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Sample records for complex biochemical reaction

  1. Probabilistic sensitivity analysis of biochemical reaction systems.

    Science.gov (United States)

    Zhang, Hong-Xuan; Dempsey, William P; Goutsias, John

    2009-09-07

    Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology. We develop here a probabilistic approach to sensitivity analysis of biochemical reaction systems. The proposed technique employs a biophysically derived model for parameter fluctuations and, by using a recently suggested variance-based approach to sensitivity analysis [Saltelli et al., Chem. Rev. (Washington, D.C.) 105, 2811 (2005)], it leads to a powerful sensitivity analysis methodology for biochemical reaction systems. The approach presented in this paper addresses many problems associated with derivative-based sensitivity analysis techniques. Most importantly, it produces thermodynamically consistent sensitivity analysis results, can easily accommodate appreciable parameter variations, and allows for systematic investigation of high-order interaction effects. By employing a computational model of the mitogen-activated protein kinase signaling cascade, we demonstrate that our approach is well suited for sensitivity analysis of biochemical reaction systems and can produce a wealth of information about the sensitivity properties of such systems. The price to be paid, however, is a substantial increase in computational complexity over derivative-based techniques, which must be effectively addressed in order to make the proposed approach to sensitivity analysis more practical.

  2. Biochemical reactions of the organism

    International Nuclear Information System (INIS)

    Fedorova, A.V.

    1984-01-01

    Effects of mercury, strontium chloride, GMDA, trichlorfon as well as some radionuclides ( 89 Sr, 137 Cs, 203 Hg) were studied on rats. Changes in biochemical parameters (histamine content, activity of cholinesterase and histaminase) are noted. Most noticeable changes were observed in enzymatic activity. Distortion of enzymatic systems and accumulation of intermediate exchange and decay products of tissues in excess quantities affecting other systems can be the reason for changes in the organism. The observed changes in biochemical parameters should be necessarily taken into account at hygienic regulations of harmful effects of enviroment

  3. Explorations into Chemical Reactions and Biochemical Pathways.

    Science.gov (United States)

    Gasteiger, Johann

    2016-12-01

    A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Simulation studies in biochemical signaling and enzyme reactions

    Science.gov (United States)

    Nelatury, Sudarshan R.; Vagula, Mary C.

    2014-06-01

    Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

  5. Characterizing multistationarity regimes in biochemical reaction networks.

    Directory of Open Access Journals (Sweden)

    Irene Otero-Muras

    Full Text Available Switch like responses appear as common strategies in the regulation of cellular systems. Here we present a method to characterize bistable regimes in biochemical reaction networks that can be of use to both direct and reverse engineering of biological switches. In the design of a synthetic biological switch, it is important to study the capability for bistability of the underlying biochemical network structure. Chemical Reaction Network Theory (CRNT may help at this level to decide whether a given network has the capacity for multiple positive equilibria, based on their structural properties. However, in order to build a working switch, we also need to ensure that the bistability property is robust, by studying the conditions leading to the existence of two different steady states. In the reverse engineering of biological switches, knowledge collected about the bistable regimes of the underlying potential model structures can contribute at the model identification stage to a drastic reduction of the feasible region in the parameter space of search. In this work, we make use and extend previous results of the CRNT, aiming not only to discriminate whether a biochemical reaction network can exhibit multiple steady states, but also to determine the regions within the whole space of parameters capable of producing multistationarity. To that purpose we present and justify a condition on the parameters of biochemical networks for the appearance of multistationarity, and propose an efficient and reliable computational method to check its satisfaction through the parameter space.

  6. Conservation Laws in Biochemical Reaction Networks

    DEFF Research Database (Denmark)

    Mahdi, Adam; Ferragut, Antoni; Valls, Claudia

    2017-01-01

    We study the existence of linear and nonlinear conservation laws in biochemical reaction networks with mass-action kinetics. It is straightforward to compute the linear conservation laws as they are related to the left null-space of the stoichiometry matrix. The nonlinear conservation laws...... are difficult to identify and have rarely been considered in the context of mass-action reaction networks. Here, using the Darboux theory of integrability, we provide necessary structural (i.e., parameterindependent) conditions on a reaction network to guarantee the existence of nonlinear conservation laws...

  7. Modeling of uncertainties in biochemical reactions.

    Science.gov (United States)

    Mišković, Ljubiša; Hatzimanikatis, Vassily

    2011-02-01

    Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual reactions. However, kinetic data acquired from experimental observations bring along uncertainties due to various experimental conditions and measurement methods. In this contribution, we propose a novel way to model the uncertainty in the enzyme kinetics and to predict quantitatively the responses of metabolic reactions to the changes in enzyme activities under uncertainty. The proposed methodology accounts explicitly for mechanistic properties of enzymes and physico-chemical and thermodynamic constraints, and is based on formalism from systems theory and metabolic control analysis. We achieve this by observing that kinetic responses of metabolic reactions depend: (i) on the distribution of the enzymes among their free form and all reactive states; (ii) on the equilibrium displacements of the overall reaction and that of the individual enzymatic steps; and (iii) on the net fluxes through the enzyme. Relying on this observation, we develop a novel, efficient Monte Carlo sampling procedure to generate all states within a metabolic reaction that satisfy imposed constrains. Thus, we derive the statistics of the expected responses of the metabolic reactions to changes in enzyme levels and activities, in the levels of metabolites, and in the values of the kinetic parameters. We present aspects of the proposed framework through an example of the fundamental three-step reversible enzymatic reaction mechanism. We demonstrate that the equilibrium displacements of the individual enzymatic steps have an important influence on kinetic responses of the enzyme. Furthermore, we derive the conditions that must be satisfied by a reversible three-step enzymatic reaction operating far away from the equilibrium in order to respond to

  8. Modeling stochasticity in biochemical reaction networks

    International Nuclear Information System (INIS)

    Constantino, P H; Vlysidis, M; Smadbeck, P; Kaznessis, Y N

    2016-01-01

    Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts. (topical review)

  9. The human sunburn reaction: histologic and biochemical studies

    International Nuclear Information System (INIS)

    Gilchrest, B.A.; Soter, N.A.; Stoff, J.S.; Mihm, M.C. Jr.

    1981-01-01

    The ultraviolet-induced erythema reaction was investigated histologically and biochemically in four subjects, utilizing suction blister aspirates, analyzed for histamine and prostaglandin E2 (PGE2), and Epon-embedded 1-mu skin biopsy sections from control skin and from irradiated skin at intervals for 72 hours after exposure to a Hanovia lamp. Major histologic alterations in the epidermis included dyskeratotic and vacuolated keratinocytes (sunburn cells), and disappearance of Langerhans cells. In the dermis the major changes were vascular, involving both the superficial and deep venular plexuses. Endothelial cell enlargement was first apparent within 30 minutes of irradiation, peaked at 24 hours, and persisted throughout the 72-hour study period. Mast cell degranulation and associated perivenular edema were first apparent at 1 hour and striking at the onset of erythema, 3 to 4 hours postirradiation; edema was absent and mast cells were again normal in number and granule content at 24 hours. Histamine levels rose approximately fourfold above control values immediately after the onset of erythema and returned to baseline within 24 hours. PGE2 levels were statistically elevated even before the onset of erythema and reached approximately 150% of the control value at 24 hours. These data provide the first evidence that histamine may mediate the early phase of the human sunburn reaction and increase our understanding of its complex histologic and biochemical sequelae

  10. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

    Science.gov (United States)

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

    2011-09-01

    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

  11. Mean field interaction in biochemical reaction networks

    KAUST Repository

    Tembine, Hamidou; Tempone, Raul; Vilanova, Pedro

    2011-01-01

    In this paper we establish a relationship between chemical dynamics and mean field game dynamics. We show that chemical reaction networks can be studied using noisy mean field limits. We provide deterministic, noisy and switching mean field limits

  12. Substitution reactions of technetium complexes

    International Nuclear Information System (INIS)

    Omori, T.

    1997-01-01

    Substitution reactions of a series of technetium complexes are considered in comparison with corresponding reactions of rhenium. Rhenium and technetium complexes are rather inert in substitution reactions, the latter are characterized by greater rate constants when they proceed according to dissociative mechanism. In rare cases when k Tc /k Re id little it is assumed that the reaction proceeds according to the associative mechanism. (author)

  13. Mean field interaction in biochemical reaction networks

    KAUST Repository

    Tembine, Hamidou

    2011-09-01

    In this paper we establish a relationship between chemical dynamics and mean field game dynamics. We show that chemical reaction networks can be studied using noisy mean field limits. We provide deterministic, noisy and switching mean field limits and illustrate them with numerical examples. © 2011 IEEE.

  14. Accurate atom-mapping computation for biochemical reactions.

    Science.gov (United States)

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  15. Characterising Complex Enzyme Reaction Data.

    Directory of Open Access Journals (Sweden)

    Handan Melike Dönertaş

    Full Text Available The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG. Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution.

  16. Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

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    Goutsias John

    2010-11-01

    Full Text Available Abstract Background Estimating the rate constants of a biochemical reaction system with known stoichiometry from noisy time series measurements of molecular concentrations is an important step for building predictive models of cellular function. Inference techniques currently available in the literature may produce rate constant values that defy necessary constraints imposed by the fundamental laws of thermodynamics. As a result, these techniques may lead to biochemical reaction systems whose concentration dynamics could not possibly occur in nature. Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable. Results We introduce a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. Our method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations. The proposed method employs a maximization-expectation-maximization algorithm that provides thermodynamically feasible estimates of the rate constant values and computes appropriate measures of estimation accuracy. We demonstrate various aspects of the proposed method on synthetic data obtained by simulating a subset of a well-known model of the EGF/ERK signaling pathway, and examine its robustness under conditions that violate key assumptions. Software, coded in MATLAB®, which implements all Bayesian analysis techniques discussed in this paper, is available free of charge at http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.html. Conclusions Our approach provides an attractive statistical methodology for

  17. Reaction mechanisms of metal complexes

    CERN Document Server

    Hay, R W

    2000-01-01

    This text provides a general background as a course module in the area of inorganic reaction mechanisms, suitable for advanced undergraduate and postgraduate study and/or research. The topic has important research applications in the metallurgical industry and is of interest in the science of biochemistry, biology, organic, inorganic and bioinorganic chemistry. In addition to coverage of substitution reactions in four-, five- and six-coordinate complexes, the book contains further chapters devoted to isomerization and racemization reactions, to the general field of redox reactions, and to the reactions of coordinated ligands. It is relevant in other fields such as organic, bioinorganic and biological chemistry, providing a bridge to organic reaction mechanisms. The book also contains a chapter on the kinetic background to the subject with many illustrative examples which should prove useful to those beginning research. Provides a general background as a course module in the area of inorganic reaction mechanis...

  18. Effect of Modifying Factors on Radiosensitive Biochemical Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Romantsev, E. F.; Filippovich, I. V.; Zhulanova, Z. I.; Blokhina, V. D.; Trebenok, Z. A.; Kolesnikov, E. E.; Sheremetyevskaya, T. N.; Nikolsky, A. V.; Zymaleva, O. G. [Institute of Biophysics, USSR Ministry of Health, Moscow, USSR (Russian Federation)

    1971-03-15

    Some of the radioprotective aminothiols are now routine pharmacopoeial drugs and are used in clinics to decrease the radiation reaction which appears as a side effect during the radiotherapy of cancer. The action of effective modifying agents on radiosensitive biochemical reactions in the organisms of mammals, in principle, cannot be different from the same effects of the protectors on biochemical systems of the human organism. The effect of modifying agents is mediated by biochemical systems. The administration of radioprotective doses of MEA to rats before irradiation results in a significant normalization of the excretion in urine of degradation products of nucleic acids (so-called Dische-positive compounds), the excretion of which sharply rises after irradiation. The curve of the radioprotective effect of MEA (survival rate after administration of radioprotectors at different intervals of time) completely corresponds to curves of the accumulation of MEA which is bound (by mixed disulphide links) to the proteins of liver mitochondria, to proteins of the nuclear-sap, to the hyaloplasm of rat thymus and to the nuclear ribosomes of the spleen. After MEA administration the curve of the biosynthesis of deoxycytidine represents a mirror reflection of the curve of MEA bound to proteins of the thymus hyaloplasm by means of mixed disulphide links. The mechanism of action of such modifying factors as MEA in experiments on mammals is mediated to a great degree through the temporary formation of mixed disulphide links between the aminothiol and the protein component of enzymes in different biochemical systems. (author)

  19. Modelling biochemical reaction systems by stochastic differential equations with reflection.

    Science.gov (United States)

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan

    2016-05-07

    In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

    Directory of Open Access Journals (Sweden)

    Luca Marchetti

    2017-01-01

    Full Text Available HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA. HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA.

  1. Markovian dynamics on complex reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Goutsias, J., E-mail: goutsias@jhu.edu; Jenkinson, G., E-mail: jenkinson@jhu.edu

    2013-08-10

    Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.

  2. Markovian dynamics on complex reaction networks

    International Nuclear Information System (INIS)

    Goutsias, J.; Jenkinson, G.

    2013-01-01

    Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples

  3. A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems

    Directory of Open Access Journals (Sweden)

    Goutsias John

    2010-05-01

    Full Text Available Abstract Background Sensitivity analysis is an indispensable tool for the analysis of complex systems. In a recent paper, we have introduced a thermodynamically consistent variance-based sensitivity analysis approach for studying the robustness and fragility properties of biochemical reaction systems under uncertainty in the standard chemical potentials of the activated complexes of the reactions and the standard chemical potentials of the molecular species. In that approach, key sensitivity indices were estimated by Monte Carlo sampling, which is computationally very demanding and impractical for large biochemical reaction systems. Computationally efficient algorithms are needed to make variance-based sensitivity analysis applicable to realistic cellular networks, modeled by biochemical reaction systems that consist of a large number of reactions and molecular species. Results We present four techniques, derivative approximation (DA, polynomial approximation (PA, Gauss-Hermite integration (GHI, and orthonormal Hermite approximation (OHA, for analytically approximating the variance-based sensitivity indices associated with a biochemical reaction system. By using a well-known model of the mitogen-activated protein kinase signaling cascade as a case study, we numerically compare the approximation quality of these techniques against traditional Monte Carlo sampling. Our results indicate that, although DA is computationally the most attractive technique, special care should be exercised when using it for sensitivity analysis, since it may only be accurate at low levels of uncertainty. On the other hand, PA, GHI, and OHA are computationally more demanding than DA but can work well at high levels of uncertainty. GHI results in a slightly better accuracy than PA, but it is more difficult to implement. OHA produces the most accurate approximation results and can be implemented in a straightforward manner. It turns out that the computational cost of the

  4. Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory.

    Science.gov (United States)

    Pantazis, Yannis; Katsoulakis, Markos A; Vlachos, Dionisios G

    2013-10-22

    Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks. Typically, such mathematical models involve networks of coupled jump stochastic processes with a large number of parameters that need to be suitably calibrated against experimental data. In this direction, the parameter sensitivity analysis of reaction networks is an essential mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. However, existing sensitivity analysis approaches such as variants of the finite difference method can have an overwhelming computational cost in models with a high-dimensional parameter space. We develop a sensitivity analysis methodology suitable for complex stochastic reaction networks with a large number of parameters. The proposed approach is based on Information Theory methods and relies on the quantification of information loss due to parameter perturbations between time-series distributions. For this reason, we need to work on path-space, i.e., the set consisting of all stochastic trajectories, hence the proposed approach is referred to as "pathwise". The pathwise sensitivity analysis method is realized by employing the rigorously-derived Relative Entropy Rate, which is directly computable from the propensity functions. A key aspect of the method is that an associated pathwise Fisher Information Matrix (FIM) is defined, which in turn constitutes a gradient-free approach to quantifying parameter sensitivities. The structure of the FIM turns out to be block-diagonal, revealing hidden parameter dependencies and sensitivities in reaction networks. As a gradient-free method, the proposed sensitivity analysis provides a significant advantage when dealing with complex stochastic systems with a large number of parameters. In addition, the knowledge of the structure of the FIM can allow to efficiently address

  5. Complexity of generic biochemical circuits: topology versus strength of interactions

    Science.gov (United States)

    Tikhonov, Mikhail; Bialek, William

    2016-12-01

    The historical focus on network topology as a determinant of biological function is still largely maintained today, illustrated by the rise of structure-only approaches to network analysis. However, biochemical circuits and genetic regulatory networks are defined both by their topology and by a multitude of continuously adjustable parameters, such as the strength of interactions between nodes, also recognized as important. Here we present a class of simple perceptron-based Boolean models within which comparing the relative importance of topology versus interaction strengths becomes a quantitatively well-posed problem. We quantify the intuition that for generic networks, optimization of interaction strengths is a crucial ingredient of achieving high complexity, defined here as the number of fixed points the network can accommodate. We propose a new methodology for characterizing the relative role of parameter optimization for topologies of a given class.

  6. SABIO-RK: A data warehouse for biochemical reactions and their kinetics

    Directory of Open Access Journals (Sweden)

    Krebs Olga

    2007-03-01

    Full Text Available Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics, a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.

  7. A moment-convergence method for stochastic analysis of biochemical reaction networks.

    Science.gov (United States)

    Zhang, Jiajun; Nie, Qing; Zhou, Tianshou

    2016-05-21

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  8. A moment-convergence method for stochastic analysis of biochemical reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jiajun [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China); Nie, Qing [Department of Mathematics, University of California at Irvine, Irvine, California 92697 (United States); Zhou, Tianshou, E-mail: mcszhtsh@mail.sysu.edu.cn [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China); Guangdong Province Key Laboratory of Computational Science and School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China)

    2016-05-21

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  9. Predictive hypotheses are ineffectual in resolving complex biochemical systems.

    Science.gov (United States)

    Fry, Michael

    2018-03-20

    Scientific hypotheses may either predict particular unknown facts or accommodate previously-known data. Although affirmed predictions are intuitively more rewarding than accommodations of established facts, opinions divide whether predictive hypotheses are also epistemically superior to accommodation hypotheses. This paper examines the contribution of predictive hypotheses to discoveries of several bio-molecular systems. Having all the necessary elements of the system known beforehand, an abstract predictive hypothesis of semiconservative mode of DNA replication was successfully affirmed. However, in defining the genetic code whose biochemical basis was unclear, hypotheses were only partially effective and supplementary experimentation was required for its conclusive definition. Markedly, hypotheses were entirely inept in predicting workings of complex systems that included unknown elements. Thus, hypotheses did not predict the existence and function of mRNA, the multiple unidentified components of the protein biosynthesis machinery, or the manifold unknown constituents of the ubiquitin-proteasome system of protein breakdown. Consequently, because of their inability to envision unknown entities, predictive hypotheses did not contribute to the elucidation of cation theories remained the sole instrument to explain complex bio-molecular systems, the philosophical question of alleged advantage of predictive over accommodative hypotheses became inconsequential.

  10. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal

    1997-01-01

    Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown...... that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction...... of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can...

  11. Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays

    Energy Technology Data Exchange (ETDEWEB)

    Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Department of Mathematics, University of Trento (Italy); Zunino, Roberto, E-mail: roberto.zunino@unitn.it [Department of Mathematics, University of Trento (Italy)

    2014-10-07

    We propose a new exact stochastic rejection-based simulation algorithm for biochemical reactions and extend it to systems with delays. Our algorithm accelerates the simulation by pre-computing reaction propensity bounds to select the next reaction to perform. Exploiting such bounds, we are able to avoid recomputing propensities every time a (delayed) reaction is initiated or finished, as is typically necessary in standard approaches. Propensity updates in our approach are still performed, but only infrequently and limited for a small number of reactions, saving computation time and without sacrificing exactness. We evaluate the performance improvement of our algorithm by experimenting with concrete biological models.

  12. Photoinitiated reactions in weakly bonded complexes

    International Nuclear Information System (INIS)

    Wittig, C.

    1993-01-01

    This paper discusses photoinitiated reactions in weakly bonded binary complexes in which the constituents are only mildly perturbed by the intermolecular bond. Such complexes, with their large zero point excursions, set the stage for events that occur following electronic excitation of one of the constituents. This can take several forms, but in all cases, entrance channel specificity is imposed by the character of the complex as well as the nature of the photoinitiation process. This has enabled us to examine aspects of bimolecular processes: steric effects, chemical branching ratios, and inelastic scattering. Furthermore, monitoring reactions directly in the time domain can reveal mechanisms that cannot be inferred from measurements of nascent product excitations. Consequently, we examined several systems that had been studied previously by our group with product state resolution. With CO 2 /HI, in which reaction occurs via a HOCO intermediate, the rates agree with RRKM predictions. With N 2 O/HI, the gas phase single collision reaction yielding OH + N 2 has been shown to proceed mainly via an HNNO intermediate that undergoes a 1,3-hydrogen shift to the OH + N 2 channel. With complexes, ab initio calculations and high resolution spectroscopic studies of analogous systems suggest that the hydrogen, while highly delocalized, prefers the oxygen to the nitrogen. We observe that OH is produced with a fast risetime (< 250 fs) which can be attributed to either direct oxygen-side attack or rapid HNNO decomposition and/or a termolecular contribution involving the nearby iodine

  13. A Simple Approach to Study Designs in Complex Biochemical ...

    Indian Academy of Sciences (India)

    Somdatta Sinha

    Protein sequences. • Biochemical & Genetic information. REVERSE ENGINEERING. LARGE NETWORKS. FORWARD ENGINEERING. All designs that are not physically forbidden are realizable, but not all realizable designs are functionally effective. (in relation to context and constraints of the system and environment).

  14. Contributions of cell growth and biochemical reactions to nongenetic variability of cells.

    NARCIS (Netherlands)

    Schwabe, A.; Bruggeman, F.J.

    2014-01-01

    Cell-to-cell variability in the molecular composition of isogenic, steady-state growing cells arises spontaneously from the inherent stochasticity of intracellular biochemical reactions and cell growth. Here, we present a general decomposition of the total variance in the copy number per cell of a

  15. Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes.

    Science.gov (United States)

    Kulasiri, Don

    2011-01-01

    We discuss the quantification of molecular fluctuations in the biochemical reaction systems within the context of intracellular processes associated with gene expression. We take the molecular reactions pertaining to circadian rhythms to develop models of molecular fluctuations in this chapter. There are a significant number of studies on stochastic fluctuations in intracellular genetic regulatory networks based on single cell-level experiments. In order to understand the fluctuations associated with the gene expression in circadian rhythm networks, it is important to model the interactions of transcriptional factors with the E-boxes in the promoter regions of some of the genes. The pertinent aspects of a near-equilibrium theory that would integrate the thermodynamical and particle dynamic characteristics of intracellular molecular fluctuations would be discussed, and the theory is extended by using the theory of stochastic differential equations. We then model the fluctuations associated with the promoter regions using general mathematical settings. We implemented ubiquitous Gillespie's algorithms, which are used to simulate stochasticity in biochemical networks, for each of the motifs. Both the theory and the Gillespie's algorithms gave the same results in terms of the time evolution of means and variances of molecular numbers. As biochemical reactions occur far away from equilibrium-hence the use of the Gillespie algorithm-these results suggest that the near-equilibrium theory should be a good approximation for some of the biochemical reactions. © 2011 Elsevier Inc. All rights reserved.

  16. Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Department of Mathematics, University of Trento, Trento (Italy)

    2015-08-07

    We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajectory is exact by exploiting the rejection-based mechanism. We benchmark tRSSA on different biological systems with varying forms of reaction rates to demonstrate its applicability and efficiency. We reveal that for nontrivial cases, the selection of reaction firings in existing algorithms introduces approximations because the integration of reaction rates is very computationally demanding and simplifying assumptions are introduced. The selection of the next reaction firing by our approach is easier while preserving the exactness.

  17. Accelerating rejection-based simulation of biochemical reactions with bounded acceptance probability

    Energy Technology Data Exchange (ETDEWEB)

    Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Department of Mathematics, University of Trento, Trento (Italy); Zunino, Roberto, E-mail: roberto.zunino@unitn.it [Department of Mathematics, University of Trento, Trento (Italy)

    2016-06-14

    Stochastic simulation of large biochemical reaction networks is often computationally expensive due to the disparate reaction rates and high variability of population of chemical species. An approach to accelerate the simulation is to allow multiple reaction firings before performing update by assuming that reaction propensities are changing of a negligible amount during a time interval. Species with small population in the firings of fast reactions significantly affect both performance and accuracy of this simulation approach. It is even worse when these small population species are involved in a large number of reactions. We present in this paper a new approximate algorithm to cope with this problem. It is based on bounding the acceptance probability of a reaction selected by the exact rejection-based simulation algorithm, which employs propensity bounds of reactions and the rejection-based mechanism to select next reaction firings. The reaction is ensured to be selected to fire with an acceptance rate greater than a predefined probability in which the selection becomes exact if the probability is set to one. Our new algorithm improves the computational cost for selecting the next reaction firing and reduces the updating the propensities of reactions.

  18. Prediction of bakery products nutritive value based on mathematical modeling of biochemical reactions

    Directory of Open Access Journals (Sweden)

    E. I. Ponomareva

    2013-01-01

    Full Text Available Researches are devoted to identifying changes in the chemical composition of whole-grain wheat bread during baking and to forecasting of food value of bakery products by mathematical modeling of biochemical transformations. The received model represents the invariant composition, considering speed of biochemical reactions at a batch of bakery products, and allowing conduct virtual experiments to develop new types of bread for various categories of the population, including athletes. The offered way of modeling of biochemical transformations at a stage of heat treatment allows to predict food value of bakery products, without spending funds for raw materials and large volume of experiment that will provide possibility of economy of material resources at a stage of development of new types of bakery products and possibility of production efficiency increase.

  19. HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

    International Nuclear Information System (INIS)

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

    2016-01-01

    This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

  20. HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Marchetti, Luca, E-mail: marchetti@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy); University of Trento, Department of Mathematics (Italy); Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy)

    2016-07-15

    This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

  1. Physics of positronium acceptor complex formation reactions

    International Nuclear Information System (INIS)

    Gangopadhyay, Debarshi; Ganguly, Bichitra Nandi; Mukherjee, Tapas; Dutta-Roy, Binayak

    2002-01-01

    Positronium (P s ) reaction rates (κ) with weak Acceptors (Ac) leading to the formation of Ps-Ac complexes show several interesting features: non-monotonic temperature dependence of κ(departing from the usual Arrhenius behaviour), considerable variability of κ with respect to different solvents, and anomalies in response to external pressure at ambient temperature. The object of this work is to explain all these phenomena using a remarkably simple bubble model (the widely used model for the pick-off component of ortho-positronium decay in liquids), which has been revisited several times in the context and as a result smooth diffuse boundary of the bubble was suggested that yields reasonable agreement of the experimental data. The contractile force on the bubble relies much on the surface tension of the liquid, through our calculation the notion of critical surface tension emerges and enables us to explain the experimental observations satisfactorily. (author)

  2. Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components.

    Science.gov (United States)

    Timasheff, Serge N

    2002-07-23

    Solvent additives (cosolvents, osmolytes) modulate biochemical reactions if, during the course of the reaction, there is a change in preferential interactions of solvent components with the reacting system. Preferential interactions can be expressed in terms of preferential binding of the cosolvent or its preferential exclusion (preferential hydration). The driving force is the perturbation by the protein of the chemical potential of the cosolvent. It is shown that the measured change of the amount of water in contact with protein during the course of the reaction modulated by an osmolyte is a change in preferential hydration that is strictly a measure of the cosolvent chemical potential perturbation by the protein in the ternary water-protein-cosolvent system. It is not equal to the change in water of hydration, because water of hydration is a reflection strictly of protein-water forces in a binary system. There is no direct relation between water of preferential hydration and water of hydration.

  3. SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

    Science.gov (United States)

    Rey, Maja; Weidemann, Andreas; Kania, Renate; Müller, Wolfgang

    2018-01-01

    Abstract SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012). (i) The website has been completely revised and (ii) allows now also free text search for kinetics data. (iii) Additional interlinkages with other databases in our field have been established; this enables users to gain directly comprehensive knowledge about the properties of enzymes and kinetics beyond SABIO-RK. (iv) Vice versa, direct access to SABIO-RK data has been implemented in several systems biology tools and workflows. (v) On request of our experimental users, the data can be exported now additionally in spreadsheet formats. (vi) The newly established SABIO-RK Curation Service allows to respond to specific data requirements. PMID:29092055

  4. Efficient Characterization of Parametric Uncertainty of Complex (Biochemical Networks.

    Directory of Open Access Journals (Sweden)

    Claudia Schillings

    2015-08-01

    Full Text Available Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative deterministic methodology that relies on sparse polynomial approximations. We propose a deterministic computational interpolation scheme which identifies most significant expansion coefficients adaptively. We present its performance in kinetic model equations from computational systems biology with several hundred parameters and state variables, leading to numerical approximations of the parametric solution on the entire parameter space. The scheme is based on adaptive Smolyak interpolation of the parametric solution at judiciously and adaptively chosen points in parameter space. As Monte-Carlo sampling, it is "non-intrusive" and well-suited for massively parallel implementation, but affords higher convergence rates. This opens up new avenues for large-scale dynamic network analysis by enabling scaling for many applications, including parameter estimation, uncertainty quantification, and systems design.

  5. Reaction factoring and bipartite update graphs accelerate the Gillespie Algorithm for large-scale biochemical systems.

    Directory of Open Access Journals (Sweden)

    Sagar Indurkhya

    Full Text Available ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1 a small number of reactions tend to occur a disproportionately large percentage of the time, and (2 a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models.

  6. Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

    Science.gov (United States)

    Indurkhya, Sagar; Beal, Jacob

    2010-01-01

    ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of the time, and (2) a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models. PMID:20066048

  7. Reaction factoring and bipartite update graphs accelerate the Gillespie Algorithm for large-scale biochemical systems.

    Science.gov (United States)

    Indurkhya, Sagar; Beal, Jacob

    2010-01-06

    ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of the time, and (2) a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models.

  8. Survey on bio-chemical complex harmonized with global environment. 3; Kankyo chowagata seibutsu kagaku konbinato ni kansuru chosa. 3

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-03-01

    A survey was conducted of bio-chemical complex harmonized with the global environment for the purpose of constructing the material production process harmonized with the environment by the process fusion between biological conversion and chemical reaction. Palm oil was taken up as renewable raw material plant resource. The process utilizing bio-chemical reaction advances at normal temperature and pressure and is high in reaction specificity and selectivity. This is a recycling, circulation and environmental harmony type production technology which brings high yield, energy conservation, resource conservation, and low environmental loads. Waste water treatment and production of useful substances from sludge were thought as elementary technology. A possibility was studied of enzyme production by culturing solid waste, and the enzyme was applied to the hydrolysis process. The paper indicated trace components in the palm oil and the extraction method and proposed the production process of new derivatives for adding value to hydrolysate. A study was also made of the overall process flow which integrated these new processes and the material balance. The comprehensive evaluation of this new process was made from the aspect of the product structure, the market, construction cost, economical efficiency, and the environment. 133 refs., 65 figs., 56 tabs.

  9. Methods for forming complex oxidation reaction products including superconducting articles

    International Nuclear Information System (INIS)

    Rapp, R.A.; Urquhart, A.W.; Nagelberg, A.S.; Newkirk, M.S.

    1992-01-01

    This patent describes a method for producing a superconducting complex oxidation reaction product of two or more metals in an oxidized state. It comprises positioning at least one parent metal source comprising one of the metals adjacent to a permeable mass comprising at least one metal-containing compound capable of reaction to form the complex oxidation reaction product in step below, the metal component of the at least one metal-containing compound comprising at least a second of the two or more metals, and orienting the parent metal source and the permeable mass relative to each other so that formation of the complex oxidation reaction product will occur in a direction towards and into the permeable mass; and heating the parent metal source in the presence of an oxidant to a temperature region above its melting point to form a body of molten parent metal to permit infiltration and reaction of the molten parent metal into the permeable mass and with the oxidant and the at least one metal-containing compound to form the complex oxidation reaction product, and progressively drawing the molten parent metal source through the complex oxidation reaction product towards the oxidant and towards and into the adjacent permeable mass so that fresh complex oxidation reaction product continues to form within the permeable mass; and recovering the resulting complex oxidation reaction product

  10. Open complex-balanced mass action chemical reaction networks

    NARCIS (Netherlands)

    Rao, Shodhan; van der Schaft, Arjan; Jayawardhana, Bayu

    We consider open chemical reaction networks, i.e. ones with inflows and outflows. We assume that all the inflows to the network are constant and all outflows obey the mass action kinetics rate law. We define a complex-balanced open reaction network as one that admits a complex-balanced steady state.

  11. Electron transfer reactions of metal complexes in solution

    International Nuclear Information System (INIS)

    Sutin, N.

    1977-01-01

    A few representative electron-transfer reactions are selected and their kinetic parameters compared with the predictions of activated complex models. Since Taube has presented an elegant treatment of intramolecular electron-transfer reactions, emphasis is on bimolecular reactions. The latter electron-transfer reactions are more complicated to treat theoretically since the geometries of their activated complexes are not as well known as for the intramolecular case. In addition in biomolecular reactions, the work required to bring the two reactants together needs to be calculated. Since both reactants generally carry charges this presents a non-trivial problem at the ionic strengths usually used to study bimolecular electron transfer

  12. Biochemical characterization of enzyme fidelity of influenza A virus RNA polymerase complex.

    Directory of Open Access Journals (Sweden)

    Shilpa Aggarwal

    2010-04-01

    Full Text Available It is widely accepted that the highly error prone replication process of influenza A virus (IAV, together with viral genome assortment, facilitates the efficient evolutionary capacity of IAV. Therefore, it has been logically assumed that the enzyme responsible for viral RNA replication process, influenza virus type A RNA polymerase (IAV Pol, is a highly error-prone polymerase which provides the genomic mutations necessary for viral evolution and host adaptation. Importantly, however, the actual enzyme fidelity of IAV RNA polymerase has never been characterized.Here we established new biochemical assay conditions that enabled us to assess both polymerase activity with physiological NTP pools and enzyme fidelity of IAV Pol. We report that IAV Pol displays highly active RNA-dependent RNA polymerase activity at unbiased physiological NTP substrate concentrations. With this robust enzyme activity, for the first time, we were able to compare the enzyme fidelity of IAV Pol complex with that of bacterial phage T7 RNA polymerase and the reverse transcriptases (RT of human immunodeficiency virus (HIV-1 and murine leukemia virus (MuLV, which are known to be low and high fidelity enzymes, respectively. We observed that IAV Pol displayed significantly higher fidelity than HIV-1 RT and T7 RNA polymerase and equivalent or higher fidelity than MuLV RT. In addition, the IAV Pol complex showed increased fidelity at lower temperatures. Moreover, upon replacement of Mg(++ with Mn(++, IAV Pol displayed increased polymerase activity, but with significantly reduced processivity, and misincorporation was slightly elevated in the presence of Mn(++. Finally, when the IAV nucleoprotein (NP was included in the reactions, the IAV Pol complex exhibited enhanced polymerase activity with increased fidelity.Our study indicates that IAV Pol is a high fidelity enzyme. We envision that the high fidelity nature of IAV Pol may be important to counter-balance the multiple rounds of

  13. Heterogeneous catalysis in complex, condensed reaction media

    Energy Technology Data Exchange (ETDEWEB)

    Cantu, David C.; Wang, Yang-Gang; Yoon, Yeohoon; Glezakou, Vassiliki-Alexandra; Rousseau, Roger; Weber, Robert S.

    2017-07-01

    Many reactions required for the upgrading of biomass into fuels and chemicals—hydrogenation, hydrodeoxygenation, hydrocracking—are ostensibly similar to those practiced in the upgrading of petroleum into fuels. But, repurposing hydroprocessing catalysts from refinery operations to treat bio-oil has proved to be unsatisfactory. New catalysts are needed because the composition of the biogenic reactants differs from that of petroleum-derived feedstocks (e.g. the low concentration of sulfur in cellulose-derived biomass precludes use of metal sulfide catalysts unless sulfur is added to the reaction stream). New processes are needed because bio-oils oligomerize rapidly, forming intractable coke and “gunk”, at temperatures so low that the desired upgrading reactions are impractically slow, and so low that the bio-oil upgrading must be handled as a condensed fluid. Ideally, the new catalysts and processes would exploit the properties of the multiple phases present in condensed bio-oil, notably the polarizability and structure of the fluid near a catalyst’s surface in the cybotactic region. The results of preliminary modeling of the cybotactic region of different catalyst surfaces in the hydrogenation of phenol suggest that Pd catalysts supported on hydrophilic surfaces are more active than catalysts based on lipophilic supports because the former serve to enhance the concentration of the phenol in the vicinity of the Pd. The effect stems from thermodynamics, not the rate of mass transport. This work was supported by the US Department of Energy, Office of Energy Efficiency and Renewable Energy, Bioenergy Technologies Office. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.

  14. Organotellurium ligands – designing and complexation reactions

    Indian Academy of Sciences (India)

    Unknown

    membered rings it is negative and ~30 ppm only. Keywords. Organotellurium ligands; hybrid telluroether; platinum metal complexes; tellurium-125 NMR. 1. Introduction. Tellurium is the noblest metalloid which may act as a Lewis acid as well as Lewis base. The ligand chemistry of tellurium, which acts as a 'soft' donor, was ...

  15. Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation

    KAUST Repository

    Mélykúti, Bence

    2010-01-01

    The Chemical Langevin Equation (CLE), which is a stochastic differential equation driven by a multidimensional Wiener process, acts as a bridge between the discrete stochastic simulation algorithm and the deterministic reaction rate equation when simulating (bio)chemical kinetics. The CLE model is valid in the regime where molecular populations are abundant enough to assume their concentrations change continuously, but stochastic fluctuations still play a major role. The contribution of this work is that we observe and explore that the CLE is not a single equation, but a parametric family of equations, all of which give the same finite-dimensional distribution of the variables. On the theoretical side, we prove that as many Wiener processes are sufficient to formulate the CLE as there are independent variables in the equation, which is just the rank of the stoichiometric matrix. On the practical side, we show that in the case where there are m1 pairs of reversible reactions and m2 irreversible reactions there is another, simple formulation of the CLE with only m1 + m2 Wiener processes, whereas the standard approach uses 2 m1 + m2. We demonstrate that there are considerable computational savings when using this latter formulation. Such transformations of the CLE do not cause a loss of accuracy and are therefore distinct from model reduction techniques. We illustrate our findings by considering alternative formulations of the CLE for a human ether a-go-go related gene ion channel model and the Goldbeter-Koshland switch. © 2010 American Institute of Physics.

  16. Complex Reaction Kinetics in Chemistry: A Unified Picture Suggested by Mechanics in Physics

    Directory of Open Access Journals (Sweden)

    Elena Agliari

    2018-01-01

    Full Text Available Complex biochemical pathways can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. Among the elementary reactions so far extensively investigated, we recall the Michaelis-Menten and the Hill positive-cooperative kinetics, which apply to molecular binding and are characterized by the absence and the presence, respectively, of cooperative interactions between binding sites. However, there is evidence of reactions displaying a more complex pattern: these follow the positive-cooperative scenario at small substrate concentration, yet negative-cooperative effects emerge as the substrate concentration is increased. Here, we analyze the formal analogy between the mathematical backbone of (classical reaction kinetics in Chemistry and that of (classical mechanics in Physics. We first show that standard cooperative kinetics can be framed in terms of classical mechanics, where the emerging phenomenology can be obtained by applying the principle of least action of classical mechanics. Further, since the saturation function plays in Chemistry the same role played by velocity in Physics, we show that a relativistic scaffold naturally accounts for the kinetics of the above-mentioned complex reactions. The proposed formalism yields to a unique, consistent picture for cooperative-like reactions and to a stronger mathematical control.

  17. SCScore: Synthetic Complexity Learned from a Reaction Corpus.

    Science.gov (United States)

    Coley, Connor W; Rogers, Luke; Green, William H; Jensen, Klavs F

    2018-02-26

    Several definitions of molecular complexity exist to facilitate prioritization of lead compounds, to identify diversity-inducing and complexifying reactions, and to guide retrosynthetic searches. In this work, we focus on synthetic complexity and reformalize its definition to correlate with the expected number of reaction steps required to produce a target molecule, with implicit knowledge about what compounds are reasonable starting materials. We train a neural network model on 12 million reactions from the Reaxys database to impose a pairwise inequality constraint enforcing the premise of this definition: that on average, the products of published chemical reactions should be more synthetically complex than their corresponding reactants. The learned metric (SCScore) exhibits highly desirable nonlinear behavior, particularly in recognizing increases in synthetic complexity throughout a number of linear synthetic routes.

  18. Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems—an analytical theory

    International Nuclear Information System (INIS)

    Qian, Hong

    2011-01-01

    The nonlinear dynamics of biochemical reactions in a small-sized system on the order of a cell are stochastic. Assuming spatial homogeneity, the populations of n molecular species follow a multi-dimensional birth-and-death process on Z n . We introduce the Delbrück–Gillespie process, a continuous-time Markov jump process, whose Kolmogorov forward equation has been known as the chemical master equation, and whose stochastic trajectories can be computed via the Gillespie algorithm. Using simple models, we illustrate that a system of nonlinear ordinary differential equations on R n emerges in the infinite system size limit. For finite system size, transitions among multiple attractors of the nonlinear dynamical system are rare events with exponentially long transit times. There is a separation of time scales between the deterministic ODEs and the stochastic Markov jumps between attractors. No diffusion process can provide a global representation that is accurate on both short and long time scales for the nonlinear, stochastic population dynamics. On the short time scale and near deterministic stable fixed points, Ornstein–Uhlenbeck Gaussian processes give linear stochastic dynamics that exhibit time-irreversible circular motion for open, driven chemical systems. Extending this individual stochastic behaviour-based nonlinear population theory of molecular species to other biological systems is discussed. (invited article)

  19. Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks.

    Science.gov (United States)

    Rumschinski, Philipp; Borchers, Steffen; Bosio, Sandro; Weismantel, Robert; Findeisen, Rolf

    2010-05-25

    Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge available for such processes is frequently limited, and measurements are often subject to inherent and possibly large uncertainties. This results in competing model hypotheses, whose kinetic parameters may not be experimentally determinable. Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding of the considered process, and to benefit from the analytical tools at hand. In this work we present a set-based framework that allows to discriminate between competing model hypotheses and to provide guaranteed outer estimates on the model parameters that are consistent with the (possibly sparse and uncertain) experimental measurements. This is obtained by means of exact proofs of model invalidity that exploit the polynomial/rational structure of biochemical reaction networks, and by making use of an efficient strategy to balance solution accuracy and computational effort. The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of measurement sparsity, uncertainty, and prior knowledge on the parameter estimates. This can help in designing further experiments leading to improved parameter estimates.

  20. Design of experiments for identification of complex biochemical systems with applications to mitochondrial bioenergetics.

    Science.gov (United States)

    Vinnakota, Kalyan C; Beard, Daniel A; Dash, Ranjan K

    2009-01-01

    Identification of a complex biochemical system model requires appropriate experimental data. Models constructed on the basis of data from the literature often contain parameters that are not identifiable with high sensitivity and therefore require additional experimental data to identify those parameters. Here we report the application of a local sensitivity analysis to design experiments that will improve the identifiability of previously unidentifiable model parameters in a model of mitochondrial oxidative phosphorylation and tricaboxylic acid cycle. Experiments were designed based on measurable biochemical reactants in a dilute suspension of purified cardiac mitochondria with experimentally feasible perturbations to this system. Experimental perturbations and variables yielding the most number of parameters above a 5% sensitivity level are presented and discussed.

  1. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

    Science.gov (United States)

    Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

    2014-03-11

    While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

  2. ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

    Science.gov (United States)

    Kayala, Matthew A; Baldi, Pierre

    2012-10-22

    Proposing reasonable mechanisms and predicting the course of chemical reactions is important to the practice of organic chemistry. Approaches to reaction prediction have historically used obfuscating representations and manually encoded patterns or rules. Here we present ReactionPredictor, a machine learning approach to reaction prediction that models elementary, mechanistic reactions as interactions between approximate molecular orbitals (MOs). A training data set of productive reactions known to occur at reasonable rates and yields and verified by inclusion in the literature or textbooks is derived from an existing rule-based system and expanded upon with manual curation from graduate level textbooks. Using this training data set of complex polar, hypervalent, radical, and pericyclic reactions, a two-stage machine learning prediction framework is trained and validated. In the first stage, filtering models trained at the level of individual MOs are used to reduce the space of possible reactions to consider. In the second stage, ranking models over the filtered space of possible reactions are used to order the reactions such that the productive reactions are the top ranked. The resulting model, ReactionPredictor, perfectly ranks polar reactions 78.1% of the time and recovers all productive reactions 95.7% of the time when allowing for small numbers of errors. Pericyclic and radical reactions are perfectly ranked 85.8% and 77.0% of the time, respectively, rising to >93% recovery for both reaction types with a small number of allowed errors. Decisions about which of the polar, pericyclic, or radical reaction type ranking models to use can be made with >99% accuracy. Finally, for multistep reaction pathways, we implement the first mechanistic pathway predictor using constrained tree-search to discover a set of reasonable mechanistic steps from given reactants to given products. Webserver implementations of both the single step and pathway versions of Reaction

  3. Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space

    Directory of Open Access Journals (Sweden)

    St Laurent Georges

    2010-03-01

    signaling network is capable of performing information processing in a robust manner, a functional property that is independent of the signaling task required to be executed. Nevertheless, it was found that the robust performance of the network is not solely determined by its design principle (topology, but this may be heavily dependent on the network's current position in biochemical reaction space. Ultimately, our results enabled us the identification of key rate limiting steps which most effectively control the performance of the system under diverse dynamical regimes. Conclusions Overall, our in silico study suggests that biologically relevant and non-intuitive aspects on the general behavior of a complex biomolecular network can be elucidated only when taking into account a wide spectrum of dynamical regimes attainable by the system. Most importantly, this strategy provides the means for a suitable assessment of the inherent variational constraints imposed by the structure of the system when systematically probing its parameter space.

  4. Kinetics of the reactions of hydrated electrons with metal complexes

    International Nuclear Information System (INIS)

    Korsse, J.

    1983-01-01

    The reactivity of the hydrated electron towards metal complexes is considered. Experiments are described involving metal EDTA and similar complexes. The metal ions studied are mainly Ni 2+ , Co 2+ and Cu 2+ . Rates of the reactions of the complexes with e - (aq) were measured using the pulse radiolysis technique. It is shown that the reactions of e - (aq) with the copper complexes display unusually small kinetic salt effects. The results suggest long-range electron transfer by tunneling. A tunneling model is presented and the experimental results are discussed in terms of this model. Results of approximate molecular orbital calculations of some redox potentials are given, for EDTA chelates as well as for series of hexacyano and hexaquo complexes. Finally, equilibrium constants for the formation of ternary complexes are reported. (Auth./G.J.P.)

  5. PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list.

    Science.gov (United States)

    Kotera, Masaaki; Nishimura, Yosuke; Nakagawa, Zen-ichi; Muto, Ai; Moriya, Yuki; Okamoto, Shinobu; Kawashima, Shuichi; Katayama, Toshiaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2014-12-01

    Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been verified, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been verified. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies. Instead, most of the bioinformatics studies simply use the identifiers of the enzymes, i.e. the Enzyme Commission (EC) numbers. We investigated the actual usage of terminology throughout the Enzyme List, and demonstrated that the partial characteristics of reactions cannot be retrieved by simply using EC numbers. Thus, we developed a novel ontology, named PIERO, for annotating biochemical transformations as follows. First, the terminology describing enzymatic reactions was retrieved from the Enzyme List, and was grouped into those related to overall reactions and biochemical transformations. Consequently, these terms were mapped onto the actual transformations taken from enzymatic reaction equations. This ontology was linked to Gene Ontology (GO) and EC numbers, allowing the extraction of common partial reaction characteristics from given sets of orthologous genes and the elucidation of possible enzymes from the given transformations. Further future development of the PIERO ontology should enhance the Enzyme List to promote the integration of genomics and metabolomics.

  6. Biochemical characterization of native Usher protein complexes from a vesicular subfraction of tracheal epithelial cells.

    Science.gov (United States)

    Zallocchi, Marisa; Sisson, Joseph H; Cosgrove, Dominic

    2010-02-16

    Usher syndrome is the major cause of deaf/blindness in the world. It is a genetic heterogeneous disorder, with nine genes already identified as causative for the disease. We noted expression of all known Usher proteins in bovine tracheal epithelial cells and exploited this system for large-scale biochemical analysis of Usher protein complexes. The dissected epithelia were homogenized in nondetergent buffer and sedimented on sucrose gradients. At least two complexes were evident after the first gradient: one formed by specific isoforms of CDH23, PCDH15, and VLGR-1 and a different one at the top of the gradient that included all of the Usher proteins and rab5, a transport vesicle marker. TEM analysis of these top fractions found them enriched in 100-200 nm vesicles, confirming a vesicular association of the Usher complex(es). Immunoisolation of these vesicles confirmed some of the associations already predicted and identified novel interactions. When the vesicles are lysed in the presence of phenylbutyrate, most of the Usher proteins cosediment into the gradient at a sedimentation coefficient of approximately 50 S, correlating with a predicted molecular mass of 2 x 10(6) Da. Although it is still unclear whether there is only one complex or several independent complexes that are trafficked within distinct vesicular pools, this work shows for the first time that native Usher protein complexes occur in vivo. This complex(es) is present primarily in transport vesicles at the apical pole of tracheal epithelial cells, predicting that Usher proteins may be directionally transported as complexes in hair cells and photoreceptors.

  7. BIOCHEMICAL CHARACTERIZATION OF NATIVE USHER PROTEIN COMPLEXES FROM A VESICULAR SUBFRACTION OF TRACHEAL EPITHELIAL CELLS†

    Science.gov (United States)

    Zallocchi, Marisa; Sisson, Joseph H.; Cosgrove, Dominic

    2010-01-01

    Usher syndrome is the major cause of deaf/blindness in the world. It is a genetic heterogeneous disorder, with nine genes already identified as causative for the disease. We noted expression of all known Usher proteins in bovine tracheal epithelial cells, and exploited this system for large-scale biochemical analysis of Usher protein complexes. The dissected epithelia were homogenized in non-detergent buffer, and sedimented on sucrose gradients. At least two complexes were evident after the first gradient: one formed by specific isoforms of CDH23, PCDH15 and VLGR-1, and a different one at the top of the gradient that included all the Usher proteins and rab5, a transport vesicle marker. TEM analysis of these top fractions found them enriched in 100–200 nm vesicles, confirming a vesicular association of the Usher complex(es). Immunoisolation of these vesicles confirmed some of the associations already predicted and identified novel interactions. When the vesicles are lysed in the presence of phenylbutyrate, most of the Usher proteins co-sediment into the gradient at a sedimentation coefficient of approximately 50S, correlating with a predicted molecular mass of 2 × 106 Daltons. Although it is still unclear whether there is only one complex or several independent complexes that are trafficked within distinct vesicular pools, this work shows for the first time that native Usher proteins complexes occur in vivo. This complex(es) is present primarily in transport vesicles at the apical pole of tracheal epithelial cells, predicting that Usher proteins may be directionally transported as complexes in hair cells and photoreceptors. PMID:20058854

  8. Light induced electron transfer reactions of metal complexes

    International Nuclear Information System (INIS)

    Sutin, N.; Creutz, C.

    1980-01-01

    Properties of the excited states of tris(2,2'-bipyridine) and tris(1,10-phenanthroline) complexes of chromium(III), iron(II), ruthenium(II), osmium(II), rhodium(III), and iridium(III) are described. The electron transfer reactions of the ground and excited states are discussed and interpreted in terms of the driving force for the reaction and the distortions of the excited states relative to the corresponding ground states. General considerations relevant to the conversion of light into chemical energy are presented and progress in the use of polypyridine complexes to effect the light decomposition of water into hydrogen and oxygen is reviewed

  9. Reduced linear noise approximation for biochemical reaction networks with time-scale separation: The stochastic tQSSA+

    Science.gov (United States)

    Herath, Narmada; Del Vecchio, Domitilla

    2018-03-01

    Biochemical reaction networks often involve reactions that take place on different time scales, giving rise to "slow" and "fast" system variables. This property is widely used in the analysis of systems to obtain dynamical models with reduced dimensions. In this paper, we consider stochastic dynamics of biochemical reaction networks modeled using the Linear Noise Approximation (LNA). Under time-scale separation conditions, we obtain a reduced-order LNA that approximates both the slow and fast variables in the system. We mathematically prove that the first and second moments of this reduced-order model converge to those of the full system as the time-scale separation becomes large. These mathematical results, in particular, provide a rigorous justification to the accuracy of LNA models derived using the stochastic total quasi-steady state approximation (tQSSA). Since, in contrast to the stochastic tQSSA, our reduced-order model also provides approximations for the fast variable stochastic properties, we term our method the "stochastic tQSSA+". Finally, we demonstrate the application of our approach on two biochemical network motifs found in gene-regulatory and signal transduction networks.

  10. Reaction-diffusion controlled growth of complex structures

    Science.gov (United States)

    Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna

    2013-03-01

    Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support

  11. Adverse reaction to veterinary multivitamins and vitamin B complex ...

    African Journals Online (AJOL)

    It has been reported that dogs in South-western Nigeria react adversely to injectable veterinary multivitamins and human vitamin B complex preparations. Experimentation and interview survey were concurrently conducted to identify the type of Adverse Drug Reactions (ADRs) that the indications produced. For the survey ...

  12. Reactions of sigma-bonded organochromium(III)complexes

    International Nuclear Information System (INIS)

    Leslie, J.P. II.

    1975-12-01

    Three projects were carried out, each dealing with the kinetics and mechanism of reactions of sigma-bonded organochromium(III) complexes of the form (H 2 O) 5 CrR 2+ . Part I describes the kinetics of the reaction of dichloromethylchromium(III) ion with chromium(II) ion in aqueous acid. Part II deals with the radioexchange of 4-pyridinomethylchromium(III) ion with 51 Cr 2+ and the kinetics of formation of the organochromium species at 55 0 in 1 M H + . Part III deals with the reactions of Hg 2+ and CH 3 Hg + with a series of (H 2 O) 5 CrR 2+ complexes, in which R is an aliphatic alkyl group, a haloalkyl group, or an aralkyl group

  13. Reaction of nitriles intercalation in tantalum pentachloride complexes with amines

    International Nuclear Information System (INIS)

    Glushkova, M.A.; Chumaevskij, N.A.; Khmelevskaya, L.V.; Ershova, M.M.; Buslaev, Yu.A.

    1987-01-01

    Data on the study of aceto-, propio- and benzonitrile intercalation in TaCl 5 complexes with diethyl- and triethylamines in CCl 4 solution are discussed. Using the methods of IR and Raman spectroscopy it has been established that it is the nature of ligand, and not nitrile intercalated in the complex, that affects greatly the composition of final products. In contrast to acetonitrile, intercalation in the complex of propio- and benzonitriles is observed already at room temperature. On the basis of spectral data a supposition is made that carbon tetrachloride used as a solvent accelerates the reaction of nitrile intercalation and promotes their deprotonation in the presence of aprotonic amine

  14. Identifying Slow Molecular Motions in Complex Chemical Reactions.

    Science.gov (United States)

    Piccini, GiovanniMaria; Polino, Daniela; Parrinello, Michele

    2017-09-07

    We have studied the cyclization reaction of deprotonated 4-chloro-1-butanethiol to tetrahydrothiophene by means of well-tempered metadynamics. To properly select the collective variables, we used the recently proposed variational approach to conformational dynamics within the framework of metadyanmics. This allowed us to select the appropriate linear combinations from a set of collective variables representing the slow degrees of freedom that best describe the slow modes of the reaction. We performed our calculations at three different temperatures, namely, 300, 350, and 400 K. We show that the choice of such collective variables allows one to easily interpret the complex free-energy surface of such a reaction by univocal identification of the conformers belonging to reactants and product states playing a fundamental role in the reaction mechanism.

  15. Dynamics of Clinical and Biochemical Parameters in Patients with Liver Cirrhosis Under the Influence of Complex Therapy with Ursodeoxycholic Acid

    Directory of Open Access Journals (Sweden)

    M.I. Shved

    2013-11-01

    Full Text Available It was studied dynamics of clinical and biochemical parameters in patients with liver cirrhosis under the influence of complex treatment using ursosan. It is found that the inclusion of ursosan in complex treatment improves clinical and laboratory parameters, significantly reduces the manifestations of general inflammatory liver syndrome, which prevents the progression of the disease.

  16. Hydrogen transfer reactions of interstellar Complex Organic Molecules

    Science.gov (United States)

    Álvarez-Barcia, S.; Russ, P.; Kästner, J.; Lamberts, T.

    2018-06-01

    Radical recombination has been proposed to lead to the formation of complex organic molecules (COMs) in CO-rich ices in the early stages of star formation. These COMs can then undergo hydrogen addition and abstraction reactions leading to a higher or lower degree of saturation. Here, we have studied 14 hydrogen transfer reactions for the molecules glyoxal, glycoaldehyde, ethylene glycol, and methylformate and an additional three reactions where CHnO fragments are involved. Over-the-barrier reactions are possible only if tunneling is invoked in the description at low temperature. Therefore the rate constants for the studied reactions are calculated using instanton theory that takes quantum effects into account inherently. The reactions were characterized in the gas phase, but this is expected to yield meaningful results for CO-rich ices due to the minimal alteration of reaction landscapes by the CO molecules. We found that rate constants should not be extrapolated based on the height of the barrier alone, since the shape of the barrier plays an increasingly larger role at decreasing temperature. It is neither possible to predict rate constants based only on considering the type of reaction, the specific reactants and functional groups play a crucial role. Within a single molecule, though, hydrogen abstraction from an aldehyde group seems to be always faster than hydrogen addition to the same carbon atom. Reactions that involve heavy-atom tunneling, e.g., breaking or forming a C-C or C-O bond, have rate constants that are much lower than those where H transfer is involved.

  17. Characterization of reversible reactions of isocyanides with molybdenum dithiolate complexes

    International Nuclear Information System (INIS)

    Miller, D.J.; DuBois, M.R.

    1980-01-01

    Dimeric molybdenum complexes with bridging dithiocarbonimidate ligands of the formula [C 5 H 5 MoS 2 CNR] 2 (where R = CH 3 , CH 2 C 6 H 5 , C 6 H 11 , and n-C 4 H 9 ) have been synthesized and characterized. The syntheses involve the room-temperature reactions of excess isocyanides with solutions of the dimeric complex [C 5 H 5 MoSC 3 H 6 S] 2 . During the course of these reactions, propene is displaced from the sulfur atoms of the bridging dithiolate ligands. Addition of excess alkene reverses the above reactions. Equilibrium constants have been calculated for the following reactions by integration of NMR resonances: [CH 3 C 5 H 4 MoSC 2 H 4 S] 2 + RNC reversible (CH 3 C 5 H 4 Mo) 2 (SC 2 H 4 S)(S 2 CNR) + C == C, K 1 = 2.9 +- 0.2; (CH 3 C 5 H 4 Mo) 2 (SC 2 H 4 S)(S 2 CNR) + RNC reversible [CH 3 C 5 H 4 MoS 2 CNR] 2 + C == C, K 2 = 0.7 +- 0.1 (R = CH 2 C 6 H 5 ). The dithiocarbonimidate complexes react cleanly with the electrophiles CH 3 OSO 2 F and HOSO 2 CF 3 to form [C 5 H 5 MoS 2 CNRR'] 2 2+ where R' = H or CH 3 . These products have been characterized by spectral and conductivity methods. The reactions of the dithiocarbonimidate complexes with reducing agents and with carbon monoxide are discussed. 1 figure, 2 tables

  18. Mass transfer with complex reversible chemical reactions. II: Parallel reversible chemical reactions

    NARCIS (Netherlands)

    Versteeg, Geert; van Beckum, F.P.H.; Kuipers, J.A.M.; van Swaaij, Willibrordus Petrus Maria

    1990-01-01

    An absorption model has been developed which can be used to calculate rapidly absorption rates for the phenomenon mass transfer accompanied by multiple complex parallel reversible chemical reactions. This model can be applied for the calculation of the mass transfer rates, enhancement factors and

  19. Mass transfer with complex reversible chemical reactions. II: parallel reversible chemical reactions

    NARCIS (Netherlands)

    Versteeg, G.F.; Kuipers, J.A.M.; Beckum, van F.P.H.; van Swaaij, W.P.M.

    1990-01-01

    An absorption model has been developed which can be used to calculate rapidly absorption rates for the phenomenon mass transfer accompanied by multiple complex parallel reversible chemical reactions. This model can be applied for the calculation of the mass transfer rates, enhancement factors and

  20. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

    NARCIS (Netherlands)

    De Wispelaere, K.; Ensing, B.; Ghysels, A.; Meijer, E.J.; van Van Speybroeck, V.

    2015-01-01

    The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first

  1. Successes and failures of DFT functionals in acid/base and redox reactions of organic and biochemical interest

    OpenAIRE

    Silva, Pedro J.; Ramos, Maria João

    2011-01-01

    The performance of 18 different DFT functionals in the prediction of absolute and relative energies of organic and biochemical acid/base and redox reactions was evaluated, using MP2 extrapolated to the complete basis set limit and CCSD(T)/aug-cc-pVTZ energies as benchmark. Absolute reduction energies were predicted with relatively large average errors (2–4 kcal mol−1) except for the best functional, PBE0 (1.3 ± 1.2 kcal mol−1). The DFT predictions of relative reduction energies afforded mean ...

  2. Studies of complex fragment emission in heavy ion reactions

    International Nuclear Information System (INIS)

    Charity, R.J.; Sobotka, L.G.

    1993-01-01

    The study of intermediate-energy heavy-ion nuclear reactions is reported. This work has two foci: the properties of nuclear matter under abnormal conditions, in this energy domain, predominately low densities and the study of the relevant reaction mechanisms. Nuclear matter properties, such as phase transitions, are reflected in the dynamics of the reactions. The process leads to an understanding of the reaction mechanism themselves and therefore to the response characteristics of finite, perhaps non-equilibrium, strongly interacting systems. The program has the following objectives: to study energy, mass, and angular momentum deposition by studying incomplete fusion reactions; to gain confidence in the understanding of how highly excited systems decompose by studying all emissions from the highly excited systems; to push these kinds of studies into the intermediate energy domain (where intermediate mass fragment emission is not improbable) with excitation function studies; and to learn about the dynamics of the decays using particle-particle correlations. The last effort focuses on simple systems, where definitive statements are possible. These avenues of research share a common theme, large complex fragment production. It is this feature, more than any other, which distinguishes the intermediate energy domain

  3. Fabrication of a pen-shaped portable biochemical reaction system based on magnetic bead manipulation

    International Nuclear Information System (INIS)

    Shikida, Mitsuhiro; Inagaki, Noriyuki; Okochi, Mina; Honda, Hiroyuki; Sato, Kazuo

    2011-01-01

    A pen-shaped platform that is similar to a mechanical pencil is proposed for producing a portable reaction system. A reaction unit, as the key component in the system, was produced by using a heat shrinkable tube. A mechanical pencil supplied by Mitsubishi Pencil Co. Ltd was used as the pen-shaped platform for driving the reaction cylinder. It was actuated using an inchworm motion. We confirmed that the magnetic beads were successfully manipulated in the droplet in the cylinder-shaped reaction units. (technical note)

  4. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  5. BlenX-based compositional modeling of complex reaction mechanisms

    Directory of Open Access Journals (Sweden)

    Judit Zámborszky

    2010-02-01

    Full Text Available Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality.

  6. Reactions of diiron m-aminocarbyne complexes containing nitrile ligands

    Directory of Open Access Journals (Sweden)

    Busetto Luigi

    2003-01-01

    Full Text Available The acetonitrile ligand in the mu-aminocarbyne complexes [Fe2{mu-CN(MeR}(mu-CO(CO(NCMe(Cp2][SO 3CF3] (R = Me, 2a, CH2Ph, 2b, Xyl, 2c (Xyl = 2,6-Me2C6H3 is readily displaced by halides and cyanide anions affording the corresponding neutral species [Fe2{mu-CN(MeR}(mu-CO(CO(X(Cp2 ] (X = Br, I, CN. Complexes 2 undergo deprotonation and rearrangement of the coordinated MeCN upon treatment with organolithium reagents. Trimethylacetonitrile, that does not contain acidic alpha hydrogens has been used in place of MeCN to form the complexes [Fe2{mu-CN(MeR}(mu-CO(CO(NCCMe3 (Cp2][SO3CF3] (7a-c. Attempts to replace the nitrile ligand in 3 with carbon nucleophiles (by reaction with RLi failed, resulting in decomposition products. However the reaction of 7c with LiCºCTol (Tol = C6H4Me, followed by treatment with HSO3CF3, yielded the imino complex [Fe2{mu-CN(MeXyl}(mu-CO(CO {N(HC(CºCC6H4Me-4CMe3}(Cp 2][SO3CF3 ] (8, obtained via acetilyde addition at the coordinated NCCMe3.

  7. Real-time nonlinear feedback control of pattern formation in (bio)chemical reaction-diffusion processes: a model study.

    Science.gov (United States)

    Brandt-Pollmann, U; Lebiedz, D; Diehl, M; Sager, S; Schlöder, J

    2005-09-01

    Theoretical and experimental studies related to manipulation of pattern formation in self-organizing reaction-diffusion processes by appropriate control stimuli become increasingly important both in chemical engineering and cellular biochemistry. In a model study, we demonstrate here exemplarily the application of an efficient nonlinear model predictive control (NMPC) algorithm to real-time optimal feedback control of pattern formation in a bacterial chemotaxis system modeled by nonlinear partial differential equations. The corresponding drift-diffusion model type is representative for many (bio)chemical systems involving nonlinear reaction dynamics and nonlinear diffusion. We show how the computed optimal feedback control strategy exploits the system inherent physical property of wave propagation to achieve desired control aims. We discuss various applications of our approach to optimal control of spatiotemporal dynamics.

  8. Studies of complex fragment emission in heavy ion reactions

    International Nuclear Information System (INIS)

    Charity, R.J.; Sobotka, L.G.

