the RBX of HB has started. Since mid-June, electricity and cooling are back in S1 and S2, allowing us to turn equipment back on, at least during the day. 24/7 shifts are not foreseen in the next weeks, and safety tours are mandatory to keep equipment on overnight, but re-commissioning activities are slowly being resumed. Given the (slight) delays accumulated in LS1, it was decided to merge the two global runs initially foreseen into a single exercise during the week of 4 November 2013. The aim of the global run is to check that we can run (parts of) CMS after several months switched off, with the new VME PCs installed, th...
Christophe Delaere
2013-01-01
The focus of Run Coordination during LS1 is to monitor closely the advance of maintenance and upgrade activities, to smooth interactions between subsystems and to ensure that all are ready in time to resume operations in 2015 with a fully calibrated and understood detector. After electricity and cooling were restored to all equipment, at about the time of the last CMS week, recommissioning activities were resumed for all subsystems. On 7 October, DCS shifts began 24/7 to allow subsystems to remain on to facilitate operations. That culminated with the Global Run in November (GriN), which took place as scheduled during the week of 4 November. The GriN has been the first centrally managed operation since the beginning of LS1, and involved all subdetectors but the Pixel Tracker presently in a lab upstairs. All nights were therefore dedicated to long stable runs with as many subdetectors as possible. Among the many achievements in that week, three items may be highlighted. First, the Strip...
Rokhina, E.V.; Makarova, K.; Golovina, E.A.; As, van H.; Virkutyte, J.
2010-01-01
The homolysis of peracetic acid (PAA) as a relevant source of free radicals (e.g., •OH) was studied in detail. Radicals formed as a result of chain radical reactions were detected with electron spin resonance and nuclear magnetic resonance spin trapping techniques and subsequently identified by mean
Beccaceci, Sonya; Armata, Nerina; Ogden, J Steven; Dyke, John M; Rhyman, Lydia; Ramasami, Ponnadurai
2012-02-21
The reactions of dimethylsulfide (DMS) with molecular iodine (I(2)) and iodine monochloride (ICl) have been studied by infrared matrix isolation spectroscopy by co-condensation of the reagents in an inert gas matrix. Molecular adducts of DMS + I(2) and DMS + ICl have also been prepared using standard synthetic methods. The vapour above each of these adducts trapped in an inert gas matrix gave the same infrared spectrum as that recorded for the corresponding co-condensation reaction. In each case, the infrared spectrum has been interpreted in terms of a van der Waals adduct, DMS : I(2) and DMS : ICl, with the aid of infrared spectra computed for their minimum energy structures at the MP2 level. Computed relative energies of minima and transition states on the potential energy surfaces of these reactions were used to understand why they do not proceed further than the reactant complexes DMS : I(2) and DMS : ICl. The main findings of this research are compared with results obtained earlier for the DMS + Cl(2) and DMS + Br(2) reactions, and the atmospheric implications of the conclusions are also considered.
Ouk, Chanda-Malis; Zvereva-Loëte, Natalia; Scribano, Yohann; Bussery-Honvault, Béatrice
2012-10-30
Multireference single and double configuration interaction (MRCI) calculations including Davidson (+Q) or Pople (+P) corrections have been conducted in this work for the reactants, products, and extrema of the doublet ground state potential energy surface involved in the N((2)D) + CH(4) reaction. Such highly correlated ab initio calculations are then compared with previous PMP4, CCSD(T), W1, and DFT/B3LYP studies. Large relative differences are observed in particular for the transition state in the entrance channel resolving the disagreement between previous ab initio calculations. We confirm the existence of a small but positive potential barrier (3.86 ± 0.84 kJ mol(-1) (MR-AQCC) and 3.89 kJ mol(-1) (MRCI+P)) in the entrance channel of the title reaction. The correlation is seen to change significantly the energetic position of the two minima and five saddle points of this system together with the dissociation channels but not their relative order. The influence of the electronic correlation into the energetic of the system is clearly demonstrated by the thermal rate constant evaluation and it temperature dependance by means of the transition state theory. Indeed, only MRCI values are able to reproduce the experimental rate constant of the title reaction and its behavior with temperature. Similarly, product branching ratios, evaluated by means of unimolecular RRKM theory, confirm the NH production of Umemoto et al., whereas previous works based on less accurate ab initio calculations failed. We confirm the previous findings that the N((2)D) + CH(4) reaction proceeds via an insertion-dissociation mechanism and that the dominant product channels are CH(2)NH + H and CH(3) + NH.
Xu, Bing; Shi, Peipei; Huang, Tengfei; Wang, Xuefeng
2017-10-01
Reactions of laser-ablated cerium atoms with silane were investigated by matrix isolation infrared spectroscopy and theoretical calculations. The reaction products, Si(μ-H)3CeH, H3SiCeH, H2Si(μ-H)CeH and HSi(μ-H)2CeH were identified on the basis of the SiD4 isotopic substitutions and DFT frequency calculations. In the solid argon or krypton matrix, the inserted H3SiCeH molecule was observed as initial product on deposition, which rearranged to hydrogen bridge species Si(μ-H)3CeH on follow-up annealing through H2Si(μ-H)CeH and HSi(μ-H)2CeH species. The Sisbnd Hsbnd Ce hydrogen bridge was investigated by NBO and ELF analysis. Calculation suggested that in Si(μ-H)3CeH molecule Ce atom donated one electron to Si atom, resulting in electron-rich SiH3 subunit, which was confirmed by ESP and AIM analysis. The increased basicity of Sisbnd H bond facilitates the formation of hydrogen bridge bond between Si and Ce. For comparison only insertion H3CCeH structure was obtained from the reaction of Ce atoms with CH4.
Goodson, D Z; Chiang, W T; Valone, S M; Doll, J D; Goodson, David Z.; Roelse, Dustin W.; Chiang, Wan-Ting; Valone, Steven M.
1997-01-01
The temperature dependence of the rate of the reaction CH_4+H \\to CH_3+H_2 is studied using classical collision theory with a temperature-dependent effective potential derived from a path integral analysis. Analytical expressions are obtained for the effective potential and for the rate constant. The rate constant expressions use a temperature-dependent activation energy. They give better agreement with the available experimental results than do previous empirical fits. Since all but one of the parameters in the present expressions are obtained from theory, rather than by fitting to experimental reaction rates, the expressions can be expected to be more dependable than purely empirical expressions at temperatures above 2000 K or below 350 K, where experimental results are not available.
Yang, Limin
2014-08-01
A facile N-heterocyclic carbene catalytic enantioselective aza-Diels-Alder reaction of oxodiazenes with α-chloroaldehydes as dienophile precursors is reported, with excellent enantioselectivity (ee > 99%) and excellent yield (up to 93%). DFT study showed that cis-TSa, formed from a top face approach of oxodiazene to cis-IIa, is the most favorable transition state and is consistent with the experimental observations. © 2014 American Chemical Society.
Harmonic Vibrational Analysis in Delocalized Internal Coordinates.
Jensen, Frank; Palmer, David S
2011-01-11
It is shown that a principal component analysis of a large set of internal coordinates can be used to define a nonredundant set of delocalized internal coordinates suitable for the calculation of harmonic vibrational normal modes. The selection of internal coordinates and the principal component analysis provide large degrees of freedom in extracting a nonredundant set of coordinates, and thus influence how the vibrational normal modes are described. It is shown that long-range coordinates may be especially suitable for describing low-frequency global deformation modes in proteins.
Jensen, L; van Duijnen, PT
2005-01-01
We have calculated the frequency-dependent refractive index and the third-order nonlinear susceptibility for C-60 in the condensed phase, which is related to third-harmonic generation (THG) and degenerate four-wave mixing (DFWM) experiments. This was done using the recently developed discrete solven
Nishioka, Hirotaka; Ando, Koji
2011-05-28
By making use of an ab initio fragment-based electronic structure method, fragment molecular orbital-linear combination of MOs of the fragments (FMO-LCMO), developed by Tsuneyuki et al. [Chem. Phys. Lett. 476, 104 (2009)], we propose a novel approach to describe long-distance electron transfer (ET) in large system. The FMO-LCMO method produces one-electron Hamiltonian of whole system using the output of the FMO calculation with computational cost much lower than conventional all-electron calculations. Diagonalizing the FMO-LCMO Hamiltonian matrix, the molecular orbitals (MOs) of the whole system can be described by the LCMOs. In our approach, electronic coupling T(DA) of ET is calculated from the energy splitting of the frontier MOs of whole system or perturbation method in terms of the FMO-LCMO Hamiltonian matrix. Moreover, taking into account only the valence MOs of the fragments, we can considerably reduce computational cost to evaluate T(DA). Our approach was tested on four different kinds of model ET systems with non-covalent stacks of methane, non-covalent stacks of benzene, trans-alkanes, and alanine polypeptides as their bridge molecules, respectively. As a result, it reproduced reasonable T(DA) for all cases compared to the reference all-electron calculations. Furthermore, the tunneling pathway at fragment-based resolution was obtained from the tunneling current method with the FMO-LCMO Hamiltonian matrix.
曹晴; 李槐树; 周羽; 周石
2015-01-01
Models based on Schwarz–Christoffel's transformation of a salient PMSM with rotor eccentricity is presented. At first, motor's direct-quadrature (d-q) axis's armature-reaction field under square wave magnetomotive force is calculated. Then, d-q armature-reaction field under magnetomotive force without regular distribution is analyzed. Finally, armature-reaction field can be obtained by superposing them. This method can be applied to magnet calculation of different types of motors with rotor eccentricity. Armature-reaction field of this motor was calculated by using this analytical method and Finite Element Method (FEM). The results shows that the two cases agree well, and the validity and accuracy of the presented method are verified.%本文基于许-克变换针对转子偏心凸极永磁电机建立了磁场计算模型.首先计算方波磁势作用下电机的直、交轴电枢磁场;然后计算不规则磁势分布条件下的直、交轴电枢磁场;电枢磁场即为两者叠加.该方法适用于各种偏心情况下的电机磁场计算.将本模型计算的电枢磁场分布与有限元比较,结果吻合,证明其准确性和有效性.
葛自明; 周雅君; 吕志伟; 王治文
2002-01-01
The triple differential cross sections of the 2p electron of argon in a coplanar highly asymmetric geometry have beencalculated with the modified distorted wave Born approximation (DWBA) and the target Hartree-Fock approximationmethods. The damping polarization of the semi-classical short-range potentials and the Mee factor are included in thedistorting potentials of the modified DWBA. Theoretical results are compared with a recent experiment. The dynamicmechanism of inner shell ionization in a coplanar highly asymmetric geometry (e, 2e) reaction are also discussed.
Motor coordination: a local hub for coordination.
Calabrese, Ronald L
2014-03-31
A local interneuron of a crayfish central pattern generator serves as a hub that integrates ascending and descending coordinating information and passes it on to a local oscillatory microcircuit to coordinate a series of segmental appendages known as swimmerets.
Sihver, L; Mancusi, D [Chalmers University of Technology, Gothenburg, Sweden, (Sweden); Matthiae, D [German Aerospace Center, Cologne (Germany); Koi, T [SLAC, Stanford, CA (United States)], E-mail: sihver@chalmers.se
2008-10-15
Radiation exposure of aircrew is more and more recognized as an occupational hazard. The ionizing environment at standard commercial aircraft flight altitudes consists mainly of secondary particles, of which the neutrons give a major contribution to the dose equivalent. Accurate estimations of neutron spectra in the atmosphere are therefore essential for correct calculations of aircrew doses. Energetic solar particle events (SPE) could also lead to significantly increased dose rates, especially at routes close to the North Pole, e.g. for flights between Europe and USA. It is also well known that the radiation environment encountered by personnel aboard low Earth orbit (LEO) spacecraft or aboard a spacecraft traveling outside the Earth's protective magnetosphere is much harsher compared with that within the atmosphere since the personnel are exposed to radiation from both galactic cosmic rays (GCR) and SPE. The relative contribution to the dose from GCR when traveling outside the Earth's magnetosphere, e.g. to the Moon or Mars, is even greater, and reliable and accurate particle and heavy ion transport codes are essential to calculate the radiation risks for both aircrew and personnel on spacecraft. We have therefore performed calculations of neutron distributions in the atmosphere, total dose equivalents, and quality factors at different depths in a water sphere in an imaginary spacecraft during solar minimum in a geosynchronous orbit. The calculations were performed with the GEANT4 Monte Carlo (MC) code using both the binary cascade (BIC) model, which is part of the standard GEANT4 package, and the JQMD model, which is used in the particle and heavy ion transport code PHITS GEANT4.
Balaganesh, M; Rajakumar, B
2012-10-11
The rate coefficients of ((E)-CF(3)CH═CHF, (Z)-CF(3)CH═CHF, (E)-CF(3)CF═CHF, and (Z)-CF(3)CF═CHF) + OH reactions were computed using M06-2X/6-31+G(d,p) theory in the temperature range of 200 and 400 K. The possible reaction mechanisms of the ((E)-CF(3)CH═CHF, (Z)-CF(3)CH═CHF, (E)-CF(3)CF═CHF, and (Z)-CF(3)CF═CHF) + OH reactions were examined. The rate coefficients for the addition and abstraction reactions were calculated using canonical variational transition state theory (CVT) and conventional transition state theory (CTST), respectively, and we concluded that abstraction reactions are negligible within the temperature range and addition reactions take the lead role. The small curvature tunnelling (SCT) was included in the computation of the rate coefficients. The temperature dependent rate expressions (in cm(3) molecule(-1) s(-1)) of the (E)-CF(3)CH═CHF, (Z)-CF(3)CH═CHF, (E)-CF(3)CF═CHF, and (Z)-CF(3)CF═CHF + OH reactions between 200 and 400 K are presented. The atmospheric lifetimes and global warming potentials (GWPs) of the test molecules were computed using the rate coefficients obtained in this study, and it is concluded that these molecules are very short-lived in the Earth's atmosphere with low GWPs.
