Synthesis, characterization and properties of copper(I) complexes with bis(diphenylphosphino)-ferrocene ancillary ligand

NASA Astrophysics Data System (ADS)

Liu, Xinfang; Zhang, Songlin; Ding, Yuqiang

2012-06-01

Three copper(I) complexes (2-4) containing dppf ancillary ligand (dppf = bis(diphenylphosphino)-ferrocene) were synthesized when chloride-bridged copper(I) complex 1 reacted with acetanilide and characterized by IR, element analysis and NMR spectrum. And the crystal structures of complexes 2 and 4 have been determined by X-ray diffraction method. Complex 2, an acetate-bridged copper(I) complex, was obtained under N2 atmosphere in un-dried solvent; the acetate ion came from the hydrolysis reaction of acetanilide due to residual water in solvent. Acetanilide was deprotonated and coordinated with the copper(I) centre to form a copper(I) amidate complex 3 when reacted in pre-dried solvent. In addition, a known complex 4, the oxidation product of dppf, was isolated from the same reaction system when reacted in air atmosphere. CV and TG experiments were carried out to check the electron transfer properties and thermal stabilities of complexes 2-3. Finally, the arylation reaction of complex 3 with iodobenzene was performed to study the reaction mechanism of copper(I) catalyzed Goldberg reaction.

Rule-based spatial modeling with diffusing, geometrically constrained molecules.

PubMed

Gruenert, Gerd; Ibrahim, Bashar; Lenser, Thorsten; Lohel, Maiko; Hinze, Thomas; Dittrich, Peter

2010-06-07

We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly.

Rule-based spatial modeling with diffusing, geometrically constrained molecules

PubMed Central

2010-01-01

Background We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Results Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. Conclusions We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly. PMID:20529264

Signal transduction in a covalent post-assembly modification cascade

NASA Astrophysics Data System (ADS)

Pilgrim, Ben S.; Roberts, Derrick A.; Lohr, Thorsten G.; Ronson, Tanya K.; Nitschke, Jonathan R.

2017-12-01

Natural reaction cascades control the movement of biomolecules between cellular compartments. Inspired by these systems, we report a synthetic reaction cascade employing post-assembly modification reactions to direct the partitioning of supramolecular complexes between phases. The system is composed of a self-assembled tetrazine-edged FeII8L12 cube and a maleimide-functionalized FeII4L6 tetrahedron. Norbornadiene (NBD) functions as the stimulus that triggers the cascade, beginning with the inverse-electron-demand Diels-Alder reaction of NBD with the tetrazine moieties of the cube. This reaction generates cyclopentadiene as a transient by-product, acting as a relay signal that subsequently undergoes a Diels-Alder reaction with the maleimide-functionalized tetrahedron. Cyclooctyne can selectively inhibit the cascade by outcompeting NBD as the initial trigger. Initiating the cascade with 2-octadecyl NBD leads to selective alkylation of the tetrahedron upon cascade completion. The increased lipophilicity of the C18-tagged tetrahedron drives this complex into a non-polar phase, allowing its isolation from the initially inseparable mixture of complexes.

Catalysis of Photochemical Reactions.

ERIC Educational Resources Information Center

Albini, A.

1986-01-01

Offers a classification system of catalytic effects in photochemical reactions, contrasting characteristic properties of photochemical and thermal reactions. Discusses catalysis and sensitization, examples of catalyzed reactions of excepted states, complexing ground state substrates, and catalysis of primary photoproducts. (JM)

Reaction-diffusion controlled growth of complex structures

NASA Astrophysics Data System (ADS)

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

Modification of heterogeneous chemistry by complex substrate morphology

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

Henson, B.F.; Buelow, S.J.; Robinson, J.M.

1998-12-31

This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). Chemistry in many environmental systems is determined at some stage by heterogeneous reaction with a surface. Typically the surface exists as a dispersion or matrix of particulate matter or pores, and a determination of the heterogeneous chemistry of the system must address the extent to which the complexity of the environmental surface affects the reaction rates. Reactions that are of current interest are the series of chlorine nitrate reactions important in polar ozone depletion. The authors have applied surfacemore » spectroscopic techniques developed at LANL to address the chemistry of chlorine nitrate reactions on porous nitric and sulfuric acid ice surfaces as a model study of the measurement of complex, heterogeneous reaction rates. The result of the study is an experimental determination of the surface coverage of one adsorbed reagent and a mechanism of reactivity based on the dependence of this coverage on temperature and vapor pressure. The resulting mechanism allows the first comprehensive modeling of chlorine nitrate reaction probability data from several laboratories.« less

Reactivity of [K₃(phen)₈][Cu(NPh₂)₂]₃--a possible intermediate in the copper(I)-catalyzed N-arylation of N-phenylaniline.

PubMed

Tseng, Chia-Kai; Lee, Chi-Rung; Tseng, Mei-Chun; Han, Chien-Chung; Shyu, Shin-Guang

2014-05-21

Complex [K3(phen)8][Cu(NPh2)2]3 (1, phen = phenanthroline) was isolated from the catalytic C-N cross coupling reaction based on the CuI-phen-tBuOK catalytic system. Complex 1 can react with 4-iodotoluene to give 4-methyl-N,N-diphenylaniline (3a) in 50% yield (based on all available NPh2(-) ligands of complex 1). In addition, 1 can also work as an effective catalyst for the C-N coupling reactions under the same reaction conditions, indicating that 1 may be an effective intermediate of the catalytic system. In the presence of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO), a radical scavenger, the stoichiometric reaction between complex 1 and 4-iodotoluene was significantly quenched to give a low yield of 12%. The results suggest that the radical path dominates in the reaction, with (phen)KNPh2 as the possible radical source. The structures of 1 and (phen)KNPh2 were both determined by single crystal X-ray diffraction studies.

The kinetics of lanthanide complexation by EDTA and DTPA in lactate media.

PubMed

Nash, K L; Brigham, D; Shehee, T C; Martin, A

2012-12-28

The interaction of trivalent lanthanide and actinide cations with polyaminopolycarboxylic acid complexing agents in lactic acid buffer systems is an important feature of the chemistry of the TALSPEAK process for the separation of trivalent actinides from lanthanides. To improve understanding of metal ion coordination chemistry in this process, the results of an investigation of the kinetics of lanthanide complexation by ethylenediamine-N,N,N',N'-tetraacetic acid (EDTA) and diethylenetriamine-N,N,N',N'',N''-pentaacetic acid (DTPA) in 0.3 M lactic acid/0.3 M ionic strength solution are reported. Progress of the reaction was monitored using the distinctive visible spectral changes attendant to lanthanide complexation by the colorimetric indicator ligand Arsenazo III, which enables the experiment but plays no mechanistic role. Under the conditions of these experiments, the reactions occur in a time regime suitable for study by stopped-flow spectrophotometric techniques. Experiments have been conducted as a function of EDTA/DTPA ligand concentration, total lactic acid concentration, and pH. The equilibrium perturbation reaction proceeds as a first order approach to equilibrium over a wide range of conditions, allowing the simultaneous determination of complex formation and dissociation rate constants. The rate of the complexation reaction has been determined for the entire lanthanide series (except Pm(3+)). The predominant pathway for lanthanide-EDTA and lanthanide-DTPA dissociation is inversely dependent on the total lactate concentration; the complex formation reaction demonstrates a direct dependence on [H(+)]. Unexpectedly, the rate of the complex formation reaction is seen in both ligand systems to be fastest for Gd(3+). Correlation of these results indicates that in 0.3 M lactate solutions the exchange of lanthanide ions between lactate complexes and the polyaminopolycarboxylate govern the process.

Transition Manifolds of Complex Metastable Systems: Theory and Data-Driven Computation of Effective Dynamics.

PubMed

Bittracher, Andreas; Koltai, Péter; Klus, Stefan; Banisch, Ralf; Dellnitz, Michael; Schütte, Christof

2018-01-01

We consider complex dynamical systems showing metastable behavior, but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics.

Transition Manifolds of Complex Metastable Systems

NASA Astrophysics Data System (ADS)

Bittracher, Andreas; Koltai, Péter; Klus, Stefan; Banisch, Ralf; Dellnitz, Michael; Schütte, Christof

2018-04-01

We consider complex dynamical systems showing metastable behavior, but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics.

Convergence to equilibrium of renormalised solutions to nonlinear chemical reaction–diffusion systems

NASA Astrophysics Data System (ADS)

Fellner, Klemens; Tang, Bao Quoc

2018-06-01

The convergence to equilibrium for renormalised solutions to nonlinear reaction-diffusion systems is studied. The considered reaction-diffusion systems arise from chemical reaction networks with mass action kinetics and satisfy the complex balanced condition. By applying the so-called entropy method, we show that if the system does not have boundary equilibria, i.e. equilibrium states lying on the boundary of R_+^N, then any renormalised solution converges exponentially to the complex balanced equilibrium with a rate, which can be computed explicitly up to a finite-dimensional inequality. This inequality is proven via a contradiction argument and thus not explicitly. An explicit method of proof, however, is provided for a specific application modelling a reversible enzyme reaction by exploiting the specific structure of the conservation laws. Our approach is also useful to study the trend to equilibrium for systems possessing boundary equilibria. More precisely, to show the convergence to equilibrium for systems with boundary equilibria, we establish a sufficient condition in terms of a modified finite-dimensional inequality along trajectories of the system. By assuming this condition, which roughly means that the system produces too much entropy to stay close to a boundary equilibrium for infinite time, the entropy method shows exponential convergence to equilibrium for renormalised solutions to complex balanced systems with boundary equilibria.

Hybrid deterministic/stochastic simulation of complex biochemical systems.

PubMed

Lecca, Paola; Bagagiolo, Fabio; Scarpa, Marina

2017-11-21

In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects. Moreover, it should be implemented by efficient algorithms requiring the shortest possible execution time, to avoid enlarging excessively the time elapsing between data analysis and any subsequent experiment. Besides the features of their topological structure, the complexity of biological networks also refers to their dynamics, that is often non-linear and stiff. The stiffness is due to the presence of molecular species whose abundance fluctuates by many orders of magnitude. A fully stochastic simulation of a stiff system is computationally time-expensive. On the other hand, continuous models are less costly, but they fail to capture the stochastic behaviour of small populations of molecular species. We introduce a new efficient hybrid stochastic-deterministic computational model and the software tool MoBioS (MOlecular Biology Simulator) implementing it. The mathematical model of MoBioS uses continuous differential equations to describe the deterministic reactions and a Gillespie-like algorithm to describe the stochastic ones. Unlike the majority of current hybrid methods, the MoBioS algorithm divides the reactions' set into fast reactions, moderate reactions, and slow reactions and implements a hysteresis switching between the stochastic model and the deterministic model. Fast reactions are approximated as continuous-deterministic processes and modelled by deterministic rate equations. Moderate reactions are those whose reaction waiting time is greater than the fast reaction waiting time but smaller than the slow reaction waiting time. A moderate reaction is approximated as a stochastic (deterministic) process if it was classified as a stochastic (deterministic) process at the time at which it crosses the threshold of low (high) waiting time. A Gillespie First Reaction Method is implemented to select and execute the slow reactions. The performances of MoBios were tested on a typical example of hybrid dynamics: that is the DNA transcription regulation. The simulated dynamic profile of the reagents' abundance and the estimate of the error introduced by the fully deterministic approach were used to evaluate the consistency of the computational model and that of the software tool.

A benchmark for reaction coordinates in the transition path ensemble

PubMed Central

2016-01-01

The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems. PMID:27059559

Photochemistry and reactivity of the phenyl radical-water system: a matrix isolation and computational study.

PubMed

Mardyukov, Artur; Crespo-Otero, Rachel; Sanchez-Garcia, Elsa; Sander, Wolfram

2010-08-02

The reaction of the phenyl radical 1 with water has been investigated by using matrix isolation spectroscopy and quantum chemical calculations. The primary thermal product of the reaction between 1 and water is a weakly bound complex stabilized by an OH...pi interaction. This complex is photolabile, and visible-light irradiation (lambda>420 nm) results in hydrogen atom transfer from water to radical 1 and the formation of a highly labile complex between benzene and the OH radical. This complex is stable under the conditions of matrix isolation, however, continuous irradiation with lambda>420 nm light results in the complete destruction of the aromatic system and formation of an acylic unsaturated ketene. The mechanisms of all reaction steps are discussed in the light of ab initio and DFT calculations.

Dynamic control and information processing in chemical reaction systems by tuning self-organization behavior

NASA Astrophysics Data System (ADS)

Lebiedz, Dirk; Brandt-Pollmann, Ulrich

2004-09-01

Specific external control of chemical reaction systems and both dynamic control and signal processing as central functions in biochemical reaction systems are important issues of modern nonlinear science. For example nonlinear input-output behavior and its regulation are crucial for the maintainance of the life process that requires extensive communication between cells and their environment. An important question is how the dynamical behavior of biochemical systems is controlled and how they process information transmitted by incoming signals. But also from a general point of view external forcing of complex chemical reaction processes is important in many application areas ranging from chemical engineering to biomedicine. In order to study such control issues numerically, here, we choose a well characterized chemical system, the CO oxidation on Pt(110), which is interesting per se as an externally forced chemical oscillator model. We show numerically that tuning of temporal self-organization by input signals in this simple nonlinear chemical reaction exhibiting oscillatory behavior can in principle be exploited for both specific external control of dynamical system behavior and processing of complex information.

Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends.

PubMed

Snowden, Thomas J; van der Graaf, Piet H; Tindall, Marcus J

2017-07-01

Complex models of biochemical reaction systems have become increasingly common in the systems biology literature. The complexity of such models can present a number of obstacles for their practical use, often making problems difficult to intuit or computationally intractable. Methods of model reduction can be employed to alleviate the issue of complexity by seeking to eliminate those portions of a reaction network that have little or no effect upon the outcomes of interest, hence yielding simplified systems that retain an accurate predictive capacity. This review paper seeks to provide a brief overview of a range of such methods and their application in the context of biochemical reaction network models. To achieve this, we provide a brief mathematical account of the main methods including timescale exploitation approaches, reduction via sensitivity analysis, optimisation methods, lumping, and singular value decomposition-based approaches. Methods are reviewed in the context of large-scale systems biology type models, and future areas of research are briefly discussed.

New Developments in the Field of Reaction Technology: The Multiparallel Reactor HPMR 50-96

PubMed Central

Allwardt, Arne; Wendler, Christian; Thurow, Kerstin

2005-01-01

Catalytic high-pressure reactions play an important role in classic bulk chemistry. The optimization of common reactions, the search for new and more effective catalysts, and the increasing use of catalytic pressure reactions in the field of drug development call for high-parallel reaction systems. A crucial task of current developments, apart from the parameters of pressure, temperature, and number of reaction chambers, is, in this respect, the systems' integration into complex laboratory automation environments. PMID:18924722

Oxidation of benzoin catalyzed by oxovanadium(IV) schiff base complexes

PubMed Central

2013-01-01

Background The oxidative transformation of benzoin to benzil has been accomplished by the use of a wide variety of reagents or catalysts and different reaction procedures. The conventional oxidizing agents yielded mainly benzaldehyde or/and benzoic acid and only a trace amount of benzil. The limits of practical utilization of these reagents involves the use of stoichiometric amounts of corrosive acids or toxic metallic reagents, which in turn produce undesirable waste materials and required high reaction temperatures. In recent years, vanadium complexes have attracted much attention for their potential utility as catalysts for various types of reactions. Results Active and selective catalytic systems of new unsymmetrical oxovanadium(IV) Schiff base complexes for the oxidation of benzoin is reported. The Schiff base ligands are derived between 2-aminoethanol and 2-hydroxy-1-naphthaldehyde (H2L1) or 3-ethoxy salicylaldehyde (H2L3); and 2-aminophenol and 3-ethoxysalicylaldehyde (H2L2) or 2-hydroxy-1-naphthaldehyde (H2L4). The unsymmetrical Schiff bases behave as tridentate dibasic ONO donor ligands. Reaction of these Schiff base ligands with oxovanadyl sulphate afforded the mononuclear oxovanadium(IV) complexes (VIVOLx.H2O), which are characterized by various physico-chemical techniques. The catalytic oxidation activities of these complexes for benzoin were evaluated using H2O2 as an oxidant. The best reaction conditions are obtained by considering the effect of solvent, reaction time and temperature. Under the optimized reaction conditions, VOL4 catalyst showed high conversion (>99%) with excellent selectivity to benzil (~100%) in a shorter reaction time compared to the other catalysts considered. Conclusion Four tridentate ONO type Schiff base ligands were synthesized. Complexation of these ligands with vanadyl(IV) sulphate leads to the formation of new oxovanadium(IV) complexes of type VIVOL.H2O. Elemental analyses and spectral data of the free ligands and their oxovanadium(IV) complexes were found to be in good agreement with their structures, indicating high purity of all the compounds. Oxovanadium complexes were screened for the oxidation of benzoin to benzil using H2O2 as oxidant. The effect of time, solvent and temperature were optimized to obtain maximum yield. The catalytic activity results demonstrate that these catalytic systems are both highly active and selective for the oxidation of benzoin under mild reaction conditions. PMID:23294561

Oxidation of benzoin catalyzed by oxovanadium(IV) schiff base complexes.

PubMed

Alsalim, Tahseen A; Hadi, Jabbar S; Ali, Omar N; Abbo, Hanna S; Titinchi, Salam Jj

2013-01-07

The oxidative transformation of benzoin to benzil has been accomplished by the use of a wide variety of reagents or catalysts and different reaction procedures. The conventional oxidizing agents yielded mainly benzaldehyde or/and benzoic acid and only a trace amount of benzil. The limits of practical utilization of these reagents involves the use of stoichiometric amounts of corrosive acids or toxic metallic reagents, which in turn produce undesirable waste materials and required high reaction temperatures.In recent years, vanadium complexes have attracted much attention for their potential utility as catalysts for various types of reactions. Active and selective catalytic systems of new unsymmetrical oxovanadium(IV) Schiff base complexes for the oxidation of benzoin is reported. The Schiff base ligands are derived between 2-aminoethanol and 2-hydroxy-1-naphthaldehyde (H2L1) or 3-ethoxy salicylaldehyde (H2L3); and 2-aminophenol and 3-ethoxysalicylaldehyde (H2L2) or 2-hydroxy-1-naphthaldehyde (H2L4). The unsymmetrical Schiff bases behave as tridentate dibasic ONO donor ligands. Reaction of these Schiff base ligands with oxovanadyl sulphate afforded the mononuclear oxovanadium(IV) complexes (VIVOLx.H2O), which are characterized by various physico-chemical techniques.The catalytic oxidation activities of these complexes for benzoin were evaluated using H2O2 as an oxidant. The best reaction conditions are obtained by considering the effect of solvent, reaction time and temperature. Under the optimized reaction conditions, VOL4 catalyst showed high conversion (>99%) with excellent selectivity to benzil (~100%) in a shorter reaction time compared to the other catalysts considered. Four tridentate ONO type Schiff base ligands were synthesized. Complexation of these ligands with vanadyl(IV) sulphate leads to the formation of new oxovanadium(IV) complexes of type VIVOL.H2O.Elemental analyses and spectral data of the free ligands and their oxovanadium(IV) complexes were found to be in good agreement with their structures, indicating high purity of all the compounds.Oxovanadium complexes were screened for the oxidation of benzoin to benzil using H2O2 as oxidant. The effect of time, solvent and temperature were optimized to obtain maximum yield. The catalytic activity results demonstrate that these catalytic systems are both highly active and selective for the oxidation of benzoin under mild reaction conditions.

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

DOE R&D Accomplishments Database

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.

Associative charge transfer reactions. Temperature effects and mechanism of the gas-phase polymerization of propene initiated by a benzene radical cation.

PubMed

Ibrahim, Yehia; Meot-Ner Mautner, Michael; El-Shall, M Samy

2006-07-13

In associative charge transfer (ACT) reactions, a core ion activates ligand molecules by partial charge transfer. The activated ligand polymerizes, and the product oligomer takes up the full charge from the core ion. In the present system, benzene(+*) (Bz(+*)) reacts with two propene (Pr) molecules to form a covalently bonded ion, C(6)H(6)(+*) + 2 C(3)H(6) --> C(6)H(12)(+*) + C(6)H(6). The ACT reaction is activated by a partial charge transfer from Bz(+*) to Pr in the complex, and driven to completion by the formation of a covalent bond in the polymerized product. An alternative channel forms a stable association product (Bz.Pr)(+*), with an ACT/association product ratio of 60:40% that is independent of pressure and temperature. In contrast to the Bz(+*)/propene system, ACT polymerization is not observed in the Bz(+*)/ethylene (Et) system since charge transfer in the Bz(+*)(Et) complex is inefficient to activate the reaction. The roles of charge transfer in these complexes are verified by ab initio calculations. The overall reaction of Bz(+*) with Pr follows second-order kinetics with a rate constant of k (304 K) = 2.1 x 10(-12) cm(3) s(-1) and a negative temperature coefficient of k = aT(-5.9) (or an activation energy of -3 kcal/mol). The kinetic behavior is similar to sterically hindered reactions and suggests a [Bz(+*) (Pr)]* activated complex that proceeds to products through a low-entropy transition state. The temperature dependence shows that ACT reactions can reach a unit collision efficiency below 100 K, suggesting that ACT can initiate polymerization in cold astrochemical environments.

Signals of monocyte activation in patients with SLE.

PubMed Central

Kávai, M; Zsindely, A; Sonkoly, I; Major, M; Demján, I; Szegedi, G

1983-01-01

The Fc receptor mediated reaction, the beta-glucuronidase and the lactic dehydrogenase activities of monocytes and the serum lysozyme level were tested together with the circulating immune complex content of patients with systemic lupus erythematosus. Simultaneously with the increasing FC receptor-mediated reaction and the elevated enzyme activities of patient monocytes, the secretion of lysozyme and the immune complex content of the sera were higher than those of the controls. A positive correlation was demonstrated between the Fc receptor-mediated reaction, the beta-glucuronidase activity, the lysozyme secretion and the immune complex content of the sera. Thus, the monocytes of patients appeared to be activated by the circulating immune complexes. PMID:6839541

GCKP84-general chemical kinetics code for gas-phase flow and batch processes including heat transfer effects

NASA Technical Reports Server (NTRS)

Bittker, D. A.; Scullin, V. J.

1984-01-01

A general chemical kinetics code is described for complex, homogeneous ideal gas reactions in any chemical system. The main features of the GCKP84 code are flexibility, convenience, and speed of computation for many different reaction conditions. The code, which replaces the GCKP code published previously, solves numerically the differential equations for complex reaction in a batch system or one dimensional inviscid flow. It also solves numerically the nonlinear algebraic equations describing the well stirred reactor. A new state of the art numerical integration method is used for greatly increased speed in handling systems of stiff differential equations. The theory and the computer program, including details of input preparation and a guide to using the code are given.

Structural modulation of silver complexes and their distinctive catalytic properties.

PubMed

Zhao, Yue; Chen, Kai; Fan, Jian; Okamura, Taka-aki; Lu, Yi; Luo, Li; Sun, Wei-Yin

2014-02-07

A family of silver(I) complexes, [Ag2(L)2(OOCCF3)2] (1), [Ag(L)0.5(OOCCF3)] (2), [Ag(L)2](OOCCF3)(H2O)2 (3), was obtained by reactions of 4,4'-di(2-oxazolinyl)biphenyl (L) and AgOOCCF3 in different reaction media. Compound 1 has a 1D chain structure with alternative connections between the Ag(I) and L ligand. When the crystal nucleation inductor, pyrazine, was added into the reaction system, complex 2 was isolated with no pyrazine observed in its structure. In 2, the 1D inorganic chains formed by Ag(I) cations and OOCCF3(-) anions were connected by the L ligand to produce a 2D network. When a different inductor, imidazole, was added into the reaction system, 3 with (4,4) topology was synthesized, and again no imidazole was found in 3. When 1-3 were used as catalysts for cycloaddition reactions between imino esters and methyl acrylate, 3 affords the highest yield, in which the particular size of the channels in 3 led to its selective catalytic performance.

Lagrangian simulation of mixing and reactions in complex geochemical systems

NASA Astrophysics Data System (ADS)

Engdahl, Nicholas B.; Benson, David A.; Bolster, Diogo

2017-04-01

Simulations of detailed geochemical systems have traditionally been restricted to Eulerian reactive transport algorithms. This note introduces a Lagrangian method for modeling multicomponent reaction systems. The approach uses standard random walk-based methods for the particle motion steps but allows the particles to interact with each other by exchanging mass of their various chemical species. The colocation density of each particle pair is used to calculate the mass transfer rate, which creates a local disequilibrium that is then relaxed back toward equilibrium using the reaction engine PhreeqcRM. The mass exchange is the only step where the particles interact and the remaining transport and reaction steps are entirely independent for each particle. Several validation examples are presented, which reproduce well-known analytical solutions. These are followed by two demonstration examples of a competitive decay chain and an acid-mine drainage system. The source code, entitled Complex Reaction on Particles (CRP), and files needed to run these examples are hosted openly on GitHub (https://github.com/nbengdahl/CRP), so as to enable interested readers to readily apply this approach with minimal modifications.

Hardware-Software Complex for Measurement of Energy and Angular Distributions of Charged Particles Formed in Nuclear Reactions

NASA Astrophysics Data System (ADS)

Vikhlyantsev, O. P.; Generalov, L. N.; Kuryakin, A. V.; Karpov, I. A.; Gurin, N. E.; Tumkin, A. D.; Fil'chagin, S. V.

2017-12-01

A hardware-software complex for measurement of energy and angular distributions of charged particles formed in nuclear reactions is presented. Hardware and software structures of the complex, the basic set of the modular nuclear-physical apparatus of a multichannel detecting system on the basis of Δ E- E telescopes of silicon detectors, and the hardware of experimental data collection, storage, and processing are presented and described.

Sealable femtoliter chamber arrays for cell-free biology

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

Retterer, Scott T.; Fowlkes, Jason Davidson; Collier, Charles Patrick

Cell-free systems provide a flexible platform for probing specific networks of biological reactions isolated from the complex resource sharing (e.g. global gene expression, cell division) encountered within living cells. However, such systems, used in conventional macro-scale bulk reactors, often fail to exhibit the dynamic behaviors and efficiencies characteristic of their living micro-scale counterparts. Understanding the impact of internal cell structure and scale on reaction dynamics is crucial to understanding complex gene networks. Here we report a microfabricated device that confines cell-free reactions in cellular scale volumes while allowing flexible characterization of the enclosed molecular system. This multilayered poly(dimethylsiloxane) (PDMS) devicemore » contains femtoliter-scale reaction chambers on an elastomeric membrane which can be actuated (open and closed). When actuated, the chambers confine Cell-Free Protein Synthesis (CFPS) reactions expressing a fluorescent protein, allowing for the visualization of the reaction kinetics over time using time-lapse fluorescent microscopy. Lastly, we demonstrate how this device may be used to measure the noise structure of CFPS reactions in a manner that is directly analogous to those used to characterize cellular systems, thereby enabling the use of noise biology techniques to characterize CFPS gene circuits and their interactions with the cell-free environment.« less

Sealable femtoliter chamber arrays for cell-free biology

DOE PAGES

Retterer, Scott T.; Fowlkes, Jason Davidson; Collier, Charles Patrick; ...

2015-03-11

Cell-free systems provide a flexible platform for probing specific networks of biological reactions isolated from the complex resource sharing (e.g. global gene expression, cell division) encountered within living cells. However, such systems, used in conventional macro-scale bulk reactors, often fail to exhibit the dynamic behaviors and efficiencies characteristic of their living micro-scale counterparts. Understanding the impact of internal cell structure and scale on reaction dynamics is crucial to understanding complex gene networks. Here we report a microfabricated device that confines cell-free reactions in cellular scale volumes while allowing flexible characterization of the enclosed molecular system. This multilayered poly(dimethylsiloxane) (PDMS) devicemore » contains femtoliter-scale reaction chambers on an elastomeric membrane which can be actuated (open and closed). When actuated, the chambers confine Cell-Free Protein Synthesis (CFPS) reactions expressing a fluorescent protein, allowing for the visualization of the reaction kinetics over time using time-lapse fluorescent microscopy. Lastly, we demonstrate how this device may be used to measure the noise structure of CFPS reactions in a manner that is directly analogous to those used to characterize cellular systems, thereby enabling the use of noise biology techniques to characterize CFPS gene circuits and their interactions with the cell-free environment.« less

Features of proteolytic properties of tetraphenylporphyrin complex with lanthanide group metals

NASA Astrophysics Data System (ADS)

Tobolkina, Elena A.; Skripnikova, Tatiana A.; Starikova, Anna A.; Shumilova, Galina I.; Pendin, Andrey A.

2018-01-01

Demetallation of metalloporphyrin molecules is one of the essential degradation reactions in photosynthesis. The effect of metalloporphyrin nature on removal of central metals from tetraphenylporphyrin complexes based on lanthanide group metals (Dy, Er, Lu, Ho) has been studied. pH values, at which the metal ions leave the metalloporphyrin complex were established using two-phase spectrophotometric titration with potentiometric pH-control. The pH values decrease with the increase of atomic numbers of lanthanide groups, as well as with increase of 4f-electrons. The reaction of an extra ligand exchange for the hydroxide ion was studied. For Dy-, Er- and Ho-tetraphenylporphyrin complexes one particle of extra ligand coordinates with one porphyrin complex. A complex with dimeric particles can be formed for the system of Lu-tetraphenylporphyrin. Constants of the ion exchange reactions were calculated.

A Networks Approach to Modeling Enzymatic Reactions.

PubMed

Imhof, P

2016-01-01

Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. © 2016 Elsevier Inc. All rights reserved.

Oxygen-Evolving Porous Glass Plates Containing the Photosynthetic Photosystem II Pigment-Protein Complex.

PubMed

Noji, Tomoyasu; Kawakami, Keisuke; Shen, Jian-Ren; Dewa, Takehisa; Nango, Mamoru; Kamiya, Nobuo; Itoh, Shigeru; Jin, Tetsuro

2016-08-09

The development of artificial photosynthesis has focused on the efficient coupling of reaction at photoanode and cathode, wherein the production of hydrogen (or energy carriers) is coupled to the electrons derived from water-splitting reactions. The natural photosystem II (PSII) complex splits water efficiently using light energy. The PSII complex is a large pigment-protein complex (20 nm in diameter) containing a manganese cluster. A new photoanodic device was constructed incorporating stable PSII purified from a cyanobacterium Thermosynechococcus vulcanus through immobilization within 20 or 50 nm nanopores contained in porous glass plates (PGPs). PSII in the nanopores retained its native structure and high photoinduced water splitting activity. The photocatalytic rate (turnover frequency) of PSII in PGP was enhanced 11-fold compared to that in solution, yielding a rate of 50-300 mol e(-)/(mol PSII·s) with 2,6-dichloroindophenol (DCIP) as an electron acceptor. The PGP system realized high local concentrations of PSII and DCIP to enhance the collisional reactions in nanotubes with low disturbance of light penetration. The system allows direct visualization/determination of the reaction inside the nanotubes, which contributes to optimize the local reaction condition. The PSII/PGP device will substantively contribute to the construction of artificial photosynthesis using water as the ultimate electron source.

Light charged particle multiplicities in fusion and quasifission reactions

NASA Astrophysics Data System (ADS)

Kalandarov, Sh. A.; Adamian, G. G.; Antonenko, N. V.; Lacroix, D.; Wieleczko, J. P.

2018-01-01

The light charged particle evaporation from the compound nucleus and from the complex fragments in the reactions 32S+100Mo, 121Sb+27Al, 40Ar+164Dy, and 40Ar+ nat Ag is studied within the dinuclear system model. The possibility to distinguish the reaction products from different reaction mechanisms is discussed.

A new synthesis route for Os-complex modified redox polymers for potential biofuel cell applications.

PubMed

Pöller, Sascha; Beyl, Yvonne; Vivekananthan, Jeevanthi; Guschin, Dmitrii A; Schuhmann, Wolfgang

2012-10-01

A new synthesis route for Os-complex modified redox polymers was developed. Instead of ligand exchange reactions for coordinative binding of suitable precursor Os-complexes at the polymer, Os-complexes already exhibiting the final ligand shell containing a suitable functional group were bound to the polymer via an epoxide opening reaction. By separation of the polymer synthesis from the ligand exchange reaction at the Os-complex, the modification of the same polymer backbone with different Os-complexes or the binding of the same Os-complex to a number of different polymer backbones becomes feasible. In addition, the Os-complex can be purified and characterized prior to its binding to the polymer. In order to further understand and optimize suitable enzyme/redox polymer systems concerning their potential application in biosensors or biofuel cells, a series of redox polymers was synthesized and used as immobilization matrix for Trametes hirsuta laccase. The properties of the obtained biofuel cell cathodes were compared with similar biocatalytic interfaces derived from redox polymers obtained via ligand exchange reaction of the parent Os-complex with a ligand integrated into the polymer backbone during the polymer synthesis. Copyright © 2011 Elsevier B.V. All rights reserved.

A transformation theory of stochastic evolution in Red Moon methodology to time evolution of chemical reaction process in the full atomistic system.

PubMed

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H 2 + I 2  ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H 2 and I 2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H 2 ] eq and equilibrium constants K eq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H 2 ] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

Electronic Structure Theory Study of the Microsolvated F(-)(H2O) + CH3I SN2 Reaction.

PubMed

Zhang, Jiaxu; Yang, Li; Sheng, Li

2016-05-26

The potential energy profile of microhydrated fluorine ion reaction with methyl iodine has been characterized by extensive electronic structure calculations. Both hydrogen-bonded F(-)(H2O)---HCH2I and ion-dipole F(-)(H2O)---CH3I complexes are formed for the reaction entrance and the PES in vicinity of these complexes is very flat, which may have important implications for the reaction dynamics. The water molecule remains on the fluorine side until the reactive system goes to the SN2 saddle point. It can easily move to the iodine side with little barrier, but in a nonsynchronous reaction path after the dynamical bottleneck to the reaction, which supports the previous prediction for microsolvated SN2 systems. The influence of solvating water molecule on the reaction mechanism is probed by comparing with the influence of the nonsolvated analogue and other microsolvated SN2 systems. Taking the CCSD(T) single-point calculations based on MP2-optimized geometries as benchmark, the DFT functionals B97-1 and B3LYP are found to better characterize the potential energy profile for the title reaction and are recommended as the preferred methods for the direct dynamics simulations to uncover the dynamic behaviors.

THE INFLUENCE OF MINERAL REACTIONS ON THE ENVIRONMENTAL FATE OF METALS IN SOILS AND SEDIMENTS

EPA Science Inventory

Significant progress has been made in elucidating sorption reactions that control the partitioning of metals from solution to mineral surfaces in contaminated soil/sediment systems. Surface complexation models have been developed to quantify the forward reaction, however, these ...

Unraveling reaction pathways and specifying reaction kinetics for complex systems.

PubMed

Vinu, R; Broadbelt, Linda J

2012-01-01

Many natural and industrial processes involve a complex set of competing reactions that include several different species. Detailed kinetic modeling of such systems can shed light on the important pathways involved in various transformations and therefore can be used to optimize the process conditions for the desired product composition and properties. This review focuses on elucidating the various components involved in modeling the kinetics of pyrolysis and oxidation of polymers. The elementary free radical steps that constitute the chain reaction mechanism of gas-phase/nonpolar liquid-phase processes are outlined. Specification of the rate coefficients of the various reaction families, which is central to the theme of kinetics, is described. Construction of the reaction network on the basis of the types of end groups and reactive moieties in a polymer chain is discussed. Modeling frameworks based on the method of moments and kinetic Monte Carlo are evaluated using illustrations. Finally, the prospects and challenges in modeling biomass conversion are addressed.

Vacuum Ultraviolet Photoionization of Complex Chemical Systems

DOE PAGES

Kostko, Oleg; Bandyopadhyay, Biswajit; Ahmed, Musahid

2016-02-24

Tunable vacuum ultraviolet (VUV) radiation coupled to mass spectrometry is applied to the study of complex chemical systems in this paper. The identification of novel reactive intermediates and radicals is revealed in flame, pulsed photolysis, and pyrolysis reactors, leading to the elucidation of spectroscopy, reaction mechanisms, and kinetics. Mass-resolved threshold photoelectron photoion coincidence measurements provide unprecedented access to vibrationally resolved spectra of free radicals present in high-temperature reactors. Photoionization measurements in water clusters, nucleic acid base dimers, and their complexes with water provide signatures of proton transfer in hydrogen-bonded and π-stacked systems. Experimental and theoretical methods to track ion–molecule reactionsmore » and fragmentation pathways in intermolecular and intramolecular hydrogen-bonded systems in sugars and alcohols are described. Photoionization of laser-ablated molecules, clusters, and their reaction products inform thermodynamics and spectroscopy that are relevant to astrochemistry and catalysis. Finally, new directions in coupling VUV radiation to interrogate complex chemical systems are discussed.« less

A Class of Multiresponsive Colorimetric and Fluorescent pH Probes via Three Different Reaction Mechanisms of Salen Complexes: A Selective and Accurate pH Measurement.

PubMed

Cheng, Jinghui; Gou, Fei; Zhang, Xiaohong; Shen, Guangyu; Zhou, Xiangge; Xiang, Haifeng

2016-09-19

We report a class of multiresponsive colorimetric and fluorescent pH probes based on three different reaction mechanisms including cation exchange, protonation, and hydrolysis reaction of K(I), Ca(II), Zn(II), Cu(II), Al(III), and Pd(II) Salen complexes. Compared with traditional pure organic pH probes, these complex-based pH probes exhibited a much better selectivity due to the shielding function of the filled-in metal ion in the complex. Their pH sensing performances were affected by the ligand structure and the central metal ion. This work is the first report of "off-on-on'-off" colorimetric and fluorescent pH probes that possess three different reaction mechanisms and should inspire the design of multiple-responsive probes for important analytes in biological systems.

Double Reformatsky reaction: divergent synthesis of δ-hydroxy-β-ketoesters.

PubMed

Mineno, Masahiro; Sawai, Yasuhiro; Kanno, Kazuaki; Sawada, Naotaka; Mizufune, Hideya

2013-06-21

The double Reformatsky reaction, tandem addition of two molecules of zinc alkanoate to a carbonyl compound, and its synthetic application to a series of δ-hydroxy-β-ketoesters has been developed. The key to accelerate the double Reformatsky reaction is considered to be a complex-induced proximity effect of the in situ generated zinc alkoxide coordinated with the pyridyl group of the substrate or bidentate amines. A noteworthy feature of the reaction system is its high tolerance of functional groups due to the moderate nucleophilicity of organozinc reagents and the mild reaction conditions. Moreover, spectroscopic and crystallographic analyses of the zinc complex of the double Reformatsky product support the proposed mechanism of reaction site discrimination for ketones, aldehydes, nitriles, carboxylic acid anhydrides, and esters.

Mechanism of Ferric Oxalate Photolysis

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

Mangiante, David. M.; Schaller, Richard D.; Zarzycki, Piotr

Iron(III) oxalate, Fe 3+(C 2O 4) 3 3–, is a photoactive metal organic complex found in natural systems and used to quantify photon flux as a result of its high absorbance and reaction quantum yield. It also serves as a model complex to understand metal carboxylate complex photolysis because the mechanism of photolysis and eventual production of CO 2 is not well understood for any system. Here, we employed pump/probe mid-infrared transient absorption spectroscopy to study the photolysis reaction of the iron(III) oxalate ion in D 2O and H 2O up to 3 ns following photoexcitation. We find that intramolecularmore » electron transfer from oxalate to iron occurs on a sub-picosecond time scale, creating iron(II) complexed by one oxidized and two spectator oxalate ligands. Within 40 ps following electron transfer, the oxidized oxalate molecule dissociates to form free solvated CO 2(aq) and a species inferred to be CO 2 •– based on the appearance of a new vibrational absorption band and ab initio simulation. Our work provides direct spectroscopic evidence for the first mechanistic steps in the photolysis reaction and presents a technique to analyze other environmentally relevant metal carboxylate photolysis reactions.« less

Mechanism of Ferric Oxalate Photolysis

DOE PAGES

Mangiante, David. M.; Schaller, Richard D.; Zarzycki, Piotr; ...