    1992-01-01

    Our work involves the study of intermediate energy heavy-ion nuclear reactions. This work has two foci. On the one hand, we desire to learn about the properties of nuclear matter under abnormal conditions, in this energy domain, predominately low densities. This purpose runs abreast of the second, which is the study of the relevant reaction mechanisms. The two objectives are inexorably linked because our experimental laboratory for studying nuclear matter properties is a dynamic one. We are forced to ask how nuclear matter properties, such as phase transitions, are reflected in the dynamics of the reactions. It may be that irrefutable information about nuclear matter will not be extracted from the reaction work. Nevertheless, we are compelled to undertake this effort not only because it is the only game in town and as yet we do not know that information cannot be extracted, but also because of our second objective. The process leads to an understanding of the reaction mechanism themselves and therefore to the response characteristics of finite, perhaps non-equilibrium, strongly interacting systems. Our program has been: To study energy, mass, and angular momentum deposition by studying incomplete fusion reactions. To gain confidence that we understand how highly excited systems decompose by studying all emissions from the highly excited systems. To push these kinds of studies into the intermediate energy domain, with excitation function studies. And attempt to learn about the dynamics of the decays using particle-particle correlations. In the last effort, we have decided to focus on simple systems, where we believe, definitive statements are possible. These avenues of research share a common theme, large complex fragment production

  9. The effect of menstruation on chosen physiological and biochemical reactions caused by the physical effort with the submaximal intensity

    Directory of Open Access Journals (Sweden)

    P Zieliński

    2003-03-01

    Full Text Available The aim of this work was to determine the influence of the menstruation phase on changes of respective indicators of the gas exchange and on biochemical parameters of blood during physical efforts with the sub-maximal intensity. Fifteen female students of the Academy of Physical Education took part in the study. Girls were aged from 19 to 22 years old and did not practice sports. The effort tests were conducted in the follicular and luteal phase of two succeeding menstrual cycles. As far the aerobic capacity determination is concerned, one cyclo-ergometric test with graded effort was conducted and it was performed till the “refusal”. It allowed to mark a threshold (TDMA and a maximal level of physiological and biochemical indicators. Basing on the results of the graded test individual loads were determined for every next effort trial (repeated 4 times in every phase of the two succeeding menstrual cycles. The aim of this trial was to evaluate the reaction of women’s constitution on work with the sub-maximal intensity. The above trial consisted on two 10 min efforts divided with the 2 min pause (the first effort with the intensity of 80% of the TDMA threshold, second with the intensity bigger about 30-40% of difference between TDMA and a maximal load established by the graded test. The research did not reveal statistically significant differentiation as considering effort changes of basic physiological and biochemical indicators, determining reaction of women’s organisms on work with the sub- and over- threshold intensity (TDMA. It showed that menstruation has not significant effect on the level of changes of analysed parameters caused by the physical effort with the sub-maximal intensity.

  10. (γ,2n) reactions in complexe nuclei at intermediate energies

    International Nuclear Information System (INIS)

    Pinheiro Filho, J. de D.

    1976-01-01

    The Monte Carlo Method has been used in the intranuclear cascade model for the calculation of the cross sections of the (γ,2n) reactions in complex nuclei 9 Be, 12 C, 16 O, 59 Co, 103 Rh, 127 I, 197 Au and 209 Bi at intermediate energies (200MeV-1000MeV). The initial photon-interaction via the photomesonic and quasi-deuteron mechanisms have been taken into account. The nuclear model used was a degenerate Fermi gas of nucleons, and the Pauli exclusion principle was considered in all secondary interactions. To improve accuracy in the results of the calculations, 30000 cascades have been followed for each target nucleus at a given incident photon energy. The probabilities of the various (γ,2n) reactions, as well as the correspondent cross section obtained, are summarized in tables and graphs. New data on the cross sections of the 59 Co (γ,2n) and 209 Bi (γ,2n) reactions at photon energies between 300 MeV and 1000MeV are also reported. These measurements were obtained with the Bremsstrahlung beams of the Frascati 1 GeV Electron Synchrotron. A comparison between all existing data in the literature on the (γ,2n) reaction cross sections and the estimates by the Monte Carlo Method, is presented. (Author) [pt

  11. Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation

    KAUST Repository

    Mélykúti, Bence; Burrage, Kevin; Zygalakis, Konstantinos C.

    2010-01-01

    The Chemical Langevin Equation (CLE), which is a stochastic differential equation driven by a multidimensional Wiener process, acts as a bridge between the discrete stochastic simulation algorithm and the deterministic reaction rate equation when

  12. Some biochemical reactions of strawberry plants to infection with Botrytis cinerea and salicylic acid treatment

    Directory of Open Access Journals (Sweden)

    Urszula Małolepsza

    2013-12-01

    Full Text Available The reactions of strawberry plants to infection with B. cinerea and treatment with salicylic acid has been studied. Infection of leaves with B. cinerea resulted in early increases in active oxygen species generation, superoxide dismutase and peroxidase activities and phenolic compounds content. Some increases of the above reactions were noticed in plants treated with salicylic acid but not in the plants treated with SA and then later infected with B. cinerea.

  13. A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

    Science.gov (United States)

    Miwa, Makoto; Ohta, Tomoko; Rak, Rafal; Rowley, Andrew; Kell, Douglas B.; Pyysalo, Sampo; Ananiadou, Sophia

    2013-01-01

    Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. Contact: makoto.miwa@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813008

  14. Reactions and mass spectra of complex particles using Aerosol CIMS

    Science.gov (United States)

    Hearn, John D.; Smith, Geoffrey D.

    2006-12-01

    Aerosol chemical ionization mass spectrometry (CIMS) is used both on- and off-line for the analysis of complex laboratory-generated and ambient particles. One of the primary advantages of Aerosol CIMS is the low degree of ion fragmentation, making this technique well suited for investigating the reactivity of complex particles. To demonstrate the usefulness of this "soft" ionization, particles generated from meat cooking were reacted with ozone and the composition was monitored as a function of reaction time. Two distinct kinetic regimes were observed with most of the oleic acid in these particles reacting quickly but with 30% appearing to be trapped in the complex mixture. Additionally, detection limits are measured to be sufficiently low (100-200 ng/m3) to detect some of the more abundant constituents in ambient particles, including sulfate, which is measured in real-time at 1.2 [mu]g/m3. To better characterize complex aerosols from a variety of sources, a novel off-line collection method was also developed in which non-volatile and semi-volatile organics are desorbed from particles and concentrated in a cold U-tube. Desorption from the U-tube followed by analysis with Aerosol CIMS revealed significant amounts of nicotine in cigarette smoke and levoglucosan in oak and pine smoke, suggesting that this may be a useful technique for monitoring particle tracer species. Additionally, secondary organic aerosol formed from the reaction of ozone with R-limonene and volatile organics from orange peel were analyzed off-line showing large molecular weight products (m/z > 300 amu) that may indicate the formation of oligomers. Finally, mass spectra of ambient aerosol collected offline reveal a complex mixture of what appears to be highly processed organics, some of which may contain nitrogen.

  15. Event timing in associative learning: from biochemical reaction dynamics to behavioural observations.

    Directory of Open Access Journals (Sweden)

    Ayse Yarali

    Full Text Available Associative learning relies on event timing. Fruit flies for example, once trained with an odour that precedes electric shock, subsequently avoid this odour (punishment learning; if, on the other hand the odour follows the shock during training, it is approached later on (relief learning. During training, an odour-induced Ca(++ signal and a shock-induced dopaminergic signal converge in the Kenyon cells, synergistically activating a Ca(++-calmodulin-sensitive adenylate cyclase, which likely leads to the synaptic plasticity underlying the conditioned avoidance of the odour. In Aplysia, the effect of serotonin on the corresponding adenylate cyclase is bi-directionally modulated by Ca(++, depending on the relative timing of the two inputs. Using a computational approach, we quantitatively explore this biochemical property of the adenylate cyclase and show that it can generate the effect of event timing on associative learning. We overcome the shortage of behavioural data in Aplysia and biochemical data in Drosophila by combining findings from both systems.

  16. Stochastic analysis of complex reaction networks using binomial moment equations.

    Science.gov (United States)

    Barzel, Baruch; Biham, Ofer

    2012-09-01

    The stochastic analysis of complex reaction networks is a difficult problem because the number of microscopic states in such systems increases exponentially with the number of reactive species. Direct integration of the master equation is thus infeasible and is most often replaced by Monte Carlo simulations. While Monte Carlo simulations are a highly effective tool, equation-based formulations are more amenable to analytical treatment and may provide deeper insight into the dynamics of the network. Here, we present a highly efficient equation-based method for the analysis of stochastic reaction networks. The method is based on the recently introduced binomial moment equations [Barzel and Biham, Phys. Rev. Lett. 106, 150602 (2011)]. The binomial moments are linear combinations of the ordinary moments of the probability distribution function of the population sizes of the interacting species. They capture the essential combinatorics of the reaction processes reflecting their stoichiometric structure. This leads to a simple and transparent form of the equations, and allows a highly efficient and surprisingly simple truncation scheme. Unlike ordinary moment equations, in which the inclusion of high order moments is prohibitively complicated, the binomial moment equations can be easily constructed up to any desired order. The result is a set of equations that enables the stochastic analysis of complex reaction networks under a broad range of conditions. The number of equations is dramatically reduced from the exponential proliferation of the master equation to a polynomial (and often quadratic) dependence on the number of reactive species in the binomial moment equations. The aim of this paper is twofold: to present a complete derivation of the binomial moment equations; to demonstrate the applicability of the moment equations for a representative set of example networks, in which stochastic effects play an important role.

  17. Post-prior equivalence for transfer reactions with complex potentials

    Science.gov (United States)

    Lei, Jin; Moro, Antonio M.

    2018-01-01

    In this paper, we address the problem of the post-prior equivalence in the calculation of inclusive breakup and transfer cross sections. For that, we employ the model proposed by Ichimura et al. [Phys. Rev. C 32, 431 (1985), 10.1103/PhysRevC.32.431], conveniently generalized to include the part of the cross section corresponding the transfer to bound states. We pay particular attention to the case in which the unobserved particle is left in a bound state of the residual nucleus, in which case the theory prescribes the use of a complex potential, responsible for the spreading width of the populated single-particle states. We see that the introduction of this complex potential gives rise to an additional term in the prior cross-section formula, not present in the usual case of real binding potentials. The equivalence is numerically tested for the 58Ni(d ,p X ) reaction.

  18. Biochemical principles underlying the stable maintenance of LTP by the CaMKII/NMDAR complex.

    Science.gov (United States)

    Lisman, John; Raghavachari, Sridhar

    2015-09-24

    Memory involves the storage of information at synapses by an LTP-like process. This information storage is synapse specific and can endure for years despite the turnover of all synaptic proteins. There must, therefore, be special principles that underlie the stability of LTP. Recent experimental results suggest that LTP is maintained by the complex of CaMKII with the NMDAR. Here we consider the specifics of the CaMKII/NMDAR molecular switch, with the goal of understanding the biochemical principles that underlie stable information storage by synapses. Consideration of a variety of experimental results suggests that multiple principles are involved. One switch requirement is to prevent spontaneous transitions from the off to the on state. The highly cooperative nature of CaMKII autophosphorylation by Ca(2+) (Hill coefficient of 8) and the fact that formation of the CaMKII/NMDAR complex requires release of CaMKII from actin are mechanisms that stabilize the off state. The stability of the on state depends critically on intersubunit autophosphorylation, a process that restores any loss of pT286 due to phosphatase activity. Intersubunit autophosphorylation is also important in explaining why on state stability is not compromised by protein turnover. Recent evidence suggests that turnover occurs by subunit exchange. Thus, stability could be achieved if a newly inserted unphosphorylated subunit was autophosphorylated by a neighboring subunit. Based on other recent work, we posit a novel mechanism that enhances the stability of the on state by protection of pT286 from phosphatases. We posit that the binding of the NMNDAR to CaMKII forces pT286 into the catalytic site of a neighboring subunit, thereby protecting pT286 from phosphatases. A final principle concerns the role of structural changes. The binding of CaMKII to the NMDAR may act as a tag to organize the binding of further proteins that produce the synapse enlargement that underlies late LTP. We argue that these

  19. Identification of alterations in the Jacobian of biochemical reaction networks from steady state covariance data at two conditions.

    Science.gov (United States)

    Kügler, Philipp; Yang, Wei

    2014-06-01

    Model building of biochemical reaction networks typically involves experiments in which changes in the behavior due to natural or experimental perturbations are observed. Computational models of reaction networks are also used in a systems biology approach to study how transitions from a healthy to a diseased state result from changes in genetic or environmental conditions. In this paper we consider the nonlinear inverse problem of inferring information about the Jacobian of a Langevin type network model from covariance data of steady state concentrations associated to two different experimental conditions. Under idealized assumptions on the Langevin fluctuation matrices we prove that relative alterations in the network Jacobian can be uniquely identified when comparing the two data sets. Based on this result and the premise that alteration is locally confined to separable parts due to network modularity we suggest a computational approach using hybrid stochastic-deterministic optimization for the detection of perturbations in the network Jacobian using the sparsity promoting effect of [Formula: see text]-penalization. Our approach is illustrated by means of published metabolomic and signaling reaction networks.

  20. From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions.

    Science.gov (United States)

    Nikel, Pablo I; Chavarría, Max; Danchin, Antoine; de Lorenzo, Víctor

    2016-10-01

    The soil bacterium Pseudomonas putida is endowed with a central carbon metabolic network capable of fulfilling high demands of reducing power. This situation arises from a unique metabolic architecture that encompasses the partial recycling of triose phosphates to hexose phosphates-the so-called EDEMP cycle. In this article, the value of P. putida as a bacterial chassis of choice for contemporary, industrially-oriented metabolic engineering is addressed. The biochemical properties that make this bacterium adequate for hosting biotransformations involving redox reactions as well as toxic compounds and intermediates are discussed. Finally, novel developments and open questions in the continuous quest for an optimal microbial cell factory are presented at the light of current and future needs in the area of biocatalysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Biochemical parameters in Tubifex tubifex as an integral part of complex sediment toxicity assessment

    Energy Technology Data Exchange (ETDEWEB)

    Smutna, M.; Hilscherova, K.; Paskova, V. [Masaryk Univ., Brno (CZ). RECETOX (Research Centre for Environmental Chemistry and Ecotoxicology); Marsalek, B [Czech Academy of Science, Brno (Czech Republic). Centre for Cyanobacteria and their Toxins

    2008-06-15

    Background, aim, and scope Restoration of lakes and reservoirs with extensive cyanobacterial water bloom often requires evaluation of the sediment quality. Next to the chemical analysis of known pollutants, sediment bioassays should be employed to assess toxicity of the present contaminants and to make predictions of associated risk. Brno reservoir in the Czech Republic is a typical example of water bodies with long-term problems concerning cyanobacterial water blooms. Comprehensive assessment of reservoir sediment quality was conducted since successful reservoir restoration might require sediment removal. An important part of this survey focused on an examination of the utility of Tubifex tubifex and its sublethal biochemical markers for the assessment of direct sediment toxicity. Materials and methods This complex study included chemical analysis of contaminants (heavy metals, organic pollutants), ecotoxicity testing of sediment elutriates (tests with Daphnia magna, Pseudomonas putida, Sinapis alba, Scenedesmus subspicatus), and other parameters. We have tested in more detail the applicability of T. tubifex as a test organism for direct evaluation of contact sediment toxicity. Survival tests after 14 days of exposure were complemented by an assessment of parameters serving as biomarkers for sublethal effects [such as total glutathione content (GSH), activities of the enzymes glutathione transferase (GST), glutathione peroxidase (GPx), and glutathione reductase (GR)]. The data matrix was subjected to multivariate analysis to interpret relationships between different parameters and possible differences among locations. Results The multivariate statistical techniques helped to clearly identify the more contaminated upstream sites and separate them from the less contaminated and reference samples. The data document closer relationships of the detected sediment contamination with results of direct sediment exposure in the T. tubifex test regarding mortality but namely

  2. Communication: Limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks

    Science.gov (United States)

    Thomas, Philipp; Straube, Arthur V.; Grima, Ramon

    2011-11-01

    It is commonly believed that, whenever timescale separation holds, the predictions of reduced chemical master equations obtained using the stochastic quasi-steady-state approximation are in very good agreement with the predictions of the full master equations. We use the linear noise approximation to obtain a simple formula for the relative error between the predictions of the two master equations for the Michaelis-Menten reaction with substrate input. The reduced approach is predicted to overestimate the variance of the substrate concentration fluctuations by as much as 30%. The theoretical results are validated by stochastic simulations using experimental parameter values for enzymes involved in proteolysis, gluconeogenesis, and fermentation.

  3. Measuring the complex behavior of the SO2 oxidation reaction

    Directory of Open Access Journals (Sweden)

    Muhammad Shahzad

    2015-09-01

    Full Text Available The two step reversible chemical reaction involving five chemical species is investigated. The quasi equilibrium manifold (QEM and spectral quasi equilibrium manifold (SQEM are used for initial approximation to simplify the mechanisms, which we want to utilize in order to investigate the behavior of the desired species. They show a meaningful picture, but for maximum clarity, the investigation method of invariant grid (MIG is employed. These methods simplify the complex chemical kinetics and deduce low dimensional manifold (LDM from the high dimensional mechanism. The coverage of the species near equilibrium point is investigated and then we shall discuss moving along the equilibrium of ODEs. The steady state behavior is observed and the Lyapunov function is utilized to study the stability of ODEs. Graphical results are used to describe the physical aspects of measurements.

  4. A Comparison of Deterministic and Stochastic Modeling Approaches for Biochemical Reaction Systems: On Fixed Points, Means, and Modes.

    Science.gov (United States)

    Hahl, Sayuri K; Kremling, Andreas

    2016-01-01

    In the mathematical modeling of biochemical reactions, a convenient standard approach is to use ordinary differential equations (ODEs) that follow the law of mass action. However, this deterministic ansatz is based on simplifications; in particular, it neglects noise, which is inherent to biological processes. In contrast, the stochasticity of reactions is captured in detail by the discrete chemical master equation (CME). Therefore, the CME is frequently applied to mesoscopic systems, where copy numbers of involved components are small and random fluctuations are thus significant. Here, we compare those two common modeling approaches, aiming at identifying parallels and discrepancies between deterministic variables and possible stochastic counterparts like the mean or modes of the state space probability distribution. To that end, a mathematically flexible reaction scheme of autoregulatory gene expression is translated into the corresponding ODE and CME formulations. We show that in the thermodynamic limit, deterministic stable fixed points usually correspond well to the modes in the stationary probability distribution. However, this connection might be disrupted in small systems. The discrepancies are characterized and systematically traced back to the magnitude of the stoichiometric coefficients and to the presence of nonlinear reactions. These factors are found to synergistically promote large and highly asymmetric fluctuations. As a consequence, bistable but unimodal, and monostable but bimodal systems can emerge. This clearly challenges the role of ODE modeling in the description of cellular signaling and regulation, where some of the involved components usually occur in low copy numbers. Nevertheless, systems whose bimodality originates from deterministic bistability are found to sustain a more robust separation of the two states compared to bimodal, but monostable systems. In regulatory circuits that require precise coordination, ODE modeling is thus still

  5. Biochemical toxicology studies of methomyl and its kinetic reaction with cholinesterase in rats

    International Nuclear Information System (INIS)

    Tawfik, S.M.; Abdel-Hamid, F.M.

    2001-01-01

    The effect of the pesticide methomyl on acetylcholinesterase activities in brain and blood of male rats in vivo and the kinetics involved in their reaction in vitro were studied. Also, its effect on peroxidase action of catalase in vivo was studied using 14C - formate. The results showed that methomyl is a competitive inhibitor for acetylcholinesterase and the concentration levels that caused 50% inhibition of the enzyme activity were 2.1 x 10-2 M and 1.9 x 10-4 for brain and blood- Ache, respectively. The inhibition of acetylcholinesterase activity decreased to 67.5 % at the time of appearance of toxicity symptoms. The radioactivity eliminated in both the expired air and in urine was reduced

  6. Genetic and biochemical identification of a novel single-stranded DNA binding complex in Haloferax volcanii

    Directory of Open Access Journals (Sweden)

    Amy eStroud

    2012-06-01

    Full Text Available Single-stranded DNA binding proteins play an essential role in DNA replication and repair. They use oligosaccharide-binding folds, a five-stranded ß-sheet coiled into a closed barrel, to bind to single-stranded DNA thereby protecting and stabilizing the DNA. In eukaryotes the single-stranded DNA binding protein is known as replication protein A (RPA and consists of three distinct subunits that function as a heterotrimer. The bacterial homolog is termed single-stranded DNA-binding protein (SSB and functions as a homotetramer. In the archaeon Haloferax volcanii there are three genes encoding homologs of RPA. Two of the rpa genes (rpa1 and rpa3 exist in operons with a novel gene specific to Euryarchaeota, this gene encodes a protein that we have termed rpa-associated protein (RPAP. The rpap genes encode proteins belonging to COG3390 group and feature oligosaccharide-binding folds, suggesting that they might cooperate with RPA in binding to single-stranded DNA. Our genetic analysis showed that rpa1 and rpa3 deletion mutants have differing phenotypes; only ∆rpa3 strains are hypersensitive to DNA damaging agents. Deletion of the rpa3-associated gene rpap3 led to similar levels of DNA damage sensitivity, as did deletion of the rpa3 operon, suggesting that RPA3 and RPAP3 function in the same pathway. Protein pull-downs involving recombinant hexahistidine-tagged RPAs showed that RPA3 co-purifies with RPAP3, and RPA1 co-purifies with RPAP1. This indicates that the RPAs interact only with their respective associated proteins; this was corroborated by the inability to construct rpa1 rpap3 and rpa3 rpap1 double mutants. This is the first report investigating the individual function of the archaeal COG3390 RPA-associated proteins. We have shown genetically and biochemically that the RPAPs interact with their respective RPAs, and have uncovered a novel single-stranded DNA binding complex that is unique to Euryarchaeota.

  7. Multiscale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Burke, Michael P.; Goldsmith, C. Franklin; Klippenstein, Stephen J.; Welz, Oliver; Huang, Haifeng; Antonov, Ivan O.; Savee, John D.; Osborn, David L.; Zádor, Judit; Taatjes, Craig A.; Sheps, Leonid

    2015-07-16

    We have developed a multi-scale approach (Burke, M. P.; Klippenstein, S. J.; Harding, L. B. Proc. Combust. Inst. 2013, 34, 547–555.) to kinetic model formulation that directly incorporates elementary kinetic theories as a means to provide reliable, physics-based extrapolation to unexplored conditions. Here, we extend and generalize the multi-scale modeling strategy to treat systems of considerable complexity – involving multi-well reactions, potentially missing reactions, non-statistical product branching ratios, and non-Boltzmann (i.e. non-thermal) reactant distributions. The methodology is demonstrated here for a subsystem of low-temperature propane oxidation, as a representative system for low-temperature fuel oxidation. A multi-scale model is assembled and informed by a wide variety of targets that include ab initio calculations of molecular properties, rate constant measurements of isolated reactions, and complex systems measurements. Active model parameters are chosen to accommodate both “parametric” and “structural” uncertainties. Theoretical parameters (e.g. barrier heights) are included as active model parameters to account for parametric uncertainties in the theoretical treatment; experimental parameters (e.g. initial temperatures) are included to account for parametric uncertainties in the physical models of the experiments. RMG software is used to assess potential structural uncertainties due to missing reactions. Additionally, branching ratios among product channels are included as active model parameters to account for structural uncertainties related to difficulties in modeling sequences of multiple chemically activated steps. The approach is demonstrated here for interpreting time-resolved measurements of OH, HO2, n-propyl, i-propyl, propene, oxetane, and methyloxirane from photolysis-initiated low-temperature oxidation of propane at pressures from 4 to 60 Torr and temperatures from 300 to 700 K. In particular, the multi-scale informed

  8. Complexation Key to a pH Locked Redox Reaction

    Science.gov (United States)

    Rizvi, Masood Ahmad; Dangat, Yuvraj; Shams, Tahir; Khan, Khaliquz Zaman

    2016-01-01

    An unfavorable pH can block a feasible electron transfer for a pH dependent redox reaction. In this experiment, a series of potentiometric titrations demonstrate the sequential loss in feasibility of iron(II) dichromate redox reaction over a pH range of 0-4. The pH at which this reaction failed to occur was termed as a pH locked reaction. The…

  9. An effective rate equation approach to reaction kinetics in small volumes: theory and application to biochemical reactions in nonequilibrium steady-state conditions.

    Science.gov (United States)

    Grima, R

    2010-07-21

    Chemical master equations provide a mathematical description of stochastic reaction kinetics in well-mixed conditions. They are a valid description over length scales that are larger than the reactive mean free path and thus describe kinetics in compartments of mesoscopic and macroscopic dimensions. The trajectories of the stochastic chemical processes described by the master equation can be ensemble-averaged to obtain the average number density of chemical species, i.e., the true concentration, at any spatial scale of interest. For macroscopic volumes, the true concentration is very well approximated by the solution of the corresponding deterministic and macroscopic rate equations, i.e., the macroscopic concentration. However, this equivalence breaks down for mesoscopic volumes. These deviations are particularly significant for open systems and cannot be calculated via the Fokker-Planck or linear-noise approximations of the master equation. We utilize the system-size expansion including terms of the order of Omega(-1/2) to derive a set of differential equations whose solution approximates the true concentration as given by the master equation. These equations are valid in any open or closed chemical reaction network and at both the mesoscopic and macroscopic scales. In the limit of large volumes, the effective mesoscopic rate equations become precisely equal to the conventional macroscopic rate equations. We compare the three formalisms of effective mesoscopic rate equations, conventional rate equations, and chemical master equations by applying them to several biochemical reaction systems (homodimeric and heterodimeric protein-protein interactions, series of sequential enzyme reactions, and positive feedback loops) in nonequilibrium steady-state conditions. In all cases, we find that the effective mesoscopic rate equations can predict very well the true concentration of a chemical species. This provides a useful method by which one can quickly determine the

  10. Biochemical Characterisation of TSC1 and TSC2 Variants Identified in Patients with Tuberous Sclerosis Complex

    Science.gov (United States)

    2010-07-01

    autism -spectrum disorders. Mutations in either the TSC1 gene on chromosome 9q34 [van Slegtenhorst et al., 1997], or the TSC2 gene on chromosome 16p13.3...cell-based phospho-ERK assay for dopamine D2 and D3 receptors. Anal Biochem 2004; 333: 265–272. 14 Selkirk JV, Nottebaum LM, Ford IC et al: A novel cell

  11. On determination of enthalpies of complex formation reactions by means of temperature coefficient of complexing degree

    International Nuclear Information System (INIS)

    Povar, I.G.

    1995-01-01

    Equations describing the relation between temperature coefficient of ∂lnα/∂T complexing degree and the sum of changes in the enthalpy of complex formation of the composition M m L n δH mn multiplied by the weight coefficients k mm , are presented. A method to determine changes in the enthalpy of certain ΔH mm reactions from ∂lnα/∂T derivatives has been suggested. The best approximating equation from lnα/(T) dependence has been found. Errors of thus determined δH mm values are estimated and the results of calculation experiment for the system In 3+ -F - are provided. 10 refs., 2 figs., 3 tabs

  12. Fiber-Optic Bio-sniffer (Biochemical Gas Sensor) Using Reverse Reaction of Alcohol Dehydrogenase for Exhaled Acetaldehyde.

    Science.gov (United States)

    Iitani, Kenta; Chien, Po-Jen; Suzuki, Takuma; Toma, Koji; Arakawa, Takahiro; Iwasaki, Yasuhiko; Mitsubayashi, Kohji

    2018-02-23

    Volatile organic compounds (VOCs) exhaled in breath have huge potential as indicators of diseases and metabolisms. Application of breath analysis for disease screening and metabolism assessment is expected since breath samples can be noninvasively collected and measured. In this research, a highly sensitive and selective biochemical gas sensor (bio-sniffer) for gaseous acetaldehyde (AcH) was developed. In the AcH bio-sniffer, a reverse reaction of alcohol dehydrogenase (ADH) was employed for reducing AcH to ethanol and simultaneously consuming a coenzyme, reduced form of nicotinamide adenine dinucleotide (NADH). The concentration of AcH can be quantified by fluorescence detection of NADH that was consumed by reverse reaction of ADH. The AcH bio-sniffer was composed of an ultraviolet light-emitting diode (UV-LED) as an excitation light source, a photomultiplier tube (PMT) as a fluorescence detector, and an optical fiber probe, and these three components were connected with a bifurcated optical fiber. A gas-sensing region of the fiber probe was developed with a flow-cell and an ADH-immobilized membrane. In the experiment, after optimization of the enzyme reaction conditions, the selectivity and dynamic range of the AcH bio-sniffer were investigated. The AcH bio-sniffer showed a short measurement time (within 2 min) and a broad dynamic range for determination of gaseous AcH, 0.02-10 ppm, which encompassed a typical AcH concentration in exhaled breath (1.2-6.0 ppm). Also, the AcH bio-sniffer exhibited a high selectivity to gaseous AcH based on the specificity of ADH. The sensor outputs were observed only from AcH-contained standard gaseous samples. Finally, the AcH bio-sniffer was applied to measure the concentration of AcH in exhaled breath from healthy subjects after ingestion of alcohol. As a result, a significant difference of AcH concentration between subjects with different aldehyde dehydrogenase type 2 (ALDH2) phenotypes was observed. The AcH bio-sniffer can be

  13. Dinuclear Tetrapyrazolyl Palladium Complexes Exhibiting Facile Tandem Transfer Hydrogenation/Suzuki Coupling Reaction of Fluoroarylketone

    KAUST Repository

    Dehury, Niranjan; Maity, Niladri; Tripathy, Suman Kumar; Basset, Jean-Marie; Patra, Srikanta

    2016-01-01

    Herein, we report an unprecedented example of dinuclear pyrazolyl-based Pd complexes exhibiting facile tandem catalysis for fluoroarylketone: Tetrapyrazolyl di-palladium complexes with varying Pd-Pd distances efficiently catalyze the tandem reaction

  14. Microfluidic technology platforms for synthesizing, labeling and measuring the kinetics of transport and biochemical reactions for developing molecular imaging probes

    Energy Technology Data Exchange (ETDEWEB)

    Phelps, Michael E. [Univ. of California, Los Angeles, CA (United States)

    2009-09-01

    Radiotracer techniques are used in environmental sciences, geology, biology and medicine. Radiotracers with Positron Emission Tomography (PET) provided biological examinations of ~3 million patients 2008. Despite the success of positron labeled tracers in many sciences, there is limited access in an affordable and convenient manner to develop and use new tracers. Integrated microfluidic chips are a new technology well matched to the concentrations of tracers. Our goal is to develop microfluidic chips and new synthesis approaches to enable wide dissemination of diverse types of tracers at low cost, and to produce new generations of radiochemists for which there are many unfilled jobs. The program objectives are to: 1. Develop an integrated microfluidic platform technology for synthesizing and 18F-labeling diverse arrays of different classes of molecules. 2. Incorporate microfluidic chips into small PC controlled devices (“Synthesizer”) with a platform interfaced to PC for electronic and fluid input/out control. 3. Establish a de-centralized model with Synthesizers for discovering and producing molecular imaging probes, only requiring delivery of inexpensive [18F]fluoride ion from commercial PET radiopharmacies vs the centralized approach of cyclotron facilities synthesizing and shipping a few different types of 18F-probes. 4. Develop a position sensitive avalanche photo diode (PSAPD) camera for beta particles embedded in a microfluidic chip for imaging and measuring transport and biochemical reaction rates to valid new 18F-labeled probes in an array of cell cultures. These objectives are met within a research and educational program integrating radio-chemistry, synthetic chemistry, biochemistry, engineering and biology in the Crump Institute for Molecular Imaging. The Radiochemistry Training Program exposes PhD and post doctoral students to molecular imaging in vitro in cells and microorganisms in microfluidic chips and in vivo with PET, from new technologies

  15. On the Complexity of Reconstructing Chemical Reaction Networks

    DEFF Research Database (Denmark)

    Fagerberg, Rolf; Flamm, Christoph; Merkle, Daniel

    2013-01-01

    The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network properties are typically made on standard graphs derived from...... the full hypergraph description, e.g. on the so-called species and reaction graphs. However, a reconstruction of the underlying hypergraph from these graphs is not necessarily unique. In this paper, we address the problem of reconstructing a hypergraph from its species and reaction graph and show NP...

  16. Bio-Photoelectrochemical Solar Cells Incorporating Reaction Center and Reaction Center Plus Light Harvesting Complexes

    Science.gov (United States)

    Yaghoubi, Houman

    Harvesting solar energy can potentially be a promising solution to the energy crisis now and in the future. However, material and processing costs continue to be the most important limitations for the commercial devices. A key solution to these problems might lie within the development of bio-hybrid solar cells that seeks to mimic photosynthesis to harvest solar energy and to take advantage of the low material costs, negative carbon footprint, and material abundance. The bio-photoelectrochemical cell technologies exploit biomimetic means of energy conversion by utilizing plant-derived photosystems which can be inexpensive and ultimately the most sustainable alternative. Plants and photosynthetic bacteria harvest light, through special proteins called reaction centers (RCs), with high efficiency and convert it into electrochemical energy. In theory, photosynthetic RCs can be used in a device to harvest solar energy and generate 1.1 V open circuit voltage and ~1 mA cm-2 short circuit photocurrent. Considering the nearly perfect quantum yield of photo-induced charge separation, efficiency of a protein-based solar cell might exceed 20%. In practice, the efficiency of fabricated devices has been limited mainly due to the challenges in the electron transfer between the protein complex and the device electrodes as well as limited light absorption. The overarching goal of this work is to increase the power conversion efficiency in protein-based solar cells by addressing those issues (i.e. electron transfer and light absorption). This work presents several approaches to increase the charge transfer rate between the photosynthetic RC and underlying electrode as well as increasing the light absorption to eventually enhance the external quantum efficiency (EQE) of bio-hybrid solar cells. The first approach is to decrease the electron transfer distance between one of the redox active sites in the RC and the underlying electrode by direct attachment of the of protein complex

  17. Biochemical characterization of the prolyl 3-hydroxylase 1.cartilage-associated protein.cyclophilin B complex.

    Science.gov (United States)

    Ishikawa, Yoshihiro; Wirz, Jackie; Vranka, Janice A; Nagata, Kazuhiro; Bächinger, Hans Peter

    2009-06-26

    The rough endoplasmic reticulum-resident protein complex consisting of prolyl 3-hydroxylase 1 (P3H1), cartilage-associated protein (CRTAP), and cyclophilin B (CypB) can be isolated from chick embryos on a gelatin-Sepharose column, indicating some involvement in the biosynthesis of procollagens. Prolyl 3-hydroxylase 1 modifies a single proline residue in the alpha chains of type I, II, and III collagens to (3S)-hydroxyproline. The peptidyl-prolyl cis-trans isomerase activity of cyclophilin B was shown previously to catalyze the rate of triple helix formation. Here we show that cyclophilin B in the complex shows peptidyl-prolyl cis-trans isomerase activity and that the P3H1.CRTAP.CypB complex has another important function: it acts as a chaperone molecule when tested with two classical chaperone assays. The P3H1.CRTAP.CypB complex inhibited the thermal aggregation of citrate synthase and was active in the denatured rhodanese refolding and aggregation assay. The chaperone activity of the complex was higher than that of protein-disulfide isomerase, a well characterized chaperone. The P3H1.CRTAP.CypB complex also delayed the in vitro fibril formation of type I collagen, indicating that this complex is also able to interact with triple helical collagen and acts as a collagen chaperone.

  18. Studies of complex fragment emission in heavy ion reactions

    International Nuclear Information System (INIS)

    Sobotka, L.G.

    1989-01-01

    The production of large fragments, fragments with mass between light particles and fission fragments, in intermediate and high energy nuclear reactions has fostered the proposal of a number of novel reaction mechanisms. These include liquid-vapor equilibrium and nuclear shattering. Temporarily left in the wake of these exciting proposed mechanisms was the old standard, statistical decay of compound nuclei. To be sure, the standard treatment of compound nucleus decay did not deal with large fragment production. However, this omission was not due to any fundamental deficiency of statistical models, but rather an uncertainty concerning exactly how to splice large fragment emission into statistical models. A large portion of our program deals with this problem. Specifically, by studying the yields of large fragments produced in sufficiently low energy reactions we are attempting to deduce the asymmetry and l-wave dependence of large fragment emission from compound nuclear intermediates. This, however, is only half of the problem. Since the novel mechanisms proposed for large fragment emission were spawned by intermediate and high energy reaction data, we must also realize the relevance of the compound nucleus mechanisms at high energies. It is not unreasonable to suspect that compound nucleus-like objects are formed with less than complete momentum transfer and perhaps less than complete mass transfer. Therefore the study of energy, mass, and angular momentum transfer in incomplete fusion and non-compound reactions. This thread joins the apparently divergent subjects covered in this report

  19. Wave Packet Based Statistical Approach to Complex-Forming Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Hua [Univ. of New Mexico, Albuquerque, NM (United States). Dept. of Chemistry and Chemical Biology

    2017-12-06

    Combustion represents a key chemical process in energy consumption in modern societies and a clear and comprehensive understanding of the elemental reactions in combustion is of great importance to a number of challenging areas such as engine efficiency and environmental protection. In this award, we proposed to develop new theoretical tools to understand elemental chemical processes in combustion environments. With the support of this DOE grant, we have made significant advances in developing new and more efficient and accurate algorithms to characterize reaction dynamics.

  20. Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus

    OpenAIRE

    Kiyonari, Shinichi; Tahara, Saki; Shirai, Tsuyoshi; Iwai, Shigenori; Ishino, Sonoko; Ishino, Yoshizumi

    2009-01-01

    Apurinic/apyrimidinic (AP) sites are the most frequently found mutagenic lesions in DNA, and they arise mainly from spontaneous base loss or modified base removal by damage-specific DNA glycosylases. AP sites are cleaved by AP endonucleases, and the resultant gaps in the DNA are repaired by DNA polymerase/DNA ligase reactions. We identified the gene product that is responsible for the AP endonuclease activity in the hyperthermophilic euryarchaeon, Pyrococcus furiosus. Furthermore, we detected...

  1. Reactions of transition metal complexes with cyclic ethers

    International Nuclear Information System (INIS)

    Milstein, D.

    1977-02-01

    Three novel reactions of epoxides with homogeneous transition-metal catalysts have been explored: (a) the selective rearrangement of internal epoxides to ketones; (b) the cleavage of C-C bond in epoxides having electron-attracting substituents; (c) the transformation of terminal epoxides into esters. Based on an intensive kinetic study, a general mechanism for the transformations of epoxides is postulated

  2. Possible self-complexity and affective reactions to goal-relevant evaluation.

    Science.gov (United States)

    Niedenthal, P M; Setterlund, M B; Wherry, M B

    1992-07-01

    The complexity of people's self-concept appears to be inversely related to the intensity of their reactions to evaluative feedback about present goals and abilities (Linville, 1985, 1987). The idea that the complexity of individuals' possible self-concept similarly mediates reactions to feedback regarding future goals was investigated. Two preliminary studies suggested that complexity of the actual self only explains 20% to 30% of the variance in possible self-complexity. Three studies were conducted. Support was found for the idea that possible self-complexity mediates affective reactions to evaluative feedback about future goals and actual self-complexity mediates affective reactions to evaluative feedback about present goals. The findings underscore the independent roles of the organization of actual and possible self-concepts in affective processes.

  3. Biochemical reconstitution and phylogenetic comparison of human SET1 family core complexes involved in histone methylation.

    Science.gov (United States)

    Shinsky, Stephen A; Monteith, Kelsey E; Viggiano, Susan; Cosgrove, Michael S

    2015-03-06

    Mixed lineage leukemia protein-1 (MLL1) is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases that are required for metazoan development. MLL1 is the best characterized human SET1 family member, which includes MLL1-4 and SETd1A/B. MLL1 assembles with WDR5, RBBP5, ASH2L, DPY-30 (WRAD) to form the MLL1 core complex, which is required for H3K4 dimethylation and transcriptional activation. Because all SET1 family proteins interact with WRAD in vivo, it is hypothesized they are regulated by similar mechanisms. However, recent evidence suggests differences among family members that may reflect unique regulatory inputs in the cell. Missing is an understanding of the intrinsic enzymatic activities of different SET1 family complexes under standard conditions. In this investigation, we reconstituted each human SET1 family core complex and compared subunit assembly and enzymatic activities. We found that in the absence of WRAD, all but one SET domain catalyzes at least weak H3K4 monomethylation. In the presence of WRAD, all SET1 family members showed stimulated monomethyltransferase activity but differed in their di- and trimethylation activities. We found that these differences are correlated with evolutionary lineage, suggesting these enzyme complexes have evolved to accomplish unique tasks within metazoan genomes. To understand the structural basis for these differences, we employed a "phylogenetic scanning mutagenesis" assay and identified a cluster of amino acid substitutions that confer a WRAD-dependent gain-of-function dimethylation activity on complexes assembled with the MLL3 or Drosophila trithorax proteins. These results form the basis for understanding how WRAD differentially regulates SET1 family complexes in vivo. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Generalization of the Activated Complex Theory of Reaction Rates. I. Quantum Mechanical Treatment

    Science.gov (United States)

    Marcus, R. A.

    1964-01-01

    In its usual form activated complex theory assumes a quasi-equilibrium between reactants and activated complex, a separable reaction coordinate, a Cartesian reaction coordinate, and an absence of interaction of rotation with internal motion in the complex. In the present paper a rate expression is derived without introducing the Cartesian assumption. The expression bears a formal resemblance to the usual one and reduces to it when the added assumptions of the latter are introduced.

  5. Vinylogous Nicholas reactions in the synthesis of bi- and tricyclic cycloheptynedicobalt complexes.

    Science.gov (United States)

    Kolodziej, Izabela; Green, James R

    2015-11-28

    The Lewis acid mediated intramolecular Nicholas reactions of allylic acetate enyne-Co2(CO)6 complexes afford cycloheptenyne-Co2(CO)6 complexes in three manifestations. Electron rich aryl substituted alkyne complexes give tricyclic 6,7,x-benzocycloheptenyne complexes, with x = 5, 6, or 7. Allylsilane substituted complexes afford exo methylene bicyclic x,7-cycloheptenyne complexes (x = 6,7). The allyl acetate function may also be replaced by a benzylic acetate, to afford dibenzocycloheptyne-Co2(CO)6 complexes. Following reductive complexation, the methodology may be applied to the synthesis of the icetexane diterpene carbon framework.

  6. N-Heterocyclic Carbene Complexes in Dehalogenation Reactions

    Science.gov (United States)

    Mas-Marzá, Elena; Page, Michael J.; Whittlesey, Michael K.

    Catalytic dehalogenation represents an underdeveloped transformation in M-NHC chemistry with a small number of reports detailing the reactivity of Co, Ru, Ni and Pd catalysts. In situ generated nickel and palladium NHC complexes catalyse the hydrodechlorination of aryl chlorides. Lower coordinate Ni complexes are proposed to operate in the hydrodefluorination of mono- and poly-fluorinated substrates. The single example of Ru-NHC catalysed hydrodefluorination of fully and partially fluorinated aromatic substrates is characterised by an unusual regioselectivity. The highly regioselective dehydrohalogenation of relatively unreactive alkyl halide substrates is achieved with a cobalt NHC catalyst.

  7. Biochemical Characterisation of TSC1 and TSC2 Variants Identifiedd in Patients with Tuberous sclerosis Complex

    Science.gov (United States)

    2008-07-01

    different species (human, chimpanzee, macacca, cow, dog, horse, mouse, rat, chicken, pufferfish, honey bee , fruitfly, mosquito and fission yeast). The...by mutations in either the TSC1 or TSC2 tumour suppressor genes (2, 3). The TSC1 and TSC2 gene products form a protein complex that inhibits the...quantitative estimate of TSC1-TSC2 levels and S6K phosphorylation, the blots were scanned. 3. Phosphorylation of ribosomal protein S6 in Tsc1 -/- and

  8. Proton exchange in acid–base complexes induced by reaction coordinates with heavy atom motions

    International Nuclear Information System (INIS)

    Alavi, Saman; Taghikhani, Mahdi

    2012-01-01

    Highlights: ► Proton exchange in acid–base complexes is studied. ► The structures, binding energies, and normal mode vibrations are calculated. ► Transition state structures of proton exchange mechanism are determined. ► In the complexes studied, the reaction coordinate involves heavy atom rocking. ► The reaction coordinate is not simply localized in the proton movements. - Abstract: We extend previous work on nitric acid–ammonia and nitric acid–alkylamine complexes to illustrate that proton exchange reaction coordinates involve the rocking motion of the base moiety in many double hydrogen-bonded gas phase strong acid–strong base complexes. The complexes studied involve the biologically and atmospherically relevant glycine, formic, acetic, propionic, and sulfuric acids with ammonia/alkylamine bases. In these complexes, the magnitude of the imaginary frequencies associated with the proton exchange transition states are −1 . This contrasts with widely studied proton exchange reactions between symmetric carboxylic acid dimers or asymmetric DNA base pair and their analogs where the reaction coordinate is localized in proton motions and the magnitude of the imaginary frequencies for the transition states are >1100 cm −1 . Calculations on complexes of these acids with water are performed for comparison. Variations of normal vibration modes along the reaction coordinate in the complexes are described.

  9. Theoretical aspects of electron transfer reactions of complex molecules

    DEFF Research Database (Denmark)

    Kuznetsov, A. M.; Ulstrup, Jens

    2001-01-01

    Features of electron transfer involving complex molecules are discussed. This notion presently refers to molecular reactants where charge transfer is accompanied by large molecular reorganization, and commonly used displaced harmonic oscillator models do not apply. It is shown that comprehensive...... theory of charge transfer in polar media offers convenient tools for the treatment of experimental data for such systems, with due account of large-amplitude strongly anharmonic intramolecular reorganization. Equations for the activation barrier and free energy relationships are provided, incorporating...

  10. Psychological reactions to catastrophes: fear as a reaction to accidents and emergencies in industriel complexes

    International Nuclear Information System (INIS)

    Wernli, G.

    1989-01-01

    This paper addresses the subject 'stress' and its effects on the personality. Specific types of behavior, which the human develops in a fearful situation are demonstrated by means of the psychoanalytical personality model. In the conclusion possible methods of alleviating fear, shock and panic reactions are described. 7 figs., 2 tabs., 9 refs

  11. Arenethiolatecopper(I) complexes as homogeneous catalysts for Michael addition reactions

    NARCIS (Netherlands)

    Koten, G. van; Klaveren, M. van; Lambert, F.; Eijkelkamp, D.J.F.M.; Grove, D.M.

    1994-01-01

    Arenethiolatocopper(I) complexes are shown to be efficient homogeneous catalysts in Michael addition reactions of several Grignard reagents to acyclic enones; the addition products are formed with excellent chemoselectivity (>99%) and good enantioselectivity (76% e.e.).

  12. Probing the Energy Transfer Dynamics of Photosynthetic Reaction Center Complexes Through Hole-Burning and Single-Complex Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Kerry Joseph [Iowa State Univ., Ames, IA (United States)

    2007-01-01

    Photosynthesis is the process by which light energy is used to drive reactions that generate sugars to supply energy for cellular processes. It is one of the most important fundamental biological reactions and occurs in both prokaryotic (e.g. bacteria) and eukaryotic (e.g. plants and algae) organisms. Photosynthesis is also remarkably intricate, requiring the coordination of many different steps and reactions in order to successfully transform absorbed solar energy into a biochemical usable form of energy. However, the net reaction for all photosynthetic organisms can be reduced to the following, deceptively general, equation developed by Van Niel[1] H2 - D + Aimplieshv A - H2 + D where H2-D is the electron donor, e.g. H2O, H2S. A is the electron acceptor, e.g. CO2, and A-H2 is the synthesized sugar. Amazingly, this simple net equation is responsible for creating the oxidizing atmosphere of Earth and the recycling of CO2, both of which are necessary for the sustainment of the global ecosystem.

  13. Kinetic and mechanism formation reaction of complex compound Cu with di-n-buthildithiocarbamate (dbdtc) ligand

    Science.gov (United States)

    Haryani, S.; Kurniawan, C.; Kasmui

    2018-04-01

    Synthesis of complex compound is one field of research which intensively studied. Metal-dithiocarbamate complexes find wide-ranging applications in nanomaterial and metal separation science, and have potential use as chemotherapeutic, pesticides, and as additives to lubricants. However, the information about is reaction kinetic and mechanism are very much lacking. The research and analyzes results show that reaction synthesis ligand DBDTC and complex compounds Cu-DBDTC. Optimum reaction condition of formation of complex compounds Cu with DBDTC at pH=3, [DBDTC] = 4.10-3 M, and the time of reaction 5 minutes. Based the analysis varian reaction of complex compounds at pH 3 and 4, diffrence significance at the other pH: 5; 5,5; 6; 6,5 ; 7; and 8. The various of mole with reactants comosition difference sigbificance, those the time reaction for 5 and 6 minutes diffrence by significance with the other time, it is 3,4,8, and 10 minutes. The great product to at condition pH 6, the time optimum at 5 minutes and molar ratio of logam: ligand = 1:2. The reaction kinetic equation of complex compound Cu with chelathing ligand DBDTC is V=0.917106 [Cu2+]0.87921 [DBDTC]2.03021. Based on the kinetic data, and formed complex compounds estimation, the mechanism explaining by 2 stages. In the first stage formation of [Cu(DBDTC)], and then [Cu(DBDTC)2] with the last structure geomethry planar rectangle. The result of this research will be more useful if an effort is being done in reaction mechanism by chemical computation method for obtain intermediate, and for constant “k” in same stage, k1.k2. and compound complex constanta (β).

  14. Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.

    Science.gov (United States)

    Schillings, Claudia; Sunnåker, Mikael; Stelling, Jörg; Schwab, Christoph

    2015-08-01

    Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative deterministic methodology that relies on sparse polynomial approximations. We propose a deterministic computational interpolation scheme which identifies most significant expansion coefficients adaptively. We present its performance in kinetic model equations from computational systems biology with several hundred parameters and state variables, leading to numerical approximations of the parametric solution on the entire parameter space. The scheme is based on adaptive Smolyak interpolation of the parametric solution at judiciously and adaptively chosen points in parameter space. As Monte-Carlo sampling, it is "non-intrusive" and well-suited for massively parallel implementation, but affords higher convergence rates. This opens up new avenues for large-scale dynamic network analysis by enabling scaling for many applications, including parameter estimation, uncertainty quantification, and systems design.

  15. Combining measurements to estimate properties and characterization extent of complex biochemical mixtures; applications to Heparan Sulfate

    Science.gov (United States)

    Pradines, Joël R.; Beccati, Daniela; Lech, Miroslaw; Ozug, Jennifer; Farutin, Victor; Huang, Yongqing; Gunay, Nur Sibel; Capila, Ishan

    2016-04-01

    Complex mixtures of molecular species, such as glycoproteins and glycosaminoglycans, have important biological and therapeutic functions. Characterization of these mixtures with analytical chemistry measurements is an important step when developing generic drugs such as biosimilars. Recent developments have focused on analytical methods and statistical approaches to test similarity between mixtures. The question of how much uncertainty on mixture composition is reduced by combining several measurements still remains mostly unexplored. Mathematical frameworks to combine measurements, estimate mixture properties, and quantify remaining uncertainty, i.e. a characterization extent, are introduced here. Constrained optimization and mathematical modeling are applied to a set of twenty-three experimental measurements on heparan sulfate, a mixture of linear chains of disaccharides having different levels of sulfation. While this mixture has potentially over two million molecular species, mathematical modeling and the small set of measurements establish the existence of nonhomogeneity of sulfate level along chains and the presence of abundant sulfate repeats. Constrained optimization yields not only estimations of sulfate repeats and sulfate level at each position in the chains but also bounds on these levels, thereby estimating the extent of characterization of the sulfation pattern which is achieved by the set of measurements.

  16. Biogeochemical stability and reactions of iron-organic carbon complexes

    Science.gov (United States)

    Yang, Y.; Adhikari, D.; Zhao, Q.; Dunham-Cheatham, S.; Das, K.; Mejia, J.; Huang, R.; Wang, X.; Poulson, S.; Tang, Y.; Obrist, D.; Roden, E. E.

    2017-12-01

    Our core hypothesis is that the degradation rate of soil organic carbon (OC) is governed by the amount of iron (Fe)-bound OC, and the ability of microbial communities to utilize OC as an energy source and electron shuttle for Fe reduction that in turn stimulates reductive release of Fe-bound labile dissolved OC. This hypothesis is being systematically evaluated using model Fe-OC complexes, natural soils, and microcosm system. We found that hematite-bound aliphatic C was more resistant to reduction release, although hematite preferred to sorb more aromatic C. Resistance to reductive release represents a new mechanism that aliphatic soil OC was stabilized by association with Fe oxide. In other studies, pyrogenic OC was found to facilitate the reduction of hematite, by enhancing extracellular electron transport and sorbing Fe(II). For ferrihydrite-OC co-precipitates, the reduction of Fe and release of OC was closely governed by the C/Fe ratio in the system. Based on the XPS, XANES and XAFS analysis, the transformation of Fe speciation was heterogeneous, depending on the conformation and composition of Fe-OC complexes. For natural soils, we investigated the quantity, characteristics, and reactivity of Fe-bound OC in soils collected from 14 forests in the United States. Fe-bound OC contributed up to 57.8% of total OC in the forest soils. Under the anaerobic conditions, the reduction of Fe was positively correlated to the electron accepting capacity of OC. Our findings highlight the closely coupled dynamics of Fe and OC, with broad implications on the turnover of OC and biogeochemical cycles of Fe.

  17. Complex reactions of excitable tissue on radio-, photo- and thermostimulation

    International Nuclear Information System (INIS)

    Neu, E.; Bischof, R.; Seidenbusch, W.; Willich, N.

    2003-01-01

    Photo-, radio and thermotherapies are an essential part of modern treatment. A summary of some selected earlier and resent data about motor reactions of non- and vascular preparations is given [1-4, incl. methods]. Radiostimulation: X-irradiation (50-150 kV: 1-50 Gy, 10-30 Gy/min) induced in frog and rat aorta (helical strips) as well as guinea pig (GP) (and rat) detrusor, t. coli, frog lung and neuro-muscle prep. of hirudo med. reversible contractions. Photostimulation: After UV-irradiation (450 W Xenon lamp) frog aorta and hirudo (max. 267-308 nm) and frog lung (max. 294-335 nm) also reacted with reversible contr., but rat aorta and GP t. coli (max. 294-335 nm) with a photorelaxation. Laser (He-Ne 632.8 nm, 10 mW) induced photocontractions in detrusor and hirudo. Thermostimulation: After hypothermia (37 to 25/5 deg C) a relaxation of frog and rat aorta appeared: X-ray contr. of frog aorta and GP detrusor was potentiated, but of rat aorta - abolished; hyperthermic (37 to 42/45 deg C) tonic contr. of rat rct. were observed. Differences in the radio-, photo- and thermosensitizing / -inhibitory effects by drugs and ions are observed. The influence of non-ionizing radiation (infrared laser 9.5-11.5 μm and 50 μm-1 mm) as well as of micro- (cm) and ultrashort (m) waves (MHz, GHz) on excitable tissue in context of combined effects with ionizing radiation and signal transduction will be studied. Lit.: Furchgott et al [a] J Gen Physiol 44, 499, 1961; [b] Nature 218, 682, 1968. [2] Michailov et al, Strahlenther [a] 167, 5, 311-318, 1991 and 165, 860-5, 1989 and 159, 448-451, 1983; [b] Proc. ICRR Dublin, 234, 1999 and Wuerzburg 400, 1995. [3] Neu et al [a] in: IORT, Vg 'Blaue Eule' 27-39, 1993; [b] Gyn Rdsch 33/S1, 206-7, 1993. [4] Welscher et al [a] Front Rad Ther Oncol 31, Karger 22-35, 1997; [b] Proc ICRR Wuerzburg 434, 1995 and Toronto 265, 1991; [c] Physiol Res 48, S138, 1999; [d] Eur J. Physiol 430/S, 604, 1995?

  18. Computational Analyses of Complex Flows with Chemical Reactions

    Science.gov (United States)

    Bae, Kang-Sik

    missiles. The comprehensive skeletal mechanism consists of 58 species and 315 reactions including in CPD, Benzene formation process by the theory for polycyclic aromatic hydrocarbons (PAH) and soot formation process on the constant volume combustor, premixed flame characteristics.

  19. Synthesis of sp3-rich scaffolds for molecular libraries through complexity-generating cascade reactions

    DEFF Research Database (Denmark)

    Flagstad, Thomas; Min, Geanna; Bonnet, K.

    2016-01-01

    An efficient strategy for the synthesis of complex small molecules from simple building blocks is presented. Key steps of the strategy include tandem Petasis and Diels–Alder reactions, and divergent complexity-generating cyclization cascades from a key dialdehyde intermediate. The methodology...

  20. Functional LH1 antenna complexes influence electron transfer in bacterial photosynthetic reaction centers

    NARCIS (Netherlands)

    Visschers, R.W.; Vulto, S.I.E.; Jones, M.R.; van Grondelle, R.; Kraayenhof, R.

    1999-01-01

    The effect of the light harvesting 1 (LH1) antenna complex on the driving force for light-driven electron transfer in the Rhodobacter sphaeroides reaction center has been examined. Equilibrium redox titrations show that the presence of the LH1 antenna complex influences the free energy change for

  1. Functional LH1 antenna complexes influence electron transfer in bacterial photosynthetic reaction centers.

    NARCIS (Netherlands)

    Visschers, R.W.; Vulto, S.I.E.; Jones, M.R.; van Grondelle, R.; Kraayenhof, R.

    1999-01-01

    The effect of the light harvesting 1 (LH1) antenna complex on the driving force for light-driven electron transfer in the Rhodobacter sphaeroides reaction center has been examined. Equilibrium redox titrations show that the presence of the LH1 antenna complex influences the free energy change for

  2. Reaction of tantalum-alkyne complexes with isocyanates or acyl cyanides

    International Nuclear Information System (INIS)

    Kataoka, Yasutaka; Oguchi, Yoshiyuki; Yoshizumi, Kazuyuki; Miwatashi, Seiji; Takai, Kazuhiko; Utimoto, Kiitiro

    1992-01-01

    Treatment of alkynes with low-valent tantalum derived from TiCl 5 and zinc produces tantalum-alkyne complexes (not isolated), which react in situ with phenyl isocyanate (or butyl isocyanate) to give (E)-α, β-unsaturated amides stereoselectively. The tantalum-alkyne complexes also react with acyl cyanides in the presence of BF 3 ·OEt 2 to give α-cyanohydrins. In both reactions, filtration of the reaction mixture containing the tantalum-alkyne complexes before addition of isocyanates (or acyl cyanides) is indispensable to obtain good yields. (author)

  3. Mechanisms of reactions of organoaluminium compounds with alkenes and alkynes catalyzed by Zr complexes

    International Nuclear Information System (INIS)

    Parfenova, L V; Khalilov, Leonard M; Dzhemilev, Usein M

    2012-01-01

    The results of studies dealing with mechanisms of hydro-, carbo- and cycloalumination of alkenes and alkynes catalyzed by zirconium complexes are generalized and systematized for the first time. Data about the structures of intermediates responsible for the formation of the target compounds are presented and the available data on the effect of the structure of organoaluminium compounds and the electronic and steric factors determining the catalytic activity of metal complexes in these reactions are considered in detail. Much attention is paid to studies of the influence of reaction conditions on the chemo-, regio- and stereoselectivity of the Zr-containing complex catalysts. The bibliography includes 217 references.

  4. Anticancer system created by acrolein and hydroxyl radical generated in enzymatic oxidation of spermine and other biochemical reactions.

    Science.gov (United States)

    Alarcon, R A

    2012-10-01

    A hypothesis suggesting the existence of a ubiquitous physiological anticancer system created by two highly reactive oxidative stress inducers with anticancer properties, acrolein and hydroxyl radical, is reported in this communication. Both components can originate separately or together in several biochemical interactions, among them, the enzymatic oxidation of the polyamine spermine, which appear to be their main source. The foundations of this hypothesis encompass our initial search for growth-inhibitors or anticancer compounds in biological material leading to the isolation of spermine, a polyamine that became highly cytotoxic through the generation of acrolein, when enzymatically oxidized. Findings complemented with pertinent literature data by other workers and observed anticancer activities by sources capable of producing acrolein and hydroxyl radical. This hypothesis obvious implication: spermine enzymatic oxidations or other biochemical interactions that would co-generate acrolein and hydroxyl radical, the anticancer system components, should be tried as treatments for any given cancer. The biochemical generation of acrolein observed was totally unexpected, since this aldehyde was known; as a very toxic and highly reactive xenobiotic chemical produced in the pyrolysis of fats and other organic material, found as an atmospheric pollutant, in tobacco smoke and car emissions, and mainly used as a pesticide or aquatic herbicide. Numerous studies on acrolein, considered after our work a biological product, as well, followed. In them, acrolein widespread presence, its effects on diverse cellular proteins, such as, growth factors, and its anticancer activities, were additionally reported. Regarding hydroxyl radical, the second component of the proposed anticancer system, and another cytotoxic product in normal cell metabolism, it co-generates with acrolein in several biochemical interactions, occurrences suggesting that these products might jointly fulfill some

  5. Chiral PEPPSI Complexes: Synthesis, Characterization, and Application in Asymmetric Suzuki–Miyaura Coupling Reactions

    KAUST Repository

    Benhamou, Laure

    2014-01-13

    PEPPSI complexes incorporating chiral N-heterocyclic carbene (NHC) ligands based on 2,2-dimethyl-1-(o-substituted aryl)propan-1-amines were synthesized. Two complexes, with one saturated and one unsaturated NHC ligand, were structurally characterized. The chiral PEPPSI complexes were used in asymmetric Suzuki-Miyaura reactions, giving atropisomeric biaryl products in modest to good enantiomeric ratios. © 2013 American Chemical Society.

  6. An isoelectronic NO dioxygenase reaction using a nonheme iron(III)-peroxo complex and nitrosonium ion.

    Science.gov (United States)

    Yokoyama, Atsutoshi; Han, Jung Eun; Karlin, Kenneth D; Nam, Wonwoo

    2014-02-18

    Reaction of a nonheme iron(III)-peroxo complex, [Fe(III)(14-TMC)(O2)](+), with NO(+), a transformation which is essentially isoelectronic with that for nitric oxide dioxygenases [Fe(III)(O2˙(-)) + NO], affords an iron(IV)-oxo complex, [Fe(IV)(14-TMC)(O)](2+), and nitrogen dioxide (NO2), followed by conversion to an iron(III)-nitrato complex, [Fe(III)(14-TMC)(NO3)(F)](+).

  7. An isoelectronic NO dioxygenase reaction using a nonheme iron(III)-peroxo complex and nitrosonium ion†

    Science.gov (United States)

    Yokoyama, Atsutoshi; Han, Jung Eun; Karlin, Kenneth D.; Nam, Wonwoo

    2014-01-01

    Reaction of a nonheme iron(III)-peroxo complex, [FeIII(14-TMC)(O2)]+, with NO+, a transformation which is essentially isoelectronic with that for nitric oxide dioxygenases [Fe(III)(O2•−) + NO], affords an iron(IV)-oxo complex, [FeIV(14-TMC)(O)]2+, and nitrogen dioxide (NO2), followed by conversion to an iron(III)-nitrato complex, [FeIII(14-TMC)(NO3)(F)]+. PMID:24394960

  8. An isoelectronic NO dioxygenase reaction using a nonheme iron(III)-peroxo complex and nitrosonium ion†

    OpenAIRE

    Yokoyama, Atsutoshi; Han, Jung Eun; Karlin, Kenneth D.; Nam, Wonwoo

    2014-01-01

    Reaction of a nonheme iron(III)-peroxo complex, [FeIII(14-TMC)(O2)]+, with NO+, a transformation which is essentially isoelectronic with that for nitric oxide dioxygenases [Fe(III)(O2•−) + NO], affords an iron(IV)-oxo complex, [FeIV(14-TMC)(O)]2+, and nitrogen dioxide (NO2), followed by conversion to an iron(III)-nitrato complex, [FeIII(14-TMC)(NO3)(F)]+.

  9. Chiral PEPPSI Complexes: Synthesis, Characterization, and Application in Asymmetric Suzuki–Miyaura Coupling Reactions

    KAUST Repository

    Benhamou, Laure; Besnard, Cé line; Kü ndig, E. Peter

    2014-01-01

    PEPPSI complexes incorporating chiral N-heterocyclic carbene (NHC) ligands based on 2,2-dimethyl-1-(o-substituted aryl)propan-1-amines were synthesized. Two complexes, with one saturated and one unsaturated NHC ligand, were structurally characterized. The chiral PEPPSI complexes were used in asymmetric Suzuki-Miyaura reactions, giving atropisomeric biaryl products in modest to good enantiomeric ratios. © 2013 American Chemical Society.

  10. Aza-crown ether complex cation ionic liquids: preparation and applications in organic reactions.

    Science.gov (United States)

    Song, Yingying; Cheng, Chen; Jing, Huanwang

    2014-09-26

    Aza-crown ether complex cation ionic liquids (aCECILs) were devised, fabricated, and characterized by using NMR spectroscopy, MS, thermogravimetric differential thermal analysis (TG-DTA), elemental analysis and physical properties. These new and room-temperature ILs were utilized as catalysts in various organic reactions, such as the cycloaddition reaction of CO2 to epoxides, esterification of acetic acid and alcohols, the condensation reaction of aniline and propylene carbonate, and Friedel-Crafts alkylation of indole with aldehydes were investigated carefully. In these reactions, the ionic liquid exhibited cooperative catalytic activity between the anion and cation. In addition, the aza-[18-C-6HK][HSO4]2 was the best acidic catalyst in the reactions of esterification and Friedel-Crafts alkylation under mild reaction conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. To address surface reaction network complexity using scaling relations machine learning and DFT calculations

    International Nuclear Information System (INIS)

    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. Lastly, propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations.