Characteristics of Trivalent Lanthanides in Coordination Chemistry
Xue Dongfeng(薛冬峰); Zuo Sen(左森); Henryk Ratajczak
2004-01-01
Some basic characteristics of lanthanide-oxygen bonds in various trivalent lanthanide metal-organic complexes are quantitatively studied by the bond valence model. Some important relationships among the electronegativity, bond valence parameter, bond length and lanthanide coordination number in these complexes are generally found , which show that for each trivalent lanthanide cation all calculated parameters may well be correlated with its coordination number in their coordination complexes. Specifically,32 new data for the bond valence parameter are first calculated in this work.An approximate linear relationship between the Ln-O bond valence parameter and the coordination number of Ln3+ is obtained.The Ln-O bond length increases with the increase in the lanthanide coordination number.The difference of electronegative values decreases with the increase in the lanthanide coordination number.
Pritychenko, B.; Mughabghab, S. F.
2012-12-01
We present calculations of neutron thermal cross sections, Westcott factors, resonance integrals, Maxwellian-averaged cross sections and astrophysical reaction rates for 843 ENDF materials using data from the major evaluated nuclear libraries and European activation file. Extensive analysis of newly-evaluated neutron reaction cross sections, neutron covariances, and improvements in data processing techniques motivated us to calculate nuclear industry and neutron physics quantities, produce s-process Maxwellian-averaged cross sections and astrophysical reaction rates, systematically calculate uncertainties, and provide additional insights on currently available neutron-induced reaction data. Nuclear reaction calculations are discussed and new results are presented. Due to space limitations, the present paper contains only calculated Maxwellian-averaged cross sections and their uncertainties. The complete data sets for all results are published in the Brookhaven National Laboratory report.
Pritychenko, B. [National Nuclear Data Center, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Mughabghab, S.F. [National Nuclear Data Center, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States)
2012-12-15
We present calculations of neutron thermal cross sections, Westcott factors, resonance integrals, Maxwellian-averaged cross sections and astrophysical reaction rates for 843 ENDF materials using data from the major evaluated nuclear libraries and European activation file. Extensive analysis of newly-evaluated neutron reaction cross sections, neutron covariances, and improvements in data processing techniques motivated us to calculate nuclear industry and neutron physics quantities, produce s-process Maxwellian-averaged cross sections and astrophysical reaction rates, systematically calculate uncertainties, and provide additional insights on currently available neutron-induced reaction data. Nuclear reaction calculations are discussed and new results are presented. Due to space limitations, the present paper contains only calculated Maxwellian-averaged cross sections and their uncertainties. The complete data sets for all results are published in the Brookhaven National Laboratory report.
Fonseca, A. C.
1990-02-01
Four-body integral equations are used to calculate the binding energy of 4He as well as dd → dd and dd → p 3H amplitudes using a single term separable nucleon-nucleon potential in channels 1S 0 and 3S 1- 3D 1, together with the energy dependent pole expansion to set up an N term representation of all (3)+1 subamplitudes of interest. The (2)+(2) subamplitudes are treated exactly by convolution. The 4He binding energy is obtained from the exact solution of the equations. In the scattering region first order perturbation theory is used to separate the contribution of the s-wave components of the N-N t-matrix and s- and p-wave three-nucleon channels to the tour-nucleon Kernel, from the contribution of d-wave two- and three-nucleon channel components that result from the tensor-force. Cross sections and analysing powers are calculated using all positive and negative parity four-body amplitudes with total angular momentum J⩽4. Comparison with data is presented.
Cheng, Tao; Xiao, Hai; Goddard, William A
2016-10-11
Copper is the only elemental metal that reduces a significant fraction of CO2 to hydrocarbons and alcohols, but the atomistic reaction mechanism that controls the product distributions are not known because it has not been possible to detect the reaction intermediates on the electrode surface experimentally, or carry out Quantum Mechanics (QM) calculations with a realistic description of the electrolyte (water). Here, we carry out Quantum Mechanics (QM) calculations with an explicit description of water on the Cu(100) surface (experimentally shown to be stable under CO2RR conditions) to examine the initial reaction pathways to form CO and formate (HCOO(-)) from CO2 through free energy calculations at 298K and pH 7. We find that CO formation proceeds from physisorbed CO2 to chemisorbed CO2 (*CO2(δ-)), with a free energy barrier of ΔG(‡)=0.43 eV, the rate determining step (RDS). The subsequent barriers of protonating *CO2(δ-) to form COOH* and then dissociating COOH* to form *CO are 0.37 eV and 0.30 eV, respectively. HCOO(-) formation proceeds through a very different pathway in which physisorbed CO2 reacts directly with a surface H* (along with electron transfer), leading to ΔG(‡) = 0.80 eV. Thus, the competition between CO formation and HCOO(-) formation occurs in the first electron transfer step. On Cu(100), the RDS for CO formation is lower, making CO the predominant product. Thus, to alter the product distribution we need to control this first step of CO2 binding, which might involve alloying or changing the structure at the nanoscale.
Lara, Manuel, E-mail: manuel.lara@uam.es [Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid (Spain); Jambrina, P. G.; Aoiz, F. J. [Departamento de Química Física, Facultad de Química, Universidad Complutense, 28040 Madrid (Spain); Launay, J.-M. [Institut de Physique de Rennes, UMR CNRS 6251, Université de Rennes I, F-35042 Rennes (France)
2015-11-28
Quantum reactive and elastic cross sections and rate coefficients have been calculated for D{sup +} + H{sub 2} (v = 0, j = 0) collisions in the energy range from 10{sup −8} K (deep ultracold regime), where only one partial wave is open, to 150 K (Langevin regime) where many of them contribute. In systems involving ions, the ∼R{sup −4} behavior extends the interaction up to extremely long distances, requiring a special treatment. To this purpose, we have used a modified version of the hyperspherical quantum reactive scattering method, which allows the propagations up to distances of 10{sup 5} a{sub 0} needed to converge the elastic cross sections. Interpolation procedures are also proposed which may reduce the cost of exact dynamical calculations at such low energies. Calculations have been carried out on the PES by Velilla et al. [J. Chem. Phys. 129, 084307 (2008)] which accurately reproduces the long range interactions. Results on its prequel, the PES by Aguado et al. [J. Chem. Phys. 112, 1240 (2000)], are also shown in order to emphasize the significance of the inclusion of the long range interactions. The calculated reaction rate coefficient changes less than one order of magnitude in a collision energy range of ten orders of magnitude, and it is found in very good agreement with the available experimental data in the region where they exist (10-100 K). State-to-state reaction probabilities are also provided which show that for each partial wave, the distribution of HD final states remains essentially constant below 1 K.
New form of geodetic coordinate system taking two length quantity as coordinate parameters
Yimin SHI; Ziyang ZHU; Yeming FAN
2009-01-01
A new form of geodetic coordinate system based on geodesic coordinates instead of geodetic long-itude and latitude was proposed. The vertical and horizontal geodesic coordinates measured with length were defined as coordinate parameters, but the two families of coordinate curves were still meridians and parallel circles. The first fundamental form on the ellipsoidal surface and its three coefficients were deduced by the geodesic coordinate. The formula for the latitudinal scale factor of length for geodetic parallel lines was derived, by which the obtained result conformed to that standard value calculated from geodetic latitude, and it is applicable in the range of 400 km from north to south. Therefore, it lays the foundation for establishing the differential equation and differential relationship based on this type of coordinate parameters; and consequently, it is convenient and accurate enough to operate on the ellipsoidal surface in this new form of geodetic coordinate system.
Wang, Tianfang; Bowie, John H
2011-01-01
A number of linear cumulenes and heterocumulenes have been made by charge stripping of anions of known bond connectivity in the source of a mass spectrometer. Some of these reactive molecules have been identified in interstellar molecular clouds. The structures of these neutrals may be investigated by reionization to a decomposing positive ion [the neutralization-reionization technique ((-)NR(+))], and/or by ab initio calculations. Energized linear cumulenes and heterocumulenes may undergo cyclization to form stable cyclic isomers. To cite a selection of the examples described in this review: (i) four-atom systems CCCC and some heterocumulenes CCCX (X=B, N, Al, Si, P) involve the formation of stable four-membered ring rhombic (also called kite and fan) structures. One of the cyclic molecules, cyclo-C(3) Si, has been detected in interstellar molecular clouds, (ii) five-atom cumulene and heterocumulene systems are more complex. Linear CCCCC rearranges the carbon skeleton by forming a C substituted rhomboid system, CCCCO forms a three-membered cyclic isomer, while nitrogen containing five-atom cumulenes effect nitrile to isonitrile interconversion via three-centered cyclized intermediates, and (iii) CCCCCC and CCCCBO cyclize to give unique six-membered ring systems.
Limitations of Radar Coordinates
Bini, Donato; Lusanna, Luca; Mashhoon, Bahram
2004-01-01
The construction of a radar coordinate system about the world line of an observer is discussed. Radar coordinates for a hyperbolic observer as well as a uniformly rotating observer are described in detail. The utility of the notion of radar distance and the admissibility of radar coordinates are investigated. Our results provide a critical assessment of the physical significance of radar coordinates.
李尚俊; 谈宁馨; 姚倩; 李泽荣; 李象远
2015-01-01
Intramolecular hydrogen migration in alkylperoxy reactions is one of the most important reaction classes in hydrocarbon combustion at low temperatures. In this study, the kinetic parameters for reactions in this class were calculated using the isodesmic reaction method. The geometries for al the reactants, transition states, and products were optimized at the B3LYP/6-311+G(d,p) level. A criterion based on conservation of the reaction-center geometry of the transition state was proposed for the reaction class, and the intramolecular hydrogen migration reactions studied were divided into four classes, i.e., (1,3), (1,4), (1,5), and (1,n) (n=6, 7, 8) hydrogen migration. The simplest reaction system for each reaction class was defined as the principal reaction;the approximate single-point energies were obtained at the low level of B3LYP/6-311+G(d,p) and accurate single-point energies were obtained at the high level of CBS-QB3. The other reactions in this class were chosen as the target reactions and the approximate single-point energies were obtained at the B3LYP/6-311+G(d,p) level. The energy barriers and rate constants of these target reactions were corrected using the isodesmic reaction method. The results showed that accurate energy barriers and rate constants for the reactions of large molecules can be obtained by a relatively low level method using the isodesmic reaction method. In this study, classification of the basic isodesmic reaction showed the essential features of the reaction classes. The present work provides accurate kinetic parameters for modeling intramolecular hydrogen migration reactions of hydrocarbons at low temperatures.%过氧烷基自由基分子内氢迁移是低温燃烧反应中的一类重要基元反应。本文用等键反应方法计算了该类反应的动力学参数。所有反应物、过渡态、产物的几何结构均在B3LYP/6-311+G(d,p)水平下优化得到。本文提出了用过渡态反应中心几何结构守恒作为反
Quantum dynamics of the abstraction reaction of H with cyclopropane.
Shan, Xiao; Clary, David C
2014-10-30
The dynamics of the abstraction reaction of H atoms with the cyclopropane molecule is studied using quantum mechanical scattering theory. The quantum scattering calculations are performed in hyperspherical coordinates with a two-dimensional (2D) potential energy surface. The ab initio energy calculations are carried out with CCSD(T)-F12a/cc-pVTZ-F12 level of theory with the geometry and frequency calculations at the MP2/cc-pVTZ level. The contribution to the potential energy surface from the spectator modes is included as the projected zero-point energy correction to the ab initio energy. The 2D surface is fitted with a 29-parameter double Morse potential. An R-matrix propagation scheme is carried out to solve the close-coupled equations. The adiabatic energy barrier and reaction enthalpy are compared with high level computational calculations as well as experimental data. The calculated reaction rate constants shows very good agreement when compared with the experimental data, especially at lower temperature highlighting the importance of quantum tunnelling. The reaction probabilities are also presented and discussed. The special features of performing quantum dynamics calculation on the chemical reaction of a cyclic molecule are discussed.
S. Tolosa
2013-01-01
Full Text Available A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described using ab initio solute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3 via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.
Novel Intramolecular Coordination Chemistry of Some New Metallocene Complexes
钱延龙; 黄吉玲
2001-01-01
This article summarizes the recent results of systematic study on the novel intramolecular cordination chemistry of some new substituted metallocene complexes made by our research group.It deals with the syntheses,reactions,structures of 65 new substituted metallocene complexes and some application of such coordination in homogeneous ctalysis,especially the structural chemistry of such novel intramolecular coordination complexes,and the mechanism of elimination and cyclization of such coordination compounds,as well as their control action in catalytic reactions.