2017-06-08

Iron(III) oxalate, Fe 3+(C 2O 4) 3 3–, is a photoactive metal organic complex found in natural systems and used to quantify photon flux as a result of its high absorbance and reaction quantum yield. It also serves as a model complex to understand metal carboxylate complex photolysis because the mechanism of photolysis and eventual production of CO 2 is not well understood for any system. Here, we employed pump/probe mid-infrared transient absorption spectroscopy to study the photolysis reaction of the iron(III) oxalate ion in D 2O and H 2O up to 3 ns following photoexcitation. We find that intramolecularmore » electron transfer from oxalate to iron occurs on a sub-picosecond time scale, creating iron(II) complexed by one oxidized and two spectator oxalate ligands. Within 40 ps following electron transfer, the oxidized oxalate molecule dissociates to form free solvated CO 2(aq) and a species inferred to be CO 2 •– based on the appearance of a new vibrational absorption band and ab initio simulation. Our work provides direct spectroscopic evidence for the first mechanistic steps in the photolysis reaction and presents a technique to analyze other environmentally relevant metal carboxylate photolysis reactions.« less

Design criteria for extraction with chemical reaction and liquid membrane permeation

NASA Technical Reports Server (NTRS)

Bart, H. J.; Bauer, A.; Lorbach, D.; Marr, R.

1988-01-01

The design criteria for heterogeneous chemical reactions in liquid/liquid systems formally correspond to those of classical physical extraction. More complex models are presented which describe the material exchange at the individual droplets in an extraction with chemical reaction and in liquid membrane permeation.

XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes

PubMed Central

Blinov, Michael L.; Moraru, Ion I.

2011-01-01

Multi-state molecules and multi-component complexes are commonly involved in cellular signaling. Accounting for molecules that have multiple potential states, such as a protein that may be phosphorylated on multiple residues, and molecules that combine to form heterogeneous complexes located among multiple compartments, generates an effect of combinatorial complexity. Models involving relatively few signaling molecules can include thousands of distinct chemical species. Several software tools (StochSim, BioNetGen) are already available to deal with combinatorial complexity. Such tools need information standards if models are to be shared, jointly evaluated and developed. Here we discuss XML conventions that can be adopted for modeling biochemical reaction networks described by user-specified reaction rules. These could form a basis for possible future extensions of the Systems Biology Markup Language (SBML). PMID:21464833

Real-time monitoring of enzyme-free strand displacement cascades by colorimetric assays

NASA Astrophysics Data System (ADS)

Duan, Ruixue; Wang, Boya; Hong, Fan; Zhang, Tianchi; Jia, Yongmei; Huang, Jiayu; Hakeem, Abdul; Liu, Nannan; Lou, Xiaoding; Xia, Fan

2015-03-01

The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications.The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications. Electronic supplementary information (ESI) available: Experimental procedures and analytical data are provided. See DOI: 10.1039/c5nr00697j

Waterflooding injectate design systems and methods

DOEpatents

Brady, Patrick V.; Krumhansl, James L.

2014-08-19

A method of designing an injectate to be used in a waterflooding operation is disclosed. One aspect includes specifying data representative of chemical characteristics of a liquid hydrocarbon, a connate, and a reservoir rock, of a subterranean reservoir. Charged species at an interface of the liquid hydrocarbon are determined based on the specified data by evaluating at least one chemical reaction. Charged species at an interface of the reservoir rock are determined based on the specified data by evaluating at least one chemical reaction. An extent of surface complexation between the charged species at the interfaces of the liquid hydrocarbon and the reservoir rock is determined by evaluating at least one surface complexation reaction. The injectate is designed and is operable to decrease the extent of surface complexation between the charged species at interfaces of the liquid hydrocarbon and the reservoir rock. Other methods, apparatus, and systems are disclosed.

Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks.

PubMed

Morgado, Gaspar; Gerngross, Daniel; Roberts, Tania M; Panke, Sven

Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity. The scale of these initial attempts remains small, suggesting that more robust control of such systems and more efficient optimization are currently major bottlenecks. To this end, the very nature of enzyme cascade reactions as multi-membered systems requires novel approaches for implementation and optimization, some of which can be obtained from in vivo disciplines (such as pathway refactoring and DNA assembly), and some of which can be built on the unique, cell-free properties of cascade reactions (such as easy analytical access to all system intermediates to facilitate modeling).

Quantitative computational models of molecular self-assembly in systems biology

PubMed Central

Thomas, Marcus; Schwartz, Russell

2017-01-01

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally. PMID:28535149

Quantitative computational models of molecular self-assembly in systems biology.

PubMed

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

A network dynamics approach to chemical reaction networks

NASA Astrophysics Data System (ADS)

van der Schaft, A. J.; Rao, S.; Jayawardhana, B.

2016-04-01

A treatment of a chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption, the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in the chemical reaction network theory, and which directly relates to the thermodynamics and port-Hamiltonian formulation of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This immediately leads to the characterisation of the set of equilibria and their stability. Furthermore, the assumption of complex balancedness is revisited from the point of view of Kirchhoff's matrix tree theorem. Both the form of the dynamics and the deduced behaviour are very similar to consensus dynamics, and provide additional perspectives to the latter. Finally, using the classical idea of extending the graph of chemical complexes by a 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action kinetics outflows is given, and a unified framework is provided for structure-preserving model reduction of this important class of open reaction networks.

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

NASA Astrophysics Data System (ADS)

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.

Metals and lipid oxidation. Contemporary issues.

PubMed

Schaich, K M

1992-03-01

Lipid oxidation is now recognized to be a critically important reaction in physiological and toxicological processes as well as in food products. This provides compelling reasons to understand what causes lipid oxidation in order to be able to prevent or control the reactions. Redox-active metals are major factors catalyzing lipid oxidation in biological systems. Classical mechanisms of direct electron transfer to double bonds by higher valence metals and of reduction of hydroperoxides by lower valence metals do not always account for patterns of metal catalysis of lipid oxidation in multiphasic or compartmentalized biological systems. To explain why oxidation kinetics, mechanisms, and products in molecular environments which are both chemically and physically complex often do not follow classical patterns predicted by model system studies, increased consideration must be given to five contemporary issues regarding metal catalysis of lipid oxidation: hypervalent non-heme iron or iron-oxygen complexes, heme catalysis mechanism(s), compartmentalization of reactions and lipid phase reactions of metals, effects of metals on product mixes, and factors affecting the mode of metal catalytic action.

PumpKin: A tool to find principal pathways in plasma chemical models

NASA Astrophysics Data System (ADS)

Markosyan, A. H.; Luque, A.; Gordillo-Vázquez, F. J.; Ebert, U.

2014-10-01

PumpKin is a software package to find all principal pathways, i.e. the dominant reaction sequences, in chemical reaction systems. Although many tools are available to integrate numerically arbitrarily complex chemical reaction systems, few tools exist in order to analyze the results and interpret them in relatively simple terms. In particular, due to the large disparity in the lifetimes of the interacting components, it is often useful to group reactions into pathways that recycle the fastest species. This allows a researcher to focus on the slow chemical dynamics, eliminating the shortest timescales. Based on the algorithm described by Lehmann (2004), PumpKin automates the process of finding such pathways, allowing the user to analyze complex kinetics and to understand the consumption and production of a certain species of interest. We designed PumpKin with an emphasis on plasma chemical systems but it can also be applied to atmospheric modeling and to industrial applications such as plasma medicine and plasma-assisted combustion.

STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python

PubMed Central

Wils, Stefan; Schutter, Erik De

2008-01-01

We describe how the use of the Python language improved the user interface of the program STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions. Setting up such models is a complicated process that consists of many phases. Initial versions of STEPS relied on a static input format that did not cleanly separate these phases, limiting modelers in how they could control the simulation and becoming increasingly complex as new features and new simulation algorithms were added. We solved all of these problems by tightly integrating STEPS with Python, using SWIG to expose our existing simulation code. PMID:19623245

Efficient Constant-Time Complexity Algorithm for Stochastic Simulation of Large Reaction Networks.

PubMed

Thanh, Vo Hong; Zunino, Roberto; Priami, Corrado

2017-01-01

Exact stochastic simulation is an indispensable tool for a quantitative study of biochemical reaction networks. The simulation realizes the time evolution of the model by randomly choosing a reaction to fire and update the system state according to a probability that is proportional to the reaction propensity. Two computationally expensive tasks in simulating large biochemical networks are the selection of next reaction firings and the update of reaction propensities due to state changes. We present in this work a new exact algorithm to optimize both of these simulation bottlenecks. Our algorithm employs the composition-rejection on the propensity bounds of reactions to select the next reaction firing. The selection of next reaction firings is independent of the number reactions while the update of propensities is skipped and performed only when necessary. It therefore provides a favorable scaling for the computational complexity in simulating large reaction networks. We benchmark our new algorithm with the state of the art algorithms available in literature to demonstrate its applicability and efficiency.

Synthesis, characterization and solid-state properties of [Zn(Hdmmthiol)2]\\cdot2H2O complex

NASA Astrophysics Data System (ADS)

Dagdelen, Fethi; Aydogdu, Yildirim; Dey, Kamalendu; Biswas, Susobhan

2016-05-01

The zinc(II) complex with tridentate thiohydrazone ligand have been prepared by metal template reaction. The metal template reaction was used to prepare the zinc (II) complex with tridentate thiohydrazone ligand. The reaction of diacetylmonoxime and, morpholine N-thiohydrazidewith Zn(OAc)2 \\cdot2H2O under reflux yielded the formation of the [Zn(Hdmmthiol )2]\\cdot2H2O complex. The complex was characterized by a combination of protocols including elemental analysis, UV+vis, FT-IR, TG and PXRD. The temperature dependence of the electrical conductivity and the optical property of the [Zn(Hdmmthiol )2] \\cdot2H2O complex is called H2dammthiol was studied. Powder X-ray diffraction (PXRD) method was used to investigate the crystal structure of the sample. The zinc complex was shown to be a member of the triclinic system. The zinc complex was determined to have n-type conductivity as demonstrated in the hot probe measurements. The complex was determined to display direct optical transition with band gaps of 2.52eV as determined by the optical absorption analysis.

Moving bed reactor setup to study complex gas-solid reactions.

PubMed

Gupta, Puneet; Velazquez-Vargas, Luis G; Valentine, Charles; Fan, Liang-Shih

2007-08-01

A moving bed scale reactor setup for studying complex gas-solid reactions has been designed in order to obtain kinetic data for scale-up purpose. In this bench scale reactor setup, gas and solid reactants can be contacted in a cocurrent and countercurrent manner at high temperatures. Gas and solid sampling can be performed through the reactor bed with their composition profiles determined at steady state. The reactor setup can be used to evaluate and corroborate model parameters accounting for intrinsic reaction rates in both simple and complex gas-solid reaction systems. The moving bed design allows experimentation over a variety of gas and solid compositions in a single experiment unlike differential bed reactors where the gas composition is usually fixed. The data obtained from the reactor can also be used for direct scale-up of designs for moving bed reactors.

Theoretical stusy of the reaction between 2,2',4' - trihydroxyazobenzene-5-sulfonic acid and zirconium

USGS Publications Warehouse

Fletcher, Mary H.

1960-01-01

Zirconium reacts with 2,2',4'-trihydroxyazobenzene-5-sulfonic acid in acid solutions to Form two complexes in which the ratios of dye to zirconium are 1 to 1 and 2 to 1. Both complexes are true chelates, with zirconium acting as a bridge between the two orthohydroxy dye groups. Apparent equilibrium constants for the reactions to form each of the complexes are determined. The reactions are used as a basis for the determination of the active component in the dye and a graphical method for the determination of reagent purity is described. Four absorption spectra covering the wave length region from 350 to 750 mu are given, which completely define the color system associated with the reactions in solutions where the hydrochloric acid concentration ranges from 0.0064N to about 7N.

STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies.

PubMed

Hepburn, Iain; Chen, Weiliang; Wils, Stefan; De Schutter, Erik

2012-05-10

Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. We describe STEPS, a stochastic reaction-diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction-diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. STEPS simulates models of cellular reaction-diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/

On the deduction of chemical reaction pathways from measurements of time series of concentrations.

PubMed

Samoilov, Michael; Arkin, Adam; Ross, John

2001-03-01

We discuss the deduction of reaction pathways in complex chemical systems from measurements of time series of chemical concentrations of reacting species. First we review a technique called correlation metric construction (CMC) and show the construction of a reaction pathway from measurements on a part of glycolysis. Then we present two new improved methods for the analysis of time series of concentrations, entropy metric construction (EMC), and entropy reduction method (ERM), and illustrate (EMC) with calculations on a model reaction system. (c) 2001 American Institute of Physics.

Iterated reaction graphs: simulating complex Maillard reaction pathways.

PubMed

Patel, S; Rabone, J; Russell, S; Tissen, J; Klaffke, W

2001-01-01

This study investigates a new method of simulating a complex chemical system including feedback loops and parallel reactions. The practical purpose of this approach is to model the actual reactions that take place in the Maillard process, a set of food browning reactions, in sufficient detail to be able to predict the volatile composition of the Maillard products. The developed framework, called iterated reaction graphs, consists of two main elements: a soup of molecules and a reaction base of Maillard reactions. An iterative process loops through the reaction base, taking reactants from and feeding products back to the soup. This produces a reaction graph, with molecules as nodes and reactions as arcs. The iterated reaction graph is updated and validated by comparing output with the main products found by classical gas-chromatographic/mass spectrometric analysis. To ensure a realistic output and convergence to desired volatiles only, the approach contains a number of novel elements: rate kinetics are treated as reaction probabilities; only a subset of the true chemistry is modeled; and the reactions are blocked into groups.

Final Technical Report of Research

DOE R&D Accomplishments Database

Taube, H.

1972-04-03

The studies conducted embrace the following subject areas: ion solvation, mechanistic studies on substitution reactions in metal complexes, oxidation of coordinated ligands, mechanistic studies on electron transfer reactions, preparation and characterization of new species in the aquo and ammino systems.

CoBr2-TMTU-zinc catalysed-Pauson-Khand reaction.

PubMed

Wang, Yuefan; Xu, Lingmin; Yu, Ruocheng; Chen, Jiahua; Yang, Zhen

2012-08-25

A cobalt-TMTU complex, derived from the in situ reduction of CoBr(2) with Zn in the presence of TMTU, can catalyze Pauson-Khand reaction at a balloon pressure of CO, which enables the synthesis of structurally diverse cyclopentenones. This catalytic system works efficiently for both intermolecular and intramolecular PK reactions.

Active control of complex, multicomponent self-assembly processes

NASA Astrophysics Data System (ADS)

Schulman, Rebecca

The kinetics of many complex biological self-assembly processes such as cytoskeletal assembly are precisely controlled by cells. Spatiotemporal control over rates of filament nucleation, growth and disassembly determine how self-assembly occurs and how the assembled form changes over time. These reaction rates can be manipulated by changing the concentrations of the components needed for assembly by activating or deactivating them. I will describe how we can use these principles to design driven self-assembly processes in which we assemble and disassemble multiple types of components to create micron-scale networks of semiflexible filaments assembled from DNA. The same set of primitive components can be assembled into many different, structures depending on the concentrations of different components and how designed, DNA-based chemical reaction networks manipulate these concentrations over time. These chemical reaction networks can in turn interpret environmental stimuli to direct complex, multistage response. Such a system is a laboratory for understanding complex active material behaviors, such as metamorphosis, self-healing or adaptation to the environment that are ubiquitous in biological systems but difficult to quantitatively characterize or engineer.

An experimental design method leading to chemical Turing patterns.

PubMed

Horváth, Judit; Szalai, István; De Kepper, Patrick

2009-05-08

Chemical reaction-diffusion patterns often serve as prototypes for pattern formation in living systems, but only two isothermal single-phase reaction systems have produced sustained stationary reaction-diffusion patterns so far. We designed an experimental method to search for additional systems on the basis of three steps: (i) generate spatial bistability by operating autoactivated reactions in open spatial reactors; (ii) use an independent negative-feedback species to produce spatiotemporal oscillations; and (iii) induce a space-scale separation of the activatory and inhibitory processes with a low-mobility complexing agent. We successfully applied this method to a hydrogen-ion autoactivated reaction, the thiourea-iodate-sulfite (TuIS) reaction, and noticeably produced stationary hexagonal arrays of spots and parallel stripes of pH patterns attributed to a Turing bifurcation. This method could be extended to biochemical reactions.

Three-Component Reactions of Diazoesters, Aldehydes, and Imines Using a Dual Catalytic System Consisting of a Rhodium(II) Complex and a Lewis Acid.

PubMed

Toda, Yasunori; Kaku, Wakatake; Tsuruoka, Makoto; Shinogaki, Sho; Abe, Tomoka; Kamiya, Hideaki; Kikuchi, Ayaka; Itoh, Kennosuke; Suga, Hiroyuki

2018-05-04

A dual catalytic system, dirhodium tetrapivalate/ytterbium(III) triflate, enables the three-component reactions of α-alkyl-α-diazoesters, aromatic aldehydes, and N-benzylidenebenzylamine derivatives to afford the corresponding β-amino alcohols in good yields after hydrolysis of the oxazolidine cycloadducts, whereas no β-amino alcohols are obtained in the absence of ytterbium(III) triflate. A similar dual catalytic system, dirhodium tetraacetate/ytterbium(III) triflate, is found to be effective in accelerating the reactions of α-aryl-α-diazoesters in high yields. Furthermore, the reactions using dimethyl diazomalonate are described.

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

PubMed Central

2016-01-01

Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition. PMID:27004858

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

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

Li, Wenjin; Ma, Ao, E-mail: aoma@uic.edu

Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C{sub 7eq} → C{sub 7ax} transition of themore » alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.« less

Adaptive Correction from Virtually Complex Dynamic Libraries: The Role of Noncovalent Interactions in Structural Selection and Folding.

PubMed

Lafuente, Maria; Atcher, Joan; Solà, Jordi; Alfonso, Ignacio

2015-11-16

The hierarchical self-assembling of complex molecular systems is dictated by the chemical and structural information stored in their components. This information can be expressed through an adaptive process that determines the structurally fittest assembly under given environmental conditions. We have set up complex disulfide-based dynamic covalent libraries of chemically and topologically diverse pseudopeptidic compounds. We show how the reaction evolves from very complex mixtures at short reaction times to the almost exclusive formation of a major compound, through the establishment of intramolecular noncovalent interactions. Our experiments demonstrate that the systems evolve through error-check and error-correction processes. The nature of these interactions, the importance of the folding and the effects of the environment are also discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nonlinear Systems.

ERIC Educational Resources Information Center

Seider, Warren D.; Ungar, Lyle H.

1987-01-01

Describes a course in nonlinear mathematics courses offered at the University of Pennsylvania which provides an opportunity for students to examine the complex solution spaces that chemical engineers encounter. Topics include modeling many chemical processes, especially those involving reaction and diffusion, auto catalytic reactions, phase…

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

NASA Astrophysics Data System (ADS)

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).

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.

PubMed

Yang, Qian; Sing-Long, Carlos A; Reed, Evan J

2017-08-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

PubMed Central

Sing-Long, Carlos A.

2017-01-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates. PMID:28989618

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

DOE PAGES

Yang, Qian; Sing-Long, Carlos A.; Reed, Evan J.

2017-06-19

Here, we propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. Conversely, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our methodmore » on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. Furthermore, we describe a framework in this work that paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.« less

Controlling Complex Systems and Developing Dynamic Technology

NASA Astrophysics Data System (ADS)

Avizienis, Audrius Victor

In complex systems, control and understanding become intertwined. Following Ilya Prigogine, we define complex systems as having control parameters which mediate transitions between distinct modes of dynamical behavior. From this perspective, determining the nature of control parameters and demonstrating the associated dynamical phase transitions are practically equivalent and fundamental to engaging with complexity. In the first part of this work, a control parameter is determined for a non-equilibrium electrochemical system by studying a transition in the morphology of structures produced by an electroless deposition reaction. Specifically, changing the size of copper posts used as the substrate for growing metallic silver structures by the reduction of Ag+ from solution under diffusion-limited reaction conditions causes a dynamical phase transition in the crystal growth process. For Cu posts with edge lengths on the order of one micron, local forces promoting anisotropic growth predominate, and the reaction produces interconnected networks of Ag nanowires. As the post size is increased above 10 microns, the local interfacial growth reaction dynamics couple with the macroscopic diffusion field, leading to spatially propagating instabilities in the electrochemical potential which induce periodic branching during crystal growth, producing dendritic deposits. This result is interesting both as an example of control and understanding in a complex system, and as a useful combination of top-down lithography with bottom-up electrochemical self-assembly. The second part of this work focuses on the technological development of devices fabricated using this non-equilibrium electrochemical process, towards a goal of integrating a complex network as a dynamic functional component in a neuromorphic computing device. Self-assembled networks of silver nanowires were reacted with sulfur to produce interfacial "atomic switches": silver-silver sulfide junctions, which exhibit complex dynamics (e.g. both short- and long-term changes in conductivity) in response to applied voltage signals. Characterization of these atomic switch networks (ASNs) brought out interesting parallels to biological neural networks, including power-law scaling in the statistics of electrical signal propagation and dynamic self-organization of differentiated subnetworks. A reservoir computing (RC) strategy was employed to utilize measurements of electrical signals dynamically generated in ASNs to perform time-series memory and manipulation tasks including a parity test and arbitrary waveform generation. These results represent the useful integration of a complex network into a dynamic physical RC device.

About the Barriers to Reaction of CCl4 with HFeOH and FeCl2

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

Ginovska-Pangovska, Bojana; Camaioni, Donald M.; Dupuis, Michel

2011-08-11

The reactivity of iron nanoparticles in aqueous environments has received considerable attention due to their potential utilization in environmental remediation technologies. As part of a broader program aiming at an improved understanding of the mechanisms involved in the degradation of harmful chlorocarbons, joint experimental and computational studies of model systems were initiated. We previously reported on the reaction of one and two Fe atoms reactions with carbon tetrachloride (CCl4) in direct mimic of “atom-dropping” experiments, with insights into the formation of novel iron-carbon-chlorine complexes, their structures and possible reaction mechanisms. Increasing the level of complexity, we report here on themore » modeling of the reaction of HFeOH and CCl4 as companion research of recent ultra high vacuum experiments of the reaction of Fe with water and CCl4. HFeOH is a stable molecular species formed in the reaction of Fe with H2O. Experimentally the (Fe, H2O, CCl4) system showed no reactivity up to the desorption temperature of CCl4. Electron correlated CCSD(T) calculations (at DFT(B3LYP) optimized structures) indicated an energy barrier to reactivity of 24.5 kcal/mol following the formation of a stable ( 7.5 kcal/mol) long-range precursor complex. This finding is consistent with the lack of experimentally detected reaction products. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

Supraglacial sulfur springs and associated biological activity in the Canadian high arctic - signs of life beneath the ice

USGS Publications Warehouse

Grasby, Stephen E.; Allen, Carlton C.; Longazo, Teresa G.; Lisle, John T.; Griffin, Dale W.; Beauchamp, Benoit

2003-01-01

Unique springs, discharging from the surface of an arctic glacier, release H2S and deposit native sulfur, gypsum, and calcite. The presence of sulfur in three oxidation states indicates a complex series of redox reactions. Physical and chemical conditions of the spring water and surrounding environment, as well as mineralogical and isotopic signatures, suggest biologically mediated reactions. Cell counts and DNA analyses confirm bacteria are present in the spring system, and a limited number of sequenced isolates suggests that complex communities of bacteria live within the glacial system.

Chemical composition of donor-acceptor complexes of hydroxyoxo(5,10,15,20-tetraphenylporphinato)molybdenum(V) with 3,5-dimethylpyrazole and equilibrium constants for their formation

NASA Astrophysics Data System (ADS)

Motorina, E. V.; Lomova, T. N.

2017-11-01

The results from a quantitative study of reactions between hydroxyoxo(5,10,15,20-tetraphenylporphinato)molybdenum(V) (O=Mo(OH)TPP) and 3,5-dimethylpyrazole, a biologically active base, in toluene are presented. The chemical structure and key parameters of intermediates and reaction products are determined by spectral means. The equilibrium constant ( K = 51.3 L/mol) is calculated and a full kinetic description of simple reactions that occur in this system during complex transformation is obtained. The prospect of using a mixed porphyrin-containing complex as a receptor for 3,5-dimethylpyrazole, a building block for alkaloids and pharmaceutical preparations, is substantiated.

Biphasic catalysis in water/carbon dioxide micellar systems

DOEpatents

Jacobson, Gunilla B.; Tumas, William; Johnston, Keith P.

2002-01-01

A process is provided for catalyzing an organic reaction to form a reaction product by placing reactants and a catalyst for the organic reaction, the catalyst of a metal complex and at least one ligand soluble within one of the phases of said aqueous biphasic system, within an aqueous biphasic system including a water phase, a dense phase fluid, and a surfactant adapted for forming an emulsion or microemulsion within the aqueous biphasic system, the reactants soluble within one of the phases of the aqueous biphasic system and convertible in the presence of the catalyst to a product having low solubility in the phase in which the catalyst is soluble; and, maintaining the aqueous biphasic system under pressures, at temperatures, and for a period of time sufficient for the organic reaction to occur and form the reaction product and to maintain sufficient density on the dense phase fluid, the reaction product characterized as having low solubility in the phase in which the catalyst is soluble.

Interface Reactions and Synthetic Reaction of Composite Systems

PubMed Central

Park, Joon Sik; Kim, Jeong Min

2010-01-01

Interface reactions in composite systems often determine their overall properties, since product phases usually formed at interfaces during composite fabrication processing make up a large portion of the composites. Since most composite materials represent a ternary or higher order materials system, many studies have focused on analyses of diffusion phenomena and kinetics in multicomponent systems. However, the understanding of the kinetic behavior increases the complexity, since the kinetics of each component during interdiffusion reactions need to be defined for interpreting composite behaviors. From this standpoint, it is important to clarify the interface reactions for producing compatible interfaces with desired product phases. A thermodynamic evaluation such as a chemical potential of involving components can provide an understanding of the diffusion reactions, which govern diffusion pathways and product phase formation. A strategic approach for designing compatible interfaces is discussed in terms of chemical potential diagrams and interface morphology, with some material examples.

Aminopyridinate-FI hybrids, their hafnium and titanium complexes, and their application in the living polymerization of 1-hexene.

PubMed

Haas, Isabelle; Dietel, Thomas; Press, Konstantin; Kol, Moshe; Kempe, Rhett

2013-10-11

Based on two well-established ligand systems, the aminopyridinato (Ap) and the phenoxyimine (FI) ligand systems, new Ap-FI hybrid ligands were developed. Four different Ap-FI hybrid ligands were synthesized through a simple condensation reaction and fully characterized. The reaction of hafnium tetrabenzyl with all four Ap-FI hybrid ligands exclusively led to mono(Ap-FI) complexes of the type [(Ap-FI)HfBn2 ]. The ligands acted as tetradentate dianionic chelates. Upon activation with tris(pentafluorophenyl)borane, the hafnium-dibenzyl complexes led to highly active catalysts for the polymerization of 1-hexene. Ultrahigh molecular weights and extremely narrow polydispersities support the living nature of this polymerization process. A possible deactivation product of the hafnium catalysts was characterized by single-crystal X-ray analysis and is discussed. The coordination modes of these new ligands were studied with the help of model titanium complexes. The reaction of titanium(IV) isopropoxide with ligand 1 led to a mono(Ap-FI) complex, which showed the desired fac-mer coordination mode. Titanium (IV) isopropoxide reacted with ligand 4 to give a complex of the type [(ApH-FI)2 Ti(OiPr)2 ], which featured the ligand in its monoanionic form. The two titanium complexes were characterized by X-ray crystal-structure analysis. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pattern dynamics of the reaction-diffusion immune system.

PubMed

Zheng, Qianqian; Shen, Jianwei; Wang, Zhijie

2018-01-01

In this paper, we will investigate the effect of diffusion, which is ubiquitous in nature, on the immune system using a reaction-diffusion model in order to understand the dynamical behavior of complex patterns and control the dynamics of different patterns. Through control theory and linear stability analysis of local equilibrium, we obtain the optimal condition under which the system loses stability and a Turing pattern occurs. By combining mathematical analysis and numerical simulation, we show the possible patterns and how these patterns evolve. In addition, we establish a bridge between the complex patterns and the biological mechanism using the results from a previous study in Nature Cell Biology. The results in this paper can help us better understand the biological significance of the immune system.

Short relaxation times but long transient times in both simple and complex reaction networks

PubMed Central

Henry, Adrien; Martin, Olivier C.

2016-01-01

When relaxation towards an equilibrium or steady state is exponential at large times, one usually considers that the associated relaxation time τ, i.e. the inverse of the decay rate, is the longest characteristic time in the system. However, that need not be true, other times such as the lifetime of an infinitesimal perturbation can be much longer. In the present work, we demonstrate that this paradoxical property can arise even in quite simple systems such as a linear chain of reactions obeying mass action (MA) kinetics. By mathematical analysis of simple reaction networks, we pin-point the reason why the standard relaxation time does not provide relevant information on the potentially long transient times of typical infinitesimal perturbations. Overall, we consider four characteristic times and study their behaviour in both simple linear chains and in more complex reaction networks taken from the publicly available database ‘Biomodels’. In all these systems, whether involving MA rates, Michaelis–Menten reversible kinetics, or phenomenological laws for reaction rates, we find that the characteristic times corresponding to lifetimes of tracers and of concentration perturbations can be significantly longer than τ. PMID:27411726

Generic strategies for chemical space exploration.

PubMed

Andersen, Jakob L; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F

2014-01-01

The chemical universe of molecules reachable from a set of start compounds by iterative application of a finite number of reactions is usually so vast, that sophisticated and efficient exploration strategies are required to cope with the combinatorial complexity. A stringent analysis of (bio)chemical reaction networks, as approximations of these complex chemical spaces, forms the foundation for the understanding of functional relations in Chemistry and Biology. Graphs and graph rewriting are natural models for molecules and reactions. Borrowing the idea of partial evaluation from functional programming, we introduce partial applications of rewrite rules. A framework for the specification of exploration strategies in graph-rewriting systems is presented. Using key examples of complex reaction networks from carbohydrate chemistry we demonstrate the feasibility of this high-level strategy framework. While being designed for chemical applications, the framework can also be used to emulate higher-level transformation models such as illustrated in a small puzzle game.

[The changes of physiological reactivity of cardiorespiratory system to respiratory homeostasis with the use of complex stimulation of special work capacity].

PubMed

Lysenko, O M

2012-01-01

We present the influence of the program of special additional stimulation of work capacity of high-performance athletes on the sensitivity of cardiorespiratory system to hypercapnic and hypoxic shifts in respiratory homeostasis. We found that under the influence of the pre-start complex a decrease in the sensitivity of ventilator responses to CO2-H+ stimuli in combination with a reduction in the thresholds of the reaction take place. This creates conditions for increased mobilization properties of the cardiorespiratory system and economization of its reaction under conditions of changes of respiratory homeostasis characteristic of intense training and competitive loads in the sport.

An integrated cell-free metabolic platform for protein production and synthetic biology

PubMed Central

Jewett, Michael C; Calhoun, Kara A; Voloshin, Alexei; Wuu, Jessica J; Swartz, James R

2008-01-01

Cell-free systems offer a unique platform for expanding the capabilities of natural biological systems for useful purposes, i.e. synthetic biology. They reduce complexity, remove structural barriers, and do not require the maintenance of cell viability. Cell-free systems, however, have been limited by their inability to co-activate multiple biochemical networks in a single integrated platform. Here, we report the assessment of biochemical reactions in an Escherichia coli cell-free platform designed to activate natural metabolism, the Cytomim system. We reveal that central catabolism, oxidative phosphorylation, and protein synthesis can be co-activated in a single reaction system. Never before have these complex systems been shown to be simultaneously activated without living cells. The Cytomim system therefore promises to provide the metabolic foundation for diverse ab initio cell-free synthetic biology projects. In addition, we describe an improved Cytomim system with enhanced protein synthesis yields (up to 1200 mg/l in 2 h) and lower costs to facilitate production of protein therapeutics and biochemicals that are difficult to make in vivo because of their toxicity, complexity, or unusual cofactor requirements. PMID:18854819

A self-organized ensemble of fluorescent 3-hydroxyflavone-Al (III) complex as sensor for fluoride and acetate ions.

PubMed

Sathish, Sai; Narayan, Govindh; Rao, Nageswara; Janardhana, Chelli

2007-01-01

Aluminum chloride addition results in a self-organized TURN-ON fluorescence of 3-hydroxyflavone (3HF) by a complexation reaction in MeOH and subsequent ligand exchange reaction with fluoride or acetate ions causes a fluorescence TURN-OFF of this complex, delivering a quantitative estimation route for fluoride and acetate ions. The ternary complex of 3HF with Al (III), a hard acid provides for a sensitive signalling system for fluoride ion, a hard base in the concentration range from 6 muM to 50 mM by a concerted co-ordination of fluoride ion involving an intermediate mechanistic pathway, while the complex is sensitive to acetate addition between 0-68 muM. The ligand exchange reaction of Al (3HF)(2) complex by fluoride or acetate ion, without interference from other common anions, has been investigated by UV-visible and fluorescence spetroscopies. The structure of the in-situ intermediate isolated at higher Al (3HF)(2) complex and acetate concentrations was inferred from the FT-IR spectrum and ESI-MS of the sample.

Bromamine Decomposition Revisited: A Holistic Approach for Analyzing Acid and Base Catalysis Kinetics.

PubMed

Wahman, David G; Speitel, Gerald E; Katz, Lynn E

2017-11-21

Chloramine chemistry is complex, with a variety of reactions occurring in series and parallel and many that are acid or base catalyzed, resulting in numerous rate constants. Bromide presence increases system complexity even further with possible bromamine and bromochloramine formation. Therefore, techniques for parameter estimation must address this complexity through thoughtful experimental design and robust data analysis approaches. The current research outlines a rational basis for constrained data fitting using Brønsted theory, application of the microscopic reversibility principle to reversible acid or base catalyzed reactions, and characterization of the relative significance of parallel reactions using fictive product tracking. This holistic approach was used on a comprehensive and well-documented data set for bromamine decomposition, allowing new interpretations of existing data by revealing that a previously published reaction scheme was not robust; it was not able to describe monobromamine or dibromamine decay outside of the conditions for which it was calibrated. The current research's simplified model (3 reactions, 17 constants) represented the experimental data better than the previously published model (4 reactions, 28 constants). A final model evaluation was conducted based on representative drinking water conditions to determine a minimal model (3 reactions, 8 constants) applicable for drinking water conditions.

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

PubMed

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.

DYNAMICS OF MINERAL STRUCTURES AND THE FATE OF METALS IN SOILS AND SEDIMENTS

EPA Science Inventory

Significant progress has been made in elucidating sorption reactions that control the partitioning of metals from solution to mineral surfaces in contaminated soil/sediment systems. Surface complexation models have been developed to quantify the forward reaction with reasonable ...

Several necessary conditions for the evolution of complex forms of life in an artificial environment.

PubMed

Suzuki, Hideaki; Ono, Naoaki; Yuta, Kikuo

2003-01-01

In order for an artificial life (Alife) system to evolve complex creatures, an artificial environment prepared by a designer has to satisfy several conditions. To clarify this requirement, we first assume that an artificial environment implemented in the computational medium is composed of an information space in which elementary symbols move around and react with each other according to human-prepared elementary rules. As fundamental properties of these factors (space, symbols, transportation, and reaction), we present ten criteria from a comparison with the biochemical reaction space in the real world. Then, in the latter half of the article, we take several computational Alife systems one by one, and assess them in terms of the proposed criteria. The assessment can be used not only for improving previous Alife systems but also for devising new Alife models in which complex forms of artificial creatures can be expected to evolve.

Non-Archimedean reaction-ultradiffusion equations and complex hierarchic systems

NASA Astrophysics Data System (ADS)

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.

Theoretical study of the kinetics of chlorine atom abstraction from chloromethanes by atomic chlorine.

PubMed

Brudnik, Katarzyna; Twarda, Maria; Sarzyński, Dariusz; Jodkowski, Jerzy T

2013-10-01

Ab initio calculations at the G3 level were used in a theoretical description of the kinetics and mechanism of the chlorine abstraction reactions from mono-, di-, tri- and tetra-chloromethane by chlorine atoms. The calculated profiles of the potential energy surface of the reaction systems show that the mechanism of the studied reactions is complex and the Cl-abstraction proceeds via the formation of intermediate complexes. The multi-step reaction mechanism consists of two elementary steps in the case of CCl4 + Cl, and three for the other reactions. Rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The temperature dependencies of the calculated rate constants can be expressed, in temperature range of 200-3,000 K as [Formula: see text]. The rate constants for the reverse reactions CH3/CH2Cl/CHCl2/CCl3 + Cl2 were calculated via the equilibrium constants derived theoretically. The kinetic equations [Formula: see text] allow a very good description of the reaction kinetics. The derived expressions are a substantial supplement to the kinetic data necessary to describe and model the complex gas-phase reactions of importance in combustion and atmospheric chemistry.

Origin of Complexity in Multicellular Organisms

NASA Astrophysics Data System (ADS)

Furusawa, Chikara; Kaneko, Kunihiko

2000-06-01

Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems can exhibit complex pattern formation with spontaneous cell differentiation. Such systems employ a ``cooperative'' use of resources and maintain a larger growth speed than simple cell systems, which exist in a homogeneous state and behave ``selfishly.'' The relevance of the diversity of chemicals and reaction dynamics to the growth of a multicellular organism is demonstrated. Chaotic biochemical dynamics are found to provide the multipotency of stem cells.

Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

PubMed

Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

2016-02-01

Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Comparing 2-nt 3' overhangs against blunt-ended siRNAs: a systems biology based study.

PubMed

Ghosh, Preetam; Dullea, Robert; Fischer, James E; Turi, Tom G; Sarver, Ronald W; Zhang, Chaoyang; Basu, Kalyan; Das, Sajal K; Poland, Bradley W

2009-07-07

In this study, we formulate a computational reaction model following a chemical kinetic theory approach to predict the binding rate constant for the siRNA-RISC complex formation reaction. The model allowed us to study the potency difference between 2-nt 3' overhangs against blunt-ended siRNA molecules in an RNA interference (RNAi) system. The rate constant predicted by this model was fed into a stochastic simulation of the RNAi system (using the Gillespie stochastic simulator) to study the overall potency effect. We observed that the stochasticity in the transcription/translation machinery has no observable effects in the RNAi pathway. Sustained gene silencing using siRNAs can be achieved only if there is a way to replenish the dsRNA molecules in the cell. Initial findings show about 1.5 times more blunt-ended molecules will be required to keep the mRNA at the same reduced level compared to the 2-nt overhang siRNAs. However, the mRNA levels jump back to saturation after a longer time when blunt-ended siRNAs are used. We found that the siRNA-RISC complex formation reaction rate was 2 times slower when blunt-ended molecules were used pointing to the fact that the presence of the 2-nt overhangs has a greater effect on the reaction in which the bound RISC complex cleaves the mRNA.

Comparing 2-nt 3' overhangs against blunt-ended siRNAs: a systems biology based study

PubMed Central

Ghosh, Preetam; Dullea, Robert; Fischer, James E; Turi, Tom G; Sarver, Ronald W; Zhang, Chaoyang; Basu, Kalyan; Das, Sajal K; Poland, Bradley W

2009-01-01

In this study, we formulate a computational reaction model following a chemical kinetic theory approach to predict the binding rate constant for the siRNA-RISC complex formation reaction. The model allowed us to study the potency difference between 2-nt 3' overhangs against blunt-ended siRNA molecules in an RNA interference (RNAi) system. The rate constant predicted by this model was fed into a stochastic simulation of the RNAi system (using the Gillespie stochastic simulator) to study the overall potency effect. We observed that the stochasticity in the transcription/translation machinery has no observable effects in the RNAi pathway. Sustained gene silencing using siRNAs can be achieved only if there is a way to replenish the dsRNA molecules in the cell. Initial findings show about 1.5 times more blunt-ended molecules will be required to keep the mRNA at the same reduced level compared to the 2-nt overhang siRNAs. However, the mRNA levels jump back to saturation after a longer time when blunt-ended siRNAs are used. We found that the siRNA-RISC complex formation reaction rate was 2 times slower when blunt-ended molecules were used pointing to the fact that the presence of the 2-nt overhangs has a greater effect on the reaction in which the bound RISC complex cleaves the mRNA. PMID:19594876

New Complexity-Building Reactions of Alpha-Keto Esters

NASA Astrophysics Data System (ADS)

Bartlett, Samuel L.