  12. Redox reactions of Cu(II)-amine complexes in aqueous solutions

    International Nuclear Information System (INIS)

    Kumbhar, A.G.; Kishore, Kamal

    2003-01-01

    A number of amines can be employed for all volatile treatment (AVT) of steam generator (SG) systems of nuclear power reactors. These amines form complexes with Cu 2+ and Ni 2+ ions which come into water due to corrosion. The redox reactions of a number of Cu(II)-AVT amine complexes and the stability of the transient species formed have been studied by pulse radiolysis technique. Rate constants for the reaction of e aq - with a number of Cu(II)-amine complexes have been determined by following the decay of e aq - absorption. Stability of Cu(I)-amine complexes was studied by following the kinetics of the bleaching signal formed at the λ max of the Cu(II) amine complex. Except for Cu(I)-triethanolamine complex all other Cu(I)-amine complexes were found to be stable. One-electron oxidation of Cu(II) amine complexes was studied using azidyl radicals for the oxidation reaction as OH radicals react with the alcohol groups present in the amines used in this study. Cu(III)-amine complexes were found to be unstable and decayed by second-order kinetics

  13. Dinuclear Tetrapyrazolyl Palladium Complexes Exhibiting Facile Tandem Transfer Hydrogenation/Suzuki Coupling Reaction of Fluoroarylketone

    KAUST Repository

    Dehury, Niranjan

    2016-07-18

    Herein, we report an unprecedented example of dinuclear pyrazolyl-based Pd complexes exhibiting facile tandem catalysis for fluoroarylketone: Tetrapyrazolyl di-palladium complexes with varying Pd-Pd distances efficiently catalyze the tandem reaction involving transfer hydrogenation of fluoroarylketone to the corresponding alcohol and Suzuki-Miyaura cross coupling reaction of the resulting fluoroarylalcohol under moderate reaction conditions, to biaryl alcohol. The complex with the shortest Pd-Pd distance exhibits the highest tandem activity among its di-metallic analogues, and exceeds in terms of activity and selectivity the analogous mononuclear compound. The kinetics of the reaction indicates clearly that reductive transformation of haloarylketone into haloaryalcohol is the rate determining step in the tandem reaction. Interestingly while fluoroarylketone undergoes the multistep tandem catalysis, the chloro- and bromo-arylketones undergo only a single step C-C coupling reaction resulting in biarylketone as the final product. Unlike the pyrazole based Pd compounds, the precursor PdCl2 and the phosphine based relevant complexes (PPh3)2PdCl2 and (PPh3)4Pd are found to be unable to exhibit the tandem catalysis.

  14. Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations

    International Nuclear Information System (INIS)

    Zahn, Dirk

    2004-01-01

    The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom follows as a separate reaction step. Since the nucleophilic attack involves the breaking and formation of several bonds, the underlying reaction coordinate is rather complex. We investigate this reaction step from path sampling Car-Parrinello molecular dynamics simulations. This approach does not require the predefinition of reaction coordinates and is thus particularly suited for investigating reaction mechanisms. From our simulations the most relevant components of the reaction coordinate are elaborated. Though the C···O distance of the oxygen atom of the water molecule performing the nucleophilic attack and the corresponding amide carbon atom is a descriptor of the reaction progress, a complete picture of the reaction coordinate must include all three molecules taking part in the reaction. Moreover, the proton transfer is found to depend on favorable solvent configurations. Thus, also the arrangement of non-reacting, i.e. solvent water molecules needs to be considered in the reaction coordinate

  15. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

    Directory of Open Access Journals (Sweden)

    Le Novère Nicolas

    2010-03-01

    Full Text Available Abstract Background Most cellular signal transduction mechanisms depend on a few molecular partners whose roles depend on their position and movement in relation to the input signal. This movement can follow various rules and take place in different compartments. Additionally, the molecules can form transient complexes. Complexation and signal transduction depend on the specific states partners and complexes adopt. Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes. Results Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time. Conclusions Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at http://meredys.sourceforge.net/.

  16. Recoil implantation reactions in binary mixtures of catcher complexes and in mixed ligand catchers

    International Nuclear Information System (INIS)

    Sekine, Tsutomu; Sano, Masaaki; Yoshihara, Kenji

    1989-01-01

    Recoil implantation reactions were studied in binary mixtures of catcher complexes of tris(β-diketonato)metal(III) and in single-component catcher complexes of Cr(acac) n (dbm) 3-n where n=1 and 2. For the mixtures of M(acac) 3 and M(dbm) 3 , the products of 51 Cr(acac) 3 and 51 Cr(dbm) 3 were obtained as major components while 51 Cr(acac) 2 (dbm) and 51 Cr(acac)(dbm) 2 were seen as minor components. For the single component catcher complexes, predominant chemical species were parent retention type compounds. In addition to retentions there were product distributions which indicated a strong preference for acac pickup. The results were interpreted by a model which involves displacement reaction as a main process and ligand pickup reactions as side processes. (orig.)

  17. Aryldiazo complexes. Syntheses and reactions of new complexes of osmium and ruthenium

    International Nuclear Information System (INIS)

    Haymore, B.L.; Ibers, J.A.

    1975-01-01

    Aryldiazo complexes, [M(CO) 2 (NNPh)(PPh 3 ) 2 ][PF 6 ](M = Os, Ru; Ph = C 6 H 5 ), were prepared by allowing diazonium salts to react with M(CO) 3 (PPh 3 ) 2 . Infrared spectra of the Ru complex suggest the presence of two isomers both in solution and in the solid state. These complexes react with a variety of coordinating anions (X - ), to form MX(CO) 2 (NNPh)(PPh 3 ) 2 . The osmium derivatives have ν(NN) near 1455 cm -1 , which is the lowest value yet reported for a nonbridging aryldiazo ligand. The first aryldiazo--hydrido complexes, MH(CO) 2 (NNPh)(PPh 3 ) 2 and MH(CO)(NNPh)(PPh 3 ) 2 , were prepared by deprotonation of the respective phenyldiazene complexes, MH(CO) 2 (HNNPh)(PPh 3 ) 2 + and MH(CO)(HNNPh)(PPh 3 ) 3 + . The compound OsCl 3 (NNPh)(PPh 3 ) 2 was also prepared. A large number of the foregoing complexes were synthesized with selective 2 H and 15 N labels. Infrared and NMR spectra show MX(CO) 2 (NNPh)(PPh 3 ) 2 and the analogous hydrido complex to be pseudooctahedral with trans phosphine ligands, cis carbonyl ligands, and a doubly bent phenyldiazenido (NNPh - ) ligand. Similarly, MH(CO)(NNPh)(PPh 3 ) 2 possesses a trigonal-bipyramidal geometry with trans phosphine ligands and an equatorial, singly bent phenyldiazoniumato (NNPh + ) ligand. Isotopic substitution of the diazo ligand shows that ν(NN) is often vibrationally coupled with phenyl vibrational modes and that two or three bands sometimes shift upon 15 N substitution. Vibrational coupling was also observed in the higher energy region (1850 to 1900 cm -1 ) in the compound RuCl 3 (NNC 6 D 5 )(PPh 3 ) 2 . The wide range in the values of ν(NN), RuCl 3 (NNPh)(PPh 3 ) 2 (1882 cm -1 ) vs. RuCl(CO) 2 (NNPh)(PPh 3 ) 2 (1462 cm -1 ), indicates that the N--N stretching frequencies are sensitive to the electronic and steric environment of the diazo ligand. The aryldiazo complexes are compared with analogous, isoelectronic nitrosyl complexes of Os and Ru

  18. Complex nuclear-structure phenomena revealed from the nuclide production in fragmentation reactions

    International Nuclear Information System (INIS)

    Ricciardi, M.V.; Kelic, A.; Napolitani, P.; Schmidt, K.H.; Yordanov, O.; Ignatyuk, A.V.; Rejmund, F.

    2003-12-01

    Complex structural effects in the nuclide production from the projectile fragmentation of 1 A GeV 238 U nuclei in a titanium target are reported. The structure seems to be insensitive to the excitation energy induced in the reaction. This is in contrast to the prominent structural features found in nuclear fission and in transfer reactions, which gradually disappear with increasing excitation energy. Using the statistical model of nuclear reactions, relations to structural effects in nuclear binding and in the nuclear level density are demonstrated. (orig.)

  19. Interest of uranium complexes for the mechanism study of the McMurry reaction

    International Nuclear Information System (INIS)

    Maury, O.

    1997-01-01

    The reducing coupling reactions of ketones in diols and olefins are generally carried out with titanium or samarium compounds. In this work uranium complexes have been used. They have allowed to study the chemical reaction mechanism. This thesis is divided into three parts: 1) the reduction mechanism of uranium tetrachloride by cyclic voltametry has been studied at first. It has been shown that this reduction is followed by a transfer reaction of chlorides between the reduced specie of the higher electronic density and UCl . 2) In the second part is described: the synthesis, the crystal structure, the reactivity of the chemical agents, the stereochemistry of diols and alkenes formation and the pinacolisation reaction catalysis. 3) In the last part, the limits of the McMurry reaction are given by the study of the aromatic ketones pinacolisation reaction by-products. The obtained results show that the complexes of the metals which present a high reducing and oxo-philic (Ti, Sm, U..) character react in a similar way with the carbonyl compounds. If the uranium compounds are less used than those of the titanium in the field of the organic synthesis applications, they are precious auxiliaries and excellent models for reactions mechanisms study and for the synthesis methods optimization. (O.M.)

  20. Biochemical identification of residues that discriminate between 3,4-dihydroxyphenylalanine decarboxylase and 3,4-dihydroxyphenylacetaldehyde synthase-mediated reactions.

    Science.gov (United States)

    Liang, Jing; Han, Qian; Ding, Haizhen; Li, Jianyong

    2017-12-01

    In available insect genomes, there are several L-3,4-dihydroxyphenylalanine (L-dopa) decarboxylase (DDC)-like or aromatic amino acid decarboxylase (AAAD) sequences. This contrasts to those of mammals whose genomes contain only one DDC. Our previous experiments established that two DDC-like proteins from Drosophila actually mediate a complicated decarboxylation-oxidative deamination process of dopa in the presence of oxygen, leading to the formation of 3,4-dihydroxyphenylacetaldehyde (DHPA), CO 2 , NH 3, and H 2 O 2 . This contrasts to the typical DDC-catalyzed reaction, which produces CO 2 and dopamine. These DDC-like proteins were arbitrarily named DHPA synthases based on their critical role in insect soft cuticle formation. Establishment of reactions catalyzed by these AAAD-like proteins solved a puzzle that perplexed researchers for years, but to tell a true DHPA synthase from a DDC in the insect AAAD family remains problematic due to high sequence similarity. In this study, we performed extensive structural and biochemical comparisons between DHPA synthase and DDC. These comparisons identified several target residues potentially dictating DDC-catalyzed and DHPA synthase-catalyzed reactions, respectively. Comparison of DHPA synthase homology models with crystal structures of typical DDC proteins, particularly residues in the active sites, provided further insights for the roles these identified target residues play. Subsequent site-directed mutagenesis of the tentative target residues and activity evaluations of their corresponding mutants determined that active site His192 and Asn192 are essential signature residues for DDC- and DHPA synthase-catalyzed reactions, respectively. Oxygen is required in DHPA synthase-mediated process and this oxidizing agent is reduced to H 2 O 2 in the process. Biochemical assessment established that H 2 O 2 , formed in DHPA synthase-mediated process, can be reused as oxidizing agent and this active oxygen species is reduced to H 2

  1. Ruthenium(II) pincer complexes with oxazoline arms for efficient transfer hydrogenation reactions

    KAUST Repository

    Chen, Tao

    2012-08-01

    Well-defined P NN CN pincer ruthenium complexes bearing both strong phosphine and weak oxazoline donors were developed. These easily accessible complexes exhibit significantly better catalytic activity in transfer hydrogenation of ketones compared to their PN 3P analogs. These reactions proceed under mild and base-free conditions via protonation- deprotonation of the \\'NH\\' group in the aromatization-dearomatization process. © 2012 Elsevier Ltd. All rights reserved.

  2. Facile reactions of gold(i) complexes with tri(tert-butyl)azadiboriridine.

    Science.gov (United States)

    Shang, Rong; Saito, Souta; Jimenez-Halla, J Oscar C; Yamamoto, Yohsuke

    2018-04-17

    Direct structural evidence for group 11 metal-mediated B-B bond activation was obtained from reactions of tri(tert-butyl)azadiboriridine (1) with AuCl(L) complexes. The AuCl(SMe2) reaction afforded [η2-B,B-B(tBu)N(tBu)B(tBu)]AuCl (2) by ligand displacement. More donating phosphines as co-ligands led to B-B bond cleavage accompanied by either halide or L migration to form boron-gold complexes 3 (L = PPh3) and 4 (L = PMe3). A similar product 5, which is isostructural to 4, was obtained by the addition of dimethylaminopyridine (DMAP) to 2-4. Complexes 2-5 constitute rare examples of metal complexes bearing two Lewis acidic centres. The effect of the boryl ligand was demonstrated in the formation of a gold(i) complex 6 bearing a 5-membered heterocycle from 3 and tert-butylisonitrile. Plausible reaction mechanisms that led to these complexes and their bonding situation were explored computationally at the DFT level.

  3. Visible lights induced polymerization reactions: interactions between rose bengal and iron aren complex

    International Nuclear Information System (INIS)

    Burget, D.; Grotzinger, C.; Jacques, P.; Fouassier, J.P.

    1999-01-01

    The present paper is devoted to an investigation of the interactions between Rose Bengal (RB) and an Iron aren (Irg(+)) complex that are usable in visible light induced polymerization reactions. Steady state and flash photolysis experiments were performed in order to elucidate the nature of the intermediates formed after light excitation. A complete scheme of evolution of the excited states is discussed

  4. Mass transfer with complex reversible chemical reactions—I. Single reversible chemical reaction

    NARCIS (Netherlands)

    Versteeg, G.F.; Kuipers, J.A.M.; Beckum, F.P.H. van; Swaaij, W.P.M. van

    1989-01-01

    An improved numerical technique was used in order to develop an absorption model with which it is possible to calculate rapidly absorption rates for the phenomenon of mass transfer accompanied by a complex reversible chemical reaction. This model can be applied for the calculation of the mass

  5. Mass transfer with complex reversible chemical reactions—II. parallel reversible chemical reactions

    NARCIS (Netherlands)

    Versteeg, G.F.; Kuipers, J.A.M.; Beckum, F.P.H. van; Swaaij, W.P.M. van

    1990-01-01

    An absorption model has been developed which can be used to calculate rapidly absorption rates for the phenomenon mass transfer accompanied by multiple complex parallel reversible chemical reactions. This model can be applied for the calculation of the mass transfer rates, enhancement factors and

  6. Study of the competitive reaction ability of harmine and harmaline during complex formation with transition metals

    International Nuclear Information System (INIS)

    Chepulsky, S.A.; Kadirova, Z.Ch.; Parpiev, N.A.

    2006-01-01

    New coordination compounds of d-metals (Zn(II), Co(II), Mn(II), Mo(VI), Cr(VI)) β-carboline alkaloids were synthesized. The structure of obtained substances was established by IR, PMR spectroscopy. The quantum-chemical assessment of the harmine and harmaline reactivity in complexation reactions with d-metals was carried out. (author)

  7. Characterization of ESIPT reactions with instant spectra of fluorescence and complexation processes

    International Nuclear Information System (INIS)

    Tomin, Vladimir I.; Ushakou, Dzmitryi V.

    2016-01-01

    Proton transfer processes and especially excited-state intramolecular proton transfer (ESIPT) are of interest not only in physical studies but in a wide range of biological and chemical researches, since they play an important role in different fundamental reactions. Moreover, occurrence of ESIPT very often causes two-bands emission spectra corresponding to the normal and photoproduct (tautomer) forms of molecular structure. It allows carrying out unique measurement of microcharacteristics in chemical and biological researches by using substances with ESIPT as molecular probes, because its dual emission is very sensitive to parameters of microenvironment. Dual fluorescence signal is very convenient for two wavelength ratiometric measurements as they are more sensitive to variations of sample characteristics. Recently new approach for revealing type of excited state reaction which is based on analysis of dynamic changes of relative intensities in instant spectra of fluorescence ESIPT solutes was suggested and tested for neat solutions. Now we generalize this method on solutions in which ESIPT solute may participate also in creating fluorescent complexes. We demonstrate that relative intensities of instant spectra of fluorescence registered with high time resolution allow to get valuable information referring to type of excited state reaction in which dye may undergo complexation reactions with ions in solvent. In addition we show how it is possible in such case to determine characteristics of complexation as, for example, stability constant and efficiency of complexation.

  8. Generalization of the Activated Complex Theory of Reaction Rates. II. Classical Mechanical Treatment

    Science.gov (United States)

    Marcus, R. A.

    1964-01-01

    In its usual classical form activated complex theory assumes a particular expression for the kinetic energy of the reacting system -- one associated with a rectilinear motion along the reaction coordinate. The derivation of the rate expression given in the present paper is based on the general kinetic energy expression.

  9. Cleaning of small components of complex geometry by means of the sodium-alcohol reaction

    International Nuclear Information System (INIS)

    De Luca, B.; Grasso, C.; Spadoni, M.

    1978-01-01

    The results of some experiments on the vacuum reaction between butylcellosolve and sodium, contained in small diameter capillaries, are reported. The effects on the cleaning rate of the temperature, amount of solvent, diameter and position of the capillaries are analyzed. The facility, used for the cleaning of small components of complex geometry, is described. (author)

  10. Linear constraint relations in biochemical reaction systems: I. Classification of the calculability and the balanceability of conversion rates.

    Science.gov (United States)

    van der Heijden, R T; Heijnen, J J; Hellinga, C; Romein, B; Luyben, K C

    1994-01-05

    Measurements provide the basis for process monitoring and control as well as for model development and validation. Systematic approaches to increase the accuracy and credibility of the empirical data set are therefore of great value. In (bio)chemical conversions, linear conservation relations such as the balance equations for charge, enthalpy, and/or chemical elements, can be employed to relate conversion rates. In a pactical situation, some of these rates will be measured (in effect, be calculated directly from primary measurements of, e.g., concentrations and flow rates), as others can or cannot be calculated from the measured ones. When certain measured rates can also be calculated from other measured rates, the set of equations, the accuracy and credibility of the measured rates can indeed be improved by, respectively, balancing and gross error diagnosis. The balanced conversion rates are more accurate, and form a consistent set of data, which is more suitable for further application (e.g., to calculate nonmeasured rates) than the raw measurements. Such an approach has drawn attention in previous studies. The current study deals mainly with the problem of mathematically classifying the conversion rates into balanceable and calculable rates, given the subset of measured rates. The significance of this problem is illustrated with some examples. It is shown that a simple matrix equation can be derived that contains the vector of measured conversion rates and the redundancy matrix R. Matrix R plays a predominant role in the classification problem. In supplementary articles, significance of the redundancy matrix R for an improved gross error diagnosis approach will be shown. In addition, efficient equations have been derived to calculate the balanceable and/or calculable rates. The method is completely based on matrix algebra (principally different from the graph-theoretical approach), and it is easily implemented into a computer program. (c) 1994 John Wiley & Sons

  11. Biochemical parameters as monitoring markers of the inflammatory reaction by patients with chronic obstructive pulmonary disease (COPD)

    Science.gov (United States)

    Lenártová, Petra; Kopčeková, Jana; Gažarová, Martina; Mrázová, Jana; Wyka, Joanna

    Chronic obstructive pulmonary disease (COPD) is an airway inflammatory disease caused by inhalation of toxic particles, mainly cigarette smoking, and now is accepted as a disease associated with systemic characteristics. The aim of this work was to investigate and compare selected biochemical parameters in patients with and without COPD. Observation group consisted of clinically stable patients with COPD (n = 60). The control group was healthy persons from the general population, without COPD, who were divided into two subgroups – smokers (n = 30) and non-smokers (n = 30). Laboratory parameters were investigated by automated clinical chemistry analyzer LISA 200th. Albumin in our measurements showed an average value of 39.55 g.l-1 in the patient population; 38.89 g.l-1 in smokers and in non-smokers group 44.65 g.l-1. The average value of pre-albumin in the group of patients was 0.28 ± 0.28 g.l-1 and 0.30 ± 0.04 g.l-1 in smokers group. The average value of the orosomucoid in patients was about 1.11 ± 0.90 mg.ml-1. In the group of smokers, the mean value of orosomucoid was 0.60 ± 0.13 mg.ml-1. The level of C-reactive protein (CRP) in the patient group reached an average value of 15.31 ± 22.04 mg.l-1, in the group of smokers was 5.18 ± 4.58 mg. l-1. Prognostic inflammatory and nutritional index (PINI) in the group of patients showed a mean value of 4.65 ± 10.77 and 0.026 ± 0.025 in smokers. The results of this work show, that the values of index PINI in COPD patients are significantly higher than in smokers (P COPD.

  12. The mechanism distinguishability problem in biochemical kinetics: the single-enzyme, single-substrate reaction as a case study.

    Science.gov (United States)

    Schnell, Santiago; Chappell, Michael J; Evans, Neil D; Roussel, Marc R

    2006-01-01

    A theoretical analysis of the distinguishability problem of two rival models of the single enzyme-single substrate reaction, the Michaelis-Menten and Henri mechanisms, is presented. We also outline a general approach for analysing the structural indistinguishability between two mechanisms. The approach involves constructing, if possible, a smooth mapping between the two candidate models. Evans et al. [N.D. Evans, M.J. Chappell, M.J. Chapman, K.R. Godfrey, Structural indistinguishability between uncontrolled (autonomous) nonlinear analytic systems, Automatica 40 (2004) 1947-1953] have shown that if, in addition, either of the mechanisms satisfies a particular criterion then such a transformation always exists when the models are indistinguishable from their experimentally observable outputs. The approach is applied to the single enzyme-single substrate reaction mechanism. In principle, mechanisms can be distinguished using this analysis, but we show that our ability to distinguish mechanistic models depends both on the precise measurements made, and on our knowledge of the system prior to performing the kinetics experiments.

  13. Complement activation in leprosy: a retrospective study shows elevated circulating terminal complement complex in reactional leprosy.

    Science.gov (United States)

    Bahia El Idrissi, N; Hakobyan, S; Ramaglia, V; Geluk, A; Morgan, B Paul; Das, P Kumar; Baas, F

    2016-06-01

    Mycobacterium leprae infection gives rise to the immunologically and histopathologically classified spectrum of leprosy. At present, several tools for the stratification of patients are based on acquired immunity markers. However, the role of innate immunity, particularly the complement system, is largely unexplored. The present retrospective study was undertaken to explore whether the systemic levels of complement activation components and regulators can stratify leprosy patients, particularly in reference to the reactional state of the disease. Serum samples from two cohorts were analysed. The cohort from Bangladesh included multi-bacillary (MB) patients with (n = 12) or without (n = 46) reaction (R) at intake and endemic controls (n = 20). The cohort from Ethiopia included pauci-bacillary (PB) (n = 7) and MB (n = 23) patients without reaction and MB (n = 15) patients with reaction. The results showed that the activation products terminal complement complex (TCC) (P ≤ 0·01), C4d (P ≤ 0·05) and iC3b (P ≤ 0·05) were specifically elevated in Bangladeshi patients with reaction at intake compared to endemic controls. In addition, levels of the regulator clusterin (P ≤ 0·001 without R; P < 0·05 with R) were also elevated in MB patients, irrespective of a reaction. Similar analysis of the Ethiopian cohort confirmed that, irrespective of a reaction, serum TCC levels were increased significantly in patients with reactions compared to patients without reactions (P ≤ 0·05). Our findings suggests that serum TCC levels may prove to be a valuable tool in diagnosing patients at risk of developing reactions. © 2016 British Society for Immunology.

  14. Genetic and Biochemical Identification of a Novel Single-Stranded DNA-Binding Complex in Haloferax volcanii.

    Science.gov (United States)

    Stroud, Amy; Liddell, Susan; Allers, Thorsten

    2012-01-01

    Single-stranded DNA (ssDNA)-binding proteins play an essential role in DNA replication and repair. They use oligonucleotide/oligosaccharide-binding (OB)-folds, a five-stranded β-sheet coiled into a closed barrel, to bind to ssDNA thereby protecting and stabilizing the DNA. In eukaryotes the ssDNA-binding protein (SSB) is known as replication protein A (RPA) and consists of three distinct subunits that function as a heterotrimer. The bacterial homolog is termed SSB and functions as a homotetramer. In the archaeon Haloferax volcanii there are three genes encoding homologs of RPA. Two of the rpa genes (rpa1 and rpa3) exist in operons with a novel gene specific to Euryarchaeota; this gene encodes a protein that we have termed RPA-associated protein (rpap). The rpap genes encode proteins belonging to COG3390 group and feature OB-folds, suggesting that they might cooperate with RPA in binding to ssDNA. Our genetic analysis showed that rpa1 and rpa3 deletion mutants have differing phenotypes; only Δrpa3 strains are hypersensitive to DNA damaging agents. Deletion of the rpa3-associated gene rpap3 led to similar levels of DNA damage sensitivity, as did deletion of the rpa3 operon, suggesting that RPA3 and RPAP3 function in the same pathway. Protein pull-downs involving recombinant hexahistidine-tagged RPAs showed that RPA3 co-purifies with RPAP3, and RPA1 co-purifies with RPAP1. This indicates that the RPAs interact only with their respective associated proteins; this was corroborated by the inability to construct rpa1 rpap3 and rpa3 rpap1 double mutants. This is the first report investigating the individual function of the archaeal COG3390 RPA-associated proteins (RPAPs). We have shown genetically and biochemically that the RPAPs interact with their respective RPAs, and have uncovered a novel single-stranded DNA-binding complex that is unique to Euryarchaeota.

  15. Event-triggered synchronization for reaction-diffusion complex networks via random sampling

    Science.gov (United States)

    Dong, Tao; Wang, Aijuan; Zhu, Huiyun; Liao, Xiaofeng

    2018-04-01

    In this paper, the synchronization problem of the reaction-diffusion complex networks (RDCNs) with Dirichlet boundary conditions is considered, where the data is sampled randomly. An event-triggered controller based on the sampled data is proposed, which can reduce the number of controller and the communication load. Under this strategy, the synchronization problem of the diffusion complex network is equivalently converted to the stability of a of reaction-diffusion complex dynamical systems with time delay. By using the matrix inequality technique and Lyapunov method, the synchronization conditions of the RDCNs are derived, which are dependent on the diffusion term. Moreover, it is found the proposed control strategy can get rid of the Zeno behavior naturally. Finally, a numerical example is given to verify the obtained results.

  16. Study of substitution reactions of ligands in VO2+ complexes in toluene solutions by ESR method

    International Nuclear Information System (INIS)

    Lundkvist, R.; Panfilov, A.T.; Kalinichenko, N.B.; Marov, I.N.; AN SSSR, Moscow. Inst. Geokhimii i Analiticheskoj Khimii)

    1976-01-01

    Kinetics and equilibrium of stepwise substitution of ligands have been investigated at different temperatures for the complexes of oxovanadium (4) with salicylaldoxime, 8-oxyquinoline, acetylacetone, benzoylacetone, and tenoyltrifluoroacetone. The relative complexability of these ligands in toluene has been studied. The parameters of spin-Hamiltonian of EPR spectra of the VO 2+ complexes have been determined. The equilibrium constants, the rate constants, and activation energy have been found for the substitution reactions of ligands in the complexes VOA 2 : VOA 2 +HB=VOAB+HA; VOAB+HB=VOB 2 +HA, where HA and HB are the ligands with different donor atoms. The mixed complexes have been detected of the general formula VOAB, where HA is salicylaldoxime or 8-oxyquinoline and HB is β-diketone

  17. EXAFS studies on the reaction of gold (III) chloride complex ions with sodium hydroxide and glucose.

    Science.gov (United States)

    Pacławski, K; Zajac, D A; Borowiec, M; Kapusta, Cz; Fitzner, K

    2010-11-11

    EXAFS and QEXAFS experiments were carried out at Hasylab laboratory in DESY center (X1 beamline, Hamburg, Germany) to monitor the course of the hydrolysis reactions of [AuCl(4)](-) complex ions as well as their reduction using glucose. As a result, changes in the spectra of [AuCl(4)](-) ions and disappearance of absorption Au-L(3) edge were registered. From the results of the experiments we have carried out, the changes in bond lengths between Au(3+) central ion and Cl(-) ligands as well as the reduction of Au(3+) to metallic form (colloidal gold was formed in the system) are evident. Good quality spectra obtained before and after the reactions gave a chance to determine the bond length characteristic of Au-Cl, Au-OH and Au-Au pairs. Additionally, the obtained results were compared with the simulated spectra of different gold (III) complex ions, possibly present in the solution. Finally, the mechanism of these reactions was suggested. Unfortunately, it was not possible to detect the changes in the structure of gold (III) complex ions within the time of reaction, because of too high rates of both processes (hydrolysis and reduction) as compared with the detection time.

  18. Electrochemical study of quinone redox cycling: A novel application of DNA-based biosensors for monitoring biochemical reactions.

    Science.gov (United States)

    Ensafi, Ali A; Jamei, Hamid Reza; Heydari-Bafrooei, Esmaeil; Rezaei, B

    2016-10-01

    This paper presents the results of an experimental investigation of voltammetric and impedimetric DNA-based biosensors for monitoring biological and chemical redox cycling reactions involving free radical intermediates. The concept is based on associating the amounts of radicals generated with the electrochemical signals produced, using differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). For this purpose, a pencil graphite electrode (PGE) modified with multiwall carbon nanotubes and poly-diallydimethlammonium chloride decorated with double stranded fish sperm DNA was prepared to detect DNA damage induced by the radicals generated from a redox cycling quinone (i.e., menadione (MD; 2-methyl-1,4-naphthoquinone)). Menadione was employed as a model compound to study the redox cycling of quinones. A direct relationship was found between free radical production and DNA damage. The relationship between MD-induced DNA damage and free radical generation was investigated in an attempt to identify the possible mechanism(s) involved in the action of MD. Results showed that DPV and EIS were appropriate, simple and inexpensive techniques for the quantitative and qualitative comparisons of different reducing reagents. These techniques may be recommended for monitoring DNA damages and investigating the mechanisms involved in the production of redox cycling compounds. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Follow-up of some biochemical parameters to detect adaptive reactions induced in vivo by tritium contamination

    International Nuclear Information System (INIS)

    Petcu, I.; Moisoi, N.; Savu, D.; Constantinescu, B.

    1999-01-01

    The experiment intended to examine whether adaptive response could be elicited in vivo by low level internal contamination of rats with tritiated water and subsequently observed after a challenging irradiation with fast neutrons. Rats have been pre-contaminated for 3 weeks to total doses of 7 cGy and 35 cGy. Subsequently they were irradiated 1 Gy by fast neutrons obtained from deuterons (13.5 MeV) on a Be target. After 24 h the rats were sacrificed and the lipid peroxidation level was determined in liver, kidney, small intestine, spleen, bone marrow and plasma. The reduced glutathion and the glucose-6-phosphate dehydrogenase activity was determined in erythrocytes. Concurrently an in vivo assay was performed to observe the modifications of the thymidine intake in the isolated bone marrow cells. For the rats pre-exposed to tritiated water the lipid peroxides level was significantly decreased only for liver and kidney and only after the highest preirradiation dose (35 cGy). The thymidine incorporation assay revealed a putative adaptive reaction also for the 35 cGy preirradiated rats. The glutathion content was found to be increased (back to the normal level) for the tritium pre-contaminated and neutron irradiated animals as compared to those exposed only to fast neutrons. (authors)

  20. Actinide complexation kinetics: rate and mechanism of dioxoneptunium (V) reaction with chlorophosphonazo III

    International Nuclear Information System (INIS)

    Fugate, G.; Feil-Jenkins, J.F.; Sullivan, J.C.; Nash, K.L.

    1996-12-01

    Rates of complex formation and dissociation in NpO 2 + - Chlorophosphonazo III (2,7-bis(4-chloro-2-phosphonobenzeneazo)-1,8- dihydroxynapthalene-3,6-disulfonic acid)(CLIII) were investigated by stopped-flow spectrophotometry. Also, limited studies were made of the rates of reaction of La 3+ , Eu 3+ , Dy 3+ , and Fe 3+ with CLIII. Rate determining step in each system is an intramolecular process, the NpO 2 + -CLIII reaction proceeding by a first order approach to equilibrium in the acid range from 0.1 to 1.0 M. Complex formation occurs independent of acidity, while both acid dependent and independent dissociation pathways are observed. Activation parameters for the complex formation reaction are ΔH=46.2±0.3 kJ/m and ΔS=7± J/mK (I=1.0 M); these for the acid dependent and independent dissociation pathways are ΔH=38.8±0.6 kJ/m, ΔS=-96±18 J/mK, ΔH=70.0± kJ/m, and ΔS=17±1 J/mK, respectively. An isokinetic relationship is observed between the activation parameters for CLIII complex formation with NpO 2 + , UO 2 2+ , Th 4+ , and Zr 4+ . Rates of CLIII complex formation reactions for Fe 3+ , Zr 4+ , NpO 2 + , UO 2 2+ , Th 4+ , La 3+ , Eu 3+ , and Dy 3+ correlate with cation radius rather than charge/radius ratio

  1. A study of fundamental reaction pathways for transition metal alkyl complexes. I. The reaction of a nickel methyl complex with alkynes. Ii. The mechanism of aldehyde formation in the reaction of a molybdenum hydride with molybdenum alkyls

    Energy Technology Data Exchange (ETDEWEB)

    Huggins, John Mitchell [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

    1980-06-12

    I. This study reports the rapid reaction under mild conditions of internal or terminal alkynes with methyl (acetyl-acetonato) (triphenylphosphine) nickel (1) in either aromatic or ether solvents. In all cases vinylnickel products 2 are formed by insertion of the alkyne into the nickel=methyl bond. These complexes may be converted into a variety of organic products (e.g. alkenes, esters, vinyl halides) by treatment with appropriate reagents. Unsymmetrical alkynes give selectively the one regioisomer with the sterically largest substituent next to the nickel atom. In order to investigate the stereochemistry of the initial insertion, a x-ray diffraction study of the reaction of 1 with diphenylacetylene was carried out. This showed that the vinylnickel complex formed by overall trans insertion was the product of the reaction. Furthermore, subsequent slow isomerization of this complex, to a mixture of it and the corresponding cis isomer, demonstrated that this trans addition product is the kinetic product of the reaction. In studies with other alkynes, the product of trans addition was not always exclusively (or even predominantly) formed, but the ratio of the stereoisomers formed kinetically was substantially different from the thermodynamic ratio. Isotope labeling, added phosphine, and other experiments have allowed us to conclude that the mechanism of this reaction does involve initial cis addition. However, a coordinatively unsaturated vinylnickel complex is initially formed which can undergo rapid, phosphine-catalyzed cis-trans isomerization in competition with its conversion to the isolable phosphine-substituted kinetic reaction products. II. The reaction of CpMo(CO)3H (1a) with CpMo(CO)3R (2, R= CH3, C2H5) at 50°C in THF gives the aldehyde RCHO and the dimers [CpMo(CO)3]2 (3a) and [CpMo(CO)2]2 (4a). Labeling one of the reactants with a methylcyclopentadienyl ligand

  2. Studies on the ruthenium complexes. IX. Kinetic studies on the deaquation-anation reaction of aquapentaammineruthenium(III) complexes

    Energy Technology Data Exchange (ETDEWEB)

    Ohyoshi, A; Hiraki, S I; Odate, T; Kohata, S; Oda, J [Kumamoto Univ. (Japan). Faculty of Engineering

    1975-01-01

    The deaquation-anation reaction of (Ru(OH/sub 2/)(NH/sub 3/)/sub 5/)X/sub 3/-type complexes in the solid state, as shown by the (Ru(OH/sub 2/)(NH/sub 3/)/sub 5/)X/sub 3/(s)..-->..(RuX(NH/sub 3/)/sub 5/)X/sub 2/(s)+H/sub 2/O(g) equation, where X is Cl, Br, I, and NO/sub 3/ respectively, was kinetically studied by means of thermogravimetry (TG) along with differential thermal analysis (DTA). The activation energy and entropy in the reaction process (Esub(a) kcal/mol, ..delta..S c.u.) are, respectively, found by isothermal kinetic study to be (22.7, - 7.1) for the chloride, (23.4, - 5.2) for the bromide, (26.7, 5.8) for the iodide, and (19.3 - 15.9) for the nitrate. The reaction seems to proceed through the following two steps, except in the case of the iodide: (Ru(OH/sub 2/)(NH/sub 3/)/sub 5/)X/sub 3/..-->..(RuX(OH/sub 2/)(NH/sub 3/)/sub 5/)X/sub 2/..-->..(RuX(NH/sub 3/)/sub 5/)X/sub 2/+H/sub 2/O. The first step is regarded as the rate-determining one.

  3. Metadislocation reactions and metadislocation networks in the complex metallic alloy ξ'-Al-Pd-Mn

    International Nuclear Information System (INIS)

    Heggen, Marc; Feuerbacher, Michael

    2005-01-01

    Metadislocations are novel structural defects firstly observed in the complex metallic alloy ξ'-Al-Pd-Mn. We present a transmission electron microscopy study on metadislocation reactions and networks. It is shown that metadislocations can dissociate into partials, which leads to a decrease of the elastic line energy. Connected groups of metadislocations can assume large and complex network structures with large total Burgers vectors. However, the local elastic strain at the individual metadislocation cores as well as the fault-plane energies remain small. By this mechanism, effective large Burgers vectors, contributing massively to plastic strain, can be distributed over a large portion of the material

  4. Application of adjustable pulse lasers to studying rapid reaction kinetics of excited lanthanide complexing

    Energy Technology Data Exchange (ETDEWEB)

    Gruzdev, V.P. (Gosudarstvennyj Opticheskij Inst., Leningrad (USSR))

    1983-12-01

    Using some europium (3) ion complexes new possibilities to be opened by application of adjustable pulse lasers for studying rapid reactions of electron-excited metal ion complexing are demonstrated. The 6Zh rhodamine pulse laser is used as a source of nonequilibrium photoexcitation of an array of Eu/sup 3 +/ complexes in the luminescent kinetic spectroscopy method. The following results are obtained: for the first time the rate of reaction of acetate ion substitution for water molecules of an excited (/sup 5/D/sub 0/) ion of Eu/sup 3 +/ was measured to be (0.7+-0.2)x10/sup 7/ s/sup -1/; using direct experiments the lower limit for the rate of transition of one isomeric form of the excited Eu x EDTA complex into another one in an aqueous solution is determined to be 5x10/sup 5/ s/sup -1/ at 295 K; the kinetics of the excitation energy migration beteen aqueous solvates of Eu/sup 3 +/ and EuxEDTA complexes is investigated.

  5. Insights into the Halogen Oxidative Addition Reaction to Dinuclear Gold(I) Di(NHC) Complexes

    KAUST Repository

    Baron, Marco

    2016-06-14

    Gold(I) dicarbene complexes [Au2(MeIm-Y-ImMe)2](PF6)2(Y=CH2(1), (CH2)2(2), (CH2)4(4), MeIm=1-methylimidazol-2-ylidene) react with iodine to give the mixed-valence complex [Au(MeIm-CH2-ImMe)2AuI2](PF6)2(1 aI) and the gold(III) complexes [Au2I4(MeIm-Y-ImMe)2](PF6)2(2 cIand 4 cI). Reaction of complexes 1 and 2 with an excess of ICl allows the isolation of the tetrachloro gold(III) complexes [Au2Cl4(MeIm-CH2-ImMe)2](PF6)2(1 cCl) and [Au2Cl4(MeIm-(CH2)2-ImMe)2](Cl)2(2 cCl-Cl) (as main product); remarkably in the case of complex 2, the X-ray molecular structure of the crystals also shows the presence of I-Au-Cl mixed-sphere coordination. The same type of coordination has been observed in the main product of the reaction of complexes 3 or 4 with ICl. The study of the reactivity towards the oxidative addition of halogens to a large series of dinuclear bis(dicarbene) gold(I) complexes has been extended and reviewed. The complexes react with Cl2, Br2and I2to give the successive formation of the mixed-valence gold(I)/gold(III) n aXand gold(III) n cX(excluding compound 1 cI) complexes. However, complex 3 affords with Cl2and Br2the gold(II) complex 3 bX[Au2X2(MeIm-(CH2)3-ImMe)2](PF6)2(X=Cl, Br), which is the predominant species over compound 3 cXeven in the presence of free halogen. The observed different relative stabilities of the oxidised complexes of compounds 1 and 3 have also been confirmed by DFT calculations. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Metal halide-phosphorus halide-alkyl halide complexes: reaction with niobium and tantalum pentachlorides

    International Nuclear Information System (INIS)

    Puri, D.M.; Saini, M.S.

    1978-01-01

    The reactions of niobium and tantalum pentachlorides with trichlorophosphine and phenyldichlorophosphine have been studied in presence of alkylating agents such as sec-butyl chloride, iso-butyl chloride, tert-butyl chloride, tert-anylchloride, cyclohexyl chloride and triphenylmethyl chloride. Solid products have been isolated and characterised by vibrational spectroscopy as ionic complexes of alkyl- and/or aryl-phosphonium cations with hexachloroniobate and hexachlorotantalate anions. (author)

  7. Sources and characteristics of complex fragments in La-induced reactions

    International Nuclear Information System (INIS)

    Roussel-Chomaz, P.; Blumenfeld, Y.; Charity, R.; Colonna, M.; Colonna, N.; Libby, B.; Hanold, K.; Moretto, L.; Peaslee, G.; Wozniak, G.

    1991-01-01

    Complex fragment emission has been studied for a variety of reactions at intermediate energies. Multifragment events are shown to be associated with specific sources characterized by their mass and excitation energy through the incomplete fusion model. Excitation functions for the different multifragment decay channels are found to be almost independent of the system and the incident energy. Preliminary comparisons of the data with dynamical calculations followed by statistical decay calculations are discussed. 11 refs., 7 figs

  8. Mass transfer with complex reversible chemical reactions—II. parallel reversible chemical reactions

    OpenAIRE

    Versteeg, G.F.; Kuipers, J.A.M.; Beckum, F.P.H. van; Swaaij, W.P.M. van

    1990-01-01

    An absorption model has been developed which can be used to calculate rapidly absorption rates for the phenomenon mass transfer accompanied by multiple complex parallel reversible chemical reactions. This model can be applied for the calculation of the mass transfer rates, enhancement factors and concentration profiles for a wide range of processes and conditions, for both film and penetration model. With the aid of this mass transfer model it is demonstrated that the absorption rates in syst...

  9. Chiral Nickel(II) Complex Catalyzed Enantioselective Doyle-Kirmse Reaction of α-Diazo Pyrazoleamides.

    Science.gov (United States)

    Lin, Xiaobin; Tang, Yu; Yang, Wei; Tan, Fei; Lin, Lili; Liu, Xiaohua; Feng, Xiaoming

    2018-03-07

    Although high enantioselectivity of [2,3]-sigmatropic rearrangement of sulfonium ylides (Doyle-Kirmse reaction) has proven surprisingly elusive using classic chiral Rh(II) and Cu(I) catalysts, in principle it is due to the difficulty in fine discrimination of the heterotopic lone pairs of sulfur and chirality inversion at sulfur of sulfonium ylides. Here, we show that the synergistic merger of new α-diazo pyrazoleamides and a chiral N, N'-dioxide-nickel(II) complex catalyst enables a highly enantioselective Doyle-Kirmse reaction. The pyrazoleamide substituent serves as both an activating and a directing group for the ready formation of a metal-carbene- and Lewis-acid-bonded ylide intermediate in the assistance of a dual-tasking nickel(II) complex. An alternative chiral Lewis-acid-bonded ylide pathway greatly improves the product enantiopurity even for the reaction of a symmetric diallylsulfane. The majority of transformations over a series of aryl- or vinyl-substituted α-diazo pyrazoleamindes and sulfides proceed rapidly (within 5-20 min in most cases) with excellent results (up to 99% yield and 96% ee), providing a breakthrough in enantioselective Doyle-Kirmse reaction.

  10. Reactions, accuracy and response complexity of numerical typing on touch screens.

    Science.gov (United States)

    Lin, Cheng-Jhe; Wu, Changxu

    2013-01-01

    Touch screens are popular nowadays as seen on public kiosks, industrial control panels and personal mobile devices. Numerical typing is one frequent task performed on touch screens, but this task on touch screen is subject to human errors and slow responses. This study aims to find innate differences of touch screens from standard physical keypads in the context of numerical typing by eliminating confounding issues. Effects of precise visual feedback and urgency of numerical typing were also investigated. The results showed that touch screens were as accurate as physical keyboards, but reactions were indeed executed slowly on touch screens as signified by both pre-motor reaction time and reaction time. Provision of precise visual feedback caused more errors, and the interaction between devices and urgency was not found on reaction time. To improve usability of touch screens, designers should focus more on reducing response complexity and be cautious about the use of visual feedback. The study revealed that slower responses on touch screens involved more complex human cognition to formulate motor responses. Attention should be given to designing precise visual feedback appropriately so that distractions or visual resource competitions can be avoided to improve human performance on touch screens.

  11. Equilibria and partitioning of complexes in the S-adenosylmethionine synthetase reaction

    International Nuclear Information System (INIS)

    Markham, G.D.

    1987-01-01

    S-adenosylmethionine synthetase (ATP: L-methionine S-adenosyltransferase) catalyzes a reaction in which the [enzyme-ATP-methionine] complex reacts to form an intermediate [enzyme-AdoMet-PPPi] complex: hydrolysis of PPPi yields an [enzyme-AdoMet-PPi-Pi] complex from which AdoMet is the last product to dissociate. Analysis of reaction mixtures which were quenched with acid during turnover of E. coli AdoMet synthetase with saturating substrates containing [α - 32 P]ATP showed that PPPi is present in an amount corresponding to 45% of the total enzyme active sites, reflecting the portion of enzyme present in an [enzyme-AdoMet-PPPi] complex. Similar experiments in which excess pyrophosphatase was included (to hydrolyze PPi as it was released from AdoMet synthetase), showed that enzyme-bound PPi is present in an amount corresponding to 22% of the total AdoMet synthetase. The enzyme not present in complexes with PPPi or PPi is probably distributed between the [enzyme-ATP-methionine] and the [enzyme-AdoMet] complexes. AdoMet synthetase forms enzyme-bound 32 PPPi from added 32 PPi and Pi; the equilibrium constant [enzyme-AdoMet-PPi-Pi]/[enzyme-AdoMet-PPPi] is 2.0, greatly displaced from the equilibrium for hydrolysis of free PPPi. Since the ratio of enzyme-bound PPi to PPPi is 0.5 during the steady state, the PPPi hydrolysis step is not at equilibrium during turnover. Formation of [ 32 P]ATP from the [enzyme-AdoMet- 32 PPPi] complex was not detected

  12. The single-process biochemical reaction of Rubisco: a unified theory and model with the effects of irradiance, CO₂ and rate-limiting step on the kinetics of C₃ and C₄ photosynthesis from gas exchange.

    Science.gov (United States)

    Farazdaghi, Hadi

    2011-02-01

    Photosynthesis is the origin of oxygenic life on the planet, and its models are the core of all models of plant biology, agriculture, environmental quality and global climate change. A theory is presented here, based on single process biochemical reactions of Rubisco, recognizing that: In the light, Rubisco activase helps separate Rubisco from the stored ribulose-1,5-bisphosphate (RuBP), activates Rubisco with carbamylation and addition of Mg²(+), and then produces two products, in two steps: (Step 1) Reaction of Rubisco with RuBP produces a Rubisco-enediol complex, which is the carboxylase-oxygenase enzyme (Enco) and (Step 2) Enco captures CO₂ and/or O₂ and produces intermediate products leading to production and release of 3-phosphoglycerate (PGA) and Rubisco. PGA interactively controls (1) the carboxylation-oxygenation, (2) electron transport, and (3) triosephosphate pathway of the Calvin-Benson cycle that leads to the release of glucose and regeneration of RuBP. Initially, the total enzyme participates in the two steps of the reaction transitionally and its rate follows Michaelis-Menten kinetics. But, for a continuous steady state, Rubisco must be divided into two concurrently active segments for the two steps. This causes a deviation of the steady state from the transitional rate. Kinetic models are developed that integrate the transitional and the steady state reactions. They are tested and successfully validated with verifiable experimental data. The single-process theory is compared to the widely used two-process theory of Farquhar et al. (1980. Planta 149, 78-90), which assumes that the carboxylation rate is either Rubisco-limited at low CO₂ levels such as CO₂ compensation point, or RuBP regeneration-limited at high CO₂. Since the photosynthesis rate cannot increase beyond the two-process theory's Rubisco limit at the CO₂ compensation point, net photosynthesis cannot increase above zero in daylight, and since there is always respiration at

  13. Systems biology and the origins of life? part II. Are biochemical networks possible ancestors of living systems? networks of catalysed chemical reactions: non-equilibrium, self-organization and evolution.

    Science.gov (United States)

    Ricard, Jacques

    2010-01-01

    The present article discusses the possibility that catalysed chemical networks can evolve. Even simple enzyme-catalysed chemical reactions can display this property. The example studied is that of a two-substrate proteinoid, or enzyme, reaction displaying random binding of its substrates A and B. The fundamental property of such a system is to display either emergence or integration depending on the respective values of the probabilities that the enzyme has bound one of its substrate regardless it has bound the other substrate, or, specifically, after it has bound the other substrate. There is emergence of information if p(A)>p(AB) and p(B)>p(BA). Conversely, if p(A)equilibrium. Moreover, in such systems, emergence results in an increase of the energy level of the ternary EAB complex that becomes closer to the transition state of the reaction, thus leading to the enhancement of catalysis. Hence a drift from quasi-equilibrium is, to a large extent, responsible for the production of information and enhancement of catalysis. Non-equilibrium of these simple systems must be an important aspect that leads to both self-organization and evolutionary processes. These conclusions can be extended to networks of catalysed chemical reactions. Such networks are, in fact, networks of networks, viz. meta-networks. In this formal representation, nodes are chemical reactions catalysed by poorly specific proteinoids, and links can be identified to the transport of metabolites from proteinoid to proteinoid. The concepts of integration and emergence can be applied to such situations and can be used to define the identity of these networks and therefore their evolution. Defined as open non-equilibrium structures, such biochemical networks possess two remarkable properties: (1) the probability of occurrence of their nodes is dependant upon the input and output of matter in, and from, the system and (2) the probability of occurrence of the nodes is strictly linked to their degree of

  14. Organodioxygen complexes of some heavy metal ions and their oxygen transfer reactions

    International Nuclear Information System (INIS)

    Tarafder, M.T.H.; Mei Ling; Gino Mariotto

    2003-09-01

    Several novel organodioxygen complexes of lanthanide ions, viz., lanthanum(m) and cerium(IV) have been synthesized containing a number of organic co- ligands. The complexes characterized were, [La(0 2 )(det)(N0 3 ) 2 ] (1), [La(O 2 )(tet)(NO 3 ) 2 ] (2), [La(O 2 )(C 5 H 5 N)2NO 3 ] (3), [La(O 2 )(C 6 H 18 N 3 PO) 2 (NO 3 ) 2 ] (4), [La(0 2 )(OPPh 3 ) 2 (N0 3 ) 2 ] (5), [La(O 2 ) 2 (NH 2 CH 2 CH 2 NH 2 ) 2 NO 3 ] (6), [La(O 2 )(PPh 3 ) 2 (NO 3 ) 2 ] (7) and [Ce(O 2 )(C 6 H 18 N 3 PO) 2 (NO 3 ) 3 ] (8). IR and Raman spectra revealed that (3) was a peroxo complex while the others were, in particular, superoxo type. The IR spectrum of (3) gives V 1 (O-O) at 851 cm -1 while the Raman spectra of (4), (5), (7) and (8) give V 1 (O 2 ) bands at 1046 cm -1 , 1032 cm 1 , 1100 cm -1 and 1046 cm -1 , respectively. The oxygen transfer reactions of two selected complexes were carried out under stoichiometric conditions. The complex containing a bidentate ligand, (6), was found to oxidize triphenylphosphine and trans-stilbene to their oxides while the complex containing tridentate ligand (1) was stable and inert towards oxidation. (author)

  15. Spectroscopic properties of reaction center pigments in photosystem II core complexes: revision of the multimer model.

    Science.gov (United States)

    Raszewski, Grzegorz; Diner, Bruce A; Schlodder, Eberhard; Renger, Thomas

    2008-07-01

    Absorbance difference spectra associated with the light-induced formation of functional states in photosystem II core complexes from Thermosynechococcus elongatus and Synechocystis sp. PCC 6803 (e.g., P(+)Pheo(-),P(+)Q(A)(-),(3)P) are described quantitatively in the framework of exciton theory. In addition, effects are analyzed of site-directed mutations of D1-His(198), the axial ligand of the special-pair chlorophyll P(D1), and D1-Thr(179), an amino-acid residue nearest to the accessory chlorophyll Chl(D1), on the spectral properties of the reaction center pigments. Using pigment transition energies (site energies) determined previously from independent experiments on D1-D2-cytb559 complexes, good agreement between calculated and experimental spectra is obtained. The only difference in site energies of the reaction center pigments in D1-D2-cytb559 and photosystem II core complexes concerns Chl(D1). Compared to isolated reaction centers, the site energy of Chl(D1) is red-shifted by 4 nm and less inhomogeneously distributed in core complexes. The site energies cause primary electron transfer at cryogenic temperatures to be initiated by an excited state that is strongly localized on Chl(D1) rather than from a delocalized state as assumed in the previously described multimer model. This result is consistent with earlier experimental data on special-pair mutants and with our previous calculations on D1-D2-cytb559 complexes. The calculations show that at 5 K the lowest excited state of the reaction center is lower by approximately 10 nm than the low-energy exciton state of the two special-pair chlorophylls P(D1) and P(D2) which form an excitonic dimer. The experimental temperature dependence of the wild-type difference spectra can only be understood in this model if temperature-dependent site energies are assumed for Chl(D1) and P(D1), reducing the above energy gap from 10 to 6 nm upon increasing the temperature from 5 to 300 K. At physiological temperature, there are

  16. Oxygen atom transfer reactions from Mimoun complexes to sulfides and sulfoxides. A bonding evolution theory analysis.

    Science.gov (United States)

    González-Navarrete, Patricio; Sensato, Fabricio R; Andrés, Juan; Longo, Elson

    2014-08-07

    In this research, a comprehensive theoretical investigation has been conducted on oxygen atom transfer (OAT) reactions from Mimoun complexes to sulfides and sulfoxides. The joint use of the electron localization function (ELF) and Thom's catastrophe theory (CT) provides a powerful tool to analyze the evolution of chemical events along a reaction pathway. The progress of the reaction has been monitored by structural stability domains from ELF topology while the changes between them are controlled by turning points derived from CT which reveal that the reaction mechanism can be separated in several steps: first, a rupture of the peroxo O1-O2 bond, then a rearrangement of lone pairs of the sulfur atom occurs and subsequently the formation of S-O1 bond. The OAT process involving the oxidation of sulfides and sulfoxides is found to be an asynchronous process where O1-O2 bond breaking and S-O1 bond formation processes do not occur simultaneously. Nucleophilic/electrophilic characters of both dimethyl sulfide and dimethyl sulfoxide, respectively, are sufficiently described by our results, which hold the key to unprecedented insight into the mapping of electrons that compose the bonds while the bonds change.

  17. Formation of quinones, indanones and furans by the reaction of molybdenum carbene complexes with alkynes

    International Nuclear Information System (INIS)

    Doetz, K.H.; Larbig, H.

    1992-01-01

    (Alkoxy)carbene complexes of molybdenum react with terminal alkynes to give carbene annulation of cycloaddition products, the skeleton of which depends on the carbene substitution pattern and the alkyne used. (CO) 5 Mo=C(OMe)-p-tol undergoes carbene annulation upon reaction with trimethylsilylacetylene leading to naphthoquinone after oxidative work-up. Similar products are obtained from (CO) 5 Mo=C(OMe)2-furyl and hex-1-yne or oct-1-yne. The reaction of these alkynes results in the formation of indanones as five-membered annulation products. In the presence of 3.3-dimethylbut-1-yne the (phenyl) carbene ligands act as a C 1 -synthon, which is incorporated into the furan cycloaddition products

  18. Spectrophotometric study of the complexation reaction between niobium(V) and 5-sulpho-3-nitro-salicylic acid

    Energy Technology Data Exchange (ETDEWEB)

    Parmar, D S; Shivahare, G C [Rajasthan Univ., Jaipur (India). Dept. of Chemistry

    1975-04-01

    5-sulpho-3 nitro-salicylic acid forms a yellow complex with niobium(V) at pH 8.5 and the reaction has been successfully studied spectrophotometrically. The results of the Job's continuous variation method and the molar ratio method indicate a composition of 1:2 for the complex. Stability constant of the complex has also been determined. (auth)

  19. DHA- RICH FISH OIL IMPROVES COMPLEX REACTION TIME IN FEMALE ELITE SOCCER PLAYERS

    Directory of Open Access Journals (Sweden)

    José F. Guzmán

    2011-06-01

    Full Text Available Omega-3 fatty acids (n-3 has shown to improve neuromotor function. This study examined the effects of docosahexaenoic acid (DHA on complex reaction time, precision and efficiency, in female elite soccer players. 24 players from two Spanish female soccer Super League teams were randomly selected and assigned to two experimental groups, then administered, in a double-blind manner, 3.5 g·day-1 of either DHA-rich fish oil (FO =12 or olive oil (OO = 12 over 4 weeks of training. Two measurements (pre- and post-treatment of complex reaction time and precision were taken. Participants had to press different buttons and pedals with left and right hands and feet, or stop responding, according to visual and auditory stimuli. Multivariate analysis of variance displayed an interaction between supplement administration (pre/post and experimental group (FO/OO on complex reaction time (FO pre = 0.713 ± 0.142 ms, FO post = 0.623 ± 0.109 ms, OO pre = 0.682 ± 1.132 ms, OO post = 0.715 ± 0.159 ms; p = 0.004 and efficiency (FO pre = 40.88 ± 17.41, FO post = 57.12 ± 11.05, OO pre = 49.52 ± 14.63, OO post = 49. 50 ± 11.01; p = 0.003. It was concluded that after 4 weeks of supplementation with FO, there was a significant improvement in the neuromotor function of female elite soccer players

  20. Reversible alkyne insertion in the benzannulation reaction of Fischer carbene complexes with alkynes

    Energy Technology Data Exchange (ETDEWEB)

    Waters, M.L.; Bos, M.E.; Wulff, W.D. [Univ. of Chicago, IL (United States)

    1995-12-31

    The benzannulation reaction of Fischer carbene complexes with alkynes to give phenols is highly regioselective with terminal alkynes, and reasonably regioselective with internal alkynes. This has been attributed to steric factors in intermediates, where one form is favored due to close contact between the R substituent and a cis-CO ligand. Whether alkyne insertion is kinetically or thermodynamically controlled has not been determined. The authors now have evidence from regioselectivity studies that alkyne insertion into the metal-carbon bond is reversible. Implications of these results and further mechanistic considerations will be presented.

  1. URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.

    Science.gov (United States)

    Drawert, Brian; Engblom, Stefan; Hellander, Andreas

    2012-06-22

    Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at

  2. Neutron-induced complex reaction analysis with 3D nuclear track simulation

    International Nuclear Information System (INIS)

    Sajo-Bohus, L.; Palfalvi, J.K.; Akatov, Yu.; Arevalo, O.; Greaves, E.D.; Nemeth, P.; Palacios, D.; Szabo, J.; Eoerdoegh, I.

    2005-01-01

    Complex (multiple) etched tracks are analysed through digitised images and 3D simulation by a purpose-built algorithm. From a binary track image an unfolding procedure is followed to generate a 3D track model, from which several track parameters are estimated. The method presented here allows the deposited energy, that originated from particle fragmentation or carbon spallation by means of induced tracks in commercially available PADC detectors, to be estimated. Results of evaluated nuclear tracks related to 12 C (n,3αn ' ) reaction are presented here. The detectors were exposed on the ISS in 2001

  3. Populations of excited states and reaction mechanisms in the emission of complex fragments

    International Nuclear Information System (INIS)

    Gomez del Campo, J.

    1990-01-01

    Cross sections for emission of complex fragments (Z>2) in their ground and excited states are presented for several heavy-ion reactions at bombarding energies above 10 MeV/nucleon. Data presented are mostly on the cross sections extracted by γ-ray techniques. It is shown that a simple statistical approach to associate the ratio, of cross sections for excited states and ground states, to the temperature of the emitter fails to give the expected temperatures. However, it is shown that this is mostly due to the fact that the fragments that γ decay are secondary fragments, produced by the particle decay of the primary emitted complex fragments. A Hauser-Feshbach analysis accounts well for the cross sections and extracted temperatures. 22 refs., 6 figs

  4. Chemical proprieties of the iron-quinone complex in mutated reaction centers of Rb. sphaeroides

    International Nuclear Information System (INIS)

    Hałas, Agnieszka; Derrien, Valerie; Sebban, Pierre; Matlak, Krzysztof; Korecki, Józef; Kruk, Jerzy; Burda, Kvĕtoslava

    2012-01-01

    We investigated type II bacterial photosynthetic reaction centers, which contain a quinone - iron complex (Q A -Fe-Q B ) on their acceptor side. Under physiological conditions it was observed mainly in a reduced high spin state but its low spin ferrous states were also observed. Therefore, it was suggested that it might regulate the dynamical properties of the iron–quinone complex and the protonation and deprotonation events in its neighbourhood. In order to get insight into the molecular mechanism of the NHFe low spin state formation, we preformed Mössbauer studies of a wild type of Rb. sphaeroides and its two mutated forms. Our Mössbauer measurements show that the hydrophobicity of the Q A binding site can be crucial for stabilization of the high spin ferrous state of NHFe.

  5. Alumina plate containing photosystem I reaction center complex oriented inside plate-penetrating silica nanopores.

    Science.gov (United States)

    Kamidaki, Chihiro; Kondo, Toru; Noji, Tomoyasu; Itoh, Tetsuji; Yamaguchi, Akira; Itoh, Shigeru

    2013-08-22

    The photosynthetic photosystem I reaction center complex (PSI-RC), which has a molecular diameter of 21 nm with 100 pigments, was incorporated into silica nanopores with a 100-nm diameter that penetrates an alumina plate of 60-μm thickness to make up an inorganic-biological hybrid photocell. PSI-RCs, purified from a thermophilic cyanobacterium, were stable inside the nanopores and rapidly photoreduced a mediator dye methyl viologen. The reduced dye was more stable inside nanopores suggesting the decrease of dissolved oxygen. The analysis by a cryogenic electron spin paramagnetic resonance indicated the oriented arrangement of RCs inside the 100-nm nanopores, with their surface parallel to the silica wall and perpendicular to the plane of the alumina plate. PSI RC complex in the semicrystalline orientation inside silica nanopores can be a new type of light energy conversion unit to supply strong reducing power selectively to other molecules inside or outside nanopores.

  6. Spectroscopy and dynamics of chemical reactions in van der Waals complexes

    International Nuclear Information System (INIS)

    Soorkia, Satchin

    2008-09-01

    Transition metal elements have d valence electrons and are characterized by a great variety of electronic configurations responsible for their specific reactivity. The elements of the second row in particular have 4d and 5s atomic orbitals of similar size and energy which can be both involved in chemical processes. We have been interested in the reactivity of a transition metal element, zirconium, combined with a simple organic functionalized molecule in a van der Waals complex formed in a supersonic molecular beam in the model reaction Zr + CH 3 F. In this context, one of the chemicals reactions that we are interested in leads to the formation of ZrF. The electronic spectroscopy of ZrF in the spectral domain 400 - 470 nm is extremely rich and surprising for a diatomic molecule. With this study, we have been able to identify the ground state of ZrF (X 2 Δ) by simulating the observed rotational structures and obtain essential information on the electronic structure. These experimental results are in agreement with ab initio calculations. The excited states of the complex Zr...F-CH 3 have been studied with a depopulation method. The spectral domain 615 - 700 nm is particularly interesting because it reveals a group of diffuse bands red-shifted and broadened with respect to the transition a 3 F → z 3 F in the metal. This transition is forbidden from the ground state a 3 F 2 of zirconium but allowed from the a 3 F 4 state. Complexation of the metal atom with a CH 3 F molecule allows coupling of these two states to occur which ensures the optical transition from the ground state of the complex. (author)

  7. Photochemical redox reactions of copper(II)-alanine complexes in aqueous solutions.

    Science.gov (United States)

    Lin, Chen-Jui; Hsu, Chao-Sheng; Wang, Po-Yen; Lin, Yi-Liang; Lo, Yu-Shiu; Wu, Chien-Hou

    2014-05-19

    The photochemical redox reactions of Cu(II)/alanine complexes have been studied in deaerated solutions over an extensive range of pH, Cu(II) concentration, and alanine concentration. Under irradiation, the ligand-to-metal charge transfer results in the reduction of Cu(II) to Cu(I) and the concomitant oxidation of alanine, which produces ammonia and acetaldehyde. Molar absorptivities and quantum yields of photoproducts for Cu(II)/alanine complexes at 313 nm are characterized mainly with the equilibrium Cu(II) speciation where the presence of simultaneously existing Cu(II) species is taken into account. By applying regression analysis, individual Cu(I) quantum yields are determined to be 0.094 ± 0.014 for the 1:1 complex (CuL) and 0.064 ± 0.012 for the 1:2 complex (CuL2). Individual quantum yields of ammonia are 0.055 ± 0.007 for CuL and 0.036 ± 0.005 for CuL2. Individual quantum yields of acetaldehyde are 0.030 ± 0.007 for CuL and 0.024 ± 0.007 for CuL2. CuL always has larger quantum yields than CuL2, which can be attributed to the Cu(II) stabilizing effect of the second ligand. For both CuL and CuL2, the individual quantum yields of Cu(I), ammonia, and acetaldehyde are in the ratio of 1.8:1:0.7. A reaction mechanism for the formation of the observed photoproducts is proposed.