Fleming, Donald G; Arseneau, Donald J; Sukhorukov, Oleksandr; Brewer, Jess H; Mielke, Steven L; Truhlar, Donald G; Schatz, George C; Garrett, Bruce C; Peterson, Kirk A
2011-11-14
The neutral muonic helium atom (4)Heμ, in which one of the electrons of He is replaced by a negative muon, may be effectively regarded as the heaviest isotope of the hydrogen atom, with a mass of 4.115 amu. We report details of the first muon spin rotation (μSR) measurements of the chemical reaction rate constant of (4)Heμ with molecular hydrogen, (4)Heμ + H(2) → (4)HeμH + H, at temperatures of 295.5, 405, and 500 K, as well as a μSR measurement of the hyperfine coupling constant of muonic He at high pressures. The experimental rate constants, k(Heμ), are compared with the predictions of accurate quantum mechanical (QM) dynamics calculations carried out on a well converged Born-Huang (BH) potential energy surface, based on complete configuration interaction calculations and including a Born-Oppenheimer diagonal correction. At the two highest measured temperatures the agreement between the quantum theory and experiment is good to excellent, well within experimental uncertainties that include an estimate of possible systematic error, but at 295.5 K the quantum calculations for k(Heμ) are below the experimental value by 2.1 times the experimental uncertainty estimates. Possible reasons for this discrepancy are discussed. Variational transition state theory calculations with multidimensional tunneling have also been carried out for k(Heμ) on the BH surface, and they agree with the accurate QM rate constants to within 30% over a wider temperature range of 200-1000 K. Comparisons between theory and experiment are also presented for the rate constants for both the D + H(2) and Mu + H(2) reactions in a novel study of kinetic isotope effects for the H + H(2) reactions over a factor of 36.1 in isotopic mass of the atomic reactant. © 2011 American Institute of Physics
黄少伟; 陈颖; 沈沉; 梅生伟
2012-01-01
With the considerations of the dynamic characteristics of loads and generators, the dynamic power flow is one of the most important functions of EMS and DTS. To achieve the on-line power flow analysis of the multi-area interconnected power systems, a new algorithm of the distributed dynamic power flow is proposed in this work. By setting up the implicit boundary equations, the unified power flow of the whole power system is modeled in the de composition and coordination manner, which can handle the power balance and distribution of imbalance power at the same time. Then, a Jacobian-Free Newton-GMRES method is used to solve the boundary equations, which re quires the simple interfaces of the data exchanges during the coordination procedures. Test results in wide area net work communication environment show that the proposed algorithm can archive such high-performances both on the computation and communication aspects that it is practical and feasible for the online power flow analysis applica tions.%考虑负荷和发电机调节特性的动态潮流是EMS和DTS系统的基础功能之一.采用分解协调方式的多调度中心间分布式动态潮流计算是全网在线一体化潮流分析的一种新的途径.本文以隐函数形式的边界协调方程对全网动态潮流方程协调求解问题建模.该模型可统一考虑边界节点功率平衡和不平衡功率在分区电网间的合理分配问题.进一步,本文采用Jacobian Free NewtonGMRES方法实现协调求解过程.广域网络通信环境中的测试结果表明所提算法通信接口简单、通信次数较少,能够满足在线应用的需求.
Godlewska, P.; Ban-Oganowska, H.; Macalik, L.; Hanuza, J.; Oganowski, W.; Roszak, S.; Lipkowski, P.
2006-01-01
The results of the FT-Raman and FT-IR studies of the LnCl 3(LNO) 3 type complexes (where Ln=Pr, Nd, Sm, Eu, Gd, Dy and LNO=3-Br-4-CH 3OC 7H 7NO) are presented. The spectral contours observed in the regions of the lanthanide-oxygen, lanthanide-chlorine and nitrogen-oxygen vibrations are employed in the discussion of the molecular structure of the complex ions and the local symmetry of the LnCl 3(ON) 3 polyhedron. The discussion of the vibrational spectra is based on the classical normal coordinate analysis and its results are compared to the results of DFT quantum chemical calculations performed for complete molecule. The normal coordinate analysis has been performed for PrCl 3(ON) 3 and DyCl 3(ON) 3 molecular systems, which have been treated as a different 'isotopic units'. Basing on the predominant PED contributions of the respective internal coordinates the assignment of the normal vibrations has been proposed.
Practical astronomy with your calculator
Duffett-Smith, Peter
1989-01-01
Practical Astronomy with your Calculator, first published in 1979, has enjoyed immense success. The author's clear and easy to follow routines enable you to solve a variety of practical and recreational problems in astronomy using a scientific calculator. Mathematical complexity is kept firmly in the background, leaving just the elements necessary for swiftly making calculations. The major topics are: time, coordinate systems, the Sun, the planetary system, binary stars, the Moon, and eclipses. In the third edition there are entirely new sections on generalised coordinate transformations, nutr
瞿志荣
2007-01-01
The reaction of CoCl2· 6H2O with 4-cyanopyridine N-oxide in the present of NaN3 affords two novel complexes, {[(POTZ)(H2O)2N3]Co(H2O)} (1) and Co(POTZ)2(H2O)4 (2) (POTZ=4-tetrazolyl pyridine N-oxide), which are two different phases yielded at different stages of a single Demko-Sharpless' tetrazole synthesis reaction.Surprisingly the 1D chain coordination polymer 1 is almost completely converted into monomeric complex 2 in this reaction, and, in a separate test, 2 also can be converted into 1. CCDC: 641222, 1; 641223, 2.
Lapouge, Christine; Cornard, Jean-Paul
2010-04-01
We investigated the unknown interaction of Pb(II) with catechol ligand in diluted aqueous solution by electronic spectroscopies combined with quantum chemical calculations. The aim of this work is the determination of the complete structure of the complex formed and particularly the metal coordination sphere. Three successive steps have been necessary to reach this goal: (i) the comparison of the experimental electronic absorption spectrum with theoretical spectra calculated from various hypothetical structures, (ii) complexation reaction pathways calculations in vacuum and with taking into account the solvent effects and finally (iii) the fluorescence emission wavelength calculations. All these investigations led to identify a monodentate complex with the monodeprotonated ligand, in which the Pb atom presents a coordination number of five. The formula of the complex is [Pb(Hcat)(HO)4]mono+.
王娜; 瓮长水; 朱才兴; 刘立明; 焦伟国; 王秋华; 郭燕梅
2011-01-01
Objective To study the relationship between age and lower limb neuromuscular function in elderly people under the closed chain environment. Methods 45 cases met the criteria for inclusion were divided into the 60-69 years group, 70~74 years group, and > 75 years group, 15 patients in each group. With the Functional Squat Systems (FSS), the subjects were measured isometric lower limb strength, reaction time and coordination. The maximum isometric extension strength standard value (MISS), the average isometric extension strength standard value (AISS), the overall average response time (OART), the average migration distance (AMD) were recorded. Results With the Pearson's correlation analysis, the age significantly correlated with all the other indexes (P75 years group. There was no significant difference between the 70-74 years group and >75 years group. Conclusion The lower limb neuromuscular function in elderly showed age-related significance.%目的 研究闭链动作下老年人下肢神经肌肉功能的年龄相关性.方法 45例符合人选条件的老年人分成60～69岁组、70～74岁组和≥75岁组,每组15例.应用功能性蹲屈测试系统(FSS)分别测试受试者下肢的等长肌力、反应时间和协调性.采集记录最大等长伸展肌力标准值、平均等长伸展肌力标准值、总体平均反应时间、平均偏移距离.结果 经Pearson相关分析,年龄与各项指标均有显著相关性(P＜0.05～0.01)；经组间方差分析,协调性在各组人群中均无显著性差异；最大肌力标准值和平均肌力标准值在60～69组均优于其他两组(P＜0.05)；60～69岁组的总体平均反应时间优于≥75岁组(P＜0.05)；70～74岁组与≥75岁组各项指标均无显著性差异(P＞0.05).结论 老年人的下肢神经肌肉功能具有年龄相关性.
Spin Resonance Strength Calculations
Courant, E. D.
2009-08-01
In calculating the strengths of depolarizing resonances it may be convenient to reformulate the equations of spin motion in a coordinate system based on the actual trajectory of the particle, as introduced by Kondratenko, rather than the conventional one based on a reference orbit. It is shown that resonance strengths calculated by the conventional and the revised formalisms are identical. Resonances induced by radiofrequency dipoles or solenoids are also treated; with rf dipoles it is essential to consider not only the direct effect of the dipole but also the contribution from oscillations induced by it.
Spin resonance strength calculations
Courant,E.D.
2008-10-06
In calculating the strengths of depolarizing resonances it may be convenient to reformulate the equations of spin motion in a coordinate system based on the actual trajectory of the particle, as introduced by Kondratenko, rather than the conventional one based on a reference orbit. It is shown that resonance strengths calculated by the conventional and the revised formalisms are identical. Resonances induced by radiofrequency dipoles or solenoids are also treated; with rf dipoles it is essential to consider not only the direct effect of the dipole but also the contribution from oscillations induced by it.
... Español Text Size Email Print Share Movement and Coordination Page Content Article Body At this age, your ... level will strengthen his body and develop his coordination. In the months ahead, your child’s running will ...
Developmental coordination disorder
... page: //medlineplus.gov/ency/article/001533.htm Developmental coordination disorder To use the sharing features on this page, please enable JavaScript. Developmental coordination disorder is a childhood disorder. It leads to ...
National Oceanic and Atmospheric Administration, Department of Commerce — Declination is calculated using the current International Geomagnetic Reference Field (IGRF) model. Declination is calculated using the current World Magnetic Model...
Janssen, Maarten
2003-01-01
textabstractThis comment makes four related points. First, explaining coordination is different from explaining cooperation. Second, solving the coordination problem is more important for the theory of games than solving the cooperation problem. Third, a version of the Principle of Coordination can be rationalized on individualistic grounds. Finally, psychological game theory should consider how players perceive their gaming situation. ---------------------------------------------------------...
Processing Coordination Ambiguity
Engelhardt, Paul E.; Ferreira, Fernanda
2010-01-01
We examined temporarily ambiguous coordination structures such as "put the butter in the bowl and the pan on the towel." Minimal Attachment predicts that the ambiguous noun phrase "the pan" will be interpreted as a noun-phrase coordination structure because it is syntactically simpler than clausal coordination. Constraint-based theories assume…
Processing Coordination Ambiguity
Engelhardt, Paul E.; Ferreira, Fernanda
2010-01-01
We examined temporarily ambiguous coordination structures such as "put the butter in the bowl and the pan on the towel." Minimal Attachment predicts that the ambiguous noun phrase "the pan" will be interpreted as a noun-phrase coordination structure because it is syntactically simpler than clausal coordination. Constraint-based…
M.C.W. Janssen (Maarten)
2003-01-01
textabstractThis comment makes four related points. First, explaining coordination is different from explaining cooperation. Second, solving the coordination problem is more important for the theory of games than solving the cooperation problem. Third, a version of the Principle of Coordination can
M.C.W. Janssen (Maarten)
2003-01-01
textabstractThis comment makes four related points. First, explaining coordination is different from explaining cooperation. Second, solving the coordination problem is more important for the theory of games than solving the cooperation problem. Third, a version of the Principle of Coordination can
匡秀洪; 庄圣贤; 熊冬情
2012-01-01
采用三维有限元方法对一台爪极发电机的电枢反应进行了研究.基于ANSOFT软件对电机气隙磁场和电感矩阵进行了计算仿真,通过对电感矩阵进行派克变换,进而得到交、直轴的电枢反应电抗.所得结果与用相量图方法计算的结果进行了比较,证明了解的正确性与可行性,为爪极发电机的优化设计奠定了理论基础.%The armature reaction of a claw-pole alternator using three dimensional finite element method was analyzed. Air-gap magnetic fields and inductance matrix were calculated by Ansoft. The quadrature-axis and direct-axis armature reaction reactance were obtained through the Park transformation. The results between this method and phasor diagram method were compared and verified. Its validity and feasibility were indicated, which was the theoretic foundation for the optimum design of claw-pole alternators.
Koten, G. van; Klerks, J.M.; Stufkens, D.J.; Vrieze, K.
1979-01-01
Reaction of R-N=CH-CH=N-R with [(CH{3}){3}Al]{2} affords the coordination product (CH{3}){3}AlRN=CH-CH=NR (A) for R = 2, 6-(CH{3}){2}C{6}H{3} and 2,4,6(CH{3}){3}C{6}H{2}. For R = 4 ClC{6}H{4}, 4-CH{3}C{6}H{4} and 4-CH{3}OC{6}H{4}, insertion takes place, giving the complexes (CH{3}){2}AlRN-CH(CH{3})-
Efficient path sampling on multiple reaction channels
van Erp, Titus S.
2007-01-01
Due to the time scale problem, rare events are not accessible by straight forward molecular dynamics. The presence of multiple reaction channels complicates the problem even further. The feasibility of the standard free energy based methods relies strongly on the success in finding a proper reaction coordinate. This can be very difficult task in high-dimensional complex systems and even more if several distinct reaction channels exist. Moreover, even if a proper reaction coordinate can be fou...
Hybrid Optimized and Localized Vibrational Coordinates.