I. Introduction: Importance of Asymmetric Catalysis and the Reactivity Patterns of alpha-Keto Esters. II. Synthesis of Complex Tertiary Glycolates by Enantioconvergent Arylation of Stereochemically Labile alpha-Keto Esters. Enantioconvergent arylation reactions of boronic acids and racemic ?-stereogenic alpha-keto esters have been developed. The reactions are catalyzed by a chiral (diene)Rh(I) complex and provide a wide array of beta-stereogenic tertiary aryl glycolate derivatives with high levels of diastereo- and enantioselectivity. Racemization studies employing a series of sterically differentiated tertiary amines suggest that the steric nature of the amine base additive exerts a significant influence on the rate of substrate racemization. III. Palladium-Catalyzed beta-Arylation of alpha-Keto Esters . A catalyst system derived from commercially available Pd2(dba) 3 and PtBu3 has been applied to the coupling of alpha-keto ester enolates and aryl bromides. The reaction provides access to an array of beta-stereogenic alpha-keto ester derivatives. When the air stable ligand precursor PtBu 3˙HBF4 is employed, the reaction can be carried out without use of a glovebox. The derived products are of broad interest given the prevalence of the alpha-keto acid substructure in biologically important molecules. IV. Catalytic Enantioselective [3+2] Cycloaddition of alpha-Keto Ester Enolates and Nitrile Oxides. An enantioselective [3+2] cycloaddition reaction between nitrile oxides and transiently generated enolates of alpha-keto esters has been developed. The catalyst system was found to be compatible with in situ nitrile oxide generation conditions. A versatile array of nitrile oxides and alpha-keto esters could participate in the cycloaddition, providing novel 5-hydroxy-2-isoxazolines in high chemical yield with high levels of diastereo- and enantioselectivity. Notably, the optimal reaction conditions circumvented concurrent reaction via O-imidoylation and hetero-[3+2] pathways.

Gas-phase chemical kinetics: Three is the magic number

NASA Astrophysics Data System (ADS)

Skodje, Rex T.

2017-11-01

Although predicted many years ago, chemically reactive termolecular reactions were thought to be unimportant in defining the behaviour of combustion systems. Now, calculations have shown that such reactions between radicals and long-lived bimolecular complexes can actually play an important role in hydrogen combustion.

Method and apparatus for purifying nucleic acids and performing polymerase chain reaction assays using an immiscible fluid

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

Koh, Chung-Yan; Light, Yooli Kim; Piccini, Matthew Ernest

Embodiments of the present invention are directed toward devices, systems, and methods for purifying nucleic acids to conduct polymerase chain reaction (PCR) assays. In one example, a method includes generating complexes of silica beads and nucleic acids in a lysis buffer, transporting the complexes through an immiscible fluid to remove interfering compounds from the complexes, further transporting the complexes into a density medium containing components required for PCR where the nucleic acids disassociate from the silica beads, and thermocycling the contents of the density medium to achieve PCR. Signal may be detected from labeling agents in the components required formore » PCR.« less

Mode Reduction and Upscaling of Reactive Transport Under Incomplete Mixing

NASA Astrophysics Data System (ADS)

Lester, D. R.; Bandopadhyay, A.; Dentz, M.; Le Borgne, T.

2016-12-01

Upscaling of chemical reactions in partially-mixed fluid environments is a challenging problem due to the detailed interactions between inherently nonlinear reaction kinetics and complex spatio-temporal concentration distributions under incomplete mixing. We address this challenge via the development of an order reduction method for the advection-diffusion-reaction equation (ADRE) via projection of the reaction kinetics onto a small number N of leading eigenmodes of the advection-diffusion operator (the so-called "strange eigenmodes" of the flow) as an N-by-N nonlinear system, whilst mixing dynamics only are projected onto the remaining modes. For simple kinetics and moderate Péclet and Damkhöler numbers, this approach yields analytic solutions for the concentration mean, evolving spatio-temporal distribution and PDF in terms of the well-mixed reaction kinetics and mixing dynamics. For more complex kinetics or large Péclet or Damkhöler numbers only a small number of modes are required to accurately quantify the mixing and reaction dynamics in terms of the concentration field and PDF, facilitating greatly simplified approximation and analysis of reactive transport. Approximate solutions of this low-order nonlinear system provide quantiative predictions of the evolving concentration PDF. We demonstrate application of this method to a simple random flow and various mass-action reaction kinetics.

Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data.

PubMed

Gu, Deqing; Jian, Xingxing; Zhang, Cheng; Hua, Qiang

2017-01-01

Genome-scale metabolic network models (GEMs) have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, most algorithms have limited capabilities with respect to directly predicting accurate genetic design for metabolic engineering. In particular, methods that predict reaction knockout strategies leading to overproduction are often impractical in terms of gene manipulations. Recently, we proposed a method named logical transformation of model (LTM) to simplify the gene-reaction associations by introducing intermediate pseudo reactions, which makes it possible to generate genetic design. Here, we propose an alternative method to relieve researchers from deciphering complex gene-reactions by adding pseudo gene controlling reactions. In comparison to LTM, this new method introduces fewer pseudo reactions and generates a much smaller model system named as gModel. We showed that gModel allows two seldom reported applications: identification of minimal genomes and design of minimal cell factories within a modified OptKnock framework. In addition, gModel could be used to integrate expression data directly and improve the performance of the E-Fmin method for predicting fluxes. In conclusion, the model transformation procedure will facilitate genetic research based on GEMs, extending their applications.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2011-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier. Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2010-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier.Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

Mixing and reactions in multiphase flow through porous media

NASA Astrophysics Data System (ADS)

Jimenez-Martinez, J.; Le Borgne, T.; Meheust, Y.; Porter, M. L.; De Anna, P.; Hyman, J.; Tabuteau, H.; Turuban, R.; Carey, J. W.; Viswanathan, H. S.

2016-12-01

The understanding and quantification of flow and transport processes in multiphase systems remains a grand scientific and engineering challenge in natural and industrial systems (e.g., soils and vadose zone, CO2 sequestration, unconventional oil and gas extraction, enhanced oil recovery). Beyond the kinetic of the chemical reactions, mixing processes in porous media play a key role in controlling both fluid-fluid and fluid-solid reactions. However, conventional continuum-scale models and theories oversimplify and/or ignore many important pore-scale processes. Multiphase flows, with the creation of highly heterogeneous fluid velocity fields (i.e., low velocities regions or stagnation zones, and high velocity regions or preferential paths), makes conservative and reactive transport more complex. We present recent multi-scale experimental developments and theoretical approaches to quantify transport, mixing, and reaction and their coupling with multiphase flows. We discuss our main findings: i) the sustained concentration gradients and enhanced reactivity in a two-phase system for a continuous injection, and the comparison with a pulse line injection; ii) the enhanced mixing by a third mobile-immiscible phase; and iii) the role that capillary forces play in the localization of the fluid-solid reactions. These experimental results are for highly-idealized geometries, however, the proposed models are related to basic porous media and unsaturated flow properties, and could be tested on more complex systems.

Scandium(III) catalysis of transimination reactions. Independent and constitutionally coupled reversible processes.

PubMed

Giuseppone, Nicolas; Schmitt, Jean-Louis; Schwartz, Evan; Lehn, Jean-Marie

2005-04-20

Sc(OTf)(3) efficiently catalyzes the self-sufficient transimination reaction between various types of C=N bonds in organic solvents, with turnover frequencies up to 3600 h(-)(1) and rate accelerations up to 6 x 10(5). The mechanism of the crossover reaction in mixtures of amines and imines is studied, comparing parallel individual reactions with coupled equilibria. The intrinsic kinetic parameters for isolated reactions cannot simply be added up when several components are mixed, and the behavior of the system agrees with the presence of a unique mediator that constitutes the core of a network of competing reactions. In mixed systems, every single amine or imine competes for the same central hub, in accordance with their binding affinity for the catalyst metal ion center. More generally, the study extends the basic principles of constitutional dynamic chemistry to interconnected chemical transformations and provides a step toward dynamic systems of increasing complexity.

Reactions of cisplatin with cysteine and methionine at constant pH; a computational study.

PubMed

Zimmermann, Tomás; Burda, Jaroslav V

2010-02-07

Interactions of hydrated cisplatin complexes cis-[Pt(NH(3))(2)Cl(H(2)O)](+) and cis-[Pt(NH(3))(2)(OH)(H(2)O)](+) with cysteine and methionine in an aqueous solution at constant pH were explored using computational methods. Thermodynamic parameters of considered reactions were studied in a broad pH range, taking up to 4 protonation states of each molecule into account. Reaction free energies at constant pH were obtained from standard Gibbs free energies using the Legendre transformation. Solvation free energies and pK(a) values were calculated using the PCM model with UAHF cavities, recently adapted by us for transition metal complexes. The root mean square error of pK(a) values on a set of model platinum complexes and amino acids was equal to 0.74. At pH 7, the transformed Gibbs free energies differ by up to 15 kcal mol(-1) from the Gibbs free energies of model reactions with a constant number of protons. As for cysteine, calculations confirmed a strong preference for kappaS monodenate bonding in a broad pH range. The most stable product of the second reaction step, which proceeds from monodentate to chelate complex, is the kappa(2)S,N coordinated chelate. The reaction with methionine is more complex. In the first step all three considered methionine donor atoms (N, S and O) are thermodynamically preferred products depending on the platinum complex and the pH. This is in accordance with the experimental observation of a pH dependent migration between N and S donor atoms in a chemically related system. The most stable chelates of platinum with methionine are kappa(2)S,N and kappa(2)N,O bonded complexes. The comparison of reaction free energies of both amino acids suggests, that the bidentate methionine ligand can be displaced even by the monodentate cysteine ligand under certain conditions.

Virtually Instantaneous, Room-temperature [11C]-Cyanation Using Biaryl Phosphine Pd(0) Complexes

PubMed Central

Lee, Hong Geun; Milner, Phillip J.; Placzek, Michael S.; Buchwald, Stephen L.; Hooker, Jacob M.

2015-01-01

A new radiosynthetic protocol for the preparation of [11C]aryl nitriles has been developed. This process is based on the direct reaction of in situ prepared L•Pd(Ar)X complexes (L=biaryl phosphine) with [11C]HCN. The strategy is operationally simple, exhibits a remarkably wide substrate scope with short reaction times, and demonstrates superior reactivity compared to previously reported systems. With this procedure, a variety of [11C]nitrile-containing pharmaceuticals were prepared with high radiochemical efficiency. PMID:25565277

[IMMUNE SYSTEM INTERNSHIP WITH SYMBIOTIC MICROORGANISMS IN GNOTOBIOTIC ANIMAL'S INTESTINUM ILEUM].

PubMed

Kochlamasashvili, B; Gogiashvili, L; Jandieri, K

2017-11-01

Structures, responsible for acceptive (comensaling relation) and protective (pathogenic defense) immunity, were studied and compared in small intestine - to ileum mucosa. Data shown, that main application of the both domains of immune system is to support the correlation between body and foreign microbes, but they response is different. Most significant differences are as follows: in acceptive reactions presented only in aseptic animals - gnotobionts, inflammatory changes absent, so immune reaction complex develops into physiological condition. Symbiotic reactions release in mucosa epithelial cells, also in cells, responsible for adaptive and congenital immune reactivity. Thus, acceptive immune reactions contribute symbiotic biocenosis versus elimination; which is function of protective immunity.

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

Nagaoka, Masataka; Core Research for Evolutional Science and Technology; ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520

A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

Controlled Ring-Opening Metathesis Polymerization by Molybdenum and Tungsten Alkylidene Complexes

DTIC Science & Technology

1988-07-29

weights and low polydispersities (as low as 1.03) consistent with a living catalyst system employing 50, 100, 200, and 400 eq of monomer. The reactions are...secondary metathesis of polymer chains Bulky alkoxide ligands Wittig-like reaction Ring-opening metathesis polymerization (ROMP) Feast monomer Cyclic...olefins Retro Diels-Alder reaction Norbornene (NBE) Low temperature column chromatography Endo-,endo-5,6-dicarbomethoxynorbornene Discrete, soluble

Hypothesized diprotomeric enzyme complex supported by stochastic modelling of palytoxin-induced Na/K pump channels

PubMed Central

Vilallonga, Gabriel D.; de Almeida, Antônio-Carlos G.; Ribeiro, Kelison T.; Campos, Sergio V. A.

2018-01-01

The sodium–potassium pump (Na+/K+ pump) is crucial for cell physiology. Despite great advances in the understanding of this ionic pumping system, its mechanism is not completely understood. We propose the use of a statistical model checker to investigate palytoxin (PTX)-induced Na+/K+ pump channels. We modelled a system of reactions representing transitions between the conformational substates of the channel with parameters, concentrations of the substates and reaction rates extracted from simulations reported in the literature, based on electrophysiological recordings in a whole-cell configuration. The model was implemented using the UPPAAL-SMC platform. Comparing simulations and probabilistic queries from stochastic system semantics with experimental data, it was possible to propose additional reactions to reproduce the single-channel dynamic. The probabilistic analyses and simulations suggest that the PTX-induced Na+/K+ pump channel functions as a diprotomeric complex in which protein–protein interactions increase the affinity of the Na+/K+ pump for PTX. PMID:29657808

Electrochemical immobilization of Fluorescent labelled probe molecules on a FTO surface for affinity detection based on photo-excited current

NASA Astrophysics Data System (ADS)

Haruyama, Tetsuya; Wakabayashi, Ryo; Cho, Takeshi; Matsuyama, Sho-taro

2011-10-01

Photo-excited current can be generated at a molecular interface between a photo-excited molecules and a semi-conductive material in appropriate condition. The system has been recognized for promoting photo-energy devices such as an organic dye sensitized solar-cell. The photo-current generated reactions are totally dependent on the interfacial energy reactions, which are in a highly fluctuated interfacial environment. The authors investigated the photo-excited current reaction to develop a smart affinity detection method. However, in order to perform both an affinity reaction and a photo-excited current reaction at a molecular interface, ordered fabrications of the functional (affinity, photo-excitation, etc.) molecules layer on a semi-conductive surface is required. In the present research, we would like to present the fabrication and functional performance of photo-excited current-based affinity assay device and its application for detection of endocrine disrupting chemicals. On the FTO surface, fluorescent pigment labelled affinity peptide was immobilized through the EC tag (electrochemical-tag) method. The modified FTO produced a current when it was irradiated with diode laser light. However, the photo current decreased drastically when estrogen (ES) coexisted in the reaction solution. In this case, immobilized affinity probe molecules formed a complex with ES and estrogen receptor (ER). The result strongly suggests that the photo-excited current transduction between probe molecule-labelled cyanine pigment and the FTO surface was partly inhibited by a complex that formed at the affinity oligo-peptide region in a probe molecule on the FTO electrode. The bound bulky complex may act as an impediment to perform smooth transduction of photo-excited current in the molecular interface. The present system is new type of photo-reaction-based analysis. This system can be used to perform simple high-sensitive homogeneous assays.

Final Technical Report: Metal—Organic Surface Catalyst for Low-temperature Methane Oxidation: Bi-functional Union of Metal—Organic Complex and Chemically Complementary Surface

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

Tait, Steven L.

Stabilization and chemical control of transition metal centers is a critical problem in the advancement of heterogeneous catalysts to next-generation catalysts that exhibit high levels of selectivity, while maintaining strong activity and facile catalyst recycling. Supported metal nanoparticle catalysts typically suffer from having a wide range of metal sites with different coordination numbers and varying chemistry. This project is exploring new possibilities in catalysis by combining features of homogeneous catalysts with those of heterogeneous catalysts to develop new, bi-functional systems. The systems are more complex than traditional heterogeneous catalysts in that they utilize sequential active sites to accomplish the desiredmore » overall reaction. The interaction of metal—organic catalysts with surface supports and their interactions with reactants to enable the catalysis of critical reactions at lower temperatures are at the focus of this study. Our work targets key fundamental chemistry problems. How do the metal—organic complexes interact with the surface? Can those metal center sites be tuned for selectivity and activity as they are in the homogeneous system by ligand design? What steps are necessary to enable a cooperative chemistry to occur and open opportunities for bi-functional catalyst systems? Study of these systems will develop the concept of bringing together the advantages of heterogeneous catalysis with those of homogeneous catalysis, and take this a step further by pursuing the objective of a bi-functional system. The use of metal-organic complexes in surface catalysts is therefore of interest to create well-defined and highly regular single-site centers. While these are not likely to be stable in the high temperature environments (> 300 °C) typical of industrial heterogeneous catalysts, they could be applied in moderate temperature reactions (100-300 °C), made feasible by lowering reaction temperatures by better catalyst control. They also serve as easily tuned model systems for exploring the chemistry of single-site transition metals and tandem catalysts that could then be developed into a zeolite or other stable support structures. In this final technical report, three major advances our described that further these goals. The first is a study demonstrating the ability to tune the oxidation state of V single-site centers on a surface by design of the surrounding ligand field. The synthesis of the single-site centers was developed in a previous reporting period of this project and this new advance shows a distinct new ability of the systems to have a designed oxidation state of the metal center. Second, we demonstrate metal complexation at surfaces using vibrational spectroscopy and also show a metal replacement reaction on Ag surfaces. Third, we demonstrate a surface-catalyzed dehydrocyclization reaction important for metal-organic catalyst design at surfaces.« less

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

NASA Astrophysics Data System (ADS)

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.

Theorems and application of local activity of CNN with five state variables and one port.

PubMed

Xiong, Gang; Dong, Xisong; Xie, Li; Yang, Thomas

2012-01-01

Coupled nonlinear dynamical systems have been widely studied recently. However, the dynamical properties of these systems are difficult to deal with. The local activity of cellular neural network (CNN) has provided a powerful tool for studying the emergence of complex patterns in a homogeneous lattice, which is composed of coupled cells. In this paper, the analytical criteria for the local activity in reaction-diffusion CNN with five state variables and one port are presented, which consists of four theorems, including a serial of inequalities involving CNN parameters. These theorems can be used for calculating the bifurcation diagram to determine or analyze the emergence of complex dynamic patterns, such as chaos. As a case study, a reaction-diffusion CNN of hepatitis B Virus (HBV) mutation-selection model is analyzed and simulated, the bifurcation diagram is calculated. Using the diagram, numerical simulations of this CNN model provide reasonable explanations of complex mutant phenomena during therapy. Therefore, it is demonstrated that the local activity of CNN provides a practical tool for the complex dynamics study of some coupled nonlinear systems.

A parallel reaction-transport model applied to cement hydration and microstructure development

NASA Astrophysics Data System (ADS)

Bullard, Jeffrey W.; Enjolras, Edith; George, William L.; Satterfield, Steven G.; Terrill, Judith E.

2010-03-01

A recently described stochastic reaction-transport model on three-dimensional lattices is parallelized and is used to simulate the time-dependent structural and chemical evolution in multicomponent reactive systems. The model, called HydratiCA, uses probabilistic rules to simulate the kinetics of diffusion, homogeneous reactions and heterogeneous phenomena such as solid nucleation, growth and dissolution in complex three-dimensional systems. The algorithms require information only from each lattice site and its immediate neighbors, and this localization enables the parallelized model to exhibit near-linear scaling up to several hundred processors. Although applicable to a wide range of material systems, including sedimentary rock beds, reacting colloids and biochemical systems, validation is performed here on two minerals that are commonly found in Portland cement paste, calcium hydroxide and ettringite, by comparing their simulated dissolution or precipitation rates far from equilibrium to standard rate equations, and also by comparing simulated equilibrium states to thermodynamic calculations, as a function of temperature and pH. Finally, we demonstrate how HydratiCA can be used to investigate microstructure characteristics, such as spatial correlations between different condensed phases, in more complex microstructures.

2010 Precision Strike Annual Review Held in Springfield, Virginia on April 20-21, 2010

DTIC Science & Technology

2010-04-21

Reaction Technology Office Fogg (Acting) Director, Rapid Fielding Wyatt PD - Riley Program Oversight Dipetto Program Guidance And Assessment TBD Director...warfighters Joint Rapid Acquisition Cell Mr Thomas P Dee Complex Systems Dr Charles W Perkins Rapid Reaction Technology Office Mr Glenn A Fogg (Acting

The kinetics of thermal generation of flavour.

PubMed

Parker, Jane K

2013-01-01

Control and optimisation of flavour is the ultimate challenge for the food and flavour industry. The major route to flavour formation during thermal processing is the Maillard reaction, which is a complex cascade of interdependent reactions initiated by the reaction between a reducing sugar and an amino compound. The complexity of the reaction means that researchers turn to kinetic modelling in order to understand the control points of the reaction and to manipulate the flavour profile. Studies of the kinetics of flavour formation have developed over the past 30 years from single- response empirical models of binary aqueous systems to sophisticated multi-response models in food matrices, based on the underlying chemistry, with the power to predict the formation of some key aroma compounds. This paper discusses in detail the development of kinetic models of thermal generation of flavour and looks at the challenges involved in predicting flavour. Copyright © 2012 Society of Chemical Industry.

Coding the Assembly of Polyoxotungstates with a Programmable Reaction System.

PubMed

Ruiz de la Oliva, Andreu; Sans, Victor; Miras, Haralampos N; Long, De-Liang; Cronin, Leroy

2017-05-01

Chemical transformations are normally conducted in batch or flow mode, thereby allowing the chemistry to be temporally or spatially controlled, but these approaches are not normally combined dynamically. However, the investigation of the underlying chemistry masked by the self-assembly processes that often occur in one-pot reactions and exploitation of the potential of complex chemical systems requires control in both time and space. Additionally, maintaining the intermediate constituents of a self-assembled system "off equilibrium" and utilizing them dynamically at specific time intervals provide access to building blocks that cannot coexist under one-pot conditions and ultimately to the formation of new clusters. Herein, we implement the concept of a programmable networked reaction system, allowing us to connect discrete "one-pot" reactions that produce the building block{W 11 O 38 } ≡ {W 11 } under different conditions and control, in real time, the assembly of a series of polyoxometalate clusters {W 12 O 42 } ≡ {W 12 }, {W 22 O 74 } ≡ {W 22 } 1a, {W 34 O 116 } ≡ {W 34 } 2a, and {W 36 O 120 } ≡ {W 36 } 3a, using pH and ultraviolet-visible monitoring. The programmable networked reaction system reveals that is possible to assemble a range of different clusters using {W 11 }-based building blocks, demonstrating the relationship between the clusters within the family of iso-polyoxotungstates, with the final structural motif being entirely dependent on the building block libraries generated in each separate reaction space within the network. In total, this approach led to the isolation of five distinct inorganic clusters using a "fixed" set of reagents and using a fully automated sequence code, rather than five entirely different reaction protocols. As such, this approach allows us to discover, record, and implement complex one-pot reaction syntheses in a more general way, increasing the yield and reproducibility and potentially giving access to nonspecialists.

Coding the Assembly of Polyoxotungstates with a Programmable Reaction System

PubMed Central

2017-01-01

Chemical transformations are normally conducted in batch or flow mode, thereby allowing the chemistry to be temporally or spatially controlled, but these approaches are not normally combined dynamically. However, the investigation of the underlying chemistry masked by the self-assembly processes that often occur in one-pot reactions and exploitation of the potential of complex chemical systems requires control in both time and space. Additionally, maintaining the intermediate constituents of a self-assembled system “off equilibrium” and utilizing them dynamically at specific time intervals provide access to building blocks that cannot coexist under one-pot conditions and ultimately to the formation of new clusters. Herein, we implement the concept of a programmable networked reaction system, allowing us to connect discrete “one-pot” reactions that produce the building block{W11O38} ≡ {W11} under different conditions and control, in real time, the assembly of a series of polyoxometalate clusters {W12O42} ≡ {W12}, {W22O74} ≡ {W22} 1a, {W34O116} ≡ {W34} 2a, and {W36O120} ≡ {W36} 3a, using pH and ultraviolet–visible monitoring. The programmable networked reaction system reveals that is possible to assemble a range of different clusters using {W11}-based building blocks, demonstrating the relationship between the clusters within the family of iso-polyoxotungstates, with the final structural motif being entirely dependent on the building block libraries generated in each separate reaction space within the network. In total, this approach led to the isolation of five distinct inorganic clusters using a “fixed” set of reagents and using a fully automated sequence code, rather than five entirely different reaction protocols. As such, this approach allows us to discover, record, and implement complex one-pot reaction syntheses in a more general way, increasing the yield and reproducibility and potentially giving access to nonspecialists. PMID:28414229

A new initiating system based on [(SiMes)Ru(PPh3)(Ind)Cl2] combined with azo-bis-isobutyronitrile in the polymerization and copolymerization of styrene and methyl methacrylate.

PubMed

Al-Majid, Abdullah M; Shamsan, Waseem Sharaf; Al-Odayn, Abdel-Basit Mohammed; Nahra, Fady; Aouak, Taieb; Nolan, Steven P

2017-01-01

The homopolymerization and copolymerization of styrene and methyl methacrylate, initiated for the first time by the combination of azo-bis-isobutyronitrile (AIBN) with [(SiMes)Ru(PPh 3 )(Ind)Cl 2 ] complex. The reactions were successfully carried out, on a large scale, in presence this complex at 80 °C. It was concluded from the data obtained that the association of AIBN with the ruthenium complex reduces considerably the transfer reactions and leads to the controlled radical polymerization and the well-defined polymers.

Dynamics of localized structures in reaction-diffusion systems induced by delayed feedback

NASA Astrophysics Data System (ADS)

Gurevich, Svetlana V.

2013-05-01

We are interested in stability properties of a single localized structure in a three-component reaction-diffusion system subjected to the time-delayed feedback. We shall show that variation in the product of the delay time and the feedback strength leads to complex dynamical behavior of the system, including formation of target patterns, spontaneous motion, and spontaneous breathing as well as various complex structures, arising from combination of different oscillatory instabilities. In the case of spontaneous motion, we provide a bifurcation analysis of the delayed system and derive an order parameter equation for the position of the localized structure, explicitly describing its temporal evolution in the vicinity of the bifurcation point. This equation is a subject to a nonlinear delay differential equation, which can be transformed to the normal form of the pitchfork drift bifurcation.

System and process for pulsed multiple reaction monitoring

DOEpatents

Belov, Mikhail E

2013-05-17

A new pulsed multiple reaction monitoring process and system are disclosed that uses a pulsed ion injection mode for use in conjunction with triple-quadrupole instruments. The pulsed injection mode approach reduces background ion noise at the detector, increases amplitude of the ion signal, and includes a unity duty cycle that provides a significant sensitivity increase for reliable quantitation of proteins/peptides present at attomole levels in highly complex biological mixtures.

Molnets: An Artificial Chemistry Based on Neural Networks

NASA Technical Reports Server (NTRS)

Colombano, Silvano; Luk, Johnny; Segovia-Juarez, Jose L.; Lohn, Jason; Clancy, Daniel (Technical Monitor)

2002-01-01

The fundamental problem in the evolution of matter is to understand how structure-function relationships are formed and increase in complexity from the molecular level all the way to a genetic system. We have created a system where structure-function relationships arise naturally and without the need of ad hoc function assignments to given structures. The idea was inspired by neural networks, where the structure of the net embodies specific computational properties. In this system networks interact with other networks to create connections between the inputs of one net and the outputs of another. The newly created net then recomputes its own synaptic weights, based on anti-hebbian rules. As a result some connections may be cut, and multiple nets can emerge as products of a 'reaction'. The idea is to study emergent reaction behaviors, based on simple rules that constitute a pseudophysics of the system. These simple rules are parameterized to produce behaviors that emulate chemical reactions. We find that these simple rules show a gradual increase in the size and complexity of molecules. We have been building a virtual artificial chemistry laboratory for discovering interesting reactions and for testing further ideas on the evolution of primitive molecules. Some of these ideas include the potential effect of membranes and selective diffusion according to molecular size.

Formation, aggregation and reactivity of amorphous ferric oxyhydroxides on dissociation of Fe(III)-organic complexes in dilute aqueous suspensions

NASA Astrophysics Data System (ADS)

Bligh, Mark W.; Waite, T. David

2010-10-01

While chemical reactions that take place at the surface of amorphous ferric oxides (AFO) are known to be important in aquatic systems, incorporation of these reactions into kinetic models is hindered by a lack of ability to reliably quantify the reactivity of the surface and the changes in reactivity that occur over time. Long term decreases in the reactivity of iron oxides may be considered to result from changes in the molecular structure of the solid, however, over shorter time scales where substantial aggregation may occur, the mechanisms of reactivity loss are less clear. Precipitation of AFO may be described as a combination of homogeneous and heterogeneous reactions, however, despite its potentially significant role, the latter reaction is usually neglected in kinetic models of aquatic processes. Here, we investigate the role of AFO in scavenging dissolved inorganic ferric (Fe(III)) species (Fe') via the heterogeneous precipitation reaction during the net dissociation of organically complexed Fe(III) in seawater. Using sulfosalicylic acid (SSA) as a model ligand, AFO was shown to play a significant role in inducing the net dissociation of the Fe-SSA complexes with equations describing both the heterogeneous precipitation reaction and the aging of AFO being required to adequately describe the experimental data. An aggregation based mechanism provided a good description of AFO aging over the short time scale of the experiments. The behaviour of AFO described here has implications for the bioavailability of iron in natural systems as a result of reactions involving AFO which are recognised to occur over time scales of minutes, including adsorption of Fe' and AFO dissolution, precipitation and ageing.

Sites of superoxide and hydrogen peroxide production during fatty acid oxidation in rat skeletal muscle mitochondria

PubMed Central

Perevoshchikova, Irina V.; Quinlan, Casey L.; Orr, Adam L.; Gerencser, Akos A.; Brand, Martin D.

2013-01-01

H2O2 production by skeletal muscle mitochondria oxidizing palmitoylcarnitine was examined under two conditions: the absence of respiratory chain inhibitors and the presence of myxothiazol to inhibit complex III. Without inhibitors, respiration and H2O2 production were low unless carnitine or malate was added to limit acetyl-CoA accumulation. With palmitoylcarnitine alone, H2O2 production was dominated by complex II (44% from site IIF in the forward reaction); the remainder was mostly from complex I (34%, superoxide from site IF). With added carnitine, H2O2 production was about equally shared between complexes I, II, and III. With added malate, it was 75% from complex III (superoxide from site IIIQo) and 25% from site IF. Thus complex II (site IIF in the forward reaction) is a major source of H2O2 production during oxidation of palmitoylcarnitine ± carnitine. Under the second condition (myxothiazol present to keep ubiquinone reduced), the rates of H2O2 production were highest in the presence of palmitoylcarnitine ± carnitine and were dominated by complex II (site IIF in the reverse reaction). About half the rest was from site IF, but a significant portion, ~40 pmol H2O2 · min−1 · mg protein−1, was not from complex I, II, or III and was attributed to the proteins of β-oxidation (electron-transferring flavoprotein (ETF) and ETF-ubiquinone oxidoreductase). The maximum rate from the ETF system was ~200 pmol H2O2 · min−1 ~ mg protein−1 under conditions of compromised antioxidant defense and reduced ubiqui-none pool. Thus complex II and the ETF system both contribute to H2O2 production during fatty acid oxidation under appropriate conditions. PMID:23583329

Cycloaddition Reactions of Cobalt-Complexed Macrocyclic Alkynes: The Transannular Pauson-Khand Reaction.

PubMed

Karabiyikoglu, Sedef; Boon, Byron A; Merlic, Craig A

2017-08-04

The Pauson-Khand reaction is a powerful tool for the synthesis of cyclopentenones through the efficient [2 + 2 + 1] cycloaddition of dicobalt alkyne complexes with alkenes. While intermolecular and intramolecular variants are widely known, transannular versions of this reaction are unknown and the basis of this study. Macrocyclic enyne and dienyne complexes were readily synthesized by palladium(II)-catalyzed oxidative macrocyclizations of bis(vinyl boronate esters) or ring-closing metathesis reactions followed by complexation with dicobalt octacarbonyl. Several reaction modalities of these macrocyclic complexes were uncovered. In addition to the first successful transannular Pauson-Khand reactions, other intermolecular and transannular cycloaddition reactions included intermolecular Pauson-Khand reactions, transannular [4 + 2] cycloaddition reactions, intermolecular [2 + 2 + 2] cycloaddition reactions, and intermolecular [2 + 2 + 1 + 1] cycloaddition reactions. The structural and reaction requirements for each process are presented.

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

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

Burke, Michael P.; Goldsmith, C. Franklin; Klippenstein, Stephen J.

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 andmore » 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 model provides a consistent quantitative explanation of both ab initio calculations and time-resolved species measurements. The present results show that interpretations of OH measurements are significantly more complicated than previously thought – in addition to barrier heights for key transition states considered previously, OH profiles also depend on additional theoretical parameters for R + O2 reactions, secondary reactions, QOOH + O2 reactions, and treatment of non-Boltzmann reaction sequences. Extraction of physically rigorous information from those measurements may require more sophisticated treatment of all of those model aspects, as well as additional experimental data under more conditions, to discriminate among possible interpretations and ensure model reliability. Keywords: Optimization, Uncertainty quantification, Chemical mechanism, Low-Temperature Oxidation, Non-Boltzmann« less

Generative complexity of Gray-Scott model

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2018-03-01

In the Gray-Scott reaction-diffusion system one reactant is constantly fed in the system, another reactant is reproduced by consuming the supplied reactant and also converted to an inert product. The rate of feeding one reactant in the system and the rate of removing another reactant from the system determine configurations of concentration profiles: stripes, spots, waves. We calculate the generative complexity-a morphological complexity of concentration profiles grown from a point-wise perturbation of the medium-of the Gray-Scott system for a range of the feeding and removal rates. The morphological complexity is evaluated using Shannon entropy, Simpson diversity, approximation of Lempel-Ziv complexity, and expressivity (Shannon entropy divided by space-filling). We analyse behaviour of the systems with highest values of the generative morphological complexity and show that the Gray-Scott systems expressing highest levels of the complexity are composed of the wave-fragments (similar to wave-fragments in sub-excitable media) and travelling localisations (similar to quasi-dissipative solitons and gliders in Conway's Game of Life).

Real-time monitoring of enzyme-free strand displacement cascades by colorimetric assays.

PubMed

Duan, Ruixue; Wang, Boya; Hong, Fan; Zhang, Tianchi; Jia, Yongmei; Huang, Jiayu; Hakeem, Abdul; Liu, Nannan; Lou, Xiaoding; Xia, Fan

2015-03-19

The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications.

Definitions of Complexity are Notoriously Difficult

NASA Astrophysics Data System (ADS)

Schuster, Peter

Definitions of complexity are notoriously difficult if not impossible at all. A good working hypothesis might be: Everything is complex that is not simple. This is precisely the way in which we define nonlinear behavior. Things appear complex for different reasons: i) Complexity may result from lack of insight, ii) complexity may result from lack of methods, and (iii) complexity may be inherent to the system. The best known example for i) is celestial mechanics: The highly complex Pythagorean epicycles become obsolete by the introduction of Newton's law of universal gravitation. To give an example for ii), pattern formation and deterministic chaos became not really understandable before extensive computer simulations became possible. Cellular metabolism may serve as an example for iii) and is caused by the enormous complexity of biochemical reaction networks with up to one hundred individual reaction fluxes. Nevertheless, only few fluxes are dominant in the sense that using Pareto optimal values for them provides near optimal values for all the others...

Determination of equilibrium and rate constants for complex formation by fluorescence correlation spectroscopy supplemented by dynamic light scattering and Taylor dispersion analysis.

PubMed

Zhang, Xuzhu; Poniewierski, Andrzej; Jelińska, Aldona; Zagożdżon, Anna; Wisniewska, Agnieszka; Hou, Sen; Hołyst, Robert

2016-10-04

The equilibrium and rate constants of molecular complex formation are of great interest both in the field of chemistry and biology. Here, we use fluorescence correlation spectroscopy (FCS), supplemented by dynamic light scattering (DLS) and Taylor dispersion analysis (TDA), to study the complex formation in model systems of dye-micelle interactions. In our case, dyes rhodamine 110 and ATTO-488 interact with three differently charged surfactant micelles: octaethylene glycol monododecyl ether C 12 E 8 (neutral), cetyltrimethylammonium chloride CTAC (positive) and sodium dodecyl sulfate SDS (negative). To determine the rate constants for the dye-micelle complex formation we fit the experimental data obtained by FCS with a new form of the autocorrelation function, derived in the accompanying paper. Our results show that the association rate constants for the model systems are roughly two orders of magnitude smaller than those in the case of the diffusion-controlled limit. Because the complex stability is determined by the dissociation rate constant, a two-step reaction mechanism, including the diffusion-controlled and reaction-controlled rates, is used to explain the dye-micelle interaction. In the limit of fast reaction, we apply FCS to determine the equilibrium constant from the effective diffusion coefficient of the fluorescent components. Depending on the value of the equilibrium constant, we distinguish three types of interaction in the studied systems: weak, intermediate and strong. The values of the equilibrium constant obtained from the FCS and TDA experiments are very close to each other, which supports the theoretical model used to interpret the FCS data.

Reactions of monodithiolene tungsten(VI) sulfido complexes with copper(I) in relation to the structure of the active site of carbon monoxide dehydrogenase.

PubMed

Groysman, Stanislav; Majumdar, Amit; Zheng, Shao-Liang; Holm, R H

2010-02-01

Reactions directed at the synthesis of structural analogues of the active site of molybdenum-containing carbon monoxide dehydrogenase have been investigated utilizing [WO(2)S(bdt)](2-) (1) and [WOS(2)(bdt)](2-) (2) and sterically hindered [Cu(R)L] or [Cu(SSiR'(3))(2)](-) as reactants. All successful reactions of 2 afford the binuclear W(VI)/Cu(I) products [WO(bdt)(mu(2)-S)(2)Cu(L)](2-/-) with L = carbene (3), Ar*S (4), Ar* (7), SSiR(3) (R = Ph (5), Pr(i) (6)). Similarly, [W(bdt)(OSiPh(3))S(2)](-) leads to [W(bdt)(OSiPh(3))(mu(2)-S)(2)Cu(SAr*)](-) (8). These complexes, with apical oxo and basal dithiolato and sulfido coordination (excluding 8), terminal thiolate ligation at Cu(I) (4-6, 8), and W-(mu(2)-S)-Cu bridging, bear a structural resemblance to the enzyme site. Differences include two bridges instead of one and the absence of basal oxo/hydroxo ligation. Complex 8 differs from the others by utilizing apical and basal sulfido ligands in bridge formation. Related reaction systems based on 1 gave 4 in small yield or product mixtures in which the desired monobridged complex [WO(2)(bdt)(mu(2)-S)Cu(R)](2-) was not detected. Mass spectrometric analysis of the reaction system with L = carbene suggests that any monobridged species forms may converted to the dibridged form by disproportionation. In these experiments, the use of W(VI) preserves the structural integrity of Mo(VI), whose analogues of 1 and 2 have not been isolated. (Ar* = 2,6-bis(2,4,6-triisopropylphenyl)phenyl, bdt = benzene-1,2-dithiolate(2-)).

Probing ‘Spin-Forbidden’ Oxygen Atom Transfer: Gas-Phase Reactions of Chromium-Porphyrin Complexes

PubMed Central

Fornarini, Simonetta; Lanucara, Francesco; Warren, Jeffrey J.

2010-01-01

Oxygen-atom transfer reactions of metalloporphyrin species play an important role in biochemical and synthetic oxidation reactions. An emerging theme in this chemistry is that spin-state changes can play important roles, and a ‘two-state’ reactivity model has been extensively applied especially in iron-porphyrin systems. Herein we explore the gas phase oxygen-atom transfer chemistry of meso-tetrakis(pentafluorophenyl)porphyrin (TPFPP) chromium complexes, as well as some other tetradentate macrocyclic ligands. Electrospray ionization in concert with Fourier transform ion cyclotron resonance (FT-ICR) spectrometry has been used to characterize and observe reactivity of the ionic species [(TPFPP)CrIII]+ (1) and [(TPFPP)CrVO]+ (2). These are an attractive system to examine the effects of spin state change on oxygen atom transfer because the d1 CrV species are doublets while the CrIII complexes have quartet ground states with high-lying doublet excited states. In the gas phase, [(TPFPP)CrIII]+ forms adducts with a variety of neutral donors but O-atom transfer is only observed for NO2. Pyridine N-oxide adducts of 1 do yield 2 upon collision induced dissociation (CID), but the ethylene oxide, DMSO, and TEMPO analogs do not. [(TPFPP)CrVO]+ is shown by its reactivity and by CID experiments to be a terminal metal-oxo with a single vacant coordination site. It also displays limited reaction chemistry, being deoxygenated only by the very potent reductant P(OMe)3. In general, [(TPFPP)CrVO]+ species are much less reactive than the Fe and Mn analogs. Thermochemical analysis of the reactions points towards the involvement of spin issues in the lower observed reactivity of the chromium complexes. PMID:20218631

A continuous-exchange cell-free protein synthesis system based on extracts from cultured insect cells.