  8. Biochemical Characterization of the Prolyl 3-Hydroxylase 1·Cartilage-associated Protein·Cyclophilin B Complex*

    Science.gov (United States)

    Ishikawa, Yoshihiro; Wirz, Jackie; Vranka, Janice A.; Nagata, Kazuhiro; Bächinger, Hans Peter

    2009-01-01

    The rough endoplasmic reticulum-resident protein complex consisting of prolyl 3-hydroxylase 1 (P3H1), cartilage-associated protein (CRTAP), and cyclophilin B (CypB) can be isolated from chick embryos on a gelatin-Sepharose column, indicating some involvement in the biosynthesis of procollagens. Prolyl 3-hydroxylase 1 modifies a single proline residue in the α chains of type I, II, and III collagens to (3S)-hydroxyproline. The peptidyl-prolyl cis-trans isomerase activity of cyclophilin B was shown previously to catalyze the rate of triple helix formation. Here we show that cyclophilin B in the complex shows peptidyl-prolyl cis-trans isomerase activity and that the P3H1·CRTAP·CypB complex has another important function: it acts as a chaperone molecule when tested with two classical chaperone assays. The P3H1·CRTAP·CypB complex inhibited the thermal aggregation of citrate synthase and was active in the denatured rhodanese refolding and aggregation assay. The chaperone activity of the complex was higher than that of protein-disulfide isomerase, a well characterized chaperone. The P3H1·CRTAP·CypB complex also delayed the in vitro fibril formation of type I collagen, indicating that this complex is also able to interact with triple helical collagen and acts as a collagen chaperone. PMID:19419969

  9. Computational and experimental studies on stabilities, reactions and reaction rates of cations and ion-dipole complexes

    NARCIS (Netherlands)

    Ervasti, H.K.

    2008-01-01

    In this thesis, ion stability, ion-molecule reactions and reaction rates are studied using mass spectrometry and molecular modelling. In Chapter 2 the effect of functional group substitution on neutral and ionised ketene are studied. Electron-donating substituents show a stabilising positive

  10. Crystal structure of an EAL domain in complex with reaction product 5'-pGpG.

    Directory of Open Access Journals (Sweden)

    Julien Robert-Paganin

    Full Text Available FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686: one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

  11. Method for Determining the Activation Energy Distribution Function of Complex Reactions by Sieving and Thermogravimetric Measurements.

    Science.gov (United States)

    Bufalo, Gennaro; Ambrosone, Luigi

    2016-01-14

    A method for studying the kinetics of thermal degradation of complex compounds is suggested. Although the method is applicable to any matrix whose grain size can be measured, herein we focus our investigation on thermogravimetric analysis, under a nitrogen atmosphere, of ground soft wheat and ground maize. The thermogravimetric curves reveal that there are two well-distinct jumps of mass loss. They correspond to volatilization, which is in the temperature range 298-433 K, and decomposition regions go from 450 to 1073 K. Thermal degradation is schematized as a reaction in the solid state whose kinetics is analyzed separately in each of the two regions. By means of a sieving analysis different size fractions of the material are separated and studied. A quasi-Newton fitting algorithm is used to obtain the grain size distribution as best fit to experimental data. The individual fractions are thermogravimetrically analyzed for deriving the functional relationship between activation energy of the degradation reactions and the particle size. Such functional relationship turns out to be crucial to evaluate the moments of the activation energy distribution, which is unknown in terms of the distribution calculated by sieve analysis. From the knowledge of moments one can reconstruct the reaction conversion. The method is applied first to the volatilization region, then to the decomposition region. The comparison with the experimental data reveals that the method reproduces the experimental conversion with an accuracy of 5-10% in the volatilization region and of 3-5% in the decomposition region.

  12. Crystal structure of an EAL domain in complex with reaction product 5'-pGpG.

    Science.gov (United States)

    Robert-Paganin, Julien; Nonin-Lecomte, Sylvie; Réty, Stéphane

    2012-01-01

    FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686): one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

  13. Chemistry by nanocatalysis: First example of a solid-supported RAPTA complex for organic reactions in aqueous medium

    KAUST Repository

    Garcí a-Garrido, Sergio E.; Francos, Javier; Cadierno, Victorio; Basset, Jean-Marie; Polshettiwar, Vivek

    2010-01-01

    , with no use at all of organic solvent during or after the reactions, and microwaves as an alternative energy source renders the synthetic processes reported herein "truly" green and sustainable. RAPTA's delight: A nano-RAPTA complex supported on silica

  14. Fluoridonitrosyl complexes of technetium(I) and technetium(II). Synthesis, characterization, reactions, and DFT calculations.

    Science.gov (United States)

    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+).

  15. Biochemical investigation of yttrium(III) complex containing 1,10-phenanthroline: DNA binding and antibacterial activity.

    Science.gov (United States)

    Khorasani-Motlagh, Mozhgan; Noroozifar, Meissam; Moodi, Asieh; Niroomand, Sona

    2013-03-05

    Characterization of the interaction between yttrium(III) complex containing 1,10-phenanthroline as ligand, [Y(phen)2Cl(OH2)3]Cl2⋅H2O, and DNA has been carried out by UV absorption, fluorescence spectra and viscosity measurements in order to investigate binding mode. The experimental results indicate that the yttrium(III) complex binds to DNA and absorption is decreasing in charge transfer band with the increase in amount of DNA. The binding constant (Kb) at different temperatures as well as thermodynamic parameters, enthalpy change (ΔH°) and entropy change (ΔS°), were calculated according to relevant fluorescent data and Vant' Hoff equation. The results of interaction mechanism studies, suggested that groove binding plays a major role in the binding of the complex and DNA. The activity of yttrium(III) complex against some bacteria was tested and antimicrobial screening tests shown growth inhibitory activity in the presence of yttrium(III) complex. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Exquisite Modulation of the Active Site of Methanocaldococcus jannaschii Adenylosuccinate Synthetase in Forward Reaction Complexes.

    Science.gov (United States)

    Karnawat, Vishakha; Mehrotra, Sonali; Balaram, Hemalatha; Puranik, Mrinalini

    2016-05-03

    In enzymes that conduct complex reactions involving several substrates and chemical transformations, the active site must reorganize at each step to complement the transition state of that chemical step. Adenylosuccinate synthetase (ADSS) utilizes a molecule each of guanosine 5'-monophosphate (GTP) and aspartate to convert inosine 5'-monophosphate (IMP) into succinyl adenosine 5'-monophosphate (sAMP) through several kinetic intermediates. Here we followed catalysis by ADSS through high-resolution vibrational spectral fingerprints of each substrate and intermediate involved in the forward reaction. Vibrational spectra show differential ligand distortion at each step of catalysis, and band positions of substrates are influenced by binding of cosubstrates. We found that the bound IMP is distorted toward its N1-deprotonated form even in the absence of any other ligands. Several specific interactions between GTP and active-site amino acid residues result in large Raman shifts and contribute substantially to intrinsic binding energy. When both IMP and GTP are simultaneously bound to ADSS, IMP is converted into an intermediate 6-phosphoryl inosine 5'-monophosphate (6-pIMP). The 6-pIMP·ADSS complex was found to be stable upon binding of the third ligand, hadacidin (HDA), an analogue of l-aspartate. We find that in the absence of HDA, 6-pIMP is quickly released from ADSS, is unstable in solution, and converts back into IMP. HDA allosterically stabilizes ADSS through local conformational rearrangements. We captured this complex and determined the spectra and structure of 6-pIMP in its enzyme-bound state. These results provide important insights into the exquisite tuning of active-site interactions with changing substrate at each kinetic step of catalysis.

  17. Reaction

    African Journals Online (AJOL)

    abp

    19 oct. 2017 ... Reaction to Mohamed Said Nakhli et al. concerning the article: "When the axillary block remains the only alternative in a 5 year old child". .... Bertini L1, Savoia G, De Nicola A, Ivani G, Gravino E, Albani A et al ... 2010;7(2):101-.

  18. Bis(pentamethylcyclopentadienyl) ytterbium: Electron-transfer reactions with organotransition metal complexes

    Energy Technology Data Exchange (ETDEWEB)

    Matsunaga, P.T.

    1991-11-01

    The divalent lanthanide complex, (Me{sub 5}C{sub 5}){sub 2}Yb, reacts with methylcopper to produce the base-free, ytterbium-methyl complex, (Me{sub 5}C{sub 5}){sub 2}YbMe. This product forms a asymmetric, methyl-bridged dimer in the solid state. The bulky alkyl complex, (Me{sub 5}C{sub 5}){sub 2}YbCH(SiMe{sub 3}){sub 2}, displays similar chemistry to (Me{sub 5}C{sub 5}){sub 2}YbMe, but at a reduced reaction rate due to the limited accessibility of the metal in (Me{sub 5}C{sub 5}){sub 2}YbCH(SiMe{sub 3}){sub 2}. Copper and silver halide salts react with (Me{sub 5}C{sub 5}){sub 2}V to produce the trivalent halide derivatives, (Me{sub 5}C{sub 5}){sub 2}VX (X + F, Cl, Br, I). The chloride complex, (Me{sub 5}C{sub 5}){sub 2}VCl, reacts with lithium reagents to form the phenyl and borohydride species. Nitrous oxide transfers an oxygen atom to (Me{sub 5}C{sub 5}){sub 2}V producing the vanadium-oxo complex, (Me{sub 5}Ce{sub 5}){sub 2}VO. The trivalent titanium species, (Me{sub 5}C{sub 5}){sub 2}TiX (X = Cl, Br, Me, BH{sub 4}), form bimetallic coordination complexes with (Me{sub 5}C{sub 5}){sub 2}Yb. The magnetic behavior of the products indicates that electron transfer has not occurred. The solid state structures of the chloride and bromide complexes show unusual bend angles for the halide bridges between ytterbium and titanium. A model based on frontier orbital theory has been proposed to account for the bending behavior in these species. The bimetallic methyl complex contains a linear methyl bridge between ytterbium and titanium.

  19. Bis(pentamethylcyclopentadienyl) ytterbium: Electron-transfer reactions with organotransition metal complexes

    Energy Technology Data Exchange (ETDEWEB)

    Matsunaga, Phillip Thomas [Univ. of California, Berkeley, CA (United States)

    1991-11-01

    The divalent lanthanide complex, (Me5C5)2Yb, reacts with methylcopper to produce the base-free, ytterbium-methyl complex, (Me5C5)2YbMe. This product forms a asymmetric, methyl-bridged dimer in the solid state. The bulky alkyl complex, (Me5C5)2YbCH(SiMe3)2, displays similar chemistry to (Me5C5)2YbMe, but at a reduced reaction rate due to the limited accessibility of the metal in (Me5C5)3YbCH(SiMe5)2. Copper and silver halide salts react with (Me5C5)2V to produce the trivalent halide derivatives, (Me5C5)2VX (X + F, Cl, Br, I). The chloride complex, (Me5C5)2VCl, reacts with lithium reagents to form the phenyl and borohydride species. Nitrous oxide transfers an oxygen atom to (Me5C5)2V producing the vanadium-oxo complex, (Me5Ce5)2VO. The trivalent titanium species, (Me5C5)2TiX (X = Cl, Br, Me, BH4), form bimetallic coordination complexes with (Me5C5)2Yb. The magnetic behavior of the products indicates that electron transfer has not occurred. The solid state structures of the chloride and bromide complexes show unusual bend angles for the halide bridges between ytterbium and titanium. A model based on frontier orbital theory has been proposed to account for the bending behavior in these species. The bimetallic methyl complex contains a linear methyl bridge between ytterbium and titanium.

  20. Systematics of complex fragment emission from La induced reactions at E/A = 47 MeV

    International Nuclear Information System (INIS)

    Kehoe, W.L.; Mignerey, A.C.; Bradley, S.

    1989-03-01

    Complex fragment (Z > 2) emission was studied in the reverse kinematics reactions of 139 La on 27 Al and /sup nat./Cu at a bombarding energy of E/A = 47 MeV. Experimental results from inclusive and coincidence measurements for two- and three-fold complex fragments events are presented. Measured cross sections and Z 1 -Z 2 correlations show a predominately binary-decay process for the La + Al reaction, while the La + Cu reaction is dominated by multi-body decay. 18 refs., 9 figs., 1 tab

  1. The complex reaction kinetics of neptunium including redox and extraction process in 30% TBP-nitric acid system

    International Nuclear Information System (INIS)

    Hu Zhang; Zhan-yuan Liu; Xian-ming Zhou; Li Li

    2017-01-01

    In order to understand the complex and dynamic neptunium process chemistry in the TBP-HNO_3 system, the kinetics involved reversible redox reaction and extraction mass transfer was investigated. The results indicates that the mass transfer rate of Np(VI) is much faster than the redox reaction in aqueous solution. The concentrations of nitric acid and nitrous acid not only can change the Np(V) oxidation reaction and Np(VI) reduction reaction rate, but also can ultimately determine the distribution of neptunium extraction equilibrium. The variety of temperature can only influence the extraction equilibrium time, but cannot alter the equilibrium state of neptunium. (author)

  2. Reaction of cyanide with Pt-nucleobase complexes: preparative, spectroscopic, and structural studies. Unexpected stability of Pt-thymine and Pt-uracil complexes

    International Nuclear Information System (INIS)

    Raudaschl-Sieber, G.; Lippert, B.

    1985-01-01

    In order to improve the understanding of the nature of the strongly bound cisplatin on DNA, the reactivity of a large number of complexes of cis-(NH 3 ) 2 Pt/sup II/ with the model nucleobases, 9-ethylguanine, 9-methyladenine, 1-methylcytisine, 1-methylthymine, and i-methyluracil, toward a large excess of cyanide was studied. The behavior of Pt-nucleobase complexes toward CN - is compared with that of simple Pt-amine complexes, and reactions of thiourea with two selected nucleobase complexes is reported. The relevance of these findings with respect to substitution reactions of Pt-nucleobase complexes and the nature of the tightly DNA-bound Pt, which cannot be removed by excess KCN, is discussed

  3. Method of investigation of nuclear reactions in charge-nonsymmetrical muonic complexes

    CERN Document Server

    Bystritsky, V M; Penkov, F M

    1999-01-01

    A method for experimental determination of the nuclear fusion rates in the d mu He molecules in the states with J=0 and J=1 (J is the orbital moment of the system) and of the effective rate of transition between these states (rotational transition 1-0) is proposed. It is shown that information on the desired characteristics can be found from joint analysis of the time distribution and yield of products of nuclear fusion reactions in deuterium-helium muonic molecules and muonic X-ray obtained in experiments with the D sub 2 +He mixture at three (and more) appreciably different densities. The planned experiments with the D sub 2 +He mixture at the meson facility PSI (Switzerland) are optimized to gain more accurate information about the desired parameters on the assumption that different mechanisms for the 1-0 transition of the d mu He complex are realized. (author)

  4. Baseline simple and complex reaction times in female compared to male boxers.

    Science.gov (United States)

    Bianco, M; Ferri, M; Fabiano, C; Giorgiano, F; Tavella, S; Manili, U; Faina, M; Palmieri, V; Zeppilli, P

    2011-06-01

    The aim of the study was to compare baseline cognitive performance of female in respect to male amateur boxers. Study population included 28 female amateur boxers. Fifty-six male boxers, matched for age, employment and competitive level to female athletes, formed the control group. All boxers had no history of head concussions (except boxing). Each boxer was requested to: 1) fulfill a questionnaire collecting demographic data, level of education, occupational status, boxing record and number of head concussions during boxing; 2) undergo a baseline computerized neuropsychological (NP) test (CogSport) measuring simple and complex reaction times (RT). Female were lighter than male boxers (56±7 vs. 73.1±9.8 kg, Pknock-outs, etc.) correlated with NP scores. Female and male Olympic-style boxers have no (or minimal) differences in baseline cognitive performance. Further research with larger series of female boxers is required to confirm these findings.

  5. Biochemical indicators of nephrotoxicity in blood serum of rats treated with novel 4-thiazolidinone derivatives or their complexes with polyethylene glycol-containing nanoscale polymeric carrier

    Directory of Open Access Journals (Sweden)

    L. I. Kоbylinska

    2016-02-01

    Full Text Available The aim of this study was to compare the effect of new synthetic 4-thiazolidinone derivatives (potential anticancer compounds denoted as 3882, 3288 and 3833 and doxorubicin (positive control in free form and in their complexes with synthetic polyethylene glycol-containing nanoscale polymeric carrier on the biochemical indicators of nephrotoxicity in blood serum of rats. The concentration of total protein, urea, creatinine, glucose, ions of sodium, potassium, calcium, iron and chloride was measured. It was found that after injection of the investigated compounds, the concentration of sodium cations and chloride anions in blood serum was increased compared with control (untreated animals. Doxorubicin’s injection was accompanied by a decrease in the concentration of iron cations. The concentration of total protein, urea and creatinine decreased under the influence of the studied compounds. Complexation of these аntineoplastic substances with a synthetic polymeric nanocarrier lowered the concentration of the investigated metabolites substantially compared to the effect of these compounds in free form. The normalization of concentration of total protein, urea and creatinine in blood serum of rats treated with complexes of the studied compounds with the polymeric carrier comparing with increased concentration of these indicators at the introduction of such compounds in free form was found.

  6. Time-dependent--S-matrix Hartree-Fock theory of complex reactions

    International Nuclear Information System (INIS)

    Griffin, J.J.; Lichtner, P.C.; Dworzecka, M.

    1980-01-01

    Some limitations of the conventional time-dependent Hartree-Fock method for describing complex reactions are noted, and one particular ubiquitous defect is discussed in detail: the post-breakup spurious cross channel correlations which arise whenever several asymptotic reaction channels must be simultaneously described by a single determinant. A reformulated time-dependent--S-matrix Hartree-Fock theory is proposed, which obviates this difficulty. Axiomatic requirements minimal to assure that the time-dependent--S-matrix Hartree-Fock theory represents an unambiguous and physically interpretable asymptotic reaction theory are utilized to prescribe conditions upon the definition of acceptable asymptotic channels. That definition, in turn, defines the physical range of the time-dependent--S-matrix Hartree-Fock theory to encompass the collisions of mathematically well-defined ''time-dependent Hartree-Fock droplets.'' The physical properties of these objects then circumscribe the content of the Hartree-Fock single determinantal description. If their periodic vibrations occur for continuous ranges of energy then the resulting ''classical'' time-dependent Hartree-Fock droplets are seen to be intrinsically dissipative, and the single determinantal description of their collisions reduces to a ''trajectory'' theory which can describe the masses and relative motions of the fragments but can provide no information about specific asymptotic excited states beyond their constants of motion, or the average properties of the limit, if it exists, of their equilibrization process. If, on the other hand, the periodic vibrations of the time-dependent Hartree-Fock droplets are discrete in energy, then the time-dependent--S-matrix Hartree-Fock theory can describe asymptotically the time-average properties of the whole spectrum of such periodic vibrations

  7. Microencapsulation of stearidonic acid soybean oil in Maillard reaction-modified complex coacervates.

    Science.gov (United States)

    Ifeduba, Ebenezer A; Akoh, Casimir C

    2016-05-15

    The antioxidant capacity of Maillard reaction (MR)-modified gelatin (GE)-gum arabic (GA) coacervates was optimized to produce microcapsules with superior oxidative stability compared to the unmodified control. MR was used to crosslink GE and GA, with or without maltodextrin (MD), to produce anti-oxidative Maillard reaction products (MRP) which was used to encapsulate stearidonic acid soybean oil (SDASO) by complex coacervation. Biopolymer blends (GE-GA [1:1, w/w] or GE-GA-MD [2:2:1, w/w/w]) were crosslinked by dry-heating at 80°C for 4, 8, or 16h. Relationships between the extent of browning, Trolox equivalent antioxidant capacity (TEAC), and the total oxidation (TOTOX) of encapsulated SDASO were fitted to quadratic models. The [GE-GA-MD] blends exhibited higher browning rates and TEAC values than corresponding [GE-GA] blends. Depending on the type of biopolymer blend and dry-heating time, TOTOX values of SDASO in MRP-derived microcapsules were 29-87% lower than that of the non-crosslinked control after 30 days of storage. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Theoretical investigation of elementary reaction of complexing LiH+BeH/sub 2/. -->. LiBeH/sub 3/

    Energy Technology Data Exchange (ETDEWEB)

    Charkin, O P; Boldyrev, A I; Sukhanov, L P [AN SSSR, Chernogolovka. Inst. Novykh Khimicheskikh Problem

    1979-01-01

    In the framework of non-empirical Hartree-Fock-Roothaan method on the basis of gauss functions of Roos and Siegbahn made are calculations of different sections of potential surface elementary reaction of complexing LiH+BeH/sub 2/ ..-->.. LiBeH/sub 3/. Charts of potential surface are presented. Questions of the elementary mechanism of elementary processes of complexing and effect of mutual orientation of the reagents upon the reaction mechanism are considered. Stability of LiBeH/sub 3/ molecule to different dissociation channels and different aspects of structural non-rigidity of the L(MXsub(k+1)) complexes at super barrier excitation are discussed.

  9. Theoretical investigation of elementary reaction of complexing LiH+BeH2 → LiBeH3

    International Nuclear Information System (INIS)

    Charkin, O.P.; Boldyrev, A.I.; Sukhanov, L.P.

    1979-01-01

    In the framework of non-empiric Hartree-Fock-Roothaan method on the basis of gauss functions of Roos and Siegbahn made are calculations of different sections of potential surface elementary reaction of complexing LiH+BeH 2 → LiBeH 3 . Charts of potential surface are presented. Questions of the elementary mechanism of elementary processes of complexing and effect of mutual orientation of the reagents upon the reaction mechanism are considered. Stability of LiBeH 3 molecule to different dissociation channels and different aspects of structural non-rigidity of the L[MXsub(k+1)] complexes at super barrier excitation are discussed

  10. Investigations of nuclear structure and nuclear reactions induced by complex projectiles

    International Nuclear Information System (INIS)

    Sarantites, D.G.

    1990-01-01

    This report discusses research in the following areas: nuclear structure; fusion reactions near and below the barrier; incomplete fusion and fragmentation reactions; and instrumentation and analysis. (LSP)

  11. Non-Archimedean reaction-ultradiffusion equations and complex hierarchic systems

    Science.gov (United States)

    Zúñiga-Galindo, W. A.

    2018-06-01

    We initiate the study of non-Archimedean reaction-ultradiffusion equations and their connections with models of complex hierarchic systems. From a mathematical perspective, the equations studied here are the p-adic counterpart of the integro-differential models for phase separation introduced by Bates and Chmaj. Our equations are also generalizations of the ultradiffusion equations on trees studied in the 1980s by Ogielski, Stein, Bachas, Huberman, among others, and also generalizations of the master equations of the Avetisov et al models, which describe certain complex hierarchic systems. From a physical perspective, our equations are gradient flows of non-Archimedean free energy functionals and their solutions describe the macroscopic density profile of a bistable material whose space of states has an ultrametric structure. Some of our results are p-adic analogs of some well-known results in the Archimedean setting, however, the mechanism of diffusion is completely different due to the fact that it occurs in an ultrametric space.

  12. The feasibility of using complex wastewater from a monosodium glutamate factory to cultivate Spirulina subsalsa and accumulate biochemical composition.

    Science.gov (United States)

    Jiang, Liqun; Pei, Haiyan; Hu, Wenrong; Ji, Yan; Han, Lin; Ma, Guixia

    2015-03-01

    This paper is mainly observations on the growth and biomass accumulation of Spirulina subsalsa in modified Zarrouk medium supplemented with complex wastewater (CW, from a monosodium glutamate factory) in different concentrations. High ammonia in 75% and 100% CW inhibits algae growth, but maximum biomass production (2.86mgL(-1)) was obtained in 25% CW (concentration of CW in medium was 25%). Different CW concentration promoted biomass composition accumulation at different degrees, 41% of protein content in 25% CW and 18% of carbohydrate in 50% CW. In terms of economy, a concentration of 25% CW was suitable for protein production and 50% for lipid and carbohydrate production. These results suggested that CW is a feasible replacement in part for cultivation of S. subsalsa to economize input of water and nutrients. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Oxidoreduction reactions involving the electrostatic and the covalent complex of cytochrome c and plastocyanin: Importance of the protein rearrangement for the intracomplex electron-transfer reaction

    International Nuclear Information System (INIS)

    Peerey, L.M.; Kostic, N.M.

    1989-01-01

    Horse heart cytochrome c and French bean plastocyanin are cross-linked one-to-one by a carbodiimide in the same general orientation in which they associate electrostatically. The reduction potentials of the Fe and Cu atoms in the covalent diprotein complex are respectively 245 and 385 mV vs NHE; the EPR spectra of the two metals are not perturbed by cross-linking. For isomers of the covalent diprotein complex, which probably differ slightly from one another in the manner of cross-linking, are separated efficiently by cation-exchange chromatography. Stopped-flow spectrophotometric experiments with the covalent diprotein complex show that the presence of plastocyanin somewhat inhibits oxidation of ferrocytochrome c by [Fe(CN) 6 ] 3- and somewhat promotes oxidation of this protein by [Fe(C 5 H 5 ) 2 ] + . These changes in reactivity are explained in terms of electrostatic and steric effects. Pulse-radiolysis experiments with the electrostatic diprotein complex yield association constants of ≥5 x 10 6 and 1 x 10 5 M -1 at ionic strengths of 1 and 40 mM, respectively, and the rate constant of 1.05 x 10 3 s -1 , regardless of the ionic strength, for the intracomplex electron-transfer reaction. Analogous pulse-radiolysis experiments with each of the four isomers of the covalent diprotein complex, at ionic strengths of both 2 and 200 mM, show an absence of the intracomplex electron-transfer reaction. A rearrangement of the proteins for this reaction seems to be possible (or unnecessary) in the electrostatic complex but impossible in the covalent complex

  14. Ductular reaction or hepatic reparative complex: immunohistochemical features in liver cirrhosis in patients with chronic hepatitis

    Directory of Open Access Journals (Sweden)

    V. A. Tumanskiy

    2018-04-01

    Full Text Available Until recently, a discussion about the mechanisms of development and the biological role of the ductular reaction, which develops in patients with chronic liver diseases continues among hepatologists and pathomorphologists. Purpose of the study. To characterize the pathomorphological features and significance of the ductular response in liver cirrhosis in patients with chronic non-alcoholic, alcoholic and viral hepatitis in hepatobioptats with the use of immunohistochemical (IHC techniques. Material and methods of investigation. Histological, histochemical and IHC study of the ductular liver reaction in liver biopsies of 52 patients aged 24 to 66 years with cirrhosis of the liver on the background of non-alcoholic steatohepatitis (13 patients, and alcoholic steatohepatitis (13 patients and on the background of chronic viral hepatitis C (10 patients, 26–47 years, as well as those suffering from severe biliostasis (8 patients and focal nodular liver hyperplasia (8 patients. Results. The ductular reaction can be detected in the active phase with maximum manifestations in patients with liver cirrhosis on the background of chronic hepatitis, it may have an average or weak degree of severity; in a significant number of patients, the effects of the ductular reaction of the liver are revealed. Cellular chains and groups of cells with the immunophenotype of the progenitor cells of the liver appear in the active phase of the ductular reaction at the periphery of the hepatic lobules in the projection of the Goering canals, in the fibrotically altered portal tracts, in the subcapsular zone of the liver and in the thickened fibrosis septa (c-kit CD117+, CD34+, CD56+ CK7-, CK19-, Hepar- without presence of figures of mitosis or increased level of expression of Кі-67 in them. In small ductules localized in the projection of the Goering canals, single cells with the expression of c-kit CD 117+, CD44 Std./HCAM+, CD34+, CD56+, expressing the markers of

  15. Interest of uranium complexes for the mechanism study of the McMurry reaction; Interet des complexes de l`uranium pour l`etude du mecanisme de la reaction de McMurry

    Energy Technology Data Exchange (ETDEWEB)

    Maury, O

    1997-07-04

    The reducing coupling reactions of ketones in diols and olefins are generally carried out with titanium or samarium compounds. In this work uranium complexes have been used. They have allowed to study the chemical reaction mechanism. This thesis is divided into three parts: 1) the reduction mechanism of uranium tetrachloride by cyclic voltametry has been studied at first. It has been shown that this reduction is followed by a transfer reaction of chlorides between the reduced specie of the higher electronic density and UCl . 2) In the second part is described: the synthesis, the crystal structure, the reactivity of the chemical agents, the stereochemistry of diols and alkenes formation and the pinacolisation reaction catalysis. 3) In the last part, the limits of the McMurry reaction are given by the study of the aromatic ketones pinacolisation reaction by-products. The obtained results show that the complexes of the metals which present a high reducing and oxo-philic (Ti, Sm, U..) character react in a similar way with the carbonyl compounds. If the uranium compounds are less used than those of the titanium in the field of the organic synthesis applications, they are precious auxiliaries and excellent models for reactions mechanisms study and for the synthesis methods optimization. (O.M.). 284 refs.

  16. Cell phone ringtone, but not landline phone ringtone, affects complex reaction time

    Directory of Open Access Journals (Sweden)

    Radosław Zajdel

    2013-02-01

    Full Text Available Introduction: Legislation systems of most countries prohibited using the handheld mobile phone while driving due to the fact that it disturbs concentration and causes hand involvement. Every phone owner is accustomed to the ringtone of his phone and almost involuntarily endeavors to pick it up or check who calls. This engages one’s psychomotor skills, which in our opinion contributes to the attenuation of reaction time needed for performing other crucial functions. Objectives: The aim of the study was: (1 to evaluate the infl uence of the sound of a ringing mobile phone on the complex reaction time (RT score in healthy subjects (owners, and (2 to check if there are any differences in RT when a landline phone and mobile phone ring. Methods: To assess RT we used our system and protocol of examination, previously validated. The examination conditions were standardized. All tests were performed in the same room with the same light and general acoustic conditions. The test group consisted of 23 women and 24 men, aged 19–24 years. The examination comprised 4 sessions: Training Session (TS during which the subjects were accustomed with the application and sample stimuli, Control Session (CS with no telephone ringing, Landline Session (LS with landline phone ringing, Mobile Session (MS with mobile phone ringing. Results: The median RT in the study population was signifi cantly elongated (p 0.05. Conclusions: We think that the specifi c ‘bond’ between a person and their private phone can signifi cantly disrupt their attention and thus affect the attention-demanding activities.

  17. Membrane Processes Based on Complexation Reactions of Pollutants as Sustainable Wastewater Treatments

    Directory of Open Access Journals (Sweden)

    Teresa Poerio

    2009-11-01

    Full Text Available Water is today considered to be a vital and limited resource due to industrial development and population growth. Developing appropriate water treatment techniques, to ensure a sustainable management, represents a key point in the worldwide strategies. By removing both organic and inorganic species using techniques based on coupling membrane processes and appropriate complexing agents to bind pollutants are very important alternatives to classical separation processes in water treatment. Supported Liquid Membrane (SLM and Complexation Ultrafiltration (CP-UF based processes meet the sustainability criteria because they require low amounts of energy compared to pressure driven membrane processes, low amounts of complexing agents and they allow recovery of water and some pollutants (e.g., metals. A more interesting process, on the application point of view, is the Stagnant Sandwich Liquid Membrane (SSwLM, introduced as SLM implementation. It has been studied in the separation of the drug gemfibrozil (GEM and of copper(II as organic and inorganic pollutants in water. Obtained results showed in both cases the higher efficiency of SSwLM with respect to the SLM system configuration. Indeed higher stability (335.5 vs. 23.5 hours for GEM; 182.7 vs. 49.2 for copper(II and higher fluxes (0.662 vs. 0.302 mmol·h-1·m-2 for GEM; 43.3 vs. 31.0 for copper(II were obtained by using the SSwLM. Concerning the CP-UF process, its feasibility was studied in the separation of metals from waters (e.g., from soil washing, giving particular attention to process sustainability such as water and polymer recycle, free metal and water recovery. The selectivity of the CP-UF process was also validated in the separate removal of copper(II and nickel(II both contained in synthetic and real aqueous effluents. Thus, complexation reactions involved in the SSwLM and the CP-UF processes play a key role to meet the sustainability criteria.

  18. MECHANISMS OF THE COMPLEX FORMATION BY d-METALS ON POROUS SUPPORTS AND THE CATALYTIC ACTIVITY OF THE FORMED COMPLEXES IN REDOX REACTIONS

    Directory of Open Access Journals (Sweden)

    T. L. Rakitskaya

    2015-11-01

    Full Text Available The catalytic activity of supported complexes of d metals in redox reactions with participation of gaseous toxicants, PH3, CO, O3, and SO2, depends on their composition. Owing to the variety of physicochemical and structural-adsorption properties of available supports, their influence on complex formation processes, the composition and catalytic activity of metal complexes anchored on them varies over a wide range. The metal complex formation on sup-ports with weak ion-exchanging properties is similar to that in aqueous solutions. In this case, the support role mainly adds up to the ability to reduce the activity of water adsorbed on them. The interaction between a metal complex and a support surface occurs through adsorbed water molecules. Such supports can also affect complex formation processes owing to protolytic reactions on account of acidic properties of sorbents used as supports. The catalytic activity of metal complexes supported on polyphase natural sorbents considerably depends on their phase relationship. In the case of supports with the nonsimple structure and pronounced ion-exchanging properties, for instance, zeolites and laminar silicates, it is necessary to take into account the variety of places where metal ions can be located. Such location places determine distinctions in the coordination environment of the metal ions and the strength of their bonding with surface adsorption sites and, therefore, the catalytic activity of surface complexes formed by theses metal ions. Because of the energy surface inhomogeneity, it is important to determine a relationship between the strength of a metal complex bonding with a support surface and its catalytic activity. For example, bimetallic complexes are catalytically active in the reactions of oxidation of the above gaseous toxicants. In particular, in the case of carbon monoxide oxidation, the most catalytic activity is shown by palladium-copper complexes in which copper(II is strongly

  19. An Investigation of the Complexity of Maillard Reaction Product Profiles from the Thermal Reaction of Amino Acids with Sucrose Using High Resolution Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Agnieszka Golon

    2014-08-01

    Full Text Available Thermal treatment of food changes its chemical composition drastically with the formation of “so-called” Maillard reaction products, being responsible for the sensory properties of food, along with detrimental and beneficial health effects. In this contribution, we will describe the reactivity of several amino acids, including arginine, lysine, aspartic acid, tyrosine, serine and cysteine, with carbohydrates. The analytical strategy employed involves high and ultra-high resolution mass spectrometry followed by chemometric-type data analysis. The different reactivity of amino acids towards carbohydrates has been observed with cysteine and serine, resulting in complex MS spectra with thousands of detectable reaction products. Several compounds have been tentatively identified, including caramelization reaction products, adducts of amino acids with carbohydrates, their dehydration and hydration products, disproportionation products and aromatic compounds based on molecular formula considerations.

  20. The Possibility of Ce3+ and Mn2+ Complex Ions Formation With Iodine Species in a Dushman Reaction

    Directory of Open Access Journals (Sweden)

    Iurie Ungureanu

    2018-06-01

    Full Text Available This contribution presents investigations into possible effects of Ce3+ and Mn2+ on the reduction of UV-spectral signal for I3- observed e.g. in the Dushman reaction. The potential of the metal ions to form complexes with iodine-containing species was analysed. It was shown that no complex ions are formed between Ce3+ and Mn2+ metals ions with IO3-, I-, I2 species. Only the formation of a very weak CeI32+ complex ion was found to occur. An effect of a complex formation on the studied systems could be excluded.

  1. Efficient transfer hydrogenation reaction Catalyzed by a dearomatized PN 3P ruthenium pincer complex under base-free Conditions

    KAUST Repository

    He, Lipeng

    2012-03-01

    A dearomatized complex [RuH(PN 3P)(CO)] (PN 3PN, N′-bis(di-tert-butylphosphino)-2,6-diaminopyridine) (3) was prepared by reaction of the aromatic complex [RuH(Cl)(PN 3P)(CO)] (2) with t-BuOK in THF. Further treatment of 3 with formic acid led to the formation of a rearomatized complex (4). These new complexes were fully characterized and the molecular structure of complex 4 was further confirmed by X-ray crystallography. In complex 4, a distorted square-pyramidal geometry around the ruthenium center was observed, with the CO ligand trans to the pyridinic nitrogen atom and the hydride located in the apical position. The dearomatized complex 3 displays efficient catalytic activity for hydrogen transfer of ketones in isopropanol. © 2011 Elsevier B.V. All rights reserved.

  2. The Mechanism of Redox Reaction between Palladium(II Complex Ions and Potassium Formate in Acidic Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Wojnicki M.

    2017-06-01

    Full Text Available The kinetics studies of redox reaction between palladium(II chloride complex ions and potassium formate in acidic aqueous solutions was investigated. It was shown, that the reduction reaction of Pd(II is selective in respect to Pd(II complex structure. The kinetic of the process was monitored spectrophotometrically. The influence of chloride ions concentration, Pd(II initial concentration, reductant concentration, ionic strength as well as the temperature were investigated in respect to the process dynamics. Arrhenius equation parameters were determined and are equal to 65.8 kJ/mol, and A = 1.12×1011 s−1.

  3. Complex ion kinetics. Reaction rates on ion-exchange resins compared to those in water

    International Nuclear Information System (INIS)

    Liss, I.B.; Murmann, R.K.

    1975-01-01

    A comparison has been made between the rates in water and on an ion-exchange resin for the aquation of [(NH 3 ) 5 CoOReO 3 ] 2+ and [(H 2 O) 5 CrCl] 2+ and for the 18 O isotopic exchange of water with [(NH 3 ) 5 Co(OH 2 )] 3+ and ReO 4 - . The rate of water exchange on [(NH 3 ) 5 Co(OH 2 )] 3+ was not changed by association with Dowex 50W resins. Aquation of [(NH 3 ) 5 CoOReO 3 ] 2+ and water exchange on ReO 4 - had modified pH dependencies when associated with a resin. With the cobalt complex the rates were faster on the resin in the acidic region and slower on the resin in the basic region. A new term in the rate equation was observed when ReO 4 - was on the resin, first order in H + , while the other terms appear to be unchanged. Aquation of [(H 2 O) 5 CrCl] 2+ was much slower when it was absorbed on the resin. This was related to the known ionic strength effect of the reaction. (auth)

  4. Surface reaction of SnII on goethite (α-FeOOH): surface complexation, redox reaction, reductive dissolution, and phase transformation.

    Science.gov (United States)

    Dulnee, Siriwan; Scheinost, Andreas C

    2014-08-19

    To elucidate the potential risk of (126)Sn migration from nuclear waste repositories, we investigated the surface reactions of Sn(II) on goethite as a function of pH and Sn(II) loading under anoxic condition with O2 level redox state and surface structure were investigated by Sn K edge X-ray absorption spectroscopy (XAS), goethite phase transformations were investigated by high-resolution transmission electron microscopy and selected area electron diffraction. The results demonstrate the rapid and complete oxidation of Sn(II) by goethite and formation of Sn(IV) (1)E and (2)C surface complexes. The contribution of (2)C complexes increases with Sn loading. The Sn(II) oxidation leads to a quantitative release of Fe(II) from goethite at low pH, and to the precipitation of magnetite at higher pH. To predict Sn sorption, we applied surface complexation modeling using the charge distribution multisite complexation approach and the XAS-derived surface complexes. Log K values of 15.5 ± 1.4 for the (1)E complex and 19.2 ± 0.6 for the (2)C complex consistently predict Sn sorption across pH 2-12 and for two different Sn loadings and confirm the strong retention of Sn(II) even under anoxic conditions.

  5. Nickel(II) complexes containing ONS donor ligands: Synthesis ...

    Indian Academy of Sciences (India)

    MS received 23 July 2014; revised 28 November 2014; accepted 28 November 2014 ... Nickel(II) complexes; X-ray structure; Kumada-Corriu reaction; Suzuki reaction; ...... 29 75. 37. Kovala-Demertzi D, Demertzis M A, Miller J R,. Papadopoulou C ... Biochem. 86 555. 38. Bellamy L J 1985 In The Infrared Spectra of Complex.

  6. Influence of chitosan and melanin-glucan complex onto gamma-exposure with low doses and acute stressful reaction

    International Nuclear Information System (INIS)

    Senyuk, O.F.; Tarasenko, P.D.; Pazukhin, Eh.M.; Gorovoj, L.F.; Varlamov, V.P.

    2004-01-01

    Possibilities of prevention and reduction of consequences of acute exposure on the background of immobilization stress with the help of chitosan preparations and of melanin - glucan complex of highest bazidiomicetes (fungi) were studied. Tested preparations were capable to protect hematological and immunological homeostasis of line BALB/c mice from stressful reaction provoked by acute exposure and two-hour immobilization. The most expressed normalizing and adapting effect had the mixture composed of chitosan and melanin-glucan complex

  7. Catecholase activity of dicopper(II)-bispidine complexes: stabilities and structures of intermediates, kinetics and reaction mechanism.

    Science.gov (United States)

    Born, Karin; Comba, Peter; Daubinet, André; Fuchs, Alexander; Wadepohl, Hubert

    2007-01-01

    A mechanism for the oxidation of 3,5-di-tert-butylcatechol (dtbc) with dioxygen to the corresponding quinone (dtbq), catalyzed by bispidine-dicopper complexes (bispidines are various mono- and dinucleating derivatives of 3,7-diazabicyclo[3.3.1]nonane with bis-tertiary-amine-bispyridyl or bis-tertiary-amine-trispyridyl donor sets), is proposed on the basis of (1) the stoichiometry of the reaction as well as the stabilities and structures [X-ray, density functional theory (B3LYP, TZV)] of the bispidine-dicopper(II)-3,4,5,6-tetrachlorcatechol intermediates, (2) formation kinetics and structures (molecular mechanics, MOMEC) of the end-on peroxo-dicopper(II) complexes and (3) kinetics of the stoichiometric (anaerobic) and catalytic (aerobic) copper-complex-assisted oxidation of dtbc. This involves (1) the oxidation of the dicopper(I) complexes with dioxygen to the corresponding end-on peroxo-dicopper(II) complexes, (2) coordination of dtbc as a bridging ligand upon liberation of H(2)O(2) and (3) intramolecular electron transfer to produce dtbq, which is liberated, and the dicopper(I) catalyst. Although the bispidine complexes have reactivities comparable to those of recently published catalysts with macrocyclic ligands, which seem to reproduce the enzyme-catalyzed process in various reaction sequences, a strikingly different oxidation mechanism is derived from the bispidine-dicopper-catalyzed reaction.

  8. Pulse radiolysis studies of the reactions of bromine atoms and dimethyl sulfoxide bromine atom complexes with alcohols

    Science.gov (United States)

    Sumiyoshi, Takashi; Fujiyoshi, Ryoko; Katagiri, Miho; Sawamura, Sadashi

    2007-05-01

    Dimethylsulfoxide (DMSO)-Br complexes were generated by pulse radiolysis of DMSO/bromomethane mixtures and the formation mechanism and spectral characteristics of the formed complexes were investigated in detail. The rate constant for the reaction of bromine atoms with DMSO and the extinction coefficient of the complex were obtained to be 4.6×10 9 M -1 s -1 and 6300 M -1 cm -1 at the absorption maximum of 430 nm. Rate constants for the reaction of bromine atoms with a series of alcohols were determined in CBrCl 3 solutions applying a competitive kinetic method using the DMSO-Br complex as the reference system. The obtained rate constants were ˜10 8 M -1 s -1, one or two orders larger than those reported for highly polar solvents. Rate constants of DMSO-Br complexes with alcohols were determined to be ˜ 10 7 M -1 s -1. A comparison of the reactivities of Br atoms and DMSO-Br complexes with those of chlorine atoms and chlorine atom complexes which are ascribed to hydrogen abstracting reactants strongly indicates that hydrogen abstraction from alcohols is not the rate determining step in the case of Br atoms and DMSO-Br complexes.

  9. Mechanism of redox reactions induced by light and electron pulse in solutions of mixed ligand iron(II) complex cyanides

    International Nuclear Information System (INIS)

    Horvath, A.; Szoeke, J.; Wojnarovits, L.

    1991-01-01

    Redox reactions induced by light and electron pulse have been studied in aqueous solutions of mixed ligand iron(II) complex cyanides. The short lived intermediates have been identified by time resolved specroscopy, the results of detailed kinetic analysis have been discussed. (author) 6 refs.; 3 figs.; 2 tabs

  10. Stability and Reactivity of Cyclometallated Naphthylamine Complexes in Pd-C Bond Insertion Reactions with Coordinated Alkynylphosphanes

    KAUST Repository

    Chen, Shuli; Chiew, Jun Xuan; Pullarkat, Sumod A.; Li, Yongxin; Leung, Pak Hing

    2013-01-01

    , 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

  11. Analysis of mechanism of complex chemical reaction taking radiation chemical purification of gases from impurities as an example

    International Nuclear Information System (INIS)

    Gerasimov, G.Ya.; Makarov, V.N.

    1997-01-01

    Algorithm of selecting optimal mechanism of complex chemical reaction, enabling to reduce the number of its stages, is suggested. Main steps of constructing the kinetic model of the medium are considered, taking the radiation chemical purification (using fast electron radiation) of gases (N 2 , CO 2 , O 2 and others) from impurities as an example. 17 refs., 3 figs., 2 tabs

  12. Purification and spectroscopic characterization of photosystem II reaction center complexes isolated with or without Triton X-100.

    NARCIS (Netherlands)

    Eijckelhoff, C.; van Roon, H.; Groot, M.L.; van Grondelle, R.; Dekker, J.P.

    1996-01-01

    The pigment composition of the isolated photosystem II reaction center complex in its most stable and pure form currently is a matter of considerable debate. In this contribution, we present a new method based on a combination of gel filtration chromatography and diode array detection to analyze the

  13. Applicability of the Reaction Layer Principle to Nanoparticulate Metal Complexes at a Macroscopic Reactive (Bio)Interface

    NARCIS (Netherlands)

    Duval, Jérôme F.L.; Town, Raewyn M.; Leeuwen, Van Herman P.

    2017-01-01

    The reaction layer concept is commonly adopted to estimate the contribution of metal complexes to the flux of free metal ions (M) toward a macroscopic M-accumulating (bio)interface, e.g., a biosurface (microorganism) or a sensor (electrode). This concept is well-established for molecular ligands

  14. Diphosphinoazine Palladium(II) Complexes as Catalysts for the Heck Reaction of Bromides and an Activated Chloride

    Czech Academy of Sciences Publication Activity Database

    Včelák, Jaroslav; Storch, Jan; Czakoová, Marie; Čermák, Jan

    2004-01-01

    Roč. 222, 1-2 (2004), s. 121-126 ISSN 1381-1169 R&D Projects: GA ČR GA203/01/0554; GA AV ČR IAA4072205 Institutional research plan: CEZ:AV0Z4072921 Keywords : heck reaction * amido complex es * palladium Subject RIV: CA - Inorganic Chemistry Impact factor: 2.316, year: 2004

  15. Influence of Ligand Architecture in Tuning Reaction Bifurcation Pathways for Chlorite Oxidation by Non-Heme Iron Complexes

    NARCIS (Netherlands)

    Barman, Prasenjit; Faponle, Abayomi S; Vardhaman, Anil Kumar; Angelone, Davide; Löhr, Anna-Maria; Browne, Wesley R; Comba, Peter; Sastri, Chivukula V; de Visser, Sam P

    2016-01-01

    Reaction bifurcation processes are often encountered in the oxidation of substrates by enzymes and generally lead to a mixture of products. One particular bifurcation process that is common in biology relates to electron transfer versus oxygen atom transfer by high-valent iron(IV)-oxo complexes,

  16. Reaction of carbon dioxide with a palladium–alkyl complex supported by a bis–NHC framework†

    Science.gov (United States)

    Ariyananda, Piyal W. G.; Yap, Glenn P. A.

    2012-01-01

    The reactivity of a dimethyl palladium complex supported by a dicarbene chelate (MDCMes)PdMe2 towards CO2 has been investigated. In the presence of trace H2O, this reaction yields the corresponding methyl bicarbonate complex (MDCMes)PdMe(O2COH), which goes on to give the corresponding κ2-carbonato complex upon crystallization (MDCMes)Pd(CO3). This chemistry, as well as related protonolysis by acetic acid was monitored by a combination of techniques including React-IR spectroscopy. PMID:22643651

  17. Reaction of carbon dioxide with a palladium-alkyl complex supported by a bis-NHC framework.

    Science.gov (United States)

    Ariyananda, Piyal W G; Yap, Glenn P A; Rosenthal, Joel

    2012-07-14

    The reactivity of a dimethyl palladium complex supported by a dicarbene chelate (MDC(Mes))PdMe(2) towards CO(2) has been investigated. In the presence of trace H(2)O, this reaction yields the corresponding methyl bicarbonate complex (MDC(Mes))PdMe(O(2)COH), which goes on to give the corresponding κ(2)-carbonato complex upon crystallization (MDC(Mes))Pd(CO(3)). This chemistry, as well as related protonolysis by acetic acid was monitored by a combination of techniques including React-IR spectroscopy.

  18. Features of E-Z-photoisomerization reversible reaction of 4-styrylpyridine crown-containing complexes with different cations

    International Nuclear Information System (INIS)

    Fedorov, Yu.V.; Shepel', N.Eh.; Chernikova, E.Yu.; Fedorova, O.A.; Gulakova, E.N.; Avakyan, V.G.; Jonushauskas, G.

    2008-01-01

    E-Z-Photoisomerization reversible reaction of crown-containing 4-styrylpyridine in the presence of alkali metal perchlorates (Ca 2+ , Mg 2+ , Ba 2+ ) gifted in the formation of complexes with crown-ether fragments, as well as heavy metal perchlorates (Hg 2+ , Cd 2+ ) gifted in the coordination with nitrogen atom of heterocyclic residuum has been studied. Effect of complexing on the photoisomerization is determined by electron spectroscopy and NMR 1 H, structures of the formed Z-isomers are established. The possibility of the E-Z-isomerization control with the use of supramolecular complexing is confirmed by the investigations [ru

  19. Cationic Tungsten(VI) Penta-Methyl Complex: Synthesis, Characterization and its Application in Olefin Metathesis Reaction

    KAUST Repository

    Dey, Raju

    2016-04-13

    Tungsten-hexa-methyl readily reacts with B(C6F5)3 in dichloromethane and generates the corresponding well-defined cationic tungsten-penta-methyl complex which was identified precisely by 1H NMR, 13C NMR, 1H-13C NMR correlation spectroscopy. Unlike WMe6, this cationic complex has low energy barrier to form tungsten carbene intermediate, which was further supported by the fact that WMe6 alone has no activity in olefin metathesis reaction whereas the cationic complex shows catalytic activity for self-metathesis of 1-octene.

  20. Cationic Tungsten(VI) Penta-Methyl Complex: Synthesis, Characterization and its Application in Olefin Metathesis Reaction

    KAUST Repository

    Dey, Raju; Samantaray, Manoja; Callens, Emmanuel; Hamieh, Ali Imad Ali; Emwas, Abdul-Hamid M.; Abou-Hamad, Edy; Kavitake, Santosh Giridhar; Basset, Jean-Marie

    2016-01-01

    Tungsten-hexa-methyl readily reacts with B(C6F5)3 in dichloromethane and generates the corresponding well-defined cationic tungsten-penta-methyl complex which was identified precisely by 1H NMR, 13C NMR, 1H-13C NMR correlation spectroscopy. Unlike WMe6, this cationic complex has low energy barrier to form tungsten carbene intermediate, which was further supported by the fact that WMe6 alone has no activity in olefin metathesis reaction whereas the cationic complex shows catalytic activity for self-metathesis of 1-octene.

  1. Cerimetric determination of simvastatin in pharmaceuticals based on redox and complex formation reactions

    International Nuclear Information System (INIS)

    Basavaiah, K.; Devi, O.Z

    2008-01-01

    Two sensitive spectrophotometric methods are described for the determination of simvastatin (SMT) in bulk drug and in tablets. The methods are based on the oxidation of SMT by a measured excess of cerium (IV) in acid medium followed by determination of unreacted oxidant by two different reaction schemes. In one procedure (method A), the residual cerium (IV) is reacted with a fixed concentration of ferroin and the increase in absorbance is measured at 510 nm. The second approach (method B) involves the reduction of the unreacted cerium (IV) with a fixed quantity of iron (II), and the resulting iron (III) is complexed with thiocyanate and the absorbance measured at 470 nm. In both methods, the amount of cerium (IV) reacted corresponds to SMT concentration. The experimental conditions for both methods were optimized. In method A, the absorbance is found to increase linearly with SMT concentration (r = 0.9995) whereas in method B, the same decreased (r = -0.9943). The systems obey Beer's law for 0.6-7.5 and 0.5-5.0 μg mL -1 for method A and method B, respectively. The calculated molar absorptivity values are 2.7 X 104 and 1.06 X 105 Lmol -1 cm -1 , respectively; and the corresponding sandel sensitivity values are 0.0153 and 0.0039 μg cm -2 , respectively. The limit of detection (LOD) and quantification (LOQ) are reported for both methods. Intra-day and inter-day precision, and accuracy of the methods were established as per the current ICH guidelines. The methods were successfully applied to the determination of SMT in tablets and the results were statistically compared with those of the reference method by applying the Student's t-test and F-test. No interference was observed from the common excipients added to tablets. The accuracy and validity of the methods were further ascertained by performing recovery experiments via standard addition procedure. (author)

  2. Ácido L-ascórbico: reações de complexação e de óxido-redução com alguns íons metálicos de transição L-ascorbic acid: complexation and redox reactions with some transition metal ions

    OpenAIRE

    Adalgiza Fornaro; Nina Coichev

    1998-01-01

    The strong reducing action of L-ascorbic acid (Vitamin C) are of fundamental interest in biochemical and related process. The oxidation of ascorbic acid by molecular oxygen and others oxidants are of fundamental importance, involving the intervention of transition metal ions as catalysts and the formation transition metal complexes of ascorbic acid as intermediates. The present article is intended to cover some aspects of the reactions of ascorbic acid and related compounds involving some tra...

  3. Aqueous complexation, precipitation, and adsorption reactions of cadmium in the geologic environment

    International Nuclear Information System (INIS)

    Zachara, J.M.; Rai, D.; Felmy, A.R.; Cowan, C.E.; Smith, S.C.; Moore, D.A.; Resch, C.T.

    1992-06-01

    This report contains new laboratory data and equilibrium constants for important solubility and adsorption reactions of Cd that occur in soil and groundwater and attenuate Cd migration. In addition, extensive interaction experiments with Cd and soils from electric utility sites are described. These experiments show the importance of precipitation and adsorption reactions in soil and demonstrate how such reactions can be modeled to predict Cd attenuation near utility sites

  4. Quantum chemical and thermodynamic calculations of fulvic and humic copper complexes in reactions of malachite and azurite formation

    International Nuclear Information System (INIS)

    Fomin, Vitaliy N.; Gogol, Daniil B.; Rozhkovoy, Ivan E.; Ponomarev, Dmitriy L.

    2017-01-01

    This article provides a thermodynamic evaluation of the reactions of humic and fulvic acids in the process of malachite and azurite mineralogenesis. Semi-empirical methods AM/1, MNDO, PM3, PM5, PM6 and PM7 were used to compute the heat of formation, enthalpy and entropy for thermodynamic calculations of the reactions performed on the basis of Hess's law. It is shown that methods PM6 and PM7 in the MOPAC software package provide good compliance with experimental and calculated heats of formation for copper complexes and alkaline earth metal complexes with organic acids. It is found that the malachite and azurite formation processes involving humus complexing substances are thermodynamically possible. - Highlights: • Copper and alkali-earth metal complexes with humic and fulvic acids are considered. • Quantum chemical calculation of thermodynamics for the structures was performed. • Semi-empirical methods PM6 and PM7 provide best correlation for the properties. • Parameters of basic copper carbonate formation reactions were obtained by Hess's law. • Processes of malachite and azurite formation from humus complexes are possible.

  5. Factors affecting hydrogen-tunneling contribution in hydroxylation reactions promoted by oxoiron(IV) porphyrin π-cation radical complexes.

    Science.gov (United States)

    Cong, Zhiqi; Kinemuchi, Haruki; Kurahashi, Takuya; Fujii, Hiroshi

    2014-10-06

    Hydrogen atom transfer with a tunneling effect (H-tunneling) has been proposed to be involved in aliphatic hydroxylation reactions catalyzed by cytochrome P450 and synthetic heme complexes as a result of the observation of large hydrogen/deuterium kinetic isotope effects (KIEs). In the present work, we investigate the factors controlling the H-tunneling contribution to the H-transfer process in hydroxylation reaction by examining the kinetics of hydroxylation reactions at the benzylic positions of xanthene and 1,2,3,4-tetrahydronaphthalene by oxoiron(IV) 5,10,15,20-tetramesitylporphyrin π-cation radical complexes ((TMP(+•))Fe(IV)O(L)) under single-turnover conditions. The Arrhenius plots for these hydroxylation reactions of H-isotopomers have upwardly concave profiles. The Arrhenius plots of D-isotopomers, clear isosbestic points, and product analysis rule out the participation of thermally dependent other reaction processes in the concave profiles. These results provide evidence for the involvement of H-tunneling in the rate-limiting H-transfer process. These profiles are simulated using an equation derived from Bell's tunneling model. The temperature dependence of the KIE values (k(H)/k(D)) determined for these reactions indicates that the KIE value increases as the reaction temperature becomes lower, the bond dissociation energy (BDE) of the C-H bond of a substrate becomes higher, and the reactivity of (TMP(+•))Fe(IV)O(L) decreases. In addition, we found correlation of the slope of the ln(k(H)/k(D)) - 1/T plot and the bond strengths of the Fe═O bond of (TMP(+•))Fe(IV)O(L) estimated from resonance Raman spectroscopy. These observations indicate that these factors modulate the extent of the H-tunneling contribution by modulating the ratio of the height and thickness of the reaction barrier.

  6. Reactions of guanine with methyl chloride and methyl bromide: O6-methylation versus charge transfer complex formation

    Science.gov (United States)

    Shukla, P. K.; Mishra, P. C.; Suhai, S.

    Density functional theory (DFT) at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels was employed to study O6-methylation of guanine due to its reactions with methyl chloride and methyl bromide and to obtain explanation as to why the methyl halides cause genotoxicity and possess mutagenic and carcinogenic properties. Geometries of the various isolated species involved in the reactions, reactant complexes (RCs), and product complexes (PCs) were optimized in gas phase. Transition states connecting the reactant complexes with the product complexes were also optimized in gas phase at the same levels of theory. The reactant complexes, product complexes, and transition states were solvated in aqueous media using the polarizable continuum model (PCM) of the self-consistent reaction field theory. Zero-point energy (ZPE) correction to total energy and the corresponding thermal energy correction to enthalpy were made in each case. The reactant complexes of the keto form of guanine with methyl chloride and methyl bromide in water are appreciably more stable than the corresponding complexes involving the enol form of guanine. The nature of binding in the product complexes was found to be of the charge transfer type (O6mG+ · X-, X dbond Cl, Br). Binding of HCl, HBr, and H2O molecules to the PCs obtained with the keto form of guanine did not alter the positions of the halide anions in the PCs, and the charge transfer character of the PCs was also not modified due to this binding. Further, the complexes obtained due to the binding of HCl, HBr, and H2O molecules to the PCs had greater stability than the isolated PCs. The reaction barriers involved in the formation of PCs were found to be quite high (?50 kcal/mol). Mechanisms of genotoxicity, mutagenesis and carcinogenesis caused by the methyl halides appear to involve charge transfer-type complex formation. Thus the mechanisms of these processes involving the methyl halides appear to be quite different from those that involve the

  7. Energy, Electron Transfer and Photocatalytic Reactions of Visible Light Absorbing Transition Metal Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Schmehl, Russell H. [Tulane Univ., New Orleans, LA (United States)

    2016-03-02

    This is the final technical report for a project carried out at Tulane University of New Orleans that describes the development of light induced (solar) reactions geared toward decomposing water into its component elements : hydrogen and oxygen. Much of the work involved optimizing systems for absorbing visible light and undergoing light promoted reactions to generate very strong reducing agents that are capable of reacting with water to produce hydrogen. Additional portions of the research were collaborative efforts to put the strong reducing agents to work in reaction with hydrogen generation catalysts prepared elsewhere. Time resolved laser spectroscopic methods were used to evaluate the light induced reactions and characterize very reactive intermediate substances formed during the reactions.

  8. Novel heterometallic metal–azido complex synthesized by “one-step” reaction: synthetic strategy and magnetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Jiao, Yong-Kun [School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384 (China); Li, Xiu-Ping [Technical center for safety of industrial products of Tianjin entry-exit inspection and quarantine bureau, Tianjin 300201 (China); Zhao, Cui; Wang, Hai-Chao; Xue, Min [School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384 (China); Zhao, Jiong-Peng, E-mail: horryzhao@yahoo.com [School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384 (China); Liu, Fu-Chen, E-mail: fuchenliutj@yahoo.com [School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384 (China); Lanzhou Petrochemical College of Vocational Technology, Lanzhou 730060 (China)

    2013-06-15

    A novel heterometallic complex, [Ni{sub 2}Mn(N{sub 3}){sub 2}(nic){sub 4}·(H{sub 2}O){sub 2}]{sub n} (1) (nic=nicotinate), was obtained by assembling MnCl{sub 2}·4H{sub 2}O, Ni(NO{sub 3}){sub 2}·6H{sub 2}O, NaN{sub 3} and nicotinic acid with a “one step” synthetic strategy—hydrothermal reaction. The 3D structure of the complex can be described as end-on (EO) azido and syn,syn carboxylates mixed bridged by alternate Ni–Mn–Ni trimers linked by the nicotinate. Dominant ferromagnetic interactions were observed between the Ni{sup II} and Mn{sup II} ions in the trimer. - Graphical abstract: A novel heterometallic 3D complex [Ni{sub 2}Mn(N{sub 3}){sub 2}(nic){sub 4}·(H{sub 2}O){sub 2}]{sub n} (1) (nic=nicotinate) was synthesized by hydrothermal reaction. This complex exhibits interesting structural and magnetic properties. - Highlights: • It is difficult to construct simple coordination complexes with azide as “ligands” to obtain heterometallic metal–azido compounds. • A “one-step” method—hydrothermal reaction— was introduced to avoid the disadvantages of azide mentioned above. • The magnetic property is different with the isostructural homometal–azido complex due to the changed metal center.

  9. Novel heterometallic metal–azido complex synthesized by “one-step” reaction: synthetic strategy and magnetic properties

    International Nuclear Information System (INIS)

    Jiao, Yong-Kun; Li, Xiu-Ping; Zhao, Cui; Wang, Hai-Chao; Xue, Min; Zhao, Jiong-Peng; Liu, Fu-Chen

    2013-01-01

    A novel heterometallic complex, [Ni 2 Mn(N 3 ) 2 (nic) 4 ·(H 2 O) 2 ] n (1) (nic=nicotinate), was obtained by assembling MnCl 2 ·4H 2 O, Ni(NO 3 ) 2 ·6H 2 O, NaN 3 and nicotinic acid with a “one step” synthetic strategy—hydrothermal reaction. The 3D structure of the complex can be described as end-on (EO) azido and syn,syn carboxylates mixed bridged by alternate Ni–Mn–Ni trimers linked by the nicotinate. Dominant ferromagnetic interactions were observed between the Ni II and Mn II ions in the trimer. - Graphical abstract: A novel heterometallic 3D complex [Ni 2 Mn(N 3 ) 2 (nic) 4 ·(H 2 O) 2 ] n (1) (nic=nicotinate) was synthesized by hydrothermal reaction. This complex exhibits interesting structural and magnetic properties. - Highlights: • It is difficult to construct simple coordination complexes with azide as “ligands” to obtain heterometallic metal–azido compounds. • A “one-step” method—hydrothermal reaction— was introduced to avoid the disadvantages of azide mentioned above. • The magnetic property is different with the isostructural homometal–azido complex due to the changed metal center

  10. Activation energies as the validity criterion of a model for complex reactions that can be in oscillatory states

    Directory of Open Access Journals (Sweden)

    Anić S.

    2007-01-01

    Full Text Available Modeling of any complex reaction system is a difficult task. If the system under examination can be in various oscillatory dynamic states, the apparent activation energies corresponding to different pathways may be of crucial importance for this purpose. In that case the activation energies can be determined by means of the main characteristics of an oscillatory process such as pre-oscillatory period, duration of the oscillatory period, the period from the beginning of the process to the end of the last oscillation, number of oscillations and others. All is illustrated on the Bray-Liebhafsky oscillatory reaction.

  11. Reactions of dihydridotetrakis(triphenylphosphine)ruthenium(II) with olefins and isolation of new ruthenium-olefin complexes

    International Nuclear Information System (INIS)

    Komiya, Sanshiro; Yamamoto, Akio

    1976-01-01

    Dihydridotetrakis(triphenylphosphine)ruthenium (II), RuH 2 (PPh 3 ) 4 , reacts with olefins (ethylene, propylene, stylene and butadiene) to give olefin-coordinated complexes of the type, Ru(olefin)(PPh 3 ) 3 and equimolar amounts of their hydrogenation products per mol of the dihydride complex. The olefin coordinated with ruthenium can be exchanged with other olefins. Olefin-coordinated complexes easily react with molecular hydrogen to afford tetrahydridotris(triphenylphosphine)ruthenium, RuH 4 (PPh 3 ) 3 , releasing alkane at room temperature, Under hydrogen atmosphere catalytic hydrogenation of the olefins smoothly takes place with RuH 2 (PPh 3 ) 4 . (Ethylene)tris(triphenylphosphine)ruthenium(0) reacts with methyl iodide to give propylene and a trace of butadiene along with methane, ethylene, and small amounts of ethane and butenes. The formation of propylene suggests that oxidative addition involving cleavage of the C-H bond of ethylene to ruthenium giving a hydridovinyl complex may be taking place. Reactions of Ru(C 2 H 4 )(PPh 3 ) 3 with methyl-d 3 iodide and ethyl iodide, and of Ru(C 3 H 6 )(PPh 3 ) 3 with methyl iodide were examined to test the generality of this type of reaction. The reaction of Ru(C 2 H 4 )(PPh 3 ) 3 with CD 3 I released CD 4 and CD 2 H 2 together with CD 3 H suggesting the involvement of α-hydrogen abstraction. (auth.)