Klinting, Emil Lund; König, Carolin; Christiansen, Ove
2015-11-01
We present a new type of vibrational coordinates denoted hybrid optimized and localized coordinates (HOLCs) aiming at a good set of rectilinear vibrational coordinates supporting fast convergence in vibrational stucture calculations. The HOLCs are obtained as a compromise between the recently promoted optimized coordinates (OCs) and localized coordinates (LCs). The three sets of coordinates are generally different from each other and differ from standard normal coordinates (NCs) as well. In determining the HOLCs, we optimize the vibrational self-consistent field (VSCF) energy with respect to orthogonal transformation of the coordinates, which is similar to determining OCs but for HOLCs we additionally introduce a penalty for delocalization, by using a measure of localization similar to that employed in determining LCs. The same theory and implementation covers OCs, LCs, and HOLCs. It is shown that varying one penalty parameter allows for connecting OCs and LCs. The HOLCs are compared to NCs, OCs, and LCs in their nature and performance as basis for vibrational coupled cluster (VCC) response calculations of vibrational anharmonic energies for a small set of simple systems comprising water, formaldehyde, and ethylene. It is found that surprisingly good results can be obtained with HOLCs by using potential energy surfaces as simple as quadratic Taylor expansions. Quite similar coordinates are found for the already established OCs but obtaining these OCs requires much more elaborate and expensive potential energy surfaces and localization is generally not guaranteed. The ability to compute HOLCs for somewhat larger systems is demonstrated for coumarin and the alanine quadramer. The good agreement between HOLCs and OCs, together with the much easier applicability of HOLCs for larger systems, suggests that HOLCs may be a pragmatically very interesting option for anharmonic calculations on medium to large molecular systems.
Quantum theory of chemical reactions in the presence of electromagnetic fields
Tscherbul, T V
2008-01-01
We present a theory for rigorous quantum scattering calculations of probabilities for chemical reactions of atoms with diatomic molecules in the presence of an external electric field. The approach is based on the fully uncoupled basis set representation of the total wave function in the space-fixed coordinate frame, the Fock-Delves hyperspherical coordinates and adiabatic partitioning of the total Hamiltonian of the reactive system. The adiabatic channel wave functions are expanded in basis sets of hyperangular functions corresponding to different reaction arrangements and the interactions with external fields are included in each chemical arrangement separately. We apply the theory to examine the effects of electric fields on the chemical reactions of LiF molecules with H atoms and HF molecules with Li atoms at low temperatures and show that electric fields may enhance the probability of chemical reactions and modify reactive scattering resonances by coupling the rotational states of the reactants. Our prel...
Schäfer, Harald
2013-01-01
Chemical Transport Reactions focuses on the processes and reactions involved in the transport of solid or liquid substances to form vapor phase reaction products. The publication first offers information on experimental and theoretical principles and the transport of solid substances and its special applications. Discussions focus on calculation of the transport effect of heterogeneous equilibria for a gas motion between equilibrium spaces; transport effect and the thermodynamic quantities of the transport reaction; separation and purification of substances by means of material transport; and
ARTICLE Mechanistic Investigation on the Reaction of O- with CH3CN Using Density Functional Theory
Yu, Feng; Wu, Li-xia; Zhou, Xiao-guo; Liu, Shi-lin
2010-12-01
The potential energy profile of the reaction between the atomic oxygen radical anion and acetonitrile has been mapped at the G3MP2B3 level of theory. Geometries of the reactants, products, intermediate complexes, and transition states involved in this reaction have been optimized at the (U)B3LYP/6-31+G(d,p) level, and then their accurate relative energies have been improved using the G3MP2B3 method. The potential energy profile is confirmed via intrinsic reaction coordinate calculations of transition states. Four possible production channels are examined respectively, as H+ transfer, H-atom transfer, H2+ transfer, and bi-molecular nucleophilic substitution (SN2) reaction pathways. Based on present calculations, the H2+ transfer reaction is major among these four channels, which agrees with previous experimental conclusions.
State Space Path Integrals for Electronically Nonadiabatic Reaction Rates
Duke, Jessica Ryan
2016-01-01
We present a state-space-based path integral method to calculate the rate of electron transfer (ET) in multi-state, multi-electron condensed-phase processes. We employ an exact path integral in discrete electronic states and continuous Cartesian nuclear variables to obtain a transition state theory (TST) estimate to the rate. A dynamic recrossing correction to the TST rate is then obtained from real-time dynamics simulations using mean field ring polymer molecular dynamics. We employ two different reaction coordinates in our simulations and show that, despite the use of mean field dynamics, the use of an accurate dividing surface to compute TST rates allows us to achieve remarkable agreement with Fermi's golden rule rates for nonadiabatic ET in the normal regime of Marcus theory. Further, we show that using a reaction coordinate based on electronic state populations allows us to capture the turnover in rates for ET in the Marcus inverted regime.
Mechanisms that underlie coordination in children with developmental coordination disorder.
O'Brien, Jane Clifford; Williams, Harriet G; Bundy, Anita; Lyons, Jim; Mittal, Amita
2008-01-01
The authors examined potential mechanisms underlying motor coordination in children with developmental coordination disorder (DCD). Because children with DCD experience difficulty processing visual, auditory, and vibrotactile information, the authors explored patterns of choice reaction time (RT) in young (6-7 years) and older (9-10 years) children with and without DCD by using a compatibility-incompatibility paradigm and different sensory modalities. Young children responded more slowly than older children to visual, auditory, and vibrotactile stimuli. Children with DCD took longer than typical children to process visual and vibrotactile stimuli under more complex stimulus-response mappings. Young children with DCD responded more slowly than typical children to visual and vibrotactile information under incompatible conditions. Children with DCD responded faster than unaffected children to auditory stimuli. The results suggest that there is a developmental nature in the processing of visual and auditory input and imply that the vibrotactile sensory modality may be key to the motor coordination difficulties of children with DCD.
Gimondi, Ilaria; Cavallotti, Carlo; Vanuzzo, Gianmarco; Balucani, Nadia; Casavecchia, Piergiorgio
2016-07-14
The mechanism of the O((3)P) + CH3CCH reaction was investigated using a combined experimental/theoretical approach. Experimentally the reaction dynamics was studied using crossed molecular beams (CMB) with mass-spectrometric detection and time-of-flight analysis at 9.2 kcal/mol collision energy. Theoretically master equation (ME) simulations were performed on a potential energy surface (PES) determined using high-level ab initio electronic structure calculations. In this paper (II) the theoretical results are described and compared with experiments, while in paper (I) are reported and discussed the results of the experimental study. The PES was investigated by determining structures and vibrational frequencies of wells and transition states at the CASPT2/aug-cc-pVTZ level using a minimal active space. Energies were then determined at the CASPT2 level increasing systematically the active space and at the CCSD(T) level extrapolating to the complete basis set limit. Two separate portions of the triplet PES were investigated, as O((3)P) can add either on the terminal or the central carbon of the unsaturated propyne bond. Minimum energy crossing points (MECPs) between the triplet and singlet PESs were searched at the CASPT2 level. The calculated spin-orbit coupling constants between the T1 and S0 electronic surfaces were ∼25 cm(-1) for both PESs. The portions of the singlet PES that can be accessed from the MECPs were investigated at the same level of theory. The system reactivity was predicted integrating stochastically the one-dimensional ME using Rice-Ramsperger-Kassel-Marcus theory to determine rate constants on the full T1/S0 PESs, accounting explicitly for intersystem crossing (ISC) using the Landau-Zener model. The computational results are compared both with the branching ratios (BRs) determined experimentally in the companion paper (I) and with those estimated in a recent kinetic study at 298 K. The ME results allow to interpret the main system reactivity: CH
Calculating Free Energies Using Average Force
Darve, Eric; Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
A new, general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived. The instantaneous force is defined as the force acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero. The formula applies to simulations in which the selected coordinates are either unconstrained or constrained to fixed values. It is shown that in the latter case the formula reduces to the expression previously derived by den Otter and Briels. If simulations are carried out without constraining the coordinates of interest, the formula leads to a new method for calculating the free energy changes along these coordinates. This method is tested in two examples - rotation around the C-C bond of 1,2-dichloroethane immersed in water and transfer of fluoromethane across the water-hexane interface. The calculated free energies are compared with those obtained by two commonly used methods. One of them relies on determining the probability density function of finding the system at different values of the selected coordinate and the other requires calculating the average force at discrete locations along this coordinate in a series of constrained simulations. The free energies calculated by these three methods are in excellent agreement. The relative advantages of each method are discussed.
Compilation report of VHTRC temperature coefficient benchmark calculations
Yasuda, Hideshi; Yamane, Tsuyoshi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment
1995-11-01
A calculational benchmark problem has been proposed by JAERI to an IAEA Coordinated Research Program, `Verification of Safety Related Neutronic Calculation for Low-enriched Gas-cooled Reactors` to investigate the accuracy of calculation results obtained by using codes of the participating countries. This benchmark is made on the basis of assembly heating experiments at a pin-in block type critical assembly, VHTRC. Requested calculation items are the cell parameters, effective multiplication factor, temperature coefficient of reactivity, reaction rates, fission rate distribution, etc. Seven institutions from five countries have joined the benchmark works. Calculation results are summarized in this report with some remarks by the authors. Each institute analyzed the problem by applying the calculation code system which was prepared for the HTGR development of individual country. The values of the most important parameter, k{sub eff}, by all institutes showed good agreement with each other and with the experimental ones within 1%. The temperature coefficient agreed within 13%. The values of several cell parameters calculated by several institutes did not agree with the other`s ones. It will be necessary to check the calculation conditions again for getting better agreement. (J.P.N.).
Enhanced time overcurrent coordination
Enriquez, Arturo Conde; Martinez, Ernesto Vazquez [Universidad Autonoma de Nuevo Leon, Facultad de Ingenieria Mecanica y Electrica, Apdo. Postal 114-F, Ciudad Universitaria, CP 66450 San Nicolas de los Garza, Nuevo Leon (Mexico)
2006-04-15
In this paper, we recommend a new coordination system for time overcurrent relays. The purpose of the coordination process is to find a time element function that allows it to operate using a constant back-up time delay, for any fault current. In this article, we describe the implementation and coordination results of time overcurrent relays, fuses and reclosers. Experiments were carried out in a laboratory test situation using signals of a power electrical system physics simulator. (author)
Zenkina, Olena V; Gidron, Ori; Shimon, Linda J W; Iron, Mark A; van der Boom, Milko E
2015-11-01
This contribution describes the reactivity of a zero-valent palladium phosphine complex with substrates that contain both an aryl halide moiety and an unsaturated carbon-carbon bond. Although η(2) -coordination of the metal center to a C=C or C≡C unit is kinetically favored, aryl halide bond activation is favored thermodynamically. These quantitative transformations proceed under mild reaction conditions in solution or in the solid state. Kinetic measurements indicate that formation of η(2) -coordination complexes are not nonproductive side-equilibria, but observable (and in several cases even isolated) intermediates en route to aryl halide bond cleavage. At the same time, DFT calculations show that the reaction with palladium may proceed through a dissociation-oxidative addition mechanism rather than through a haptotropic intramolecular process (i.e., ring walking). Furthermore, the transition state involves coordination of a third phosphine to the palladium center, which is lost during the oxidative addition as the C-halide bond is being broken. Interestingly, selective activation of aryl halides has been demonstrated by adding reactive aryl halides to the η(2) -coordination complexes. The product distribution can be controlled by the concentration of the reactants and/or the presence of excess phosphine.
Calibration of transformation matrix in object body coordinate and camera coordinate
Song, Jincheng; Sun, Zengyu; Guo, Lei; Wang, Dongwei
2013-01-01
In this paper, a new coordinate system calibration is proposed in order to define the dependence of position between object body coordinate and camera coordinate which can be used in object measurement by the formation of image. Due to existing the fabrication and installation error, it is difficult to make system parallel between object body coordinate and camera coordinate. To resolve it, the deviation of the two coordinate system is demanded to measure detailed. The deviation compensation in the image processing software can ensure the accuracy the pitch angle and azimuth in the destination image of camera measurement system. In order to definite the position, a base coordinate system of theodolite is set by mutual-space measurement principle. After the measurement of theodolite system, a transformation matrix of the base coordinate system can be deduced. Changing the position of the theodolite station and adjusting the cross-screw to infinity, the transformation matrix between the base coordinate and star-sensor coordinate can be deduced by image formation of the destination at infinity. The position relation between object body and camera can be calculated by the transformation matrix. The results of the measurement experiment show that the gauging repeatability is 6' which can meet the system gauging demands.
张智晟; 温令云; 李国; 张伟
2014-01-01
To mitigate the impact of fluctuation of renewable generation output on power grid and accelerate the population of electric vehicles (EV), taking the minimized output fluctuation of renewable generation and the maximized income of EV users as objective function and considering the constraints of the electricity quantity stored in the battery, the charging/discharging power and the charging/discharging times, a multi-objective coordinated scheduling model, in which the grid-connectible EV, wind power generation system and photovoltaic (PV) generation system are taken into account simultaneously, is established. A virtual ideal molecular based multi-objective improved chemical reaction optimization algorithm(CROA) is proposed, and the established model is solved by the proposed algorithm. In allusion to such defects of CROA as slow convergence and low accuracy, the update mode of particle swarm optimization algorithm is integrated with the improved CROA. Results of calculation example show that through reasonably arranging the charging/discharging of EV, the output fluctuation of renewable generation can be effectively suppressed and the income of EV users can be increased. Comparison results show that the virtual ideal molecular based improved multi-objective CROA possesses strong searching ability.%为减小可再生能源出力波动对电网的影响以及加快电动汽车的普及速率，以最小化可再生能源的出力波动和最大化电动汽车用户收益为目标函数，计及电池储存电量约束、充放电功率约束和充放电次数约束等条件，建立了同时计及可入网电动汽车、风力发电和光伏发电系统的多目标协同调度模型。提出了基于虚拟理想分子的多目标改进化学反应优化算法(chemical reaction optimization algorithm ， CROA)，并用该算法对模型进行了求解，针对化学反应算法收敛速度慢、精度低的缺陷，在算法中融入了粒子群优化算法的更
Guo, Bingkun; Kong, Qingyu; Zhu, Ying; Mao, Ya; Wang, Zhaoxiang; Wan, Meixiang; Chen, Liquan
2011-12-23
Current lithium-ion battery (LIB) technologies are all based on inorganic electrode materials, though organic materials have been used as electrodes for years. Disadvantages such as limited thermal stability and low specific capacity hinder their applications. On the other hand, the transition metal oxides that provide high lithium-storage capacity by way of electrochemical conversion reaction suffer from poor cycling stability. Here we report a novel high-performance, organic, lithium-storage material, a polypyrrole-cobalt-oxygen (PPy-Co-O) coordination complex, with high lithium-storage capacity and excellent cycling stability. Extended X-ray absorption fine structure and Raman spectroscopy and other physical and electrochemical characterizations demonstrate that this coordination complex can be electrochemically fabricated by cycling PPy-coated Co(3)O(4) between 0.0 V and 3.0 V versus Li(+)/Li. Density functional theory (DFT) calculations indicate that each cobalt atom coordinates with two nitrogen atoms within the PPy-Co coordination layer and the layers are connected with oxygen atoms between them. Coordination weakens the C-H bonds on PPy and makes the complex a novel lithium-storage material with high capacity and high cycling stability.