PubMed

Stech, Marlitt; Quast, Robert B; Sachse, Rita; Schulze, Corina; Wüstenhagen, Doreen A; Kubick, Stefan

2014-01-01

In this study, we present a novel technique for the synthesis of complex prokaryotic and eukaryotic proteins by using a continuous-exchange cell-free (CECF) protein synthesis system based on extracts from cultured insect cells. Our approach consists of two basic elements: First, protein synthesis is performed in insect cell lysates which harbor endogenous microsomal vesicles, enabling a translocation of de novo synthesized target proteins into the lumen of the insect vesicles or, in the case of membrane proteins, their embedding into a natural membrane scaffold. Second, cell-free reactions are performed in a two chamber dialysis device for 48 h. The combination of the eukaryotic cell-free translation system based on insect cell extracts and the CECF translation system results in significantly prolonged reaction life times and increased protein yields compared to conventional batch reactions. In this context, we demonstrate the synthesis of various representative model proteins, among them cytosolic proteins, pharmacological relevant membrane proteins and glycosylated proteins in an endotoxin-free environment. Furthermore, the cell-free system used in this study is well-suited for the synthesis of biologically active tissue-type-plasminogen activator, a complex eukaryotic protein harboring multiple disulfide bonds.

A Continuous-Exchange Cell-Free Protein Synthesis System Based on Extracts from Cultured Insect Cells

PubMed Central

Stech, Marlitt; Quast, Robert B.; Sachse, Rita; Schulze, Corina; Wüstenhagen, Doreen A.; Kubick, Stefan

2014-01-01

In this study, we present a novel technique for the synthesis of complex prokaryotic and eukaryotic proteins by using a continuous-exchange cell-free (CECF) protein synthesis system based on extracts from cultured insect cells. Our approach consists of two basic elements: First, protein synthesis is performed in insect cell lysates which harbor endogenous microsomal vesicles, enabling a translocation of de novo synthesized target proteins into the lumen of the insect vesicles or, in the case of membrane proteins, their embedding into a natural membrane scaffold. Second, cell-free reactions are performed in a two chamber dialysis device for 48 h. The combination of the eukaryotic cell-free translation system based on insect cell extracts and the CECF translation system results in significantly prolonged reaction life times and increased protein yields compared to conventional batch reactions. In this context, we demonstrate the synthesis of various representative model proteins, among them cytosolic proteins, pharmacological relevant membrane proteins and glycosylated proteins in an endotoxin-free environment. Furthermore, the cell-free system used in this study is well-suited for the synthesis of biologically active tissue-type-plasminogen activator, a complex eukaryotic protein harboring multiple disulfide bonds. PMID:24804975

Simulation of anaerobic digestion processes using stochastic algorithm.

PubMed

Palanichamy, Jegathambal; Palani, Sundarambal

2014-01-01

The Anaerobic Digestion (AD) processes involve numerous complex biological and chemical reactions occurring simultaneously. Appropriate and efficient models are to be developed for simulation of anaerobic digestion systems. Although several models have been developed, mostly they suffer from lack of knowledge on constants, complexity and weak generalization. The basis of the deterministic approach for modelling the physico and bio-chemical reactions occurring in the AD system is the law of mass action, which gives the simple relationship between the reaction rates and the species concentrations. The assumptions made in the deterministic models are not hold true for the reactions involving chemical species of low concentration. The stochastic behaviour of the physicochemical processes can be modeled at mesoscopic level by application of the stochastic algorithms. In this paper a stochastic algorithm (Gillespie Tau Leap Method) developed in MATLAB was applied to predict the concentration of glucose, acids and methane formation at different time intervals. By this the performance of the digester system can be controlled. The processes given by ADM1 (Anaerobic Digestion Model 1) were taken for verification of the model. The proposed model was verified by comparing the results of Gillespie's algorithms with the deterministic solution for conversion of glucose into methane through degraders. At higher value of 'τ' (timestep), the computational time required for reaching the steady state is more since the number of chosen reactions is less. When the simulation time step is reduced, the results are similar to ODE solver. It was concluded that the stochastic algorithm is a suitable approach for the simulation of complex anaerobic digestion processes. The accuracy of the results depends on the optimum selection of tau value.

ECUT: Energy Conversion and Utilization Technologies program. Heterogeneous catalysis modeling program concept

NASA Technical Reports Server (NTRS)

Voecks, G. E.

1983-01-01

Insufficient theoretical definition of heterogeneous catalysts is the major difficulty confronting industrial suppliers who seek catalyst systems which are more active, selective, and stable than those currently available. In contrast, progress was made in tailoring homogeneous catalysts to specific reactions because more is known about the reaction intermediates promoted and/or stabilized by these catalysts during the course of reaction. However, modeling heterogeneous catalysts on a microscopic scale requires compiling and verifying complex information on reaction intermediates and pathways. This can be achieved by adapting homogeneous catalyzed reaction intermediate species, applying theoretical quantum chemistry and computer technology, and developing a better understanding of heterogeneous catalyst system environments. Research in microscopic reaction modeling is now at a stage where computer modeling, supported by physical experimental verification, could provide information about the dynamics of the reactions that will lead to designing supported catalysts with improved selectivity and stability.

Non-covalent and coordination interactions in Cu(II) systems with uridine, uridine 5'-monophosphate and triamine or tetramine as biogenic amine analogues in aqueous solutions.

PubMed

Łomozik, Lechosław; Jastrzab, Renata

2003-10-01

Reactions of metallation and non-covalent interactions have been studied in ternary systems of Cu(II) ions with uridine, uridine 5'-monophosphate and diamines or triamines. It has been found that in metal-free systems the reaction centres of the nucleoside with the polyamine are the donor nitrogen atoms N(3) and protonated -NH(x) groups of the amines. In comparison to systems with adenosine or cytidine, the pH range of complex formation is shifted towards higher values. It is a consequence of significantly higher basicity of uridine and in agreement with the ion-ion, ion-dipole interaction model assumed. Formation of molecular complexes of uridine 5'-monophosphate with polyamines at a low pH is the result of activity of the phosphate group which plays the role of a negatively charged reaction site. Non-covalent interactions interfere in processes of bioligand metallation. Centres of weak interactions are simultaneously binding sites of metal ions. In protonated Cu(Urd)(PA)H(x) complexes, coordination has been found to involve the N(3) atom from the nucleoside and two donor nitrogen atoms from the polyamine (PA). In the heteroligand species Cu(Urd)(PA), despite deprotonation of all amine groups, one of these groups is located outside the inner coordination sphere. In complexes with uridine-5'-monophosphate, the phosphate group is active in metallation. Moreover, in certain coordination compounds this group is engaged in non-covalent interactions with PA molecules, despite binding Cu ions, as has been shown on the basis of equilibrium and spectral studies.

Antenna complexes protect Photosystem I from Photoinhibition

PubMed Central

Alboresi, Alessandro; Ballottari, Matteo; Hienerwadel, Rainer; Giacometti, Giorgio M; Morosinotto, Tomas

2009-01-01

Background Photosystems are composed of two moieties, a reaction center and a peripheral antenna system. In photosynthetic eukaryotes the latter system is composed of proteins belonging to Lhc family. An increasing set of evidences demonstrated how these polypeptides play a relevant physiological function in both light harvesting and photoprotection. Despite the sequence similarity between antenna proteins associated with the two Photosystems, present knowledge on their physiological role is mostly limited to complexes associated to Photosystem II. Results In this work we analyzed the physiological role of Photosystem I antenna system in Arabidopsis thaliana both in vivo and in vitro. Plants depleted in individual antenna polypeptides showed a reduced capacity for photoprotection and an increased production of reactive oxygen species upon high light exposure. In vitro experiments on isolated complexes confirmed that depletion of antenna proteins reduced the resistance of isolated Photosystem I particles to high light and that the antenna is effective in photoprotection only upon the interaction with the core complex. Conclusion We show that antenna proteins play a dual role in Arabidopsis thaliana Photosystem I photoprotection: first, a Photosystem I with an intact antenna system is more resistant to high light because of a reduced production of reactive oxygen species and, second, antenna chlorophyll-proteins are the first target of high light damages. When photoprotection mechanisms become insufficient, the antenna chlorophyll proteins act as fuses: LHCI chlorophylls are degraded while the reaction center photochemical activity is maintained. Differences with respect to photoprotection strategy in Photosystem II, where the reaction center is the first target of photoinhibition, are discussed. PMID:19508723

Sensitivity and network topology in chemical reaction systems

NASA Astrophysics Data System (ADS)

Okada, Takashi; Mochizuki, Atsushi

2017-08-01

In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses to enzyme perturbations only from network topology, and then proved a theorem, called the law of localization, explaining response patterns in terms of network topology. In this paper, we generalize these results to reaction networks with conserved concentrations, which allows us to study any reaction system. We also propose network characteristics quantifying robustness. We compare E. coli metabolic network with randomly rewired networks, and find that the robustness of the E. coli network is significantly higher than that of the random networks.

Strategies and Rubrics for Teaching Complex Systems Theory to Novices (Invited)

NASA Astrophysics Data System (ADS)

Fichter, L. S.

2010-12-01

Bifurcation. Self-similarity. Fractal. Sensitive dependent. Agents. Self-organized criticality. Avalanche behavior. Power laws. Strange attractors. Emergence. The language of complexity is fundamentally different from the language of equilibrium. If students do not know these phenomena, and what they tell us about the pulse of dynamic systems, complex systems will be opaque. A complex system is a group of agents. (individual interacting units, like birds in a flock, sand grains in a ripple, or individual friction units along a fault zone), existing far from equilibrium, interacting through positive and negative feedbacks, following simple rules, forming interdependent, dynamic, evolutionary networks. Complex systems produce behaviors that cannot be predicted deductively from knowledge of the behaviors of the individual components themselves; they must be experienced. What complexity theory demonstrates is that, by following simple rules, all the agents end up coordinating their behavior—self organizing—so that what emerges is not chaos, but meaningful patterns. How can we introduce Freshman, non-science, general education students to complex systems theories, in 3 to 5 classes; in a way they really get it, and can use the principles to understand real systems? Complex systems theories are not a series of unconnected or disconnected equations or models; they are developed as narratives that makes sense of how all the pieces and properties are interrelated. The principles of complex systems must be taught as deliberately and systematically as the equilibrium principles normally taught; as, say, the systematic training from pre-algebra and geometry to algebra. We have developed a sequence of logically connected narratives (strategies and rubrics) that introduce complex systems principles using models that can be simulated in a computer, in class, in real time. The learning progression has a series of 12 models (e.g. logistic system, bifurcation diagrams, genetic algorithms, etc.) leading to 19 learning outcomes that encompass most of the universality properties that characterize complex systems. They are developed in a specific order to achieve specific ends of understanding. We use these models in various depths and formats in courses ranging from gened courses, to evolutionary systems and environmental systems, to upper level geology courses. Depending on the goals of a course, the learning outcomes can be applied to understanding many other complex systems; e.g. oscillating chemical reactions (reaction-diffusion and activator-inhibitor systems), autocatalytic networks, hysteresis (bistable) systems, networks, and the rise/collapse of complex societies. We use these and other complex systems concepts in various classes to talk about the origin of life, ecosystem organization, game theory, extinction events, and environmental system behaviors. The applications are almost endless. The complete learning progression with models, computer programs, experiments, and learning outcomes is available at: www.jmu.edu/geology/ComplexEvolutionarySystems/

Reaction Analysis of Shocked Nitromethane using Extended Lagrangian Born-Oppenheimer Molecular Dynamics

NASA Astrophysics Data System (ADS)

Perriot, Romain; Kober, Ed; Mniszewski, Sue; Martinez, Enrique; Niklasson, Anders; Yang, Ping; McGrane, Shawn; Cawkwell, Marc

2017-06-01

Characterizing the complex, rapid reactions of energetic materials under conditions of high temperatures and pressures presents strong experimental and computational challenges. The recently developed extended Lagrangian Born-Oppenheimer molecular dynamics formalism enables the long-term conservation of the total energy in microcanonical trajectories, and using a density functional tight binding formulation provides good chemical accuracy. We use this combined approach to study the evolution of temperature, pressure, and chemical species in shock-compressed liquid nitromethane over hundreds of picoseconds. The chemical species seen in nitromethane under shock compression are compared with those seen under static high temperature conditions. A reduced-order representation of the complex sequence of chemical reactions that characterize this system has been developed from the molecular dynamics simulations by focusing on classes of chemical reactions rather than specific molecular species. Time-resolved infra-red vibrational spectra were also computed from the molecular trajectories and compared to the chemical analysis. These spectra provide a time history of the species present in the system that can be compared directly with recent experiments at LANL.

Approximate Matching as a Key Technique in Organization of Natural and Artificial Intelligence

NASA Technical Reports Server (NTRS)

Mack, Marilyn; Lapir, Gennadi M.; Berkovich, Simon

2000-01-01

The basic property of an intelligent system, natural or artificial, is "understanding". We consider the following formalization of the idea of "understanding" among information systems. When system I issues a request to system 2, it expects a certain kind of desirable reaction. If such a reaction occurs, system I assumes that its request was "understood". In application to simple, "push-button" systems the situation is trivial because in a small system the required relationship between input requests and desired outputs could be specified exactly. As systems grow, the situation becomes more complex and matching between requests and actions becomes approximate.

Functional complexity and ecosystem stability: an experimental approach

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

Van Voris, P.; O'Neill, R.V.; Shugart, H.H.

1978-01-01

The complexity-stability hypothesis was experimentally tested using intact terrestrial microcosms. Functional complexity was defined as the number and significance of component interactions (i.e., population interactions, physical-chemical reactions, biological turnover rates) influenced by nonlinearities, feedbacks, and time delays. It was postulated that functional complexity could be nondestructively measured through analysis of a signal generated from the system. Power spectral analysis of hourly CO/sub 2/ efflux, from eleven old-field microcosms, was analyzed for the number of low frequency peaks and used to rank the functional complexity of each system. Ranking of ecosystem stability was based on the capacity of the system tomore » retain essential nutrients and was measured by net loss of Ca after the system was stressed. Rank correlation supported the hypothesis that increasing ecosystem functional complexity leads to increasing ecosystem stability. The results indicated that complex functional dynamics can serve to stabilize the system. The results also demonstrated that microcosms are useful tools for system-level investigations.« less

The effect of caffeine on the reactions of the excited singlet state of pyrene in micellar sodium lauryl sulfate

NASA Astrophysics Data System (ADS)

Hashimoto, Shuichi; Thomas, J. Kerry

1984-08-01

The effect of caffeine on a few photo-induced reactions of pyrene in micellar sodium lauryl sulfate (NaLS) has been studied. In these systems caffeine complexes with the pyrene (K asso = 85 ± 10 M -1 and also with the other reactants, e.g. Cu 2+ or TI +. The efficiencies of reactions which involve contact, i.e. pyrene excimer formation, and quenching by TI + ions to give the triplet state of pyrene, are significantly reduced in the presence of caffeine, due to geometric inhibitions formed by the complexation processes. The kinetics of photo-induced electron transfer, e.g. between excited pyrene and Cu 2+, are not affected. However, the subsequent reactions of the products are modified and the yield of ionic products is markedly increased.

Mechanisms of proton transfer in Nafion: elementary reactions at the sulfonic acid groups.

PubMed

Sagarik, Kritsana; Phonyiem, Mayuree; Lao-ngam, Charoensak; Chaiwongwattana, Sermsiri

2008-04-21

Proton transfer reactions at the sulfonic acid groups in Nafion were theoretically studied, using complexes formed from triflic acid (CF3SO3H), H3O+ and H2O, as model systems. The investigations began with searching for potential precursors and transition states at low hydration levels, using the test-particle model (T-model), density functional theory (DFT) and ab initio calculations. They were employed as starting configurations in Born-Oppenheimer molecular dynamics (BOMD) simulations at 298 K, from which elementary reactions were analyzed and categorized. For the H3O+-H2O complexes, BOMD simulations suggested that a quasi-dynamic equilibrium could be established between the Eigen and Zundel complexes, and that was considered to be one of the most important elementary reactions in the proton transfer process. The average lifetime of H3O+ obtained from BOMD simulations is close to the lowest limit, estimated from low-frequency vibrational spectroscopy. It was demonstrated that proton transfer reactions at -SO3H are not concerted, due to the thermal energy fluctuation and the existence of various quasi-dynamic equilibria, and -SO3H could directly and indirectly mediate proton transfer reactions through the formation of proton defects, as well as the -SO3- and -SO3H2+ transition states.

Single-Molecule Analysis for RISC Assembly and Target Cleavage.

PubMed

Sasaki, Hiroshi M; Tadakuma, Hisashi; Tomari, Yukihide

2018-01-01

RNA-induced silencing complex (RISC) is a small RNA-protein complex that mediates silencing of complementary target RNAs. Biochemistry has been successfully used to characterize the molecular mechanism of RISC assembly and function for nearly two decades. However, further dissection of intermediate states during the reactions has been warranted to fill in the gaps in our understanding of RNA silencing mechanisms. Single-molecule analysis with total internal reflection fluorescence (TIRF) microscopy is a powerful imaging-based approach to interrogate complex formation and dynamics at the individual molecule level with high sensitivity. Combining this technique with our recently established in vitro reconstitution system of fly Ago2-RISC, we have developed a single-molecule observation system for RISC assembly. In this chapter, we summarize the detailed protocol for single-molecule analysis of chaperone-assisted assembly of fly Ago2-RISC as well as its target cleavage reaction.

Multifunctional Composites of Chiral Valine Derivative Schiff Base Cu(II) Complexes and TiO2

PubMed Central

Takeshita, Yuki; Takakura, Kazuya; Akitsu, Takashiro

2015-01-01

We have prepared four new Cu(II) complexes containing valine moieties with imidazole ligands at the fourth coordination sites and examined their photo-induced reactions with TiO2 in order of understanding the reaction mechanisms. Under a nitrogen atmosphere, the intermolecular electron transfer reactions (essentially supramolecular interactions) of these systems, which resulted in the reduction of Cu(II) species to Cu(I) ones, occurred after UV light irradiation. In this study, we have investigated the conditions of the redox reactions in view of substituent effects of aldehyde moieties. The results of cyclic voltammetry (CV) on an rotating ring-disk electrode (RRDE) suggested that the substitution effects and redox potentials were correlated. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were also performed to simulate the UV–Vis and circular dichroism (CD) spectra; the results revealed a reasonably good correlation between the substituent effects and the highest occupied molecular orbitals and the lowest unoccupied molecular orbitals (HOMO-LUMO) gaps associated with the most intense transition bands. In addition, we summarized the substitution effects of Cu(II) complexes for their corresponding UV light-induced reactions. PMID:25686033

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

PubMed

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.

Direct Observation of Energy Detrapping in LH1-RC Complex by Two-Dimensional Electronic Spectroscopy.

PubMed

Ma, Fei; Yu, Long-Jiang; Hendrikx, Ruud; Wang-Otomo, Zheng-Yu; van Grondelle, Rienk

2017-01-18

The purple bacterial core light harvesting antenna-reaction center (LH1-RC) complex is the simplest system able to achieve the entire primary function of photosynthesis. During the past decade, a variety of photosynthetic proteins were studied by a powerful technique, two-dimensional electronic spectroscopy (2DES). However, little attention has been paid to LH1-RC, although its reversible uphill energy transfer, trapping, and backward detrapping processes, represent a crucial step in the early photosynthetic reaction dynamics. Thus, in this work, we employed 2DES to study two LH1-RC complexes of Thermochromatium (Tch.) tepidum. By direct observation of detrapping, the complex reversible process was clearly identified and an overall scheme of the excitation evolution in LH1-RC was obtained.

Catalytic transformation of dinitrogen into ammonia and hydrazine by iron-dinitrogen complexes bearing pincer ligand

PubMed Central

Kuriyama, Shogo; Arashiba, Kazuya; Nakajima, Kazunari; Matsuo, Yuki; Tanaka, Hiromasa; Ishii, Kazuyuki; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki

2016-01-01

Synthesis and reactivity of iron-dinitrogen complexes have been extensively studied, because the iron atom plays an important role in the industrial and biological nitrogen fixation. As a result, iron-catalyzed reduction of molecular dinitrogen into ammonia has recently been achieved. Here we show that an iron-dinitrogen complex bearing an anionic PNP-pincer ligand works as an effective catalyst towards the catalytic nitrogen fixation, where a mixture of ammonia and hydrazine is produced. In the present reaction system, molecular dinitrogen is catalytically and directly converted into hydrazine by using transition metal-dinitrogen complexes as catalysts. Because hydrazine is considered as a key intermediate in the nitrogen fixation in nitrogenase, the findings described in this paper provide an opportunity to elucidate the reaction mechanism in nitrogenase. PMID:27435503

Catalytic asymmetric Michael reactions promoted by a lithium-free lanthanum-BINOL complex

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

Sasai, Hiroaki; Arai, Takayoshi; Shibasaki, Masakatsu

1994-02-23

In this communication, we report about a new lithium-free BINOL-lanthanum complex, which is quite effective in catalytic asymmetric Michael reaction. We have succeeded in developing effective asymmetric base catalysts, in particular, asymmetric ester enolate catalysts for asymmetric Michael reactions. Two asymmetric lanthanum complexes are now available, namely, BINOL-lanthanum-lithium complex, which is quite effective in catalytic asymmetric nitrosaldol reactions, and a new lithium-free BINOL-lanthanum ester enolate complex, that is very effective in catalytic asymmetric Michael reactions. The two complexes complement each other in their ability to catalyze asymmetric nitroaldol and asymmetric Michael reactions. 14 refs., 1 fig., 2 tabs.

Polynuclear complexes of copper(I) halides: coordination chemistry and catalytic transformations of alkynes

NASA Astrophysics Data System (ADS)

Mykhalichko, B. M.; Temkin, Oleg N.; Mys'kiv, M. G.

2000-11-01

Characteristic features of the coordination chemistry of Cu(I) and mechanisms of catalytic conversions of alkynes in the CuCl-MCl-H2O-HC≡CR system (MCl is alkali metal or ammonium chloride or amine hydrochloride; R=H, CH2OH, CH=CH2, etc.) are analysed based on studies of the compositions and structures of copper(I) chloride (bromide) complexes, alkyne π-complexes and ethynyl organometallic polynuclear compounds formed in this system in solutions and in the crystalline state. The role of polynuclear complexes in various reactions of alkynes is discussed. The bibliography includes 149 references.

Systems Biocatalysis: Development and engineering of cell-free "artificial metabolisms" for preparative multi-enzymatic synthesis.

PubMed

Fessner, Wolf-Dieter

2015-12-25

Systems Biocatalysis is an emerging concept of organizing enzymes in vitro to construct complex reaction cascades for an efficient, sustainable synthesis of valuable chemical products. The strategy merges the synthetic focus of chemistry with the modular design of biological systems, which is similar to metabolic engineering of cellular production systems but can be realized at a far lower level of complexity from a true reductionist approach. Such operations are free from material erosion by competing metabolic pathways, from kinetic restrictions by physical barriers and regulating circuits, and from toxicity problems with reactive foreign substrates, which are notorious problems in whole-cell systems. A particular advantage of cell-free concepts arises from the inherent opportunity to construct novel biocatalytic reaction systems for the efficient synthesis of non-natural products ("artificial metabolisms") by using enzymes specifically chosen or engineered for non-natural substrate promiscuity. Examples illustrating the technology from our laboratory are discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

The algorithm of numerical calculation of constraints reactions in a dynamic system of transport machine

NASA Astrophysics Data System (ADS)

Akhtulov, A. L.

2018-01-01

The questions of construction and practical application of the automation system for the design of components and aggregates for the construction of transport vehicles are considered, taking into account their dynamic characteristics. Based on the results of the studies, a unified method for determining the reactions of bonds of a complex spatial structure is proposed. The technique, based on the method of substructures, allows us to determine the values of the transfer functions taking into account the reactions of the bonds. After the carried out researches it is necessary to note, that such approach gives the most satisfactory results and can be used for calculations of complex mechanical systems of machines and units of different purposes. The directions of increasing the degree of validity of technical decisions are shown, especially in the early stages of design, when the cost of errors is high, with careful thorough working out of all the elements of the design, which is really feasible only on the basis of automation of design and technological work.

Some special features of the le chatelier-braun principle

NASA Astrophysics Data System (ADS)

Nesis, E. I.; Skibin, Yu. N.

2000-07-01

The relaxation reaction of a system that follows from the Le Chatelier-Braun principle and weakens the result of an external influence turns out to be more intense under a complex action. A method for quantitative determination of the weakening effect for simple and complex actions is suggested.

Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism.

PubMed

Holme, Petter; Huss, Mikael; Lee, Sang Hoon

2011-05-06

The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.

Harnessing Thin-Film Continuous-Flow Assembly Lines.

PubMed

Britton, Joshua; Castle, Jared W; Weiss, Gregory A; Raston, Colin L

2016-07-25

Inspired by nature's ability to construct complex molecules through sequential synthetic transformations, an assembly line synthesis of α-aminophosphonates has been developed. In this approach, simple starting materials are continuously fed through a thin-film reactor where the intermediates accrue molecular complexity as they progress through the flow system. Flow chemistry allows rapid multistep transformations to occur via reaction compartmentalization, an approach not amenable to using conventional flasks. Thin film processing can also access facile in situ solvent exchange to drive reaction efficiency, and through this method, α-aminophosphonate synthesis requires only 443 s residence time to produce 3.22 g h(-1) . Assembly-line synthesis allows unprecedented reaction flexibility and processing efficiency. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Predictor - Predictive Reaction Design via Informatics, Computation and Theories of Reactivity

DTIC Science & Technology

2017-10-10

into more complex and valuable molecules, but are limited by: 1. The extensive time it takes to design and optimize a synthesis 2. Multi-step...system. As it is fully compatible to the industry standard SQL, designing a server- based system at a later time will be trivial. Producing a JAVA front...Report: PREDICTOR - Predictive REaction Design via Informatics, Computation and Theories of Reactivity The goal of this program was to create a cyber

Propagation failures, breathing pulses, and backfiring in an excitable reaction-diffusion system.

PubMed

Manz, Niklas; Steinbock, Oliver

2006-09-01

We report results from experiments with a pseudo-one-dimensional Belousov-Zhabotinsky reaction that employs 1,4-cyclohexanedione as its organic substrate. This excitable system shows traveling oxidation pulses and pulse trains that can undergo complex sequences of propagation failures. Moreover, we present examples for (i) breathing pulses that undergo periodic changes in speed and size and (ii) backfiring pulses that near their back repeatedly generate new pulses propagating in opposite direction.

Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach.

PubMed

van Roekel, Hendrik W H; Rosier, Bas J H M; Meijer, Lenny H H; Hilbers, Peter A J; Markvoort, Albert J; Huck, Wilhelm T S; de Greef, Tom F A

2015-11-07

Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli. It has become apparent that these biological responses are regulated by complex chemical reaction networks (CRNs). Unravelling the function of these circuits is a key topic of both systems biology and synthetic biology. Recent progress at the interface of chemistry and biology together with the realisation that current experimental tools are insufficient to quantitatively understand the molecular logic of pathways inside living cells has triggered renewed interest in the bottom-up development of CRNs. This builds upon earlier work of physical chemists who extensively studied inorganic CRNs and showed how a system of chemical reactions can give rise to complex spatiotemporal responses such as oscillations and pattern formation. Using purified biochemical components, in vitro synthetic biologists have started to engineer simplified model systems with the goal of mimicking biological responses of intracellular circuits. Emulation and reconstruction of system-level properties of intracellular networks using simplified circuits are able to reveal key design principles and molecular programs that underlie the biological function of interest. In this Tutorial Review, we present an accessible overview of this emerging field starting with key studies on inorganic CRNs followed by a discussion of recent work involving purified biochemical components. Finally, we review recent work showing the versatility of programmable biochemical reaction networks (BRNs) in analytical and diagnostic applications.

Are Nonadiabatic Reaction Dynamics the Key to Novel Organosilicon Molecules? The Silicon (Si(3P))-Dimethylacetylene (C4H6(X1A1g)) System as a Case Study.

PubMed

Thomas, Aaron M; Dangi, Beni B; Yang, Tao; Kaiser, Ralf I; Lin, Lin; Chou, Tzu-Jung; Chang, Agnes H H

2018-06-06

The bimolecular gas phase reaction of ground-state silicon (Si; 3 P) with dimethylacetylene (C 4 H 6 ; X 1 A 1g ) was investigated under single collision conditions in a crossed molecular beams machine. Merged with electronic structure calculations, the data propose nonadiabatic reaction dynamics leading to the formation of singlet SiC 4 H 4 isomer(s) and molecular hydrogen (H 2 ) via indirect scattering dynamics along with intersystem crossing (ISC) from the triplet to the singlet surface. The reaction may lead to distinct energetically accessible singlet SiC 4 H 4 isomers ( 1 p8- 1 p24) in overall exoergic reaction(s) (-107 -20 +12 kJ mol -1 ). All feasible reaction products are either cyclic, carry carbene analogous silylene moieties, or carry C-Si-H or C-Si-C bonds that would require extensive isomerization from the initial collision complex(es) to the fragmenting singlet intermediate(s). The present study demonstrates the first successful crossed beams study of an exoergic reaction channel arising from bimolecular collisions of silicon, Si( 3 P), with a hydrocarbon molecule.

Kinetic study of lipase-catalyzed glycerolysis of palm olein using Lipozyme TLIM in solvent-free system

PubMed Central

Phuah, Eng-Tong; Lee, Yee-Ying; Tang, Teck-Kim

2018-01-01

Diacylglycerol (DAG) and monoacylglycerol (MAG) are two natural occurring minor components found in most edible fats and oils. These compounds have gained increasing market demand owing to their unique physicochemical properties. Enzymatic glycerolysis in solvent-free system might be a promising approach in producing DAG and MAG-enriched oil. Understanding on glycerolysis mechanism is therefore of great importance for process simulation and optimization. In this study, a commercial immobilized lipase (Lipozyme TL IM) was used to catalyze the glycerolysis reaction. The kinetics of enzymatic glycerolysis reaction between triacylglycerol (TAG) and glycerol (G) were modeled using rate equation with unsteady-state assumption. Ternary complex, ping-pong bi-bi and complex ping-pong bi-bi models were proposed and compared in this study. The reaction rate constants were determined using non-linear regression and sum of square errors (SSE) were minimized. Present work revealed satisfactory agreement between experimental data and the result generated by complex ping-pong bi-bi model as compared to other models. The proposed kinetic model would facilitate understanding on enzymatic glycerolysis for DAG and MAG production and design optimization of a pilot-scale reactor. PMID:29401481

From isolated light-harvesting complexes to the thylakoid membrane: a single-molecule perspective

NASA Astrophysics Data System (ADS)

Gruber, J. Michael; Malý, Pavel; Krüger, Tjaart P. J.; Grondelle, Rienk van

2018-01-01

The conversion of solar radiation to chemical energy in plants and green algae takes place in the thylakoid membrane. This amphiphilic environment hosts a complex arrangement of light-harvesting pigment-protein complexes that absorb light and transfer the excitation energy to photochemically active reaction centers. This efficient light-harvesting capacity is moreover tightly regulated by a photoprotective mechanism called non-photochemical quenching to avoid the stress-induced destruction of the catalytic reaction center. In this review we provide an overview of single-molecule fluorescence measurements on plant light-harvesting complexes (LHCs) of varying sizes with the aim of bridging the gap between the smallest isolated complexes, which have been well-characterized, and the native photosystem. The smallest complexes contain only a small number (10-20) of interacting chlorophylls, while the native photosystem contains dozens of protein subunits and many hundreds of connected pigments. We discuss the functional significance of conformational dynamics, the lipid environment, and the structural arrangement of this fascinating nano-machinery. The described experimental results can be utilized to build mathematical-physical models in a bottom-up approach, which can then be tested on larger in vivo systems. The results also clearly showcase the general property of biological systems to utilize the same system properties for different purposes. In this case it is the regulated conformational flexibility that allows LHCs to switch between efficient light-harvesting and a photoprotective function.

Optimization of information content in a mass spectrometry based flow-chemistry system by investigating different ionization approaches.

PubMed

Martha, Cornelius T; Hoogendoorn, Jan-Carel; Irth, Hubertus; Niessen, Wilfried M A

2011-05-15

Current development in catalyst discovery includes combinatorial synthesis methods for the rapid generation of compound libraries combined with high-throughput performance-screening methods to determine the associated activities. Of these novel methodologies, mass spectrometry (MS) based flow chemistry methods are especially attractive due to the ability to combine sensitive detection of the formed reaction product with identification of introduced catalyst complexes. Recently, such a mass spectrometry based continuous-flow reaction detection system was utilized to screen silver-adducted ferrocenyl bidentate catalyst complexes for activity in a multicomponent synthesis of a substituted 2-imidazoline. Here, we determine the merits of different ionization approaches by studying the combination of sensitive detection of product formation in the continuous-flow system with the ability to simultaneous characterize the introduced [ferrocenyl bidentate+Ag](+) catalyst complexes. To this end, we study the ionization characteristics of electrospray ionization (ESI), atmospheric-pressure chemical ionization (APCI), no-discharge APCI, dual ESI/APCI, and dual APCI/no-discharge APCI. Finally, we investigated the application potential of the different ionization approaches by the investigation of ferrocenyl bidentate catalyst complex responses in different solvents. Copyright © 2011 Elsevier B.V. All rights reserved.

What Controls the "Off/On Switch" in the Toehold-Mediated Strand Displacement Reaction on DNA Conjugated Gold Nanoparticles?

PubMed

Yao, Dongbao; Wang, Bei; Xiao, Shiyan; Song, Tingjie; Huang, Fujian; Liang, Haojun

2015-06-30

In DNA dynamic nanotechnology, a toehold-mediated DNA strand-displacement reaction has demonstrated its capability in building complex autonomous system. In most cases, the reaction is performed in pure DNA solution that is essentially a one-phase system. In the present work, we systematically investigated the reaction in a heterogeneous media, in which the strand that implements a displacing action is conjugated on gold nanoparticles. By monitoring the kinetics of spherical nucleic acid (SNA) assembly driven by toehold-mediated strand displacement reaction, we observed significant differences, i.e., the abrupt jump in behavior of an "off/on switch", in the reaction rate when the invading toehold was extended to eight bases from seven bases. These phenomena are attributed to the effect of steric hindrance arising from the high density of invading strand conjugated to AuNPs. Based on these studies, an INHIBIT logic gate presenting good selectivity was developed.

Enzymatic reactions in confined environments

NASA Astrophysics Data System (ADS)

Küchler, Andreas; Yoshimoto, Makoto; Luginbühl, Sandra; Mavelli, Fabio; Walde, Peter

2016-05-01

Within each biological cell, surface- and volume-confined enzymes control a highly complex network of chemical reactions. These reactions are efficient, timely, and spatially defined. Efforts to transfer such appealing features to in vitro systems have led to several successful examples of chemical reactions catalysed by isolated and immobilized enzymes. In most cases, these enzymes are either bound or adsorbed to an insoluble support, physically trapped in a macromolecular network, or encapsulated within compartments. Advanced applications of enzymatic cascade reactions with immobilized enzymes include enzymatic fuel cells and enzymatic nanoreactors, both for in vitro and possible in vivo applications. In this Review, we discuss some of the general principles of enzymatic reactions confined on surfaces, at interfaces, and inside small volumes. We also highlight the similarities and differences between the in vivo and in vitro cases and attempt to critically evaluate some of the necessary future steps to improve our fundamental understanding of these systems.

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

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; Bittker, David A.

1993-01-01

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

Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe–S Assembly Complex

PubMed Central

Fox, Nicholas G.; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A.; Barondeau, David P.

2015-01-01

Iron–sulfur (Fe–S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe–S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe–S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe–S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe–S assembly complex. Here the kinetics of Fe–S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe–S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe–S assembly complex. PMID:26016518

Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe-S Assembly Complex.

PubMed

Fox, Nicholas G; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A; Barondeau, David P

2015-06-30

Iron-sulfur (Fe-S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe-S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe-S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe-S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe-S assembly complex. Here the kinetics of Fe-S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe-S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe-S assembly complex.

Zirconocene-iridium hydrido complexes: arene carbon-hydrogen bond activation and formation of a planar square Zr2Ir2 complex.

PubMed

Oishi, Masataka; Suzuki, Hiroharu

2009-03-16

New early-late heterobimetallic hydrides (L(2)ZrCl)(Cp*Ir)(mu-H)(3) (1; L = Cp derivative, Cp* = eta(5)-C(5)Me(5)) were synthesized from zirconocene derivatives (L(2)ZrCl(2)) and LiCp*IrH(3) via a salt elimination reaction and structurally characterized by NMR and X-ray analyses. Upon treatment of 1 with an alkyllithium reagent, hydride abstraction complex 4 underwent thermolytic ligand elimination at the Zr-Ir system to yield a novel planar square complex (L(2)Zr)(2)(Cp*Ir)(2)(mu(3)-H)(4) (2). When a labeling study of the reaction was conducted, it was found that the conversion of 1 to 2 involves rapid aromatic and benzylic C-H activation by a coordinatively unsaturated dinuclear complex (L(2)Zr)(Cp*Ir)(H)(2) (3).

Chemical Memory Reactions Induced Bursting Dynamics in Gene Expression

PubMed Central

Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems. PMID:23349679

Chemical memory reactions induced bursting dynamics in gene expression.

PubMed

Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.

Coupled enzyme reactions performed in heterogeneous reaction media: experiments and modeling for glucose oxidase and horseradish peroxidase in a PEG/citrate aqueous two-phase system.

PubMed

Aumiller, William M; Davis, Bradley W; Hashemian, Negar; Maranas, Costas; Armaou, Antonios; Keating, Christine D

2014-03-06

The intracellular environment in which biological reactions occur is crowded with macromolecules and subdivided into microenvironments that differ in both physical properties and chemical composition. The work described here combines experimental and computational model systems to help understand the consequences of this heterogeneous reaction media on the outcome of coupled enzyme reactions. Our experimental model system for solution heterogeneity is a biphasic polyethylene glycol (PEG)/sodium citrate aqueous mixture that provides coexisting PEG-rich and citrate-rich phases. Reaction kinetics for the coupled enzyme reaction between glucose oxidase (GOX) and horseradish peroxidase (HRP) were measured in the PEG/citrate aqueous two-phase system (ATPS). Enzyme kinetics differed between the two phases, particularly for the HRP. Both enzymes, as well as the substrates glucose and H2O2, partitioned to the citrate-rich phase; however, the Amplex Red substrate necessary to complete the sequential reaction partitioned strongly to the PEG-rich phase. Reactions in ATPS were quantitatively described by a mathematical model that incorporated measured partitioning and kinetic parameters. The model was then extended to new reaction conditions, i.e., higher enzyme concentration. Both experimental and computational results suggest mass transfer across the interface is vital to maintain the observed rate of product formation, which may be a means of metabolic regulation in vivo. Although outcomes for a specific system will depend on the particulars of the enzyme reactions and the microenvironments, this work demonstrates how coupled enzymatic reactions in complex, heterogeneous media can be understood in terms of a mathematical model.

Uncovering Oscillations, Complexity, and Chaos in Chemical Kinetics Using Mathematica

NASA Astrophysics Data System (ADS)

Ferreira, M. M. C.; Ferreira, W. C., Jr.; Lino, A. C. S.; Porto, M. E. G.

1999-06-01

Unlike reactions with no peculiar temporal behavior, in oscillatory reactions concentrations can rise and fall spontaneously in a cyclic or disorganized fashion. In this article, the software Mathematica is used for a theoretical study of kinetic mechanisms of oscillating and chaotic reactions. A first simple example is introduced through a three-step reaction, called the Lotka model, which exhibits a temporal behavior characterized by damped oscillations. The phase plane method of dynamic systems theory is introduced for a geometric interpretation of the reaction kinetics without solving the differential rate equations. The equations are later numerically solved using the built-in routine NDSolve and the results are plotted. The next example, still with a very simple mechanism, is the Lotka-Volterra model reaction, which oscillates indefinitely. The kinetic process and rate equations are also represented by a three-step reaction mechanism. The most important difference between this and the former reaction is that the undamped oscillation has two autocatalytic steps instead of one. The periods of oscillations are obtained by using the discrete Fourier transform (DFT)-a well-known tool in spectroscopy, although not so common in this context. In the last section, it is shown how a simple model of biochemical interactions can be useful to understand the complex behavior of important biological systems. The model consists of two allosteric enzymes coupled in series and activated by its own products. This reaction scheme is important for explaining many metabolic mechanisms, such as the glycolytic oscillations in muscles, yeast glycolysis, and the periodic synthesis of cyclic AMP. A few of many possible dynamic behaviors are exemplified through a prototype glycolytic enzymatic reaction proposed by Decroly and Goldbeter. By simply modifying the initial concentrations, limit cycles, chaos, and birhythmicity are computationally obtained and visualized.

Scale-Dependent Rates of Uranyl Surface Complexation Reaction in Sediments

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

Liu, Chongxuan; Shang, Jianying; Kerisit, Sebastien N.