  12. Biochemical and Functional Studies on the Burkholderia cepacia Complex bceN Gene, Encoding a GDP-D-Mannose 4,6-Dehydratase

    Science.gov (United States)

    Pinheiro, Pedro F.; Leitão, Jorge H.

    2013-01-01

    This work reports the biochemical and functional analysis of the Burkholderia cenocepacia J2315 bceN gene, encoding a protein with GDP-D-mannose 4,6-dehydratase enzyme activity (E.C.4.2.1.47). Data presented indicate that the protein is active when in the tetrameric form, catalyzing the conversion of GDP-D-mannose into GDP-4-keto-6-deoxy-D-mannose. This sugar nucleotide is the intermediary necessary for the biosynthesis of GDP-D-rhamnose, one of the sugar residues of cepacian, the major exopolysaccharide produced by environmental and human, animal and plant pathogenic isolates of the Burkholderia cepacia complex species. Vmax and Km values of 1.5±0.2 µmol.min−1.mg−1 and 1024±123 µM, respectively, were obtained from the kinetic characterization of the B. cenocepacia J2315 BceN protein by NMR spectroscopy, at 25°C and in the presence of 1 mol MgCl2 per mol of protein. The enzyme activity was strongly inhibited by the substrate, with an estimated Ki of 2913±350 µM. The lack of a functional bceN gene in a mutant derived from B. cepacia IST408 slightly reduced cepacian production. However, in the B. multivorans ATCC17616 with bceN as the single gene in its genome with predicted GMD activity, a bceN mutant did not produce cepacian, indicating that this gene product is required for cepacian biosynthesis. PMID:23460819

  13. Biochemical and functional studies on the Burkholderia cepacia complex bceN gene, encoding a GDP-D-mannose 4,6-dehydratase.

    Directory of Open Access Journals (Sweden)

    Sílvia A Sousa

    Full Text Available This work reports the biochemical and functional analysis of the Burkholderia cenocepacia J2315 bceN gene, encoding a protein with GDP-D-mannose 4,6-dehydratase enzyme activity (E.C.4.2.1.47. Data presented indicate that the protein is active when in the tetrameric form, catalyzing the conversion of GDP-D-mannose into GDP-4-keto-6-deoxy-D-mannose. This sugar nucleotide is the intermediary necessary for the biosynthesis of GDP-D-rhamnose, one of the sugar residues of cepacian, the major exopolysaccharide produced by environmental and human, animal and plant pathogenic isolates of the Burkholderia cepacia complex species. Vmax and Km values of 1.5±0.2 µmol.min(-1.mg(-1 and 1024±123 µM, respectively, were obtained from the kinetic characterization of the B. cenocepacia J2315 BceN protein by NMR spectroscopy, at 25°C and in the presence of 1 mol MgCl2 per mol of protein. The enzyme activity was strongly inhibited by the substrate, with an estimated Ki of 2913±350 µM. The lack of a functional bceN gene in a mutant derived from B. cepacia IST408 slightly reduced cepacian production. However, in the B. multivorans ATCC17616 with bceN as the single gene in its genome with predicted GMD activity, a bceN mutant did not produce cepacian, indicating that this gene product is required for cepacian biosynthesis.

  14. From simple to complex and backwards. Chemical reactions under very high pressure

    International Nuclear Information System (INIS)

    Bini, Roberto; Ceppatelli, Matteo; Citroni, Margherita; Schettino, Vincenzo

    2012-01-01

    Highlights: ► High pressure reactivity of several molecular systems. ► Reaction kinetics and dynamics in high density conditions. ► Key role of optical pumping and electronic excitation. ► Perspectives for the synthesis of hydrogen. - Abstract: High pressure chemical reactions of molecular systems are discussed considering the various factors that can affect the reactivity. These include steric hindrance and geometrical constraints in the confined environment of crystals at high pressure, changes of the free energy landscape with pressure, photoactivation by two-photon absorption, local and collective effects. A classification of the chemical reactions at high pressure is attempted on the basis of the prevailing factors.

  15. Modeling of catalytically active metal complex species and intermediates in reactions of organic halides electroreduction.

    Science.gov (United States)

    Lytvynenko, Anton S; Kolotilov, Sergey V; Kiskin, Mikhail A; Eremenko, Igor L; Novotortsev, Vladimir M

    2015-02-28

    The results of quantum chemical modeling of organic and metal-containing intermediates that occur in electrocatalytic dehalogenation reactions of organic chlorides are presented. Modeling of processes that take place in successive steps of the electrochemical reduction of representative C1 and C2 chlorides - CHCl3 and Freon R113 (1,1,2-trifluoro-1,2,2-trichloroethane) - was carried out by density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2). It was found that taking solvation into account using an implicit solvent model (conductor-like screening model, COSMO) or considering explicit solvent molecules gave similar results. In addition to modeling of simple non-catalytic dehalogenation, processes with a number of complexes and their reduced forms, some of which were catalytically active, were investigated by DFT. Complexes M(L1)2 (M = Fe, Co, Ni, Cu, Zn, L1H = Schiff base from 2-pyridinecarbaldehyde and the hydrazide of 4-pyridinecarboxylic acid), Ni(L2) (H2L2 is the Schiff base from salicylaldehyde and 1,2-ethylenediamine, known as salen) and Co(L3)2Cl2, representing a fragment of a redox-active coordination polymer [Co(L3)Cl2]n (L3 is the dithioamide of 1,3-benzenedicarboxylic acid), were considered. Gradual changes in electronic structure in a series of compounds M(L1)2 were observed, and correlations between [M(L1)2](0) spin-up and spin-down LUMO energies and the relative energies of the corresponding high-spin and low-spin reduced forms, as well as the shape of the orbitals, were proposed. These results can be helpful for determination of the nature of redox-processes in similar systems by DFT. No specific covalent interactions between [M(L1)2](-) and the R113 molecule (M = Fe, Co, Ni, Zn) were found, which indicates that M(L1)2 electrocatalysts act rather like electron transfer mediators via outer-shell electron transfer. A relaxed surface scan of the adducts {M(L1)2·R113}(-) (M = Ni or Co) versus the distance between the

  16. Recoil properties of radionuclides formed in photospallation reactions on complex nuclei at intermediate energies

    International Nuclear Information System (INIS)

    Haba, Hiromitsu; Oura, Yasuji; Shibata, Seiichi; Furukawa, Michiaki; Fujiwara, Ichiro

    2001-01-01

    A short review is given on our studies of recoil properties of radionuclides formed in photospallation reactions induced by bremsstrahlung of end-point energies (E 0 ) from 600 to 1100 MeV, in which the thick-target thick-catcher method was employed. The measurements have been successful on 14, 24, 26, 31, 21 and 20 nuclides from nat V, nat Cu, 93 Nb, nat Ag, nat Ta, and 197 Au, respectively. Reflecting the resonance character in a photonuclear reaction, the mean ranges FW and BW in the forward and backward directions, respectively, are E 0 -independent at the studied energies and classified into two groups accounting for the (γ, xn) (x ≥ 1) and (γ, xnyp) (x, y ≥ 1) processes. The forward-to-backward ratios (F/B) are independent of the mass difference (ΔA) between a product (A p ) and a target (A t ) and also of A t . The kinematic properties of the product nuclei were analyzed by the two-step vector velocity model. The forward velocity ν after the first step of photon-reaction is quite different from that of proton-reaction at proton energies of E p ≤ 3 GeV, though the difference disappears at higher energies. On the other hand, the mean kinetic energy T of the residual nucleus in the second step is almost equal to that of proton-reaction irrespective of E p . A comparison with T values calculated by the PICA (Photon-Induced Intranuclear Cascade Analysis) code at E 0 =400 MeV was also performed. It was found that although the code well reproduces the experimental results of nat V and nat Cu, the same calculation for heavier targets gives T values lower than the experimental results, indicating some nuclear-structure effect, such as a medium effect notably at A t ≥ 100. An average kinetic energy carried off by the emitted particles ε s =T/(ΔA/A t ) of both photon- and proton-reactions seem to increase with an increase of A t up to around A t =100, and become almost constant at larger A t , implying some change in the nuclear structure effect in this

  17. Investigations of nuclear structure and nuclear reactions induced by complex projectiles

    International Nuclear Information System (INIS)

    Sarantites, D.G.

    1991-01-01

    The research program of our group touches five areas of nuclear physics: (1) Nuclear structure studies at high spin; (2) Studies at the interface between structure and reactions; (3) Production and study of hot nuclei; (4) Incomplete fusion and fragmentation reactions; and (5) Development and use of novel techniques and instrumentation in the above areas of research. The papers from these areas are discussed in this report

  18. Structural zinc(II thiolate complexes relevant to the modeling of Ada repair protein: Application toward alkylation reactions

    Directory of Open Access Journals (Sweden)

    Mohamed M. Ibrahim

    2014-11-01

    Full Text Available The TtZn(II-bound perchlorate complex [TtZn–OClO3] 1 (Ttxyly = hydrotris[N-xylyl-thioimidazolyl]borate was used for the synthesis of zinc(II-bound ethanthiothiol complex [TtZn–SCH2CH3] 2 and its hydrogen-bond containing analog Tt–ZnSCH2CH2–NH(COOC(CH33 3. These thiolate complexes were examined as structural models for the active sites of Ada repair protein toward methylation reactions. The Zn[S3O] coordination sphere in complex 1 includes three thione donors from the ligand Ttixyl and one oxygen donor from the perchlorate coligand in ideally tetrahedral arrangement around the zinc center. The average Zn(1–S(thione bond length is 2.344 Å, and the Zn(1–O(1 bond length is 1.917 Å.

  19. Thermodynamic Characteristics of Reactions of the Formation of Complexes between Triglycine and Ni2+ Ions in Aqueous Solution

    Science.gov (United States)

    Gorboletova, G. G.; Metlin, A. A.; Bychkova, S. A.

    2018-05-01

    Thermal effects of reactions of the formation of complexes between Ni(II) and triglycine are determined via direct calorimetry in aqueous solutions at 298.15 K and ionic strengths of 0.2, 0.5, and 1.0 (KNO3). Standard thermodynamic characteristics (Δr H°, Δr G°, Δr S°) of complexing processes in the investigated systems are calculated. The structures of triglycinate complexes NiL+, NiH-1L, NiL2, NiH-2L2- 2, NiL- 3, and NiH-3L4- 3 are introduced to compare the obtained values and data on the thermodynamics of triglycinate complexes of Ni(II).

  20. Determination of transport and reaction swarm coefficients from the analysis of complex transient pulses from the pulsed Townsend experiment

    International Nuclear Information System (INIS)

    Bekstein, A; De Urquijo, J; Rodríguez-Luna, J C; Juárez, A M; Ducasse, O

    2012-01-01

    We present in this paper the interpretation and analysis of transient pulses from a pulsed Townsend experiment by solving the continuity equations of the charged carriers (electrons and ions) involved in the avalanche. The set of second order partial differential equations is solved by SIMAV, a simulator designed specifically for the pulsed Townsend avalanche. Complex situations involving processes such as electron detachment, ion-molecule reactions, Penning ionization and secondary electron emission from ion impact at the cathode, virtually impossible to solve analytically, are discussed here to illustrate the capability of the simulator to help explain the various reaction processes involved in the avalanche, and also to derive some of the transport and reaction coefficients.

  1. Production of complex particles in low energy spallation and in fragmentation reactions by in-medium random clusterization

    International Nuclear Information System (INIS)

    Lacroix, D.; Durand, D.

    2005-09-01

    Rules for in-medium complex particle production in nuclear reactions are proposed. These rules have been implemented in two models to simulate nucleon-nucleus and nucleus-nucleus reactions around the Fermi energy. Our work emphasizes the effect of randomness in cluster formation, the importance of the nucleonic Fermi motion as well as the role of conservation laws. The concepts of total available phase-space and explored phase-space under constraint imposed by the reaction are clarified. The compatibility of experimental observations with a random clusterization is illustrated in a schematic scenario of a proton-nucleus collision. The role of randomness under constraint is also illustrated in the nucleus-nucleus case. (authors)

  2. Emission of complex fragments in the reaction Ar+Au at 44 and 77 A.MeV

    International Nuclear Information System (INIS)

    Sokolov, A.; Guerreau, D.; Jiang, D.X.; Cramer, B.; Ingold, G.; Gatty, B.; Lott, B.; Piasecki, E.

    1992-01-01

    Complex fragment emission from the 44 and 77 A.MeV 40 Ar + 197 Au reaction was investigated, and complex fragments have been detected, together with the associated neutron multiplicity distributions, and are seen to be preferentially emitted in violent collisions. Equilibrium and non-equilibrium components were identified which are discussed in terms of statistical emission from the hot target-like fragment and of a possible persistence of a deep-inelastic process. (R.P.) 45 refs.; 16 figs.; 1 tab

  3. Electrochemical reactions of uranyl(VI) complexes in aqueous solution, non-aqueous solvents, and ionic liquids

    International Nuclear Information System (INIS)

    Ikeda, Yasuhisa

    2006-01-01

    Author's recent experimental results on the chemistry of U(V) in aqueous solution, non-aqueous solvents, and ionic solvents by cyclic voltametry are described. The U(V) was produced by electrochemical reduction of uranyl U(VI) ions or complexes such as carbonates, DMF(N, N-dimethylformamide), DMSO(dimethylsulfoxide), acetylacetonato, and other organic polydental ligands. The produced U(V) complexes were studied by spectrophotometry using optical-transmission thin-layer electrode. The U(V) complexes in non-aqueous solvents were found to be rather stable, they undergo ligand-dissociation reaction but not disproportionation reaction. The structure and electronic spectra as well as IR spectra of the complexes were studied. The present method was further developed to study the behavior of U(V) complexes in ionic liquids as molten salts, e.g., alkaline metals chlorides. Thus, the present research contributes to understanding the chemistry of 5fl system. Application to such nuclear technology as spent fuel reprocessing is discussed. (S. Ohno)

  4. The complex transfer reaction (14C, 15O) on Ni, Zn and Ge targets: existence and mass of 69Ni

    International Nuclear Information System (INIS)

    Dessagne, P.; Bernas, M.; Langevin, M.; Pougheon, F.; Roussel, P.; Morrison, G.C.

    1984-01-01

    The ( 14 C, 15 O) complex transfer reaction has been studied at 72 MeV incident energy on 58 Ni, 60 Ni, 62 Ni, 64 Ni, 68 Zn, 70 Zn and 74 Ge, 76 Ge targets. Spectra and differential cross sections have been measured in a 5 0 angular range centred around a laboratory angle of 6 0 . The nucleus 69 Ni has been observed and its mass determined for the first time

  5. Kinetic modeling of electron transfer reactions in photosystem I complexes of various structures with substituted quinone acceptors.

    Science.gov (United States)

    Milanovsky, Georgy E; Petrova, Anastasia A; Cherepanov, Dmitry A; Semenov, Alexey Yu

    2017-09-01

    The reduction kinetics of the photo-oxidized primary electron donor P 700 in photosystem I (PS I) complexes from cyanobacteria Synechocystis sp. PCC 6803 were analyzed within the kinetic model, which considers electron transfer (ET) reactions between P 700 , secondary quinone acceptor A 1 , iron-sulfur clusters and external electron donor and acceptors - methylviologen (MV), 2,3-dichloro-naphthoquinone (Cl 2 NQ) and oxygen. PS I complexes containing various quinones in the A 1 -binding site (phylloquinone PhQ, plastoquinone-9 PQ and Cl 2 NQ) as well as F X -core complexes, depleted of terminal iron-sulfur F A /F B clusters, were studied. The acceleration of charge recombination in F X -core complexes by PhQ/PQ substitution indicates that backward ET from the iron-sulfur clusters involves quinone in the A 1 -binding site. The kinetic parameters of ET reactions were obtained by global fitting of the P 700 + reduction with the kinetic model. The free energy gap ΔG 0 between F X and F A /F B clusters was estimated as -130 meV. The driving force of ET from A 1 to F X was determined as -50 and -220 meV for PhQ in the A and B cofactor branches, respectively. For PQ in A 1A -site, this reaction was found to be endergonic (ΔG 0  = +75 meV). The interaction of PS I with external acceptors was quantitatively described in terms of Michaelis-Menten kinetics. The second-order rate constants of ET from F A /F B , F X and Cl 2 NQ in the A 1 -site of PS I to external acceptors were estimated. The side production of superoxide radical in the A 1 -site by oxygen reduction via the Mehler reaction might comprise ≥0.3% of the total electron flow in PS I.

  6. Organoplatinum complex promoted the asymmetric endo stereochemically controlled Diels-Alder reaction between 3-diphenylphosphinofuran and diphenylvinylphosphine.

    Science.gov (United States)

    Liu, Fengli; Pullarkat, Sumod A; Tan, Kien-Wee; Li, Yongxin; Leung, Pak-Hing

    2009-12-07

    The organoplatinum complex containing ortho-metalated (R)-(1-(dimethylamino)ethyl)-naphthalene as the chiral auxiliary has been used efficiently to promote the asymmetric [4 + 2] Diels-Alder reaction between diphenylvinylphosphine and 3-diphenylphosphinofuran to generate two chelating diphosphine endocycloadducts in the ratio 17:1. The absolute configurations of the three newly generated stereocenters have been assigned by single-crystal X-ray analysis.

  7. Metal–Organic Frameworks Stabilize Mono(phosphine)–Metal Complexes for Broad-Scope Catalytic Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Sawano, Takahiro; Lin, Zekai; Boures, Dean; An, Bing; Wang, Cheng; Lin, Wenbin (UC); (Xiamen)

    2016-08-10

    Mono(phosphine)–M (M–PR3; M = Rh and Ir) complexes selectively prepared by postsynthetic metalation of a porous triarylphosphine-based metal–organic framework (MOF) exhibited excellent activity in the hydrosilylation of ketones and alkenes, the hydrogenation of alkenes, and the C–H borylation of arenes. The recyclable and reusable MOF catalysts significantly outperformed their homogeneous counterparts, presumably via stabilizing M–PR3 intermediates by preventing deleterious disproportionation reactions/ligand exchanges in the catalytic cycles.

  8. Nucleophilic reactions of hydrazido(2-) complexes of molybdenum and tungsten with succinyl dichloride and phenyl isocyanate

    International Nuclear Information System (INIS)

    Iwanami, Kiyotaka; Mizobe, Yasushi; Takahashi, Tamotsu; Kodama, Teruyuki; Uchida, Yasuzo

    1981-01-01

    Nucleophilic attack of the WNNH 2 group in the hydrazido(2-) complex [WF(NNH 2 )(dpe) 2 ][BF 4 ] (dpe = Ph 2 PCH 2 CH 2 PPh 2 ) on succinyl dichloride gives a novel ethanedioylhydrazido(2-) complex, [WF(NNCOCH 2 CH 2 CO)(dpe) 2 ][BF 4 ]. X-Ray structural analysis shows that the carbon, nitrogen, and oxygen atoms of the ethanedioylhydrazido(2-) ligand lie nearly in the same plane, indicating sp 2 character of the nitrogen atom bearing the two carbonyl groups. Phenyl isocyanate also undergoes nucleophilic attack by the hydrazido(2-) complex [MBr(NNH 2 )(dpe) 2 ]Br (M = Mo or W) to yield the phenylsemicarbazido(2-) type complex, [MBr(NNHCONHPh)(dpe) 2 ]Br. Treatment of the semicarbazido(2-) complex with triethylamine gives a new diazenido complex [MBr(NNCONHPh)(dpe) 2 ]. (author)

  9. Influence of Proton Acceptors on the Proton-Coupled Electron Transfer Reaction Kinetics of a Ruthenium-Tyrosine Complex.

    Science.gov (United States)

    Lennox, J Christian; Dempsey, Jillian L

    2017-11-22

    A polypyridyl ruthenium complex with fluorinated bipyridine ligands and a covalently bound tyrosine moiety was synthesized, and its photo-induced proton-coupled electron transfer (PCET) reactivity in acetonitrile was investigated with transient absorption spectroscopy. Using flash-quench methodology with methyl viologen as an oxidative quencher, a Ru 3+ species is generated that is capable of initiating the intramolecular PCET oxidation of the tyrosine moiety. Using a series of substituted pyridine bases, the reaction kinetics were found to vary as a function of proton acceptor concentration and identity, with no significant H/D kinetic isotope effect. Through analysis of the kinetics traces and comparison to a control complex without the tyrosine moiety, PCET reactivity was found to proceed through an equilibrium electron transfer followed by proton transfer (ET-PT) pathway in which irreversible deprotonation of the tyrosine radical cation shifts the ET equilibrium, conferring a base dependence on the reaction. Comprehensive kinetics modeling allowed for deconvolution of complex kinetics and determination of rate constants for each elementary step. Across the five pyridine bases explored, spanning a range of 4.2 pK a units, a linear free-energy relationship was found for the proton transfer rate constant with a slope of 0.32. These findings highlight the influence that proton transfer driving force exerts on PCET reaction kinetics.

  10. How computational methods and relativistic effects influence the study of chemical reactions involving Ru-NO complexes?

    Science.gov (United States)

    Orenha, Renato Pereira; Santiago, Régis Tadeu; Haiduke, Roberto Luiz Andrade; Galembeck, Sérgio Emanuel

    2017-05-05

    Two treatments of relativistic effects, namely effective core potentials (ECP) and all-electron scalar relativistic effects (DKH2), are used to obtain geometries and chemical reaction energies for a series of ruthenium complexes in B3LYP/def2-TZVP calculations. Specifically, the reaction energies of reduction (A-F), isomerization (G-I), and Cl - negative trans influence in relation to NH 3 (J-L) are considered. The ECP and DKH2 approaches provided geometric parameters close to experimental data and the same ordering for energy changes of reactions A-L. From geometries optimized with ECP, the electronic energies are also determined by means of the same ECP and basis set combined with the computational methods: MP2, M06, BP86, and its derivatives, so as B2PLYP, LC-wPBE, and CCSD(T) (reference method). For reactions A-I, B2PLYP provides the best agreement with CCSD(T) results. Additionally, B3LYP gave the smallest error for the energies of reactions J-L. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  11. Characterization and reaction studies of dimeric molybdenum(III) complexes with bridging dithiolate ligands. Catalytic reduction of acetylene to ethylene

    International Nuclear Information System (INIS)

    DuBois, M.R.; Haltiwanger, R.C.; Miller, D.J.; Glatzmaier, G.

    1979-01-01

    The complexes [C 5 H 5 MoSC/sub n/H/sub 2n/S] 2 (where n = 2 and 3) have been prepared by the reaction of ethylene sulfide and propylene sulfide, respectively, with C 5 H 5 MoH(CO) 3 or with [C 5 H 5 Mo(CO) 3 ] 2 . Cyclic voltammetry shows that each complex undergoes two reversible oxidations at 0.13 and 0.79 V vs. SCE (in acetonitrile with 0.1 M Bu 4 NBF 4 ). Both the one-electron and two-electron oxidation products have been synthesized and characterized by spectral and magnetic data. Electrochemical data for the oxidized complexes support the conclusion that the complexes have the same gross structural features in all three oxidation states. A single crystal of the monocation [C 5 H 5 MoSC 3 H 6 S] 2 BF 4 has been characterized by an x-ray diffraction study. The compound crystallizes in the space group C2/c with a = 18.266 (1) A, b = 9.206 (4) A, c = 12.911 (5) A, β = 100.83 (3) 0 , and V = 2128 A 3 . The metal ions of the cation are bridged by two 1,2-propanedithiolate ligands. The four sulfur atoms of these ligands form a plane which bisects the metal-metal distance. The neutral dimeric complexes undergo a unique reaction with alkenes and alkynes in which the hydrocarbon portion of the bridging dithiolate ligands is exchanged. The reaction has been characterized with olefinswith both electron-withdrawing and electron-donating substituents. When [C 5 H 5 MoSC 2 H 4 S] 2 (1) is reacted with acetylene at 25 0 C, ethene is produced and the complex [C 5 H 5 MoSC 2 H 2 S] 2 is isolated. The latter complex is reduced by hydrogen (2 atm) at 60 0 C to re-form 1. The utility of these reactions in the catalytic reduction of acetylene to ethylene has been investigated. The role of the sulfur ligands in this catalytic cycle is discussed. 50 references, 2 figures, 5 tables

  12. Reaction of Non-Symmetric Schiff Base Metallo-Ligand Complexes Possessing an Oxime Function with Ln Ions

    Directory of Open Access Journals (Sweden)

    Jean-Pierre Costes

    2018-03-01

    Full Text Available The preparation of non-symmetric Schiff base ligands possessing one oxime function that is associated to a second function such as pyrrole or phenol function is first described. These ligands, which possess inner N4 or N3O coordination sites, allow formation of cationic or neutral non-symmetric CuII or NiII metallo-ligand complexes under their mono- or di-deprotonated forms. In presence of Lanthanide ions the neutral complexes do not coordinate to the LnIII ions, the oxygen atom of the oxime function being only hydrogen-bonded to a water molecule that is linked to the LnIII ion. This surprising behavior allows for the isolation of LnIII ions by non-interacting metal complexes. Reaction of cationic NiII complexes possessing a protonated oxime function with LnIII ions leads to the formation of original and dianionic (Gd(NO352− entities that are well separated from each other. This work highlights the preparation of well isolated mononuclear LnIII entities into a matrix of diamagnetic metal complexes. These new complexes complete our previous work dealing with the complexing ability of the oxime function toward Lanthanide ions. It could open the way to the synthesis of new entities with interesting properties, such as single-ion magnets for example.

  13. Aqueous Complexation Reactions Governing the Rate and Extent of Biogeochemical U(VI) Reduction

    International Nuclear Information System (INIS)

    Scott C. Brooks; Wenming Dong; Sue Carroll; James K. Fredrickson; Kenneth M. Kemner; Shelly D. Kelly

    2006-01-01

    The proposed research will elucidate the principal biogeochemical reactions that govern the concentration, chemical speciation, and reactivity of the redox-sensitive contaminant uranium. The results will provide an improved understanding and predictive capability of the mechanisms that govern the biogeochemical reduction of uranium in subsurface environments. In addition, the work plan is designed to: (1) Generate fundamental scientific understanding on the relationship between U(VI) chemical speciation and its susceptibility to biogeochemical reduction reactions. (2) Elucidate the controls on the rate and extent of contaminant reactivity. (3) Provide new insights into the aqueous and solid speciation of U(VI)/U(IV) under representative groundwater conditions

  14. The first experimental confirmation of the fractional kinetics containing the complex-power-law exponents: Dielectric measurements of polymerization reactions

    Science.gov (United States)

    Nigmatullin, R. R.; Arbuzov, A. A.; Salehli, F.; Giz, A.; Bayrak, I.; Catalgil-Giz, H.

    2007-01-01

    For the first time we achieved incontestable evidence that the real process of dielectric relaxation during the polymerization reaction of polyvinylpyrrolidone (PVP) is described in terms of the fractional kinetic equations containing complex-power-law exponents. The possibility of the existence of the fractional kinetics containing non-integer complex-power-law exponents follows from the general theory of dielectric relaxation that has been suggested recently by one of the authors (R.R.N). Based on the physical/geometrical meaning of the fractional integral with complex exponents there is a possibility to develop a general theory of dielectric relaxation based on the self-similar (fractal) character of the reduced (averaged) microprocesses that take place in the mesoscale region. This theory contains some essential predictions related to existence of the non-integer power-law kinetics and the results of this paper can be considered as the first confirmation of existence of the kinetic phenomena that are described by fractional derivatives with complex-power-law exponents. We want to stress here that with the help of a new complex fitting function for the complex permittivity it becomes possible to describe the whole process for real and imaginary parts simultaneously throughout the admissible frequency range (30 Hz-13 MHz). The fitting parameters obtained for the complex permittivity function for three temperatures (70, 90 and 110 °C) confirm in general the picture of reaction that was known qualitatively before. They also reveal some new features, which improve the interpretation of the whole polymerization process. We hope that these first results obtained in the paper will serve as a good stimulus for other researches to find the traces of the existence of new fractional kinetics in other relaxation processes unrelated to the dielectric relaxation. These results should lead to the reconsideration and generalization of irreversibility and kinetic phenomena that

  15. pincer complex in Suzuki–Miyaura cross-coupling reaction under

    Indian Academy of Sciences (India)

    The recent focus of interest on pincer complexes is due to their extended utility in the field of homogeneous catalysis.1 Pincer complexes offer interesting possibili- ties both in terms of mechanistic understanding and cat- alytic performance.1b The high catalytic efficiency is attributed to the stable and compact geometry of the.

  16. Simple reactions to nearby neighbours and complex social behaviour in primates

    NARCIS (Netherlands)

    Hemelrijk, Charlotte; Menzel, Randolf; Fischer, Julia

    Compared to many other animal taxa, the social behavior of primates is generally regarded to be more complex in its patterns and underlying cognition. This complexity has often been overestimated, because the same patterns of social behavior are found in taxa that are supposed to be cognitively less

  17. Organoruthenium (II) complexes produced by insertion reactions of substituted olefins into a hydrido-ruthenium bond

    Energy Technology Data Exchange (ETDEWEB)

    Hiraki, Katsuma; Sasada, Yoko; Kitamura, Tsuneyuki [Nagasaki Univ. (Japan)

    1980-04-01

    Dimethyl fumarate, 2-vinylpyridine, and acrylonitrile insert into a H-Ru bond of (RuClH(CO)(PPh/sub 3/)/sub 3/) (1) to yield new substituted alkylruthenium(II) complexes. Methyl sorbate also reacted with 1 to give a new substituted eta/sup 3/-allylruthenium(II) complex.

  18. Mathematical treatment of isotopologue and isotopomer speciation and fractionation in biochemical kinetics

    Science.gov (United States)

    Maggi, Federico; Riley, William J.

    2010-03-01

    We present a mathematical treatment of the kinetic equations that describe isotopologue and isotopomer speciation and fractionation during enzyme-catalyzed biochemical reactions. These equations, presented here with the name GEBIK (general equations for biochemical isotope kinetics) and GEBIF (general equations for biochemical isotope fractionation), take into account microbial biomass and enzyme dynamics, reaction stoichiometry, isotope substitution number, and isotope location within each isotopologue and isotopomer. In addition to solving the complete GEBIK and GEBIF, we also present and discuss two approximations to the full solutions under the assumption of biomass-free and enzyme steady-state, and under the quasi-steady-state assumption as applied to the complexation rate. The complete and approximate approaches are applied to observations of biological denitrification in soils. Our analysis highlights that the full GEBIK and GEBIF provide a more accurate description of concentrations and isotopic compositions of substrates and products throughout the reaction than do the approximate forms. We demonstrate that the isotopic effects of a biochemical reaction depend, in the most general case, on substrate and complex concentrations and, therefore, the fractionation factor is a function of time. We also demonstrate that inverse isotopic effects can occur for values of the fractionation factor smaller than 1, and that reactions that do not discriminate isotopes do not necessarily imply a fractionation factor equal to 1.

  19. Development of indirect spectrophotometric method for quantification of cephalexin in pure form and commercial formulation using complexation reaction

    International Nuclear Information System (INIS)

    Khan, M.N.; Hussain, R.; Kalsoom, S.; Saadiq, M.

    2016-01-01

    A simple, accurate and indirect spectrophotometric method was developed for the quantification of cephalexin in pure form and pharmaceutical products using complexation reaction. The developed method is based on the oxidation of the cephalexin with Fe/sup 3+/ in acidic medium. Then 1, 10- phenanthroline reacts with Fe/sup 2+/ and a red colored complex was formed. The absorbance of the complex was measured at 510 nm by spectrophotometer. Different experimental parameters affecting the complexation reactions were studied and optimized. Beer law was obeyed in the concentration range 0.4 -10 micro gmL/sup -1/ with a good correlation of 0.992. The limit of detection and limit of quantification were found to be 0.065 micro gmL/sup -1/ and 0.218 micro gmL/sup -1/ , respectively. The method have good reproducibility with a relative standard deviation of 6.26 percent (n = 6). The method was successfully applied for the determination of cephalexin in bulk powder and commercial formulation. Percent recoveries were found to range from 95.47 to 103.87 percent for the pure form and 98.62 to 103.35 percent for commercial formulations. (author)

  20. Aqueous complexation reactions governing the rate and extent of biogeochemical U(VI) reduction

    International Nuclear Information System (INIS)

    Kemner, K.M.; Kelly, S.D.; Brooks, Scott C.; Dong, Wenming; Carroll, Sue; Fredrickson, James K.

    2006-01-01

    The proposed research will elucidate the principal biogeochemical reactions that govern the concentration, chemical speciation, and reactivity of the redox-sensitive contaminant uranium. The results will provide an improved understanding and predictive capability of the mechanisms that govern the biogeochemical reduction of uranium in subsurface environments

  1. Investigations of nuclear structure and nuclear reactions induced by complex projectiles

    International Nuclear Information System (INIS)

    Sarantites, D.G.

    1993-01-01

    This is a progress report on activities of the Washington University group in nuclear reaction studies for the period Sept 1, 1992 to Aug 31, 1993. This group has a research program which touches five areas of nuclear physics: nuclear structure studies at high spin; studies at the interface between structure and reactions; production and study of hot nuclei; reaction mechanism studies; development and use of novel techniques and instrumentation in the above areas of research. Specific activities of the group include in part: superdeformation in 82 Sr; structure of and identical bands in 182 Hg and 178 Pt; a highly deformed band in 136 Pm; particle decay of the 164 Yb compound nucleus; fusion reactions; proton evaporation; two-proton decay of 12 O; modeling and theoretical studies; excited 16 O disassembly into four alpha particles; 209 Bi + 136 Xe collisions at 28.2 MeV/amu; and development work on 4π solid angle gamma detectors, and x-ray detectors

  2. Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc1 Complex

    DEFF Research Database (Denmark)

    Barragan, Angela M; Schulten, Klaus; Solov'yov, Ilia A

    2016-01-01

    , the quinol-protein interaction, which initiates the Q-cycle, has not yet been completely described. Furthermore, the initial charge transfer reactions of the Q-cycle lack a physical description. The present investigation utilizes classical molecular dynamics simulations in tandem with quantum density...

  3. Insights into the Halogen Oxidative Addition Reaction to Dinuclear Gold(I) Di(NHC) Complexes

    KAUST Repository

    Baron, Marco; Tubaro, Cristina; Basato, Marino; Isse, Abdirisak Ahmed; Gennaro, Armando; Cavallo, Luigi; Graiff, Claudia; Dolmella, Alessandro; Falivene, Laura; Caporaso, Lucia

    2016-01-01

    Gold(I) dicarbene complexes [Au2(MeIm-Y-ImMe)2](PF6)2(Y=CH2(1), (CH2)2(2), (CH2)4(4), MeIm=1-methylimidazol-2-ylidene) react with iodine to give the mixed-valence complex [Au(MeIm-CH2-ImMe)2AuI2](PF6)2(1 aI) and the gold(III) complexes [Au2I4(Me

  4. Reactivity of N-heterocyclic carbene-pyridine palladacyclopentadiene complexes toward halogen addition. The unpredictable course of the reaction.

    Science.gov (United States)

    Visentin, Fabiano; Santo, Claudio; Scattolin, Thomas; Demitri, Nicola; Canovese, Luciano

    2017-08-08

    As an extension of a previously published work we have reacted some palladacyclopentadiene complexes stabilized by bidentate N-heterocyclic carbene-pyridine or monodentate N-heterocyclic carbene-pyridine and isocyanide ligands with the halogens I 2 and Br 2 . All the bidentate and monodentate complexes react with halogens to give at first the expected σ-coordinated butadienyl fragment. However, two of the less hindered NHC carbene-pyridine bidentate butadienyl iodo derivatives undergo a further rearrangement and novel Pd(ii) complexes characterized by a ten term coordinative ring were isolated and characterized. In the most favorable case we were able to carry out the kinetics of rearrangement and measure its reaction rate. Moreover, we have surmised a plausible mechanism on the basis of a dedicated computational approach and in one case the surprising structure characterized by the ten term coordinative ring was resolved by X-ray diffraction.

  5. Synthesis and substitution reactions of palladium(II) complexes with 2,2'-Bipyridine and 1,10-Phenanthroline

    International Nuclear Information System (INIS)

    Zaghal, M. H.; Al-Lawatia, S.

    1996-01-01

    The complexes cis-[Pd (Nn)CI 2 ] [Nn=2,2'-bipyridine (b py) and 1,10-phenanthroline (phen)] have been prepared via a new method by reacting the benzonitrile complex cis-[Pd(Ph CN) 2 CI 2 ] with the ligands. This method gives the products rapidly, in a pure state and in high yields. The substitution reactions of cis-[Pd(Nn)CI 2 ] (Nn=b py and phen) with Br - and I - have been attempted. The complexes cis-[Pd(Nn)X 2 ] (Nn=b py or phen; X Br, I) have been isolated. The products have been characterized by elemental analysis, conductivity measurements, and infrared, electronics absorption and 1 H NMR spectra. (authors). 26 refs., 1 tab

  6. Hemoglobin and Myoglobin as Reducing Agents in Biological Systems. Redox Reactions of Globins with Copper and Iron Salts and Complexes.

    Science.gov (United States)

    Postnikova, G B; Shekhovtsova, E A

    2016-12-01

    In addition to reversible O2 binding, respiratory proteins of the globin family, hemoglobin (Hb) and myoglobin (Mb), participate in redox reactions with various metal complexes, including biologically significant ones, such as those of copper and iron. HbO 2 and MbO 2 are present in cells in large amounts and, as redox agents, can contribute to maintaining cell redox state and resisting oxidative stress. Divalent copper complexes with high redox potentials (E 0 , 200-600 mV) and high stability constants, such as [Cu(phen) 2 ] 2+ , [Cu(dmphen) 2 ] 2+ , and CuDTA oxidize ferrous heme proteins by the simple outer-sphere electron transfer mechanism through overlapping π-orbitals of the heme and the copper complex. Weaker oxidants, such as Cu2+, CuEDTA, CuNTA, CuCit, CuATP, and CuHis (E 0 ≤ 100-150 mV) react with HbO 2 and MbO 2 through preliminary binding to the protein with substitution of the metal ligands with protein groups and subsequent intramolecular electron transfer in the complex (the site-specific outer-sphere electron transfer mechanism). Oxidation of HbO 2 and MbO 2 by potassium ferricyanide and Fe(3) complexes with NTA, EDTA, CDTA, ATP, 2,3-DPG, citrate, and pyrophosphate PP i proceeds mainly through the simple outer-sphere electron transfer mechanism via the exposed heme edge. According to Marcus theory, the rate of this reaction correlates with the difference in redox potentials of the reagents and their self-exchange rates. For charged reagents, the reaction may be preceded by their nonspecific binding to the protein due to electrostatic interactions. The reactions of LbO 2 with carboxylate Fe complexes, unlike its reactions with ferricyanide, occur via the site-specific outer-sphere electron transfer mechanism, even though the same reagents oxidize structurally similar MbO 2 and cytochrome b 5 via the simple outer-sphere electron transfer mechanism. Of particular biological interest is HbO 2 and MbO 2 transformation into met-forms in the presence

  7. Electron transfer reactions in some complexes of V+2, Co+3 and Eu+3

    International Nuclear Information System (INIS)

    Lellis, F.T.P.

    1983-01-01

    The stability constants β 1 , β 2 , β 3 for the mono-,bis-and tris-substituted complexes from vanadium (III) ions with the pyridine-2-carboxilate liquid are determined potentiometrically. The tris-substituted complex in aqueous solutions by electronic spectra and reversible cyclic voltammetry using gold electrodes is extensively characterized. In the investigation of electron tranfer kinetics involving mild oxidizing complexes, such as Co(NH 3 ) 3+ 6 , Co(en) 3+ 3 , Co(en) 2 gly 2+ , Co (histidinate) + 2 , Ru(NH 3 ) 3+ 6 and Eu 3+ ions, the tris (picolinate) vanadate (III) complex is used. Electron transfer kinetics for the Eu 3+ / 2+ couple in terms of a pseudo-first order process is analysed. The results, in terms of a tunneling mechanism, involving a set of similar, nuclear coordinates for the reactants and products, are explained. (M.J.C.) [pt

  8. Ouroboros - Playing A Biochemical

    Directory of Open Access Journals (Sweden)

    D. T. Rodrigues

    2014-08-01

    Full Text Available Ouroboros: Playing A Biochemical RODRIGUES,D.T.1,2;GAYER, M.C.1,2; ESCOTO, D.F.1; DENARDIN, E.L.G.2, ROEHRS, R.1,2 1Interdisciplinary Research Group on Teaching Practice, Graduate Program in Biochemistry, Unipampa, RS, Brazil 2Laboratory of Physicochemical Studies and Natural Products, Post Graduate Program in Biochemistry, Unipampa, RS, Brazil Introduction: Currently, teachers seek different alternatives to enhance the teaching-learning process. Innovative teaching methodologies are increasingly common tools in educational routine. The use of games, electronic or conventional, is an effective tool to assist in learning and also to raise the social interaction between students. Objective: In this sense our work aims to evaluate the card game and "Ouroboros" board as a teaching and learning tool in biochemistry for a graduating class in Natural Sciences. Materials and methods: The class gathered 22 students of BSc in Natural Sciences. Each letter contained a question across the board that was drawn to a group to answer within the allotted time. The questions related concepts of metabolism, organic and inorganic chemical reactions, bioenergetics, etc.. Before the game application, students underwent a pre-test with four issues involving the content that was being developed. Soon after, the game was applied. Then again questions were asked. Data analysis was performed from the ratio of the number of correct pre-test and post-test answers. Results and discussion: In the pre-test 18.1% of the students knew all issues, 18.1% got 3 correct answers, 40.9% answered only 2 questions correctly and 22.7% did not hit any. In post-test 45.4% answered all the questions right, 31.8% got 3 questions and 22.7% got 2 correct answers. The results show a significant improvement of the students about the field of content taught through the game. Conclusion: Generally, traditional approaches of chemistry and biochemistry are abstract and complex. Thus, through games

  9. Investigations of nuclear structure and nuclear reactions induced by complex projectiles

    International Nuclear Information System (INIS)

    Sarantites, D.G.

    1986-01-01

    The research conducted by the program is: (1) to investigate in detail the role of energy and angular momentum dissipation in the mechanisms of subbarrier fusion, in fusion at and above the barrier, in quasi-elastic and in strongly damped reactions of heavy ions; (2) to extend the above reaction mechanism studies in the regime of 10 to 50 MeV/amu employing techniques of complete detection including γ-rays, light charged particles, neutrons and heavy ions in real or kinematic 4π counting when possible; (3) the study of structural and shape changes of nuclei at very high spins and excitations; and (4) the development and use of novel techniques and instrumentation in the above studies. 76 refs., 27 figs

  10. Chemistry by nanocatalysis: First example of a solid-supported RAPTA complex for organic reactions in aqueous medium

    KAUST Repository

    García-Garrido, Sergio E.

    2010-11-18

    A ruthenium-arene-PTA (RAPTA) complex has been supported for the first time on an inorganic solid, that is, silica-coated ferrite nanoparticles. The resulting magnetic material proved to be a general, very efficient and easily reusable catalyst for three synthetically useful organic transformations; selective nitrile hydration, redox isomerization of allylic alcohols, and heteroannulation of (Z)-enynols. The use of low metal concentration, environmentally friendly water as a reaction medium, with no use at all of organic solvent during or after the reactions, and microwaves as an alternative energy source renders the synthetic processes reported herein "truly" green and sustainable. RAPTA\\'s delight: A nano-RAPTA complex supported on silica-coated ferrite nanoparticles proved to be a general, very efficient and easily reusable catalyst for three synthetically useful organic transformations; selective nitrile hydration, redox isomerization of allylic alcohols, and heteroannulation of (Z)-enynols. The use of low metal concentrations, water as a reaction medium, and microwaves as an energy source renders these processes green and sustainable. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Cell phone ringtone, but not landline phone ringtone, affects complex reaction time

    OpenAIRE

    Radosław Zajdel; Justyna Zajdel; Janusz Śmigielski; Dariusz Nowak

    2013-01-01

    Introduction: Legislation systems of most countries prohibited using the handheld mobile phone while driving due to the fact that it disturbs concentration and causes hand involvement. Every phone owner is accustomed to the ringtone of his phone and almost involuntarily endeavors to pick it up or check who calls. This engages one’s psychomotor skills, which in our opinion contributes to the attenuation of reaction time needed for performing other crucial functions. Objectives: The aim of the ...

  12. Some Reactions of Dinitrogen Complexes of Aryldicyclopentadienyl Titanium(III) Compounds

    NARCIS (Netherlands)

    Weij, F.W. van der; Teuben, J.H.

    1976-01-01

    The reduction of dinitrogen to NH3 and N2H4 upon thermolysis of (Cp2TiR)2N2 (R = C6H5, m-, p-CH3C6H4, CH2C6H5) is reported. The amounts of NH3 obtained from the reactions of (Cp2TiR)2N2 with sodium naphthalene, n-BuLi and i-PrMgCl are discussed.

  13. Investigations of nuclear structure and nuclear reactions induced by complex projectiles

    International Nuclear Information System (INIS)

    Sarantites, D.G.

    1992-01-01

    The research program described touches five areas of nuclear physics: nuclear structure studies at high spin (hyperdeformation in the mass A ≅ 182 region, structure of 182 Hg and 182 Au at high spin, a highly deformed band in 136 Pm and the anomalous h 11/2 proton crossing in the A∼135 superdeformed region), studies at the interface between structure and reactions (population of entry states in heavy-ion fusion reactions, nuclear structure effects in proton evaporation spectra, nuclear structure- dependent entry state population by total spectroscopy, entrance channel effects in fusion near the barrier, lifetimes of subbarrier α particles by the atomic clock method), production and study of hot nuclei (the statistical model evaporation code EVAP, statistical emission of deuterons and tritons from highly excited compound nuclei, heavy-fragment emission as a probe of the thermal properties of highly excited compound nuclei, use of incoming-wave boundary condition transmission coefficients in the statistical model: implications in the particle evaporation spectra, study of transparency in the optical model), reaction mechanism studies (binary character of highly dissipative 209 Bi + 136 Xe collisions at E/A=28.2 MeV), and development and use of novel techniques and instrumentation in these areas of research (including a 4π channel selection device, a novel x-ray detector, and a simple channel-selecting detector)

  14. Biochemical Hypermedia: Galactose Metabolism.

    Directory of Open Access Journals (Sweden)

    J.K. Sugai

    2013-05-01

    Full Text Available Introduction: Animations of biochemical processes and virtual laboratory environments lead to true molecular simulations. The use of interactive software’s in education can improve cognitive capacity, better learning and, mainly, it makes information acquisition easier. Material and Methods: This work presents the development of a biochemical hypermedia to understanding of the galactose metabolism. It was developed with the help of concept maps, ISIS Draw, ADOBE Photoshop and FLASH MX Program. Results and Discussion: A step by step animation process shows the enzymatic reactions of galactose conversion to glucose-1-phosphate (to glycogen synthesis, glucose-6-phosphate (glycolysis intermediary, UDP-galactose (substrate to mucopolysaccharides synthesis and collagen’s glycosylation. There are navigation guide that allow scrolling the mouse over the names of the components of enzymatic reactions of via the metabolism of galactose. Thus, explanatory text box, chemical structures and animation of the actions of enzymes appear to navigator. Upon completion of the module, the user’s response to the proposed exercise can be checked immediately through text box with interactive content of the answer. Conclusion: This hypermedia was presented for undergraduate students (UFSC who revealed that it was extremely effective in promoting the understanding of the theme.

  15. Electron transfer reactions of ruthenium(II) complexes with polyphenolic acids in micelles

    Energy Technology Data Exchange (ETDEWEB)

    Rajeswari, Angusamy [School of Chemistry, Madurai Kamaraj University, Madurai 625 021 (India); Department of Chemistry, Fatima College, Madurai 625 018 (India); Ramdass, Arumugam [School of Chemistry, Madurai Kamaraj University, Madurai 625 021 (India); Research Department of Chemistry, Aditanar College of Arts and Science, Tiruchendur 628 216 (India); Muthu Mareeswaran, Paulpandian [School of Chemistry, Madurai Kamaraj University, Madurai 625 021 (India); Department of Industrial Chemistry, Alagappa University, Karaikudi 630 003 (India); Rajagopal, Seenivasan, E-mail: rajagopalseenivasan@yahoo.com [School of Chemistry, Madurai Kamaraj University, Madurai 625 021 (India)

    2016-02-15

    The electron transfer in a microhetrogeneous system is a perfect mimic of biological electron transfer. The electron transfer between biologically important phenolic acids and ruthenium (II) complexes is systematically studied in the presence of anionic and cationic micelles. The photophysical properties of these ruthenium (II) complexes with anionic and cationic micelles and their binding abilities with these two type of micelles are also studies using absorption, emission and excited state lifetime spectral techniques. Pseudophase Ion Exchange (PIE) Model is applied to derive mechanism of electron transfer in two types of micelles. - Highlights: • Effect of microhetrogeneous system is studied using ruthenium (II) complexes and gallic acid is studied. • Pseudophase Ion exchange model is applied to derive the mechanism. • Binding constants are in the range of 10{sup 2}–10{sup 4} M{sup −1}.

  16. Reduced Graphene Oxide-Immobilized Tris(bipyridine)ruthenium(II) Complex for Efficient Visible-Light-Driven Reductive Dehalogenation Reaction.

    Science.gov (United States)

    Li, Xiaoyan; Hao, Zhongkai; Zhang, Fang; Li, Hexing

    2016-05-18

    A sodium benzenesulfonate (PhSO3Na)-functionalized reduced graphene oxide was synthesized via a two-step aryl diazonium coupling and subsequent NaCl ion-exchange procedure, which was used as a support to immobilize tris(bipyridine)ruthenium(II) complex (Ru(bpy)3Cl2) by coordination reaction. This elaborated Ru(bpy)3-rGO catalyst exhibited excellent catalytic efficiency in visible-light-driven reductive dehalogenation reactions under mild conditions, even for ary chloride. Meanwhile, it showed the comparable reactivity with the corresponding homogeneous Ru(bpy)3Cl2 catalyst. This high catalytic performance could be attributed to the unique two-dimensional sheet-like structure of Ru(bpy)3-rGO, which efficiently diminished diffusion resistance of the reactants. Meanwhile, the nonconjugated PhSO3Na-linkage between Ru(II) complex and the support and the very low electrical conductivity of the catalyst inhibited energy/electron transfer from Ru(II) complex to rGO support, resulting in the decreased support-induced quenching effect. Furthermore, it could be easily recycled at least five times without significant loss of catalytic reactivity.

  17. Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR)

    Science.gov (United States)

    Laszlo, Kenneth J.; Bush, Matthew F.

    2015-12-01

    Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/ z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/ z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures.

  18. Studies of transfer reactions of photosensitized electrons involving complexes of transition metals in view of solar energy storage

    International Nuclear Information System (INIS)

    Takakubo, Masaaki

    1984-01-01

    This research thesis addresses electron transfer reactions occurring during photosynthesis, for example, photosensitized reaction in which chlorophyll is the sensitizer. More specifically, the author studied experimentally electron photo-transfers with type D sensitizers (riboflavin, phenoxazine and porphyrin), and various complexes of transition metals. After a presentation of these experiments, the author describes the photosensitisation process (photo-physics of riboflavin, oxygen deactivation, sensitized photo-oxidation and photo-reduction). The theoretical aspect of electron transfer is then addressed: generalities, deactivation of the riboflavin triplet, initial efficiency of electron transfer. Experimental results on three basic processes (non-radiative deactivation, energy transfer, electron transfer) are interpreted in a unified way by using the non-radiative transfer theory. Some applications are described: photo-electrochemical batteries, photo-oxidation and photo-reduction of the cobalt ion

  19. Quantum-chemical analysis of formation reactions of Со2+ complexes

    Directory of Open Access Journals (Sweden)

    Viktor F. Vargalyuk

    2017-11-01

    Full Text Available Based on the analysis of quantum chemical calculations results (GAMESS, density functional theory, B3LYP method as to coordination compounds of Co2+ions with H2O, NH3, OH–, F–, Cl–, Br–, I–, CN–, Ac–, Ak– generally given by [Co(H2O6–nLn]2+nx, it has been demonstrated that within the selected series of ligands, there is no correlation between the amount of energy of monosubstituted cobalt aqua complexes formation(∆Е and pK1,just like between the effective nuclear charge of the central atom (z*Со and pK1. According to the behavior of ∆Е and z*Со,we identified two groups of ligands. The first group (OH–, F–, Ac–, Ak–, CN–, NH3 demonstrates logical ∆Е decrease caused by the growth of z*Со. On the contrary, the second group (Cl–, Br–, I– demonstrates ∆Е increase caused by the growth of z*Со. This phenomenon is explained by the change in electronegativity and polarizability of donor atoms in groups and periods of the periodic table. It is established that linear correlations given by lgK = A + B·z*Со can be actualized only for complexes having ligands with similar donor atoms. Referring to the literature on stepwise complex formation of hydroxide, amine and chloride cobalt complexes in combination with z*Со calculations results, we determined A and B constants of lgK, z*Со-correlations for the atoms of oxygen (30.2, –17.7; nitrogen (125.4, –69.9 and chlorine (–6.3, 5.8. The existence of the detected correlation series enables us to lean on lgK,z*М–dependence parameters for the fixed donor atom and to determine Kn values for various complexes with complex-based ligands using calculations and z*М data. This applies to complexes having central atoms of the same nature as well as simple monodentate ligands. The mentioned approach was used to calculate the stability constants for acrylate cobalt complexes (lgK1 = 1.2 и lgК2 = 4.3, which are not covered in literature.

  20. Kinetic Modeling of Complex Catalytic Reactions Modélisation cinétique des réactions catalytiques complexes

    Directory of Open Access Journals (Sweden)

    Froment G. F.

    2006-11-01

    Full Text Available The paper deals with hydrocracking on metal-loaded zeolites. A fundamental approach is presented in which the detailed reaction network of the feed components of a complex feedstock is retained to a maximum extent. The kinetics are developed in terms of the elementary steps and single events involved in the reactions. Plausible assumptions and thermodynamic constraints limit the number of kinetic parameters. These do not depend on the chain length of the hydrocarbons and are not affected by the feed composition. Certainly, chemical analysis still imposes a certain degree of lumping of components and reaction networks, but not to the extent reflected by present day models. L'article traite de l'hydrocraquage sur des zéolites chargés en métaux. Dans l'approche fondamentale qui est présentée, le réseau de réaction des composants d'une charge complexe est retenu au maximum. La cinétique est établie en suivant pas à pas le déroulement et les étapes élémentaires des réactions. Des hypothèses plausibles et des contraintes thermodynamiques limitent le nombre de paramètres cinétiques. Ceux-ci ne dépendent pas de la longueur de la chaîne des hydrocarbures et ne sont pas affectés par la composition de la charge. L'analyse chimique impose bien sûr encore un certain agrégat des composants et des réseaux de réaction, mais moins que ne reflètent les modèles actuels.

  1. Stability and Reactivity of Cyclometallated Naphthylamine Complexes in Pd-C Bond Insertion Reactions with Coordinated Alkynylphosphanes

    KAUST Repository

    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.

  2. Reaction of aromatic diazonium salts with carrier-free radioiodine and astatine, evidence for complex formation

    International Nuclear Information System (INIS)

    Meyer, G.J.; Roessler, K.; Stoecklin, G.

    1979-01-01

    Systematic studies of the astatodiazoniation reaction and a comparison with iododediazoniation under comparable conditions are reported. The yields for all astatohalobenzenes and -toluenes were nearly constant and unaffected by the nature of the diazonium compound, its isomeric form, and the number of isomers used at the same time. Only astatofluorobenzenes were obtained at higher yields. An electron-transfer mechanism is proposed for dediazoniation at these low halide concentration levels. At sufficient thermal excitation levels the electron transfer leads to the dissociation of nitrogen, while the phenyl and halogen radicals recombine. The isomer distribution found for some of the derivatives from dediazoniation may also be due to steric effects

  3. Role of carbene complexes in initiation and chain propagation in double bond redistribution reactions

    International Nuclear Information System (INIS)

    Dolgoplosk, K.L.; Makovetskij, E.I.; Tinyakova, E.I.; Golenko, T.G.; Oreshkin, I.A.

    1976-01-01

    A study has been made of the role of carbene complexes of tungsten in initiation and propagation of the ring-opening polymerization of cycloolefins. Data are given on polymerization of cyclopentene and cycloocterdiene-1,5 in the presence of the system tungsten chloride-diazo-compound (DAC)

  4. Copper(II)–imida‐salen Complexes Encapsulated into NaY Zeolite for Oxidations Reactions

    DEFF Research Database (Denmark)

    Kuźniarska‐Biernacka, Iwona; Carvalho, M. Alice; Rasmussen, Søren Birk

    2013-01-01

    The oxidation of phenol, cychohexanol and hydroquinone has been screened in the presence of copper(II) complexes with the Schiff‐base salen ligand, 1,5‐bis[(E)‐5‐chloro‐2‐hydroxybenzylideneamino]‐1H‐imidazole‐4‐carbonitrile, and encapsulated into NaY zeolite by using two different methods. The new...

  5. A pulse radiolysis study of the formation and reactions of reduced metal EDTA complexes

    International Nuclear Information System (INIS)

    Buitenhuis, R.

    1977-01-01

    The construction of a computerized pulse radiolysis system with available means appropriate for the wavelength interval between 300 and 1000 nm is described. The investigation of the radiolysis of aqueous solutions of EDTA complexes in the presence of alcohols is discussed

  6. Study of the emission oxidative reactions of ruthenium (II) complex by cationic compounds in anionic micelles

    International Nuclear Information System (INIS)

    Bonilha, J.B.S.

    1985-01-01

    The oxidative quenching of the emission of the tetraanionic complex tris (4,4' dicarboxylate - 2,2' - bipyridine ruthenium (II) in aqueous solution, by both organic and inorganic compounds in presence of anionic detergents, above and below the critical micelle concentration is studied. The organic cations, the inorganic ion and detergents used are shown. (M.J.C.) [pt

  7. Automatic analysis and reduction of reaction mechanisms for complex fuel combustion

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, Daniel

    2001-05-01

    This work concentrates on automatic procedures for simplifying chemical models for realistic fuels using skeletal mechanism construction and Quasi Steady-State Approximation (QSSA) applied to detailed reaction mechanisms. To automate the selection of species for removal or approximation, different indices for species ranking have thus been proposed. Reaction flow rates are combined with sensitivity information for targeting a certain quantity, and used to determine a level of redundancy for automatic skeletal mechanism construction by exclusion of redundant species. For QSSA reduction, a measure of species lifetime can be used for species ranking as-is, weighted by concentrations or molecular transport timescales, and/or combined with species sensitivity. Maximum values of the indices are accumulated over ranges of parameters, (e.g. fuel-air ratio and octane number), and species with low accumulated index values are selected for removal or steady-state approximation. In the case of QSSA, a model with a certain degree of reduction is automatically implemented as FORTRAN code by setting a certain index limit. The code calculates source terms of explicitly handled species from reaction rates and the steady-state concentrations by internal iteration. Homogeneous-reactor and one-dimensional laminar-flame models were used as test cases. A staged combustor fuelled by ethylene with monomethylamine addition is modelled by two homogeneous reactors in sequence, i.e. a PSR (Perfectly Stirred Reactor) followed by a PFR (Plug Flow Reactor). A modified PFR model was applied for simulation of a Homogeneous Charge Compression Ignition (HCCI) engine fuelled with four-component natural gas, whereas a two-zone model was required for a knocking Spark Ignition (SI) engine powered by Primary Reference Fuel (PRF). Finally, a laminar one-dimensional model was used to simulate premixed flames burning methane and an aeroturbine kerosene surrogate consisting of n-decane and toluene. In

  8. Detection of Maillard reaction products by a coupled HPLC-Fraction collector technique and FTIR characterization of Cu(II)-complexation with the isolated species

    Science.gov (United States)

    Ioannou, Aristos; Daskalakis, Vangelis; Varotsis, Constantinos

    2017-08-01

    The isolation of reaction products of asparagine with reducing sugars at alkaline pH and high temperature has been probed by a combination of high performance liquid chromatography (HPLC) coupled with a Fraction Collector. The UV-vis and FTIR spectra of the isolated Maillard reaction products showed structure-sensitive changes as depicted by deamination events and formation of asparagine-saccharide conjugates. The initial reaction species of the Asn-Gluc reaction were also characterized by Density Functional Theory (DFT) methods. Evidence for Cu (II) metal ion complexation with the Maillard reaction products is supported by UV-vis and FTIR spectroscopy.

  9. The complex reaction sequence of the thermal and radiolytic degradation of polyvinyl chloride

    International Nuclear Information System (INIS)

    Reichert, W.

    1983-03-01

    The degradation of PVC-foils was been tested by thermal and radiolytic stress in N 2 - and O 2 -atmosphere. Additionally was determined the influence of plasticizers, Fe-, Zn- and Cu-stearates and other additives, which partially are known as stabilizators. Complex mechanisms of degradation are proposed, which were deduced from the HCl-elimination, consumption of oxygen and the shift of the molmass by the scission and crosslinking of main chains both for PVC as combination of PVC with additives. The mechanism corresponds to other known experimental results, too. It was shown, that the radiolytical degradation caused by radicals, which initiate a radical chain mechanism, if the temperature is higher than the glass temperature (Tg). The thermical degradation in a N 2 -atmosphere was explained by an ionic complex mechanism. At the presence of oxygen the ionic mechanism was superimposed by a radical chain mechanism following the oxidation of polyene structures. (author)

  10. Novel cleavage and oligomerization reactions of nickel (o) complexes. Application to homogeneous deoxygenation and desulfurization

    International Nuclear Information System (INIS)

    Eisch, J.J.; Im, K.R.

    1979-01-01

    The ease of interaction of Ni(0) complexes with organic substrates has been shown to depend upon both the ligands on nickel and the solvent. The presence of α,α'-bipyridyl with the Ni(0) complex and the alkyne led to the isolation of a nickelacyclopropene, an observation in accord with the recently proposed metallocyclic pathway for the Ni(0)-catalyzed trimerization of alkynes. Allylic and benzylic ethers and epoxides have been observed to undergo oxidative insertion of Ni(0) into their C-O bonds with solvent (TMEDA > THF (tetrahydrofuran) > Et 2 O > C 6 H 6 ) and ligand (Et 3 P (tripthyl phosphine) > Ph 3 P (triphenyl phosphine); α,α'-bipy > COD) effects consistent with an electron-transfer attack by Ni(0). With such sulfur heterocycles as dibenzothiophene, phenoxathiin, phenothiazine, and thianthrene, a 1:1 admixture of (COD) 2 Ni with α,α'-bipyridyl gave as the principal product the desulfurized, ring-contracted cyclic product

  11. Reactions of Substituted Zirconocene-Bis(trimethylsilyl)ethyne Complexes with Terminal Alkynes

    Czech Academy of Sciences Publication Activity Database

    Horáček, Michal; Štěpnička, P.; Kubišta, Jiří; Gyepes, R.; Mach, Karel

    2004-01-01

    Roč. 23, č. 14 (2004), s. 3388-3397 ISSN 0276-7333 R&D Projects: GA ČR GA203/02/0436; GA ČR GA203/00/D037; GA ČR GA203/99/M037 Institutional research plan: CEZ:AV0Z4040901 Keywords : zirconocene complexes * titanocene * crystal structures Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.196, year: 2004

  12. New dinuclear palladium(II) complexes: Studies of the nucleophilic substitution reactions, DNA/BSA interactions and cytotoxic activity.

    Science.gov (United States)

    Ćoćić, Dušan; Jovanović, Snežana; Nišavić, Marija; Baskić, Dejan; Todorović, Danijela; Popović, Suzana; Bugarčić, Živadin D; Petrović, Biljana

    2017-10-01

    Six new dinuclear Pd(II) complexes, [{Pd(2,2'-bipy)Cl} 2 (μ-pz)](ClO 4 ) 2 (Pd1), [{Pd(dach)Cl} 2 (μ-pz)](ClO 4 ) 2 (Pd2), [{Pd(en)Cl} 2 (μ-pz)](ClO 4 ) 2 (Pd3), [{Pd(2,2'-bipy)Cl} 2 (μ-4,4'-bipy)](ClO 4 ) 2 (Pd4), [{Pd(dach)Cl} 2 (μ-4,4'-bipy)](ClO 4 ) 2 (Pd5) and [{Pd(en)Cl} 2 (μ-4,4'-bipy)](ClO 4 ) 2 (Pd6) (where 2,2'-bipy=2,2'-bipyridyl, pz=pyrazine, dach=trans-(±)-1,2-diaminocyclohexane, en=ethylenediamine, 4,4'-bipy=4,4'-bipyridyl) have been synthesized and characterized by elemental microanalysis, IR, 1 H NMR and MALDI-TOF mass spectrometry. The pK a values of corresponding diaqua complexes were determined by spectrophotometric pH titration. Substitution reactions with thiourea (Tu), l-methionine (l-Met), l-cysteine (l-Cys), l-histidine (l-His) and guanosine-5'-monophosphate (5'-GMP) were studied under the pseudo-first order conditions at pH7.2. Reactions of Pd1 with Tu, l-Met and l-Cys were followed by decomposition of complexes, while structures of dinuclear complexes were preserved during the substitution with nitrogen donors. Interactions with calf-thymus DNA (CT-DNA) were followed by absorption spectroscopy and fluorescence quenching measurements. All complexes can bind to CT-DNA exhibiting high intrinsic binding constants (K b =10 4 -10 5 M -1 ). Competitive studies with ethidium bromide (EB) have shown that complexes can displace DNA-bound EB. High values of binding constants towards bovine serum albumin protein (BSA) indicate good binding affinity. Finally, all complexes showed moderate to high cytotoxic activity against HeLa (human cervical epithelial carcinoma cell lines) and MDA-MB-231 (human breast epithelial carcinoma cell lines) tumor cell lines inducing apoptotic type cell death, whereas normal fibroblasts were significantly less sensitive. The impact on cell cycle of these cells was distinctive, where Pd4, Pd5 and Pd6 showed the most prominent effect arresting MDA-MB-231 (human lung fibroblast cell lines) cell in G1/S phase of cell

  13. Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

    NARCIS (Netherlands)

    Vijaykumar, A.; Ouldridge, T.E.; ten Wolde, P.R.; Bolhuis, P.G.