Curvilinear coordinates for full-core atoms
Putrino, Anna; Bachelet, Giovanni B.
1998-03-01
Curvilinear coordinates, first introduced by F. Gygi for valence-only electronic systems within the local-density functional theory (F. Gygi, Europhysics Letters 19), 617 (1992)., can be used to describe both core and valence electrons in electronic-structure calculations. A simple and quite general coordinate transformation results in a large, yet affordable plane-wave energy cutoff for full-core systems (e.g., ~= 120 Ryd for carbon or silicon) within the local-density functional theory, and in a reduced correlation time for full-core variational Monte Carlo calculations. Numerical examples will be presented.
Characterizing traits of coordination
Poss, R.
2013-01-01
How can one recognize coordination languages and technologies? As this report shows, the common approach that contrasts coordination with computation is intellectually unsound: depending on the selected understanding of the word "computation", it either captures too many or too few programming
Coordination models and languages
Papadopoulos, G.A.; Arbab, F.
1998-01-01
A new class of models, formalisms and mechanisms has recently evolved for describing concurrent and distributed computations based on the concept of ``coordination''. The purpose of a coordination model and associated language is to provide a means of integrating a number of possibly heterogeneous c
Gorman, Jamie C; Amazeen, Polemnia G; Cooke, Nancy J
2010-07-01
Team coordination consists of both the dynamics of team member interaction and the environmental dynamics to which a team is subjected. Focusing on dynamics, an approach is developed that contrasts with traditional aggregate-static concepts of team coordination as characterized by the shared mental model approach. A team coordination order parameter was developed to capture momentary fluctuations in coordination. Team coordination was observed in three-person uninhabited air vehicle teams across two experimental sessions. The dynamics of the order parameter were observed under changes of a team familiarity control parameter. Team members returned for the second session to either the same (Intact) or different (Mixed) team. 'Roadblock' perturbations, or novel changes in the task environment, were introduced in order to probe the stability of team coordination. Nonlinear dynamic methods revealed differences that a traditional approach did not: Intact and Mixed team coordination dynamics looked very different; Mixed teams were more stable than Intact teams and explored the space of solutions without the need for correction. Stability was positively correlated with the number of roadblock perturbations that were overcome successfully. The novel and non-intuitive contribution of a dynamical analysis was that Mixed teams, who did not have a long history working together, were more adaptive. Team coordination dynamics carries new implications for traditional problems such as training adaptive teams.
De Chiffre, Leonardo
This document is used in connection with three exercises of 2 hours duration as a part of the course GEOMETRICAL METROLOGY AND MACHINE TESTING. The exercises concern three aspects of coordinate measuring: 1) Measuring and verification of tolerances on coordinate measuring machines, 2) Traceability...
Varlet, Manuel; Marin, Ludovic; Lagarde, Julien; Bardy, Benoit G.
2011-01-01
The goal of the current study was to investigate whether a visual coupling between two people can produce spontaneous interpersonal postural coordination and change their intrapersonal postural coordination involved in the control of stance. We examined the front-to-back head displacements of participants and the angular motion of their hip and…
Varlet, Manuel; Marin, Ludovic; Lagarde, Julien; Bardy, Benoit G.
2011-01-01
The goal of the current study was to investigate whether a visual coupling between two people can produce spontaneous interpersonal postural coordination and change their intrapersonal postural coordination involved in the control of stance. We examined the front-to-back head displacements of participants and the angular motion of their hip and…
Cerar, Janez
2015-01-01
Widely cited and accepted explanation of reaction mechanism of the case study reaction of chemical kinetics between Cr(III) ions and ethylenediaminetetraacetic acid (EDTA) contradicts modern chromium(III) coordination chemistry data. Absorption UV and visible light spectra were recorded during the reaction between aqueous solution of Cr(NO(3))(3) and EDTA in order to obtain new information about this reaction. Analysis of the spectra showed that only very small fraction of intermediates may be present in solution during the course of the reaction. The reaction scheme was established and according to it calculations based on a simplified model were carried out. Literature data for constants were used if known, otherwise, adjusted values of their sound estimates were applied. Reasonable agreement of the model calculations with the experimental data was obtained for pH values 3.8 and 4.5 but the model failed to reproduce measured rate of reaction at pH 5.5, probably due to the use of the oversimplified model.
Elucidating the coordination chemistry and mechanism of biological nitrogen fixation.
Dance, Ian
2007-08-03
How does the enzyme nitrogenase reduce the inert molecule N2 to NH3 under ambient conditions that are so different from the energy-expensive conditions of the best industrial practices? This review focuses on recent theoretical investigations of the catalytic site, the iron-molybdenum cofactor FeMo-co, and the way in which it is hydrogenated by protons and electrons and then binds N2. Density functional calculations provide reaction profiles and activation energies for possible mechanistic steps. This establishes a conceptual framework and the principles for the coordination chemistry of FeMo-co that are essential to the chemical mechanism of catalysis. The model advanced herein explains relevant experimental data.
Teramoto, Hiroshi; Toda, Mikito; Takahashi, Masahiko; Kono, Hirohiko; Komatsuzaki, Tamiki
2015-08-01
We present a mechanism of global reaction coordinate switching, namely, a phenomenon in which the reaction coordinate dynamically switches to another coordinate as the total energy of the system increases. The mechanism is based on global changes in the underlying phase space geometry caused by a switching of dominant unstable modes from the original reactive mode to another nonreactive mode in systems with more than 2 degrees of freedom. We demonstrate an experimental observability to detect a reaction coordinate switching in an ionization reaction of a hydrogen atom in crossed electric and magnetic fields. For this reaction, the reaction coordinate is a coordinate along which electrons escape and its switching changes the escaping direction from the direction of the electric field to that of the magnetic field and, thus, the switching can be detected experimentally by measuring the angle-resolved momentum distribution of escaping electrons.
荚更生
2011-01-01
In this paper,the impact of a single change in transformation parameters upon GPS positioning data was analyzed,and the linear relationship formula between the two positioning values（x,y） in the horizontal direction was calculated.A group of parallel linear curves were then obtained by analyzing the changes of the two transformation parameters.These features made it possible to calculate the transformation parameters from WGS84 to Xi＇an80 Coordinate System.A set of transformation parameters were thus worked out,which,the field positioning tests showed,could meet the needs of forestry field work.%通过对单个转换参数改变对GPS定位值的影响分析,得出水平方向上的两个定位值（x,y）之间为线性关系,再通过对两个转换参数变化的分析得到一组平行的线性曲线。这些特性的存在为求算WGS84到西安80坐标系间的转换参数提供了可能。笔者利用这些特性求算出一套转换参数,并通过外业定位试验说明它们可以满足林业外业工作的需要。
Radiation reaction reexamined: bound momentum and Schott term
Galtsov, D V; Gal'tsov, Dmitri V.; Spirin, Pavel
2004-01-01
We review and compare two different approaches to radiation reaction in classical electrodynamics of point charges: a local calculation of the self-force using the charge equation of motion and a global calculation consisting in integration of the electromagnetic energy-momentum flux through a hypersurface encircling the world-line. Both approaches are complementary and, being combined together, give rise to an identity relating the locally and globally computed forces. From this identity it follows that the Schott terms in the Abraham force should arise from the bound field momentum and can not be introduced by hand as an additional term in the mechanical momentum of an accelerated charge. This is in perfect agreement with the results of Dirac and Teitelboim, but disagrees with the recent calculation of the bound momentum in the retarded coordinates. We perform an independent calculation of the bound electromagnetic momentum and verify explicitly that the Schott term is the derivative of the finite part of t...
Inter ISO Market Coordination by Calculating Border Locational Marginal Prices
BABIC, A. B.
2013-05-01
Full Text Available In this paper the methodology for solving Locational Marginal Price (LMP differences (inconsistency of LMPs that arise at the boundary buses between separate power markets is proposed. The algorithm developed enables us to obtain consistent LMP values at the boundary buses between interconnected ISOs. A Primal-Dual Interior Point based optimal power flow (OPF is applied, with complete set of power system physical limit constraints, to solve a regional spot market. The OPF is implemented such that producer and consumer behaviors are modeled simultaneously, while the welfare is maximized. In this paper a generalized methodology for multiple ISOs case is proposed and later it is practically applied on two interconnected independent entities. The algorithm for approximation of cost coefficients of generators and dispatchable loads for neighboring ISOs is proposed. The developed algorithm enables participating ISOs to obtain LMPs at the boundary buses with other interconnected ISOs. By controlling interchange of electric power at the scheduled level, regional spot markets are resolved eliminating possible exercise of market power by individual interconnected ISOs. Results of proposed methodology are tested on the IEEE 118-bus power system.
Authier, N
1998-12-01
One of the questions asked in radiation shielding problems is the estimation of the radiation level in particular to determine accessibility of working persons in controlled area (nuclear power plants, nuclear fuel reprocessing plants) or to study the dose gradients encountered in material (iron nuclear vessel, medical therapy, electronics in satellite). The flux and reaction rate estimators used in Monte Carlo codes give average values in volumes or on surfaces of the geometrical description of the system. But in certain configurations, the knowledge of punctual deposited energy and dose estimates are necessary. The Monte Carlo estimate of the flux at a point of interest is a calculus which presents an unbounded variance. The central limit theorem cannot be applied thus no easy confidencelevel may be calculated. The convergence rate is then very poor. We propose in this study a new solution for the photon flux at a point estimator. The method is based on the 'once more collided flux estimator' developed earlier for neutron calculations. It solves the problem of the unbounded variance and do not add any bias to the estimation. We show however that our new sampling schemes specially developed to treat the anisotropy of the photon coherent scattering is necessary for a good and regular behavior of the estimator. This developments integrated in the TRIPOLI-4 Monte Carlo code add the possibility of an unbiased punctual estimate on media interfaces. (author)
Evans, H.T.
1963-01-01
A review of the known crystal structures containing the uranyl ion shows that plane-pentagon coordination is equally as prevalent as plane-square or plane-hexagon. It is suggested that puckered-hexagon configurations of OH - or H2O about the uranyl group will tend to revert to plane-pentagon coordination. The concept of pentagonal coordination is invoked for possible explanations of the complex crystallography of the natural uranyl hydroxides and the unusual behavior of polynuclear ions in hydrolyzed uranyl solutions.
Mehdizadeh, Sina; Arshi, Ahmed Reza; Davids, Keith
2015-07-01
The aims of this study were to compare coordination and coordination variability in backward and forward running and to investigate the effects of speed on coordination variability in both backward and forward running. Fifteen healthy male participants took part in this study to run forwards and backwards on a treadmill at 80%, 100% and 120% of their preferred running speeds. The coordinate data of passive reflective markers attached to body segments were recorded using motion capture systems. Coordination of shank-foot and thigh-shank couplings in sagittal plane was quantified using the continuous relative phase method. Coordination variability was calculated as the standard deviation of a coordination pattern over 50 strides. Cross-correlation coefficients and associated phase shifts were determined to quantify similarity in coordination patterns between forward and backward running. Our results demonstrated that the coordination pattern in a gait cycle of backward running was in reverse to that of forward running at all speeds implying that the same neural circuitry is responsible for regulating both forward and backward running gaits. In addition, results demonstrated that there was an average of approximately 11% phase shift between the coordination patterns of backward and forward running which indicates that a single underlying mechanism might be responsible for generating motor patterns in both forward and backward running. Finally, backward running had significantly higher magnitude of coordination variability compared to forward running, signifying that more degrees of freedom were involved in backward running. Speed however, did not affect coordination variability in either task. Copyright © 2015 Elsevier B.V. All rights reserved.
Nakamoto, Kazuo
2008-01-01
The Sixth Edition of this classic work comprises the most comprehensive and current guide to infrared and Raman spectra of inorganic, organometallic, bioinorganic, and coordination compounds. From fundamental theories of vibrational spectroscopy to applications in a variety of compound types, this has been extensively updated. New topics include the theoretical calculations of vibrational frequencies (DFT method), chemical synthesis by matrix co-condensation reactions, time-resolved Raman spectroscopy, and more. This volume is a core reference for chemists and medical professionals working with infrared or Raman spectroscopies and an excellent textbook for graduate courses.