Scale-dependency of uranyl[U(VI)] surface complexation rates was investigated in stirred flow-cell and column systems using a U(VI)-contaminated sediment from the US Department of Energy, Hanford site, WA. The experimental results were used to estimate the apparent rate of U(VI) surface complexation at the grain-scale and in porous media. Numerical simulations using molecular, pore-scale, and continuum models were performed to provide insights into and to estimate the rate constants of U(VI) surface complexation at the different scales. The results showed that the grain-scale rate constant of U(VI) surface complexation was over 3 to 10 orders of magnitude smaller, dependent on themore » temporal scale, than the rate constant calculated using the molecular simulations. The grain-scale rate was faster initially and slower with time, showing the temporal scale-dependency. The largest rate constant at the grain-scale decreased additional 2 orders of magnitude when the rate was scaled to the porous media in the column. The scaling effect from the grain-scale to the porous media became less important for the slower sorption sites. Pore-scale simulations revealed the importance of coupled mass transport and reactions in both intragranular and inter-granular domains, which caused both spatial and temporal dependence of U(VI) surface complexation rates in the sediment. Pore-scale simulations also revealed a new rate-limiting mechanism in the intragranular porous domains that the rate of coupled diffusion and surface complexation reaction was slower than either process alone. The results provided important implications for developing models to scale geochemical/biogeochemical reactions.« less

Arene-chromium tricarbonyl complexes in the Pauson-Khand reaction.

PubMed

Rosillo, Marta; Domínguez, Gema; Casarrubios, Luis; Pérez-Castells, Javier

2005-12-09

[reactions: see text] We show the use of arene-chromium tricarbonyl complexes in intra- and intermolecular Pauson-Khand reactions. Both styrene and ethynylbenzene complexes react with alkynes and olefins. The synthesis of enynes connected through chromium-complexed aromatic rings is developed. The intramolecular Pauson-Khand reaction occurs in a totally diastereoselective manner.

Pulse-density modulation control of chemical oscillation far from equilibrium in a droplet open-reactor system

PubMed Central

Sugiura, Haruka; Ito, Manami; Okuaki, Tomoya; Mori, Yoshihito; Kitahata, Hiroyuki; Takinoue, Masahiro

2016-01-01

The design, construction and control of artificial self-organized systems modelled on dynamical behaviours of living systems are important issues in biologically inspired engineering. Such systems are usually based on complex reaction dynamics far from equilibrium; therefore, the control of non-equilibrium conditions is required. Here we report a droplet open-reactor system, based on droplet fusion and fission, that achieves dynamical control over chemical fluxes into/out of the reactor for chemical reactions far from equilibrium. We mathematically reveal that the control mechanism is formulated as pulse-density modulation control of the fusion–fission timing. We produce the droplet open-reactor system using microfluidic technologies and then perform external control and autonomous feedback control over autocatalytic chemical oscillation reactions far from equilibrium. We believe that this system will be valuable for the dynamical control over self-organized phenomena far from equilibrium in chemical and biomedical studies. PMID:26786848

Pulse-density modulation control of chemical oscillation far from equilibrium in a droplet open-reactor system.

PubMed

Sugiura, Haruka; Ito, Manami; Okuaki, Tomoya; Mori, Yoshihito; Kitahata, Hiroyuki; Takinoue, Masahiro

2016-01-20

The design, construction and control of artificial self-organized systems modelled on dynamical behaviours of living systems are important issues in biologically inspired engineering. Such systems are usually based on complex reaction dynamics far from equilibrium; therefore, the control of non-equilibrium conditions is required. Here we report a droplet open-reactor system, based on droplet fusion and fission, that achieves dynamical control over chemical fluxes into/out of the reactor for chemical reactions far from equilibrium. We mathematically reveal that the control mechanism is formulated as pulse-density modulation control of the fusion-fission timing. We produce the droplet open-reactor system using microfluidic technologies and then perform external control and autonomous feedback control over autocatalytic chemical oscillation reactions far from equilibrium. We believe that this system will be valuable for the dynamical control over self-organized phenomena far from equilibrium in chemical and biomedical studies.

The Complexity Trap

DTIC Science & Technology

2012-01-01

proactively and effectively to today’s international environment, prioritization is the key first step —and precisely the opposite reaction to the complacency...formidable than just endless grains of sand.”32 This is not to deny the possibility of nonlinear phenomena, butterfly effects, self-organizing systems...The first step is replac- ing the current reactive worship of complexity with proactive prioritization. To escape the complexity trap, let us dare

Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling

PubMed Central

Matsuura, Tomoaki; Tanimura, Naoki; Hosoda, Kazufumi; Yomo, Tetsuya; Shimizu, Yoshihiro

2017-01-01

To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro protein synthesis system. We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand these complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure, and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion, and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale biological reactions by visualizing complex dynamics, thereby extracting the characteristics of the reaction network, including phase transitions. PMID:28167777

Stress reaction process-based hierarchical recognition algorithm for continuous intrusion events in optical fiber prewarning system

NASA Astrophysics Data System (ADS)

Qu, Hongquan; Yuan, Shijiao; Wang, Yanping; Yang, Dan

2018-04-01

To improve the recognition performance of optical fiber prewarning system (OFPS), this study proposed a hierarchical recognition algorithm (HRA). Compared with traditional methods, which employ only a complex algorithm that includes multiple extracted features and complex classifiers to increase the recognition rate with a considerable decrease in recognition speed, HRA takes advantage of the continuity of intrusion events, thereby creating a staged recognition flow inspired by stress reaction. HRA is expected to achieve high-level recognition accuracy with less time consumption. First, this work analyzed the continuity of intrusion events and then presented the algorithm based on the mechanism of stress reaction. Finally, it verified the time consumption through theoretical analysis and experiments, and the recognition accuracy was obtained through experiments. Experiment results show that the processing speed of HRA is 3.3 times faster than that of a traditional complicated algorithm and has a similar recognition rate of 98%. The study is of great significance to fast intrusion event recognition in OFPS.

Wave reflection in a reaction-diffusion system: breathing patterns and attenuation of the echo.

PubMed

Tsyganov, M A; Ivanitsky, G R; Zemskov, E P

2014-05-01

Formation and interaction of the one-dimensional excitation waves in a reaction-diffusion system with the piecewise linear reaction functions of the Tonnelier-Gerstner type are studied. We show that there exists a parameter region where the established regime of wave propagation depends on initial conditions. Wave phenomena with a complex behavior are found: (i) the reflection of waves at a growing distance (the remote reflection) upon their collision with each other or with no-flux boundaries and (ii) the periodic transformation of waves with the jumping from one regime of wave propagation to another (the periodic trigger wave).

Wave reflection in a reaction-diffusion system: Breathing patterns and attenuation of the echo

NASA Astrophysics Data System (ADS)

Tsyganov, M. A.; Ivanitsky, G. R.; Zemskov, E. P.

2014-05-01

Formation and interaction of the one-dimensional excitation waves in a reaction-diffusion system with the piecewise linear reaction functions of the Tonnelier-Gerstner type are studied. We show that there exists a parameter region where the established regime of wave propagation depends on initial conditions. Wave phenomena with a complex behavior are found: (i) the reflection of waves at a growing distance (the remote reflection) upon their collision with each other or with no-flux boundaries and (ii) the periodic transformation of waves with the jumping from one regime of wave propagation to another (the periodic trigger wave).

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

PubMed

Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R

2014-10-14

The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a small subset of atoms within the system.

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

PubMed Central

2015-01-01

The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a small subset of atoms within the system. PMID:25328492

I + (H2O)2 → HI + (H2O)OH Forward and Reverse Reactions. CCSD(T) Studies Including Spin-Orbit Coupling.

PubMed

Wang, Hui; Li, Guoliang; Li, Qian-Shu; Xie, Yaoming; Schaefer, Henry F

2016-03-03

The potential energy profile for the atomic iodine plus water dimer reaction I + (H2O)2 → HI + (H2O)OH has been explored using the "Gold Standard" CCSD(T) method with quadruple-ζ correlation-consistent basis sets. The corresponding information for the reverse reaction HI + (H2O)OH → I + (H2O)2 is also derived. Both zero-point vibrational energies (ZPVEs) and spin-orbit (SO) coupling are considered, and these notably alter the classical energetics. On the basis of the CCSD(T)/cc-pVQZ-PP results, including ZPVE and SO coupling, the forward reaction is found to be endothermic by 47.4 kcal/mol, implying a significant exothermicity for the reverse reaction. The entrance complex I···(H2O)2 is bound by 1.8 kcal/mol, and this dissociation energy is significantly affected by SO coupling. The reaction barrier lies 45.1 kcal/mol higher than the reactants. The exit complex HI···(H2O)OH is bound by 3.0 kcal/mol relative to the asymptotic limit. At every level of theory, the reverse reaction HI + (H2O)OH → I + (H2O)2 proceeds without a barrier. Compared with the analogous water monomer reaction I + H2O → HI + OH, the additional water molecule reduces the relative energies of the entrance stationary point, transition state, and exit complex by 3-5 kcal/mol. The I + (H2O)2 reaction is related to the valence isoelectronic bromine and chlorine reactions but is distinctly different from the F + (H2O)2 system.

Intramolecular Hydroamination of Unbiased and Functionalized Primary Aminoalkenes Catalyzed by a Rhodium Aminophosphine Complex

PubMed Central

Julian, Lisa D.; Hartwig, John F.

2010-01-01

We report a rhodium catalyst that exhibits high reactivity for the hydroamination of primary aminoalkenes that are unbiased toward cyclization and that possess functional groups that would not be tolerated in hydroaminations catalyzed by more electrophilic systems. This catalyst contains an unusual diaminophosphine ligand that binds to rhodium in a κ3-P,O,P mode. The reactions catalyzed by this complex typically proceed at mild temperatures (room temperature to 70 °C), occur with primary aminoalkenes lacking substituents on the alkyl chain that bias the system toward cyclization, occur with primary aminoalkenes containing chloride, ester, ether, enolizable ketone, nitrile, and unprotected alcohol functionality, and occur with primary aminoalkenes containing internal olefins. Mechanistic data imply that these reactions occur with a turnover-limiting step that is different from that of reactions catalyzed by late transition metal complexes of Pd, Pt, and Ir. This change in the turnover-limiting step and resulting high activity of the catalyst stem from favorable relative rates for protonolysis of the M-C bond to release the hydroamination product vs reversion of the aminoalkyl intermediate to regenerate the acyclic precursor. Probes for the origin of the reactivity of the rhodium complex of L1 imply that the aminophosphine groups lead to these favorable rates by effects beyond steric demands and simple electron donation to the metal center. PMID:20839807

Quantum effects in energy and charge transfer in an artificial photosynthetic complex

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

Ghosh, Pulak Kumar; Smirnov, Anatoly Yu.; Nori, Franco

2011-06-28

We investigate the quantum dynamics of energy and charge transfer in a wheel-shaped artificial photosynthetic antenna-reaction center complex. This complex consists of six light-harvesting chromophores and an electron-acceptor fullerene. To describe quantum effects on a femtosecond time scale, we derive the set of exact non-Markovian equations for the Heisenberg operators of this photosynthetic complex in contact with a Gaussian heat bath. With these equations we can analyze the regime of strong system-bath interactions, where reorganization energies are of the order of the intersite exciton couplings. We show that the energy of the initially excited antenna chromophores is efficiently funneled tomore » the porphyrin-fullerene reaction center, where a charge-separated state is set up in a few picoseconds, with a quantum yield of the order of 95%. In the single-exciton regime, with one antenna chromophore being initially excited, we observe quantum beatings of energy between two resonant antenna chromophores with a decoherence time of {approx}100 fs. We also analyze the double-exciton regime, when two porphyrin molecules involved in the reaction center are initially excited. In this regime we obtain pronounced quantum oscillations of the charge on the fullerene molecule with a decoherence time of about 20 fs (at liquid nitrogen temperatures). These results show a way to directly detect quantum effects in artificial photosynthetic systems.« less

The sound of a mobile phone ringing affects the complex reaction time of its owner

PubMed Central

Zajdel, Justyna; Zwolińska, Anna; Śmigielski, Janusz; Beling, Piotr; Cegliński, Tomasz; Nowak, Dariusz

2012-01-01

Introduction Mobile phone conversation decreases the ability to concentrate and impairs the attention necessary to perform complex activities, such as driving a car. Does the ringing sound of a mobile phone affect the driver's ability to perform complex sensory-motor activities? We compared a subject's reaction time while performing a test either with a mobile phone ringing or without. Material and methods The examination was performed on a PC-based reaction time self-constructed system Reactor. The study group consisted of 42 healthy students. The protocol included instruction, control without phone and a proper session with subject's mobile phone ringing. The terms of the study were standardised. Results There were significant differences (p < 0.001) in reaction time in control (597 ms), mobile (633 ms) and instruction session (673 ms). The differences in female subpopulation were also significant (p < 0.01). Women revealed the longest reaction time in instruction session (707 ms), were significantly quicker in mobile (657 ms, p < 0.01) and in control session (612 ms, p < 0.001). In men, the significant difference was recorded only between instruction (622 ms) and control session (573 ms, p < 0.01). The other differences were not significant (p > 0.08). Men proofed to complete significantly quicker than women in instruction (p < 0.01) and in mobile session (p < 0.05). Differences amongst the genders in control session was not significant (p > 0.05). Conclusions The results obtained proofed the ringing of a phone exerts a significant influence on complex reaction time and quality of performed task. PMID:23185201

Solute transport with multiple equilibrium-controlled or kinetically controlled chemical reactions

USGS Publications Warehouse

Friedly, John C.; Rubin, Jacob

1992-01-01

A new approach is applied to the problem of modeling solute transport accompanied by many chemical reactions. The approach, based on concepts of the concentration space and its stoichiometric subspaces, uses elements of the subspaces as primary dependent variables. It is shown that the resulting model equations are compact in form, isolate the chemical reaction expressions from flow expressions, and can be used for either equilibrium or kinetically controlled reactions. The implications of the results on numerical algorithms for solving the equations are discussed. The application of the theory is illustrated throughout with examples involving a simple but broadly representative set of reactions previously considered in the literature. Numerical results are presented for four interconnected reactions: a homogeneous complexation reaction, two sorption reactions, and a dissolution/precipitation reaction. Three cases are considered: (1) four kinetically controlled reactions, (2) four equilibrium-controlled reactions, and (3) a system with two kinetically controlled reactions and two equilibrium-controlled reactions.

Variationally optimal selection of slow coordinates and reaction coordinates in macromolecular systems

NASA Astrophysics Data System (ADS)

Noe, Frank

To efficiently simulate and generate understanding from simulations of complex macromolecular systems, the concept of slow collective coordinates or reaction coordinates is of fundamental importance. Here we will introduce variational approaches to approximate the slow coordinates and the reaction coordinates between selected end-states given MD simulations of the macromolecular system and a (possibly large) basis set of candidate coordinates. We will then discuss how to select physically intuitive order paremeters that are good surrogates of this variationally optimal result. These result can be used in order to construct Markov state models or other models of the stationary and kinetics properties, in order to parametrize low-dimensional / coarse-grained model of the dynamics. Deutsche Forschungsgemeinschaft, European Research Council.

Spins of complex fragments in binary reactions within a dinuclear system model

NASA Astrophysics Data System (ADS)

Paşca, H.; Kalandarov, Sh. A.; Adamian, G. G.; Antonenko, N. V.

2017-10-01

The average angular momenta and widths of the spin distributions of reaction products are calculated within the dinuclear system model. The thermal excitation of rotational bearing modes is considered in the dinuclear system. The calculated fragment spins (γ multiplicities) and their variances in the reactions 20Ne (166 MeV) + 63Cu, 40Ar (280 MeV) + 58Ni, 20Ne (175 MeV) + natAg, 40Ar (237 MeV) + 89Y, 40Ar (288 and 340 MeV) + Ag,109107, and 16O (100 MeV) + 58Ni are compared with the available experimental data. The influence of the entrance channel charge (mass) asymmetry and bombarding energy on the characteristics of spin distribution is studied.

Phosphinosilylenes as a novel ligand system for heterobimetallic complexes.

PubMed

Breit, Nora C; Eisenhut, Carsten; Inoue, Shigeyoshi

2016-04-25

A dihydrophosphinosilylene iron complex [LSi{Fe(CO)4}PH2] has been prepared and utilized in the synthesis of novel heterobimetallic complexes. The phosphine moiety in this phosphinosilylene complex allows coordination towards tungsten leading to the iron-tungsten heterobimetallic complex [LSi{Fe(CO)4}PH2{W(CO)5}]. In contrast, the reaction of [LSi{Fe(CO)4}PH2] with ethylenebis(triphenylphosphine)platinum(0) results in the formation of the iron-platinum heterobimetallic complex [LSi{Fe(CO)4}PH{PtH(PPh3)2}] via oxidative addition.

Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system.

PubMed

He, Yuyang; Cao, Xiaobin; Wang, Jianwei; Bao, Huiming

2018-02-28

Although being out of equilibrium, biomolecules in organisms have the potential to approach isotope equilibrium locally because enzymatic reactions are intrinsically reversible. A rigorous approach that can describe isotope distribution among biomolecules and their apparent deviation from equilibrium state is lacking, however. Applying the concept of distance matrix in graph theory, we propose that apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference (|Δα|) matrix, in which the differences between the observed isotope composition (δ') and the calculated equilibrium fractionation factor (1000lnβ) can be more rigorously evaluated than by using a previous approach for multiple biomolecules. We tested our |Δα| matrix approach by re-analyzing published data of different amino acids (AAs) in potato and in green alga. Our re-analysis shows that biosynthesis pathways could be the reason for an apparently close-to-equilibrium relationship inside AA families in potato leaves. Different biosynthesis/degradation pathways in tubers may have led to the observed isotope distribution difference between potato leaves and tubers. The analysis of data from green algae does not support the conclusion that AAs are further from equilibrium in glucose-cultured green algae than in the autotrophic ones. Application of the |Δα| matrix can help us to locate potential reversible reactions or reaction networks in a complex system such as a metabolic system. The same approach can be broadly applied to all complex systems that have multiple components, e.g. geochemical or atmospheric systems of early Earth or other planets. Copyright © 2017 John Wiley & Sons, Ltd.

Complex dynamics and enhanced photosensitivity in a modified Belousov-Zhabotinsky reaction

NASA Astrophysics Data System (ADS)

Li, Nan; Zhao, Jinpei; Wang, Jichang

2008-06-01

This study presents an experimental investigation of nonlinear dynamics in a modified Belousov-Zhabotinsky (BZ) reaction, in which the addition of 1,4-benzoquinone induced various complex behaviors such as mixed-mode oscillations and consecutive period-adding bifurcations. In addition, the presence of 1,4-benzoquinone significantly enhanced the photosensitivity of the ferroin-catalyzed BZ system, in which light-induced transitions between simple and complex oscillations have been achieved. Mechanistic study suggests that the influence of benzoquinone may arise from its interactions with the metal catalyst ferroin/ferriin, where cyclic voltammograms illustrate that the presence of benzoquinone causes an increase in the redox potential of ferroin/ferriin couple, which may consequently alternate the oxidation and reduction paths of the catalyst.

Control of complex dynamics and chaos in distributed parameter systems

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

Chakravarti, S.; Marek, M.; Ray, W.H.

This paper discusses a methodology for controlling complex dynamics and chaos in distributed parameter systems. The reaction-diffusion system with Brusselator kinetics, where the torus-doubling or quasi-periodic (two characteristic incommensurate frequencies) route to chaos exists in a defined range of parameter values, is used as an example. Poincare maps are used for characterization of quasi-periodic and chaotic attractors. The dominant modes or topos, which are inherent properties of the system, are identified by means of the Singular Value Decomposition. Tested modal feedback control schemas based on identified dominant spatial modes confirm the possibility of stabilization of simple quasi-periodic trajectories in themore » complex quasi-periodic or chaotic spatiotemporal patterns.« less

Synthesis, characterization and catalytic activity of nanosized Ni complexed aminoclay

NASA Astrophysics Data System (ADS)

Ranchani, A. Amala Jeya; Parthasarathy, V.; Devi, A. Anitha; Meenarathi, B.; Anbarasan, R.

2017-11-01

A novel Ni complexed aminoclay (AC) catalyst was prepared by complexation method followed by reduction reaction. Various analytical techniques such as FTIR spectroscopy, UV-visible spectroscopy, DSC, TGA, SEM, HRTEM, EDX, XPS and WCA measurement are used to characterize the synthesized material. The AC-Ni catalyst system exhibited improved thermal stability and fiber-like morphology. The XPS results declared the formation of Ni nanoparticles. Thus, synthesized catalyst was tested towards the Schiff base formation reaction between various bio-medical polymers and aniline under air atmosphere at 85 °C for 24 h. The catalytic activity of the catalyst was studied by varying the % weight loading of the AC-Ni system towards the Schiff base formation. The Schiff base formation was quantitatively calculated by the 1H-NMR spectroscopy. While increasing the % weight loading of the AC-Ni catalyst, the % yield of Schiff base was also increased. The k app and Ti values were determined for the reduction of indole and α-terpineol in the presence of AC-Ni catalyst system. The experimental results were compared with the literature report.

Evolution of C−H Bond Functionalization from Methane to Methodology

PubMed Central

2016-01-01

This Perspective presents the fundamental principles, the elementary reactions, the initial catalytic systems, and the contemporary catalysts that have converted C−H bond functionalization from a curiosity to a reality for synthetic chemists. Many classes of elementary reactions involving transition-metal complexes cleave C−H bonds at typically unreactive positions. These reactions, coupled with a separate or simultaneous functionalization process lead to products containing new C−C, C−N, and C−O bonds. Such reactions were initially studied for the conversion of light alkanes to liquid products, but they have been used (and commercialized in some cases) most often for the synthesis of the more complex structures of natural products, medicinally active compounds, and aromatic materials. Such a change in direction of research in C−H bond functionalization is remarkable because the reactions must occur at an unactivated C−H bond over functional groups that are more reactive than the C−H bond toward classical reagents. The scope of reactions that form C−C bonds or install functionality at an unactivated C−H bond will be presented, and the potential future utility of these reactions will be discussed. PMID:26566092

Sites of superoxide and hydrogen peroxide production during fatty acid oxidation in rat skeletal muscle mitochondria.

PubMed

Perevoshchikova, Irina V; Quinlan, Casey L; Orr, Adam L; Gerencser, Akos A; Brand, Martin D

2013-08-01

H2O2 production by skeletal muscle mitochondria oxidizing palmitoylcarnitine was examined under two conditions: the absence of respiratory chain inhibitors and the presence of myxothiazol to inhibit complex III. Without inhibitors, respiration and H2O2 production were low unless carnitine or malate was added to limit acetyl-CoA accumulation. With palmitoylcarnitine alone, H2O2 production was dominated by complex II (44% from site IIF in the forward reaction); the remainder was mostly from complex I (34%, superoxide from site IF). With added carnitine, H2O2 production was about equally shared between complexes I, II, and III. With added malate, it was 75% from complex III (superoxide from site IIIQo) and 25% from site IF. Thus complex II (site IIF in the forward reaction) is a major source of H2O2 production during oxidation of palmitoylcarnitine ± carnitine. Under the second condition (myxothiazol present to keep ubiquinone reduced), the rates of H2O2 production were highest in the presence of palmitoylcarnitine ± carnitine and were dominated by complex II (site IIF in the reverse reaction). About half the rest was from site IF, but a significant portion, ∼40pmol H2O2·min(-1)·mg protein(-1), was not from complex I, II, or III and was attributed to the proteins of β-oxidation (electron-transferring flavoprotein (ETF) and ETF-ubiquinone oxidoreductase). The maximum rate from the ETF system was ∼200pmol H2O2·min(-1)·mg protein(-1) under conditions of compromised antioxidant defense and reduced ubiquinone pool. Thus complex II and the ETF system both contribute to H2O2 productionduring fatty acid oxidation under appropriate conditions. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantum Chemical Study of CH3 + O2 Combustion Reaction System: Catalytic Effects of Additional CO2 Molecule.

PubMed

Masunov, Artëm E; Wait, Elizabeth; Vasu, Subith S

2017-08-03

The supercritical carbon dioxide diluent is used to control the temperature and to increase the efficiency in oxycombustion fossil fuel energy technology. It may affect the rates of combustion by altering mechanisms of chemical reactions, compared to the ones at low CO 2 concentrations. Here, we investigate potential energy surfaces of the four elementary reactions in the CH 3 + O 2 reactive system in the presence of one CO 2 molecule. In the case of reaction CH 3 + O 2 → CH 2 O + OH (R1 channel), van der Waals (vdW) complex formation stabilizes the transition state and reduces the activation barrier by ∼2.2 kcal/mol. Alternatively, covalently bonded CO 2 may form a six-membered ring transition state and reduce the activation barrier by ∼0.6 kcal/mol. In case of reaction CH 3 + O 2 → CH 3 O + O (R2 channel), covalent participation of CO 2 lowers the barrier for the rate limiting step by 3.9 kcal/mol. This is expected to accelerate the R2 process, important for the branching step of the radical chain reaction mechanism. For the reaction CH 3 + O 2 → CHO + H 2 O (R3 channel) with covalent participation of CO 2 , the activation barrier is lowered by 0.5 kcal/mol. The reaction CH 2 O + OH → CHO + H 2 O (R4 channel) involves hydrogen abstraction from formaldehyde by OH radical. Its barrier is reduced from 7.1 to 0.8 kcal/mol by formation of vdW complex with spectator CO 2 . These new findings are expected to improve the kinetic reaction mechanism describing combustion processes in supercritical CO 2 medium.

Hot atoms in cosmic chemistry.

PubMed

Rossler, K; Jung, H J; Nebeling, B

1984-01-01

High energy chemical reactions and atom molecule interactions might be important for cosmic chemistry with respect to the accelerated species in solar wind, cosmic rays, colliding gas and dust clouds and secondary knock-on particles in solids. "Hot" atoms with energies ranging from a few eV to some MeV can be generated via nuclear reactions and consequent recoil processes. The chemical fate of the radioactive atoms can be followed by radiochemical methods (radio GC or HPLC). Hot atom chemistry may serve for laboratory simulation of the reactions of energetic species with gaseous or solid interstellar matter. Due to the effective measurement of 10(8)-10(10) atoms only it covers a low to medium dose regime and may add to the studies of ion implantation which due to the optical methods applied are necessarily in the high dose regime. Experimental results are given for the systems: C/H2O (gas), C/H2O (solid, 77 K), N/CH4 (solid, 77K) and C/NH3 (solid, 77 K). Nuclear reactions used for the generation of 2 to 3 MeV atoms are: N(p,alpha) 11C, 16O(p,alpha pn) 11C and 12C(d,n) 13N with 8 to 45 MeV protons or deuterons from a cyclotron. Typical reactions products are: CO, CO2, CH4, CH2O, CH3OH, HCOOH, NH3, CH3NH2, cyanamide, formamidine, guanidine etc. Products of hot reactions in solids are more complex than in corresponding gaseous systems, which underlines the importance of solid state reactions for the build-up of precursors for biomolecules in space. As one of the major mechanisms for product formation, the simultaneous or fast consecutive reactions of a hot carbon with two target molecules (reaction complex) is discussed.

A study on ?-dissipative synchronisation of coupled reaction-diffusion neural networks with time-varying delays

NASA Astrophysics Data System (ADS)

Ali, M. Syed; Zhu, Quanxin; Pavithra, S.; Gunasekaran, N.

2018-03-01

This study examines the problem of dissipative synchronisation of coupled reaction-diffusion neural networks with time-varying delays. This paper proposes a complex dynamical network consisting of N linearly and diffusively coupled identical reaction-diffusion neural networks. By constructing a suitable Lyapunov-Krasovskii functional (LKF), utilisation of Jensen's inequality and reciprocally convex combination (RCC) approach, strictly ?-dissipative conditions of the addressed systems are derived. Finally, a numerical example is given to show the effectiveness of the theoretical results.

Visualization of Proton and Electron Transfer Processes of a Biochemical Reaction by μSR

NASA Astrophysics Data System (ADS)

Kiyotani, Tamiko; Kobayashi, Masayoshi; Tanaka, Ichiro; Niimura, Nobuo

For the last several years, we have discussed and conducted experiments toward realization of visualization of electron and proton transfer process in an enzyme reaction using muon. As the first step for exploring the useful application of the μSR for the biological system, which is "μSR in Biology". A first μSR experiment on biochemical reaction was conducted using the complex of a digestive enzyme, a kind of serine-protease and the inhibitor at J-PARC and PSI.

Cox process representation and inference for stochastic reaction-diffusion processes

NASA Astrophysics Data System (ADS)

Schnoerr, David; Grima, Ramon; Sanguinetti, Guido

2016-05-01

Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to the social sciences, yet they are notoriously difficult to simulate and calibrate to observational data. Here we use ideas from statistical physics and machine learning to provide a solution to the inverse problem of learning a stochastic reaction-diffusion process from data. Our solution relies on a non-trivial connection between stochastic reaction-diffusion processes and spatio-temporal Cox processes, a well-studied class of models from computational statistics. This connection leads to an efficient and flexible algorithm for parameter inference and model selection. Our approach shows excellent accuracy on numeric and real data examples from systems biology and epidemiology. Our work provides both insights into spatio-temporal stochastic systems, and a practical solution to a long-standing problem in computational modelling.

A cascade reaction network mimicking the basic functional steps of adaptive immune response

NASA Astrophysics Data System (ADS)

Han, Da; Wu, Cuichen; You, Mingxu; Zhang, Tao; Wan, Shuo; Chen, Tao; Qiu, Liping; Zheng, Zheng; Liang, Hao; Tan, Weihong

2015-10-01

Biological systems use complex ‘information-processing cores’ composed of molecular networks to coordinate their external environment and internal states. An example of this is the acquired, or adaptive, immune system (AIS), which is composed of both humoral and cell-mediated components. Here we report the step-by-step construction of a prototype mimic of the AIS that we call an adaptive immune response simulator (AIRS). DNA and enzymes are used as simple artificial analogues of the components of the AIS to create a system that responds to specific molecular stimuli in vitro. We show that this network of reactions can function in a manner that is superficially similar to the most basic responses of the vertebrate AIS, including reaction sequences that mimic both humoral and cellular responses. As such, AIRS provides guidelines for the design and engineering of artificial reaction networks and molecular devices.

Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

DOE PAGES

Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; ...

2015-10-22

Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholinemore » catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.« less

Rational design of functional and tunable oscillating enzymatic networks

NASA Astrophysics Data System (ADS)

Semenov, Sergey N.; Wong, Albert S. Y.; van der Made, R. Martijn; Postma, Sjoerd G. J.; Groen, Joost; van Roekel, Hendrik W. H.; de Greef, Tom F. A.; Huck, Wilhelm T. S.

2015-02-01

Life is sustained by complex systems operating far from equilibrium and consisting of a multitude of enzymatic reaction networks. The operating principles of biology's regulatory networks are known, but the in vitro assembly of out-of-equilibrium enzymatic reaction networks has proved challenging, limiting the development of synthetic systems showing autonomous behaviour. Here, we present a strategy for the rational design of programmable functional reaction networks that exhibit dynamic behaviour. We demonstrate that a network built around autoactivation and delayed negative feedback of the enzyme trypsin is capable of producing sustained oscillating concentrations of active trypsin for over 65 h. Other functions, such as amplification, analog-to-digital conversion and periodic control over equilibrium systems, are obtained by linking multiple network modules in microfluidic flow reactors. The methodology developed here provides a general framework to construct dissipative, tunable and robust (bio)chemical reaction networks.

Transfer functions for protein signal transduction: application to a model of striatal neural plasticity.

PubMed

Scheler, Gabriele

2013-01-01

We present a novel formulation for biochemical reaction networks in the context of protein signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select a set of "source" species, which are interpreted as input signals. Signals are transmitted to all other species in the system (the "target" species) with a specific delay and with a specific transmission strength. The delay is computed as the maximal reaction time until a stable equilibrium for the target species is reached, in the context of all other reactions in the system. The transmission strength is the concentration change of the target species. The computed input-output transfer functions can be stored in a matrix, fitted with parameters, and even recalled to build dynamical models on the basis of state changes. By separating the temporal and the magnitudinal domain we can greatly simplify the computational model, circumventing typical problems of complex dynamical systems. The transfer function transformation of biochemical reaction systems can be applied to mass-action kinetic models of signal transduction. The paper shows that this approach yields significant novel insights while remaining a fully testable and executable dynamical model for signal transduction. In particular we can deconstruct the complex system into local transfer functions between individual species. As an example, we examine modularity and signal integration using a published model of striatal neural plasticity. The modularizations that emerge correspond to a known biological distinction between calcium-dependent and cAMP-dependent pathways. Remarkably, we found that overall interconnectedness depends on the magnitude of inputs, with higher connectivity at low input concentrations and significant modularization at moderate to high input concentrations. This general result, which directly follows from the properties of individual transfer functions, contradicts notions of ubiquitous complexity by showing input-dependent signal transmission inactivation.

Heterogeneous OH oxidation of motor oil particles causes selective depletion of branched and less cyclic hydrocarbons.

PubMed

Isaacman, Gabriel; Chan, Arthur W H; Nah, Theodora; Worton, David R; Ruehl, Chris R; Wilson, Kevin R; Goldstein, Allen H

2012-10-02

Motor oil serves as a useful model system for atmospheric oxidation of hydrocarbon mixtures typical of anthropogenic atmospheric particulate matter, but its complexity often prevents comprehensive chemical speciation. In this work we fully characterize this formerly "unresolved complex mixture" at the molecular level using recently developed soft ionization gas chromatography techniques. Nucleated motor oil particles are oxidized in a flow tube reactor to investigate the relative reaction rates of observed hydrocarbon classes: alkanes, cycloalkanes, bicycloalkanes, tricycloalkanes, and steranes. Oxidation of hydrocarbons in a complex aerosol is found to be efficient, with approximately three-quarters (0.72 ± 0.06) of OH collisions yielding a reaction. Reaction rates of individual hydrocarbons are structurally dependent: compared to normal alkanes, reaction rates increased by 20-50% with branching, while rates decreased ∼20% per nonaromatic ring present. These differences in rates are expected to alter particle composition as a function of oxidation, with depletion of branched and enrichment of cyclic hydrocarbons. Due to this expected shift toward ring-opening reactions heterogeneous oxidation of the unreacted hydrocarbon mixture is less likely to proceed through fragmentation pathways in more oxidized particles. Based on the observed oxidation-induced changes in composition, isomer-resolved analysis has potential utility for determining the photochemical age of atmospheric particulate matter with respect to heterogeneous oxidation.

IC-tagged proteins are able to interact with each other and perform complex reactions when integrated into muNS-derived inclusions.

PubMed

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.

Catalytic effects of glycine on prebiotic divaline and diproline formation.

PubMed

Plankensteiner, Kristof; Reiner, Hannes; Rode, Bernd M

2005-07-01

The catalytic effects of the simple amino acid glycine on the formation of diproline and divaline in the prebiotically relevant salt-induced peptide formation (SIPF) reaction was investigated in systems of different amino acid starting concentrations and using the two enantiomeric forms of the respective amino acid. Results show an improved applicability of the SIPF reaction to prebiotic conditions, especially at low amino acid concentrations, as presumably present in a primordial scenario, and indicate excellent conditions and resources for chemical evolution of peptides and proteins on the early earth. For valine, furthermore differences in catalytic yield increase are found indicating a chiral selectivity of the active copper complex of the reaction and showing a connection to previously found enantiomeric differences in complex formation constants with amino acids.

Co-complexes derived from alkene insertion to alkyne-dicobaltpentacarbonyl complexes: insight into the regioselectivity of pauson-khand reactions of cyclopropenes.

PubMed

Pallerla, Mahesh K; Yap, Glenn P A; Fox, Joseph M

2008-08-15

Described are the X-ray crystallographic and spectral properties of Co-complexes that were isolated from two Pauson-Khand reactions of chiral cyclopropenes. These are the first examples of isolated Co-complexes derived from the putative alkene-insertion intermediates of Pauson-Khand reactions. The binuclear Co-complexes are coordinated to mu-bonded, five-carbon "flyover" carbene ligands. It is proposed that the complexes result from cyclopropane fragmentation subsequent to alkene insertion. The observation of these metal complexes provides a rationale for the origin of regioselectivity in Pauson-Khand reactions of cyclopropenes.

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

PubMed

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 an early stage of development. In this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

Formation Mechanism of Spherical TiC in Ni-Ti-C System during Combustion Synthesis.

PubMed

Zhu, Guoliang; Wang, Wei; Wang, Rui; Zhao, Chuanbao; Pan, Weitao; Huang, Haijun; Du, Dafan; Wang, Donghong; Shu, Da; Dong, Anping; Sun, Baode; Jiang, Sheng; Pu, Yilong

2017-08-29

The formation mechanism of TiC particles in a Ni-Ti-C system were revealed by using differential thermal analysis (DTA), XRD, and SEM to identify the reaction products in different temperature ranges. The results indicated that the synthesis mechanism of TiC in Ni-Ti-C system was complex; several reactions were involved in the combustion synthesis of TiC-Ni composite. The Ni-Ti intermediate phases play important roles during the formation of TiC. Moreover, the influence of heating rate on the size range of TiC was also discussed.

Formation Mechanism of Spherical TiC in Ni-Ti-C System during Combustion Synthesis

PubMed Central

Zhu, Guoliang; Wang, Wei; Wang, Rui; Zhao, Chuanbao; Pan, Weitao; Huang, Haijun; Du, Dafan; Wang, Donghong; Shu, Da; Dong, Anping; Sun, Baode; Jiang, Sheng; Pu, Yilong

2017-01-01

The formation mechanism of TiC particles in a Ni-Ti-C system were revealed by using differential thermal analysis (DTA), XRD, and SEM to identify the reaction products in different temperature ranges. The results indicated that the synthesis mechanism of TiC in Ni-Ti-C system was complex; several reactions were involved in the combustion synthesis of TiC-Ni composite. The Ni-Ti intermediate phases play important roles during the formation of TiC. Moreover, the influence of heating rate on the size range of TiC was also discussed. PMID:28850088

Simulation of dual carbon-bromine stable isotope fractionation during 1,2-dibromoethane degradation.

PubMed

Jin, Biao; Nijenhuis, Ivonne; Rolle, Massimo

2018-06-01

We performed a model-based investigation to simultaneously predict the evolution of concentration, as well as stable carbon and bromine isotope fractionation during 1,2-dibromoethane (EDB, ethylene dibromide) transformation in a closed system. The modelling approach considers bond-cleavage mechanisms during different reactions and allows evaluating dual carbon-bromine isotopic signals for chemical and biotic reactions, including aerobic and anaerobic biological transformation, dibromoelimination by Zn(0) and alkaline hydrolysis. The proposed model allowed us to accurately simulate the evolution of concentrations and isotope data observed in a previous laboratory study and to successfully identify different reaction pathways. Furthermore, we illustrated the model capabilities in degradation scenarios involving complex reaction systems. Specifically, we examined (i) the case of sequential multistep transformation of EDB and the isotopic evolution of the parent compound, the intermediate and the reaction product and (ii) the case of parallel competing abiotic pathways of EDB transformation in alkaline solution.

Low-coordinate rare-earth complexes of the asymmetric 2,4-di-tert-butylphenolate ligand prepared by redox transmetallation/protolysis reactions, and their reactivity towards ring-opening polymerisation.

PubMed

Clark, Lawrence; Deacon, Glen B; Forsyth, Craig M; Junk, Peter C; Mountford, Philip; Townley, Josh P

2010-08-07

New trivalent lanthanoid aryloxide complexes have been prepared by redox transmetallation/protolysis (rtp) reactions using 2,4-di-tert-butylphenol (dbpH). Mononuclear octahedral complexes from tetrahydrofuran (thf) were of the type [Ln(dbp)(3)(thf)(3)] (Ln = La (1), Pr (2), Nd (3), Gd (4), Er (5)). The lanthanoid contraction results in the rather subtle change in stereochemistry from meridional (La, Pr, Nd, Gd) to facial (Er). An analogous reaction with neodymium in dimethoxyethane (dme), resulted in the isolation of the seven coordinate [Nd(dbp)(3)(dme)(2)] (6), and this is comparable with the thf complexes in terms of steric crowding. Dinuclear complexes of the type [Ln(2)(dbp)(6)(thf)(2)], (Ln = Nd (7), Er (8)) were obtained when 1 and 5 were recrystallised from toluene. These dimeric complexes contain two bridging and four terminal phenolates, as well as a single coordinated molecule of thf at each metal. A similar structural motif was observed for the products when the reaction was performed in diethyl ether, and in the absence of a solvent, yielding [Nd(2)(dbp)(6)(Et(2)O)(2)] (9) and [Nd(2)(dbp)(6)(dbpH)(2)] (10) respectively. Complexes 3 and 4 alone were efficient but poorly-controlled initiators for the ROP of rac-lactide, but with an excess of BnOH as a co-initiator they showed features consistent with immortal polymerisation. Use of BnNH(2) led to well-controlled, amine-initiated immortal ROP of rac-lactide, only the second report of this type of process for a group 3 or lanthanoid system.

Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network.

PubMed

Griffith, Mark; Courtney, Tod; Peccoud, Jean; Sanders, William H

2006-11-15

The stochastic kinetics of a well-mixed chemical system, governed by the chemical Master equation, can be simulated using the exact methods of Gillespie. However, these methods do not scale well as systems become more complex and larger models are built to include reactions with widely varying rates, since the computational burden of simulation increases with the number of reaction events. Continuous models may provide an approximate solution and are computationally less costly, but they fail to capture the stochastic behavior of small populations of macromolecules. In this article we present a hybrid simulation algorithm that dynamically partitions the system into subsets of continuous and discrete reactions, approximates the continuous reactions deterministically as a system of ordinary differential equations (ODE) and uses a Monte Carlo method for generating discrete reaction events according to a time-dependent propensity. Our approach to partitioning is improved such that we dynamically partition the system of reactions, based on a threshold relative to the distribution of propensities in the discrete subset. We have implemented the hybrid algorithm in an extensible framework, utilizing two rigorous ODE solvers to approximate the continuous reactions, and use an example model to illustrate the accuracy and potential speedup of the algorithm when compared with exact stochastic simulation. Software and benchmark models used for this publication can be made available upon request from the authors.

Monte Carlo isotopic inventory analysis for complex nuclear systems

NASA Astrophysics Data System (ADS)

Phruksarojanakun, Phiphat

Monte Carlo Inventory Simulation Engine (MCise) is a newly developed method for calculating isotopic inventory of materials. It offers the promise of modeling materials with complex processes and irradiation histories, which pose challenges for current, deterministic tools, and has strong analogies to Monte Carlo (MC) neutral particle transport. The analog method, including considerations for simple, complex and loop flows, is fully developed. In addition, six variance reduction tools provide unique capabilities of MCise to improve statistical precision of MC simulations. Forced Reaction forces an atom to undergo a desired number of reactions in a given irradiation environment. Biased Reaction Branching primarily focuses on improving statistical results of the isotopes that are produced from rare reaction pathways. Biased Source Sampling aims at increasing frequencies of sampling rare initial isotopes as the starting particles. Reaction Path Splitting increases the population by splitting the atom at each reaction point, creating one new atom for each decay or transmutation product. Delta Tracking is recommended for high-frequency pulsing to reduce the computing time. Lastly, Weight Window is introduced as a strategy to decrease large deviations of weight due to the uses of variance reduction techniques. A figure of merit is necessary to compare the efficiency of different variance reduction techniques. A number of possibilities for figure of merit are explored, two of which are robust and subsequently used. One is based on the relative error of a known target isotope (1/R 2T) and the other on the overall detection limit corrected by the relative error (1/DkR 2T). An automated Adaptive Variance-reduction Adjustment (AVA) tool is developed to iteratively define parameters for some variance reduction techniques in a problem with a target isotope. Sample problems demonstrate that AVA improves both precision and accuracy of a target result in an efficient manner. Potential applications of MCise include molten salt fueled reactors and liquid breeders in fusion blankets. As an example, the inventory analysis of a liquid actinide fuel in the In-Zinerator, a sub-critical power reactor driven by a fusion source, is examined. The result reassures MCise as a reliable tool for inventory analysis of complex nuclear systems.

Novel Visualization Approaches in Environmental Mineralogy

NASA Astrophysics Data System (ADS)

Anderson, C. D.; Lopano, C. L.; Hummer, D. R.; Heaney, P. J.; Post, J. E.; Kubicki, J. D.; Sofo, J. O.

2006-05-01

Communicating the complexities of atomic scale reactions between minerals and fluids is fraught with intrinsic challenges. For example, an increasing number of techniques are now available for the interrogation of dynamical processes at the mineral-fluid interface. However, the time-dependent behavior of atomic interactions between a solid and a liquid is often not adequately captured by two-dimensional line drawings or images. At the same time, the necessity for describing these reactions to general audiences is growing more urgent, as funding agencies are amplifying their encouragement to scientists to reach across disciplines and to justify their studies to public audiences. To overcome the shortcomings of traditional graphical representations, the Center for Environmental Kinetics Analysis is creating three-dimensional visualizations of experimental and simulated mineral reactions. These visualizations are then displayed on a stereo 3D projection system called the GeoWall. Made possible (and affordable) by recent improvements in computer and data projector technology, the GeoWall system uses a combination of computer software and hardware, polarizing filters and polarizing glasses, to present visualizations in true 3D. The three-dimensional views greatly improve comprehension of complex multidimensional data, and animations of time series foster better understanding of the underlying processes. The visualizations also offer an effective means to communicate the complexities of environmental mineralogy to colleagues, students and the public. Here we present three different kinds of datasets that demonstrate the effectiveness of the GeoWall in clarifying complex environmental reactions at the atomic scale. First, a time-resolved series of diffraction patterns obtained during the hydrothermal synthesis of metal oxide phases from precursor solutions can be viewed as a surface with interactive controls for peak scaling and color mapping. Second, the results of Rietveld analysis of cation exchange reactions in Mn oxides has provided three-dimensional difference Fourier maps. When stitched together in a temporal series, these offer an animated view of changes in atomic configurations during the process of exchange. Finally, molecular dynamical simulations are visualized as three-dimensional reactions between vibrating atoms in both the solid and the aqueous phases.

Selective CO2 reduction conjugated with H2O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

NASA Astrophysics Data System (ADS)

Morikawa, T.; Sato, S.; Arai, T.; Uemura, K.; Yamanaka, K. I.; Suzuki, T. M.; Kajino, T.; Motohiro, T.

2013-12-01

We developed a new hybrid photocatalyst for CO2 reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (ECBM) of the semiconductor and the CO2 reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO2 to formate using water as an electron donor and a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO2 reduction with a TiO2 photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.

Perspective: Two-dimensional resonance Raman spectroscopy

NASA Astrophysics Data System (ADS)

Molesky, Brian P.; Guo, Zhenkun; Cheshire, Thomas P.; Moran, Andrew M.

2016-11-01

Two-dimensional resonance Raman (2DRR) spectroscopy has been developed for studies of photochemical reaction mechanisms and structural heterogeneity in complex systems. The 2DRR method can leverage electronic resonance enhancement to selectively probe chromophores embedded in complex environments (e.g., a cofactor in a protein). In addition, correlations between the two dimensions of the 2DRR spectrum reveal information that is not available in traditional Raman techniques. For example, distributions of reactant and product geometries can be correlated in systems that undergo chemical reactions on the femtosecond time scale. Structural heterogeneity in an ensemble may also be reflected in the 2D spectroscopic line shapes of both reactive and non-reactive systems. In this perspective article, these capabilities of 2DRR spectroscopy are discussed in the context of recent applications to the photodissociation reactions of triiodide and myoglobin. We also address key differences between the signal generation mechanisms for 2DRR and off-resonant 2D Raman spectroscopies. Most notably, it has been shown that these two techniques are subject to a tradeoff between sensitivity to anharmonicity and susceptibility to artifacts. Overall, recent experimental developments and applications of the 2DRR method suggest great potential for the future of the technique.

Heterobimetallic transition metal/rare earth metal bifunctional catalysis: a Cu/Sm/Schiff base complex for syn-selective catalytic asymmetric nitro-Mannich reaction.

PubMed

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).

Chemistry with spatial control using particles and streams†

PubMed Central

Kalinin, Yevgeniy V.; Murali, Adithya

2012-01-01

Spatial control of chemical reactions, with micro- and nanometer scale resolution, has important consequences for one pot synthesis, engineering complex reactions, developmental biology, cellular biochemistry and emergent behavior. We review synthetic methods to engineer this spatial control using chemical diffusion from spherical particles, shells and polyhedra. We discuss systems that enable both isotropic and anisotropic chemical release from isolated and arrayed particles to create inhomogeneous and spatially patterned chemical fields. In addition to such finite chemical sources, we also discuss spatial control enabled with laminar flow in 2D and 3D microfluidic networks. Throughout the paper, we highlight applications of spatially controlled chemistry in chemical kinetics, reaction-diffusion systems, chemotaxis and morphogenesis. PMID:23145348

Catalysis of a 1,3-dipolar reaction by distorted DNA incorporating a heterobimetallic platinum(ii) and copper(ii) complex.

PubMed

Rivilla, Iván; de Cózar, Abel; Schäfer, Thomas; Hernandez, Frank J; Bittner, Alexander M; Eleta-Lopez, Aitziber; Aboudzadeh, Ali; Santos, José I; Miranda, José I; Cossío, Fernando P

2017-10-01

A novel catalytic system based on covalently modified DNA is described. This catalyst promotes 1,3-dipolar reactions between azomethine ylides and maleimides. The catalytic system is based on the distortion of the double helix of DNA by means of the formation of Pt(ii) adducts with guanine units. This distortion, similar to that generated in the interaction of DNA with platinum chemotherapeutic drugs, generates active sites that can accommodate N -metallated azomethine ylides. The proposed reaction mechanism, based on QM(DFT)/MM calculations, is compatible with thermally allowed concerted (but asynchronous) [π4s + π2s] mechanisms leading to the exclusive formation of racemic endo -cycloadducts.

Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum.

PubMed

Liao, Chen; Seo, Seung-Oh; Celik, Venhar; Liu, Huaiwei; Kong, Wentao; Wang, Yi; Blaschek, Hans; Jin, Yong-Su; Lu, Ting

2015-07-07

Microbial metabolism involves complex, system-level processes implemented via the orchestration of metabolic reactions, gene regulation, and environmental cues. One canonical example of such processes is acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum, during which cells convert carbon sources to organic acids that are later reassimilated to produce solvents as a strategy for cellular survival. The complexity and systems nature of the process have been largely underappreciated, rendering challenges in understanding and optimizing solvent production. Here, we present a system-level computational framework for ABE fermentation that combines metabolic reactions, gene regulation, and environmental cues. We developed the framework by decomposing the entire system into three modules, building each module separately, and then assembling them back into an integrated system. During the model construction, a bottom-up approach was used to link molecular events at the single-cell level into the events at the population level. The integrated model was able to successfully reproduce ABE fermentations of the WT C. acetobutylicum (ATCC 824), as well as its mutants, using data obtained from our own experiments and from literature. Furthermore, the model confers successful predictions of the fermentations with various network perturbations across metabolic, genetic, and environmental aspects. From foundation to applications, the framework advances our understanding of complex clostridial metabolism and physiology and also facilitates the development of systems engineering strategies for the production of advanced biofuels.

Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum

PubMed Central

Liao, Chen; Seo, Seung-Oh; Celik, Venhar; Liu, Huaiwei; Kong, Wentao; Wang, Yi; Blaschek, Hans; Jin, Yong-Su; Lu, Ting

2015-01-01

Microbial metabolism involves complex, system-level processes implemented via the orchestration of metabolic reactions, gene regulation, and environmental cues. One canonical example of such processes is acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum, during which cells convert carbon sources to organic acids that are later reassimilated to produce solvents as a strategy for cellular survival. The complexity and systems nature of the process have been largely underappreciated, rendering challenges in understanding and optimizing solvent production. Here, we present a system-level computational framework for ABE fermentation that combines metabolic reactions, gene regulation, and environmental cues. We developed the framework by decomposing the entire system into three modules, building each module separately, and then assembling them back into an integrated system. During the model construction, a bottom-up approach was used to link molecular events at the single-cell level into the events at the population level. The integrated model was able to successfully reproduce ABE fermentations of the WT C. acetobutylicum (ATCC 824), as well as its mutants, using data obtained from our own experiments and from literature. Furthermore, the model confers successful predictions of the fermentations with various network perturbations across metabolic, genetic, and environmental aspects. From foundation to applications, the framework advances our understanding of complex clostridial metabolism and physiology and also facilitates the development of systems engineering strategies for the production of advanced biofuels. PMID:26100881

Evaluation of an S-system root-finding method for estimating parameters in a metabolic reaction model.

PubMed

Iwata, Michio; Miyawaki-Kuwakado, Atsuko; Yoshida, Erika; Komori, Soichiro; Shiraishi, Fumihide

2018-02-02

In a mathematical model, estimation of parameters from time-series data of metabolic concentrations in cells is a challenging task. However, it seems that a promising approach for such estimation has not yet been established. Biochemical Systems Theory (BST) is a powerful methodology to construct a power-law type model for a given metabolic reaction system and to then characterize it efficiently. In this paper, we discuss the use of an S-system root-finding method (S-system method) to estimate parameters from time-series data of metabolite concentrations. We demonstrate that the S-system method is superior to the Newton-Raphson method in terms of the convergence region and iteration number. We also investigate the usefulness of a translocation technique and a complex-step differentiation method toward the practical application of the S-system method. The results indicate that the S-system method is useful to construct mathematical models for a variety of metabolic reaction networks. Copyright © 2018 Elsevier Inc. All rights reserved.

Functionalized Anodic Aluminum Oxide Membrane–Electrode System for Enzyme Immobilization

PubMed Central

2015-01-01

A nanoporous membrane system with directed flow carrying reagents to sequentially attached enzymes to mimic nature’s enzyme complex system was demonstrated. Genetically modified glycosylation enzyme, OleD Loki variant, was immobilized onto nanometer-scale electrodes at the pore entrances/exits of anodic aluminum oxide membranes through His6-tag affinity binding. The enzyme activity was assessed in two reactions—a one-step “reverse” sugar nucleotide formation reaction (UDP-Glc) and a two-step sequential sugar nucleotide formation and sugar nucleotide-based glycosylation reaction. For the one-step reaction, enzyme specific activity of 6–20 min–1 on membrane supports was seen to be comparable to solution enzyme specific activity of 10 min–1. UDP-Glc production efficiencies as high as 98% were observed at a flow rate of 0.5 mL/min, at which the substrate residence time over the electrode length down pore entrances was matched to the enzyme activity rate. This flow geometry also prevented an unwanted secondary product hydrolysis reaction, as observed in the test homogeneous solution. Enzyme utilization increased by a factor of 280 compared to test homogeneous conditions due to the continuous flow of fresh substrate over the enzyme. To mimic enzyme complex systems, a two-step sequential reaction using OleD Loki enzyme was performed at membrane pore entrances then exits. After UDP-Glc formation at the entrance electrode, aglycon 4-methylumbelliferone was supplied at the exit face of the reactor, affording overall 80% glycosylation efficiency. The membrane platform showed the ability to be regenerated with purified enzyme as well as directly from expression crude, thus demonstrating a single-step immobilization and purification process. PMID:25025628

Dynamics of ligand substitution in labile cobalt complexes resolved by ultrafast T-jump

PubMed Central

Ma, Hairong; Wan, Chaozhi; Zewail, Ahmed H.

2008-01-01

Ligand exchange of hydrated metal complexes is common in chemical and biological systems. Using the ultrafast T-jump, we examined this process, specifically the transformation of aqua cobalt (II) complexes to their fully halogenated species. The results reveal a stepwise mechanism with time scales varying from hundreds of picoseconds to nanoseconds. The dynamics are significantly faster when the structure is retained but becomes rate-limited when the octahedral-to-tetrahedral structural change bottlenecks the transformation. Evidence is presented, from bimolecular kinetics and energetics (enthalpic and entropic), for a reaction in which the ligand assists the displacement of water molecules, with the retention of the entering ligand in the activated state. The reaction time scale deviates by one to two orders of magnitude from that of ionic diffusion, suggesting the involvement of a collisional barrier between the ion and the much larger complex. PMID:18725628

Community detection in complex networks by using membrane algorithm

NASA Astrophysics Data System (ADS)

Liu, Chuang; Fan, Linan; Liu, Zhou; Dai, Xiang; Xu, Jiamei; Chang, Baoren

Community detection in complex networks is a key problem of network analysis. In this paper, a new membrane algorithm is proposed to solve the community detection in complex networks. The proposed algorithm is based on membrane systems, which consists of objects, reaction rules, and a membrane structure. Each object represents a candidate partition of a complex network, and the quality of objects is evaluated according to network modularity. The reaction rules include evolutionary rules and communication rules. Evolutionary rules are responsible for improving the quality of objects, which employ the differential evolutionary algorithm to evolve objects. Communication rules implement the information exchanged among membranes. Finally, the proposed algorithm is evaluated on synthetic, real-world networks with real partitions known and the large-scaled networks with real partitions unknown. The experimental results indicate the superior performance of the proposed algorithm in comparison with other experimental algorithms.

Glycine and diglycine as possible catalytic factors in the prebiotic evolution of peptides.

PubMed

Plankensteiner, Kristof; Righi, Alessandro; Rode, Bernd M

2002-06-01

Mutual catalytic effects within the Salt-Induced Peptide Formation (SIPF) Reaction might be one little puzzle piece in the complicated process of the formation of complex peptidic systems and their chemical evolution on the prebiotic earth. The catalytic effects of glycine and diglycine on the formation of dipeptides from mixed amino acid systems in the SIPF Reaction was investigated for systems with leucine, proline, valine and aspartic acid and showed to result in a significant increase of the yield of the majority of the produced dipeptides. The results of the experiments strongly confirm previous theories on the catalytic mechanism and show the ability of the SIPF Reaction to produce a very diverse set of peptide products with relevance to the formation of a biosphere.

Glycine and Diglycine as Possible Catalytic Factors in the Prebiotic Evolution of Peptides

NASA Astrophysics Data System (ADS)

Plankensteiner, Kristof; Righi, Alessandro; Rode, Bernd M.

2002-06-01

Mutual catalytic effects within the Salt-Induced Peptide Formation (SIPF) Reaction might be one little puzzle piece in the complicated process of the formation of complex peptidic systems and their chemical evolution on the prebiotic earth. The catalytic effects of glycine and diglycine on the formation of dipeptides from mixed amino acid systems in the SIPF Reaction was investigated for systems with leucine, proline, valine and aspartic acid and showed to result in a significant increase of the yield of the majority of the produced dipeptides. The results of the experiments strongly confirm previous theories on the catalytic mechanism and show the ability of the SIPF Reaction to produce a very diverse set of peptide products with relevance to the formation of a biosphere.

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

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

Schmehl, Russell H.

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 weremore » used to evaluate the light induced reactions and characterize very reactive intermediate substances formed during the reactions.« less

Co-complexes Derived from Alkene Insertion to Alkyne-dicobaltpentacarbonyl complexes: Insight into the Regioselectivity of Pauson-Khand Reactions of Cyclopropenes

PubMed Central

Pallerla, Mahesh K.; Yap, Glenn P. A.; Fox, Joseph M.

2009-01-01

Described are the X-ray crystallographic and spectral properties of Co-complexes that were isolated from two Pauson-Khand reactions of chiral cyclopropenes. These are the first examples of isolated Co-complexes derived from the putative alkene-insertion intermediates of Pauson-Khand reactions. The binuclear Co-complexes are coordinated to μ-bonded, five-carbon “flyover” carbene ligands. It is proposed that the complexes result from cyclopropane fragmentation subsequent to alkene insertion. The observation of these metal complexes provides a rationale for the origin of regioselectivity in Pauson-Khand reactions of cyclopropenes. PMID:18637694

Synthesis of branched iminosugars through a hypervalent iodine(III)-mediated radical-polar crossover reaction.

PubMed

Santana, Andrés G; Paz, Nieves R; Francisco, Cosme G; Suárez, Ernesto; González, Concepción C

2013-08-02

The synthesis of a novel type of branched iminosugars is described. This synthetic strategy is based on two key reactions: first, an aldol reaction with formaldehyde in order to introduce selectively the hydroxymethyl branch, and second, a tandem β-fragmentation-intramolecular cyclization reaction. The combination of both reactions afforded a battery of compounds exhibiting a great structural complexity, with the concomitant formation of a quaternary center, starting from readily available aldoses. With this approach we have demonstrated the usefulness of the fragmentation of anomeric alkoxyl radicals (ARF) promoted by the PhIO/I2 system for the preparation of new compounds with potential interest for both medicinal and synthetic chemists.

Mirror Me: Imitative Responses in Adults with Autism

ERIC Educational Resources Information Center

Schunke, Odette; Schöttle, Daniel; Vettorazzi, Eik; Brandt, Valerie; Kahl, Ursula; Bäumer, Tobias; Ganos, Christos; David, Nicole; Peiker, Ina; Engel, Andreas K; Brass, Marcel; Münchau, Alexander

2016-01-01

Dysfunctions of the human mirror neuron system have been postulated to underlie some deficits in autism spectrum disorders including poor imitative performance and impaired social skills. Using three reaction time experiments addressing mirror neuron system functions under simple and complex conditions, we examined 20 adult autism spectrum…

Pulse radiolysis studies of the reaction of nitrogen dioxide with the vitamin B₁₂ complexes Cob(II)alamin and nitrocobalamin

DOE PAGES

Brasch, Nicola E.; Cabelli, Diane E.; Dassanayake, Rohan S.

2014-10-06

Although now recognized to be an important reactive nitrogen species in biological systems that modifies the structures of proteins, DNA and lipids, there few studies on the reactivity of ˙NO2, including the reactions between ˙NO2 and transition metal complexes. We report kinetic studies on the reaction of ˙NO2 with two forms of vitamin B12 – cob(II)alamin and nitrocobalamin. UV-vis spectroscopy and HPLC analysis of the product solution show that ˙NO2 cleanly oxidizes the metal center of cob(II)alamin to form nitrocobalamin, with a second-order rate constant of (3.5 ± 0.3) × 10⁸ M⁻¹ s ⁻¹ (pH 7.0 and 9.0, RT, Imore » = 0.20 M). The stoichiometry of the reaction is 1:1. No reaction is detected by UV-vis spectroscopy and by HPLC analysis of the product solution when nitrocobalamin is exposed to up to 2.0 mol equiv.˙NO2.« less

Pulse radiolysis studies of the reaction of nitrogen dioxide with the vitamin B₁₂ complexes Cob(II)alamin and nitrocobalamin

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

Brasch, Nicola E.; Cabelli, Diane E.; Dassanayake, Rohan S.

Although now recognized to be an important reactive nitrogen species in biological systems that modifies the structures of proteins, DNA and lipids, there few studies on the reactivity of ˙NO2, including the reactions between ˙NO2 and transition metal complexes. We report kinetic studies on the reaction of ˙NO2 with two forms of vitamin B12 – cob(II)alamin and nitrocobalamin. UV-vis spectroscopy and HPLC analysis of the product solution show that ˙NO2 cleanly oxidizes the metal center of cob(II)alamin to form nitrocobalamin, with a second-order rate constant of (3.5 ± 0.3) × 10⁸ M⁻¹ s ⁻¹ (pH 7.0 and 9.0, RT, Imore » = 0.20 M). The stoichiometry of the reaction is 1:1. No reaction is detected by UV-vis spectroscopy and by HPLC analysis of the product solution when nitrocobalamin is exposed to up to 2.0 mol equiv.˙NO2.« less

Water oxidation catalysed by manganese compounds: from complexes to 'biomimetic rocks'.

PubMed

Wiechen, Mathias; Berends, Hans-Martin; Kurz, Philipp

2012-01-07

One of the most fundamental processes of the natural photosynthetic reaction sequence is the light-driven oxidation of water to molecular oxygen. In vivo, this reaction takes place in the large protein ensemble Photosystem II, where a μ-oxido-Mn(4)Ca- cluster, the oxygen-evolving-complex (OEC), has been identified as the catalytic site for the four-electron/four-proton redox reaction of water oxidation. This Perspective presents recent progress for three strategies which have been followed to prepare functional synthetic analogues of the OEC: (1) the synthesis of dinuclear manganese complexes designed to act as water-oxidation catalysts in homogeneous solution, (2) heterogeneous catalysts in the form of clay hybrids of such Mn(2)-complexes and (3) the preparation of manganese oxide particles of different compositions and morphologies. We discuss the key observations from the studies of such synthetic manganese systems in order to shed light upon the catalytic mechanism of natural water oxidation. Additionally, it is shown how research in this field has recently been motivated more and more by the prospect of finding efficient, robust and affordable catalysts for light-driven water oxidation, a key reaction of artificial photosynthesis. As manganese is an abundant and non-toxic element, manganese compounds are very promising candidates for the extraction of reduction equivalents from water. These electrons could consecutively be fed into the synthesis of "solar fuels" such as hydrogen or methanol.

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

Wu, Fuke, E-mail: wufuke@mail.hust.edu.cn; Tian, Tianhai, E-mail: tianhai.tian@sci.monash.edu.au; Rawlings, James B., E-mail: james.rawlings@wisc.edu

The frequently used reduction technique is based on the chemical master equation for stochastic chemical kinetics with two-time scales, which yields the modified stochastic simulation algorithm (SSA). For the chemical reaction processes involving a large number of molecular species and reactions, the collection of slow reactions may still include a large number of molecular species and reactions. Consequently, the SSA is still computationally expensive. Because the chemical Langevin equations (CLEs) can effectively work for a large number of molecular species and reactions, this paper develops a reduction method based on the CLE by the stochastic averaging principle developed in themore » work of Khasminskii and Yin [SIAM J. Appl. Math. 56, 1766–1793 (1996); ibid. 56, 1794–1819 (1996)] to average out the fast-reacting variables. This reduction method leads to a limit averaging system, which is an approximation of the slow reactions. Because in the stochastic chemical kinetics, the CLE is seen as the approximation of the SSA, the limit averaging system can be treated as the approximation of the slow reactions. As an application, we examine the reduction of computation complexity for the gene regulatory networks with two-time scales driven by intrinsic noise. For linear and nonlinear protein production functions, the simulations show that the sample average (expectation) of the limit averaging system is close to that of the slow-reaction process based on the SSA. It demonstrates that the limit averaging system is an efficient approximation of the slow-reaction process in the sense of the weak convergence.« less

Binuclear cyclometalated organoplatinum complexes containing 1,1'-bis(diphenylphosphino)ferrocene as spacer ligand: kinetics and mechanism of MeI oxidative addition.

PubMed

Jamali, Sirous; Nabavizadeh, S Masoud; Rashidi, Mehdi

2008-06-16

The binuclear complex [Pt2Me2(ppy)2(mu-dppf)], 1, in which ppy = deprotonated 2-phenylpyridyl and dppf = 1,1'-bis(diphenylphosphino)ferrocene, was synthesized by the reaction of [PtMe(SMe2)(ppy)] with 0.5 equiv of dppf at room temperature. In this reaction when 1 equiv of dppf was used, the dppf chelating complex 2, [PtMe(dppf)(ppy-kappa1C)], was obtained. The reaction of Pt(II)-Pt(II) complex 1 with excess MeI gave the Pt(IV)-Pt(IV) complex [Pt2I2Me4(ppy)2(mu-dppf)], 3. When the reaction was performed with 1 equiv of MeI, a mixture containing unreacted complex 1, a mixed-valence Pt(II)-Pt(IV) complex [PtMe(ppy)(mu-dppf)PtIMe2(ppy)], 4, and complex 3 was obtained. In a comparative study, the reaction of [PtMe(SMe2)(ppy)] with 1 equiv of monodentate phosphine PPh3 gave [PtMe(ppy)(PPh3)], A. MeI was reacted with A to give the platinum(IV) complex [PtMe2I(ppy)(PPh3)], C. All the complexes were fully characterized using multinuclear (1H, 31P, 13C, and 195Pt) NMR spectroscopy, and complex 2 was further identified by single crystal X-ray structure determination. The reaction of binuclear Pt(II)-Pt(II) complex 1 with excess MeI was monitored by low temperature 31P NMR spectroscopy and further by 1H NMR spectroscopy, and the kinetics of the reaction was studied by UV-vis spectroscopy. On the basis of the data, a mechanism has been suggested for the reaction which overall involved stepwise oxidative addition of MeI to the two Pt(II) centers. In this suggested mechanism, the reaction proceeded through a number of Pt(II)-Pt(IV) and Pt(IV)-Pt(IV) intermediates. Although MeI in each step was trans oxidatively added to one of the Pt(II) centers, further trans to cis isomerizations of Me and I groups were also identified. A comparative kinetic study of the reaction of monomeric platinum(II) complex A with MeI was also performed. The rate of reaction of MeI with complex 1 was some 3.5 times faster than that with complex A, indicating that dppf in the complex 1, as compared with PPh 3 in the complex A, has significantly enhanced the electron richness of the platinum centers.

Pt-Mechanistic Study of the β-Hydrogen Elimination from Organoplatinum(II) Enolate Complexes

PubMed Central

Alexanian, Erik J.; Hartwig, John F.

2010-01-01

A detailed mechanistic investigation of the thermal reactions of a series of bisphosphine alkylplatinum(II) enolate complexes is reported. The reactions of methylplatinum enolate complexes in the presence of added phosphine form methane and either free or coordinated enone, depending on the steric properties of the enone. Kinetic studies were conducted to determine the relationship between the rates and mechanism of β-hydrogen elimination from enolate complexes and the rates and mechanism of β-hydrogen elimination from alkyl complexes. The rates of reactions of the enolates were inversely dependent on the concentration of added phosphine, indicating that β-hydrogen elimination from the enolate complexes occurs after reversible dissociation of a phosphine. A normal, primary kinetic isotope effect was measured, and this effect was consistent with rate-limiting β-hydrogen elimination or C-H bond-forming reductive elimination to form methane. Reactions of substituted enolate complexes were also studied to determine the effect of the steric and electronic properties of the enolate complexes on the rates of β-hydrogen elimination. These studies showed that reactions of the alkylplatinum enolate complexes were retarded by electron-withdrawing substituents on the enolate and that reactions of enolate complexes possessing alkyl substituents at the β-position occurred at rates that were similar to those of complexes lacking alkyl substituents at this position. Despite the trend in electronic effects on the rates of reactions of enolate complexes and the substantial electronic differences between an enolate and an alkyl ligand, the rates of decomposition of the enolate complexes were similar to those of the analogous alkyl complexes. To the extent that the rates of reaction of the two types of complex are different, those involving β-hydrogen elimination from the enolate ligand were faster. A difference between the identity of the rate-determining step for decomposition of the two classes of complexes and an effect of stereochemistry on the selectivity for β-hydrogen elimination are possible origins of the observed phenomena. PMID:18954048

Complete characterization of the constrained geometry bimolecular reaction O(1D)+N2O-->NO+NO by three-dimensional velocity map imaging

NASA Astrophysics Data System (ADS)

Gödecke, Niels; Maul, Christof; Chichinin, Alexey I.; Kauczok, Sebastian; Gericke, Karl-Heinz

2009-08-01

The bimolecular reaction O(D1)+N2O→NO+NO was photoinitiated in the (N2O)2 dimer at a wavelength of 193 nm and was investigated by three-dimensional (3D) velocity map imaging. State selective 3D momentum vector distributions were monitored and analyzed. For the first time, kinetic energy resolution and stereodynamic information about the reaction under constrained geometry conditions is available. Directly observable NO products exhibit moderate vibrational excitation and are rotationally and translationally cold. Speed and spatial distributions suggest a pronounced backward scattering of the observed products with respect to the direction of motion of the O(D1) atom. Forward scattered partner products, which are not directly detectable are also translationally cold, but carry very large internal energy as vibration or rotation. The results confirm and extend previous studies on the complex initiated reaction system. The restricted geometry of the van der Waals complex seems to favor an abstraction reaction of the terminal nitrogen atom by the O(D1) atom, which is in striking contrast to the behavior observed for the unrestricted gas phase reaction under bulk conditions.

Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

NASA Astrophysics Data System (ADS)

Martin, Daniel R.; Matyushov, Dmitry V.

2015-04-01

Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ˜0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

Models in the Design and Validation of Eddy Current Inspection for Cracking in the Shuttle Reaction Control System Thruster

NASA Technical Reports Server (NTRS)

Aldrin, John C.; Williams, Phillip A.; Wincheski, Russell (Buzz) A.

2008-01-01

A case study is presented for using models in eddy current NDE design for crack detection in Shuttle Reaction Control System thruster components. Numerical methods were used to address the complex geometry of the part and perform parametric studies of potential transducer designs. Simulations were found to show agreement with experimental results. Accurate representation of the coherent noise associated with the measurement and part geometry was found to be critical to properly evaluate the best probe designs.

Nearside-farside, local angular momentum and resummation theories: Useful tools for understanding the dynamics of complex-mode reactions

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

Hankel, Marlies, E-mail: m.hankel@uq.edu.au, E-mail: j.n.l.connor@manchester.ac.uk; Connor, J. N. L., E-mail: m.hankel@uq.edu.au, E-mail: j.n.l.connor@manchester.ac.uk

2015-07-15

A valuable tool for understanding the dynamics of direct reactions is Nearside-Farside (NF) scattering theory. It makes a decomposition of the (resummed) partial wave series for the scattering amplitude, both for the differential cross section (DCS) and the Local Angular Momentum (LAM). This paper makes the first combined application of these techniques to complex-mode reactions. We ask if NF theory is a useful tool for their identification, in particular, can it distinguish complex-mode from direct-mode reactions? We also ask whether NF theory can identify NF interference oscillations in the full DCSs of complex-mode reactions. Our investigation exploits the fact thatmore » accurate quantum scattering matrix elements have recently become available for complex-mode reactions. We first apply NF theory to two simple models for the scattering amplitude of a complex-mode reaction: One involves a single Legendre polynomial; the other involves a single Legendre function of the first kind, whose form is suggested by complex angular momentum theory. We then study, at fixed translational energies, four state-to-state complex-mode reactions. They are: S({sup 1}D) + HD → SH + D, S({sup 1}D) + DH → SD + H, N({sup 2}D) +H{sub 2} → NH + H, and H{sup +} + D{sub 2} → HD + D{sup +}. We compare the NF results for the DCSs and LAMs with those for a state-to-state direct reaction, namely, F + H{sub 2} → FH + H. We demonstrate that NF theory is a valuable tool for identifying and analyzing the dynamics of complex-mode reactions.« less

Microhydration Effects on the Intermediates of the SN2 Reacation of Iodide Anion with Methyl Iodine

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

Doi, Keisuke; Togano, Eijiro; Xantheas, Sotiris S.

2013-04-15

Reactions of halide anions with methyl halides (X- + CH3Y → XCH3 + Y-) are bimolecular nucleophilic substitution (SN2) reactions that have been well investigated in the last few decades.[1] Figure 1 shows typical potential energy surfaces (PESs) proposed for symmetric (X- + CH3X → XCH3 + X-) SN2 reactions along the reaction coordinate. In the gas phase, the PES has two minima corresponding to the stable X-(CH3X) complexes.[2] The PES is substantially distorted by the solvation. Since the negative charge is delocalized over the [X•••CH3•••X]- moiety at the transition state the stabilization energy gained by the solvation is smallermore » for the transition state than that for the (X- + CH3X) reactants or the X- (CH3X) complexes. In solution, a large potential barrier exists between the reactants and products. The rate constants of these reactions in protic solvents were reported to be a few orders of magnitude smaller than those in aprotic solvents; this trend was explained by the formation of solvation shells of protic molecules around the halide anions.[1,3] Morokuma has previously reported a theoretical study on the PES of the (Cl- + CH3Cl → ClCH3 + Cl-) SN2 reaction with a few H2O molecules. The attachment of H2O molecules to the Cl-(CH3Cl) reactive system produces metastable isomers, which affect the reaction mechanism.[4] Johnson and coworkers extensively investigated the structure and reactions of halide anion complexes in the gas phase using photodissociation spectroscopy.« less

Static and kinetic studies of calmodulin and melittin complex.

PubMed

Itakura, M; Iio, T

1992-08-01

Ca2+ binding to calmodulin triggers conformational change of the protein which induces exposure of hydrophobic surfaces. Melittin has been believed to bind to Ca(2+)-bound calmodulin through the exposed hydrophobic surfaces. However, tryptophan fluorescence measurements and gel chromatography experiments with the melittin-calmodulin system revealed that melittin bound to calmodulin at zero salt concentration even in the absence of Ca2+; addition of salt removed melittin from Ca(2+)-free calmodulin. This means not only the hydrophobic interaction but also the electrostatic interaction contributes to the melittin-calmodulin binding. The fluorescence stopped-flow studies of the dissociation reaction of melittin-calmodulin complex revealed that Ca2+ removal from the complex induced a conformational change of calmodulin, resulting in reduction of the hydrophobic interaction between melittin and calmodulin, but the electrostatic interaction kept melittin still bound to calmodulin for a subsecond lag period, after which melittin dissociated from calmodulin. The fluorescence stopped-flow experiments on the dissociation reaction of complex of melittin and tryptic fragment(s) of calmodulin revealed that the lag period of the melittin dissociation reaction was attributable to the interaction between the C-terminal half of calmodulin and the C-terminal region of melittin.

Enhanced hydroxyl radical production by dihydroxybenzene-driven Fenton reactions: implications for wood biodegradation.

PubMed

Contreras, David; Rodríguez, Jaime; Freer, Juanita; Schwederski, Brigitte; Kaim, Wolfgang

2007-09-01

Brown rot fungi degrade wood, in initial stages, mainly through hydroxyl radicals (.OH) produced by Fenton reactions. These Fenton reactions can be promoted by dihydroxybenzenes (DHBs), which can chelate and reduce Fe(III), increasing the reactivity for different substrates. This mechanism allows the extensive degradation of carbohydrates and the oxidation of lignin during wood biodegradation by brown rot fungi. To understand the enhanced reactivity in these systems, kinetics experiments were carried out, measuring .OH formation by the spin-trapping technique of electron paramagnetic resonance spectroscopy. As models of the fungal DHBs, 1,2-dihydroxybenzene (catechol), 2,3-dihydroxybenzoic acid and 3,4-dihydroxybenzoic acid were utilized as well as 1,2-dihydroxy-3,5-benzenedisulfonate as a non-Fe(III)-reducing substance for comparison. Higher amounts and maintained concentrations of .OH were observed in the driven Fenton reactions versus the unmodified Fenton process. A linear correlation between the logarithms of complex stability constants and the .OH production was observed, suggesting participation of such complexes in the radical production.

A Nonequilibrium Rate Formula for Collective Motions of Complex Molecular Systems

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2010-09-01

We propose a compact reaction rate formula that accounts for a non-equilibrium distribution of residence times of complex molecules, based on a detailed study of the coarse-grained phase space of a reaction coordinate. We take the structural transition dynamics of a six-atom Morse cluster between two isomers as a prototype of multi-dimensional molecular reactions. Residence time distribution of one of the isomers shows an exponential decay, while that of the other isomer deviates largely from the exponential form and has multiple peaks. Our rate formula explains such equilibrium and non-equilibrium distributions of residence times in terms of the rates of diffusions of energy and the phase of the oscillations of the reaction coordinate. Rapid diffusions of energy and the phase generally give rise to the exponential decay of residence time distribution, while slow diffusions give rise to a non-exponential decay with multiple peaks. We finally make a conjecture about a general relationship between the rates of the diffusions and the symmetry of molecular mass distributions.

Oxidation of Bromide to Bromine by Ruthenium(II) Bipyridine-Type Complexes Using the Flash-Quench Technique.

PubMed

Tsai, Kelvin Yun-Da; Chang, I-Jy

2017-07-17

Six ruthenium complexes, [Ru(bpy) 3 ] 2+ (1), [Ru(bpy) 2 (deeb)] 2+ (2), [Ru(deeb) 2 (dmbpy)] 2+ (3), [Ru(deeb) 2 (bpy)] 2+ (4), [Ru(deeb) 3 ] 2+ (5), and [Ru(deeb) 2 (bpz)] 2+ (6) (bpy: 2,2'-bipyridine; deeb: 4,4'-diethylester-2,2'-bipyridine; dmbpy: 4,4'-dimethyl-2,2'-bipyridine, bpz: 2,2'-bipyrazine), have been employed to sensitize photochemical oxidation of bromide to bromine. The oxidation potential for complexes 1-6 are 1.26, 1.36, 1.42, 1.46, 1.56, and 1.66 V vs SCE, respectively. The bimolecular rate constants for the quenching of complexes 1-6 by ArN 2 + (bromobenzenediazonium) are determined as 1.1 × 10 9 , 1.6 × 10 8 , 1.4 × 10 8 , 1.2 × 10 8 , 6.4 × 10 7 , and 8.9 × 10 6 M -1 s -1 , respectively. Transient kinetics indicated that Br - reacted with photogenerated Ru(III) species at different rates. Bimolecular rate constants for the oxidation of Br - by the Ru(III) species derived from complexes 1-5 are observed as 1.2 × 10 8 , 1.3 × 10 9 , 4.0 × 10 9 , 4.8 × 10 9 , and 1.1 × 10 10 , M -1 s -1 , respectively. The last reaction kinetics observed in the three-component system consisting of a Ru sensitizer, quencher, and bromide is shown to be independent of the Ru sensitizer. The final product was identified as bromine by its reaction with hexene. The last reaction kinetics is assigned to the disproportionation reaction of Br 2 -• ions, for which the rate constant is determined as 5 × 10 9 M -1 s -1 . Though complex 6 has the highest oxidation potential in the Ru(II)/Ru(III) couple, its excited state fails to react with ArN 2 + sufficiently for subsequent reactions. The Ru(III) species derived from complex 1 reacts with Br - at the slowest rate. Complexes 2-5 are excellent photosensitizers to drive photooxidation of bromide to bromine.