    2017-01-01

    The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic

  14. Synthesis and Catalytic Hydrogen Transfer Reaction of Ruthenium(II) Complex

    International Nuclear Information System (INIS)

    Son, Jung Ik; Kim, Aram; Noh, Hui Bog; Lee, Hyun Ju; Shim, Yoon Bo; Park, Kang Hyun

    2012-01-01

    The ruthenium(II) complex [Ru(bpy) 2 -(PhenTPy)] was synthesized, and used for the transfer hydrogenation of ketones and the desired products were obtained in good yield. Based on the presented results, transition-metal complexes can be used as catalysts for a wide range of organic transformations. The relationship between the electro-reduction current density and temperature are being examined in this laboratory. Attempts to improve the catalytic activity and determine the transfer hydrogenation mechanism are currently in progress. The catalytic hydrogenation of a ketone is a basic and critical process for making many types of alcohols used as the final products and precursors in the pharmaceutical, agrochemical, flavor, fragrance, materials, and fine chemicals industries. The catalytic hydrogenation process developed by Noyori is a very attractive process. Formic acid and 2-propanol have been used extensively as hydrogenation sources. The advantage of using 2-propanol as a hydrogen source is that the only side product will be acetone, which can be removed easily during the workup process. Hydrogen transfer (HT) catalysis, which generates alcohols through the reduction of ketones, is an attractive protocol that is used widely. Ruthenium(II) complexes are the most useful catalysts for the hydrogen transfer (HT) of ketones. In this method, a highly active catalytic system employs a transition metal as a catalyst to synthesize alcohols, and is a replacement for the hydrogen-using hydrogenation process. The most active system is based on Ru, Rh and Ir, which includes a nitrogen ligand that facilitates the formation of a catalytically active hydride and phosphorus

  15. Synthesis and Catalytic Hydrogen Transfer Reaction of Ruthenium(II) Complex

    Energy Technology Data Exchange (ETDEWEB)

    Son, Jung Ik; Kim, Aram; Noh, Hui Bog; Lee, Hyun Ju; Shim, Yoon Bo; Park, Kang Hyun [Pusan National University, Busan (Korea, Republic of)

    2012-01-15

    The ruthenium(II) complex [Ru(bpy){sub 2}-(PhenTPy)] was synthesized, and used for the transfer hydrogenation of ketones and the desired products were obtained in good yield. Based on the presented results, transition-metal complexes can be used as catalysts for a wide range of organic transformations. The relationship between the electro-reduction current density and temperature are being examined in this laboratory. Attempts to improve the catalytic activity and determine the transfer hydrogenation mechanism are currently in progress. The catalytic hydrogenation of a ketone is a basic and critical process for making many types of alcohols used as the final products and precursors in the pharmaceutical, agrochemical, flavor, fragrance, materials, and fine chemicals industries. The catalytic hydrogenation process developed by Noyori is a very attractive process. Formic acid and 2-propanol have been used extensively as hydrogenation sources. The advantage of using 2-propanol as a hydrogen source is that the only side product will be acetone, which can be removed easily during the workup process. Hydrogen transfer (HT) catalysis, which generates alcohols through the reduction of ketones, is an attractive protocol that is used widely. Ruthenium(II) complexes are the most useful catalysts for the hydrogen transfer (HT) of ketones. In this method, a highly active catalytic system employs a transition metal as a catalyst to synthesize alcohols, and is a replacement for the hydrogen-using hydrogenation process. The most active system is based on Ru, Rh and Ir, which includes a nitrogen ligand that facilitates the formation of a catalytically active hydride and phosphorus.

  16. DFT study of benzyl alcohol/TiO2 interfacial surface complex: reaction pathway and mechanism of visible light absorption.

    Science.gov (United States)

    Zhao, Lei; Gu, Feng Long; Kim, Minjae; Miao, Maosheng; Zhang, Rui-Qin

    2017-09-24

    We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO 2 and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO 2 surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H 2 O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces. The effects of both acidity and solvation are included in our calculations, which demonstrate that the new pathway is competitive with a previous pathway. The electronic structure calculations based on the relaxed ISC structures reveal that the chemisorption of benzyl alcohol on the TiO 2 surface greatly alters the nature of the frontier molecular orbitals. The resulted reduced energy gap in ISC matches the energy of visible light, showing how the adsorption of benzyl alcohol sensitizes the TiO 2 surface. Graphical Abstract The chemisorption of benzyl alcohol on TiO 2 surface greatly alters the nature of the frontier molecular orbitals and the formed interfacial surface complex can be sensitized by visible light.

  17. Polystyrene copolymer supported by substituted (1R,2R)-1,2-diphenylethane-1,2-diamine-copper(II) complexes: a recyclable catalyst for asymmetric Henry reactions

    Czech Academy of Sciences Publication Activity Database

    Androvič, L.; Drabina, P.; Panov, I.; Frumarová, Božena; Kalendová, A.; Sedlák, M.

    2014-01-01

    Roč. 25, č. 9 (2014), s. 775-780 ISSN 0957-4166 Institutional support: RVO:61389013 Keywords : cooper complexes * copolymers * asymmetric Henry reaction Subject RIV: CC - Organic Chemistry Impact factor: 2.155, year: 2014

  18. N-BUTYL SUBSTITUTED N-HETEROCYCLIC CARBENE-PD(II-PYRIDINE (PEPPSI COMPLEXES: SYNTHESIS, CHARACTERIZATION AND CATALYTIC ACTIVITY IN THE SUZUKI-MIYAURA REACTION

    Directory of Open Access Journals (Sweden)

    Rukiye Fırıncı

    2016-08-01

    Full Text Available A series of N-butyl substituted imidazolium salts, (1a-c and their pyridine enhanced precatalyst preparation stabilization and initiation (PEPPSI themed palladium N-heterocyclic carbene complexes (2a-c were synthesized and characterized. Pd-NHC complexes were fully determined by elemental analysis and spectroscopic. The synthesized complexes were tested in Suzuki-Miyaura cross-coupling reaction. These complexes were found to be efficient catalysts for the Suzuki-Miyaura reaction of phenylboronic acid with aryl bromides.

  19. Stacking reactions of the borole complex Cp*Rh(η5-C4H4BPh) with the dicationic fragments [Cp*M]2+ (M = Rh or Ir)

    International Nuclear Information System (INIS)

    Loginov, D.A.; Muratov, D.V.; Starikova, Z.A.; Petrovskij, P.V.; Kudinov, A.R.

    2006-01-01

    The reaction of the (borole)rhodium iodide complex [(η-C 4 H 4 BPh)RhI] 4 with Cp*Li afforded the sandwich compound Cp*Rh(η-C 4 H 4 BPh) (1). The reactions of compound 1 with the solvated complexes [Cp*M(MeNO 2 ) 3 ] 2+ (BF 4 - ) 2 gave triple-decker cationic complexes with the central borole ligand [Cp*Rh(μ-η 5 :η 5 -C 4 H 4 BPh)MCp*] 2+ (BF 4 - ) 2 (M = Rh or Ir). The structure of complex 1 was established by X-ray diffraction [ru

  20. Spectrophotometric determination of quetiapine fumarate in pharmaceuticals and human urine by two charge-transfer complexation reactions

    Directory of Open Access Journals (Sweden)

    Vinay K.B.

    2012-01-01

    Full Text Available Two simple, rapid and accurate spectrophotometric procedures are proposed for the determination of quetiapine fumarate (QTF in pharmaceuticals and in spiked human urine. The methods are based on charge transfer complexation reactions of free base form of the drug (quetiapine, QTP, as n-electron donor (D, with either p-chloranilic acid (p-CAA (method A or 2,3-dichloro-5,6-dicyanoquinone (DDQ (method B as π-acceptors (A. The coloured charge transfer complexes produced exhibit absorption maxima at 520 and 540 nm, in method A and method B, respectively. The experimental conditions such as reagent concentration, reaction solvent and time have been carefully optimized to achieve the maximum sensitivity. Beer’s law is obeyed over the concentration ranges of 8.0 - 160 and 4.0 - 80.0 μg ml-1, for method A and method B, respectively. The calculated molar absorptivity values are 1.77 × 103 and 4.59 × 103 l mol-1cm-1, respectively, for method A and method B. The Sandell sensitivity values, limits of detection (LOD and quantification (LOQ have also been reported. The stoichiometry of the reaction in both cases was accomplished adopting the limiting logarithmic method and was found to be 1: 2 (D: A. The accuracy and precision of the methods were evaluated on intra-day and inter-day basis. The proposed methods were successfully applied for the determination of QTF in pharmaceutical formulations and spiked human urine.

  1. Formation of carbonato and hydroxo complexes in the reaction of platinum anticancer drugs with carbonate.

    Science.gov (United States)

    Di Pasqua, Anthony J; Centerwall, Corey R; Kerwood, Deborah J; Dabrowiak, James C

    2009-02-02

    The second-generation Pt(II) anticancer drug carboplatin is here shown to react with carbonate, which is present in blood, interstitial fluid, cytosol, and culture medium, to produce platinum-carbonato and -hydroxo complexes. Using [(1)H-(15)N] HSQC NMR and (15)N-labeled carboplatin, we observe that cis-[Pt(CBDCA-O)(OH)(NH(3))(2)](-), cis-[Pt(OH)(2)(NH(3))(2)], cis-[Pt(CO(3))(OH)(NH(3))(2)](-), and what may be cis-[Pt(CO(3))(NH(3))(2)] are produced when 1 is allowed to react in 23.8 mM carbonate buffer. When (15)N-labeled carboplatin is allowed to react in 0.5 M carbonate buffer, these platinum species, as well as other hydroxo and carbonato species, some of which may be dinuclear complexes, are produced. Furthermore, we show that the carbonato species cis-[Pt(CO(3))(OH)(NH(3))(2)](-) is also produced when cisplatin is allowed to react in carbonate buffer. The study outlines the conditions under which carboplatin and cisplatin form carbonato and aqua/hydroxo species in carbonate media.

  2. Electrode reactions of ruthenium–bipyridine complex in amide-type ionic liquids

    International Nuclear Information System (INIS)

    Toshimitsu, Yuichi; Katayama, Yasushi; Miura, Takashi

    2012-01-01

    The electrode kinetics of [Ru(bpy) 3 ] 3+ /[Ru(bpy) 3 ] 2+ (bpy = 2,2′-bipyridine) on a platinum electrode was investigated in room-temperature ionic liquids, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide (BMPTFSA), 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide (EMITFSA), and 1-butyl-1-methylpyrrolidinium bis(perfluoroethylsulfonyl)amide (BMPBETA) over the temperature range from 25 to 45 °C. The diffusion coefficients of [Ru(bpy) 3 ] 2+ and [Ru(bpy) 3 ] 3+ were found to be affected not only by the viscosity of ionic liquids but also by the charge density of the complex. The activation energy for the diffusion coefficients of these complexes in the ionic liquids were close to that for the viscosity of the ionic liquids. The standard rate constants of [Ru(bpy) 3 ] 3+ /[Ru(bpy) 3 ] 2+ in BMPTFSA, EMITFSA and BMPBETA were estimated by electrochemical impedance spectroscopy. The standard rate constants in the ionic liquids were estimated to be smaller than those in aqueous and organic electrolytes, probably due to the slow dynamics of the ionic liquids.

  3. Structure of choline oxidase in complex with the reaction product glycine betaine.

    Science.gov (United States)

    Salvi, Francesca; Wang, Yuan-Fang; Weber, Irene T; Gadda, Giovanni

    2014-02-01

    Choline oxidase from Arthrobacter globiformis, which is involved in the biosynthesis of glycine betaine from choline, has been extensively characterized in its mechanistic and structural properties. Despite the knowledge gained on the enzyme, the details of substrate access to the active site are not fully understood. The `loop-and-lid' mechanism described for the glucose-methanol-choline enzyme superfamily has not been confirmed for choline oxidase. Instead, a hydrophobic cluster on the solvent-accessible surface of the enzyme has been proposed by molecular dynamics to control substrate access to the active site. Here, the crystal structure of the enzyme was solved in complex with glycine betaine at pH 6.0 at 1.95 Å resolution, allowing a structural description of the ligand-enzyme interactions in the active site. This structure is the first of choline oxidase in complex with a physiologically relevant ligand. The protein structures with and without ligand are virtually identical, with the exception of a loop at the dimer interface, which assumes two distinct conformations. The different conformations of loop 250-255 define different accessibilities of the proposed active-site entrance delimited by the hydrophobic cluster on the other subunit of the dimer, suggesting a role in regulating substrate access to the active site.

  4. Detection of feline herpes virus 1 via polymerase chain reaction and immunohistochemistry in cats with ulcerative facial dermatitis, eosinophilic granuloma complex reaction patterns and mosquito bite hypersensitivity.

    Science.gov (United States)

    Persico, Paola; Roccabianca, Paola; Corona, Antonio; Vercelli, Antonella; Cornegliani, Luisa

    2011-12-01

    Ulcerative dermatitis caused by feline herpes virus 1 (FHV-1) is an uncommon disease characterized by cutaneous ulcers secondary to epidermal, adnexal and dermal necrosis. Differential diagnoses for FHV-1 lesions include, but are not limited to, mosquito bite hypersensitivity and eosinophilic granuloma complex. Histopathological diagnosis of FHV-1 dermatitis is based on the detection of the intranuclear inclusion bodies. In cases where intranuclear inclusions are missing but clinical and histological findings are compatible with FHV-1 dermatitis, immunohistochemistry (IHC) and PCRs have been used. In this retrospective study, we evaluated the presence of FHV-1 by IHC and PCR in skin biopsies and compared the results of the two tests. Sixty-four skin biopsy specimens from cats with compatible lesions were reviewed and tested via PCR and IHC for evidence of FHV-1. Polymerase chain reaction was positive in 12 of 64 biopsies; PCR and IHC were positive only in two of 64 biopsies, and these cases were considered true positive cases. The higher number of PCR-positive cases was possibly attributed to amplification of viral DNA from a live attenuated vaccination, but a previous FHV-1 infection with subsequent amplification of latently inserted FHV-1 could not be excluded. If clinical signs and histopathology suggest FHV-1 infection in the absence of typical inclusion bodies, IHC is the preferred diagnostic test; PCR may be useful for initial screening, but due to false positives is not sufficient for a definitive diagnosis. © 2011 The Authors. Veterinary Dermatology. © 2011 ESVD and ACVD.

  5. Nitric oxide reduction in coal combustion: role of char surface complexes in heterogeneous reactions.

    Science.gov (United States)

    Arenillas, Ana; Rubiera, Fernando; Pis, José J

    2002-12-15

    Nitrogen oxides are one of the major environmental problems arising from fossil fuel combustion. Coal char is relatively rich in nitrogen, and so this is an important source of nitrogen oxides during coal combustion. However, due to its carbonaceous nature, char can also reduce NO through heterogeneous reduction. The objectives of this work were on one hand to compare NO emissions from coal combustion in two different types of equipment and on the other hand to study the influence of char surface chemistry on NO reduction. A series of combustion tests were carried out in two different scale devices: a thermogravimetric analyzer coupled to a mass spectrometer and an FTIR (TG-MS-FTIR) and a fluidized bed reactor with an on line battery of analyzers. The TG-MS-FTIR system was also used to perform a specific study on NO heterogeneous reduction reactions using chars with different surface chemistry. According to the results obtained, it can be said that the TG-MS-FTIR system provides valuable information about NO heterogeneous reduction and it can give good trends of the behavior in other combustion equipments (i.e., fluidized bed combustors). It has been also pointed out that NO-char interaction depends to a large extent on temperature. In the low-temperature range (800 degrees C), a different mechanism is involved in NO heterogeneous reduction, the nature of the carbon matrix being a key factor.

  6. High Oxygen Reduction Reaction Performances of Cathode Materials Combining Polyoxometalates, Coordination Complexes, and Carboneous Supports.

    Science.gov (United States)

    Zhang, Shuangshuang; Oms, Olivier; Hao, Long; Liu, Rongji; Wang, Meng; Zhang, Yaqin; He, Hong-Yan; Dolbecq, Anne; Marrot, Jérôme; Keita, Bineta; Zhi, Linjie; Mialane, Pierre; Li, Bin; Zhang, Guangjin

    2017-11-08

    A series of carbonaceous-supported precious-metal-free polyoxometalate (POM)-based composites which can be easily synthesized on a large scale was shown to act as efficient cathode materials for the oxygen reduction reaction (ORR) in neutral or basic media via a four-electron mechanism with high durability. Moreover, exploiting the versatility of the considered system, its activity was optimized by the judicious choice of the 3d metals incorporated in the {(PW 9 ) 2 M 7 } (M = Co, Ni) POM core, the POM counterions and the support (thermalized triazine-based frameworks (TTFs), fluorine-doped TTF (TTF-F), reduced graphene oxide, or carbon Vulcan XC-72. In particular, for {(PW 9 ) 2 Ni 7 }/{Cu(ethylenediamine) 2 }/TTF-F, the overpotential required to drive the ORR compared well with those of Pt/C. This outstanding ORR electrocatalytic activity is linked with two synergistic effects due to the binary combination of the Cu and Ni centers and the strong interaction between the POM molecules and the porous and highly conducting TTF-F framework. To our knowledge, {(PW 9 ) 2 Ni 7 }/{Cu(ethylenediamine) 2 }/TTF-F represents the first example of POM-based noble-metal-free ORR electrocatalyst possessing both comparable ORR electrocatalytic activity and much higher stability than that of Pt/C in neutral medium.

  7. Identification of protein W, the elusive sixth subunit of the Rhodopseudomonas palustris reaction center-light harvesting 1 core complex.

    Science.gov (United States)

    Jackson, Philip J; Hitchcock, Andrew; Swainsbury, David J K; Qian, Pu; Martin, Elizabeth C; Farmer, David A; Dickman, Mark J; Canniffe, Daniel P; Hunter, C Neil

    2018-02-01

    The X-ray crystal structure of the Rhodopseudomonas (Rps.) palustris reaction center-light harvesting 1 (RC-LH1) core complex revealed the presence of a sixth protein component, variably referred to in the literature as helix W, subunit W or protein W. The position of this protein prevents closure of the LH1 ring, possibly to allow diffusion of ubiquinone/ubiquinol between the RC and the cytochrome bc 1 complex in analogous fashion to the well-studied PufX protein from Rhodobacter sphaeroides. The identity and function of helix W have remained unknown for over 13years; here we use a combination of biochemistry, mass spectrometry, molecular genetics and electron microscopy to identify this protein as RPA4402 in Rps. palustris CGA009. Protein W shares key conserved sequence features with PufX homologs, and although a deletion mutant was able to grow under photosynthetic conditions with no discernible phenotype, we show that a tagged version of protein W pulls down the RC-LH1 complex. Protein W is not encoded in the photosynthesis gene cluster and our data indicate that only approximately 10% of wild-type Rps. palustris core complexes contain this non-essential subunit; functional and evolutionary consequences of this observation are discussed. The ability to purify uniform RC-LH1 and RC-LH1-protein W preparations will also be beneficial for future structural studies of these bacterial core complexes. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  8. Redox reactions of the α-synuclein-Cu(2+) complex and their effects on neuronal cell viability.

    Science.gov (United States)

    Wang, Chengshan; Liu, Lin; Zhang, Lin; Peng, Yong; Zhou, Feimeng

    2010-09-21

    α-Synuclein (α-syn), a presynaptic protein believed to play an important role in neuropathology in Parkinson's disease (PD), is known to bind Cu(2+). Cu(2+) has been shown to accelerate the aggregation of α-syn to form various toxic aggregates in vitro. Copper is also a redox-active metal whose complexes with amyloidogenic proteins/peptides have been linked to oxidative stress in major neurodegenerative diseases. In this work, the formation of the Cu(2+) complex with α-syn or with an N-terminal peptide, α-syn(1-19), was confirmed with electrospray-mass spectrometry (ES-MS). The redox potentials of the Cu(2+) complex with α-syn (α-syn-Cu(2+)) and α-syn(1-19) were determined to be 0.018 and 0.053 V, respectively. Furthermore, the Cu(2+) center(s) can be readily reduced to Cu(+), and possible reactions of α-syn-Cu(2+) with cellular species (e.g., O(2), ascorbic acid, and dopamine) were investigated. The occurrence of a redox reaction can be rationalized by comparing the redox potential of the α-syn-Cu(2+) complex to that of the specific cellular species. For example, ascorbic acid can directly reduce α-syn-Cu(2+) to α-syn-Cu(+), setting up a redox cycle in which O(2) is reduced to H(2)O(2) and cellular redox species is continuously exhausted. In addition, the H(2)O(2) generated was demonstrated to reduce viability of the neuroblastoma SY-HY5Y cells. Although our results ruled out the direct oxidation of dopamine by α-syn-Cu(2+), the H(2)O(2) generated in the presence of α-syn-Cu(2+) can oxidize dopamine. Our results suggest that oxidative stress is at least partially responsible for the loss of dopaminergic cells in PD brain and reveal the multifaceted role of the α-syn-Cu(2+) complex in oxidative stress associated with PD symptoms.

  9. Multi-scale simulation of reaction-diffusion systems

    NARCIS (Netherlands)

    Vijaykumar, A.

    2017-01-01

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function

  10. Nitric oxide reduction in coal combustion: role of char surface complexes in heterogeneous reactions

    Energy Technology Data Exchange (ETDEWEB)

    Arenillas, A.; Rubiera, F.; Pis, J.J. [Instituto Nacional del Carbon, CSIC, Oviedo (Spain)

    2002-12-15

    Nitrogen oxides are one of the major environmental problems arising from fossil fuel combustion. Coal char is relatively rich in nitrogen, and so this is an important source of nitrogen oxides during coal combustion. However, due to its carbonaceous nature, char can also reduce NO through heterogeneous reduction. The objectives of this work were on one hand to compare NO emissions from coal combustion in two different types of equipment and on the other hand to study the influence of char surface chemistry on NO reduction. A series of combustion tests were carried out in two different scale devices: a thermogravimetric analyzer coupled to a mass spectrometer and an FTIR (TG-MS-FTIR) and a fluidized bed reactor with on-line battery of analyzers. According to the results obtained, it can be said that the TG-MS-FTIR system provides valuable information about NO heterogeneous reduction and it can give good trends of the behaviour in other combustion equipments, i.e. fluidized bed combustors. It has been also pointed out that NO-char interaction depends to a large extent on temperature. In the low-temperature range NO heterogeneous reduction seems to be controlled by the evolution of surface complexes. In the high-temperature range a different mechanism is involved in NO heterogeneous reduction, the nature of the carbon matrix being a key factor. 27 refs., 6 figs., 1 tab.

  11. Spectrophotometric Determination of Rifampicin in Bulk Drug and Pharmaceutical Formulations Based on Redox and Complexation Reactions

    Science.gov (United States)

    Swamy, N.; Basavaiah, K.

    2017-09-01

    Two spectrophotometric methods were developed and validated for the determination of rifampicin (RIF) in bulk form, formulations, and spiked human urine. The first method is based on the reduction of the Folin-Ciocalteu (FC) reagent by RIF to form a blue colored chromogen with λmax at 760 nm (the FCR method). In the second method, iron(III) is reduced by RIF in a neutral medium, and the resulting iron(II) is complexed with ferricyanide to form a Prussian blue peaking at 750 nm (the FFC method). Under optimum conditions, Beer's law enabled the determination of the drug in the concentration ranges 1-35 and 2.5-50 μg/mL with apparent molar absorptivities of 2.72 × 104 and 1.63×104 L/(mol × cm) for the FCR and FFC methods, respectively. The Sandell sensitivity, limits of detection (LOD), and quantification (LOQ) values were also reported for both methods. The precision of the methods, with % RSD of human urine without interference from endogenous substances. A statistical analysis indicated that there was no significant difference between the results obtained by the developed methods and the official method.

  12. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

    Science.gov (United States)

    Papin, Jason A; Reed, Jennifer L; Palsson, Bernhard O

    2004-12-01

    As reconstructed biochemical reaction networks continue to grow in size and scope, there is a growing need to describe the functional modules within them. Such modules facilitate the study of biological processes by deconstructing complex biological networks into conceptually simple entities. The definition of network modules is often based on intuitive reasoning. As an alternative, methods are being developed for defining biochemical network modules in an unbiased fashion. These unbiased network modules are mathematically derived from the structure of the whole network under consideration.

  13. Chemistry in the Dunes of Titan: Tribochemical Reactions of Complex Organics and Water Ice

    Science.gov (United States)

    Beauchamp, J. L.; Thomas, D. A.

    2010-12-01

    Titan’s N2-CH4 atmosphere provides the starting material for a wide array of organic compounds to be formed via photochemistry, and the presence of unsaturated hydrocarbon, amine, and polycyclic aromatic species has been supported by data from the Cassini-Huygens mission [1,2]. Production of tholins by UV irradiation of a simulated N2-CH4 environment has yielded products that match the observed optical properties of Titan haze, suggesting that these compounds provide suitable analogs to Titan aerosol compounds [3, 4, 5]. Organics produced in Titan’s atmosphere eventually settle to the surface and very likely contribute to the particulate matter comprising the expansive longitudinal dune features observed at mid-latitudes [6]. Once on the surface, conditions that lead to incorporation of oxygen via contact with water ice or liquid water in Titan’s low temperature environment are of particular interest and have important implications for astrobiology [7; 8]. In this work, we postulate that the mechanical energy from wind-driven grains in the dunes of Titan can ultimately drive chemical processes and lead to the incorporation of oxygen into organic compounds via tribochemical reactions [9] and describe experiments designed to test this hypothesis. While the exact composition of the dunes of Titan is unknown, it is likely that they mainly comprise organic and water ice particles approximately 0.2 mm in diameter, the ideal size for saltation by the winds of Titan [6]. During the saltation process, organic particles undergo charging due to friction between particles, leading in turn to formation of ions and free radicals in localized electrical discharges at particle interfaces [10]. These reactive intermediates can initiate processes such as free radical and ionic polymerization that further transform organics. Of particular interest is the incorporation of oxygen into organic molecules, providing a pathway to the synthesis of biologically relevant compounds

  14. Insights into the catalytic activity of [Pd(NHC)(cin)Cl] (NHC = IPr, IPrCl, IPrBr) complexes in the Suzuki-Miyaura reaction

    KAUST Repository

    Nolan, Steven Patrick; Izquierdo, Frederic; Zinser, Caroline; Minenkov, Yury; Cordes, David; Slawin, Alexandra; Cavallo, Luigi; Nahra, Fady; Cazin, Catherine

    2017-01-01

    The influence of C4,5-halogenation on palladium N-heterocyclic carbene complexes and their activity in the Suzuki-Miyaura reaction have been investigated. Two [Pd(NHC)(cin)Cl] complexes bearing IPrCl and IPrBr ligands were synthesized. After

  15. Syntheses and properties of complex resins obtained by the reaction of polyethyleneimine with maleic anhydride-isobutene copolymer

    International Nuclear Information System (INIS)

    Usami, Shiro; Hasegawa, Kiyoshi; Takata, Kyoko; Naito, Ryunosuke; Uchida, Hiroshi; Kozuka, Hiroshi.

    1985-01-01

    Complex resins obtained by the reaction of polyethyleneimine with maleic anhydride-isobutene copolymer around 100 0 C revealed selective ion adsorption depending on the equivalent ratio of nitrogen to carboxyl group (N/COOH). In detail, polyanion-excess complex resins (N/COOH 2+ , Pb 2+ , Zn 2+ and Ni 2+ , and resins containing excess polycation (N/COOH > 1) for metal complex anions such as [CrO 4 ] 2- , [Ag(S 2 O 3 ) 2 ] 3- and [Fe(CN) 6 ] 4- . Furthermore, the polycation-excess complex resins had high adsorption capacity for uranium in solution, for example, a polycationic resin (N/COOH = 1.79) had an adsorption capacity of more than 100 mg U/g-dry base resin in a 75 ppm uranium solution. It also adsorbed and recovered uranium from solution contatining such infinitesimal amounts of uranium as sea water. The results from electron probe X-ray microanalyser (EPMA) of a polycationic resin (N/COOH = 1.79) indicated that cations such as Ca 2+ and Mg 2+ , abundant in sea water, were not adsorbed at all while such anions as Cl - and S 2- were adsorbed. It was found that Br - , I - , etc. were not adsorbed from sea water while these anions were adsorbed from the solutions containing them independently. The result indicated that Cl - in sea water probably interfered the adsorption of Br - , I - , etc. However, uranium was adsorbed from sea water in spite of its extremely low concentration without any disturbance of other co-existing ions. It was found that Ni 2+ and Cu 2+ were also adsorbed. (author)

  16. Combined experimental and theoretical approach to understand the reactivity of a mononuclear Cu(II)-hydroperoxo complex in oxygenation reactions.

    Science.gov (United States)

    Kamachi, Takashi; Lee, Yong-Min; Nishimi, Tomonori; Cho, Jaeheung; Yoshizawa, Kazunari; Nam, Wonwoo

    2008-12-18

    A copper(II) complex bearing a pentadentate ligand, [Cu(II)(N4Py)(CF(3)SO(3))(2)] (1) (N4Py = N,N-bis(2-pyridylmethyl)bis(2-pyridyl)methylamine), was synthesized and characterized with various spectroscopic techniques and X-ray crystallography. A mononuclear Cu(II)-hydroperoxo complex, [Cu(II)(N4Py)(OOH)](+) (2), was then generated in the reaction of 1 and H(2)O(2) in the presence of base, and the reactivity of the intermediate was investigated in the oxidation of various substrates at -40 degrees C. In the reactivity studies, 2 showed a low oxidizing power such that 2 reacted only with triethylphosphine but not with other substrates such as thioanisole, benzyl alcohol, 1,4-cyclohexadiene, cyclohexene, and cyclohexane. In theoretical work, we have conducted density functional theory (DFT) calculations on the epoxidation of ethylene by 2 and a [Cu(III)(N4Py)(O)](+) intermediate (3) at the B3LYP level. The activation barrier is calculated to be 39.7 and 26.3 kcal/mol for distal and proximal oxygen attacks by 2, respectively. This result indicates that the direct ethylene epoxidation by 2 is not a plausible pathway, as we have observed in the experimental work. In contrast, the ethylene epoxidation by 3 is a downhill and low-barrier process. We also found that 2 cannot be a precursor to 3, since the homolytic cleavage of the O-O bond of 2 is very endothermic (i.e., 42 kcal/mol). On the basis of the experimental and theoretical results, we conclude that a mononuclear Cu(II)-hydroperoxo species bearing a pentadentate N5 ligand is a sluggish oxidant in oxygenation reactions.

  17. Simultaneous Introduction of Two Nitroxides in the Reaction: A New Approach to the Synthesis of Heterospin Complexes.

    Science.gov (United States)

    Ovcharenko, Victor; Kuznetsova, Olga; Fursova, Elena; Letyagin, Gleb; Romanenko, Galina; Bogomyakov, Artem; Zueva, Ekaterina

    2017-12-04

    A new approach to the synthesis of multispin compounds has been developed, namely, the simultaneous introduction of two different stable nitroxides (nitronyl nitroxide and imino nitroxide) in a reaction with a metal ion. An important characteristic of the new method is that nitronyl nitroxide and imino nitroxide introduced in the reaction with the metal are the products of different series; i.e., the nitronyl nitroxide molecule differs from the imino nitroxide molecule not only in one additional oxygen molecule per molecule but also in another substituent in the side chain of the organic paramagnet. This possibility was demonstrated on the synthesis of multispin compounds [Ni 2 (A 1 )(L 2 ) 2 (Piv)(MeOH)], [Ni 2 (L 1 )(A 2 ) 2 (Piv)(H 2 O)], [Co 2 (A 1 )(L 2 ) 2 (Piv)(MeOH)], and [Co 3 (L 1 ) 2 (A 2 ) 2 (Piv) 2 ], in which L n and A n differ in the substituent in the phenyl ring. The number of multispin compounds that can be synthesized by the proposed method is almost unlimited. The heterospin complexes of transition metals with coordinated nitronyl nitroxide and imino nitroxide in one molecule contain energy-different exchange interaction channels that differ in both magnitude and sign, as confirmed by the quantum-chemical analysis of exchange channels in [Ni(B 1 )(B 2 ) 2 ](NO 3 ) 2 . The series of mixed-radical complexes may include compounds with nontrivial magnetic properties such as [Co 2 (A 1 )(L 2 ) 2 (Piv)(MeOH)], which experiences bulk magnetic ordering below 3.5 K.

  18. Rate constants for the reaction of e-aq with EDTA and some metal EDTA-complexes

    International Nuclear Information System (INIS)

    Buitenhuis, R.; Bakker, C.M.N.; Stock, F.R.; Louwrier, P.W.F.

    1977-01-01

    The rate constants for the reaction e - aq + EDTA were measured as a function of the pH by the pulse-radiolysis technique. Between pH = 6and pH = 10 this rate constant can be represented by the equation k = 4.7 x 10 6 x (fraction of HEDTA 3- )+1.0 x 10 8 x (fraction H 2 EDTA 2 -)M -1 s -1 . Also the rate constants for reactions of e - aq with the following metal-EDTA complexes were measured: CuEDTA 2- , HgEDTA 2- , CoEDTA 2- , InEDTA - , NiEDTA 2- , GaEDTA - , MnEDTA 2- , ZnEDTA 2- , CdEDTA 2- , PbEDTA 2- . Ionic strength variation indicates that the reacting ions are not hydrolized to an appreciable amount at pH = 11.5. It is found that some of the products show light absorption in the region between 300 and 400 nm. (orig.) [de

  19. Capture and dissociation in the complex-forming CH + H2 → CH2 + H, CH + H2 reactions.

    Science.gov (United States)

    González, Miguel; Saracibar, Amaia; Garcia, Ernesto

    2011-02-28

    The rate coefficients for the capture process CH + H(2)→ CH(3) and the reactions CH + H(2)→ CH(2) + H (abstraction), CH + H(2) (exchange) have been calculated in the 200-800 K temperature range, using the quasiclassical trajectory (QCT) method and the most recent global potential energy surface. The reactions, which are of interest in combustion and in astrochemistry, proceed via the formation of long-lived CH(3) collision complexes, and the three H atoms become equivalent. QCT rate coefficients for capture are in quite good agreement with experiments. However, an important zero point energy (ZPE) leakage problem occurs in the QCT calculations for the abstraction, exchange and inelastic exit channels. To account for this issue, a pragmatic but accurate approach has been applied, leading to a good agreement with experimental abstraction rate coefficients. Exchange rate coefficients have also been calculated using this approach. Finally, calculations employing QCT capture/phase space theory (PST) models have been carried out, leading to similar values for the abstraction rate coefficients as the QCT and previous quantum mechanical capture/PST methods. This suggests that QCT capture/PST models are a good alternative to the QCT method for this and similar systems.

  20. Heating-induced inner-sphere substitution and reduction-oxidation reactions of the solid phenanthroline containing cobalt (2) and cobalt (3) complexes

    International Nuclear Information System (INIS)

    Palade, D.M.

    1996-01-01

    The results of the differential thermal and thermogravimetric analyses of solid phenanthroline-containing complexes of cobalt (2) and cobalt (3) in the atmosphere of the air have been analyzed. Mechanism of redox reactions occurring when cobalt (3) complexes are heated has been discussed. It is shown that some of gaseous products of the redox processes appear as a result of secondary reactions and not the processes of the ligands oxidation by Co 3+ . The influence of certain inner-sphere and coordinated anions (of I, inclusively) on cobalt (3) complexes behaviour during heating has been considered

  1. The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function

    DEFF Research Database (Denmark)

    Rowland, Paul; Bjørnberg, Olof; Nielsen, Finn S.

    1998-01-01

    Dihydroorotate dehydrogenases (DHODs) catalyze the oxidation of (S)-dihydroorotate to orotate, the fourth step and only redox reaction in the de novo biosynthesis of pyrimidine nucleotides. A description is given of the crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A (DHODA......) complexed with the product of the enzyme reaction orotate. The structure of the complex to 2.0 A resolution has been compared with the structure of the native enzyme. The active site of DHODA is known to contain a water filled cavity buried beneath a highly conserved and flexible loop. In the complex...

  2. Silica functionalized Cu(II) acetylacetonate Schiff base complex: An efficient catalyst for the oxidative condensation reaction of benzyl alcohol with amines

    Science.gov (United States)

    Anbarasu, G.; Malathy, M.; Karthikeyan, P.; Rajavel, R.

    2017-09-01

    Silica functionalized Cu(II) acetylacetonate Schiff base complex via the one pot reaction of silica functionalized 3-aminopropyltriethoxysilane with acetyl acetone and copper acetate has been reported. The synthesized material was well characterized by analytical techniques such as FT-IR, UV-DRS, XRD, SEM-EDX, HR-TEM, EPR, ICP-AES and BET analysis. The characterization results confirmed the grafting of Cu(II) Schiff base complex on the silica surface. The catalytic activity of synthesized silica functionalized Cu(II) acetylacetonate Schiff base complex was evaluated through the oxidative condensation reaction of benzyl alcohol to imine.

  3. A kinetic study of the redox reactions of complex cyanides of iron, molybdenum and tungsten with compounds of the group VI A elements

    International Nuclear Information System (INIS)

    Dennis, C.R.

    1981-01-01

    The kinetic study arises out of the fact that few is known about redox kinetics of complex cyanides of molybdenum and tungsten. The redox kinetics of the complex cyanides of iron with organic and inorganic compounds are well known in organic chemistry. This comparitive study is done to obtain more information on redox reactions of complex cyanides of molybdenum and tungsten considering its greater applicability in organic and inorganic chemistry because of the propitious reduction potential of this complex cyanide in acidic and alkaline mediums. Various redox systems are kinetically investigated regarding the influence of the oxidising agent, reducing agent hydrogen ions and alkaline-metal ions on the reaction rate. A reaction mechanism is proposed for every system

  4. Genetic variability in Brazilian populations of Biomphalaria straminea complex detected by simple sequence repeat anchored polymerase chain reaction amplification

    Directory of Open Access Journals (Sweden)

    Caldeira Roberta L

    2001-01-01

    Full Text Available Biomphalaria glabrata, B. tenagophila and B. straminea are intermediate hosts of Schistosoma mansoni, in Brazil. The latter is of epidemiological importance in the northwest of Brazil and, due to morphological similarities, has been grouped with B. intermedia and B. kuhniana in a complex named B. straminea. In the current work, we have standardized the simple sequence repeat anchored polymerase chain reaction (SSR-PCR technique, using the primers (CA8RY and K7, to study the genetic variability of these species. The similarity level was calculated using the Dice coefficient and genetic distance using the Nei and Li coefficient. The trees were obtained by the UPGMA and neighbor-joining methods. We have observed that the most related individuals belong to the same species and locality and that individuals from different localities, but of the same species, present clear heterogeneity. The trees generated using both methods showed similar topologies. The SSR-PCR technique was shown to be very efficient in intrapopulational and intraspecific studies of the B. straminea complex snails.

  5. Density functional theory studies on the structures and water-exchange reactions of aqueous Al(III)-oxalate complexes.

    Science.gov (United States)

    Jin, Xiaoyan; Yan, Yu; Shi, Wenjing; Bi, Shuping

    2011-12-01

    The structures and water-exchange reactions of aqueous aluminum-oxalate complexes are investigated using density functional theory. The present work includes (1) The structures of Al(C(2)O(4))(H(2)O)(4)(+) and Al(C(2)O(4))(2)(H(2)O)(2)(-) were optimized at the level of B3LYP/6-311+G(d,p). The geometries obtained suggest that the Al-OH(2) bond lengths trans to C(2)O(4)(2-) ligand in Al(C(2)O(4))(H(2)O)(4)(+) are much longer than the Al-OH(2) bond lengths cis to C(2)O(4)(2-). For Al(C(2)O(4))(2)(H(2)O)(2)(-), the close energies between cis and trans isomers imply the coexistence in aqueous solution. The (27)Al NMR and (13)C NMR chemical shifts computed with the consideration of sufficient solvent effect using HF GIAO method and 6-311+G(d,p) basis set are in agreement with the experimental values available, indicating the appropriateness of the applied models; (2) The water-exchange reactions of Al(III)-oxalate complexes were simulated at the same computational level. The results show that water exchange proceeds via dissociative pathway and the activation energy barriers are sensitive to the solvent effect. The energy barriers obtained indicate that the coordinated H(2)O cis to C(2)O(4)(2-) in Al(C(2)O(4))(H(2)O)(4)(+) is more labile than trans H(2)O. The water-exchange rate constants (k(ex)) of trans- and cis-Al(C(2)O(4))(2)(H(2)O)(2)(-) were estimated by four methods and their respective characteristics were explored; (3) The significance of the study on the aqueous aluminum-oxalate complexes to environmental chemistry is discussed. The influences of ubiquitous organic ligands in environment on aluminum chemistry behavior can be elucidated by extending this study to a series of Al(III)-organic system.

  6. BISEN: Biochemical simulation environment

    NARCIS (Netherlands)

    Vanlier, J.; Wu, F.; Qi, F.; Vinnakota, K.C.; Han, Y.; Dash, R.K.; Yang, F.; Beard, D.A.

    2009-01-01

    The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB® computing environment. This is the first package that can generate appropriate systems of differential equations for

  7. Biochemical and redox characterization of the mediator complex and its associated transcription factor GeBPL, a GLABROUS1 enhancer binding protein.

    Science.gov (United States)

    Shaikhali, Jehad; Davoine, Céline; Brännström, Kristoffer; Rouhier, Nicolas; Bygdell, Joakim; Björklund, Stefan; Wingsle, Gunnar

    2015-06-15

    The eukaryotic mediator integrates regulatory signals from promoter-bound transcription factors (TFs) and transmits them to RNA polymerase II (Pol II) machinery. Although redox signalling is important in adjusting plant metabolism and development, nothing is known about a possible redox regulation of mediator. In the present study, using pull-down and yeast two-hybrid assays, we demonstrate the association of mediator (MED) subunits MED10a, MED28 and MED32 with the GLABROUS1 (GL1) enhancer-binding protein-like (GeBPL), a plant-specific TF that binds a promoter containing cryptochrome 1 response element 2 (CryR2) element. All the corresponding recombinant proteins form various types of covalent oligomers linked by intermolecular disulfide bonds that are reduced in vitro by the thioredoxin (TRX) and/or glutathione/glutaredoxin (GRX) systems. The presence of recombinant MED10a, MED28 and MED32 subunits or changes of its redox state affect the DNA-binding capacity of GeBPL suggesting that redox-driven conformational changes might modulate its activity. Overall, these results advance our understanding of how redox signalling affects transcription and identify mediator as a novel actor in redox signalling pathways, relaying or integrating redox changes in combination with specific TFs as GeBPL. © The Authors Journal compilation © 2015 Biochemical Society.

  8. Formation and biochemical characterization of tube/pelle death domain complexes: critical regulators of postreceptor signaling by the Drosophila toll receptor.

    Science.gov (United States)

    Schiffmann, D A; White, J H; Cooper, A; Nutley, M A; Harding, S E; Jumel, K; Solari, R; Ray, K P; Gay, N J

    1999-09-07

    In Drosophila, the Toll receptor signaling pathway is required for embryonic dorso-ventral patterning and at later developmental stages for innate immune responses. It is thought that dimerization of the receptor by binding of the ligand spätzle causes the formation of a postreceptor activation complex at the cytoplasmic surface of the membrane. Two components of this complex are the adaptor tube and protein kinase pelle. These proteins both have "death domains", protein interaction motifs found in a number of signaling pathways, particularly those involved in apoptotic cell death. It is thought that pelle is bound by tube during formation of the activation complexes, and that this interaction is mediated by the death domains. In this paper, we show using the yeast two-hybrid system that the wild-type tube and pelle death domains bind together. Mutant tube proteins which do not support signaling in the embryo are also unable to bind pelle in the 2-hybrid assay. We have purified proteins corresponding to the death domains of tube and pelle and show that these form corresponding heterodimeric complexes in vitro. Partial proteolysis reveals a smaller core consisting of the minimal death domain sequences. We have studied the tube/pelle interaction with the techniques of surface plasmon resonance, analytical ultracentrifugation and isothermal titration calorimetry. These measurements produce a value of K(d) for the complex of about 0.5 microM.

  9. Menaquinone-7 in the reaction center complex of the green sulfur bacterium Chlorobium vibrioforme functions as the electron acceptor A1

    DEFF Research Database (Denmark)

    Kjaer, B; Frigaard, N-U; Yang, F

    1998-01-01

    Photosynthetically active reaction center complexes were prepared from the green sulfur bacterium Chlorobium vibrioforme NCIMB 8327, and the content of quinones was determined by extraction and high-performance liquid chromatography. The analysis showed a stoichiometry of 1.7 molecules of menaqui......Photosynthetically active reaction center complexes were prepared from the green sulfur bacterium Chlorobium vibrioforme NCIMB 8327, and the content of quinones was determined by extraction and high-performance liquid chromatography. The analysis showed a stoichiometry of 1.7 molecules...

  10. Accurate quantification of 5 German cockroach (GCr) allergens in complex extracts using multiple reaction monitoring mass spectrometry (MRM MS).

    Science.gov (United States)

    Mindaye, S T; Spiric, J; David, N A; Rabin, R L; Slater, J E

    2017-12-01

    German cockroach (GCr) allergen extracts are complex and heterogeneous products, and methods to better assess their potency and composition are needed for adequate studies of their safety and efficacy. The objective of this study was to develop an assay based on liquid chromatography and multiple reaction monitoring mass spectrometry (LC-MRM MS) for rapid, accurate, and reproducible quantification of 5 allergens (Bla g 1, Bla g 2, Bla g 3, Bla g 4, and Bla g 5) in crude GCr allergen extracts. We first established a comprehensive peptide library of allergens from various commercial extracts as well as recombinant allergens. Peptide mapping was performed using high-resolution MS, and the peptide library was then used to identify prototypic and quantotypic peptides to proceed with MRM method development. Assay development included a systematic optimization of digestion conditions (buffer, digestion time, and trypsin concentration), chromatographic separation, and MS parameters. Robustness and suitability were assessed following ICH (Q2 [R1]) guidelines. The method is precise (RSD  0.99, 0.01-1384 fmol/μL), and sensitive (LLOD and LLOQ MS, we quantified allergens from various commercial GCr extracts and showed considerable variability that may impact clinical efficacy. Our data demonstrate that the LC-MRM MS method is valuable for absolute quantification of allergens in GCr extracts and likely has broader applicability to other complex allergen extracts. Definitive quantification provides a new standard for labelling of allergen extracts, which will inform patient care, enable personalized therapy, and enhance the efficacy of immunotherapy for environmental and food allergies. © 2017 The Authors. Clinical & Experimental Allergy published by John Wiley & Sons Ltd. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

  11. Investigations of nuclear structure and nuclear reactions induced by complex projectiles. Technical progress report, November 1, 1978-October 31, 1979

    International Nuclear Information System (INIS)

    Sarantites, D.G.

    1979-01-01

    Experimental research on nuclear structure and reactions both published and in progress is summarized. Included are fusion reactions, strongly damped heavy ion collisions, and nuclear structure at high angular momentum. A list of publications is included

  12. Kinetics and mechanisms of the reactions of alkyl radicals with oxygen and with complexes of Co(III), Ru(III), and Ni(III)

    International Nuclear Information System (INIS)

    Kelley, D.

    1990-01-01

    The kinetics of the reactions of C 2 H 5 radical with Co(NH 3 ) 5 X 2+ , Ru(NH 3 ) 5 X 2+ , and Co(dmgH) 2 (X) (Y) (X = Br, Cl, N 3 , SCN; Y = H 2 O, CH 3 CN) complexes were studied using laser flash photolysis of ethylcobalt complexes. The kinetics were obtained by the kinetic probe method. Some relative rate constants were also determined by a competition method based on ethyl halide product ratios. The kinetics of colligation reactions of a series of alkyl radicals with β-Ni(cyclam) 2+ were studied using flaser flash photolysis of alkylcobalt complexes. Again, the kinetics were obtained by employing the kinetic probe competition method. The kinetics of the unimolecular homolysis of a series of RNi(cyclam)H 2 O 2+ were studied. Activation parameters were obtained for the unimolecular homolysis of C 2 H 5 Ni(cyclam)H 2 O 2+ . Kinetic and thermodynamic data obtained from these reactions were compared with those for the σ-bonded organometallic complexes. The kinetics of the unimolecular homolysis of a series of RNi(cyclam)H 2 O 2+ complexes were studied by monitoring the formation of the oxygen insertion product RO 2 Ni(cyclam)H 2 O 2+ . The higher rate constants for the reactions of alkyl radicals with oxygen in solution, as compared with those measured in the gas phase, were discussed. 30 refs

  13. Transition Metal Donor-Peptide-Acceptor Complexes: From Intramolecular Electron Transfer Reactions to the Study of Reactive Intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Isied, Stephan S.

    2003-03-11

    The trans-polyproline (PII) oligomers (Figure 1) are unusually rigid peptide structures which have been extensively studied by our group for peptide mediated intramolecular electron transfer (ET) at long distances. We have previously studied ET across a series of metal ion donor (D) acceptor (A) oligoproline peptides with different distances, driving forces and reorganizational energies. The majority of these experiments involve generating the ET intermediate using pulse radiolysis methods, although more recently photochemical methods are also used. Results of these studies showed that ET across peptides can vary by more than twelve orders of magnitude. Using ruthenium bipyridine donors, ET reaction rate constants across several proline residues (n = 4 - 9) occurred in the millisecond (ms) to {micro}s timescale, thus limiting the proline peptide conformational motions to only minor changes (far smaller than the large changes that occur on the ms to sec timescale, such as trans to cis proline isomerization). The present report describes our large data base of experimental results for D-peptide-A complexes in terms of a model where the involvement of both superexchange and hopping (hole and electron) mechanisms account for the long range ET rate constants observed. Our data shows that the change from superexchange to hopping mechanisms occurs at different distances depending on the type of D and A and their interactions with the peptides. Our model is also consistent with generalized models for superexchange and hopping which have been put forward by a number of theoretical groups to account for long range ET phenomena.

  14. Tantrums, Emotion Reactions and Their EEG Correlates in Childhood Benign Rolandic Epilepsy vs. Complex Partial Seizures: Exploratory Observations.

    Science.gov (United States)

    Potegal, Michael; Drewel, Elena H; MacDonald, John T

    2018-01-01

    We explored associations between EEG pathophysiology and emotional/behavioral (E/B) problems of children with two types of epilepsy using standard parent questionnaires and two new indicators: tantrums recorded by parents at home and brief, emotion-eliciting situations in the laboratory. Children with Benign Rolandic epilepsy (BRE, N = 6) reportedly had shorter, more angry tantrums from which they recovered quickly. Children with Complex Partial Seizures (CPS, N = 13) had longer, sadder tantrums often followed by bad moods. More generally, BRE correlated with anger and aggression; CPS with sadness and withdrawal. Scores of a composite group of siblings ( N = 11) were generally intermediate between the BRE and CPS groups. Across all children, high voltage theta and/or interictal epileptiform discharges (IEDs) correlated with negative emotional reactions. Such EEG abnormalities in left hemisphere correlated with greater social fear, right hemisphere EEG abnormalities with greater anger. Right hemisphere localization in CPS was also associated with parent-reported problems at home. If epilepsy alters neural circuitry thereby increasing negative emotions, additional assessment of anti-epileptic drug treatment of epilepsy-related E/B problems would be warranted.

  15. Tantrums, Emotion Reactions and Their EEG Correlates in Childhood Benign Rolandic Epilepsy vs. Complex Partial Seizures: Exploratory Observations

    Directory of Open Access Journals (Sweden)

    Michael Potegal

    2018-03-01

    Full Text Available We explored associations between EEG pathophysiology and emotional/behavioral (E/B problems of children with two types of epilepsy using standard parent questionnaires and two new indicators: tantrums recorded by parents at home and brief, emotion-eliciting situations in the laboratory. Children with Benign Rolandic epilepsy (BRE, N = 6 reportedly had shorter, more angry tantrums from which they recovered quickly. Children with Complex Partial Seizures (CPS, N = 13 had longer, sadder tantrums often followed by bad moods. More generally, BRE correlated with anger and aggression; CPS with sadness and withdrawal. Scores of a composite group of siblings (N = 11 were generally intermediate between the BRE and CPS groups. Across all children, high voltage theta and/or interictal epileptiform discharges (IEDs correlated with negative emotional reactions. Such EEG abnormalities in left hemisphere correlated with greater social fear, right hemisphere EEG abnormalities with greater anger. Right hemisphere localization in CPS was also associated with parent-reported problems at home. If epilepsy alters neural circuitry thereby increasing negative emotions, additional assessment of anti-epileptic drug treatment of epilepsy-related E/B problems would be warranted.

  16. Bio-waste corn-cob cellulose supported poly(hydroxamic acid) copper complex for Huisgen reaction: Waste to wealth approach.

    Science.gov (United States)

    Mandal, Bablu Hira; Rahman, Md Lutfor; Yusoff, Mashitah Mohd; Chong, Kwok Feng; Sarkar, Shaheen M

    2017-01-20

    Corn-cob cellulose supported poly(hydroxamic acid) Cu(II) complex was prepared by the surface modification of waste corn-cob cellulose through graft copolymerization and subsequent hydroximation. The complex was characterized by IR, UV, FESEM, TEM, XPS, EDX and ICP-AES analyses. The complex has been found to be an efficient catalyst for 1,3-dipolar Huisgen cycloaddition (CuAAC) of aryl/alkyl azides with a variety of alkynes as well as one-pot three-components reaction in the presence of sodium ascorbate to give the corresponding cycloaddition products in up to 96% yield and high turn over number (TON 18,600) and turn over frequency (TOF 930h -1 ) were achieved. The complex was easy to recover from the reaction mixture and reused six times without significant loss of its catalytic activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai [Los Alamos National Laboratory; Hengartner, Nick [Los Alamos National Laboratory

    2008-01-01

    We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, follows from the stochastic path Integral representation of the cumulant generating function of reaction events. In applications with a small number of chemIcal reactions, It produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, Interpretable representation and can be used for coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. As an example, we derive the coarse-grained description for a chain of biochemical reactions, and show that the coarse-grained and the microscopic simulations are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.

  18. Mass transfer with complex chemical reactions in gas–liquid systems : two-step reversible reactions with unit stoichiometric and kinetic orders

    NARCIS (Netherlands)

    Vas Bhat, R.D.; Kuipers, J.A.M.; Versteeg, G.F.

    2000-01-01

    An absorption model to study gas–liquid mass transfer accompanied by reversible two-step reactions in the liquid phase has been presented. This model has been used to determine mass transfer rates, enhancement factors and concentration profiles over a wide range of process conditions. Although

  19. Mass transfer with complex chemical reactions in gas-liquid systems: two-step reversible reactions with unit stoichiometric and kinetic orders

    NARCIS (Netherlands)

    Vas bhat, R.D.; Kuipers, J.A.M.; Versteeg, Geert

    2000-01-01

    An absorption model to study gas¿liquid mass transfer accompanied by reversible two-step reactions in the liquid phase has been presented. This model has been used to determine mass transfer rates, enhancement factors and concentration profiles over a wide range of process conditions. Although

  20. Synthesis of cis - and trans-diisothiocyanato-bis(NHC) complexes of nickel(II) and applications in the Kumada-Corriu reaction

    KAUST Repository

    Jothibasu, Ramasamy

    2010-09-13

    Metathetical reaction of AgSCN with a series of trans-dihalido-bis(carbene) nickel(II) complexes in CH3CN readily afforded the novel diisothiocyanato-bis(carbene) complexes [Ni(NCS)2(NHC)2] (trans-2a, NHC = 1,3-diisopropylbenzimidazolin-2-ylidene; trans-2b, NHC = 1,3-diisobutylbenzimidazolin-2-ylidene; trans-2c, NHC = 1,3- dibenzylbenzimidazolin-2-ylidene; cis-2d, NHC = 1,3-di(2-propenyl) benzimidazolin-2-ylidene; cis-2e, NHC = 1-propyl-3-methylbenzimidazolin-2- ylidene) as greenish-yellow powders in moderate to good yields. While dihalido-bis(carbene) Ni(II) complexes exclusively form trans-complexes, a trans-cis isomerization occurs upon halido-isothiocyanato exchange with complexes bearing less bulky carbene ligands, i.e., cis-2d/e. DFT calculations indicated that this isomerization can be attributed to a reduced energy difference between trans- and cis-isomers of diisothiocyanato complexes. All complexes have been characterized by multinuclear NMR spectroscopy, ESI mass spectrometry, and X-ray diffraction analysis. A catalytic study revealed that cis-complexes generally exhibit greater activities in the Kumada-Corriu coupling reaction. © 2010 American Chemical Society.

  1. Structural and biochemical analyses reveal insights into covalent flavinylation of the Escherichia coli Complex II homolog quinol:fumarate reductase

    Energy Technology Data Exchange (ETDEWEB)

    Starbird, C.A.; Maklashina, Elena; Sharma, Pankaj; Qualls-Histed, Susan; Cecchini, Gary; Iverson, T.M. (VA); (UCSF); (Vanderbilt)

    2017-06-14

    The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the E. coli QFR FrdA subunit. Using a ΔsdhE E. coli strain, we show that the requirement for the assembly factor depends on the cellular redox environment. We next identified residues important for the covalent attachment and selected the FrdAE245 residue, which contributes to proton shuttling during fumarate reduction, for detailed biophysical and structural characterization. We found that QFR complexes containing FrdAE245Q have a structure similar to that of the WT flavoprotein, but lack detectable substrate binding and turnover. In the context of the isolated FrdA subunit, the anticipated assembly intermediate during covalent flavinylation, FrdAE245 variants had stability similar to that of WT FrdA, contained noncovalent FAD, and displayed a reduced capacity to interact with SdhE. However, small-angle X-ray scattering (SAXS) analysis of WT FrdA cross-linked to SdhE suggested that the FrdAE245 residue is unlikely to contribute directly to the FrdA-SdhE protein-protein interface. We also found that no auxiliary factor is absolutely required for flavinylation, indicating that the covalent flavinylation is autocatalytic. We propose that multiple factors, including the SdhE assembly factor and bound dicarboxylates, stimulate covalent flavinylation by preorganizing the active site to stabilize the quinone-methide intermediate.

  2. Thermodynamics of axial substitution and kinetics of reactions with amino acids for the paddlewheel complex tetrakis(acetato)chloridodiruthenium(II,III).

    Science.gov (United States)

    Santos, Rodrigo L S R; van Eldik, Rudi; de Oliveira Silva, Denise

    2012-06-18

    The known paddlewheel, tetrakis(acetato)chloridodiruthenium(II,III), offers a versatile synthetic route to a novel class of antitumor diruthenium(II,III) metallo drugs, where the equatorial ligands are nonsteroidal anti-inflammatory carboxylates. This complex was studied here as a soluble starting prototype model for antitumor analogues to elucidate the reactivity of the [Ru(2)(CH(3)COO)(4)](+) framework. Thermodynamic studies on equilibration reactions for axial substitution of water by chloride and kinetic studies on reactions of the diaqua complexes with the amino acids glycine, cysteine, histidine, and tryptophan were performed. The standard thermodynamic reaction parameters ΔH°, ΔS°, and ΔV° were determined and showed that both of the sequential axial substitution reactions are enthalpy driven. Kinetic rate laws and rate constants were determined for the axial substitution reactions of coordinated water by the amino acids that gave the corresponding aqua(amino acid)-Ru(2) substituted species. The results revealed that the [Ru(2)(CH(3)COO)(4)](+) paddlewheel framework remained stable during the axial ligand substitution reactions and was also mostly preserved in the presence of the amino acids.

  3. Positive photocatalysis of a Diels-Alder reaction by quenching of excited naphthalene-indole charge-transfer complex with cyclohexadiene.

    Science.gov (United States)

    Gonzalez-Béjar, María; Stiriba, Salah-Eddine; Miranda, Miguel A; Pérez-Prieto, Julia

    2007-02-01

    [reaction: see text] Naphthalene photo-catalyzes formation of cyclohexadiene-indole cycloadducts in a wavelength-dependent process. Steady-state irradiation and time-resolved fluorescence studies agree well with NP-InH ground-state charge transfer (CT) complexes as the key species responsible for the photo-catalyzed process.

  4. Reactions of zinc hydride and magnesium hydride with pyridine; synthesis and characterization of 1,4-dihydro-1-pyridylzinc and -magnesium complexes

    NARCIS (Netherlands)

    Koning, A.J. de; Boersma, J.; Kerk, G.J.M. van der

    1980-01-01

    The synthesis and characterization of 1,4-dihydro-1-pyridylzinc and -magnesium complexes are described. Zinc hydride and magnesium hydride dissolve in and react with pyridine, and the reaction has been studied in detail in the case of zinc hydride. Evaporation of the solvent after 1–2 hours at 0°C

  5. Mixed N-Heterocyclic Carbene-Bis(oxazolinyl)borato Rhodium and Iridium Complexes in Photochemical and Thermal Oxidative Addition Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Songchen [Ames Laboratory; Manna, Kuntal [Ames Laboratory; Ellern, Arkady [Ames Laboratory; Sadow, Aaron D [Ames Laboratory

    2014-12-08

    In order to facilitate oxidative addition chemistry of fac-coordinated rhodium(I) and iridium(I) compounds, carbene–bis(oxazolinyl)phenylborate proligands have been synthesized and reacted with organometallic precursors. Two proligands, PhB(OxMe2)2(ImtBuH) (H[1]; OxMe2 = 4,4-dimethyl-2-oxazoline; ImtBuH = 1-tert-butylimidazole) and PhB(OxMe2)2(ImMesH) (H[2]; ImMesH = 1-mesitylimidazole), are deprotonated with potassium benzyl to generate K[1] and K[2], and these potassium compounds serve as reagents for the synthesis of a series of rhodium and iridium complexes. Cyclooctadiene and dicarbonyl compounds {PhB(OxMe2)2ImtBu}Rh(η4-C8H12) (3), {PhB(OxMe2)2ImMes}Rh(η4-C8H12) (4), {PhB(OxMe2)2ImMes}Rh(CO)2 (5), {PhB(OxMe2)2ImMes}Ir(η4-C8H12) (6), and {PhB(OxMe2)2ImMes}Ir(CO)2 (7) are synthesized along with ToMM(η4-C8H12) (M = Rh (8); M = Ir (9); ToM = tris(4,4-dimethyl-2-oxazolinyl)phenylborate). The spectroscopic and structural properties and reactivity of this series of compounds show electronic and steric effects of substituents on the imidazole (tert-butyl vs mesityl), effects of replacing an oxazoline in ToM with a carbene donor, and the influence of the donor ligand (CO vs C8H12). The reactions of K[2] and [M(μ-Cl)(η2-C8H14)2]2 (M = Rh, Ir) provide {κ4-PhB(OxMe2)2ImMes'CH2}Rh(μ-H)(μ-Cl)Rh(η2-C8H14)2 (10) and {PhB(OxMe2)2ImMes}IrH(η3-C8H13) (11). In the former compound, a spontaneous oxidative addition of a mesityl ortho-methyl to give a mixed-valent dirhodium species is observed, while the iridium compound forms a monometallic allyl hydride. Photochemical reactions of dicarbonyl compounds 5 and 7 result in C–H bond oxidative addition providing the compounds {κ4-PhB(OxMe2)2ImMes'CH2}RhH(CO) (12) and {PhB(OxMe2)2ImMes}IrH(Ph)CO (13). In 12, oxidative addition results in cyclometalation of the mesityl ortho-methyl similar to 10, whereas the iridium compound reacts with the benzene solvent to give a rare crystallographically characterized cis

  6. Synthesis of unsymmetric bipyridine-Pt(II) -alkynyl complexes through post-click reaction with emission enhancement characteristics and their applications as phosphorescent organic light-emitting diodes.

    Science.gov (United States)

    Li, Yongguang; Tsang, Daniel Ping-Kuen; Chan, Carmen Ka-Man; Wong, Keith Man-Chung; Chan, Mei-Yee; Yam, Vivian Wing-Wah

    2014-10-13

    Two unsymmetric bipyridine-platinum(II)-alkynyl complexes have been synthesised by a post-click reaction. These metal complexes are found to exhibit emission enhancement properties. The photoluminescence quantum yield can be significantly increased from 0.03 in solution to 0.72 in solid-state thin films. Efficient solution-processable organic light-emitting diodes have been fabricated by utilizing these complexes as phosphorescent dopants. A high external quantum efficiency of up to 5.8% has been achieved. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. A highly selective and non-reaction based chemosensor for the detection of Hg2+ ions using a luminescent iridium(III complex.

    Directory of Open Access Journals (Sweden)

    Daniel Shiu-Hin Chan

    Full Text Available We report herein a novel luminescent iridium(III complex with two hydrophobic carbon chains as a non-reaction based chemosensor for the detection of Hg(2+ ions in aqueous solution (<0.002% of organic solvent attributed to the probe solution. Upon the addition of Hg(2+ ions, the emission intensity of the complex was significantly enhanced and this change could be monitored by the naked eye under UV irradiation. The iridium(III complex shows high specificity for Hg(2+ ions over eighteen other cations. The system is capable of detecting micromolar levels of Hg(2+ ions, which is within the range of many chemical systems.

  8. Linear-dendritic supramolecular complexes as nanoscale reaction vessels for "green" chemistry. Diels-Alder reactions between fullerene C60 and polycyclic aromatic hydrocarbons in aqueous medium.