Balance training enhances motor coordination during a perturbed side-step cutting task
Oliveira, Anderson Souza; Silva, Priscila de Brito; Lund, Morten Enemark
2017-01-01
, and ground reaction forces. Motor modules were extracted from the EMG by non-negative matrix factorization. External knee abduction moments were calculated using inverse dynamics equations. Results BTR resulted in a reduction of the external knee abduction moment (33 ± 25%, p2)=0.......725), and increased the activation of trunk and proximal hip muscles in specific motor modules during perturbed cutting. BTR also increased burst duration for the motor module related to landing early in the perturbation phase (23 ± 11%, p2)=0.532). Conclusion BTR resulted in altered motor coordination...
Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin
2015-11-12
High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.
Supercritical Airfoil Coordinates
National Aeronautics and Space Administration — Rectangular Supercritical Wing (Ricketts) - design and measured locations are provided in an Excel file RSW_airfoil_coordinates_ricketts.xls . One sheet is with Non...
Understanding social motor coordination.
Schmidt, R C; Fitzpatrick, Paula; Caron, Robert; Mergeche, Joanna
2011-10-01
Recently there has been much interest in social coordination of motor movements, or as it is referred to by some researchers, joint action. This paper reviews the cognitive perspective's common coding/mirror neuron theory of joint action, describes some of its limitations and then presents the behavioral dynamics perspective as an alternative way of understanding social motor coordination. In particular, behavioral dynamics' ability to explain the temporal coordination of interacting individuals is detailed. Two experiments are then described that demonstrate how dynamical processes of synchronization are apparent in the coordination underlying everyday joint actions such as martial art exercises, hand-clapping games, and conversations. The import of this evidence is that emergent dynamic patterns such as synchronization are the behavioral order that any neural substrate supporting joint action (e.g., mirror systems) would have to sustain.
Environmental Compliance Issue Coordination
An order to establish the Department of Energy (DOE) requirements for coordination of significant environmental compliance issues to ensure timely development and consistent application of Departmental environmental policy and guidance
Yang, Mingjun; Yang, Lijiang; Gao, Yiqin; Hu, Hao
2014-07-28
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when there exist multiple parallel channels along the reaction coordinate or hidden barriers in directions perpendicular to the reaction coordinate, it is difficult for conventional umbrella sampling to reach convergent sampling within limited simulation time. Here, we propose an approach to combine umbrella sampling with the integrated tempering sampling method. The umbrella sampling method is applied to chemically more relevant degrees of freedom that possess significant barriers. The integrated tempering sampling method is used to facilitate the sampling of other degrees of freedom which may possess statistically non-negligible barriers. The combined method is applied to two model systems, butane and ACE-NME molecules, and shows significantly improved sampling efficiencies as compared to standalone conventional umbrella sampling or integrated tempering sampling approaches. Further analyses suggest that the enhanced performance of the new method come from the complemented advantages of umbrella sampling with a well-defined reaction coordinate and integrated tempering sampling in orthogonal space. Therefore, the combined approach could be useful in the simulation of biomolecular processes, which often involves sampling of complex rugged energy landscapes.
Elizalde, J; Lorente, M
2006-01-01
The progressive incorporation of organ transplants as a therapeutic resource resulted in organisational adaptation and overall transplant management, leading to the emergence of the figure of the transplant coordinator in the mid-1980s. In Spain, the National Organisation of Transplants (Organización Nacional de Transplantes - ONT) was created, establishing a system - called the "Spanish model" - based on a network of coordinators at three levels: national, the autonomous community and the hospital. This organisational structure is a point of reference at the world level. The prevalence of the Intensive Medicine specialisation amongst hospital transplant coordinators is remarkable. The majority of organs proceed from brain-dead patients with beating hearts and this requires the infrastructure offered by intensive care units. The functions of the coordinator can be summarised in guaranteeing a synchrony of all the elements and teams that come together in an organisational chain that has come to be called the "process of donation". Schematically, the crucial points that the hospital coordinator develops are the following: - Detection of the potential donor. - Maintenance of the donor. - Diagnosis of brain death. - Family consent. - Preparation of the hospital logistics. - Helping the relatives. - Direct involvement in the Program of Guarantee of Quality. - Person of reference in any activity related to the transplant. It would be desirable to achieve the creation of transplant coordination teams, with univocal messages, professionalism and a permanent input of the so-called "human factor", which is so necessary and also so close to the transplant world.
Continuous parallel coordinates.
Heinrich, Julian; Weiskopf, Daniel
2009-01-01
Typical scientific data is represented on a grid with appropriate interpolation or approximation schemes,defined on a continuous domain. The visualization of such data in parallel coordinates may reveal patterns latently contained in the data and thus can improve the understanding of multidimensional relations. In this paper, we adopt the concept of continuous scatterplots for the visualization of spatially continuous input data to derive a density model for parallel coordinates. Based on the point-line duality between scatterplots and parallel coordinates, we propose a mathematical model that maps density from a continuous scatterplot to parallel coordinates and present different algorithms for both numerical and analytical computation of the resulting density field. In addition, we show how the 2-D model can be used to successively construct continuous parallel coordinates with an arbitrary number of dimensions. Since continuous parallel coordinates interpolate data values within grid cells, a scalable and dense visualization is achieved, which will be demonstrated for typical multi-variate scientific data.
姜树海; 陆怀民; 马岩
2012-01-01
In order to improve the volume reoovery and qualified rate of veneer peeling timber,based on the theory and method of veneer peeling six points centering,and the application of robot technology and design theory,the peeling intelligent centering grasping wood robot system was developed.Combined with robot mechanism and sensor detecting system,we did some research about the mathematical description of the six points centering coordinates calculation.Combined with the mathematical description of the physical model,we obtained the coordinates of each centering point.The centering experiment was carried out combined with the data from camera,displacement sensors,and the data of the four sections and six points centering were acquired.The centering results meet the indexes of the small centering robot system and validate the correctness of our calculation method and the model.The possible errors occurred during the system process were discussed,and the compensation method was put forward.%为了提高旋切单板出材率和合格率,基于单板旋切六点定心理论与方法,应用机器人技术与设计理论,研究开发了旋切智能定心上木机器人系统。结合机器人机构和传感检测系统,对六点定心点坐标求取的数学描述做了研究与实验。结合文中物理模型的数学描述,求取各定心点的坐标。结合摄像机、位移传感器获取的数据进行定心实验,获得四截面、六点定心的数据,定心结果满足小型定心机器人系统指标,从而验证所得的计算方法和采用模型的正确性。并对系统工作过程中可能产生的误差进行讨论,提出补偿方法。
Density Function Theory Studies on Reaction of HCS with OH
PEI Ke-Mei; LI Yi-Min; LI Hai-Yang
2003-01-01
The exothermic reaction of HCS with OH on the single-state potential energy surface was explored by means of Density Function Theory(DFT). The equilibrium structural parameters, the harmonic vibrational frequencies, the total energies and the zero point energies(ZPE) of all the species in the reaction were computed. Six intermediates and seven transition states were located, three exothermic channels were found. The frequency analysis and the Intrinsic Reaction Coordinate(IRC) calculation confirm that the transitions are truthful. The results indicate that there are three exothermic channels and their corresponding products are: P1(H2O+CS), P2(H2S+CO), P3(OCS+H2), and P1 has a larger branch ratio.
Basallote, Manuel G; Feliz, Marta; Fernández-Trujillo, M Jesús; Llusar, Rosa; Safont, Vicent S; Uriel, Santiago
2004-03-19
The cluster [W(3)S(4)H(3)(dmpe)(3)](+) (1) (dmpe=1,2-bis(dimethylphosphino)ethane) reacts with HX (X=Cl, Br) to form the corresponding [W(3)S(4)X(3)(dmpe)(3)](+) (2) complexes, but no reaction is observed when 1 is treated with an excess of halide salts. Kinetic studies indicate that the hydride 1 reacts with HX in MeCN and MeCN-H(2)O mixtures to form 2 in three kinetically distinguishable steps. In the initial step, the W-H bonds are attacked by the acid to form an unstable dihydrogen species that releases H(2) and yields a coordinatively unsaturated intermediate. This intermediate adds a solvent molecule (second step) and then replaces the coordinated solvent with X(-) (third step). The kinetic results show that the first step is faster with HCl than with solvated H(+). This indicates that the rate of protonation of this metal hydride is determined not only by reorganization of the electron density at the M-H bonds but also by breakage of the H-X or H(+)-solvent bonds. It also indicates that the latter process can be more important in determining the rate of protonation.
Zinc coordination spheres in protein structures.
Laitaoja, Mikko; Valjakka, Jarkko; Jänis, Janne
2013-10-07
Zinc metalloproteins are one of the most abundant and structurally diverse proteins in nature. In these proteins, the Zn(II) ion possesses a multifunctional role as it stabilizes the fold of small zinc fingers, catalyzes essential reactions in enzymes of all six classes, or assists in the formation of biological oligomers. Previously, a number of database surveys have been conducted on zinc proteins to gain broader insights into their rich coordination chemistry. However, many of these surveys suffer from severe flaws and misinterpretations or are otherwise limited. To provide a more comprehensive, up-to-date picture on zinc coordination environments in proteins, zinc containing protein structures deposited in the Protein Data Bank (PDB) were analyzed in detail. A statistical analysis in terms of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification was performed, revealing coordination spheres from classical tetrahedral cysteine/histidine binding sites to more complex binuclear sites with carboxylated lysine residues. According to the results, coordination spheres of hundreds of crystal structures in the PDB could be misinterpreted due to symmetry-related molecules or missing electron densities for ligands. The analysis also revealed increasing average metal-to-ligand bond length as a function of crystallographic resolution, which should be taken into account when interrogating metal ion binding sites. Moreover, one-third of the zinc ions present in crystal structures are artifacts, merely aiding crystal formation and packing with no biological significance. Our analysis provides solid evidence that a minimal stable zinc coordination sphere is made up by four ligands and adopts a tetrahedral coordination geometry.
高乐华; 高强
2012-01-01
With large-scale exploitation of marine resources and expansion of the development of marine industries,marine ecosystem health is severely affected.This study was aimed to expound an internal relationship,spatial and temporal evolution rules of China’s marine eco-economic system,and build a mechanism of coordinated development for the marine eco-economic system.In order to realize these goals,the ecological footprint method,measurement capacity and sustainable development model were jointly used to build a state evaluation index system.The Analytic Hierarchy Process（AHP）,entropy method,and multi-objective decision-making power coefficient method were employed to determine the weights of the evaluation index system.Subsequently,the coercion interactive theory and non-linear regression model were applied to fit dynamic curves of spatial and temporal evolution of three sub-systems,i.e.,ecology,economy,and society,for 11 coastal provinces in China during the period 2000-2009.It was found that logarithmic curve interactions existed in both space and time between the marine economic and marine social subsystems.Inverted＂U＂curve relationships existed between marine ecology and marine economic sub-systems.Double-exponential curve relationships existed between marine ecology and marine social sub-systems.The coupled model was applied to calculate the degree of spatial and temporal coordination of the three sub-systems,resulting in fitting curves and trends in coordination degree development which appears to be able to reflect the reality of the marine eco-economic system in 11 study coastal provinces and cities.The interactive coordination degrees among marine ecological,economic,and social sub-systems were generally in line with an＂S＂ shape.Because of high dependence on marine resources and the environment,some coastal provinces and cities are currently under a deteriorated condition of marine ecological systems.%随着人类开发海洋资源、发展海
McCarty, George
1982-01-01
How THIS BOOK DIFFERS This book is about the calculus. What distinguishes it, however, from other books is that it uses the pocket calculator to illustrate the theory. A computation that requires hours of labor when done by hand with tables is quite inappropriate as an example or exercise in a beginning calculus course. But that same computation can become a delicate illustration of the theory when the student does it in seconds on his calculator. t Furthermore, the student's own personal involvement and easy accomplishment give hi~ reassurance and en couragement. The machine is like a microscope, and its magnification is a hundred millionfold. We shall be interested in limits, and no stage of numerical approximation proves anything about the limit. However, the derivative of fex) = 67.SgX, for instance, acquires real meaning when a student first appreciates its values as numbers, as limits of 10 100 1000 t A quick example is 1.1 , 1.01 , 1.001 , •••• Another example is t = 0.1, 0.01, in the functio...
Zauleck, Julius P P; Thallmair, Sebastian; Loipersberger, Matthias; de Vivie-Riedle, Regina
2016-12-13
The curse of dimensionality still remains as the central challenge of molecular quantum dynamical calculations. Either compromises on the accuracy of the potential landscape have to be made or methods must be used that reduce the dimensionality of the configuration space of molecular systems to a low dimensional one. For dynamic approaches such as grid-based wave packet dynamics that are confined to a small number of degrees of freedom this dimensionality reduction can become a major part of the overall problem. A common strategy to reduce the configuration space is by selection of a set of internal coordinates using chemical intuition. We devised two methods that increase the degree of automation of the dimensionality reduction as well as replace chemical intuition by more quantifiable criteria. Both methods reduce the dimensionality linearly and use the intrinsic reaction coordinate as guidance. The first one solely relies on the intrinsic reaction coordinate (IRC), whereas the second one uses semiclassical trajectories to identify the important degrees of freedom.