Final Technical Report: Mathematical Foundations for Uncertainty Quantification in Materials Design

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

Plechac, Petr; Vlachos, Dionisios G.

We developed path-wise information theory-based and goal-oriented sensitivity analysis and parameter identification methods for complex high-dimensional dynamics and in particular of non-equilibrium extended molecular systems. The combination of these novel methodologies provided the first methods in the literature which are capable to handle UQ questions for stochastic complex systems with some or all of the following features: (a) multi-scale stochastic models such as (bio)chemical reaction networks, with a very large number of parameters, (b) spatially distributed systems such as Kinetic Monte Carlo or Langevin Dynamics, (c) non-equilibrium processes typically associated with coupled physico-chemical mechanisms, driven boundary conditions, hybrid micro-macro systems,more » etc. A particular computational challenge arises in simulations of multi-scale reaction networks and molecular systems. Mathematical techniques were applied to in silico prediction of novel materials with emphasis on the effect of microstructure on model uncertainty quantification (UQ). We outline acceleration methods to make calculations of real chemistry feasible followed by two complementary tasks on structure optimization and microstructure-induced UQ.« less

Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

NASA Technical Reports Server (NTRS)

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

1994-01-01

Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

Ultrastructural Localization of Peroxidase Activity in Human Platelets and Megakaryocytes

PubMed Central

Breton-Gorius, Janine; Guichard, Josette

1972-01-01

Normal human platelets and megakaryocytes were examined for peroxidase activity by the diaminobenzidine (DAB) cytochemical technic. When the fixation and the incubation were adequate, a strong reaction was present in the dense tubular system of platelets suspended in plasma or spread on carbon. The black reaction product was ascribed to enzyme activity, since the reaction was completely eliminated when H2O2 or DAB were omitted, or when H2O2 was in excess. In addition, the reaction was inhibited by aminotriazole, cyanide and azide. In the human megakaryocytes, the reaction was localized in the endoplasmic reticulum including the perinuclear envelope. The Golgi complex and the clear vacuolar system were negative for the reaction. After platelet release, the reaction was always seen in the perinuclear space. The nature and function of the enzyme, as well as its possible relationships with catalase, are discussed. ImagesFig 3Fig 4Fig 5Fig 6Fig 7Fig 8Fig 9Fig 10Fig 11Fig 1Fig 2Fig 12Fig 13Fig 14Fig 15Fig 16 PMID:5009974

The mineralogic evolution of the Martian surface through time: Implications from chemical reaction path modeling studies

NASA Technical Reports Server (NTRS)

Plumlee, G. S.; Ridley, W. I.; Debraal, J. D.; Reed, M. H.

1993-01-01

Chemical reaction path calculations were used to model the minerals that might have formed at or near the Martian surface as a result of volcano or meteorite impact driven hydrothermal systems; weathering at the Martian surface during an early warm, wet climate; and near-zero or sub-zero C brine-regolith reactions in the current cold climate. Although the chemical reaction path calculations carried out do not define the exact mineralogical evolution of the Martian surface over time, they do place valuable geochemical constraints on the types of minerals that formed from an aqueous phase under various surficial and geochemically complex conditions.

A fully coupled 3D transport model in SPH for multi-species reaction-diffusion systems

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

Adami, Stefan; Hu, X. Y.; Adams, N. A.

2011-08-23

Abstract—In this paper we present a fully generalized transport model for multiple species in complex two and threedimensional geometries. Based on previous work [1] we have extended our interfacial reaction-diffusion model to handle arbitrary numbers of species allowing for coupled reaction models. Each species is tracked independently and we consider different physics of a species with respect to the bulk phases in contact. We use our SPH model to simulate the reaction-diffusion problem on a pore-scale level of a solid oxide fuel cell (SOFC) with special emphasize on the effect of surface diffusion.

Toward simulating complex systems with quantum effects

NASA Astrophysics Data System (ADS)

Kenion-Hanrath, Rachel Lynn

Quantum effects like tunneling, coherence, and zero point energy often play a significant role in phenomena on the scales of atoms and molecules. However, the exact quantum treatment of a system scales exponentially with dimensionality, making it impractical for characterizing reaction rates and mechanisms in complex systems. An ongoing effort in the field of theoretical chemistry and physics is extending scalable, classical trajectory-based simulation methods capable of capturing quantum effects to describe dynamic processes in many-body systems; in the work presented here we explore two such techniques. First, we detail an explicit electron, path integral (PI)-based simulation protocol for predicting the rate of electron transfer in condensed-phase transition metal complex systems. Using a PI representation of the transferring electron and a classical representation of the transition metal complex and solvent atoms, we compute the outer sphere free energy barrier and dynamical recrossing factor of the electron transfer rate while accounting for quantum tunneling and zero point energy effects. We are able to achieve this employing only a single set of force field parameters to describe the system rather than parameterizing along the reaction coordinate. Following our success in describing a simple model system, we discuss our next steps in extending our protocol to technologically relevant materials systems. The latter half focuses on the Mixed Quantum-Classical Initial Value Representation (MQC-IVR) of real-time correlation functions, a semiclassical method which has demonstrated its ability to "tune'' between quantum- and classical-limit correlation functions while maintaining dynamic consistency. Specifically, this is achieved through a parameter that determines the quantumness of individual degrees of freedom. Here, we derive a semiclassical correction term for the MQC-IVR to systematically characterize the error introduced by different choices of simulation parameters, and demonstrate the ability of this approach to optimize MQC-IVR simulations.

Surface-Sensitive and Bulk Studies on the Complexation and Photosensitized Degradation of Catechol by Iron(III) as a Model for Multicomponent Aerosol Systems

NASA Astrophysics Data System (ADS)

Al-abadleh, H. A.; Tofan-Lazar, J.; Situm, A.; Ruffolo, J.; Slikboer, S.

2013-12-01

Surface water plays a crucial role in facilitating or inhibiting surface reactions in atmospheric aerosols. Little is known about the role of surface water in the complexation of organic molecules to transition metals in multicomponent aerosol systems. We will show results from real time diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) experiments for the in situ complexation of catechol to Fe(III) and its photosensitized degradation under dry and humid conditions. Catechol was chosen as a simple model for humic-like substances (HULIS) in aerosols and aged polyaromatic hydrocarbons (PAH). It has also been detected in secondary organic aerosols (SOA) formed from the reaction of hydroxyl radicals with benzene. Given the importance of the iron content in aerosols and its biogeochemistry, our studies were conducted using FeCl3. For comparison, these surface-sensitive studies were complemented with bulk aqueous ATR-FTIR, UV-vis, and HPLC measurements for structural, quantitative and qualitative information about complexes in the bulk, and potential degradation products. The implications of our studies on understanding interfacial and condensed phase chemistry relevant to multicomponent aerosols, water thin islands on buildings, and ocean surfaces containing transition metals will be discussed.

A chemiluminescence method to detect hydroquinone with water-soluble sulphonato-(salen)manganese(III) complex as catalyst.

PubMed

Zhang, Guangbin; Tang, Yuhai; Sun, Yang; Yu, Hua; Du, Wei; Fu, Qiang

2016-02-01

A water-soluble sulphonato-(salen)manganese(III) complex with excellent catalytic properties was synthesized and demonstrated to greatly enhance the chemiluminescence signal of the hydrogen peroxide - luminol reaction. Coupled with flow-injection technique, a simple and sensitive chemiluminescence method was first developed to detect hydroquinone based on the chemiluminescence system of the hydrogen peroxide-luminol-sulphonato-(salen)manganese(III) complex. Under optimal conditions, the assay exhibited a wide linear range from 0.1 to 10 ng mL(-1) with a detection limit of 0.05 ng mL(-1) for hydroquinone. The method was applied successfully to detect hydroquinone in tap-water and mineral-water, with a sampling frequency of 120 times per hour. The relative standard deviation for determination of hydroquinone was less than 5.6%, and the recoveries ranged from 96.8 to 103.0%. The ultraviolet spectra, chemiluminescence spectra, and the reaction kinetics for the peroxide-luminol-sulphonato-(salen)manganese(III) complex system were employed to study the possible chemiluminescence mechanism. The proposed chemiluminescence analysis technique is rapid and sensitive, with low cost, and could be easily extended and applied to other compounds. Copyright © 2015 John Wiley & Sons, Ltd.

A DAG Scheduling Scheme on Heterogeneous Computing Systems Using Tuple-Based Chemical Reaction Optimization

PubMed Central

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems. PMID:25143977

A DAG scheduling scheme on heterogeneous computing systems using tuple-based chemical reaction optimization.

PubMed

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems.

Simultaneous Speciation, Structure, and Equilibrium Constant Determination in the Ni2+-EDTA-CN- Ternary System via High-Resolution Laboratory X-ray Absorption Fine Structure Spectroscopy and Theoretical Calculations.

PubMed

Bajnóczi, Éva G; Németh, Zoltán; Vankó, György

2017-11-20

Even quite simple chemical systems can involve many components and chemical states, and sometimes it can be very difficult to differentiate them by their hardly separable physical-chemical properties. The Ni II -EDTA-CN - (EDTA = ethylenediaminetetraacetic acid) ternary system is a good example for this problem where, in spite of its fairly simple components and numerous investigations, several molecular combinations can exist, all of them not having been identified unambiguously yet. In order to achieve a detailed understanding of the reaction steps and chemical equilibria, methods are required in which the structural transitions in the different reaction steps can be followed via element-selective complex spectral feature sets. With the help of our recently developed von Hámos type high-resolution laboratory X-ray absorption spectrometer, both the structural variations and stability constants of the forming complexes were determined from the same measurement series, proving that X-ray absorption spectroscopy can be considered as a multifaced, table-top tool in coordination chemistry. Furthermore, with the help of theoretical calculations, independent structural evidence was also given for the formation of the [NiEDTA(CN)] 3- mixed complex.

Lattice based Kinetic Monte Carlo Simulations of a complex chemical reaction network

NASA Astrophysics Data System (ADS)

Danielson, Thomas; Savara, Aditya; Hin, Celine

Lattice Kinetic Monte Carlo (KMC) simulations offer a powerful alternative to using ordinary differential equations for the simulation of complex chemical reaction networks. Lattice KMC provides the ability to account for local spatial configurations of species in the reaction network, resulting in a more detailed description of the reaction pathway. In KMC simulations with a large number of reactions, the range of transition probabilities can span many orders of magnitude, creating subsets of processes that occur more frequently or more rarely. Consequently, processes that have a high probability of occurring may be selected repeatedly without actually progressing the system (i.e. the forward and reverse process for the same reaction). In order to avoid the repeated occurrence of fast frivolous processes, it is necessary to throttle the transition probabilities in such a way that avoids altering the overall selectivity. Likewise, as the reaction progresses, new frequently occurring species and reactions may be introduced, making a dynamic throttling algorithm a necessity. We present a dynamic steady-state detection scheme with the goal of accurately throttling rate constants in order to optimize the KMC run time without compromising the selectivity of the reaction network. The algorithm has been applied to a large catalytic chemical reaction network, specifically that of methanol oxidative dehydrogenation, as well as additional pathways on CeO2(111) resulting in formaldehyde, CO, methanol, CO2, H2 and H2O as gas products.

Post-Self-Assembly Cross-Linking to Integrate Molecular Nanofibers with Copolymers in Oscillatory Hydrogels

DTIC Science & Technology

2013-05-09

The BZ reaction provides a model system to mimic a variety of complex processes, such as biological morphogenesis, in monodisperse microemulsions .15...surfaces, ion-exchange resins, membranes, and microemulsions . For example, in addition to minimizing the hydrodynamic effects and formation of bubbles...Reaction-Diffusion Microemulsions Reveals Three-Dimensional Tu- ring Patterns. Science (Washington, DC, U.S.) 2011, 331, 1309−1312. (16) Agladze, K. I

A DFT-Based Computational-Experimental Methodology for Synthetic Chemistry: Example of Application to the Catalytic Opening of Epoxides by Titanocene.

PubMed

Jaraíz, Martín; Enríquez, Lourdes; Pinacho, Ruth; Rubio, José E; Lesarri, Alberto; López-Pérez, José L

2017-04-07

A novel DFT-based Reaction Kinetics (DFT-RK) simulation approach, employed in combination with real-time data from reaction monitoring instrumentation (like UV-vis, FTIR, Raman, and 2D NMR benchtop spectrometers), is shown to provide a detailed methodology for the analysis and design of complex synthetic chemistry schemes. As an example, it is applied to the opening of epoxides by titanocene in THF, a catalytic system with abundant experimental data available. Through a DFT-RK analysis of real-time IR data, we have developed a comprehensive mechanistic model that opens new perspectives to understand previous experiments. Although derived specifically from the opening of epoxides, the prediction capabilities of the model, built on elementary reactions, together with its practical side (reaction kinetics simulations of real experimental conditions) make it a useful simulation tool for the design of new experiments, as well as for the conception and development of improved versions of the reagents. From the perspective of the methodology employed, because both the computational (DFT-RK) and the experimental (spectroscopic data) components can follow the time evolution of several species simultaneously, it is expected to provide a helpful tool for the study of complex systems in synthetic chemistry.

Universality and chaotic dynamics in reactive scattering of ultracold KRb molecules with K atoms

NASA Astrophysics Data System (ADS)

Li, Ming; Makrides, Constantinos; Petrov, Alexander; Kotochigova, Svetlana; Croft, James F. E.; Balakrishnan, Naduvalath; Kendrick, Brian K.

2017-04-01

We study the benchmark reaction between the most-celebrated ultracold polar molecule, KRb, with an ultracold K atom. For the first time we map out an accurate ab initio ground potential energy surface of the K2Rb complex in full dimensionality and performed a numerically exact quantum-mechanical calculation of reaction dynamics based on coupled-channels approach in hyperspherical coordinates. An analysis of the adiabatic hyperspherical potentials reveals a chaotic distribution for the short-range complex that plays a key role in governing the reaction outcome. The equivalent distribution for a lighter collisional system with a smaller density of states (here the Li2Yb trimer) only shows random behavior. We find an extreme sensitivity of our chaotic system to a small perturbation associated with the weak non-additive three-body potential contribution that does not affect the total reaction rate coefficient but leads to a significant change in the rotational distribution in the product molecule. In both cases the distribution of these rates is random or Poissonian. This work was supported in part by NSF Grant PHY-1505557 (N.B.) and PHY-1619788 (S.K.), ARO MURI Grant No. W911NF-12-1-0476 (N.B. & S.K.), and DOE LDRD Grant No. 20170221ER (B.K.).

Formation of mercury sulfide from Hg(II)−thiolate complexes in natural organic matter

USGS Publications Warehouse

Alain Manceau,; Cyprien Lemouchi,; Mironel Enescu,; Anne-Claire Gaillot,; Martine Lanson,; Valerie Magnin,; Pieter Glatzel,; Poulin, Brett; Ryan, Joseph N.; Aiken, George R.; Isabelle Gautier-Lunea,; Kathryn L. Nagy,

2015-01-01

Methylmercury is the environmental form of neurotoxic mercury that is biomagnified in the food chain. Methylation rates are reduced when the metal is sequestered in crystalline mercury sulfides or bound to thiol groups in macromolecular natural organic matter. Mercury sulfide minerals are known to nucleate in anoxic zones, by reaction of the thiol-bound mercury with biogenic sulfide, but not in oxic environments. We present experimental evidence that mercury sulfide forms from thiol-bound mercury alone in aqueous dark systems in contact with air. The maximum amount of nanoparticulate mercury sulfide relative to thiol-bound mercury obtained by reacting dissolved mercury and soil organic matter matches that detected in the organic horizon of a contaminated soil situated downstream from Oak Ridge, TN, in the United States. The nearly identical ratios of the two forms of mercury in field and experimental systems suggest a common reaction mechanism for nucleating the mineral. We identified a chemical reaction mechanism that is thermodynamically favorable in which thiol-bound mercury polymerizes to mercury–sulfur clusters. The clusters form by elimination of sulfur from the thiol complexes via breaking of mercury–sulfur bonds as in an alkylation reaction. Addition of sulfide is not required. This nucleation mechanism provides one explanation for how mercury may be immobilized, and eventually sequestered, in oxygenated surface environments.

Diiridium Bimetallic Complexes Function as a Redox Switch To Directly Split Carbonate into Carbon Monoxide and Oxygen.

PubMed

Chen, Tsun-Ren; Wu, Fang-Siou; Lee, Hsiu-Pen; Chen, Kelvin H-C

2016-03-23

A pair of diiridium bimetallic complexes exhibit a special type of oxidation-reduction reaction that could directly split carbonate into carbon monoxide and molecular oxygen via a low-energy pathway needing no sacrificial reagent. One of the bimetallic complexes, Ir(III)(μ-Cl)2Ir(III), can catch carbonato group from carbonate and reduce it to CO. The second complex, the rare bimetallic complex Ir(IV)(μ-oxo)2Ir(IV), can react with chlorine to release O2 by the oxidation of oxygen ions with synergistic oxidative effect of iridium ions and chlorine atoms. The activation energy needed for the key reaction is quite low (∼20 kJ/mol), which is far less than the dissociation energy of the C═O bond in CO2 (∼750 kJ/mol). These diiridium bimetallic complexes could be applied as a redox switch to split carbonate or combined with well-known processes in the chemical industry to build up a catalytic system to directly split CO2 into CO and O2.

Differences and Comparisons of the Properties and Reactivities of Iron(III)–hydroperoxo Complexes with Saturated Coordination Sphere

PubMed Central

Faponle, Abayomi S; Quesne, Matthew G; Sastri, Chivukula V; Banse, Frédéric; de Visser, Sam P

2015-01-01

Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high-valent iron(IV)–oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)–hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)–hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)–hydroperoxo reacted directly with substrates or that an initial O–O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)–hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)–hydroperoxo complex with pentadentate ligand system (L52). Direct C–O bond formation by an iron(III)–hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L52)FeIII(OOH)]2+ should be able to initiate an aromatic hydroxylation process, although a low-energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)–hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O–O bond, whereas a heterolytic O–O bond breaking in heme iron(III)–hydroperoxo is found. PMID:25399782

Rule-based modeling and simulations of the inner kinetochore structure.

PubMed

Tschernyschkow, Sergej; Herda, Sabine; Gruenert, Gerd; Döring, Volker; Görlich, Dennis; Hofmeister, Antje; Hoischen, Christian; Dittrich, Peter; Diekmann, Stephan; Ibrahim, Bashar

2013-09-01

Combinatorial complexity is a central problem when modeling biochemical reaction networks, since the association of a few components can give rise to a large variation of protein complexes. Available classical modeling approaches are often insufficient for the analysis of very large and complex networks in detail. Recently, we developed a new rule-based modeling approach that facilitates the analysis of spatial and combinatorially complex problems. Here, we explore for the first time how this approach can be applied to a specific biological system, the human kinetochore, which is a multi-protein complex involving over 100 proteins. Applying our freely available SRSim software to a large data set on kinetochore proteins in human cells, we construct a spatial rule-based simulation model of the human inner kinetochore. The model generates an estimation of the probability distribution of the inner kinetochore 3D architecture and we show how to analyze this distribution using information theory. In our model, the formation of a bridge between CenpA and an H3 containing nucleosome only occurs efficiently for higher protein concentration realized during S-phase but may be not in G1. Above a certain nucleosome distance the protein bridge barely formed pointing towards the importance of chromatin structure for kinetochore complex formation. We define a metric for the distance between structures that allow us to identify structural clusters. Using this modeling technique, we explore different hypothetical chromatin layouts. Applying a rule-based network analysis to the spatial kinetochore complex geometry allowed us to integrate experimental data on kinetochore proteins, suggesting a 3D model of the human inner kinetochore architecture that is governed by a combinatorial algebraic reaction network. This reaction network can serve as bridge between multiple scales of modeling. Our approach can be applied to other systems beyond kinetochores. Copyright © 2013 Elsevier Ltd. All rights reserved.

Chemical reaction networks as a model to describe UVC- and radiolytically-induced reactions of simple compounds.

PubMed

Dondi, Daniele; Merli, Daniele; Albini, Angelo; Zeffiro, Alberto; Serpone, Nick

2012-05-01

When a chemical system is submitted to high energy sources (UV, ionizing radiation, plasma sparks, etc.), as is expected to be the case of prebiotic chemistry studies, a plethora of reactive intermediates could form. If oxygen is present in excess, carbon dioxide and water are the major products. More interesting is the case of reducing conditions where synthetic pathways are also possible. This article examines the theoretical modeling of such systems with random-generated chemical networks. Four types of random-generated chemical networks were considered that originated from a combination of two connection topologies (viz., Poisson and scale-free) with reversible and irreversible chemical reactions. The results were analyzed taking into account the number of the most abundant products required for reaching 50% of the total number of moles of compounds at equilibrium, as this may be related to an actual problem of complex mixture analysis. The model accounts for multi-component reaction systems with no a priori knowledge of reacting species and the intermediates involved if system components are sufficiently interconnected. The approach taken is relevant to an earlier study on reactions that may have occurred in prebiotic systems where only a few compounds were detected. A validation of the model was attained on the basis of results of UVC and radiolytic reactions of prebiotic mixtures of low molecular weight compounds likely present on the primeval Earth.

Mathematical approach to nonlocal interactions using a reaction-diffusion system.

PubMed

Tanaka, Yoshitaro; Yamamoto, Hiroko; Ninomiya, Hirokazu

2017-06-01

In recent years, spatial long range interactions during developmental processes have been introduced as a result of the integration of microscopic information, such as molecular events and signaling networks. They are often called nonlocal interactions. If the profile of a nonlocal interaction is determined by experiments, we can easily investigate how patterns generate by numerical simulations without detailed microscopic events. Thus, nonlocal interactions are useful tools to understand complex biosystems. However, nonlocal interactions are often inconvenient for observing specific mechanisms because of the integration of information. Accordingly, we proposed a new method that could convert nonlocal interactions into a reaction-diffusion system with auxiliary unknown variables. In this review, by introducing biological and mathematical studies related to nonlocal interactions, we will present the heuristic understanding of nonlocal interactions using a reaction-diffusion system. © 2017 Japanese Society of Developmental Biologists.

The effect of Beta-cyclodextrin on percutaneous absorption of commonly used Eusolex® sunscreens.

PubMed

Shokri, J; Hasanzadeh, D; Ghanbarzadeh, S; Dizadji-Ilkhchi, M; Adibkia, K

2013-11-01

There is a serious concern about the topical and systemic absorption of organic ultraviolet filters in sunscreen formulations and subsequent phototoxic and photo allergic reactions. Ideally, a sunscreen should localize in the surface of stratum corneum and create a barrier against UV radiation, but not penetrate into the underlying viable tissues and systemic circulation. The objective of the present study was to determine the effects of β-cyclodextrin (β-CDX) complexation on the transdermal penetration of 3 commonly used sun blocking agents, Eusolex ® 4360 (avobenzone), Eusolex ® 9020 (Oxybenzone) and Eusolex ® 232 (Ensulizole). The complexation of the sunscreen agents with β-CDX was performed by 3 methods and confirmed by differential scanning calorimetry (DSC). Sunscreens, and their physical mixtures and complexes with β-CDX were introduced into a model cream base (o/w emulsion). To find out the influence of β-CDX, sunscreen creams were applied to the rat skin in vitro in standard Franz diffusion cells and the amount of sunscreen permeated after 6 h was assessed by HPLC. The skin penetration flux of the UV filters was significantly reduced (4–15 fold) by complexation with β-CDX. Complexation also could prolong absorption lag time of sun blocking agents to more than 150 min. Considering the ability of β-CDX complexation in the reduction of flux and enhancement ratio as well as prolongation of absorption lag time, this technique could be very helpful for reducing systemic absorption of the UV filters and subsequent toxicity and allergic reaction.

Therapeutic regulatory T-cell adoptive transfer ameliorates established murine chronic GVHD in a CXCR5-dependent manner

PubMed Central

McDonald-Hyman, Cameron; Flynn, Ryan; Panoskaltsis-Mortari, Angela; Peterson, Nicholas; MacDonald, Kelli P. A.; Hill, Geoffrey R.; Luznik, Leo; Serody, Jonathan S.; Murphy, William J.; Maillard, Ivan; Munn, David H.; Turka, Laurence A.; Koreth, John; Cutler, Corey S.; Soiffer, Robert J.; Antin, Joseph H.; Ritz, Jerome

2016-01-01

Chronic graft-versus-host disease (cGVHD) is a major complication of allogeneic hematopoietic stem cell transplantation. In cGVHD, alloreactive T cells and germinal center (GC) B cells often participate in GC reactions to produce pathogenic antibodies. Although regulatory T cells (Tregs) can inhibit GC reactions, Treg numbers are reduced in cGVHD, contributing to cGVHD pathogenesis. Here, we explored 2 means to increase Tregs in cGVHD: interleukin-2/monoclonal antibody (IL-2/mAb) complexes and donor Treg infusions. IL-2/mAb complexes given over 1 month were efficacious in expanding Tregs and treating established cGVHD in a multi-organ-system disease mouse model characterized by GC reactions, antibody deposition, and lung dysfunction. In an acute GVHD (aGVHD) model, IL-2/mAb complexes given for only 4 days resulted in rapid mortality, indicating IL-2/mAb complexes can drive conventional T-cell (Tcon)-mediated injury. In contrast, Treg infusions, which uniformly suppress aGVHD, increased Treg frequency and were effective in preventing the onset of, and treating, established cGVHD. Efficacy was dependent upon CXCR5-sufficient Tregs homing to, and inhibiting, GC reactions. These studies indicate that the infusion of Tregs, especially ones enriched for GC homing, may be desirable for cGVHD therapy. Although IL-2/mAb complexes can be efficacious in cGVHD, a cautious approach needs to be taken in settings in which aGVHD elements, and associated Tcon, are present. PMID:27385791

Thermodynamic and kinetic data for adduct formation, cis-trans isomerization and redox reactions of ML4 complexes: a case study with rhodium- and iridium-tropp complexes in d8, d9 and d10 valence electron configurations (tropp=dibenzotropylidene phosphanes).

PubMed

Breher, Frank; Rüegger, Heinz; Mlakar, Marina; Rudolph, Manfred; Deblon, Stephan; Schönberg, Hartmut; Boulmaâz, Souad; Thomaier, Jörg; Grützmacher, Hansjörg

2004-02-06

The formation of adducts of the square-planar 16-electron complexes trans-[M(tropp(ph))(2)](+) and cis-[M(tropp(ph))(2)](+) (M=Rh, Ir; tropp(Ph)=5-diphenylphosphanyldibenzo[a,d]cycloheptene) with acetonitrile (acn) and Cl(-), and the redox chemistry of these complexes was investigated by various physical methods (NMR and UV-visible spectroscopy, square-wave voltammetry), in order to obtain some fundamental thermodynamic and kinetic data for these systems. A trans/cis isomerization cannot be detected for [M(tropp(ph))(2)](+) in non-coordinating solvents. However, both isomers are connected through equilibria of the type trans-[M(tropp(ph))(2)](+)+L<==>[ML(tropp(ph))(2)](n)<==>cis-[M(tropp(ph))(2)](+)+L, involving five-coordinate intermediates [ML(tropp(ph))(2)](n) (L=acn, n=+1; L=Cl(-), n=0). Values for K(d) (K(f)), that is, the dissociation (formation) equilibrium constant, and k(d) (k(f)), that is, the dissociation (formation) rate constant, were obtained. The formation reactions are fast, especially with the trans isomers (k(f)>1x10(5) m(-1) s(-1)). The reaction with the sterically more hindered cis isomers is at least one order of magnitude slower. The stability of the five-coordinate complexes [ML(tropp(ph))(2)](n) increases with Ir>Rh and Cl(-)>acn. The dissociation reaction has a pronounced influence on the square-wave (SW) voltammograms of trans/cis-[Ir(tropp(ph))(2)](+). With the help of the thermodynamic and kinetic data independently determined by other physical means, these reactions could be simulated and allowed the setting up of a reaction sequence. Examination of the data obtained showed that the trans/cis isomerization is a process with a low activation barrier for the four-coordinate 17-electron complexes [M(tropp(ph))(2)](0) and especially that a disproportionation reaction 2 trans/cis-[M(tropp(ph))(2)](0)-->[M(tropp(ph))(2)](+)+[M(tropp(ph))(2)](-) may be sufficiently fast to mask the true reactivity of the paramagnetic species, which are probably less reactive than their diamagnetic equilibrium partners.

Moving from Batch to Field Using the RT3D Reactive Transport Modeling System

NASA Astrophysics Data System (ADS)

Clement, T. P.; Gautam, T. R.

2002-12-01

The public domain reactive transport code RT3D (Clement, 1997) is a general-purpose numerical code for solving coupled, multi-species reactive transport in saturated groundwater systems. The code uses MODFLOW to simulate flow and several modules of MT3DMS to simulate the advection and dispersion processes. RT3D employs the operator-split strategy which allows the code solve the coupled reactive transport problem in a modular fashion. The coupling between reaction and transport is defined through a separate module where the reaction equations are specified. The code supports a versatile user-defined reaction option that allows users to define their own reaction system through a Fortran-90 subroutine, known as the RT3D-reaction package. Further a utility code, known as BATCHRXN, allows the users to independently test and debug their reaction package. To analyze a new reaction system at a batch scale, users should first run BATCHRXN to test the ability of their reaction package to model the batch data. After testing, the reaction package can simply be ported to the RT3D environment to study the model response under 1-, 2-, or 3-dimensional transport conditions. This paper presents example problems that demonstrate the methods for moving from batch to field-scale simulations using BATCHRXN and RT3D codes. The first example describes a simple first-order reaction system for simulating the sequential degradation of Tetrachloroethene (PCE) and its daughter products. The second example uses a relatively complex reaction system for describing the multiple degradation pathways of Tetrachloroethane (PCA) and its daughter products. References 1) Clement, T.P, RT3D - A modular computer code for simulating reactive multi-species transport in 3-Dimensional groundwater aquifers, Battelle Pacific Northwest National Laboratory Research Report, PNNL-SA-28967, September, 1997. Available at: http://bioprocess.pnl.gov/rt3d.htm.

A novel tridentate coordination mode for the carbonatonickel system exhibited in an unusual hexanuclear nickel(II) mu3-carbonato-bridged complex.

PubMed

Anderson, James C; Blake, Alexander J; Moreno, Rafael Bou; Raynel, Guillaume; van Slageren, Joris

2009-11-14

The fixation of CO(2) at ambient temperature has been achieved by the reaction of Ni(cod)(2) and TMEDA in CO(2) saturated THF that yields a novel hexanuclear nickel(II) mu(3)-carbonato bridged complex [Ni(6)(mu(3)-CO(3))(4)(TMEDA)(6)(H(2)O)(12)](OH)(4) in 59% yield. The complex was characterised by MS analysis and the structure corroborated by single-crystal X-ray crystallography. The complex exhibits a rare carbonato binding mode for Ni(II) complexes and moderately strong antiferromagnetic interactions.

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

NASA Astrophysics Data System (ADS)

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).

A Flight-Calibrated Methodology for Determination of Cassini Thruster On-Times for Reaction Wheel Biases

NASA Technical Reports Server (NTRS)

Sarani, Sam

2010-01-01

The Cassini spacecraft, the largest and most complex interplanetary spacecraft ever built, continues to undertake unique scientific observations of planet Saturn, Titan, Enceladus, and other moons of the ring world. In order to maintain a stable attitude during the course of its mission, this three-axis stabilized spacecraft uses two different control systems: the Reaction Control System (or RCS) and the Reaction Wheel Assembly (RWA) control system. In the course of its mission, Cassini performs numerous reaction wheel momentum biases (or unloads) using its reaction control thrusters. The use of the RCS thrusters often imparts undesired velocity changes (delta Vs) on the spacecraft and it is crucial for Cassini navigation and attitude control teams to be able to, quickly but accurately, predict the hydrazine usage and delta V vector in Earth Mean Equatorial (J2000) inertial coordinates for reaction wheel bias events, without actually having to spend time and resources simulating the event in a dynamic or hardware-in-the-loop simulation environments. The flight-calibrated methodology described in this paper, and the ground software developed thereof, are designed to provide the RCS thruster on-times, with acceptable accuracy and without any form of dynamic simulation, for reaction wheel biases, along with the hydrazine usage and the delta V in EME-2000 inertial frame.

Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

DOE PAGES

Li, Y.; Zakharov, D.; Zhao, S.; ...

2015-06-29

Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. Lastly,more » this method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.« less

Phase locking route behind complex periodic windows in a forced oscillator

NASA Astrophysics Data System (ADS)

Jan, Hengtai; Tsai, Kuo-Ting; Kuo, Li-wei

2013-09-01

Chaotic systems have complex reactions against an external driving force; even in cases with low-dimension oscillators, the routes to synchronization are diverse. We proposed a stroboscope-based method for analyzing driven chaotic systems in their phase space. According to two statistic quantities generated from time series, we could realize the system state and the driving behavior simultaneously. We demonstrated our method in a driven bi-stable system, which showed complex period windows under a proper driving force. With increasing periodic driving force, a route from interior periodic oscillation to phase synchronization through the chaos state could be found. Periodic windows could also be identified and the circumstances under which they occurred distinguished. Statistical results were supported by conditional Lyapunov exponent analysis to show the power in analyzing the unknown time series.

Selective CO{sub 2} reduction conjugated with H{sub 2}O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

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

Morikawa, T., E-mail: morikawa@mosk.tytlabs.co.jp; Sato, S., E-mail: morikawa@mosk.tytlabs.co.jp; Arai, T., E-mail: morikawa@mosk.tytlabs.co.jp

2013-12-10

We developed a new hybrid photocatalyst for CO{sub 2} reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (E{sub CBM}) of the semiconductor and the CO{sub 2} reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO{sub 2} to formate using water as an electron donor andmore » a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO{sub 2} reduction with a TiO{sub 2} photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.« less

A Design Principle for an Autonomous Post-translational Pattern Formation.

PubMed

Sugai, Shuhei S; Ode, Koji L; Ueda, Hiroki R

2017-04-25

Previous autonomous pattern-formation models often assumed complex molecular and cellular networks. This theoretical study, however, shows that a system composed of one substrate with multisite phosphorylation and a pair of kinase and phosphatase can generate autonomous spatial information, including complex stripe patterns. All (de-)phosphorylation reactions are described with a generic Michaelis-Menten scheme, and all species freely diffuse without pre-existing gradients. Computational simulation upon >23,000,000 randomly generated parameter sets revealed the design motifs of cyclic reaction and enzyme sequestration by slow-diffusing substrates. These motifs constitute short-range positive and long-range negative feedback loops to induce Turing instability. The width and height of spatial patterns can be controlled independently by distinct reaction-diffusion processes. Therefore, multisite reversible post-translational modification can be a ubiquitous source for various patterns without requiring other complex regulations such as autocatalytic regulation of enzymes and is applicable to molecular mechanisms for inducing subcellular localization of proteins driven by post-translational modifications. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

MoMaS reactive transport benchmark using PFLOTRAN

NASA Astrophysics Data System (ADS)

Park, H.

2017-12-01

MoMaS benchmark was developed to enhance numerical simulation capability for reactive transport modeling in porous media. The benchmark was published in late September of 2009; it is not taken from a real chemical system, but realistic and numerically challenging tests. PFLOTRAN is a state-of-art massively parallel subsurface flow and reactive transport code that is being used in multiple nuclear waste repository projects at Sandia National Laboratories including Waste Isolation Pilot Plant and Used Fuel Disposition. MoMaS benchmark has three independent tests with easy, medium, and hard chemical complexity. This paper demonstrates how PFLOTRAN is applied to this benchmark exercise and shows results of the easy benchmark test case which includes mixing of aqueous components and surface complexation. Surface complexations consist of monodentate and bidentate reactions which introduces difficulty in defining selectivity coefficient if the reaction applies to a bulk reference volume. The selectivity coefficient becomes porosity dependent for bidentate reaction in heterogeneous porous media. The benchmark is solved by PFLOTRAN with minimal modification to address the issue and unit conversions were made properly to suit PFLOTRAN.

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

PubMed Central

Cao, Youfang; Liang, Jie

2013-01-01

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

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

NASA Astrophysics Data System (ADS)

Cao, Youfang; Liang, Jie

2013-07-01

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

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

PubMed

Cao, Youfang; Liang, Jie

2013-07-14

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

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

PubMed

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 ReactionPredictor are available via the chemoinformatics portal http://cdb.ics.uci.edu/.

Activation of dioxygen by copper metalloproteins and insights from model complexes

PubMed Central

Quist, David A.; Diaz, Daniel E.; Liu, Jeffrey J.; Karlin, Kenneth D.

2017-01-01

Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing met-alloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof. An emphasis has also been placed on cofactor biogenesis, a fundamentally important process whereby biomolecules are post-translationally modified by the pro-enzyme active site to generate cofactors which are essential for the catalytic enzymatic reaction. Significant questions remaining in copper-ion-mediated O2-activation in copper proteins are addressed. PMID:27921179

The mechanism of enantioselective ketone reduction with Noyori and Noyori–Ikariya bifunctional catalysts

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

Dub, Pavel A.; Gordon, John C.

2016-03-21

The catalytic hydrogenation of prochiral ketones with second and third-row transition metal complexes bearing chelating chiral ligands containing at least one N–H functionality has achieved unparalleled performance, delivering, in the best cases, chiral alcohols with up to 99.9% ee using extremely small catalyst loadings (~10 -5 mol%). Hence the efficacy of this reaction has closely approached that of natural enzymatic systems and the reaction itself has become one of the most efficient artificial catalytic reactions developed to date. This paper describes the current level of understanding of the mechanism of enantioselective hydrogenation and transfer hydrogenation of aromatic ketones with pioneeringmore » prototypes of bifunctional catalysts, the Noyori and Noyori–Ikariya complexes. Finally, analysis presented herein expands the concept of “metal–ligand cooperation”, redefines the term “cooperative ligand” and introduces “H –/H + outer-sphere hydrogenation” as a novel paradigm in outer-sphere hydrogenation.« less

Activation of dioxygen by copper metalloproteins and insights from model complexes.

PubMed

Quist, David A; Diaz, Daniel E; Liu, Jeffrey J; Karlin, Kenneth D

2017-04-01

Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing metalloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof. An emphasis has also been placed on cofactor biogenesis, a fundamentally important process whereby biomolecules are post-translationally modified by the pro-enzyme active site to generate cofactors which are essential for the catalytic enzymatic reaction. Significant questions remaining in copper-ion-mediated O 2 -activation in copper proteins are addressed.

Investigation of interaction between the Pt(II) ions and aminosilane-modified silica surface in heterogeneous system

NASA Astrophysics Data System (ADS)

Nowicki, Waldemar; Gąsowska, Anna; Kirszensztejn, Piotr

2016-05-01

UV-vis spectroscopy measurements confirmed the reaction in heterogeneous system between Pt(II) ions and ethylenediamine type ligand, n-(2-aminoethyl)-3-aminopropyl-trimethoxysilane, immobilized at the silica surface. The formation of complexes is a consequence of interaction between the amine groups from the ligand grafted onto SiO2 and ions of platinum. A potentiometric titration technique was to determine the stability constants of complexes of Pt(II) with immobilized insoluble ligand (SG-L), on the silica gel. The results show the formation of three surface complexes of the same type (PtHSG-L, Pt(HSG-L)2, PtSG-L) with SG-L ligand, in a wide range of pH for different Debye length. The concentration distribution of the complexes in a heterogeneous system is evaluated.

Characterising Complex Enzyme Reaction Data

PubMed Central

Rahman, Syed Asad; Thornton, Janet M.

2016-01-01

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. PMID:26840640

Global minimum profile error (GMPE) - a least-squares-based approach for extracting macroscopic rate coefficients for complex gas-phase chemical reactions.

PubMed

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.

Syntheses and Functionalizations of Porphyrin Macrocycles

PubMed Central

Vicente, Maria da G.H.; Smith, Kevin M.