    Science.gov (United States)

    Simonyan, Arsen; Gitsov, Ivan

    2008-10-21

    This study describes the first Diels-Alder (DA) reaction performed in aqueous medium with highly hydrophobic compounds-fullerene (C 60) as the dienophile and anthracene (An) or tetracene (Tet) as the dienes, respectively. The reactions are performed in nanocontainers, constructed by self-assembly of linear-dendritic amphiphilic copolymers with poly(ethylene glycol), PEG or poly(ethylene oxide), PEO as the hydrophilic blocks and poly(benzyl ether) monodendrons as the hydrophobic fragments: G3PEO13k, dG3 and dG2. Comparative studies under identical conditions are carried out with an amphiphilic linear-linear copolymer, poly(styrene)1800- block-PEO2100, PSt-PEO, and the nonionic surfactant Igepal CO-720, IP720. The binding affinity of supermolecules built of these amphiphiles toward the DA reagents decreases in the following order: G3PEO13k > dG3 > PSt-PEO > dG2 > IP720. The kinetic constant of binding is evaluated for tetracene and decreases in a similar fashion: 5 x 10 (-7) M/min (G3PEO13k), through 4 x 10 (-7) M/min (PSt-PEO) down to 1.5 x 10 (-7) M/min for IP720. The mobility of substrates encapsulated in the micellar core, estimated by pyrene fluorescence decay, is 95-121 ns for the micelles of the linear-dendritic copolymers and notably higher for PSt-PEO (152 ns), revealing the much denser interior of the linear analogue. The apparent kinetic constant for the DA reaction of C 60 and Tet within the G3PEO13k supermolecule in aqueous medium is markedly higher than in organic solvent (toluene), 208 vs 1.82 M /min. With G3PEO13k the conversions reach 49% for the DA reaction between C 60 and An, and 55% for C 60 and Tet. Besides the monoadduct (26.5% yield) the reaction with An produces exclusively increasing amounts of D 2 h -symmetric antipodal bis-adduct, whose yield reaches up to 22.5% after 48 h. In addition to the environmentally friendly conditions notable advantages of the synthetic strategy described are the extended stability of the linear

  9. Insights into the catalytic activity of [Pd(NHC)(cin)Cl] (NHC = IPr, IPrCl, IPrBr) complexes in the Suzuki-Miyaura reaction

    KAUST Repository

    Nolan, Steven Patrick

    2017-09-06

    The influence of C4,5-halogenation on palladium N-heterocyclic carbene complexes and their activity in the Suzuki-Miyaura reaction have been investigated. Two [Pd(NHC)(cin)Cl] complexes bearing IPrCl and IPrBr ligands were synthesized. After determining electronic and steric properties of these ligands, their properties were compared to those of [Pd(IPr)(cin)Cl]. The three palladium complexes were studied using DFT calculations to delineate their behaviour in the activation step leading to the putative 12-electron active catalyst. Experimentally, their catalytic activity in the Suzuki-Miyaura reaction involving a wide range of coupling partners (30 entries) at low catalyst loading was studied.

  10. Reaction of CO2 with propylene oxide and styrene oxide catalyzed by a chromium(III) amine-bis(phenolate) complex.

    Science.gov (United States)

    Dean, Rebecca K; Devaine-Pressing, Katalin; Dawe, Louise N; Kozak, Christopher M

    2013-07-07

    A diamine-bis(phenolate) chromium(III) complex, {CrCl[O2NN'](BuBu)}2 catalyzes the copolymerization of propylene oxide with carbon dioxide. The synthesis of this metal complex is straightforward and it can be obtained in high yields. This catalyst incorporates a tripodal amine-bis(phenolate) ligand, which differs from the salen or salan ligands typically used with Cr and Co complexes that have been employed as catalysts for the synthesis of such polycarbonates. The catalyst reported herein yields low molecular weight polymers with narrow polydispersities when the reaction is performed at room temperature. Performing the reaction at elevated temperatures causes the selective synthesis of propylene carbonate. The copolymerization activity for propylene oxide and carbon dioxide, as well as the coupling of carbon dioxide and styrene oxide to give styrene carbonate are presented.

  11. Studies of complex fragment emission in heavy ion reactions. Progress report, January 1, 1993 - September 1, 1995

    International Nuclear Information System (INIS)

    Charity, R.J.; Sobotka, L.G.

    1995-01-01

    This work involves the study of low and intermediate energy heavy-ion nuclear reactions. This work has two foci. First, the authors desired to learn about the properties of both nuclei and nuclear matter under abnormal conditions. Their efforts towards this end run abreast of those for their second focus which is the study of the relevant reaction mechanisms. The two objectives are inexorably linked because their experimental laboratory for studying nuclear properties is a dynamic one. Their task is to answer the questions of how nuclear and nuclear matter properties are reflected in the dynamics of the reactions. The second objective also has great intrinsic value in that they can anticipate improving upon their understanding of the reaction mechanism themselves and therefore to the response characteristics of finite, perhaps non-equilibrium, strongly interacting systems. The program has been: to study the dynamics of fusion reactions, specifically the dynamics of energy, mass, and angular momentum deposition. This work includes reactions near the Coulomb barrier, where fusion dominates the reaction cross section as well as higher energies where incomplete fusion reactions are the primary reactions. This includes the dynamics of fission, still the premier example of collective nuclear motion, as a function of excitation, spin, mass, and mass asymmetry. The authors push these kinds of studies into the intermediate energy domain, and where novel reaction scenarios are predicted. They have studied very central and peripheral collisions between very massive nuclei, and simplified projectile fragmentation reactions utilizing medium to light mass projectiles. The study of central collisions has shown us the importance of collective expansion. The study of peripheral collisions between very heavy nuclei has demonstrated the importance of dynamical production of fragments from the neck region

  12. THE RESPIRATORY SUBSTRATE RHODOQUINOL INDUCES Q-CYCLE BYPASS REACTIONS IN THE YEAST CYTOCHROME bc1 COMPLEX - MECHANISTIC AND PHYSIOLOGICAL IMPLICATIONS

    International Nuclear Information System (INIS)

    Cape, Jonathan L.; Strahan, Jeff R.; Lenaeus, Michael J.; Yuknis, Brook A.; Le, Trieu T.; Shepherd, Jennifer; Bowman, Michael K.; Kramer, David M.

    2005-01-01

    The mitochondrial cytochrome bc1 complex catalyzes the transfer of electrons from ubiquinol to cyt c, while generating a proton motive force for ATP synthesis, via the ''Qcycle'' mechanism. Under certain conditions, electron flow through the Q-cycle is blocked at the level of a reactive intermediate in the quinol oxidase site of the enzyme, resulting in ''bypass reactions'', some of which lead to superoxide production. Using analogs of the respiratory substrates, ubiquinol-3 and rhodoquinol-3, we show that the relative rates of Q-cycle bypass reactions in the Saccharomyces cerevisiae cyt bc1 complex are highly dependent, by a factor of up to one hundred-fold, on the properties of the substrate quinol. Our results suggest that the rate of Q-cycle bypass reactions is dependent on the steady state concentration of reactive intermediates produced at the quinol oxidase site of the enzyme. We conclude that normal operation of the Q-cycle requires a fairly narrow window of redox potentials, with respect to the quinol substrate, to allow normal turnover of the complex while preventing potentially damaging bypass reactions

  13. Studies of ruthenium complexes, 8. Kinetic studies of the thermal substitution reaction of hexaammine and cis--dihalogenotetraammineruthenium(III) complexes in the solid state

    Energy Technology Data Exchange (ETDEWEB)

    Ohyoshi, A; Hiraki, S; Odate, T; Kohata, S; Oda, J [Kumamoto Univ. (Japan). Faculty of Engineering

    1975-01-01

    The kinetics of the thermal substitution reaction of hexaamineruthenium (III) halides and cis-dihalogenotetraamineruthenium (III) halides have been studied in the solid state. The reaction rates and kinetic parameters were determined for these two reactions; (Ru(NH/sub 3/)/sub 6/)X/sub 3/..-->..(RuX(NH/sub 3/)/sub 5/)X/sub 2/+NH/sub 3/, (X=Br, I) and cis - (RuX/sub 2/(NH/sub 3/)/sub 4/)X..-->..(RuX/sub 3/(NH/sub 3/)/sub 3/)+NH/sub 3/, (X=Cl, Br). The values of the rate constant, the activation energy, and the activation entropy were 2.10x10/sup -5/ s/sup -1/ (at 161/sup 0/C), 23.2 kcal mol/sup -1/, and -29.3 e.u. for the hexaamine bromide, and 2.92x10/sup -5/ s/sup -1/ (at 162/sup 0/C), 31.3 kcal mol/sup -1/, and -10.1 e.u. for the cis-dibromotetraamine bromide. The Ssub(N)2 mechanism is more probable for the former reaction, while the Ssub(N)1 mechanism is more probable for the latter reaction.

  14. eQuilibrator--the biochemical thermodynamics calculator.

    Science.gov (United States)

    Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like 'how much Gibbs energy is released by ATP hydrolysis at pH 5?' are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use.

  15. eQuilibrator—the biochemical thermodynamics calculator

    Science.gov (United States)

    Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. PMID:22064852

  16. Transition metal complexes with pyrazole-based ligands.Part 29. Reactions of zinc(II and mercury(II thiocyanate with 4-acetyl-3-amino-5-methylpyrazole

    Directory of Open Access Journals (Sweden)

    KATALIN MÉSZÁROS SZÉCSÉNYI

    2009-11-01

    Full Text Available The work is concerned with the crystal and molecular structures of zinc(II and mercury(II complexes with 4-acetyl-3-amino-5-methyl-pyrazole (aamp of the coordination formulae [Zn(NCS2(aamp2] and (Haamp2[Hg(SCN4]. The zinc(II complex was obtained by the reaction of a warm methanolic solution of aamp with a mixture of zinc(II nitrate and ammonium thiocyanate, whereas the mercury(II complex was prepared by the reaction of a warm ethanolic solution of aamp and a warm, slightly acidified aqueous solution of [Hg(SCN4]2-. Both complexes have a tetrahedral geometry, which in the case of zinc complex is formed by monodentate coordination of two aamp molecules and two isothiocyanate groups. The Zn(II and Hg(II atoms have significantly deformed coordination geometry. In both crystal structures the pyrazole derivative has a planar form, probably stabilized by an intramolecular N–H···O hydrogen bond. Apart from the X-ray structural analysis, the isolated complexes were characterized by elemental analysis, IR spectroscopy, conductometric measurements and thermal analysis.

  17. Utility of Lithium in Rare-Earth Metal Reduction Reactions to Form Nontraditional Ln2+ Complexes and Unusual [Li(2.2.2-cryptand)]1+ Cations.

    Science.gov (United States)

    Huh, Daniel N; Darago, Lucy E; Ziller, Joseph W; Evans, William J

    2018-02-19

    The utility of lithium compared to other alkali metals in generating Ln 2+ rare-earth metal complexes via reduction of Ln 3+ precursors in reactions abbreviated as LnA 3 /M (Ln = rare-earth metal; A = anionic ligand; M = alkali metal) is described. Lithium reduction of Cp' 3 Ln (Cp' = C 5 H 4 SiMe 3 ; Ln = Y, Tb, Dy, Ho) under Ar in the presence of 2.2.2-cryptand (crypt) forms new examples of crystallographically characterizable Ln 2+ complexes of these metals, [Li(crypt)][Cp' 3 Ln]. In each complex, lithium is found in an N 2 O 4 donor atom coordination geometry that is unusual for the cryptand ligand. Magnetic susceptibility data on these new examples of nontraditional divalent lanthanide complexes are consistent with 4f n 5d 1 electronic configurations. The Dy and Ho complexes have exceptionally high single-ion magnetic moments, 11.35 and 11.67 μ B , respectively. Lithium reduction of Cp' 3 Y under N 2 at -35 °C forms the Y 2+ complex (Cp' 3 Y) 1- , which reduces dinitrogen upon warming to room temperature to generate the (N 2 ) 2- complex [Cp' 2 Y(THF)] 2 (μ-η 2 :η 2 -N 2 ). These results provide insight on the factors that lead to reduced dinitrogen complexes and/or stable divalent lanthanide complexes as a function of the specific reducing agent and conditions.

  18. Asymmetric synthesis of α-amino acids via homologation of Ni(II) complexes of glycine Schiff bases. Part 3: Michael addition reactions and miscellaneous transformations.

    Science.gov (United States)

    Aceña, José Luis; Sorochinsky, Alexander E; Soloshonok, Vadim

    2014-09-01

    The major goal of this review is a critical discussion of the literature data on asymmetric synthesis of α-amino acids via Michael addition reactions involving Ni(II)-complexes of amino acids. The material covered is divided into two conceptually different groups dealing with applications of: (a) Ni(II)-complexes of glycine as C-nucleophiles and (b) Ni(II)-complexes of dehydroalanine as Michael acceptors. The first group is significantly larger and consequently subdivided into four chapters based on the source of stereocontrolling element. Thus, a chiral auxiliary can be used as a part of nucleophilic glycine Ni(II) complex, Michael acceptor or both, leading to the conditions of matching vs. mismatching stereochemical preferences. The particular focus of the review is made on the practical aspects of the methodology under discussion and mechanistic considerations.

  19. Antioxidative capacity and binding affinity of the complex of green tea catechin and beta-lactoglobulin glycated by the Maillard reaction.

    Science.gov (United States)

    Perusko, Marija; Al-Hanish, Ayah; Mihailovic, Jelena; Minic, Simeon; Trifunovic, Sara; Prodic, Ivana; Cirkovic Velickovic, Tanja

    2017-10-01

    Major green tea catechin, epigallocatechin-3-gallate (EGCG), binds non-covalently to numerous dietary proteins, including beta-lactoglobulin of cow's milk. The effects of glycation of proteins via Maillard reaction on the binding capacity for polyphenols and the antiradical properties of the formed complexes have not been studied previously. Binding constant of BLG glycated by milk sugar lactose to EGCG was measured by the method of fluorophore quenching. Binding of EGCG was confirmed by CD and FTIR. The antioxidative properties of the complexes were examined by measuring ABTS radical scavenging capacity, superoxide anion scavenging capacity and total reducing power assay. Glycation of BLG does not significantly influence the binding constant of EGCG for the protein. Conformational changes were observed for both native and glycated BLG upon complexation with EGCG. Masking effect of polyphenol complexation on the antioxidative potential of the protein was of the similar degree for both glycated BLG and native BLG. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Syntheses, crystal structures and properties of novel copper(II) complexes obtained by reactions of copper(II) sulfate pentahydrate with tripodal ligands.

    Science.gov (United States)

    Zhao, Wei; Fan, Jian; Song, You; Kawaguchi, Hiroyuki; Okamura, Taka-aki; Sun, Wei-Yin; Ueyama, Norikazu

    2005-04-21

    Three novel metal-organic frameworks (MOFs), [Cu(1)SO4].H2O (4), [Cu2(2)2(SO4)2].4H2O (5) and [Cu(3)(H2O)]SO4.5.5H2O (6), were obtained by hydrothermal reactions of CuSO4.5H2O with the corresponding ligands, which have different flexibility. The structures of the synthesized complexes were determined by single-crystal X-ray diffraction analyses. Complex 4 has a 2D network structure with two types of metallacycles. Complex 5 also has a 2D network structure in which each independent 2D sheet contains two sub-layers bridged by oxygen atoms of the sulfate anions. Complex 6 has a 2D puckered structure in which the sulfate anions serve as counter anions, which are different from those in complexes 4 (terminators) and 5 (bridges). The different structures of complexes 4, 5 and 6 indicate that the nature of organic ligands affected the structures of the assemblies greatly. The magnetic behavior of complex 5 and anion-exchange properties of complex 6 were investigated.

  1. Asymmetric Diels–Alder reaction with >C=P– functionality of the 2-phosphaindolizine-η1-P-aluminium(O-menthoxy dichloride complex: experimental and theoretical results

    Directory of Open Access Journals (Sweden)

    Rajendra K. Jangid

    2013-02-01

    Full Text Available The Diels–Alder reaction of the 2-phosphaindolizine-η1-P-aluminium(O-menthoxy dichloride complex with dimethylbutadiene was investigated experimentally and computationally. The >C=P– functionality of the complex reacts with 2,3-dimethylbutadiene with complete diastereoselectivity to afford [2 + 4] cycloadducts. Calculation of the model substrate, 3-methoxycarbonyl-1-methyl-2-phosphaindolizine-P-aluminium(O-menthoxy dichloride (7a, at the DFT (B3LYP/6-31+G* level reveals that the O-menthoxy moiety blocks the Re face of the >C=P– functionality, due to which the activation barrier of the Diels–Alder reaction of 7a with 1,3-butadiene, involving its attack from the Si face, is lower. It is found that in this case, the exo approach of the diene is slightly preferred over the endo approach.

  2. Reactions of uranium (III) and (IV) compounds with ketones, nitriles and acid chlorides. Towards a use of uranium complexes in organic synthesis

    International Nuclear Information System (INIS)

    Adam, Raymond

    1993-01-01

    In this research thesis, the author shows that various organic molecules can be interestingly transformed into uranium complexes with degrees of oxidation of +3 or +4. In a first part, the author describes reactions of carbonyl compounds with the UCl 4 -Na(Hg) reducing system. Then, he addresses reductions of ketones, nitriles and acid chlorides by a uranium (III) complex: Cp 3 U(THF). The third part reports a detailed study of the reduction of ketones by U(BH 4 ) 4 [fr

  3. Program-technical complex for collection, processing and archiving of the physical information about chain nuclear reaction based on VMEbus. I. Subsystem for energy supplying control

    International Nuclear Information System (INIS)

    Alpatov, S.V.; Golovanova, Eh.Z.; Gorskaya, E.A.; Dobryanskij, V.M.; Makan'kin, A.M.; Puzynin, V.I.; Samojlov, V.N.; Cheker, A.V.

    1996-01-01

    The substantiation of choice of the hardware and software for integration in program-technical complex is given. The complex is intended for automation of the physical experiments connected with chain nuclear reaction investigations. The subsystem for energy supplying control of experiment is considered in detail. For building the subsystem the 'client-server' architecture is used. The subsystem includes the work station and VMEbus measuring modules in the net. The description of the programs and result formats are given. 5 refs., 6 figs

  4. Survey on synthesis and reaction of environmentally benign water-soluble metal complex catalysts; Kankyo chowagata suiyosei sakutai shokubai no gosei hanno no chosa

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    This report describes the research trend survey results on the synthesis and reaction of water-soluble metal complexes which are regarded as environmentally benign catalysts. For the synthesis and catalysis of water-soluble complexes, synthetic methods of water-soluble phosphines, such as sulfonated TPPMS and TPPTS, are described in detail. Synthesis and reactivity of hydroxymethylphosphines are introduced, and the application of electrospray mass spectroscopy is elucidated as a tool for the analysis of them. Changes of the application of transition metal complexes with water-soluble phosphines to catalysis are described. Dual catalysts which have both functions of phase transfer catalysts and homogeneous catalysts are introduced. Concept of counter phase transfer catalysts is also introduced, and some catalytic reactions are described. In addition, this report introduces catalysis of water-soluble polymer-supported metal complexes, immobilization of metal colloids with water-soluble ligands and their analysis, and water-soluble complexes as hybrid catalysts. 144 refs., 94 figs., 10 tabs.

  5. Pulse radiolysis and ab initio SCF MO studies of hydroxyl radical reactions with 2,2'-bipyridine and its complexes with transition metal ions

    Energy Technology Data Exchange (ETDEWEB)

    Maliyachel, A C

    1984-01-01

    In the present study, reactions of hydroxyl radical with 2,2'-bipyridine (bpy) and complexes of iron(II) and cobalt(III) containing 2,2'-bipyridine and/or cyanide as ligands have been investigated by pulse radiolysis and also by ab initio self-consistent field, molecular orbital (SCF MO) theoretical techniques for 2,2'-bipyridine and pyridines. In the pulse radiolysis experiments, the nascent products of hydroxyl radical reactions with these compounds have been characterized through their spectral and kinetic properties. All these reactions occur at near diffusion controlled rates to give transient products having absorption in the ultraviolet, visible and, in some cases, near-IR region. The primary reactions of OH are considered to take place by addition mechanisms in the cases of 2,2'-bipyridine, (Fe(bpy)/sub 3/)/sup 2 +/, (Fe(DMbpy)/sub 3/)/sup 2 +/ and (Co(bpy)/sub 3/)/sup 3 +/. With (Fe(pby)/sub 2/(CN)/sub 2/) and (Fe(bpy)(CN)/sub 4/)/sup 2 -/, both addition and charge transfer processes occur. The present study indicates that hydroxyl radical reactions with 2,2'-bipyridine can be considerably altered by complexation with metal ions such as iron(II) and cobalt(III), and the factors associated with this are discussed. In the second part of this work, ab initio SCF MO calculations have been performed for the reactions of OH with pyridine, pyridinium ion and 2,2'-bipyridine. Based on the calculated total energies for the various hydroxy radical products, the relative stability of OH addition products are found to be for pyridine, meta-C > N >> para-C > ortho-C; for pyridinium ion, meta-C >> para-C > ortho-C > N, and for 2,2'- bipyridine, C/sub 5/ > C/sub 6/ > C/sub 3/ > C/sub 4/ > N.

  6. PROCEEDINGS OF THE THIRD CONFERENCE ON REACTIONS BETWEEN COMPLEX NUCLEI, HELD AT ASILOMAR (PACIFIC GROVE, CALIFORNIA) APRIL 14-18, 1963

    Energy Technology Data Exchange (ETDEWEB)

    Ghiorso, A; Diamond, R M; Conzett, H E [eds.

    1963-07-01

    The goals of the meeting were: to provide information on the developments in the field of reactions between complex nuclei since the second conference held in Gatlinburg, TN in 1960; to allow an informal exchange of ideas bwtween scientists of universities/laboratories participating in heavy-ion research; and, to point to fruitful research for the future. Conference papers and a conference summary are included in these proceedings.

  7. Novel bipyridinyl oxadiazole-based metal coordination complexes: High efficient and green synthesis of 3,4-dihydropyrimidin-2(1H)-ones through the Biginelli reactions

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jin-Hua; Zhang, E. [Department of Chemical Engineering, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353 (China); Tang, Gui-Mei, E-mail: meiguit@163.com [Department of Chemical Engineering, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353 (China); Wang, Yong-Tao, E-mail: ceswyt@qlu.edu.cn [Department of Chemical Engineering, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353 (China); Cui, Yue-Zhi [Department of Chemical Engineering, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353 (China); Ng, Seik Weng [Department of Chemistry, University of Malaya, Kuala Lumpur 50603 (Malaysia)

    2016-09-15

    Three new metal coordination complexes, namely, [Co(BPO){sub 2}(H{sub 2}O){sub 4}](BS){sub 2}(H{sub 2}O){sub 2} (1), [Co(BPO){sub 2}(H{sub 2}O){sub 4}](ABS){sub 2}(H{sub 2}O){sub 2} (2), [Co(BPO){sub 2}(H{sub 2}O){sub 4}](MBS){sub 2}(H{sub 2}O){sub 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. - Graphical abstract: Three new metal coordination complexes with bipyridinyl-oxadiazole were obtained under hydrothermal conditions, which display a zero-dimensional motif, and show high efficiency for the green synthesis of a variety of 3,4-dihydropyrimidin-2(1H)-ones 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. Display Omitted.

  8. Reusable Polymer-Supported Terpyridine Palladium Complex for Suzuki-Miyaura, Mizoroki-Heck, Sonogashira, and Tsuji-Trost Reaction in Water

    Directory of Open Access Journals (Sweden)

    Takuya Nagamine

    2011-03-01

    Full Text Available A novel heterogeneous transition-metal catalyst comprising a polymer-supported terpyridine palladium(II complex was prepared and found to promote the Suzuki-Miyaura, Mizoroki-Heck, Sonogashira, and Tsuji-Trost, reactions in water under aerobic conditions with a high to excellent yield. The catalyst was recovered by simple filtration and directly reused several times without loss of catalytic activity.

  9. Rational Design in Catalysis: A Mechanistic Study of β-Hydride Eliminations in Gold(I) and Gold(III) Complexes Based on Features of the Reaction Valley.

    Science.gov (United States)

    Castiñeira Reis, Marta; López, Carlos Silva; Kraka, Elfi; Cremer, Dieter; Faza, Olalla Nieto

    2016-09-06

    β-Hydride eliminations for ethylgold(III) dichloride complexes are identified as reactions with an unusually long prechemical stage corresponding to the conformational preparation of the reaction complex and spanning six phases. The prechemical process is characterized by a geared rotation of the L-Au-L group (L = Cl) driving methyl group rotation and causing a repositioning of the ligands. This requires more than 28 kcal/mol of the total barrier of 34.0 kcal/mol, according to the unified reaction valley approach, which also determines that the energy requirements of the actual chemical process leading to the β-elimination product are only about 5.5 kcal/mol. A detailed mechanistic analysis was used as a basis for a rational design of substrates (via substituents on the ethyl group) and/or ligands, which can significantly reduce the reaction barrier. This strategy takes advantage of either a higher trans activity of the ligands or a tuned electronic demand of the ethyl group. The β-hydride elimination of gold(I) was found to suffer from strong Coulomb and exchange repulsion when a positively charged hydrogen atom enforces a coordination position in a d(10)-configured gold atom, thus triggering an unassisted σ-π Au(I)-C conversion.

  10. Simulation methods with extended stability for stiff biochemical Kinetics

    Directory of Open Access Journals (Sweden)

    Rué Pau

    2010-08-01

    Full Text Available Abstract Background With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (biochemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA. The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be well-behaved, leading to significantly larger step sizes. Conclusions The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (biochemical systems.

  11. Synthesis of New Chiral Benzimidazolylidene–Rh Complexes and Their Application in Asymmetric Addition Reactions of Organoboronic Acids to Aldehydes

    Directory of Open Access Journals (Sweden)

    Weiping He

    2016-09-01

    Full Text Available A series of novel chiral N-heterocyclic carbene rhodium complexes (NHC–Rh based on benzimidazole have been prepared, and all of the NHC–Rh complexes were fully characterized by NMR and mass spectrometry. These complexes could be used as catalysts for the asymmetric 1,2-addition of organoboronic acids to aldehydes, affording chiral diarylmethanols with high yields and moderate enantioselectivities.

  12. Dynamic structural change of the self-assembled lanthanum complex induced by lithium triflate for direct catalytic asymmetric aldol-Tishchenko reaction.

    Science.gov (United States)

    Horiuchi, Yoshihiro; Gnanadesikan, Vijay; Ohshima, Takashi; Masu, Hyuma; Katagiri, Kosuke; Sei, Yoshihisa; Yamaguchi, Kentaro; Shibasaki, Masakatsu

    2005-09-05

    The development of a direct catalytic asymmetric aldol-Tishchenko reaction and the nature of its catalyst are described. An aldol-Tishchenko reaction of various propiophenone derivatives with aromatic aldehydes was promoted by [LaLi3(binol)3] (LLB), and reactivity and enantioselectivity were dramatically enhanced by the addition of lithium trifluoromethanesulfonate (LiOTf). First, we observed a dynamic structural change of LLB by the addition of LiOTf using 13C NMR spectroscopy, electronspray ionization mass spectrometry (ESI-MS), and cold-spray ionization mass spectrometry (CSI-MS). X-ray crystallography revealed that the structure of the newly generated self-assembled complex was a binuclear [La2Li4(binaphthoxide)5] complex 6. A reverse structural change of complex 6 to LLB by the addition of one equivalent of Li2(binol) was also confirmed by ESI-MS and experimental results. The drastic concentration effects on the direct catalytic asymmetric aldol-Tishchenko reaction suggested that the addition of LiOTf to LLB generated an active oligomeric catalyst species.

  13. Experimental technique for study on three-particle reactions in kinematically total experiments with usage of the two-processor complex on the M-400 computer basis

    International Nuclear Information System (INIS)

    Berezin, F.N.; Kisurin, V.A.; Nemets, O.F.; Ofengenden, R.G.; Pugach, V.M.; Pavlenko, Yu.N.; Patlan', Yu.V.; Savrasov, S.S.

    1981-01-01

    Experimental technique for investigation of three-particle nuclear reactions in kinematically total experiments is described. The technique provides the storage of one-dimensional and two- dimensional energy spectra from several detectors. A block diagram of the measuring system, using this technique, is presented. The measuring system consists of analog equipment for rapid-slow coincidences and of a two-processor complex on the base of the M-400 computer with a general bus. Application of a two-processor complex, each computer of which has a possibility of direct access to memory of another computer, permits to separate functions of data collection and data operational presentation and to perform necessary physical calculations. Software of the measuring complex which includes programs written using the ASSEMBLER language for the first computer and functional programs written using the BASIC language for the second computer, is considered. Software of the first computer includes the DISPETCHER dialog control program, driver package for control of external devices, of applied program package and system modules. The technique, described, is tested in experiment on investigation of d+ 10 B→α+α+α three- particle reaction at deutron energy of 13.6 MeV. The two-dimensional energy spectrum reaction obtained with the help of the technique described is presented [ru

  14. Fragment emission in reactions of 18.5-GeV 12C ions with complex nuclei

    International Nuclear Information System (INIS)

    Porile, N.T.; Cole, G.D.

    1982-01-01

    The emission of fragments ranging from 24 Na to 52 Mn in reactions of 18.5 GeV 12 C ions with Cu, Ag, Gd, Ta, Au, and U targets has been studied by means of activation techniques. The experiments involved determination of the fragment production cross sections and thick-target recoil properties. The latter were used to obtain mean fragment kinetic energies and values of β/sub parallel to/, the forward velocity component of the struck nucleus (in units of c). The results are compared with similar data for incident protons of the same total kinetic energy. The data may be used to assess the importance of central collisions in fragment production. Such collisions lead to the near total destruction of both interacting nuclei and the resulting fragments are emitted by a system of intermediate rapidity. In such a process, the factorization hypothesis, which has been shown to be valid for target and projectile fragmentation reactions, should not be obeyed. A test for factorization is performed by means of a relation which states that the ratio of the cross sections for producing fragment /sup A/Z in 12 C reactions to that for producing the same fragment in proton reactions with the same target is unity, provided both cross sections are reduced by the values of the corresponding total reaction cross sections sigma/sub R/, and evaluated for the same total kinetic energy of the projectile. The results of this comparison for the targets studied are presented and discussed

  15. RMBNToolbox: random models for biochemical networks

    Directory of Open Access Journals (Sweden)

    Niemi Jari

    2007-05-01

    Full Text Available Abstract Background There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number of available models is still relatively small and the model sizes remain limited. The lack of kinetic information is usually the limiting factor for the construction of detailed simulation models. Results We present a computational toolbox for generating random biochemical network models which mimic real biochemical networks. The toolbox is called Random Models for Biochemical Networks. The toolbox works in the Matlab environment, and it makes it possible to generate various network structures, stoichiometries, kinetic laws for reactions, and parameters therein. The generation can be based on statistical rules and distributions, and more detailed information of real biochemical networks can be used in situations where it is known. The toolbox can be easily extended. The resulting network models can be exported in the format of Systems Biology Markup Language. Conclusion While more information is accumulating on biochemical networks, random networks can be used as an intermediate step towards their better understanding. Random networks make it possible to study the effects of various network characteristics to the overall behavior of the network. Moreover, the construction of artificial network models provides the ground truth data needed in the validation of various computational methods in the fields of parameter estimation and data analysis.

  16. Studies of complex fragment emission in heavy ion reactions: Progress report, September 1, 1986 through August 31, 1987

    International Nuclear Information System (INIS)

    Sobotka, L.G.

    1987-01-01

    The production of large fragments, fragments with mass between light particles and fission fragments, in intermediate and high energy nuclear reactions has fostered the proposal of a number of novel reaction mechanisms. These include liquid-vapor equilibrium and nuclear shattering. Temporarily left in the wake of these exciting proposed mechanisms was the old standard, statistical decay of compound nuclei. To be sure, the standard treatment of compound nucleus decay did not deal with large fragment production. However, this omission was not due to any fundamental deficiency of statistical models, but rather an uncertainty concerning exactly how to splice large fragment emission into statistical models. A large portion of our program deals with this problem. Specifically, by studying the yields of large fragments produced in sufficiently low energy reactions we are attempting to deduce the asymmetry and l-wave dependence of large fragment emission from compound nuclear intermediates. This, however, is only half of the problem. Since the novel mechanisms proposed for large fragment emission were spawned by intermediate and high energy reaction data, we must also realize the relevance of the compound nucleus mechanisms at high energies. It is not unreasonable to suspect that compound nucleus-like objects are formed with less than complete momentum transfer and perhaps less than complete mass transfer. Therefore the study of large fragment production in low energy reactions should go hand in hand with the study of energy, mass, and angular momentum transfer in non-compound reactions. This thread joins the apparently divergent subjects covered in this report. 39 refs., 24 figs., 2 tabs

  17. Studies of complex fragment emission in heavy ion reactions: Progress report, September 1, 1987--August 31, 1988

    International Nuclear Information System (INIS)

    Sobotka, L.G.

    1988-01-01

    The production of large fragments, fragments with mass between light particles and fission fragments, in intermediate and high energy nuclear reactions has fostered the proposal of a number of novel reaction mechanisms. These include liquid-vapor equilibrium and nuclear shattering. Temporarily left in the wake of these exciting proposed mechanisms was the old standard, statistical decay of compound nuclei. To be sure, the standard treatment of compound nucleus decay did not deal with large fragment production. However, this emission was not due to any fundamental deficiency of statistical models, but rather an uncertainty concerning exactly how to splice large fragment emission into statistical models. A large portion of our program deals with this problem. Specifically, by studying the yields of large fragments produced in sufficiently low energy reactions we are attempting to deduce the asymmetry and l-wave dependence of large fragment emission from compound nuclear intermediates. This, however, is only half of the problem. Since the novel mechanisms proposed for large fragment emission were spawned by intermediate and high energy reaction data, we must also realize the relevance of the compound nucleus mechanisms at high energies. It is not unreasonable to suspect that compound nucleus-like objects are formed with less than complete momentum transfer and perhaps less than complete mass transfer. Therefore the study of large fragment production in low energy reactions should go hand in hand with the study of energy, mass, and angular momentum transfer in incomplete fusion and non-compound reactions. This thread joins the apparently divergent subjects covered in this report

  18. Density-functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes

    International Nuclear Information System (INIS)

    Tateyama, Yoshitaka; Blumberger, Jochen; Sprik, Michiel; Tavernelli, Ivano

    2005-01-01

    The thermochemistry of the RuO 4 2- +MnO 4 - →RuO 4 - +MnO 4 2- redox reaction in aqueous solution is studied by separate density-functional-based ab initio molecular-dynamics simulations of the component half reactions RuO 4 2- →RuO 4 - +e - and MnO 4 2- →MnO 4 - +e - . We compare the results of a recently developed grand-canonical method for the computation of oxidation free energies to the predictions by the energy-gap relations of the Marcus theory that can be assumed to apply to these reactions. The calculated redox potentials are in good agreement. The subtraction of the half-reaction free energies gives an estimate of the free energy of the full reaction. The result obtained from the grand-canonical method is -0.4 eV, while the application of the Marcus theory gives -0.3 eV. These should be compared to the experimental value of 0.0 eV. Size effects, in response to increasing the number of water molecules in the periodic model system from 30 to 48, are found to be small (≅0.1 eV). The link to the Marcus theory also has enabled us to compute reorganization free energies for oxidation. For both the MnO 4 2- and RuO 4 2- redox reactions we find the same reorganization free energy of 0.8 eV (1.0 eV in the larger system). The results for the free energies and further analysis of solvation and electronic structure confirm that these two tetrahedral oxoanions show very similar behavior in solution in spite of the central transition-metal atoms occupying a different row and column in the periodic table

  19. Reconstructing biochemical pathways from time course data.

    Science.gov (United States)

    Srividhya, Jeyaraman; Crampin, Edmund J; McSharry, Patrick E; Schnell, Santiago

    2007-03-01

    Time series data on biochemical reactions reveal transient behavior, away from chemical equilibrium, and contain information on the dynamic interactions among reacting components. However, this information can be difficult to extract using conventional analysis techniques. We present a new method to infer biochemical pathway mechanisms from time course data using a global nonlinear modeling technique to identify the elementary reaction steps which constitute the pathway. The method involves the generation of a complete dictionary of polynomial basis functions based on the law of mass action. Using these basis functions, there are two approaches to model construction, namely the general to specific and the specific to general approach. We demonstrate that our new methodology reconstructs the chemical reaction steps and connectivity of the glycolytic pathway of Lactococcus lactis from time course experimental data.

  20. Insertion reactions into Pd[bond]O and Pd[bond]N bonds: preparation of alkoxycarbonyl, carbonato, carbamato, thiocarbamate, and thioureide complexes of palladium(II).

    Science.gov (United States)

    Ruiz, José; Martínez, M Teresa; Florenciano, Félix; Rodríguez, Venancio; López, Gregorio; Pérez, José; Chaloner, Penny A; Hitchcock, Peter B

    2003-06-02

    Mononuclear palladium hydroxo complexes of the type [Pd(N[bond]N)(C(6)F(5))(OH)] [(N[bond]N = 2,2'-bipyridine (bipy), 4,4'-dimethyl-2,2'-bipyridine (Me(2)bipy), 1,10-phenanthroline (phen), or N,N,N',N'-tetramethylethylenediamine (tmeda)] have been prepared by reaction of [Pd(N[bond]N)(C(6)F(5))(acetone)]ClO(4) with KOH in methanol. These hydroxo complexes react, in methanol, with CO (1 atm, room temperature) to yield the corresponding methoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)Me)]. Similar alkoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)R)] (N[bond]N = bis(3,5-dimethylpyrazol-1-yl)methane); R = Me, Et, or (i)Pr) are obtained when [Pd(N[bond]N)(C(6)F(5))Cl] is treated with KOH in the corresponding alcohol ROH and CO is bubbled through the solution. The reactions of [Pd(N[bond]N)(C(6)F(5))(OH)] (N[bond]N = bipy or Me(2)bipy) with CO(2), in tetrahydrofuran, lead to the formation of the binuclear carbonate complexes [(N[bond]N)(C(6)F(5))Pd(mu-eta(2)-CO(3))Pd(C(6)F(5))(N[bond]N)]. Complexes [Pd(N[bond]N)(C(6)F(5))(OH)] react in alcohol with PhNCS to yield the corresponding N-phenyl-O-alkylthiocarbamate complexes [Pd(N[bond]N)(C(6)F(5))[SC(OR)NPh

  1. Biochemical activity of fullerenes and related derivatives

    International Nuclear Information System (INIS)

    Huczko, A.; Lange, H.; Calko, E.

    1999-01-01

    An astonishing scientific interest, embodied in over 15000 research articles so far, has been encountered since 1985 when fullerenes were discovered. From new superconductors to a rich electrochemistry and reaction chemistry, fullerene nanostructures continue to excite the scientific world, and new findings continue at record pace. This review presents many examples of the biochemical activities of fullerenes and derivatives, e. g. cytotoxic activity, selective DNA cleavage and antiviral activity against HIV. We also present some results of our testing which show that, despite its chemical and biochemical activity, fullerene matter does not present any health hazard directly related to skin irritation and allergic risks. (author)

  2. The reaction of 1,2-Dichloro-4,5-dinitrobenzene with hydroxide ion: roles of Meisenheimer complexes and radical pairs

    Energy Technology Data Exchange (ETDEWEB)

    Blasko, Andrei; Bunton, Clifford A.; Gillitt, Nichollas D.; Bacaloglu, Radu [Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA (United States); Yunes, Santiago F.; Zucco, Cesar, E-mail: c.zucco@ufsc.br, E-mail: santiago.yunes@ufsc.br [Departamento de Quimica, Universidade Federal de Santa Catarina, Florianopolis-SC (Brazil)

    2013-07-15

    The reaction of 1,2-dichloro-4,5-dinitrobenzene (DCDNB) with aqueous OH{sup -} produces (after acidification) 2-nitro-4,5-dichlorophenol with loss of NO{sub 2} . Nevertheless, with > 2 mol L{sup -1} OH{sup -}, only DCDNB was recovered due to the formation of the long-lived 3,6-dihydroxy Meisenheimer complex (M{sup 2-}), and that in acid, reverted to the starting material. Fast formation of monohydroxy Meisenheimer complex (M{sup 1-}) can be followed in DMSO:H{sub 2}O 7:3 v/v and rate constants for its interconversion with DCDNB and for formation and return with M{sup 2-} complex were estimated, with evidence for these reactions in DMSO:H{sub 2}O 1:1 v/v and H{sub 2}O. The rapid hydrogen exchange in OD{sup -}/D{sub 2}O limits the use of {sup 1}H nuclear magnetic resonance (NMR) spectroscopy in identifying intermediates. {sup 1}H and {sup 13}C NMR signals of M{sup 2-} complex were observed in DMSO-H{sub 2}O-KOH. There is evidence for the formation of free radicals in DMSO:H{sub 2} O 4:1 v/v, and overall kinetics in more aqueous medium were treated in terms of the transient existence of anionic radical pairs. (author)

  3. The function of glycine decarboxylase complex is optimized to maintain high photorespiratory flux via buffering of its reaction products

    DEFF Research Database (Denmark)

    Bykova, Natalia V; Møller, Ian Max; Gardeström, Per

    2014-01-01

    oxidase. We discuss here possible mechanisms of high photorespiratory flux maintenance in mitochondria and suggest that it is fulfilled under conditions where the concentrations of glycine decarboxylase reaction products NADH and CO2 achieve an equilibrium provided by malate dehydrogenase and carbonic...

  4. Application of Box-Behnken design in the optimization of catalytic behavior of a new mixed chelate of copper (II) complex in chemiluminescence reaction of luminol

    International Nuclear Information System (INIS)

    Khajvand, Tahereh; Chaichi, Mohammad Javad; Nazari, OmLeila; Golchoubian, Hamid

    2011-01-01

    In this work, we observed an enhancement of chemiluminescence (CL) emission of luminol when a new mixed chelate of copper complex (N-(2-(2-aminoethylamino)ethyl)-1H-pyrrole-2-carboxamide-Cu(II)) was mixed with a solution containing luminol in methanol/water. The Box-Behnken design matrix and response surface methodology (RSM) have been applied to design the experiments to evaluate the interactive effects of the three most important operating variables-luminol (10 -4 -10 -2 M), fluorescein (10 -5 -10 -3 M) and hydrogen peroxide (1-3 M) concentrations on the CL emission of luminol. The total 15 experiments were conducted in the present study towards the construction of a quadratic model. Independent variables luminol and hydrogen peroxide have significant value P F less than 0.0500 indicate that model terms are significant for the CL emission of luminol. The regression equation coefficients were calculated and the data fitted to a second-order polynomial equation for CL emission of luminol. The new introduced inorganic catalyst of luminol CL reaction can be effect more than that of the common ones such as potassium hexacyanoferrate (III) and copper (II) acetate. - Research highlights: → In this study we introduce a new mixed chelate of copper complex as a catalyst of luminol chemiluminescence (CL) reaction. → The copper complex (N-(2-(2-aminoethylamino)ethyl)-1H-pyrrole-2-carboxamide-Cu(II)) catalyst luminol reaction more than that of copper acetate and potassium hexacyanoferrate (III). → The Box-Behnken design matrix and response surface methodology are used for prediction of CL intensity of luminol. → There are good correlation between experimental and expected CL intensity that predicted by the theoretical model. → Fluorescein used as a fluorescer in the luminol CL reaction in presence of the new catalyst.

  5. Mechanism of reductive elimination. Reaction of alkylpalladium(II) complexes with tetraorganotin, organolithium, and Grignard reagents. Evidence for palladium(IV) intermediacy

    International Nuclear Information System (INIS)

    Milstein, D.; Stille, J.K.

    1979-01-01

    Coupling products are obtained in good yields from the reaction of tetraorganotin compounds or Grignard reagents and organohalogenopalladium(II) complexes provided that a benzyl bromide is present. Low yields are obtained in the absence of the benzyl bromides, in which case other decomposition pathways (e.g., α elimination) take place, even in the presence of electron acceptors (e.g., oxygen, m-dinitrobenzene). The first step in the reaction of benzylhalogenobis(triphenylphosphine)-palladium(II) complexes with MeM (M = SnMe 3 , MgBr) is metathesis of the benzyl ligand rather than the halogen. This unique carbon-for-carbon transmetalation takes place at 25 0 C and is facilitated by electron-donating substituents on the benzyl ligand. The products of this reaction subsequently react at higher temperature in the presence of a benzyl bromide to afford ethylbenzene. Optically active chloro-(α-deuteriobenzyl)bis(triphenylphosphine)palladium yields, upon reaction with tetramethyltin in the presence of p-nitrobenzyl bromide, optically active α-deuterioethylbenzene in which overall retention of configuration at carbon has resulted. cis-dimethylbis(triphenylphosphine)palladium(II) reacts with benzyl bromide at 25 0 C to afford ethylbenzene and bromomethylbis(triphenylphosphine)palladium(II) rather than ethane. When optically active α-deuteriobenzyl bromide is used in this reaction, optically active α-deuterioethylbenzene is formed, and inversion of configuration at carbon takes place. The reductive elimination process is proposed to take place preferentially from a palladium(IV) intermediate with retention of configuration at carbon

  6. Nonheme Fe(IV) Oxo Complexes of Two New Pentadentate Ligands and Their Hydrogen-Atom and Oxygen-Atom Transfer Reactions.

    Science.gov (United States)

    Mitra, Mainak; Nimir, Hassan; Demeshko, Serhiy; Bhat, Satish S; Malinkin, Sergey O; Haukka, Matti; Lloret-Fillol, Julio; Lisensky, George C; Meyer, Franc; Shteinman, Albert A; Browne, Wesley R; Hrovat, David A; Richmond, Michael G; Costas, Miquel; Nordlander, Ebbe

    2015-08-03

    Two new pentadentate {N5} donor ligands based on the N4Py (N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) framework have been synthesized, viz. [N-(1-methyl-2-benzimidazolyl)methyl-N-(2-pyridyl)methyl-N-(bis-2-pyridyl methyl)amine] (L(1)) and [N-bis(1-methyl-2-benzimidazolyl)methyl-N-(bis-2-pyridylmethyl)amine] (L(2)), where one or two pyridyl arms of N4Py have been replaced by corresponding (N-methyl)benzimidazolyl-containing arms. The complexes [Fe(II)(CH3CN)(L)](2+) (L = L(1) (1); L(2) (2)) were synthesized, and reaction of these ferrous complexes with iodosylbenzene led to the formation of the ferryl complexes [Fe(IV)(O)(L)](2+) (L = L(1) (3); L(2) (4)), which were characterized by UV-vis spectroscopy, high resolution mass spectrometry, and Mössbauer spectroscopy. Complexes 3 and 4 are relatively stable with half-lives at room temperature of 40 h (L = L(1)) and 2.5 h (L = L(2)). The redox potentials of 1 and 2, as well as the visible spectra of 3 and 4, indicate that the ligand field weakens as ligand pyridyl substituents are progressively substituted by (N-methyl)benzimidazolyl moieties. The reactivities of 3 and 4 in hydrogen-atom transfer (HAT) and oxygen-atom transfer (OAT) reactions show that both complexes exhibit enhanced reactivities when compared to the analogous N4Py complex ([Fe(IV)(O)(N4Py)](2+)), and that the normalized HAT rates increase by approximately 1 order of magnitude for each replacement of a pyridyl moiety; i.e., [Fe(IV)(O)(L(2))](2+) exhibits the highest rates. The second-order HAT rate constants can be directly related to the substrate C-H bond dissociation energies. Computational modeling of the HAT reactions indicates that the reaction proceeds via a high spin transition state.

  7. Formation of nitrogen complexes when [Ru(NH3)5H2O]2+ ion reaction with diazo-acetic ester and aromatic salts of diazonium

    International Nuclear Information System (INIS)

    Shur, V.B.; Tikhonova, I.A.; Vol'pin, M.E.

    1978-01-01

    A possibility of formation of nitrogen complexes during transition metal compound interaction with aliphatic and aromatic diazo compounds is studied. It is shown that at the interaction of [Ru(NH 3 ) 5 H 2 O] 2+ with diazo-acetic ester in water (pH7) at 20 deg, quick splitting of the CN-bond in the ester molecule takes place with the formation of [Ru(NH 3 ) 5 N 2 ] 2+ and [(NH 3 ) 5 RuN 2 Ru(NH 3 ) 5 ] 4+ (NRRN) nitrogen complexes. The sum yield of complexes comprises 86% taking into acount diazo-acetic ester. Aromatic salts of diazonium, n-O 3 SC 6 H 4 N 2 and p-quinone diazide react with the [Ru(NH 3 ) 5 H 2 O] 2+ excess forming NRRN (the yield equals 40-53%). The reaction mechanism is discussed

  8. Catalytic ozonation not relying on hydroxyl radical oxidation: A selective and competitive reaction process related to metal-carboxylate complexes

    KAUST Repository

    Zhang, Tao; Croue, Jean-Philippe

    2014-01-01

    Catalytic ozonation following non-hydroxyl radical pathway is an important technique not only to degrade refractory carboxylic-containing organic compounds/matter but also to avoid catalyst deactivation caused by metal-carboxylate complexation

  9. After-Effects of the Cobalt-57-Iron-57 Electron-Capture Reaction in Hexacyanocobaltate (III) Complexes

    DEFF Research Database (Denmark)

    Fenger, Jørgen Folkvard; Siekierska, K.E.; Olsen, J.

    1973-01-01

    Isomorphous hexacyanocobaltate(III) complexes with the bivalent metal cations Mn2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, and Cd2+ have been labelled with 57Co and used as Mössbauer sources. Whilst the spectrum of the complex Fe3[57Co(CN)6]2 can be resolved into a single line corresponding to the ion Fe II...

  10. Reactions of Fischer carbene complexes with Electron-deficient olefins: Scope and limitations of this route to donor-acceptor-substituted cyclopropanes

    Energy Technology Data Exchange (ETDEWEB)

    Wienand, A.; Reissig, H.U. (Inst. fuer Organische Chemie der Technischen Hochschule Darmstadt (West Germany))

    1990-12-01

    The Fischer carbene complex ((CO){sub 5}Cr{double bond}C(OMe)Ph) (1) is able to transfer its carbene ligand to a variety of electron-deficient olefins and provides donor-acceptor-substituted cyclopropanes in good yields. Apt activating groups with respect to the alkene are ester, amide, nitrile, sulfone, and dialkyl phosphonate functions. Methyl vinyl ketone (19) affords products in low yield that may arise from an intermediate cyclopropane derivative. Phenyl vinyl sulfoxide (24) mainly acts as an oxidizing agent, transforming 1 into methyl benzoate. for olefin 24 and {alpha}-(N-methylanilino)acrylonitrile the authors found products that should be formed on an olefin metathesis pathway. The methyl-substituted carbene complex 48 also affords the expected donor-acceptor-substituted cyclopropanes; however, acyclic isomers are formed in higher amounts. The molybdenum and tungsten complexes 55 and 56, respectively, also furnish cyclopropane derivatives, but the yields are lower than with the chromium compound 1. Disubstituted olefins and complex 1 still give the cyclopropanes in moderate yields, while all trisubstituted and most of the difunctionalized alkenes do not react with this Fischer carbene complex. The cyclopropanes synthesized can be deprotonated and alkylated or transformed into ring-opened products. These model reactions demonstrate the synthetic potentials of donor-acceptor-substituted cyclopropanes prepared via Fischer carbene complexes.

  11. Isolation of an oxomanganese(V) porphyrin intermediate in the reaction of a manganese(III) porphyrin complex and H2O2 in aqueous solution.

    Science.gov (United States)

    Nam, Wonwoo; Kim, Inwoo; Lim, Mi Hee; Choi, Hye Jin; Lee, Je Seung; Jang, Ho G

    2002-05-03

    The reaction of [Mn(TF(4)TMAP)](CF(3)SO(3))(5) (TF(4)TMAP=meso-tetrakis(2,3,5,6-tetrafluoro-N,N,N-trimethyl-4-aniliniumyl)porphinato dianion) with H(2)O(2) (2 equiv) at pH 10.5 and 0 degrees C yielded an oxomanganese(V) porphyrin complex 1 in aqueous solution, whereas an oxomanganese(IV) porphyrin complex 2 was generated in the reactions of tert-alkyl hydroperoxides such as tert-butyl hydroperoxide and 2-methyl-1-phenyl-2-propyl hydroperoxide. Complex 1 was capable of epoxidizing olefins and exchanging its oxygen with H(2) (18)O, whereas 2 did not epoxidize olefins. From the reactions of [Mn(TF(4)TMAP)](5+) with various oxidants in the pH range 3-11, the O-O bond cleavage of hydroperoxides was found to be sensitive to the hydroperoxide substituent and the pH of the reaction solution. Whereas the O-O bond of hydroperoxides containing an electron-donating tert-alkyl group is cleaved homolytically, an electron-withdrawing substituent such as an acyl group in m-chloroperoxybenzoic acid (m-CPBA) facilitates O-O bond heterolysis. The mechanism of the O-O bond cleavage of H(2)O(2) depends on the pH of the reaction solution: O-O bond homolysis prevails at low pH and O-O bond heterolysis becomes a predominant pathway at high pH. The effect of pH on (18)O incorporation from H(2) (18)O into oxygenated products was examined over a wide pH range, by carrying out the epoxidation of carbamazepine (CBZ) with [Mn(TF(4)TMAP)](5+) and KHSO(5) in buffered H(2) (18)O solutions. A high proportion of (18)O was incorporated into the CBZ-10,11-oxide product at all pH values but this proportion was not affected significantly by the pH of the reaction solution.

  12. Investigations of nuclear structure and nuclear reactions induced by complex projectiles. Progress report, September 1, 1995 - August 31, 1996

    International Nuclear Information System (INIS)

    Sarantites, D.G.

    1996-01-01

    The research program of this group addresses three areas of nuclear physics: (1) nuclear structure studies at high spin; (2) nuclear reactions with emphasis on the interface between structure and reactions; (3) development and use of novel techniques and instrumentation in the above areas of research. Research with their collaborators responsible for the data analysis is also included very briefly in this report. Significant progress has been made in all the areas of their research program during the past year. The lists of publications and invited talks are given in Chapter 6. In the past 3 years the authors published 10 letters, 4 rapid communications and 7 full papers. Seven full papers have also been submitted. In addition, 12 invited talks have been delivered in professional conferences. In this report the authors highlight their accomplishments and advances in the three areas of their effort

  13. Synthesis and reactions of imines of α,β-ethylenic silicon-containing aldehydes with complex metal hydrides

    International Nuclear Information System (INIS)

    Surnin, V.A.; Stadnichuk, M.D.

    1986-01-01

    Imines of 3-trimethylsilyl-2-propenal or its hydrocarbon analog are reduced chemoselectively at the C=N double bond by sodium borohydride. The direction of lithium aluminum hydride reduction of these imines is not influenced by the nature of the element attached to the C=C bond silicon versus carbon, but rather is determined by the nature of the radical group attached to the nitrogen atom; N-arylimines undergo addition with lithium aluminum hydride at the C=N bond exclusively, whereas for N-alkylimines the addition reactions occur either partially or in full in the 1,4-position, depending on the reaction conditions, to give imines of saturated aldehydes after demetallation

  14. Selective C–C Coupling Reaction of Dimethylphenol to Tetramethyldiphenoquinone Using Molecular Oxygen Catalyzed by Cu Complexes Immobilized in Nanospaces of Structurally-Ordered Materials

    Directory of Open Access Journals (Sweden)

    Zen Maeno

    2015-02-01

    Full Text Available Two high-performance Cu catalysts were successfully developed by immobilization of Cu ions in the nanospaces of poly(propylene imine (PPI dendrimer and magadiite for the selective C–C coupling of 2,6-dimethylphenol (DMP to 3,3',5,5'-tetramethyldiphenoquinone (DPQ with O2 as a green oxidant. The PPI dendrimer encapsulated Cu ions in the internal nanovoids to form adjacent Cu species, which exhibited significantly high catalytic activity for the regioselective coupling reaction of DMP compared to previously reported enzyme and metal complex catalysts. The magadiite-immobilized Cu complex acted as a selective heterogeneous catalyst for the oxidative C–C coupling of DMP to DPQ. This heterogeneous catalyst was recoverable from the reaction mixture by simple filtration, reusable without loss of efficiency, and applicable to a continuous flow reactor system. Detailed characterization using ultraviolet-visible (UV-vis, Fourier transform infrared (FTIR, electronic spin resonance (ESR, and X-ray absorption fine structure (XAFS spectroscopies and the reaction mechanism investigation revealed that the high catalytic performances of these Cu catalysts were ascribed to the adjacent Cu species generated within the nanospaces of the PPI dendrimer and magadiite.

  15. Complexing properties of the main organic acids used in decontamination solutions and reactions involved in their degradation or elimination

    International Nuclear Information System (INIS)

    Noel, D.; Kerrec, O.; Lantes, B.; Rosset, R.; Bayri, B.; Desbarres, J.; Jardy, A.

    1994-09-01

    This paper presents a study that, parallel with the industrial development of the decontamination chemical process, has been performed more fundamentally on the chemical properties of used products: degradation reaction during process or after decontamination and during wastes treatment. In particular, results show that the organic compounds used have no interaction with resins during radioactive wastes storage and therefore they do not present leaching risk. (authors). 8 refs., 3 figs., 4 tabs

  16. The Complexity of Family Reactions to Identity among Homeless and College Lesbian, Gay, Bisexual, Transgender, and Queer Young Adults.

    Science.gov (United States)

    Schmitz, Rachel M; Tyler, Kimberly A

    2018-05-01

    Familial responses to lesbian, gay, bisexual, transgender, and queer (LGBTQ) young people's identities range on a spectrum from rejection to acceptance and these reactions strongly impact family relationships and young adult well-being. Less is known, however, about how family members' reactions may differ based on young people's contexts of socioeconomic status. Through a qualitative, life course analysis of in-depth interview data from 46 LGBTQ college students and LGBTQ homeless young adults, our study highlights the diverse, contextual nuances of young people's "linked lives" within their families. We find that the context of socioeconomic status influenced how a young person managed family rejection. Conversely, processes of familial acceptance were also connected to life course transitions that worked in some cases to enhance LGBTQ young adults' family relationships. Finally, the intricacy of familial reactions to a young person's LGBTQ identity transcended socioeconomic contexts as many respondents shared similar experiences of rejection and acceptance. These findings have implications for understanding how young people manage family relationships across different contexts of socioeconomic status and how these experiences can shape their life course trajectories. Results from this study can inform LGBTQ youth service providers by tailoring intervention programs that account for contextual social diversity.

  17. Dinuclear NHC-palladium complexes containing phosphine spacers: synthesis, X-ray structures and their catalytic activities towards the Hiyama coupling reaction.

    Science.gov (United States)

    Yang, Jin; Li, Pinhua; Zhang, Yicheng; Wang, Lei

    2014-05-21

    Six dinuclear N-heterocyclic carbene (NHC) palladium complexes, [PdCl2(IMes)]2(μ-dppe) (1), [PdCl2(IPr)]2(μ-dppe) (2), [PdCl2(IMes)]2(μ-dppb) (3), [PdCl2(IPr)]2(μ-dppb) (4), [PdCl2(IMes)]2(μ-dpph) (5), and [PdCl2(IPr)]2(μ-dpph) (6) [IMes = N,N'-bis-(2,4,6-trimethylphenyl)imidazol-2-ylidene; IPr = N,N'-bis-(2,6-di(iso-propyl)phenyl)imidazol-2-ylidene; dppe = 1,2-bis(diphenylphosphino)ethane, dppb = 1,4-bis(diphenylphosphino)butane; and dpph = 1,6-bis(diphenylphosphino)hexane], have been synthesized through bridge-cleavage reactions of chloro-bridged dimeric compounds, [Pd(μ-Cl)(Cl)(NHC)]2, with the corresponding diphosphine ligands. The obtained compounds were fully characterized by (1)H NMR, (13)C NMR and (31)P NMR spectroscopy, FT-IR, elemental analysis and single-crystal X-ray crystallography. Moreover, further explorations of the catalytic potential of the dinuclear carbene palladium complexes as catalysts for the Pd-catalyzed transformations have been performed under microwave irradiation conditions, and the complexes exhibited moderate to good catalytic activity in the Hiyama coupling reaction of trimethoxyphenylsilane with aryl chlorides.

  18. Metabonomics and medicine: the Biochemical Oracle.

    Science.gov (United States)

    Mitchell, Steve; Holmes, Elaine; Carmichael, Paul

    2002-10-01

    Occasionally, a new idea emerges that has the potential to revolutionize an entire field of scientific endeavour. It is now within our grasp to be able to detect subtle perturbations within the phenomenally complex biochemical matrix of living organisms. The discipline of metabonomics promises an all-encompassing approach to understanding total, yet fundamental, changes occurring in disease processes, drug toxicity and cell function.

  19. Synthesis of imine bond containing insoluble polymeric ligand and its transition metal complexes, structural characterization and catalytic activity on esterification reaction.

    Science.gov (United States)

    Gönül, İlyas; Ay, Burak; Karaca, Serkan; Saribiyik, Oguz Yunus; Yildiz, Emel; Serin, Selahattin

    2017-01-01

    In this study, synthesis of insoluble polymeric ligand (L) and its transition metal complexes [Cu(L)Cl 2 ]·2H 2 O (1) , [Co(L)Cl 2 (H 2 O) 2 ] (2) and [Ni(L)Cl 2 (H 2 O) 2 ] (3) , having the azomethine groups, were synthesized by the condensation reactions of the diamines and dialdehydes. The structural properties were characterized by the analytical and spectroscopic methods using by elemental analysis, Fourier Transform Infrared, Thermo Gravimetric Analysis, Powder X-ray Diffraction, magnetic susceptibility and Inductively Coupled Plasma. The solubilities of the synthesized polymeric materials were also investigated and found as insoluble some organic and inorganic solvents. Additionally, their catalytic performance was carried out for the esterification reaction of acetic acid and butyl acetate. The highest conversion rate is 75.75% by using catalyst 1 . The esterification of butanol gave butyl acetate with 100% selectivity.

  20. Comparison of hydration reactions for "piano-stool" RAPTA-B and [Ru(η6- arene)(en)Cl]+ complexes: Density functional theory computational study

    Science.gov (United States)

    Chval, Zdeněk; Futera, Zdeněk; Burda, Jaroslav V.

    2011-01-01

    The hydration process for two Ru(II) representative half-sandwich complexes: Ru(arene)(pta)Cl2 (from the RAPTA family) and [Ru(arene)(en)Cl]+ (further labeled as Ru_en) were compared with analogous reaction of cisplatin. In the study, quantum chemical methods were employed. All the complexes were optimized at the B3LYP/6-31G(d) level using Conductor Polarizable Continuum Model (CPCM) solvent continuum model and single-point (SP) energy calculations and determination of electronic properties were performed at the B3LYP/6-311++G(2df,2pd)/CPCM level. It was found that the hydration model works fairly well for the replacement of the first chloride by water where an acceptable agreement for both Gibbs free energies and rate constants was obtained. However, in the second hydration step worse agreement of the experimental and calculated values was achieved. In agreement with experimental values, the rate constants for the first step can be ordered as RAPTA-B > Ru_en > cisplatin. The rate constants correlate well with binding energies (BEs) of the Pt/Ru-Cl bond in the reactant complexes. Substitution reactions on Ru_en and cisplatin complexes proceed only via pseudoassociative (associative interchange) mechanism. On the other hand in the case of RAPTA there is also possible a competitive dissociation mechanism with metastable pentacoordinated intermediate. The first hydration step is slightly endothermic for all three complexes by 3-5 kcal/mol. Estimated BEs confirm that the benzene ligand is relatively weakly bonded assuming the fact that it occupies three coordination positions of the Ru(II) cation.

  1. Inertial effects in diffusion-limited reactions

    International Nuclear Information System (INIS)

    Dorsaz, N; Foffi, G; De Michele, C; Piazza, F

    2010-01-01

    Diffusion-limited reactions are commonly found in biochemical processes such as enzyme catalysis, colloid and protein aggregation and binding between different macromolecules in cells. Usually, such reactions are modeled within the Smoluchowski framework by considering purely diffusive boundary problems. However, inertial effects are not always negligible in real biological or physical media on typical observation time frames. This is all the more so for non-bulk phenomena involving physical boundaries, that introduce additional time and space constraints. In this paper, we present and test a novel numerical scheme, based on event-driven Brownian dynamics, that allows us to explore a wide range of velocity relaxation times, from the purely diffusive case to the underdamped regime. We show that our algorithm perfectly reproduces the solution of the Fokker-Planck problem with absorbing boundary conditions in all the regimes considered and is thus a good tool for studying diffusion-guided reactions in complex biological environments.

  2. DNA-binding, catalytic oxidation, C—C coupling reactions and antibacterial activities of binuclear Ru(II thiosemicarbazone complexes: Synthesis and spectral characterization

    Directory of Open Access Journals (Sweden)

    Arumugam Manimaran

    2012-07-01

    Full Text Available New hexa-coordinated binuclear Ru(II thiosemicarbazone complexes of the type {[(B(EPh3(COClRu]2L} (where, E = P or As; B = PPh3 or AsPh3 or pyridine; L = mononucleating NS donor of N-substituted thiosemicarbazones have been synthesized and characterized by elemental analysis, FT-IR, UV–vis and 31P{1H} NMR cyclic voltammetric studies. The DNA-binding studies of Ru(II complexes with calf thymus DNA (CT-DNA were investigated by UV–vis, viscosity measurements, gel-electrophoresis and fluorescence spectroscopy. The new complexes have been used as catalysts in C—C coupling reaction and in the oxidation of alcohols to their corresponding carbonyl compounds by using NMO as co-oxidant and molecular oxygen (O2 atmosphere at ambient temperature. Further, the new binucleating thiosemicarbazone ligands and their Ru(II complexes were also screened for their antibacterial activity against Klebsiella pneumoniae, Shigella sp., Micrococcus luteus, Escherichia coli and Salmonella typhi. From this study, it was found out that the activity of the complexes almost reaches the effectiveness of the conventional bacteriocide.

  3. Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory

    Directory of Open Access Journals (Sweden)

    Qian Hong

    2008-05-01

    Full Text Available Abstract Background: Several approaches, including metabolic control analysis (MCA, flux balance analysis (FBA, correlation metric construction (CMC, and biochemical circuit theory (BCT, have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. Results: In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RT BS and ST BS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. Conclusion: One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA.