Goze, Christine; Dupont, Nathalie; Beitler, Elvira; Leiggener, Claudia; Jia, Hongpeng; Monbaron, Philippe; Liu, Shi-Xia; Neels, Antonia; Hauser, Andreas; Decurtins, Silvio
2008-12-01
A pi-extended, redox-active bridging ligand 4',5'-bis(propylthio)tetrathiafulvenyl[i]dipyrido[2,3-a:3',2'-c]phenazine (L) was prepared via direct Schiff-base condensation of the corresponding diamine-tetrathiafulvalene (TTF) precursor with 4,7-phenanthroline-5,6-dione. Reactions of L with [Ru(bpy)(2)Cl(2)] afforded its stable mono- and dinuclear ruthenium(II) complexes 1 and 2. They have been fully characterized, and their photophysical and electrochemical properties are reported together with those of [Ru(bpy)(2)(ppb)](2+) and [Ru(bpy)(2)(mu-ppb)Ru(bpy)(2)](4+) (ppb = dipyrido[2,3-a:3',2'-c]phenazine) for comparison. In all cases, the first excited state corresponds to an intramolecular TTF --> ppb charge-transfer state. Both ruthenium(II) complexes show two strong and well-separated metal-to-ligand charge-transfer (MLCT) absorption bands, whereas the (3)MLCT luminescence is strongly quenched via electron transfer from the TTF subunit. Clearly, the transient absorption spectra illustrate the role of the TTF fragment as an electron donor, which induces a triplet intraligand charge-transfer state ((3)ILCT) with lifetimes of approximately 200 and 50 ns for mono- and dinuclear ruthenium(II) complexes, respectively.
Cobalt(II) and Cobalt(III) Coordination Compounds.
Thomas, Nicholas C.; And Others
1989-01-01
Presents a laboratory experiment which illustrates the formation of tris(phenanthroline)cobalt complexes in the 2+ and 3+ oxidation states, the effect of coordination on reactions of the ligand, and the use of a ligand displacement reaction in recovering the transformed ligand. Uses IR, UV-VIS, conductivity, and NMR. (MVL)
Coordinating Interactions: The Event Coordination Notation
Kindler, Ekkart
on a much more technical level. The Event Coordination Notation (ECNO) allows modelling the behaviour of an application on a high level of abstraction that is closer to the application’s domain than to the software realizing it. Still, these models contain all necessary details for actually executing...... implementation of ECNO, which consists of a modelling environment based on Eclipse and the Eclipse Modeling Framework (EMF) and an execution engine, which fully supports all the concepts and features of ECNO discussed in this technical report. All the examples are based on EMF, but the ECNO Engine can be used......The purpose of a domain model is to concisely capture the concepts of an application’s domain, and their relation among each other. Even though the main purpose of domain models is not on implementing the application, major parts of an application can be generated from the application’s domain...
García, José I; López-Sánchez, Beatriz; Mayoral, José A
2008-11-01
Combining the advantages of homogeneous and heterogeneous enantioselective catalysis is possible through self-supported copper coordination polymers, based on a new kind of ditopic chiral ligand bearing two azabis(oxazoline) moieties. When the coordination polymer is used to catalyze a cyclopropanation reaction, it becomes soluble in reaction conditions but precipitates after reaction completion, allowing easy recovery and efficient reuse in the same reaction up to 14 times.
Quantifying linguistic coordination
Fusaroli, Riccardo; Tylén, Kristian
). We employ nominal recurrence analysis (Orsucci et al 2005, Dale et al 2011) on the decision-making conversations between the participants. We report strong correlations between various indexes of recurrence and collective performance. We argue this method allows us to quantify the qualities......Language has been defined as a social coordination device (Clark 1996) enabling innovative modalities of joint action. However, the exact coordinative dynamics over time and their effects are still insufficiently investigated and quantified. Relying on the data produced in a collective decision...
Introduction to Coordination Chemistry
Lawrance, Geoffrey Alan
2010-01-01
Introduction to Coordination Chemistry examines and explains how metals and molecules that bind as ligands interact, and the consequences of this assembly process. This book describes the chemical and physical properties and behavior of the complex assemblies that form, and applications that may arise as a result of these properties. Coordination complexes are an important but often hidden part of our world?even part of us?and what they do is probed in this book. This book distills the essence of this topic for undergraduate students and for research scientists.
Coordinate Standard Measurement Development
Hanshaw, R.A.
2000-02-18
A Shelton Precision Interferometer Base, which is used for calibration of coordinate standards, was improved through hardware replacement, software geometry error correction, and reduction of vibration effects. Substantial increases in resolution and reliability, as well as reduction in sampling time, were achieved through hardware replacement; vibration effects were reduced substantially through modification of the machine component dampening and software routines; and the majority of the machine's geometry error was corrected through software geometry error correction. Because of these modifications, the uncertainty of coordinate standards calibrated on this device has been reduced dramatically.
Stereoselective coordination: a six-membered P,N-chelate tailored for asymmetric allylic alkylation.
Császár, Z; Farkas, G; Bényei, A; Lendvay, G; Tóth, I; Bakos, J
2015-10-01
Six-membered chelate complexes [Pd(1a-b)Cl2], (2a-b) and [Pd(1a-b)(η(3)-PhCHCHCHPh)]BF4, (3a-b) of P,N-type ligands 1a, ((2S,4S)-2-diphenyl-phosphino-4-isopropylamino-pentane) and 1b, ((2S,4S)-2-diphenyl-phosphino-4-methylamino-pentane) have been prepared. The Pd-complexes have been characterized in solution by 1D and 2D NMR spectroscopy. The observed structures were confirmed by DFT calculations and in the case of 2a also by X-ray crystallography. Unexpectedly, the coordination of the all-carbon-backbone aminophosphine 1a resulted in not only a stereospecific locking of the donor nitrogen atom into one of the two possible configurations but also the conformation of the six-membered chelate rings containing three alkyl substituents was forced into the same single chair structure showing the axially placed isopropyl group on the coordinated N-atom. The stereodiscriminative complexation of 1a led to the formation of a palladium catalyst with a conformationally rigid chelate having a configurationally fixed nitrogen and electronically different coordination sites due to the presence of P and N donors. The stereochemically fixed catalyst provided excellent ee's (up to 96%) and activities in asymmetric allylic alkylation reactions. In contrast, the chelate rings formed by 1b exist in two different chair conformations, both containing axial methyl groups, but with the opposite configurations of the coordinated N-atom. Pd-complexes of 1b provided low enantioselectivities in similar alkylations, therefore emphasizing the importance of the stereoselective coordination of N-atoms in analogous P-N chelates. The factors determining the coordination of the ligands were also studied with respect to the chelate ring conformation and the nitrogen configuration.
Basiuk, Vladimir A., E-mail: basiuk@nucleares.unam.mx [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito Exterior C.U., 04510 México D.F. (Mexico); Department of Chemistry,Tufts University, 62 Talbot Avenue, Medford, MA 02155 (United States); Alzate-Carvajal, Natalia [Centro de Ciencias Aplicadas y Desarrollo Tecnológico, Universidad Nacional Autónoma de México, Circuito Exterior C.U., 04510 México D.F. (Mexico); Henao-Holguín, Laura V. [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito Exterior C.U., 04510 México D.F. (Mexico); Rybak-Akimova, Elena V. [Department of Chemistry,Tufts University, 62 Talbot Avenue, Medford, MA 02155 (United States); Basiuk, Elena V., E-mail: elbg1111@gmail.com [Department of Chemistry,Tufts University, 62 Talbot Avenue, Medford, MA 02155 (United States); Centro de Ciencias Aplicadas y Desarrollo Tecnológico, Universidad Nacional Autónoma de México, Circuito Exterior C.U., 04510 México D.F. (Mexico)
2016-05-15
Highlights: • [Ni(cyclam)]{sup 2+} and [Ni(tet b)]{sup 2+} cations coordinate to carboxylic groups of GO. • The coordination takes place under basic conditions in aqueous-based medium. • The coordination results in the conversion from low-spin to high-spin Ni(II). • Functionalized GO samples were characterized by various instrumental techniques. - Abstract: We describe a novel approach to functionalization of graphene oxide (GO) which allows for a facile generation of paramagnetic centers from two diamagnetic components. Coordination attachment of [Ni(cyclam)]{sup 2+} or [Ni(tet b)]{sup 2+} tetraazamacrocyclic cations to carboxylic groups of GO takes place under basic conditions in aqueous-based reaction medium. The procedure is very straightforward and does not require high temperatures or other harsh conditions. Changing the coordination geometry of Ni(II) from square-planar tetracoordinated to pseudooctahedral hexacoordinated brings about the conversion from low-spin to high-spin state of the metal centers. Even though the content of tetraazamacrocyclic complexes in functionalized GO samples was found to be relatively low (nickel content of ca. 1 wt%, as determined by thermogravimetric analysis, elemental analysis and energy dispersive X-ray spectroscopy), room temperature magnetic susceptibility measurements easily detected the appearance of paramagnetic properties in GO + [Ni(cyclam)] and GO + [Ni(tet b)] nanohybrids, with effective magnetic moments of 1.95 BM and 2.2 BM for, respectively. According to density functional theory calculations, the main spin density is localized at the macrocyclic complexes, without considerable extension to graphene sheet, which suggests insignificant ferromagnetic coupling in the nanohybrids, in agreement with the results of magnetic susceptibility measurements. The coordination attachment of Ni(II) tetraazamacrocycles to GO results in considerable changes in Fourier-transform infrared and X-ray photoelectron spectra
Topochemical control in desolvation of coordination polymers
Matteo Lusi
2015-01-01
Reactions in the solid state are at the core of crystal engineering as they can result in new crystalline phases that are not always accessible by traditional solution methods. The work of Brammer and co-workers [Wright et al. (2015), IUCrJ, 2, 188–197] represents a clear example of this potential as applied to the synthesis of a silver–phenazine coordination polymer.
PIC: Protein Interactions Calculator.
Tina, K G; Bhadra, R; Srinivasan, N
2007-07-01
Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside.
Coordination failure caused by sunspots
Beugnot, Julie; Gürgüç, Zeynep; Øvlisen, Frederik Roose
2012-01-01
In a coordination game with Pareto-ranked equilibria, we study whether a sunspot can lead to either coordination on an inferior equilibrium (mis-coordination) or to out-of equilibrium behavior (dis-coordination). While much of the literature searches for mechanisms to attain coordination...... on the efficient equilibrium, we consider sunspots as a potential reason for coordination failure. We conduct an experiment with a three player 2x2x2 game in which coordination on the efficient equilibrium is easy and should normally occur. In the control session, we find almost perfect coordination on the payoff......-dominant equilibrium, but in the sunspot treatment, dis-coordination is frequent. Sunspots lead to significant inefficiency, and we conclude that sunspots can indeed cause coordination failure....
Calculating Electromagnetic Fields Of A Loop Antenna
Schieffer, Mitchell B.
1987-01-01
Approximate field values computed rapidly. MODEL computer program developed to calculate electromagnetic field values of large loop antenna at all distances to observation point. Antenna assumed to be in x-y plane with center at origin of coordinate system. Calculates field values in both rectangular and spherical components. Also solves for wave impedance. Written in MicroSoft FORTRAN 77.
Coordinating Work with Groupware
Pors, Jens Kaaber; Simonsen, Jesper
2003-01-01
One important goal of employing groupware is to make possible complex collaboration between geographically distributed groups. This requires a dual transformation of both technology and work practice. The challenge is to reduce the complexity of the coordination work by successfully integrating...
Rockin' Readers Coordinator Handbook.
Alachua County Schools, Gainesville, FL.
This coordinator's handbook describes the "Rockin' Readers" program, in which senior-citizen volunteers are matched with specifically targeted at-risk children (usually of kindergarten age or slightly older) in Alachua County, Florida, who tested below their peer group in language development and reading readiness skills. The handbook…
Hunter, G; Hunter, Geoffrey; Schlifer, Ian
2005-01-01
The recently established existence of spherical harmonic functions, $Y_\\ell^{m}(\\theta,\\phi)$ for half-odd-integer values of $\\ell$ and $m$, allows for the introduction into quantum chemistry of explicit electron spin-coordinates; i.e. spherical polar angles $\\theta_s, \\phi_s$, that specify the orientation of the spin angular momentum vector in space. In this coordinate representation the spin angular momentum operators, $S^2, S_z$, are represented by the usual differential operators in spherical polar coordinates (commonly used for $L^2, L_z$), and their electron-spin eigenfunctions are $\\sqrt{\\sin\\theta_s} \\exp(\\pm\\phi_s/2)$. This eigenfunction representation has the pedagogical advantage over the abstract spin eigenfunctions, $\\alpha, \\beta,$ that ``integration over spin coordinates'' is a true integration (over the angles $\\theta_s, \\phi_s$). In addition they facilitate construction of many electron wavefunctions in which the electron spins are neither parallel nor antiparallel, but inclined at an interme...
Equilibria with Coordination Failures
Herings, P.J.J.; van der Laan, G.; Talman, A.J.J.
2004-01-01
This paper extends the recent literature on equilibria with coordination failures to arbitrary convex sets of admissible prices.We introduce a new equilibrium concept, called quantity constrained equilibrium (QCE), giving a uni.ed treatment to all cases considered in the literature so far.At a QCE
Koh, Kyoung Moo; Wong-Foy, Antek G; Matzger, Adam J; Benin, Annabelle I; Willis, Richard R
2012-11-13
The present invention provides compositions of crystalline coordination copolymers wherein multiple organic molecules are assembled to produce porous framework materials with layered or core-shell structures. These materials are synthesized by sequential growth techniques such as the seed growth technique. In addition, the invention provides a simple procedure for controlling functionality.
Non-commutativity in polar coordinates
Edwards, James P
2016-01-01
We reconsider the fundamental commutation relations for non-commutative $\\mathbb{R}^{2}$ described in polar coordinates with non-commutativity parameter $\\theta$. Previous analysis found that the natural transition from Cartesian coordinates to polars led to a representation of $\\left[\\hat{r}, \\hat{\\varphi}\\right]$ as an everywhere diverging series. We compute the Borel resummation of this series, showing that it can subsequently be extended throughout parameter space and hence provide an interpretation of this commutator. Our analysis provides a complete solution for arbitrary $r$ and $\\theta$ that reproduces the earlier calculations at lowest order. We compare our results to previous literature in the (pseudo-)commuting limit, finding a surprising spatial dependence for the coordinate commutator when $\\theta \\gg r^{2}$. We raise some questions for future study in light of this progress.
Non-commutativity in polar coordinates
Edwards, James P. [Universidad Michoacana de San Nicolas de Hidalgo, Ciudad Universitaria, Instituto de Fisica y Matematicas, Morelia, Michoacan (Mexico)
2017-05-15
We reconsider the fundamental commutation relations for non-commutative R{sup 2} described in polar coordinates with non-commutativity parameter θ. Previous analysis found that the natural transition from Cartesian coordinates to the traditional polar system led to a representation of [r, φ] as an everywhere diverging series. In this article we compute the Borel resummation of this series, showing that it can subsequently be extended throughout parameter space and hence provide an interpretation of this commutator. Our analysis provides a complete solution for arbitrary r and θ that reproduces the earlier calculations at lowest order and benefits from being generally applicable to problems in a two-dimensional non-commutative space. We compare our results to previous literature in the (pseudo-)commuting limit, finding a surprising spatial dependence for the coordinate commutator when θ >> r{sup 2}. Finally, we raise some questions for future study in light of this progress. (orig.)
On the existence of MSA coordinates
Hernández-Pastora, J L
2009-01-01
The static solutions of the axially symmetric vacuum Einstein equations with a finite number of Relativistic Multipole Moments are described by means of a function that can be written in the same analytic form as the Newtonian gravitational multipole potential. A family of so-called MSA (Multipole-Symmetry Adapted) coordinates are introduced and calculated at any multipole order to perform the transformation of the Weyl solutions. In analogy with a previous result obtained in Newtonian gravity, the existence of a symmetry of a certain system of differential equations leading to the determination of that kind of multipole solutions in General Relativity is explored. The relationship between the existence of this kind of coordinate and the symmetries mentioned is proved for some cases, and the characterization of the MSA system of coordinates by means of this relationship is discussed.
McGinley, John; McKee, Vickie; Toftlund, Hans
2009-01-01
The simple ligand N-(2-aminoethyl)-2-hydroxy-5-nitrobenzamide () exhibits several coordination modes depending on the reaction conditions, acting as a zwitterion on its own or being ionic in the presence of acid and depending on the concentration of metal present in a reaction, it can coordinate ...
Li, Hanshan; Lei, Zhiyong
2013-01-01
To improve projectile coordinate measurement precision in fire measurement system, this paper introduces the optical fiber coding fire measurement method and principle, sets up their measurement model, and analyzes coordinate errors by using the differential method. To study the projectile coordinate position distribution, using the mathematical statistics hypothesis method to analyze their distributing law, firing dispersion and probability of projectile shooting the object center were put under study. The results show that exponential distribution testing is relatively reasonable to ensure projectile position distribution on the given significance level. Through experimentation and calculation, the optical fiber coding fire measurement method is scientific and feasible, which can gain accurate projectile coordinate position.
周传佩; 陈文生; 刘义; 屈松生; 章习哲
2001-01-01
The molar dissolution enthalpy of the reactants and the products of the coordination reaction of Samarium Chloride with Glycine have been measured by isoperihol solution calorimetry, the calorimetric solvent is 2mol·L-1 HCl solution. The standard molar reaction enthalpy △,H m (298.2K) is -7. 3381kJ ·mol-1. From the results and other auxiliary quantities, the standard molar enthalpy of formation of the new coordination compound has been calculated to be △Hm(Sm(Gly)3Cl3·3H2O, s,298.2K)= -3631.74kJ·mol-1.
Calculations in furnace technology
Davies, Clive; Hopkins, DW; Owen, WS
2013-01-01
Calculations in Furnace Technology presents the theoretical and practical aspects of furnace technology. This book provides information pertinent to the development, application, and efficiency of furnace technology. Organized into eight chapters, this book begins with an overview of the exothermic reactions that occur when carbon, hydrogen, and sulfur are burned to release the energy available in the fuel. This text then evaluates the efficiencies to measure the quantity of fuel used, of flue gases leaving the plant, of air entering, and the heat lost to the surroundings. Other chapters consi
Cameron, T Stanley; Decken, Andreas; Krossing, Ingo; Passmore, Jack; Rautiainen, J Mikko; Wang, Xinping; Zeng, Xiaoqing
2013-03-18
Two silver-cyclodimethylsiloxane cation salts [AgD6][Al] ([Al] = [Al(ORF)4](1) or [FAl(OR(F))3](2), R(F) = C(CF3)3, D = Me2SiO) were prepared by the reactions of Ag[Al] with D6 in SO2(l). For a comparison the [Ag(18-crown-6)]2[SbF6]2(3) salt was prepared by the reaction of Ag[SbF6] and 18-crown-6 in SO2(l). The compounds were characterized by IR, multinuclear NMR, and single crystal X-ray crystallography. The structures of 1 and 2 show that D6 acts as a pseudo crown ether toward Ag(+). The stabilities and bonding of [MDn](+) and [M(18-crown-6)](+) (M = Ag, Li, n = 4-8) complexes were studied with theoretical calculations. The calculations predicted that D6 adopts a puckered C(i) symmetric structure in the gas phase in contrast to previous reports. 18-Crown-6 was calculated to bind more strongly to Li(+) and Ag(+) than D6. (29)Si[(1)H] NMR results in solution, and calculations in the gas phase established that a hard Lewis acid Li(+) binds more strongly to D6 than Ag(+). A comparison of the [MD(n)](+) complex stabilities showed D7 to form the most stable metal complexes in the gas phase and the solid state and explained why [AgD7][SbF6] was isolated in a previous reaction where ring transformations resulted in an equilibrium of [AgD(n)](+) complexes. In contrast, the isolations of 1 and 2 were possible because the corresponding equilibrium of [AgD(n)](+) complexes was not observed with [Al](-) anions. The formation of the dinuclear complex salt 3 instead of the corresponding mononuclear complex salt was shown to be driven by the gain in lattice enthalpy in the solid state. The bonding to Li(+) in D6 and 18-crown-6 metal complexes was described by a quantum theory of atoms in molecules (QTAIM) analysis to be mostly electrostatic while the bonding to Ag(+) also had a significant charge transfer component. The charge transfer from both D6 and 18-crown-6 to Ag(+) and Li(+) metal ions was depicted by the QTAIM analysis to be of similar strength, and the difference in the
Diffusion Monte Carlo in internal coordinates.
Petit, Andrew S; McCoy, Anne B
2013-08-15
An internal coordinate extension of diffusion Monte Carlo (DMC) is described as a first step toward a generalized reduced-dimensional DMC approach. The method places no constraints on the choice of internal coordinates other than the requirement that they all be independent. Using H(3)(+) and its isotopologues as model systems, the methodology is shown to be capable of successfully describing the ground state properties of molecules that undergo large amplitude, zero-point vibrational motions. Combining the approach developed here with the fixed-node approximation allows vibrationally excited states to be treated. Analysis of the ground state probability distribution is shown to provide important insights into the set of internal coordinates that are less strongly coupled and therefore more suitable for use as the nodal coordinates for the fixed-node DMC calculations. In particular, the curvilinear normal mode coordinates are found to provide reasonable nodal surfaces for the fundamentals of H(2)D(+) and D(2)H(+) despite both molecules being highly fluxional.
Bourgalais, Jeremy; Kailasanathan, Ranjith Kumar Abhinavam; Osborn, David L; Hickson, Kevin M; Loison, Jean-Christophe; Wakelam, Valentine; Goulay, Fabien; Picard, Sébastien D Le
2016-01-01
The product formation channels of ground state carbon atoms, C(3P), reacting with ammonia, NH3, have been investigated using two complementary experiments and electronic structure calculations. Reaction products are detected in a gas flow tube experiment (330 K, 4 Torr) using tunable VUV photoionization coupled with time of flight mass spectrometry. Temporal profiles of the species formed and photoionization spectra are used to identify primary products of the C + NH3 reaction. In addition, H-atom formation is monitored by VUV laser induced fluorescence from room temperature to 50 K in a supersonic gas flow generated by the Laval nozzle technique. Electronic structure calculations are performed to derive intermediates, transition states and complexes formed along the reaction coordinate. The combination of photoionization and laser induced fluorescence experiments supported by theoretical calculations indicate that in the temperature and pressure range investigated, the H + H2CN production channel represents ...
1985-02-01
Time in hours at Oh UT is GAST (hours) = GMST + E (41) GAST in radians is GASTo (radians) = GAST (hours) L (42) The angle e required for transforming...inertial coordinates to ECEF is- 6(radians) GASTo + 6.3003880.99 (ti - th) (43) o ~ooUT Mod ( E 27) where St.i - tohLjT = (JD -2.4 106). (JDOE -2.4 x
International Monetary Policy Coordination
Carlberg, Michael
2005-01-01
This paper studies the international coordination of monetary policies in the world economy. It carefully discusses the process of policy competition and the structure of policy cooperation. As to policy competition, the focus is on monetary competition between Europe and America. Similarly, as to policy cooperation, the focus is on monetary cooperation between Europe and America. The spillover effects of monetary policy are negative. The policy targets are price stability and full employment.
Meson production in + reactions
H Machner; M Betigeri; J Bojowald; A Budzanowski; A Chatterjee; J Ernst; L Freindl; D Frekers; W Garske; K Grewer; A Hamacher; J Ilieva; L Jarczyk; K Kilian; S Kliczewski; W Klimala; D Kolev; T Kutsarova; J Lieb; H Machner; A Magiera; H Nann; L Pentchev; H S Plendl; D Protić; B Razen; P Von Rossen; B J Roy; R Siudak; J Smyrski; R V Srikantiah; A Strzałkowski; R Tsenov; K Zwoll
2001-08-01
Total and differential cross sections for the reactions $p+d → 3He + 0 with = ; and + → 3H + + were measured with the GEM detector at COSY for beam momenta between threshold and the maximum of the corresponding baryon resonance. For both reactions a strong forward–backward asymmetry was found. The data were compared with model calculations. The aspect of isospin symmetry breaking is studied.
陈志明; 倪天军; 宫腾; 赵永梅; 朱守荣
2012-01-01
Two 1D copper coordination polymers,{[Cu2L(4,4′-bipy)(H2O)2]·2.5H2O}n(1)and {[Cu2L(mbix)(H2O)2]·3H2O}n(2)(H4L=N,N,N′,N′-m-xylylenediamine tetracetic acid,mbix=m-bis(imidazol-1-ylmethyl)benzene)have been synthesized for the continuance of our research work on the coordination frameworks and oxidation reaction of copper(Ⅱ)complexes with ligand L4-.Compound 1 crystallizes in monoclinic system with space group P21/c and compound 2 crystallizes in space group P(1)with triclinic system,and they both form a 1D zigig-like chain.Interchain hydrogen-bonding interactions further extend the 1D arrangement to generate a 3D supramolecular architecture for 1 and 2.UV-Vis spectra shows that compound 1 and 2 both can hydroxylate the xylyl linker in the supporting ligand L4-in spite of chemical degradation of the two compounds by reaction with H2O2.CCDC:888051,1; 888052,2.%本文利用柔性的N,N,N′,N′-间-二甲苯二胺四乙酸(H4L)及不同的氮杂环配体如刚性的4-4′-联吡啶(4,4′-bipy)及柔性的间-二(咪唑-1-亚甲基)苯(mbix)构筑了2个新的一维铜配位聚合物{[Cu2L(4,4 ′-bipy)(H2O)2]·2.5H2O}n(1)和{[Cu2L(mbix)(H2O)2]·3H2O｝n(2),并对其进行了元素分析、红外光谱和X-ray单晶衍射表征.另外利用紫外-可见光谱的方法对2个化合物与H2O2的氧化反应进行了研究,结果表明虽然化合物1和2在高浓度的H2O2条件下均发生了分子断裂,但仍能使配体L4-中二甲苯基联接体C2位置发生羟基化.
Global coordination: weighted voting
Jan-Erik Lane
2014-03-01
Full Text Available In order to halt the depletion of global ecological capital, a number of different kinds of meetings between Governments of countries in the world has been scheduled. The need for global coordination of environmental policies has become ever more obvious, supported by more and more evidence of the running down of ecological capital. But there are no formal or binding arrangements in sight, as global environmental coordination suffers from high transaction costs (qualitative voting. The CO2 equivalent emissions, resulting in global warming, are driven by the unstoppable economic expansion in the global market economy, employing mainly fossil fuel generated energy, although at the same time lifting sharply the GDP per capita of several emerging countries. Only global environmental coordination on the successful model of the World Band and the IMF (quantitative voting can stem the rising emissions numbers and stop further environmental degradation. However, the system of weighted voting in the WB and the IMF must be reformed by reducing the excessive voting power disparities, for instance by reducing all member country votes by the cube root expression.