  4. Photocatalysis of the homogeneous water-gas shift reaction under ambient conditions by cationic iridium (III) complexes

    Energy Technology Data Exchange (ETDEWEB)

    Ziessel, R [Ecole Europeenne des Hautes Etudes des Industries Chimiques, 67 - Strasbourg (France)

    1991-07-01

    We describe here our results and mechanistic analysis of the first highly efficient light-assisted WGSR, which takes place under extremely mild conditions (room temperature, ambient pressure, neutral pH, visible light) and is catalyzed by novel Ir{sup III} pentamethylcyclopentadienyl complexes containing novel 4,4'-substituted bipyridine ligands. (orig./EF).

  5. Catalytic ozonation not relying on hydroxyl radical oxidation: A selective and competitive reaction process related to metal-carboxylate complexes

    KAUST Repository

    Zhang, Tao

    2014-01-01

    Catalytic ozonation following non-hydroxyl radical pathway is an important technique not only to degrade refractory carboxylic-containing organic compounds/matter but also to avoid catalyst deactivation caused by metal-carboxylate complexation. It is unknown whether this process is effective for all carboxylates or selective to special molecule structures. In this work, the selectivity was confirmed using O3/(CuO/CeO2) and six distinct ozone-resistant probe carboxylates (i.e., acetate, citrate, malonate, oxalate, pyruvate and succinate). Among these probe compounds, pyruvate, oxalate, and citrate were readily degraded following the rate order of oxalate>citrate>pyruvate, while the degradation of acetate, malonate, and succinate was not promoted. The selectivity was independent on carboxylate group number of the probe compounds and solution pH. Competitive degradation was observed for carboxylate mixtures following the preference order of citrate, oxalate, and finally pyruvate. The competitive degradation was ascribed to competitive adsorption on the catalyst surface. It was revealed that the catalytically degradable compounds formed bidentate chelating or bridging complexes with surface copper sites of the catalyst, i.e., the active sites. The catalytically undegradable carboxylates formed monodentate complexes with surface copper sites or just electrostatically adsorbed on the catalyst surface. The selectivity, relying on the structure of surface metal-carboxylate complex, should be considered in the design of catalytic ozonation process. © 2013 Elsevier B.V.

  6. Cognitive and emotional reactions to daily events: the effects of self-esteem and self-complexity.

    Science.gov (United States)

    Campbell, J D; Chew, B; Scratchley, L S

    1991-09-01

    In this article we examine the effects of self-esteem and self-complexity on cognitive appraisals of daily events and emotional lability. Subjects (n = 67) participated in a 2-week diary study; each day they made five mood ratings, described the most positive and negative events of the day, and rated these two events on six appraisal measures. Neither self-esteem nor self-complexity was related to an extremity measure of mood variability. Both traits were negatively related to measures assessing the frequency of mood change, although the effect of self-complexity dissipated when self-esteem was taken into account. Self-esteem (but not self-complexity) was also related to event appraisals: Subjects with low self-esteem rated their daily events as less positive and as having more impact on their moods. Subjects with high self-esteem made more internal, stable, global attributions for positive events than for negative events, whereas subjects low in self-esteem made similar attributions for both types of events and viewed their negative events as being more personally important than did subjects high in self-esteem. Despite these self-esteem differences in subjects' views of their daily events, naive judges (n = 63) who read the event descriptions and role-played their appraisals of them generally did not distinguish between the events that had been experienced by low self-esteem versus high self-esteem diary subjects.

  7. Mono-, di- and trimeric PS I reaction center complexes isolated from the thermophilic cyanobacterium Synechococcus sp. Size, shape and activity

    NARCIS (Netherlands)

    Rögner, M.; Mühlenhoff, U.; Boekema, E.J.; Witt, H.T.

    1990-01-01

    Photosystem I preparations from the cyanobacterium Synechococcus sp. were treated with high concentrations of Tris and octyl glucoside at alkaline pH and elevated temperature. A sucrose density gradient yielded three pigment-protein complexes; these were further purified on a HPLC anion-exchange

  8. Multi-level quantum monte Carlo wave functions for complex reactions: The decomposition of α-hydroxy-dimethylnitrosamine

    NARCIS (Netherlands)

    Fracchia, F.; Filippi, Claudia; Amovilli, C.

    2014-01-01

    We present here several novel features of our recently proposed Jastrow linear generalized valence bond (J-LGVB) wave functions, which allow a consistently accurate description of complex potential energy surfaces (PES) of medium-large systems within quantum Monte Carlo (QMC). In particular, we

  9. Radical S-adenosylmethionine (SAM) enzymes in cofactor biosynthesis: a treasure trove of complex organic radical rearrangement reactions.

    Science.gov (United States)

    Mehta, Angad P; Abdelwahed, Sameh H; Mahanta, Nilkamal; Fedoseyenko, Dmytro; Philmus, Benjamin; Cooper, Lisa E; Liu, Yiquan; Jhulki, Isita; Ealick, Steven E; Begley, Tadhg P

    2015-02-13

    In this minireview, we describe the radical S-adenosylmethionine enzymes involved in the biosynthesis of thiamin, menaquinone, molybdopterin, coenzyme F420, and heme. Our focus is on the remarkably complex organic rearrangements involved, many of which have no precedent in organic or biological chemistry. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Pd-isatin Schiff base complex immobilized onγ-Fe2O3 as a magnetically recyclable catalyst for the Heck and Suzuki cross-coupling reactions

    Institute of Scientific and Technical Information of China (English)

    Sara Sobhani; Farzaneh Zarifi

    2015-01-01

    A Pd‐isatin Schiff base complex immobilized onγ‐Fe2O3 (Pd‐isatin Schiff base‐γ‐Fe2O3) was synthe‐sized and characterized by Fourier transform infrared, scanning electron microscopy, high resolu‐tion transmission electron microscopy, X‐ray diffraction, thermogravimetric gravimetric analysis, inductively‐coupled plasma, X‐ray photoelectron spectroscopy, and elemental analysis. It was used as a magnetically reusable Pd catalyst for the Heck and Suzuki cross‐coupling reactions.

  11. Solubilization of immune complexes in complement factor deficient sera and the influence of temperature, ionic strength and divalent cations on the solubilization reaction

    DEFF Research Database (Denmark)

    Baatrup, Gunnar; Petersen, Ivan; Svehag, Svend-Erik

    1984-01-01

    The complement-mediated solubilization (CMS) of immune complexes (IC) and the initial kinetics (IKS) of this reaction in human sera depleted of or deficient in C2, C3, C8, factors B, P and I were investigated. Sera depleted of B or P and those lacking native C3 or factor I showed virtually no CMS......M. Chelation of Ca2+ in serum by Mg2+-ethylene glycol tetraacetic acid reduced the CMS capacity by up to 50% and the IKS was markedly retarded. Varying the Zn2+ or Mn2+ ion concentrations in serum influenced neither the IKS nor the CMS capacity....

  12. Kinetics and mechanism of aquation and formation reactions of carbonato complexes. XII. Deuterium solvent isotope effect on the rate of acid-catalyzed decarboxylation of the carbonatobis (ethylenediamine) cobalt(III) complex ion. A mechanistic reappraisal

    International Nuclear Information System (INIS)

    Harris, G.M.; Hyde, K.E.

    1978-01-01

    A recent study of the acid-catalyzed decarboxylation of the carbonatotetrakis(pyridine)cobalt(III) complex ion showed there to be rate acceleration in D 2 O solvent, consistent with a proton-preequilibration mechanism. This observation directly contradicts the results of a similar study made some years ago of the analogous ion, carbonatobis(ethylenediamine)cobalt(III), for which there appeared to be deceleration in D 2 O solvent. A reinvestigation of the latter reaction over a much wider acidity range has now shown the earlier work to be in error. The previously proposed generalized mechanism for aquation of chelated carbonato complex ions of the form CoN 4 CO 3 + (N 4 identical with various tetramine ligand groupings of uni-, bi-, or quadridentate type) has thus been revised to include a proton equilibration step. An unexpected complication arises in the interpretation of the data for the bis(ethylenediamine) complex ion in the acidity range 0.1 + ] + ] term, overtakes and exceeds the true first-order rate constant for CO 2 release. The interesting implications of this unusual first-order successive reaction system are fully explored in the context of the present study

  13. Zeolite-Y entrapped Ru(III and Fe(III complexes as heterogeneous catalysts for catalytic oxidation of cyclohexane reaction

    Directory of Open Access Journals (Sweden)

    Chetan K. Modi

    2017-02-01

    Full Text Available Catalysis is probably one of the greatest contributions of chemistry to both economic growth and environmental protection. Herein we report the catalytic behavior of zeolite-Y entrapped Ru(III and Fe(III complexes with general formulae [M(VTCH2·2H2O]+-Y and [M(VFCH2·2H2O]+-Y [where, VTCH = vanillin thiophene-2-carboxylic hydrazone and VFCH = vanillin furoic-2-carboxylic hydrazone] over the oxidation of cyclohexane forming cyclohexanone and cyclohexanol. The samples were corroborated by various physico-chemical techniques. These zeolite-Y based complexes are stable and recyclable under current reaction conditions. Amongst them, [Ru(VTCH2⋅2H2O]+-Y showed higher catalytic activity (41.1% with cyclohexanone (84.6% selectivity.

  14. Tetradentate N2O2 Chelated Palladium(II Complexes: Synthesis, Characterization, and Catalytic Activity towards Mizoroki-Heck Reaction of Aryl Bromides

    Directory of Open Access Journals (Sweden)

    Siti Kamilah Che Soh

    2013-01-01

    Full Text Available Four air and moisture-stable palladium(II-Schiff base complexes, N,N′-bis(α-methylsalicylidenepropane-1,3-diamine palladium(II (2a, N,N′-bis(4-methyl-α-methylsalicylidenepropane-1,3-diamine palladium(II (2b, N,N′-bis(3,5-di-tert-butylsalicylidenepropane-1,3-diamine palladium(II (2c, and N,N′-bis(4-methoxy-salicylidenepropane-1,3-diamine palladium(II (2d, have been successfully synthesised and characterised by CHN elemental analyses and conventional spectroscopic methods. These complexes were investigated as catalysts in the phosphine-free Mizoroki-Heck cross-coupling reactions of aryl bromides with methyl acrylate.

  15. Electrochemical behaviours of Eu(III/E(II and Ce(IV/Ce(III in H3PO4-H2O media : solvation and complexation reactions

    Directory of Open Access Journals (Sweden)

    Belqat B.

    2018-01-01

    Full Text Available Many kinds of rare earth elements (REE such as europium and cerium have been make them essential elements in many high-tech components. The electrochemical studies can be presented as an interesting indication for europium and cerium extraction from phosphoric solutions, including solvation and complexation reactions. The normal redox potentials of Eu3+/Eu2+ and Ce4+/Ce3+ systems have been determined in H3PO4-H2O media with various phosphoric acid concentration. The solvation of these elements in phosphoric media is characterized by their transfer activity coefficients "f" calculated from the corresponding normal redox potentials. The corresponding solvation increases with increasing the H3PO4 concentration. For each REE, the electrochemical properties depend on its number of charges and on its basic properties. Results suggest that solvation and complexation of REE phosphates are important in controlling REE concentration.

  16. Synthesis and characterization of divalent metal complexes with ligand derived from the reaction of 3-aminopyridine and biacetyl

    Directory of Open Access Journals (Sweden)

    RAMESH KUMAR

    2006-09-01

    Full Text Available Divalent cobalt, nickel and copper salts reacted in situ with 3-aminopyridine and biacetyl to form complexes of the type: [M(Ap2biac2X2], where Ap2biac is the ligand and X=Cl, Br, NO3 or NCS. The complexes were analysed and characterized as distorted octahedral by conductance, molecular weight, magnetic, electronic and IR spectral studies. The electronic spectra were interpreted and tentative aassignments made. The infrared spectral studies revealed that two molecules of 3-aminopyridine were joined by molecules of biacetyl through a two carbon atom bridge and that the ligand coordinated through azomethine nitrogen atoms, whereas the pyridine nitrogen does not participate in the coordination. In the far infrared spectra, various metal–ligand vibrations were observed and are discussed.

  17. Metathesis Polymerization Reactions Induced by the Bimetallic Complex (Ph4P2[W2(μ-Br3Br6

    Directory of Open Access Journals (Sweden)

    Despoina Chriti

    2015-12-01

    Full Text Available The reactivity of the bimetallic complex (Ph4P2[W2(μ-Br3Br6] ({W 2.5 W}7+, a′2e3 towards ring opening metathesis polymerization (ROMP of norbornene (NBE and some of its derivatives, as well as the mechanistically related metathesis polymerization of phenylacetylene (PA, is presented. Our results show that addition of a silver salt (AgBF4 is necessary for the activation of the ditungsten complex. Polymerization of PA proceeds smoothly in tetrahydrofuran (THF producing polyphenylacetylene (PPA in high yields. On the other hand, the ROMP of NBE and its derivatives is more efficient in CH2Cl2, providing high yields of polymers. 13C Cross Polarization Magic Angle Spinning (CPMAS spectra of insoluble polynorbornadiene (PNBD and polydicyclopentadiene (PDCPD revealed the operation of two mechanisms (metathetic and radical for cross-linking, with the metathesis pathway prevailing.

  18. Measures of Biochemical Sociology

    Science.gov (United States)

    Snell, Joel; Marsh, Mitchell

    2008-01-01

    In a previous article, the authors introduced a new sub field in sociology that we labeled "biochemical sociology." We introduced the definition of a sociology that encompasses sociological measures, psychological measures, and biological indicators Snell & Marsh (2003). In this article, we want to demonstrate a research strategy that would assess…

  19. Alu polymerase chain reaction: A method for rapid isolation of human-specific sequences from complex DNA sources

    International Nuclear Information System (INIS)

    Nelson, D.L.; Ledbetter, S.A.; Corbo, L.; Victoria, M.F.; Ramirez-Solis, R.; Webster, T.D.; Ledbetter, D.H.; Caskey, C.T.

    1989-01-01

    Current efforts to map the human genome are focused on individual chromosomes or smaller regions and frequently rely on the use of somatic cell hybrids. The authors report the application of the polymerase chain reaction to direct amplification of human DNA from hybrid cells containing regions of the human genome in rodent cell backgrounds using primers directed to the human Alu repeat element. They demonstrate Alu-directed amplification of a fragment of the human HPRT gene from both hybrid cell and cloned DNA and identify through sequence analysis the Alu repeats involved in this amplification. They also demonstrate the application of this technique to identify the chromosomal locations of large fragments of the human X chromosome cloned in a yeast artificial chromosome and the general applicability of the method to the preparation of DNA probes from cloned human sequences. The technique allows rapid gene mapping and provides a simple method for the isolation and analysis of specific chromosomal regions

  20. Use of radioactive tracers in chemical reactions. the displacement of zinc-nickel complexes with quantitative determination of nickel

    International Nuclear Information System (INIS)

    Mazzilli, B.; Saiki, M.

    1983-01-01

    The present paper presents a method for the determination of small quantities of nickel radioactive tracers. An analytical application of the displacement reaction between nickel and zinc ethylenediaminetetraacetate labeled with zinc-65 is pursued. This method is based on the extraction of radioactive zinc displaced by nickel from the zinc chelate into a dithizone-carbon tetrachloride solution and the subsequent measurement of the activity of an aliquot of the extract. The method is very sensitive and nickel can be measured in concentrations as small as 0.1 μg/ml or even less, depending on the specific activity of the radioreagent used. The precision and the accuracy of the method are determined. The problem of interferences is also investigated and an attempt is made in order to eliminate them by using masking agents or by means of a previous separation between nickel and other interfering metals. (Author) [pt

  1. Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB.

    Science.gov (United States)

    Ullah, M; Schmidt, H; Cho, K H; Wolkenhauer, O

    2006-03-01

    The analysis of complex biochemical networks is conducted in two popular conceptual frameworks for modelling. The deterministic approach requires the solution of ordinary differential equations (ODEs, reaction rate equations) with concentrations as continuous state variables. The stochastic approach involves the simulation of differential-difference equations (chemical master equations, CMEs) with probabilities as variables. This is to generate counts of molecules for chemical species as realisations of random variables drawn from the probability distribution described by the CMEs. Although there are numerous tools available, many of them free, the modelling and simulation environment MATLAB is widely used in the physical and engineering sciences. We describe a collection of MATLAB functions to construct and solve ODEs for deterministic simulation and to implement realisations of CMEs for stochastic simulation using advanced MATLAB coding (Release 14). The program was successfully applied to pathway models from the literature for both cases. The results were compared to implementations using alternative tools for dynamic modelling and simulation of biochemical networks. The aim is to provide a concise set of MATLAB functions that encourage the experimentation with systems biology models. All the script files are available from www.sbi.uni-rostock.de/ publications_matlab-paper.html.

  2. The biochemical, physiological and therapeutic roles of ascorbic acid

    African Journals Online (AJOL)

    Ascorbic acid is an important micronutrient necessary for a significant number of metabolic reactions in humans and other primates. It is a strong reducing agent involved in reduction reaction and it is structurally related to glucose. Experimental and epidemiological studies have documented the biochemical, physiological ...

  3. Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

    Energy Technology Data Exchange (ETDEWEB)

    MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.; Berrie, Barbara H. (NGA); (Bordeaux)

    2016-09-23

    To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K+, Zn2+, Pb2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic–inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm–1 for Pb(II) and ca. 1580 cm–1 for Zn(II) are consistent with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. These complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.

  4. Complex formation reactions of uranyl(VI) with neutral N-donors in dimethyl sulfoxide. Influence of small amounts of water

    International Nuclear Information System (INIS)

    Cassol, A.; Di Bernardo, P.; Zanonato, P.; Portanova, R.; Tolazzi, M.

    1990-01-01

    Quantitative information about the existence and thermodynamic stability of uranyl(VI) ion complexes based solely upon nitrogen coordination has been obtained in the solvent dimethyl sulfoxide. Calorimetric, potentiometric, and FT-IR investigations, under controlled anhydrous conditions, show that the uranyl(VI) ion can form both mono and bis chelates with the ethylenediamine ligand and only a mono chelate of rather low stability with propylenediamine. With the monodentate ligand n-butylamine only a very weak metal-ligand interaction has been detected. The stability constants and the enthalpy and entropy changes have been calculated for the identified coordinated species. All data refer to 25.0 degree C and a tetraethylammonium perchlorate medium of ionic strength 0.1 M. All the complexes are enthalpy stabilized whereas the entropy contributions oppose the complex formation. Calorimetric and FT-IR measurements carried out to investigate the effects of small amounts of water present show that a very low water concentration, comparable to that of the coordinating metal ion, can give rise to hydrolysis reactions that may compete with complex formation. This is due to the combined action of different factors that are discussed. 39 refs., 6 figs., 1 tab

  5. Langmuir-Blodgett and X-ray diffraction studies of isolated photosystem II reaction centers in monolayers and multilayers: physical dimensions of the complex.

    Science.gov (United States)

    Uphaus, R A; Fang, J Y; Picorel, R; Chumanov, G; Wang, J Y; Cotton, T M; Seibert, M

    1997-04-01

    The photosystem II (PSII) reaction center (RC) is a hydrophobic intrinsic protein complex that drives the water-oxidation process of photosynthesis. Unlike the bacterial RC complex, an X-ray crystal structure of the PSII RC is not available. In order to determine the physical dimensions of the isolated PSII RC complex, we applied Langmuir techniques to determine the cross-sectional area of an isolated RC in a condensed monolayer film. Low-angle X-ray diffraction results obtained by examining Langmuir-Blodgett multilayer films of alternating PSII RC/Cd stearate monolayers were used to determine the length (or height; z-direction, perpendicular to the plane of the original membrane) of the complex. The values obtained for a PSII RC monomer were 26 nm2 and 4.8 nm, respectively, and the structural integrity of the RC in the multilayer film was confirmed by several approaches. Assuming a cylindrical-type RC structure, the above dimensions lead to a predicted volume of about 125 nm3. This value is very close to the expected volume of 118 nm3, calculated from the known molecular weight and partial specific volume of the PSII RC proteins. This same type of comparison was also made with the Rhodobacter sphaeroides RC based on published data, and we conclude that the PSII RC is much shorter in length and has a more regular solid geometric structure than the bacterial RC. Furthermore, the above dimensions of the PSII RC and those of PSII core (RC plus proximal antenna) proteins protruding outside the plane of the PSII membrane into the lumenal space as imaged by scanning tunneling microscopy (Seibert, Aust. J. Pl. Physiol. 22, 161-166, 1995) fit easily into the known dimensions of the PSII core complex visualized by others as electron-density projection maps. From this we conclude that the in situ PSII core complex is a dimeric structure containing two copies of the PSII RC.

  6. Determination of microgramme amounts of osmium and ruthenium based on inhibition of the iodine-azide reaction by their complexes with 6-mercaptopurine

    International Nuclear Information System (INIS)

    Matusiewicz, H.; Kurzawa, Z.

    1976-01-01

    A new kinetic method of the determination of microamounts of osmium and ruthenium has been developed. The reaction between sodum azide and iodine induced by 6-mercaptopurine (6-MP) was used for this purpose. Under suitable experimental conditions the induction coefficient of 6-MP amounts to 1750+-40. The formed complexes of the metals are stable in the medium containing an excess of azide ions and do not induce the iodine-azide reaction. The method consists in the determination of the 6-MP not bound to the metal. The amount of osmium or ruthenium is then determined from linear relations. Before the determination osmium and ruthenium must be separated from other cations and from each other by distillation as volatile tetroxides. The iodine-azide method is simple, sensitive and does not require any apparatus. The range of the determination is 0.1-5.0 μg in 5 cm 3 of the solution of Os(8) and 0.5-5.0 μg for Ru(8). The error of the determination is +-6.4% and +- 6.1% for osmium and ruthenium, respectively. The time of the determination is 30 minutes not taking into account 2-hour waiting time necessary for the formation of the complexes. (author)

  7. Bimolecular reaction of CH3 + CO in solid p-H2: Infrared absorption of acetyl radical (CH3CO) and CH3-CO complex

    Science.gov (United States)

    Das, Prasanta; Lee, Yuan-Pern

    2014-06-01

    We have recorded infrared spectra of acetyl radical (CH3CO) and CH3-CO complex in solid para-hydrogen (p-H2). Upon irradiation at 248 nm of CH3C(O)Cl/p-H2 matrices, CH3CO was identified as the major product; characteristic intense IR absorption features at 2990.3 (ν9), 2989.1 (ν1), 2915.6 (ν2), 1880.5 (ν3), 1419.9 (ν10), 1323.2 (ν5), 836.6 (ν7), and 468.1 (ν8) cm-1 were observed. When CD3C(O)Cl was used, lines of CD3CO at 2246.2 (ν9), 2244.0 (ν1), 1866.1 (ν3), 1046.7 (ν5), 1029.7 (ν4), 1027.5 (ν10), 889.1 (ν6), and 723.8 (ν7) cm-1 appeared. Previous studies characterized only three vibrational modes of CH3CO and one mode of CD3CO in solid Ar. In contrast, upon photolysis of a CH3I/CO/p-H2 matrix with light at 248 nm and subsequent annealing at 5.1 K before re-cooling to 3.2 K, the CH3-CO complex was observed with characteristic IR features at 3165.7, 3164.5, 2150.1, 1397.6, 1396.4, and 613.0 cm-1. The assignments are based on photolytic behavior, observed deuterium isotopic shifts, and a comparison of observed vibrational wavenumbers and relative IR intensities with those predicted with quantum-chemical calculations. This work clearly indicates that CH3CO can be readily produced from photolysis of CH3C(O)Cl because of the diminished cage effect in solid p-H2 but not from the reaction of CH3 + CO because of the reaction barrier. Even though CH3 has nascent kinetic energy greater than 87 kJ mol-1 and internal energy ˜42 kJ mol-1 upon photodissociation of CH3I at 248 nm, its energy was rapidly quenched so that it was unable to overcome the barrier height of ˜27 kJ mol-1 for the formation of CH3CO from the CH3 + CO reaction; a barrierless channel for formation of a CH3-CO complex was observed instead. This rapid quenching poses a limitation in production of free radicals via bimolecular reactions in p-H2.

  8. Use of frontal analysis in ion exchange chromatography for the study of reactions of formation of complexes in solution. Application to hydrochloric complexes of nickel (II), cobalt (II) and copper (II)

    International Nuclear Information System (INIS)

    Tremillon, Bernard

    1959-01-01

    The ion exchanger column frontal analysis method provides a convenient way to study complex formation reactions when they are very unstable. It has the advantage of being much more sensitive and precise than the method (already used by other authors) of simple equilibrium between a solution and an ion exchanger. As an illustration of this method, the hydrochloric acid complexes NiCl + , CoCl + and CuCl + , have been studied, and their dissociation constants were determined (respectively 4.6 ± 0.1; 4.0 ± 0.1 and 2.5 ± 0.1, at an ionic strength substantially equal to 1.5). Reprint of a paper published in Bulletin de la Societe Chimique de France, 1958, p. 1483-1487 [fr

  9. Kinetic Isotope Effect Determination Probes the Spin of the Transition State, Its Stereochemistry, and Its Ligand Sphere in Hydrogen Abstraction Reactions of Oxoiron(IV) Complexes.

    Science.gov (United States)

    Mandal, Debasish; Mallick, Dibyendu; Shaik, Sason

    2018-01-16

    This Account outlines interplay of theory and experiment in the quest to identify the reactive-spin-state in chemical reactions that possess a few spin-dependent routes. Metalloenzymes and synthetic models have forged in recent decades an area of increasing appeal, in which oxometal species bring about functionalization of hydrocarbons under mild conditions and via intriguing mechanisms that provide a glimpse of Nature's designs to harness these reactions. Prominent among these are oxoiron(IV) complexes, which are potent H-abstractors. One of the key properties of oxoirons is the presence of close-lying spin-states, which can mediate H-abstractions. As such, these complexes form a fascinating chapter of spin-state chemistry, in which chemical reactivity involves spin-state interchange, so-called two-state reactivity (TSR) and multistate reactivity (MSR). TSR and MSR pose mechanistic challenges. How can one determine the structure of the reactive transition state (TS) and its spin state for these mechanisms? Calculations can do it for us, but the challenge is to find experimental probes. There are, however, no clear kinetic signatures for the reactive-spin-state in such reactions. This is the paucity that our group has been trying to fill for sometime. Hence, it is timely to demonstrate how theory joins experiment in realizing this quest. This Account uses a set of the H-abstraction reactions of 24 synthetic oxoiron(IV) complexes and 11 hydrocarbons, together undergoing H-abstraction reactions with TSR/MSR options, which provide experimentally determined kinetic isotope effect (KIE exp ) data. For this set, we demonstrate that comparing KIE exp results with calculated tunneling-augmented KIE (KIE TC ) data leads to a clear identification of the reactive spin-state during H-abstraction reactions. In addition, generating KIE exp data for a reaction of interest, and comparing these to KIE TC values, provides the mechanistic chemist with a powerful capability to

  10. “Covalent Hydration” Reactions in Model Monomeric Ru 2,2'-Bipyridine Complexes: Thermodynamic Favorability as a Function of Metal Oxidation and Overall Spin States

    Energy Technology Data Exchange (ETDEWEB)

    Ozkanlar, Abdullah; Cape, Jonathan L.; Hurst, James K.; Clark, Aurora E.

    2011-09-05

    Density functional theory (DFT) has been used to investigate the plausibility of water addition to the simple mononuclear ruthenium complexes, [(NH{sub 3}){sub 3}(bpy)Ru=O]{sup 2+}/{sup 3+} and [(NH{sub 3}){sub 3}(bpy)RuOH]{sup 3+}, in which the OH fragment adds to the 2,2{prime}-bipyridine (bpy) ligand. Activation of bpy toward water addition has frequently been postulated within the literature, although there exists little definitive experimental evidence for this type of 'covalent hydration'. In this study, we examine the energetic dependence of the reaction upon metal oxidation state, overall spin state of the complex, as well as selectivity for various positions on the bipyridine ring. The thermodynamic favorability is found to be highly dependent upon all three parameters, with free energies of reaction that span favorable and unfavorable regimes. Aqueous addition to [(NH{sub 3}){sub 3}(bpy)Ru=O]{sup 3+} was found to be highly favorable for the S = 1/2 state, while reduction of the formal oxidation state on the metal center makes the reaction highly unfavorable. Examination of both facial and meridional isomers reveals that when bipyridine occupies the position trans to the ruthenyl oxo atom, reactivity toward OH addition decreases and the site preferences are altered. The electronic structure and spectroscopic signatures (EPR parameters and simulated spectra) have been determined to aid in recognition of 'covalent hydration' in experimental systems. EPR parameters are found to uniquely characterize the position of the OH addition to the bpy as well as the overall spin state of the system.

  11. Origin of complex fragments from 32S + natAg reaction at 37.5 A.MeV

    International Nuclear Information System (INIS)

    Benchekroun, D.; Cheynis, B.; Demeyer, A.; Gerlic, E.; Guinet, D.; Lautesse, P.; Lebreton, L.; Magda, M.T.; Stern, M.; Chabane, A.; Desesquelles, P.; Giorni, A.; Heuer, D.; Lleres, A.; Viano, J.B.

    1996-08-01

    Fragment emission from collisions of 32 S with nat Ag at 37.5 A.MeV has been studied with the 4π multidetector AMPHORA. Production of intermediate mass and heavy fragments as well as of light charged particles has been measured. The total charged particle multiplicity and polar angular distributions have been used to select various classes of collisions. Analysis of angular and energy distributions of fragments and light particles in central collisions indicates the formation of a hot source (excitation energy of ∼ 4.4 A.MeV) with an additional contribution from a preequilibrium process at more forward angles. Azimuthal angle correlations of He - Li, Li - Li, B - B, and C - C pairs have been used as a tool to study the origin of complex fragments. Data at backward angles are well described by considering a thermalized emitter with an angular momentum around 70 h and a fragment emission time of the order of 200 fm/c. A microscopic approach of BNV type confirms these emission times and angular momenta indicating the persistence of an incomplete fusion process responsible for the emission of complex fragments at backward angles

  12. Intermolecular Dehydrative Coupling Reaction of Arylketones with Cyclic Alkenes Catalyzed by a Well-Defined Cationic Ruthenium-Hydride Complex: A Novel Ketone Olefination Method via Vinyl C–H Bond Activation

    Science.gov (United States)

    Yi, Chae S.; Lee, Do W.

    2010-01-01

    Summary The cationic ruthenium-hydride complex [(η6-C6H6)(PCy3)(CO)RuH]+BF4− was found to be a highly effective catalyst for the intermolecular olefination reaction of arylketones with cycloalkenes. The preliminary mechanistic analysis revealed that electrophilic ruthenium-vinyl complex is the key species for mediating both vinyl C–H bond activation and the dehydrative olefination steps of the coupling reaction. PMID:20567607

  13. Use of the nonsteady monotonic heating method for complex determination of thermophysical properties of chemically reacting mixture in the case of non-equilibrium proceeding of the chemical reaction

    International Nuclear Information System (INIS)

    Serebryanyj, G.Z.

    1984-01-01

    Theoretical analysis is made for the monotonic heating method as applied for complex determination of thermophysical properties of chemically reacting gases. The possibility is shown of simultaneous determination of frozen and equilibrium heat capacity, frozen and equilibrium heat conduction provided non-equilibrium occuring of the reaction in the wide range of temperatures and pressures. The monotonic heating method can be used for complex determination of thermophysical properties of chemically reacting systems in case of non-equilibrium proceeding of the chemical reaction

  14. Study of the (e,e'p) quasi-elastic reaction in complex nuclei: theory and experiment

    Energy Technology Data Exchange (ETDEWEB)

    Herraiz, Joaquin Lopez [Complutense Univ. of Madrid (Spain)

    2010-03-01

    Experimental coincidence cross section and transverse-longitudinal asymmetry ATL have been obtained for the quasielastic (e,e'p) reaction in 16O, 12C, and {sup 208}Pb in constant q-ω kinematics in the missing momentum range -350 < pmiss < 350 MeV/c. In these experiments, performed in experimental Hall A of the Thomas Jefferson National Accelerator Facility (JLAB), the beam energy and the momentum and angle of the scattered electrons were kept fixed, while the angle between the proton momentum and the momentum transfer q was varied in order to map out the missing momentum distribution. The experimental cross section and ATL asymmetry have been compared with Monte Carlo simulations based on Distorted Wave Impulse Approximation (DWIA) calculations with both relativistic and non-relativistic spinor structure. The spectroscopic factors obtained for both models are in agreement with previous experimental values, while ATL measurements favor the relativistic DWIA calculation. This thesis describes the details of the experimental setup, the calibration of the spectrometers, the techniques used in the data analysis to derive the final cross sections and the ATL, the ingredients of the theoretical calculations employed and the comparison of the results with the simulations based on these theoretical models.

  15. Complex fragment emission in the reaction 197Au → 197Au at an incident energy of 15 MeV/u

    International Nuclear Information System (INIS)

    Schmoll, R.

    1988-07-01

    For the study of the dominant decay processes in the reaction 15 MeV/u 197 Au → 197 Au in one-particle inclusive experiments the emission characteristics of all ejectiles in the mass range 24 ≤ A ≤ 197 were studied. The deflection function of the projectile-like fragments is for all energy losses at the grazing angle Θ cm gr =27.5 degrees peaked and in fact even for scattering events in which the whole available kinetic energy was dissipated in the collisions. The systematic analysis of the velocity spectra shows that the lightest fragments are formed in double-sequential fission of the highly excited gold-like fragments from the first deep inelastic reaction stage before reaching of a global equilibrium. On the other side symmetrical fission products, which are part of the narrow branch of the mass distribution, are emitted in simple-sequential non-equilibrium fission. This simple-sequential breakup is very closely limited to excitation energies of 75 ≤ E * ≤ 275 MeV of the primary, gold-like fragments, while the probability for double-sequential fission above E * ≅ 200 MeV increases very strongly. Contrarily to equilibrated compound-nucleus fission these processes are characterized by a in the source system strongly anisotropic angular distribution with distinct foreward/backward asymmetry and by an extremely asymmetric mass split. The study of the mass distribution shows that non-equilibrium fission at 15 MeV/u is both in view of the reaction cross section and regarding the creation of the complex fragments is the dominant decay process. The integral cross section of the broad four-body distribution corresponds to 60% of the total reaction cross section; the integral cross section of the narrow three-body distribution corresponds to 10%. (orig./HSI) [de

  16. Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation

    Science.gov (United States)

    Chernia, Zelig; Tsori, Yoav

    2018-03-01

    Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

  17. Gold(III) complexes with 2-substituted pyridines as experimental anticancer agents: solution behavior, reactions with model proteins, antiproliferative properties.

    Science.gov (United States)

    Maiore, Laura; Cinellu, Maria Agostina; Nobili, Stefania; Landini, Ida; Mini, Enrico; Gabbiani, Chiara; Messori, Luigi

    2012-03-01

    Gold(III) compounds form a family of promising cytotoxic and potentially anticancer agents that are currently undergoing intense preclinical investigations. Four recently synthesized and characterized gold(III) derivatives of 2-substituted pyridines are evaluated here for their biological and pharmacological behavior. These include two cationic adducts with 2-pyridinyl-oxazolines, [Au(pyox(R))Cl(2)][PF(6)], [pyox(R)=(S)-4-benzyl-2-(pyridin-2-yl)-4,5-dihydrooxazole, I; (S)-4-iso-propyl-2-(pyridin-2-yl)-4,5-dihydrooxazole, II] and two neutral complexes [Au(N,N'OH)Cl(2)], III, and [Au(N,N',O)Cl], IV, containing the deprotonated ligand N-(1-hydroxy-3-iso-propyl-2-yl)pyridine-2-carboxamide, N,N'H,OH, resulting from ring opening of bound pyox(R) ligand of complex II by hydroxide ions. The solution behavior of these compounds was analyzed. These behave as classical prodrugs: activation of the metal center typically takes place through release of the labile chloride ligands while the rest of the molecule is not altered; alternatively, activation may occur through gold(III) reduction. All compounds react eagerly with the model protein cyt c leading to extensive protein metalation. ESI MS experiments revealed details of gold-cyt c interactions and allowed us to establish the nature of protein bound metal containing fragments. The different behavior displayed by I and II compared to III and IV is highlighted. Remarkable cytotoxic properties, against the reference human ovarian carcinoma cell lines A2780/S and A2780/R were disclosed for all tested compounds with IC(50) values ranging from 1.43 to 6.18 μM in the sensitive cell line and from 1.59 to 10.86 μM in the resistant one. The common ability of these compounds to overcome cisplatin resistance is highlighted. The obtained results are thoroughly discussed in the frame of current knowledge on cytotoxic gold compounds. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Structure and function of cytochrome c2 in electron transfer complexes with the photosynthetic reaction center of Rhodobacter sphaeroides: optical linear dichroism and EPR.

    Science.gov (United States)

    Drepper, F; Mathis, P

    1997-02-11

    The photosynthetic reaction center (RC) and its secondary electron donor the water-soluble cytochrome (cyt) c2 from the purple bacterium Rhodobacter sphaeroides have been used in cross-linked and non-cross-linked complexes, oriented in compressed gels or partially dried multilayers, to study the respective orientation of the primary donor P (BChl dimer) and of cyt c2. Three methods were used: (i) Polarized optical absorption spectra at 295 and 10 K were measured and the linear dichroism of the two individual transitions (Qx, Qy), which are nearly degenerate within the alpha-band of reduced cyt c2, was determined. Attribution of the polarization directions to the molecular axes within the heme plane yielded the average cyt orientation in the complexes. (ii) Time-resolved flash absorption measurements using polarized light allowed determination of the orientation of cyt c2 in complexes which differ in their kinetics of electron transfer. (iii) EPR spectroscopy of ferricyt c2 in cross-linked RC-cyt c2 complexes was used to determine the angle between the heme and the membrane plane. The results suggest the following structural properties for the docking of cyt c2 to the RC: (i) In cross-linked complexes, the two cytochromes displaying half-lives of 0.7 and 60 micros for electron transfer to P+ are similarly oriented (difference plane is parallel to the symmetry axis of the RC (0 degrees +/- 10 degrees). Moreover, the Qy transition, which is assumed to be polarized within the ring III-ring I direction of the heme plane, makes an angle of 56 degrees +/- 1 degree with the symmetry axis. (iii) The dichroism spectrum for the fast phase (0.7 micros) for the non-cross-linked cyt c2-RC complex suggests an orientation similar to that of cross-linked cyt c2, but the heme plane is tilted about 20 degrees closer to the membrane. An alternative model is that two or more bound states of cyt c2 with heme plane tilt angles between 0 degrees and 30 degrees allow the fast electron

  19. Crystal Structures of Nitroalkane Oxidase: Insights into the Reaction Mechanism of a Covalent Complex of the Flavoenzyme Trapped During Turnover

    Energy Technology Data Exchange (ETDEWEB)

    Nagpal,A.; Valley, M.; Fitzpatrick, P.; Orville, A.

    2006-01-01

    Nitroalkane oxidase (NAO) from Fusarium oxysporum catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones with the production of H2O2 and nitrite. The flavoenzyme is a new member of the acyl-CoA dehydrogenase (ACAD) family, but it does not react with acyl-CoA substrates. We present the 2.2 Angstroms resolution crystal structure of NAO trapped during the turnover of nitroethane as a covalent N5-FAD adduct (ES*). The homotetrameric structure of ES* was solved by MAD phasing with 52 Se-Met sites in an orthorhombic space group. The electron density for the N5-(2-nitrobutyl)-1,5-dihydro-FAD covalent intermediate is clearly resolved. The structure of ES* was used to solve the crystal structure of oxidized NAO at 2.07 Angstroms resolution. The c axis for the trigonal space group of oxidized NAO is 485 Angstroms, and there are six subunits (11/2 holoenzymes) in the asymmetric unit. Four of the active sites contain spermine (EI), a weak competitive inhibitor, and two do not contain spermine (E{sup ox}). The active-site structures of E{sup ox}, EI, and ES* reveal a hydrophobic channel that extends from the exterior of the protein and terminates at Asp402 and the N5 position on the re face of the FAD. Thus, Asp402 is in the correct position to serve as the active-site base, where it is proposed to abstract the {alpha} proton from neutral nitroalkane substrates. The structures for NAO and various members of the ACAD family overlay with root-mean-square deviations between 1.7 and 3.1 Angstroms. The homologous region typically spans more than 325 residues and includes Glu376, which is the active-site base in the prototypical member of the ACAD family. However, NAO and the ACADs exhibit differences in hydrogen-bonding patterns between the respective active-site base, substrate molecules, and FAD. These likely differentiate NAO from the homologues and, consequently, are proposed to result in the unique reaction mechanism of NAO.

  20. Concentration of eicosapentaenoic acid (EPA and docosahexaenoic acid (DHA of Asian catfish oil by urea complexation: optimization of reaction conditions

    Directory of Open Access Journals (Sweden)

    Pornpisanu Thammapat

    2016-04-01

    Full Text Available Optimization of the concentrating conditions of eicosapentaenoic acid (EPA and docosahexaenoic acid (DHA extracted from Asian catfish oil was studied to obtain a maximum concentration. The crude fish oil was extracted from the belly flap and adipose tissue of Asian catfish, and the extracted oil was used as fresh crude oil. The EPA and DHA were concentrated by the urea complexation method. A hexagonal rotatable design was applied to examine the effects of crystallization temperature and urea-to-fatty acid ratio on the total content of EPA and DHA (Y1 and the liquid recovery yield (Y2 . The second order polynomial regression models for Y1 and Y2 were employed to generate the response surfaces. Under the optimum conditions of -20 °C and a urea-to-fatty acid ratio of 4 (w/w, the total concentration of EPA and DHA could be increased by up to 88%, while a liquid recovery yield of 26% was obtained.

  1. Ion chromatography of transition metals: specific alteration of retention by complexation reactions in the mobile and on the stationary phase

    International Nuclear Information System (INIS)

    Baumgartner, S.

    1992-05-01

    Ion chromatography of mono- and bivalent cations was performed on a conventional cation exchanger. The pH influence of an ethylene-diamine/citrate eluent was significant for the retention of alkaline earth and transition metals, but negligible for alkali ions. This was dealt with from a mechanistic point of view. Mobile phase optimization allowed fast isocratic analysis of mono- and bivalent cations and the separation of the radionuclides Cs-137 and Sr-90. A newly synthesized stationary phase containing iminodiacetate (IDA) function was investigated for cation chromatography using ethylenediamine/citrate eluents, polyhydroxy acid and dipicolinic acid. The column's high selectivity for transition metal ions in comparison to alkali and alkaline earth metals may be governed by the choice of complexing ability and pH of the eluent. Applications verified by atomic absorption spectroscopy include alkaline earth metals in beverages and the determination of Co, Cd and Zn in solutions containing more than 10 14 -fold excess of Na and Mg, such as sea water

  2. Biochemical thermodynamics: applications of Mathematica.

    Science.gov (United States)

    Alberty, Robert A

    2006-01-01

    reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

  3. Complex chemical composition of colored surface films formed from reactions of propanal in sulfuric acid at upper troposphere/lower stratosphere aerosol acidities.

    Science.gov (United States)

    Van Wyngarden, A L; Pérez-Montaño, S; Bui, J V H; Li, E S W; Nelson, T E; Ha, K T; Leong, L; Iraci, L T

    Particles in the upper troposphere and lower stratosphere (UT/LS) consist mostly of concentrated sulfuric acid (40-80 wt %) in water. However, airborne measurements have shown that these particles also contain a significant fraction of organic compounds of unknown chemical composition. Acid-catalyzed reactions of carbonyl species are believed to be responsible for significant transfer of gas phase organic species into tropospheric aerosols and are potentially more important at the high acidities characteristic of UT/LS particles. In this study, experiments combining sulfuric acid (H 2 SO 4 ) with propanal and with mixtures of propanal with glyoxal and/or methylglyoxal at acidities typical of UT/LS aerosols produced highly colored surface films (and solutions) that may have implications for aerosol properties. In order to identify the chemical processes responsible for the formation of the surface films, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) and 1 H nuclear magnetic resonance (NMR) spectroscopies were used to analyze the chemical composition of the films. Films formed from propanal were a complex mixture of aldol condensation products, acetals and propanal itself. The major aldol condensation products were the dimer (2-methyl-2-pentenal) and 1,3,5-trimethylbenzene that was formed by cyclization of the linear aldol condensation trimer. Additionally, the strong visible absorption of the films indicates that higher-order aldol condensation products must also be present as minor species. The major acetal species were 2,4,6-triethyl-1,3,5-trioxane and longer-chain linear polyacetals which are likely to separate from the aqueous phase. Films formed on mixtures of propanal with glyoxal and/or methylglyoxal also showed evidence of products of cross-reactions. Since cross-reactions would be more likely than self-reactions under atmospheric conditions, similar reactions of aldehydes like propanal with common aerosol organic species like glyoxal

  4. Multistate Model Builder (MSMB): a flexible editor for compact biochemical models.

    Science.gov (United States)

    Palmisano, Alida; Hoops, Stefan; Watson, Layne T; Jones, Thomas C; Tyson, John J; Shaffer, Clifford A

    2014-04-04

    Building models of molecular regulatory networks is challenging not just because of the intrinsic difficulty of describing complex biological processes. Writing a model is a creative effort that calls for more flexibility and interactive support than offered by many of today's biochemical model editors. Our model editor MSMB - Multistate Model Builder - supports multistate models created using different modeling styles. MSMB provides two separate advances on existing network model editors. (1) A simple but powerful syntax is used to describe multistate species. This reduces the number of reactions needed to represent certain molecular systems, thereby reducing the complexity of model creation. (2) Extensive feedback is given during all stages of the model creation process on the existing state of the model. Users may activate error notifications of varying stringency on the fly, and use these messages as a guide toward a consistent, syntactically correct model. MSMB default values and behavior during model manipulation (e.g., when renaming or deleting an element) can be adapted to suit the modeler, thus supporting creativity rather than interfering with it. MSMB's internal model representation allows saving a model with errors and inconsistencies (e.g., an undefined function argument; a syntactically malformed reaction). A consistent model can be exported to SBML or COPASI formats. We show the effectiveness of MSMB's multistate syntax through models of the cell cycle and mRNA transcription. Using multistate reactions reduces the number of reactions need to encode many biochemical network models. This reduces the cognitive load for a given model, thereby making it easier for modelers to build more complex models. The many interactive editing support features provided by MSMB make it easier for modelers to create syntactically valid models, thus speeding model creation. Complete information and the installation package can be found at http

  5. Characterization of the Unusual Product from the Reaction between Cobalt(II) Chloride, Ethane-1,2-diamine, and Hydrochloric Acid: An Undergraduate Project Involving an Unknown Metal Complex.

    Science.gov (United States)

    Curtis, Neil F.; And Others

    1986-01-01

    Discusses the need for student research-type chemistry projects based upon "unknown" metal complexes. Describes an experiment involving the product from the reaction between cobalt(II) chloride, ethane-1,2-diamine (en) and concentrated hydrochloric acid. Outlines the preparation of the cobalt complex, along with procedure, results and…

  6. Kinetics and Mechanism of the Reaction of a Ruthenium(VI) Nitrido Complex with HSO3 (-) and SO3 (2-) in Aqueous Solution.

    Science.gov (United States)

    Wang, Qian; Zhao, Hong Yan; Man, Wai-Lun; Lam, William W Y; Lau, Kai-Chung; Lau, Tai-Chu

    2016-07-25

    The kinetics and mechanism of the reaction of S(IV) (SO3 (2-) +HSO3 (-) ) with a ruthenium(VI) nitrido complex, [(L)Ru(VI) (N)(OH2 )](+) (Ru(VI) N, L=N,N'-bis(salicylidene)-o-cyclohexyldiamine dianion), in aqueous acidic solutions are reported. The kinetic results are consistent with parallel pathways involving oxidation of HSO3 (-) and SO3 (2-) by Ru(VI) N. A deuterium isotope effect of 4.7 is observed in the HSO3 (-) pathway. Based on experimental results and DFT calculations the proposed mechanism involves concerted N-S bond formation (partial N-atom transfer) between Ru(VI) N and HSO3 (-) and H(+) transfer from HSO3 (-) to a H2 O molecule. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Pulse radiolytic study of the oxidation reaction of uric acid in presence of bovine serum albumin: evidence of possible complex formation in the transient state

    International Nuclear Information System (INIS)

    Adhikari, S.; Gopinathan, C.

    1996-01-01

    The pulse radiolytic and spectrophotometric study of uric acid in presence of bovine serum albumin (BSA) has been carried out. In the spectrophotometric study there is no evidence for ground state interaction between BSA and uric acid. The reaction of CCl 3 OO . radical with uric acid produces a transient having absorption maximum at 330 nm and that with BSA produces transient having absorption maximum at 410 nm. In a composition of equal concentration of uric acid and BSA the CCl 3 OO . radical produces a transient absorption spectrum which shows two peaks at 330 nm and 350 nm and a shoulder at 410 nm. The peak at 350 nm is ascribed due to weak complex formation between BSA and uric acid radicals. The rate constant of CCl 3 OO . radical with uric acid increases with the increase in BSA concentration which is explained as protection of BSA by uric acid from radical attack. (author). 4 refs., 2 figs., 1 tab

  8. Global minimum profile error (GMPE) - a least-squares-based approach for extracting macroscopic rate coefficients for complex gas-phase chemical reactions.

    Science.gov (United States)

    Duong, Minh V; Nguyen, Hieu T; Mai, Tam V-T; Huynh, Lam K

    2018-01-03

    Master equation/Rice-Ramsperger-Kassel-Marcus (ME/RRKM) has shown to be a powerful framework for modeling kinetic and dynamic behaviors of a complex gas-phase chemical system on a complicated multiple-species and multiple-channel potential energy surface (PES) for a wide range of temperatures and pressures. Derived from the ME time-resolved species profiles, the macroscopic or phenomenological rate coefficients are essential for many reaction engineering applications including those in combustion and atmospheric chemistry. Therefore, in this study, a least-squares-based approach named Global Minimum Profile Error (GMPE) was proposed and implemented in the MultiSpecies-MultiChannel (MSMC) code (Int. J. Chem. Kinet., 2015, 47, 564) to extract macroscopic rate coefficients for such a complicated system. The capability and limitations of the new approach were discussed in several well-defined test cases.

  9. IC-tagged proteins are able to interact with each other and perform complex reactions when integrated into muNS-derived inclusions.

    Science.gov (United States)

    Brandariz-Nuñez, Alberto; Otero-Romero, Iria; Benavente, Javier; Martinez-Costas, Jose M

    2011-09-20

    We have recently developed a versatile tagging system (IC-tagging) that causes relocation of the tagged proteins to ARV muNS-derived intracellular globular inclusions. In the present study we demonstrate (i) that the IC-tag can be successfully fused either to the amino or carboxyl terminus of the protein to be tagged and (ii) that IC-tagged proteins are able to interact between them and perform complex reactions that require such interactions while integrated into muNS inclusions, increasing the versatility of the IC-tagging system. Also, our studies with the DsRed protein add some light on the structure/function relationship of the evolution of DsRed chromophore. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Zinc and cadmium complexes of a plant metallothionein under radical stress: desulfurisation reactions associated with the formation of trans-lipids in model membranes.

    Science.gov (United States)

    Torreggiani, Armida; Domènech, Jordi; Orihuela, Ruben; Ferreri, Carla; Atrian, Sílvia; Capdevila, Mercè; Chatgilialoglu, Chryssostomos

    2009-06-08

    Metallothioneins (MTs) are sulfur-rich proteins capable of binding metal ions to give metal clusters. The metal-MT aggregates used in this work were Zn- and Cd-QsMT, where QsMT is an MT from the plant Quercus suber. Reactions of reductive reactive species (H(*) atoms and e(aq)(-)), produced by gamma irradiation of water, with Zn- and Cd-QsMT were carried out in both aqueous solutions and vesicle suspensions, and were characterized by different approaches. By using a biomimetic model based on unsaturated lipid vesicle suspensions, the occurrence of tandem protein/lipid damage was shown. The reactions of reductive reactive species with methionine residues and/or sulfur-containing ligands afford diffusible sulfur-centred radicals, which migrate from the aqueous phase to the lipid bilayer and transform the cis double bond of the oleate moiety into the trans isomer. Tailored experiments allowed the reaction mechanism to be elucidated in some detail. The formation of sulfur-centred radicals is accompanied by the modification of the metal-QsMT complexes, which were monitored by various spectroscopic and spectrometric techniques (Raman, CD, and ESI-MS). Attack of the H(*) atom and e(aq)(-) on the metal-QsMT aggregates can induce significant structural changes such as partial deconstruction and/or rearrangement of the metal clusters and breaking of the protein backbone. Substantial differences were observed in the behaviour of the Zn- and Cd-QsMT aggregates towards the reactive species, depending on the different folding of the polypeptide in these two cases.

  11. Heterobimetallic transition metal/rare earth metal bifunctional catalysis: a Cu/Sm/Schiff base complex for syn-selective catalytic asymmetric nitro-Mannich reaction.

    Science.gov (United States)

    Handa, Shinya; Gnanadesikan, Vijay; Matsunaga, Shigeki; Shibasaki, Masakatsu

    2010-04-07

    The full details of a catalytic asymmetric syn-selective nitro-Mannich reaction promoted by heterobimetallic Cu/Sm/dinucleating Schiff base complexes are described, demonstrating the effectiveness of the heterobimetallic transition metal/rare earth metal bifunctional catalysis. The first-generation system prepared from Cu(OAc)(2)/Sm(O-iPr)(3)/Schiff base 1a = 1:1:1 with an achiral phenol additive was partially successful for achieving the syn-selective catalytic asymmetric nitro-Mannich reaction. The substrate scope and limitations of the first-generation system remained problematic. After mechanistic studies on the catalyst prepared from Sm(O-iPr)(3), we reoptimized the catalyst preparation method, and a catalyst derived from Sm(5)O(O-iPr)(13) showed broader substrate generality as well as higher reactivity and stereoselectivity compared to Sm(O-iPr)(3). The optimal system with Sm(5)O(O-iPr)(13) was applicable to various aromatic, heteroaromatic, and isomerizable aliphatic N-Boc imines, giving products in 66-99% ee and syn/anti = >20:1-13:1. Catalytic asymmetric synthesis of nemonapride is also demonstrated using the catalyst derived from Sm(5)O(O-iPr)(13).

  12. Co-formation of hydroperoxides and ultra-fine particles during the reactions of ozone with a complex VOC mixture under simulated indoor conditions

    DEFF Research Database (Denmark)

    Fan, Z.H.; Weschler, Charles J.; Han, IK

    2005-01-01

    In this study we examined the co-formation of hydrogen peroxide and other hydroperoxides (collectively presented as H2O2*) as well as submicron particles, including ultra-fine particles (UFP), resulting from the reactions of ozone (O-3) with a complex mixture of volatile organic compounds (VOCs...... higher than typical indoor levels. When O-3 was added to a 25-m(3) controlled environmental facility (CEF) containing the 23 VOC mixture, both H2O2* and submicron particles were formed. The 2-h average concentration of H2O2* was 1.89 +/- 0.30ppb, and the average total particle number concentration was 46...... to achieve saturated concentrations of the condensable organics. When the 2 terpenes were removed from the O-3/23 VOCs mixture, no H2O2* or particles were formed, indicating that the reactions of O-3 With the two terpenes were the key processes contributing to the formation of H2O2* and submicron particles...

  13. Modeling complex metabolic reactions, ecological systems, and financial and legal networks with MIANN models based on Markov-Wiener node descriptors.

    Science.gov (United States)

    Duardo-Sánchez, Aliuska; Munteanu, Cristian R; Riera-Fernández, Pablo; López-Díaz, Antonio; Pazos, Alejandro; González-Díaz, Humberto

    2014-01-27

    The use of numerical parameters in Complex Network analysis is expanding to new fields of application. At a molecular level, we can use them to describe the molecular structure of chemical entities, protein interactions, or metabolic networks. However, the applications are not restricted to the world of molecules and can be extended to the study of macroscopic nonliving systems, organisms, or even legal or social networks. On the other hand, the development of the field of Artificial Intelligence has led to the formulation of computational algorithms whose design is based on the structure and functioning of networks of biological neurons. These algorithms, called Artificial Neural Networks (ANNs), can be useful for the study of complex networks, since the numerical parameters that encode information of the network (for example centralities/node descriptors) can be used as inputs for the ANNs. The Wiener index (W) is a graph invariant widely used in chemoinformatics to quantify the molecular structure of drugs and to study complex networks. In this work, we explore for the first time the possibility of using Markov chains to calculate analogues of node distance numbers/W to describe complex networks from the point of view of their nodes. These parameters are called Markov-Wiener node descriptors of order k(th) (W(k)). Please, note that these descriptors are not related to Markov-Wiener stochastic processes. Here, we calculated the W(k)(i) values for a very high number of nodes (>100,000) in more than 100 different complex networks using the software MI-NODES. These networks were grouped according to the field of application. Molecular networks include the Metabolic Reaction Networks (MRNs) of 40 different organisms. In addition, we analyzed other biological and legal and social networks. These include the Interaction Web Database Biological Networks (IWDBNs), with 75 food webs or ecological systems and the Spanish Financial Law Network (SFLN). The calculated W

  14. Model based design of biochemical micro-reactors

    Directory of Open Access Journals (Sweden)

    Tobias eElbinger

    2016-02-01

    Full Text Available Mathematical modelling of biochemical pathways is an important resource in Synthetic Biology, as the predictive power of simulating synthetic pathways represents an important step in the design of synthetic metabolons. In this paper, we are concerned with the mathematical modeling, simulation and optimization of metabolic processes in biochemical micro-reactors able to carry out enzymatic reactions and to exchange metabolites with their surrounding medium. The results of the reported modeling approach are incorporated in the design of the first micro-reactor prototypes that are under construction. These microreactors consist of compartments separated by membranes carrying specific transporters for the input of substrates and export of products. Inside the compartments multi-enzyme complexes assembled on nano-beads by peptide adapters are used to carry out metabolic reactions.The spatially resolved mathematical model describing the ongoing processes consists of a system of diffusion equations together with boundary and initial conditions. The boundary conditions model the exchange of metabolites with the neighboring compartments and the reactions at the surface of the nano-beads carrying the multi-enzyme complexes. Efficient and accurate approaches for numerical simulation of the mathematical model and for optimal design of the micro-reactor are developed. As a proof-of-concept scenario, a synthetic pathway for the conversion of sucrose to glucose-6-phosphate (G6P was chosen. In this context, the mathematical model is employed to compute the spatio-temporal distributions of the metabolite concentrations, as well as application relevant quantities like the outflow rate of G6P. These computations are performed for different scenarios, where the number of beads as well as their loading capacity are varied. The computed metabolite distributions show spatial patterns which differ for different experimental arrangements. Furthermore, the total output

  15. Biochemical composition and methane production correlations

    OpenAIRE

    Charnier, Cyrille; Latrille, Eric; Moscoviz, Roman; Miroux, Jérémie; Steyer, Jean-Philippe

    2016-01-01

    Substrates for anaerobic digestion are composed of heterogeneous and complex organic matter. General parameters of the organic matter can be used to describe its composition such as sugar, protein and lipid contents, Chemical Oxygen Demand (COD), Biochemical Methane Potential (BMP) and kinetic of methane production. These parameters are required for the monitoring of digesters but their characterization are time consuming and expensive; thus, these parameters are rarely assessed all together....

  16. Specification, construction, and exact reduction of state transition system models of biochemical processes.

    Science.gov (United States)

    Bugenhagen, Scott M; Beard, Daniel A

    2012-10-21

    Biochemical reaction systems may be viewed as discrete event processes characterized by a number of states and state transitions. These systems may be modeled as state transition systems with transitions representing individual reaction events. Since they often involve a large number of interactions, it can be difficult to construct such a model for a system, and since the resulting state-level model can involve a huge number of states, model analysis can be difficult or impossible. Here, we describe methods for the high-level specification of a system using hypergraphs, for the automated generation of a state-level model from a high-level model, and for the exact reduction of a state-level model using information from the high-level model. Exact reduction is achieved through the automated application to the high-level model of the symmetry reduction technique and reduction by decomposition by independent subsystems, allowing potentially significant reductions without the need to generate a full model. The application of the method to biochemical reaction systems is illustrated by models describing a hypothetical ion-channel at several levels of complexity. The method allows for the reduction of the otherwise intractable example models to a manageable size.

  17. ESI-MS studies of the reactions of novel platinum(II) complexes containing O,O'-chelated acetylacetonate and sulfur ligands with selected model proteins.

    Science.gov (United States)

    Marzo, Tiziano; De Pascali, Sandra A; Gabbiani, Chiara; Fanizzi, Francesco P; Messori, Luigi; Pratesi, Alessandro

    2017-08-01

    A group of mixed-ligand Pt(II) complexes bearing acetylacetonate and sulphur ligands were recently developed in the University of Lecce as a new class of prospective anticancer agents that manifested promising pharma-cological properties in preliminary in vitro and in vivo tests. Though modelled on the basis of cisplatin, these Pt(II) complexes turned out to exhibit a profoundly distinct mode of action as they were found to act mainly on non-genomic targets rather than on DNA. Accordingly, we have explored here their reactions with two representative model proteins through an established ESI-MS procedure with the aim to describe their general interaction mechanism with protein targets. A pronounced reactivity with the tested proteins was indeed documented; the nature of the resulting metallodrug-protein interactions could be characterised in depth in the various cases. Preferential binding to protein targets compared to DNA is supported by independent ICP-OES measurements. The implications of these findings are discussed.

  18. Dembo polymerase chain reaction technique for detection of bovine abortion, diarrhea, and respiratory disease complex infectious agents in potential vectors and reservoirs.

    Science.gov (United States)

    Rahpaya, Sayed Samim; Tsuchiaka, Shinobu; Kishimoto, Mai; Oba, Mami; Katayama, Yukie; Nunomura, Yuka; Kokawa, Saki; Kimura, Takashi; Kobayashi, Atsushi; Kirino, Yumi; Okabayashi, Tamaki; Nonaka, Nariaki; Mekata, Hirohisa; Aoki, Hiroshi; Shiokawa, Mai; Umetsu, Moeko; Morita, Tatsushi; Hasebe, Ayako; Otsu, Keiko; Asai, Tetsuo; Yamaguchi, Tomohiro; Makino, Shinji; Murata, Yoshiteru; Abi, Ahmad Jan; Omatsu, Tsutomu; Mizutani, Tetsuya

    2018-05-31

    Bovine abortion, diarrhea, and respiratory disease complexes, caused by infectious agents, result in high and significant economic losses for the cattle industry. These pathogens are likely transmitted by various vectors and reservoirs including insects, birds, and rodents. However, experimental data supporting this possibility are scarce. We collected 117 samples and screened them for 44 bovine abortive, diarrheal, and respiratory disease complex pathogens by using Dembo polymerase chain reaction (PCR), which is based on TaqMan real-time PCR. Fifty-seven samples were positive for at least one pathogen, including bovine viral diarrhea virus, bovine enterovirus, Salmonella enterica ser. Dublin, Salmonella enterica ser. Typhimurium, and Neospora caninum ; some samples were positive for multiple pathogens. Bovine viral diarrhea virus and bovine enterovirus were the most frequently detected pathogens, especially in flies, suggesting an important role of flies in the transmission of these viruses. Additionally, we detected the N. caninum genome from a cockroach sample for the first time. Our data suggest that insects (particularly flies), birds, and rodents are potential vectors and reservoirs of abortion, diarrhea, and respiratory infectious agents, and that they may transmit more than one pathogen at the same time.

  19. Bayesian experts in exploring reaction kinetics of transcription circuits.

    Science.gov (United States)

    Yoshida, Ryo; Saito, Masaya M; Nagao, Hiromichi; Higuchi, Tomoyuki

    2010-09-15

    Biochemical reactions in cells are made of several types of biological circuits. In current systems biology, making differential equation (DE) models simulatable in silico has been an appealing, general approach to uncover a complex world of biochemical reaction dynamics. Despite of a need for simulation-aided studies, our research field has yet provided no clear answers: how to specify kinetic values in models that are difficult to measure from experimental/theoretical analyses on biochemical kinetics. We present a novel non-parametric Bayesian approach to this problem. The key idea lies in the development of a Dirichlet process (DP) prior distribution, called Bayesian experts, which reflects substantive knowledge on reaction mechanisms inherent in given models and experimentally observable kinetic evidences to the subsequent parameter search. The DP prior identifies significant local regions of unknown parameter space before proceeding to the posterior analyses. This article reports that a Bayesian expert-inducing stochastic search can effectively explore unknown parameters of in silico transcription circuits such that solutions of DEs reproduce transcriptomic time course profiles. A sample source code is available at the URL http://daweb.ism.ac.jp/~yoshidar/lisdas/.

  20. Regioselective aromatic substitution reactions of cyclometalated Ir(III) complexes: synthesis and photochemical properties of substituted Ir(III) complexes that exhibit blue, green, and red color luminescence emission.

    Science.gov (United States)

    Aoki, Shin; Matsuo, Yasuki; Ogura, Shiori; Ohwada, Hiroki; Hisamatsu, Yosuke; Moromizato, Shinsuke; Shiro, Motoo; Kitamura, Masanori

    2011-02-07

    In this manuscript, the regioselective halogenation, nitration, formylation, and acylation of Ir(tpy)(3) and Ir(ppy)(3) (tpy = 2-(4'-tolyl)pyridine and ppy = 2-phenylpyridine) and the subsequent conversions are described. During attempted bromination of the three methyl groups in fac-Ir(tpy)(3) using N-bromosuccinimide (NBS) and benzoyl peroxide (BPO), three protons at the 5'-position (p-position with respect to the C-Ir bond) of phenyl rings in tpy units were substituted by Br, as confirmed by (1)H NMR spectra, mass spectra, and X-ray crystal structure analysis. It is suggested that such substitution reactions of Ir complexes proceed via an ionic mechanism rather than a radical mechanism. UV-vis and luminescence spectra of the substituted Ir(III) complexes are reported. The introduction of electron-withdrawing groups such as CN and CHO groups at the 5'-position of tpy induces a blue shift of luminescence emission to about 480 nm, and the introduction of electron-donating groups such as an amino group results in a red shift to about 600 nm. A reversible change of emission for the 5'-amino derivative of Ir(tpy)(3), Ir(atpy)(3), between red and green occurs upon protonation and deprotonation.