2014-01-01

Porphyrin macrocycles have been the subject of intense study in the last century because they are widely distributed in nature, usually as metal complexes of either iron or magnesium. As such, they serve as the prosthetic groups in a wide variety of primary metabolites, such as hemoglobins, myoglobins, cytochromes, catalases, peroxidases, chlorophylls, and bacteriochlorophylls; these compounds have multiple applications in materials science, biology and medicine. This article describes current methodology for preparation of simple, symmetrical model porphyrins, as well as more complex protocols for preparation of unsymmetrically substituted porphyrin macrocycles similar to those found in nature. The basic chemical reactivity of porphyrins and metalloporphyrin is also described, including electrophilic and nucleophilic reactions, oxidations, reductions, and metal-mediated cross-coupling reactions. Using the synthetic approaches and reactivity profiles presented, eventually almost any substituted porphyrin system can be prepared for applications in a variety of areas, including in catalysis, electron transport, model biological systems and therapeutics. PMID:25484638

Thermodynamics of random reaction networks.

PubMed

Fischer, Jakob; Kleidon, Axel; Dittrich, Peter

2015-01-01

Reaction networks are useful for analyzing reaction systems occurring in chemistry, systems biology, or Earth system science. Despite the importance of thermodynamic disequilibrium for many of those systems, the general thermodynamic properties of reaction networks are poorly understood. To circumvent the problem of sparse thermodynamic data, we generate artificial reaction networks and investigate their non-equilibrium steady state for various boundary fluxes. We generate linear and nonlinear networks using four different complex network models (Erdős-Rényi, Barabási-Albert, Watts-Strogatz, Pan-Sinha) and compare their topological properties with real reaction networks. For similar boundary conditions the steady state flow through the linear networks is about one order of magnitude higher than the flow through comparable nonlinear networks. In all networks, the flow decreases with the distance between the inflow and outflow boundary species, with Watts-Strogatz networks showing a significantly smaller slope compared to the three other network types. The distribution of entropy production of the individual reactions inside the network follows a power law in the intermediate region with an exponent of circa -1.5 for linear and -1.66 for nonlinear networks. An elevated entropy production rate is found in reactions associated with weakly connected species. This effect is stronger in nonlinear networks than in the linear ones. Increasing the flow through the nonlinear networks also increases the number of cycles and leads to a narrower distribution of chemical potentials. We conclude that the relation between distribution of dissipation, network topology and strength of disequilibrium is nontrivial and can be studied systematically by artificial reaction networks.

Thermodynamics of Random Reaction Networks

PubMed Central

Fischer, Jakob; Kleidon, Axel; Dittrich, Peter

2015-01-01

Reaction networks are useful for analyzing reaction systems occurring in chemistry, systems biology, or Earth system science. Despite the importance of thermodynamic disequilibrium for many of those systems, the general thermodynamic properties of reaction networks are poorly understood. To circumvent the problem of sparse thermodynamic data, we generate artificial reaction networks and investigate their non-equilibrium steady state for various boundary fluxes. We generate linear and nonlinear networks using four different complex network models (Erdős-Rényi, Barabási-Albert, Watts-Strogatz, Pan-Sinha) and compare their topological properties with real reaction networks. For similar boundary conditions the steady state flow through the linear networks is about one order of magnitude higher than the flow through comparable nonlinear networks. In all networks, the flow decreases with the distance between the inflow and outflow boundary species, with Watts-Strogatz networks showing a significantly smaller slope compared to the three other network types. The distribution of entropy production of the individual reactions inside the network follows a power law in the intermediate region with an exponent of circa −1.5 for linear and −1.66 for nonlinear networks. An elevated entropy production rate is found in reactions associated with weakly connected species. This effect is stronger in nonlinear networks than in the linear ones. Increasing the flow through the nonlinear networks also increases the number of cycles and leads to a narrower distribution of chemical potentials. We conclude that the relation between distribution of dissipation, network topology and strength of disequilibrium is nontrivial and can be studied systematically by artificial reaction networks. PMID:25723751

The decay of hot nuclei formed in La-induced reactions at E/A=45 MeV

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

Libby, Bruce

1993-01-01

The decay of hot nuclei formed in the reactions 139La + 27Al, 51V, natCu, and 139La were studied by the coincident detection of up to four complex fragments (Z > 3) emitted in these reactions. Fragments were characterized as to their atomic number, energy and in- and out-of-plane angles. The probability of the decay by an event of a given complex fragment multiplicity as a function of excitation energy per nucleon of the source is nearly independent of the system studied. Additionally, there is no large increase in the proportion of multiple fragment events as the excitation energy of themore » source increases past 5 MeV/nucleon. This is at odds with many prompt multifragmentation models of nuclear decay. The reactions 139La + 27Al, 51V, natCu were also studied by combining a dynamical model calculation that simulates the early stages of nuclear reactions with a statistical model calculation for the latter stages of the reactions. For the reaction 139La + 27Al, these calculations reproduced many of the experimental features, but other features were not reproduced. For the reaction 139La + 51V, the calculation failed to reproduce somewhat more of the experimental features. The calculation failed to reproduce any of the experimental features of the reaction 139La + natCu, with the exception of the source velocity distributions.« less

The decay of hot nuclei formed in La-induced reactions at E/A=45 MeV

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

Libby, B.

1993-01-01

The decay of hot nuclei formed in the reactions [sup 139]La + [sup 27]Al, [sup 51]V, [sup nat]Cu, and [sup 139]La were studied by the coincident detection of up to four complex fragments (Z > 3) emitted in these reactions. Fragments were characterized as to their atomic number, energy and in- and out-of-plane angles. The probability of the decay by an event of a given complex fragment multiplicity as a function of excitation energy per nucleon of the source is nearly independent of the system studied. Additionally, there is no large increase in the proportion of multiple fragment events asmore » the excitation energy of the source increases past 5 MeV/nucleon. This is at odds with many prompt multifragmentation models of nuclear decay. The reactions [sup 139]La + [sup 27]Al, [sup 51]V, [sup nat]Cu were also studied by combining a dynamical model calculation that simulates the early stages of nuclear reactions with a statistical model calculation for the latter stages of the reactions. For the reaction [sup 139]La + [sup 27]Al, these calculations reproduced many of the experimental features, but other features were not reproduced. For the reaction [sup 139]La + [sup 51]V, the calculation failed to reproduce somewhat more of the experimental features. The calculation failed to reproduce any of the experimental features of the reaction [sup 139]La + [sup nat]Cu, with the exception of the source velocity distributions.« less

The effects of instructional sets on reactions to and performance on an intelligent tutoring system

NASA Technical Reports Server (NTRS)

Johnson, Debra Steele

1993-01-01

The effects of a contextual factor, i.e., task instructions, on performance on and reactions to an Intellegent Tutoring System (ITS) training Remote Manipulator System (RMS) tasks were examined. The results supported the first prediction that task instructions could be used to successfully induce a mastery versus an achievement orientation. Previous research suggests that a mastery orientation can result in beneficial effects on learning and performance of complex tasks. Furthermore, the results supported the second prediction that a mastery orientation would have beneficial effects on learning and performance as well as affective and cognitive reactions to the ITS tasks. Moreover, the results indicated that a mastery orientation was especially beneficial for the more complex ITS tasks and later in task practice, i.e., when a task was performed for the second time. A mastery orientation is posited to have its beneficial effects by focusing more effort and attention on task performance. Conclusions are drawn with some caution due to the small number of subjects, although the results for these subjects were consistent across multiple trials and multiple measures of performance. ITS designers are urged to consider contextual factors such as task instructions and feedback in terms of their potential to induce a mastery versus an achievement orientation.

Simulation of physiological systems in order to evaluate and predict the human condition in a space flight

NASA Technical Reports Server (NTRS)

Verigo, V. V.

1979-01-01

Simulation models were used to study theoretical problems of space biology and medicine. The reaction and adaptation of the main physiological systems to the complex effects of space flight were investigated. Mathematical models were discussed in terms of their significance in the selection of the structure and design of biological life support systems.

A two-state computational investigation of methane C--H and ethane C--C oxidative addition to [CpM(PH3)]n+ (M = Co, Rh, Ir; n = 0, 1).

PubMed

Petit, Alban; Richard, Philippe; Cacelli, Ivo; Poli, Rinaldo

2006-01-11

Reductive elimination of methane from methyl hydride half-sandwich phosphane complexes of the Group 9 metals has been investigated by DFT calculations on the model system [CpM(PH(3))(CH(3))(H)] (M = Co, Rh, Ir). For each metal, the unsaturated product has a triplet ground state; thus, spin crossover occurs during the reaction. All relevant stationary points on the two potential energy surfaces (PES) and the minimum energy crossing point (MECP) were optimized. Spin crossover occurs very near the sigma-CH(4) complex local minimum for the Co system, whereas the heavier Rh and Ir systems remain in the singlet state until the CH(4) molecule is almost completely expelled from the metal coordination sphere. No local sigma-CH(4) minimum was found for the Ir system. The energetic profiles agree with the nonexistence of the Co(III) methyl hydride complex and with the greater thermal stability of the Ir complex relative to the Rh complex. Reductive elimination of methane from the related oxidized complexes [CpM(PH(3))(CH(3))(H)](+) (M = Rh, Ir) proceeds entirely on the spin doublet PES, because the 15-electron [CpM(PH(3))](+) products have a doublet ground state. This process is thermodynamically favored by about 25 kcal mol(-1) relative to the corresponding neutral system. It is essentially barrierless for the Rh system and has a relatively small barrier (ca. 7.5 kcal mol(-1)) for the Ir system. In both cases, the reaction involves a sigma-CH(4) intermediate. Reductive elimination of ethane from [CpM(PH(3))(CH(3))(2)](+) (M = Rh, Ir) shows a similar thermodynamic profile, but is kinetically quite different from methane elimination from [CpM(PH(3))(CH(3))(H)](+): the reductive elimination barrier is much greater and does not involve a sigma-complex intermediate. The large difference in the calculated activation barriers (ca. 12.0 and ca. 30.5 kcal mol(-1) for the Rh and Ir systems, respectively) agrees with the experimental observation, for related systems, of oxidatively induced ethane elimination when M = Rh, whereas the related Ir systems prefer to decompose by alternative pathways.

Guest Commentary: Global Environmental Education: A Complex Web of Reactions and Repercussions.

ERIC Educational Resources Information Center

Stapp, William B.; Mann, Lori

1985-01-01

Argues that interdependence among all living systems on earth is a necessary element in solving environmental problems, stressing similarities among international political systems and cultures. The ultimate challenge of environmental education is to bring individuals of all ages to critical understanding of the oneness of the earth. (DH)

Reconfigurable all-dielectric metasurface based on tunable chemical systems in aqueous solution.

PubMed

Yang, Xiaoqing; Zhang, Di; Wu, Shiyue; Yin, Yang; Li, Lanshuo; Cao, Kaiyuan; Huang, Kama

2017-06-09

Dynamic control transmission and polarization properties of electromagnetic (EM) wave propagation is investigated using chemical reconfigurable all-dielectric metasurface. The metasurface is composed of cross-shaped periodical teflon tubes and inner filled chemical systems (i.e., mixtures and chemical reaction) in aqueous solution. By tuning the complex permittivity of chemical systems, the reconfigurable metasurface can be easily achieved. The transmission properties of different incident polarized waves (i.e., linear and circular polarization) were simulated and experimentally measured for static ethanol solution as volume ratio changed. Both results indicated this metasurface can serve as either tunable FSS (Frequency Selective Surface) or tunable linear-to-circular/cross Polarization Converter at required frequency range. Based on the reconfigurable laws obtained from static solutions, we developed a dynamic dielectric system and researched a typical chemical reaction with time-varying permittivity filled in the tubes experimentally. It provides new ways for realizing automatic reconfiguration of metasurface by chemical reaction system with given variation laws of permittivity.

Complex Trauma and Mental Health in Children and Adolescents Placed in Foster Care: Findings from the National Child Traumatic Stress Network

ERIC Educational Resources Information Center

Greeson, Johanna K. P.; Briggs, Ernestine C.; Kisiel, Cassandra L.; Layne, Christopher M.; Ake, George S., III; Ko, Susan J.; Gerrity, Ellen T.; Steinberg, Alan M.; Howard, Michael L.; Pynoos, Robert S.; Fairbank, John A.

2011-01-01

Many children in the child welfare system (CWS) have histories of recurrent interpersonal trauma perpetrated by caregivers early in life often referred to as "complex trauma". Children in the CWS also experience a diverse range of reactions across multiple areas of functioning that are associated with such exposure. Nevertheless, few CWSs…

Preface: Special Topic on Reaction Pathways

NASA Astrophysics Data System (ADS)

Clementi, Cecilia; Henkelman, Graeme

2017-10-01

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

Collective Autoionization in Multiply-Excited Systems: A novel ionization process observed in Helium Nanodroplets

PubMed Central

LaForge, A. C.; Drabbels, M.; Brauer, N. B.; Coreno, M.; Devetta, M.; Di Fraia, M.; Finetti, P.; Grazioli, C.; Katzy, R.; Lyamayev, V.; Mazza, T.; Mudrich, M.; O'Keeffe, P.; Ovcharenko, Y.; Piseri, P.; Plekan, O.; Prince, K. C.; Richter, R.; Stranges, S.; Callegari, C.; Möller, T.; Stienkemeier, F.

2014-01-01

Free electron lasers (FELs) offer the unprecedented capability to study reaction dynamics and image the structure of complex systems. When multiple photons are absorbed in complex systems, a plasma-like state is formed where many atoms are ionized on a femtosecond timescale. If multiphoton absorption is resonantly-enhanced, the system becomes electronically-excited prior to plasma formation, with subsequent decay paths which have been scarcely investigated to date. Here, we show using helium nanodroplets as an example that these systems can decay by a new type of process, named collective autoionization. In addition, we show that this process is surprisingly efficient, leading to ion abundances much greater than that of direct single-photon ionization. This novel collective ionization process is expected to be important in many other complex systems, e.g. macromolecules and nanoparticles, exposed to high intensity radiation fields. PMID:24406316

SCScore: Synthetic Complexity Learned from a Reaction Corpus.

PubMed

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.

Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality

PubMed Central

Sletten, Ellen M.

2010-01-01

The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules. PMID:19714693

Bioorthogonal chemistry: fishing for selectivity in a sea of functionality.

PubMed

Sletten, Ellen M; Bertozzi, Carolyn R

2009-01-01

The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.

Evolution of an RNP assembly system: A minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster

PubMed Central

Kroiss, Matthias; Schultz, Jörg; Wiesner, Julia; Chari, Ashwin; Sickmann, Albert; Fischer, Utz

2008-01-01

In vertebrates, assembly of spliceosomal uridine-rich small nuclear ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a macromolecular entity composed of the proteins SMN and Gemins 2–8. Here we have studied the evolution of this machinery using complete genome assemblies of multiple model organisms. The SMN complex has gained complexity in evolution by a blockwise addition of Gemins onto an ancestral core complex composed of SMN and Gemin2. In contrast to this overall evolutionary trend to more complexity in metazoans, orthologs of most Gemins are missing in dipterans. In accordance with these bioinformatic data a previously undescribed biochemical purification strategy elucidated that the dipteran Drosophila melanogaster contains an SMN complex of remarkable simplicity. Surprisingly, this minimal complex not only mediates the assembly reaction in a manner very similar to its vertebrate counterpart, but also prevents misassembly onto nontarget RNAs. Our data suggest that only a minority of Gemins are required for the assembly reaction per se, whereas others may serve additional functions in the context of UsnRNP biogenesis. The evolution of the SMN complex is an interesting example of how the simplification of a biochemical process contributes to genome compaction. PMID:18621711

Reaction Intermediates of Quinol Oxidation in a Photoactivatable System that Mimics Electron Transfer in the Cytochrome bc1 Complex

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

Cape, Jonathan L.; Bowman, Michael K.; Kramer, David M.

2005-03-30

Current competing models for the two-electron oxidation of quinol (QH{sub 2}) at the cytochrome bc{sub 1} complex and related complexes have different requirements for the reaction intermediate. At present, the intermediate species of the enzymatic oxidation process have not been observed or characterized, probably due to their transient nature. Here, we use a biomimetic oxidant, Ru(bpy){sub 2}(pbim)(PF6)2 (bpy = 2,2'-dipyridyl, pbim = 2-(2-benzimidazolate)pyridine) in an aprotic medium to probe the oxidation of the ubiquinol analogue, 2,3-dimethoxy-5-methyl-1,4-benzoquinol (UQH{sub 2}-0), an the plastoquinol analogue, trimethyl-1,4-benzoquinol (TMQH{sub 2}-0), using time-resolved and steady state spectroscopic techniques. This system qualitatively reproduces key features observed duringmore » ubiquinol oxidation by the mitochondrial cytochrome bc1 complex. Comparison of isotope dependent activation properties in the native and synthetic systems, as well as, analysis of the time-resolved direct-detection electron para magnetic resonance signals in the synthetic system allows us to conclude that: (1) the initial and rate-limiting step in quinol oxidation, both in the biological and biomimetic systems, involves electron and proton transfer, probably via a proton coupled electron transfer mechanism; (2) a neutral semiquinone intermediate is formed in the biomimetic system; and (3) oxidation of the QH*/QH{sub 2} couple for UQH{sub 2}-0, but not TMQH{sub 2}-0, exhibits a non-classical primary deuterium kinetic isotope effect on its Arrhenius activation energy ({Delta}G{sup TS}), where {Delta}G{sup TS} for the protiated form is larger than for the deuterated form. The same behavior is observed during steady state turnover of the cyt bc{sub 1} complex using ubiquinol, but not plastoquinol, as a substrate, leading to the conclusion that similar chemical pathways are involved in both systems. The synthetic system is an unambiguous n=1 electron acceptor and it is thus inferred that sequential oxidation of ubiquinol (by two sequential n=1 processes) is more rapid than a truly concerted (n=2) oxidation in the cyt bc{sub 1} complex.« less

Watching proton transfer in real time: Ultrafast photoionization-induced proton transfer in phenol-ammonia complex cation.

PubMed

Shen, Ching-Chi; Tsai, Tsung-Ting; Wu, Jun-Yi; Ho, Jr-Wei; Chen, Yi-Wei; Cheng, Po-Yuan

2017-10-28

In this paper, we give a full account of our previous work [C. C. Shen et al., J. Chem. Phys. 141, 171103 (2014)] on the study of an ultrafast photoionization-induced proton transfer (PT) reaction in the phenol-ammonia (PhOH-NH 3 ) complex using ultrafast time-resolved ion photofragmentation spectroscopy implemented by the photoionization-photofragmentation pump-probe detection scheme. Neutral PhOH-NH 3 complexes prepared in a free jet are photoionized by femtosecond 1 + 1 resonance-enhanced multiphoton ionization via the S 1 state. The evolving cations are then probed by delayed pulses that result in ion fragmentation, and the ionic dynamics is followed by measuring the parent-ion depletion as a function of the pump-probe delay time. By comparing with systems in which PT is not feasible and the steady-state ion photofragmentation spectra, we concluded that the observed temporal evolutions of the transient ion photofragmentation spectra are consistent with an intracomplex PT reaction after photoionization from the initial non-PT to the final PT structures. Our experiments revealed that PT in [PhOH-NH 3 ] + cation proceeds in two distinct steps: an initial impulsive wave-packet motion in ∼70 fs followed by a slower relaxation of about 1 ps that stabilizes the system into the final PT configuration. These results indicate that for a barrierless PT system, even though the initial PT motions are impulsive and ultrafast, the time scale to complete the reaction can be much slower and is determined by the rate of energy dissipation into other modes.

Computational reacting gas dynamics

NASA Technical Reports Server (NTRS)

Lam, S. H.

1993-01-01

In the study of high speed flows at high altitudes, such as that encountered by re-entry spacecrafts, the interaction of chemical reactions and other non-equilibrium processes in the flow field with the gas dynamics is crucial. Generally speaking, problems of this level of complexity must resort to numerical methods for solutions, using sophisticated computational fluid dynamics (CFD) codes. The difficulties introduced by reacting gas dynamics can be classified into three distinct headings: (1) the usually inadequate knowledge of the reaction rate coefficients in the non-equilibrium reaction system; (2) the vastly larger number of unknowns involved in the computation and the expected stiffness of the equations; and (3) the interpretation of the detailed reacting CFD numerical results. The research performed accepts the premise that reacting flows of practical interest in the future will in general be too complex or 'untractable' for traditional analytical developments. The power of modern computers must be exploited. However, instead of focusing solely on the construction of numerical solutions of full-model equations, attention is also directed to the 'derivation' of the simplified model from the given full-model. In other words, the present research aims to utilize computations to do tasks which have traditionally been done by skilled theoreticians: to reduce an originally complex full-model system into an approximate but otherwise equivalent simplified model system. The tacit assumption is that once the appropriate simplified model is derived, the interpretation of the detailed numerical reacting CFD numerical results will become much easier. The approach of the research is called computational singular perturbation (CSP).

Watching proton transfer in real time: Ultrafast photoionization-induced proton transfer in phenol-ammonia complex cation

NASA Astrophysics Data System (ADS)

Shen, Ching-Chi; Tsai, Tsung-Ting; Wu, Jun-Yi; Ho-Wei, Jr.; Chen, Yi-Wei; Cheng, Po-Yuan

2017-10-01

In this paper, we give a full account of our previous work [C. C. Shen et al., J. Chem. Phys. 141, 171103 (2014)] on the study of an ultrafast photoionization-induced proton transfer (PT) reaction in the phenol-ammonia (PhOH-NH3) complex using ultrafast time-resolved ion photofragmentation spectroscopy implemented by the photoionization-photofragmentation pump-probe detection scheme. Neutral PhOH-NH3 complexes prepared in a free jet are photoionized by femtosecond 1 + 1 resonance-enhanced multiphoton ionization via the S1 state. The evolving cations are then probed by delayed pulses that result in ion fragmentation, and the ionic dynamics is followed by measuring the parent-ion depletion as a function of the pump-probe delay time. By comparing with systems in which PT is not feasible and the steady-state ion photofragmentation spectra, we concluded that the observed temporal evolutions of the transient ion photofragmentation spectra are consistent with an intracomplex PT reaction after photoionization from the initial non-PT to the final PT structures. Our experiments revealed that PT in [PhOH-NH3]+ cation proceeds in two distinct steps: an initial impulsive wave-packet motion in ˜70 fs followed by a slower relaxation of about 1 ps that stabilizes the system into the final PT configuration. These results indicate that for a barrierless PT system, even though the initial PT motions are impulsive and ultrafast, the time scale to complete the reaction can be much slower and is determined by the rate of energy dissipation into other modes.

Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations

DOE PAGES

Pierce, Eric M.; Frugier, Pierre; Criscenti, Louise J.; ...

2014-07-12

Describing the reactions that occur at the glass-water interface and control the development of the altered layer constitutes one of the main scientific challenges impeding existing models from providing accurate radionuclide release estimates. Radionuclide release estimates are a critical component of the safety basis for geologic repositories. The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products) represents a complex region, both physically and chemically, sandwiched between two distinct boundaries pristine glass surface at the inner most interface and aqueous solution at the outer most interface. Computational models, spanning different length and time-scales, are currently being developed tomore » improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include geochemical simulations [i.e., classical reaction path simulations and glass reactivity in allowance for alteration layer (GRAAL) simulations], Monte Carlo simulations, and Molecular Dynamics methods. Finally, in this manuscript, we discuss the advances and limitations of each modeling approach placed in the context of the glass-water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers.« less

A General, Efficient and Functional-Group-Tolerant Catalyst System for the Palladium-Catalyzed Thioetherification of Aryl Bromides and Iodides

PubMed Central

Fernández-Rodríguez, Manuel A.; Hartwig, John F.

2010-01-01

The cross-coupling reaction of aryl bromides and iodides with aliphatic and aromatic thiols catalyzed by palladium complexes of the bisphosphine ligand CyPF-tBu (1) is reported. Reactions occur in excellent yields, broad scope, high tolerance of functional groups and with turnover numbers that exceed those of previous catalysts by two or three orders of magnitude. These couplings of bromo- and iodoarenes are more efficient than the corresponding reactions of chloroarenes and could be conducted with less catalyst loading and/or milder reaction conditions. Consequently, limitations regarding scope and functional group tolerance previously reported in the coupling of aryl chlorides are now overcome. PMID:19154131

Quantitative analysis of ribosome–mRNA complexes at different translation stages

PubMed Central

Shirokikh, Nikolay E.; Alkalaeva, Elena Z.; Vassilenko, Konstantin S.; Afonina, Zhanna A.; Alekhina, Olga M.; Kisselev, Lev L.; Spirin, Alexander S.

2010-01-01

Inhibition of primer extension by ribosome–mRNA complexes (toeprinting) is a proven and powerful technique for studying mechanisms of mRNA translation. Here we have assayed an advanced toeprinting approach that employs fluorescently labeled DNA primers, followed by capillary electrophoresis utilizing standard instruments for sequencing and fragment analysis. We demonstrate that this improved technique is not merely fast and cost-effective, but also brings the primer extension inhibition method up to the next level. The electrophoretic pattern of the primer extension reaction can be characterized with a precision unattainable by the common toeprint analysis utilizing radioactive isotopes. This method allows us to detect and quantify stable ribosomal complexes at all stages of translation, including initiation, elongation and termination, generated during the complete translation process in both the in vitro reconstituted translation system and the cell lysate. We also point out the unique advantages of this new methodology, including the ability to assay sites of the ribosomal complex assembly on several mRNA species in the same reaction mixture. PMID:19910372

Redox reactions of V(III) and Cr(III)picolinate complexes in aqueous solutions

NASA Astrophysics Data System (ADS)

Vinayakumar, C. K.; Dey, G. R.; Kishore, K.; Moorthy, P. N.

1996-12-01

Reactions of e aq-, H-atoms, OH, (CH 3) 2COH, and CO 2- radicals with V(III)picolinate and Cr(III)picolinate have been studied by the pulse radiolysis technique. The spectra of V(II)picolinate, V(IV)picolinate, Cr(II)picolinate, OH adduct of Cr(III)picolinate and Cr(IV)picolinate have been obtained and the rate constants of the reactions of various radicals with V(III) and Cr(III)picolinate have been determined. The implications of these results to the chemical decontamination of nuclear reactor systems are discussed.

Nickel(0)-Catalyzed Inert C-O Bond Functionalization: Organo Rare-Earth Metal Complex as the Coupling Partner.

PubMed

Yan, Xiangqian; Yang, Fanzhi; Cai, Guilong; Meng, Qingwei; Li, Xiaofang

2018-02-02

An organo rare-earth metal complex has been employed as a highly efficient nucleophile in Ni(0)-catalyzed C-O bond functionalization. The optimized catalytic system which consists of Ni(cod) 2 , PCy 3 , and t-BuONa could smoothly convert 1 equiv of naphthyl ethers to alkylated naphthalene analogues with 0.4 equiv of Ln(CH 2 SiMe 3 ) 3 (THF) 2 , delivering good to excellent yields. The reaction system could also activate the ArCH 2 -O bond with mild base.

Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics.

PubMed

Hanel, Rudolf; Pöchacker, Manfred; Thurner, Stefan

2010-12-28

Linearized catalytic reaction equations (modelling, for example, the dynamics of genetic regulatory networks), under the constraint that expression levels, i.e. molecular concentrations of nucleic material, are positive, exhibit non-trivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems, an inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity, which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems, their basic properties allow us to understand the fundamental dynamical properties of complex biological reaction networks. We analyse the Lyapunov spectrum, determine the probability of finding stationary oscillating solutions, demonstrate the effect of the nonlinearity on the effective in- and out-degree of the active interaction network, and study how the frequency distributions of oscillatory modes of such a system depend on the average connectivity.

Self-Assembly Strategies for Integrating Light Harvesting and Charge Separation in Artificial Photosynthetic Systems

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

Wasielewski, Michael R.

In natural photosynthesis, organisms optimize solar energy conversion through organized assemblies of photofunctional chromophores and catalysts within proteins that provide specifically tailored environments for chemical reactions. As with their natural counterparts, artificial photosynthetic systems for practical solar fuels production must collect light energy, separate charge, and transport charge to catalytic sites where multielectron redox processes will occur. While encouraging progress has been made on each aspect of this complex problem, researchers have not yet developed self-ordering and self-assembling components and the tailored environments necessary to realize a fully-functional artificial system. Previously researchers have used complex, covalent molecular systems comprised ofmore » chromophores, electron donors, and electron acceptors to mimic both the light-harvesting and the charge separation functions of photosynthetic proteins. These systems allow for study of the dependencies of electron transfer rate constants on donor?acceptor distance and orientation, electronic interaction, and the free energy of the reaction. The most useful and informative systems are those in which structural constraints control both the distance and the orientation between the electron donors and acceptors. Self-assembly provides a facile means for organizing large numbers of molecules into supramolecular structures that can bridge length scales from nanometers to macroscopic dimensions. The resulting structures must provide pathways for migration of light excitation energy among antenna chromophores, and from antennas to reaction centers. They also must incorporate charge conduits, that is, molecular 'wires' that can efficiently move electrons and holes between reaction centers and catalytic sites. The central scientific challenge is to develop small, functional building blocks with a minimum number of covalent linkages, which also have the appropriate molecular recognition properties to facilitate self-assembly of complete, functional artificial photosynthetic systems. In this Account, we explore how self-assembly strategies involving ?-stacking can be used to integrate light harvesting with charge separation and transport.« less

Ground-State Electronic Structure of RC-LH1 and LH2 Pigment Assemblies of Purple Bacteria via the EBF-MO Method.

PubMed

Shrestha, Kushal; Jakubikova, Elena

2015-08-20

Light-harvesting antennas are protein-pigment complexes that play a crucial role in natural photosynthesis. The antenna complexes absorb light and transfer energy to photosynthetic reaction centers where charge separation occurs. This work focuses on computational studies of the electronic structure of the pigment networks of light-harvesting complex I (LH1), LH1 with the reaction center (RC-LH1), and light-harvesting complex II (LH2) found in purple bacteria. As the pigment networks of LH1, RC-LH1, and LH2 contain thousands of atoms, conventional density functional theory (DFT) and ab initio calculations of these systems are not computationally feasible. Therefore, we utilize DFT in conjunction with the energy-based fragmentation with molecular orbitals method and a semiempirical approach employing the extended Hückel model Hamiltonian to determine the electronic properties of these pigment assemblies. Our calculations provide a deeper understanding of the electronic structure of natural light-harvesting complexes, especially their pigment networks, which could assist in rational design of artificial photosynthetic devices.

Complexes in the Photocatalytic Reaction of CO2 and H2O: Theoretical Studies

PubMed Central

Luo, Dongmei; Zhang, Ning; Hong, Sanguo; Wu, Huanwen; Liu, Zhihua

2010-01-01

Complexes (H2O/CO2, e–(H2O/CO2) and h+–(H2O/CO2)) in the reaction system of CO2 photoreduction with H2O were researched by B3LYP and MP2 methods along with natural bond orbital (NBO) analysis. Geometries of these complexes were optimized and frequencies analysis performed. H2O/CO2 captured photo-induced electron and hole produced e–(H2O/CO2) and h+–(H2O/CO2), respectively. The results revealed that CO2 and H2O molecules could be activated by the photo-induced electrons and holes, and each of these complexes possessed two isomers. Due to the effect of photo-induced electrons, the bond length of C=O and H-O were lengthened, while H-O bonds were shortened, influenced by holes. The infrared (IR) adsorption frequencies of these complexes were different from that of CO2 and H2O, which might be attributed to the synergistic effect and which could not be captured experimentally. PMID:21152274

Evidence for global processing of complex visual displays

NASA Technical Reports Server (NTRS)

Munson, Robert C.; Horst, Richard L.

1986-01-01

'Polar graphic' displays, in which changes in system status are represented by distortions in the form of a geometric figure, were presented to subjects, and reaction time (RT) to discriminate system status was recorded. Of interest was the extent to which reaction time showed evidence of global processing of these displays as the number of nodes and difficulty of discrimination were varied. When discrimination of system status was easy, RT showed no increase with increasing number of nodes, providing evidence of global processing. When discrimination was difficult, systematic differences in RT as a function of the number of nodes suggested the invocation of other (local) processes, although the data were not consistent with a node-by-node search process.

A universal surface complexation framework for modeling proton binding onto bacterial surfaces in geologic settings

USGS Publications Warehouse

Borrok, D.; Turner, B.F.; Fein, J.B.

2005-01-01

Adsorption onto bacterial cell walls can significantly affect the speciation and mobility of aqueous metal cations in many geologic settings. However, a unified thermodynamic framework for describing bacterial adsorption reactions does not exist. This problem originates from the numerous approaches that have been chosen for modeling bacterial surface protonation reactions. In this study, we compile all currently available potentiometric titration datasets for individual bacterial species, bacterial consortia, and bacterial cell wall components. Using a consistent, four discrete site, non-electrostatic surface complexation model, we determine total functional group site densities for all suitable datasets, and present an averaged set of 'universal' thermodynamic proton binding and site density parameters for modeling bacterial adsorption reactions in geologic systems. Modeling results demonstrate that the total concentrations of proton-active functional group sites for the 36 bacterial species and consortia tested are remarkably similar, averaging 3.2 ?? 1.0 (1??) ?? 10-4 moles/wet gram. Examination of the uncertainties involved in the development of proton-binding modeling parameters suggests that ignoring factors such as bacterial species, ionic strength, temperature, and growth conditions introduces relatively small error compared to the unavoidable uncertainty associated with the determination of cell abundances in realistic geologic systems. Hence, we propose that reasonable estimates of the extent of bacterial cell wall deprotonation can be made using averaged thermodynamic modeling parameters from all of the experiments that are considered in this study, regardless of bacterial species used, ionic strength, temperature, or growth condition of the experiment. The average site densities for the four discrete sites are 1.1 ?? 0.7 ?? 10-4, 9.1 ?? 3.8 ?? 10-5, 5.3 ?? 2.1 ?? 10-5, and 6.6 ?? 3.0 ?? 10-5 moles/wet gram bacteria for the sites with pKa values of 3.1, 4.7, 6.6, and 9.0, respectively. It is our hope that this thermodynamic framework for modeling bacteria-proton binding reactions will also provide the basis for the development of an internally consistent set of bacteria-metal binding constants. 'Universal' constants for bacteria-metal binding reactions can then be used in conjunction with equilibrium constants for other important metal adsorption and complexation reactions to calculate the overall distribution of metals in realistic geologic systems.

Systematic Evaluation of Bioorthogonal Reactions in Live Cells with Clickable HaloTag Ligands: Implications for Intracellular Imaging

PubMed Central

2015-01-01

Bioorthogonal reactions, including the strain-promoted azide–alkyne cycloaddition (SPAAC) and inverse electron demand Diels–Alder (iEDDA) reactions, have become increasingly popular for live-cell imaging applications. However, the stability and reactivity of reagents has never been systematically explored in the context of a living cell. Here we report a universal, organelle-targetable system based on HaloTag protein technology for directly comparing bioorthogonal reagent reactivity, specificity, and stability using clickable HaloTag ligands in various subcellular compartments. This system enabled a detailed comparison of the bioorthogonal reactions in live cells and informed the selection of optimal reagents and conditions for live-cell imaging studies. We found that the reaction of sTCO with monosubstituted tetrazines is the fastest reaction in cells; however, both reagents have stability issues. To address this, we introduced a new variant of sTCO, Ag-sTCO, which has much improved stability and can be used directly in cells for rapid bioorthogonal reactions with tetrazines. Utilization of Ag complexes of conformationally strained trans-cyclooctenes should greatly expand their usefulness especially when paired with less reactive, more stable tetrazines. PMID:26270632

Systematic Evaluation of Bioorthogonal Reactions in Live Cells with Clickable HaloTag Ligands: Implications for Intracellular Imaging.

PubMed

Murrey, Heather E; Judkins, Joshua C; Am Ende, Christopher W; Ballard, T Eric; Fang, Yinzhi; Riccardi, Keith; Di, Li; Guilmette, Edward R; Schwartz, Joel W; Fox, Joseph M; Johnson, Douglas S

2015-09-09

Bioorthogonal reactions, including the strain-promoted azide-alkyne cycloaddition (SPAAC) and inverse electron demand Diels-Alder (iEDDA) reactions, have become increasingly popular for live-cell imaging applications. However, the stability and reactivity of reagents has never been systematically explored in the context of a living cell. Here we report a universal, organelle-targetable system based on HaloTag protein technology for directly comparing bioorthogonal reagent reactivity, specificity, and stability using clickable HaloTag ligands in various subcellular compartments. This system enabled a detailed comparison of the bioorthogonal reactions in live cells and informed the selection of optimal reagents and conditions for live-cell imaging studies. We found that the reaction of sTCO with monosubstituted tetrazines is the fastest reaction in cells; however, both reagents have stability issues. To address this, we introduced a new variant of sTCO, Ag-sTCO, which has much improved stability and can be used directly in cells for rapid bioorthogonal reactions with tetrazines. Utilization of Ag complexes of conformationally strained trans-cyclooctenes should greatly expand their usefulness especially when paired with less reactive, more stable tetrazines.

Molecular gearing systems

DOE PAGES

Gakh, Andrei A.; Sachleben, Richard A.; Bryan, Jeff C.

1997-11-01

The race to create smaller devices is fueling much of the research in electronics. The competition has intensified with the advent of microelectromechanical systems (MEMS), in which miniaturization is already reaching the dimensional limits imposed by physics of current lithographic techniques. Also, in the realm of biochemistry, evidence is accumulating that certain enzyme complexes are capable of very sophisticated modes of motion. Complex synergistic biochemical complexes driven by sophisticated biomechanical processes are quite common. Their biochemical functions are based on the interplay of mechanical and chemical processes, including allosteric effects. In addition, the complexity of this interplay far exceeds thatmore » of typical chemical reactions. Understanding the behavior of artificial molecular devices as well as complex natural molecular biomechanical systems is difficult. Fortunately, the problem can be successfully resolved by direct molecular engineering of simple molecular systems that can mimic desired mechanical or electronic devices. These molecular systems are called technomimetics (the name is derived, by analogy, from biomimetics). Several classes of molecular systems that can mimic mechanical, electronic, or other features of macroscopic devices have been successfully synthesized by conventional chemical methods during the past two decades. In this article we discuss only one class of such model devices: molecular gearing systems.« less

Reaction-based Indicator displacement Assay (RIA) for the selective colorimetric and fluorometric detection of peroxynitrite.

PubMed

Sun, Xiaolong; Lacina, Karel; Ramsamy, Elena C; Flower, Stephen E; Fossey, John S; Qian, Xuhong; Anslyn, Eric V; Bull, Steven D; James, Tony D

2015-05-01

Using the self-assembly of aromatic boronic acids with Alizarin Red S (ARS), we developed a new chemosensor for the selective detection of peroxynitrite. Phenylboronic acid (PBA), benzoboroxole (BBA) and 2-( N , N -dimethylaminomethyl)phenylboronic acid (NBA) were employed to bind with ARS to form the complex probes. In particular, the ARS-NBA system with a high binding affinity can preferably react with peroxynitrite over hydrogen peroxide and other ROS/RNS due to the protection of the boron via the solvent-insertion B-N interaction. Our simple system produces a visible colorimetric change and on-off fluorescence response towards peroxynitrite. By coupling a chemical reaction that leads to an indicator displacement, we have developed a new sensing strategy, referred to herein as RIA (Reaction-based Indicator displacement Assay).

DNA-Based Enzyme Reactors and Systems

PubMed Central

Linko, Veikko; Nummelin, Sami; Aarnos, Laura; Tapio, Kosti; Toppari, J. Jussi; Kostiainen, Mauri A.

2016-01-01

During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme) cascade reactions and to regulate the enzyme functions and the reaction pathways. Moreover, sophisticated DNA structures can be utilized in encapsulating active enzymes and delivering the molecular cargo into cells. In this review, we focus on the latest enzyme systems based on novel DNA nanostructures: enzyme reactors, regulatory devices and carriers that can find uses in various biotechnological and nanomedical applications. PMID:28335267

Use of cyclodextrins in biotransformation reactions with cell cultures of Morus nigra: biosynthesis of prenylated chalcone isocordoin.

PubMed

Bolasco, Adriana; Fioravanti, Rossella; Rossi, Francesca; Rossi, Paola; Vitali, Alberto

2010-06-16

In vivo biotransformation experiments were performed by using a cell suspension culture of Morus nigra expressing a high PT (prenyltransferase) activity, fed with the target substrate 2',4'-dihydroxychalcone. In order to improve the reaction yields by enhancing the chalcone solubility, three different cyclodextrins have been used to host the substrate. The respective complexes have been studied by means of both spectroscopic and calorimetric techniques (Fourier-transform infrared, 1H-NMR and differential scanning calorimetry) and the solution behaviours have been characterized by solubility phase studies. The hydroxypropyl-beta-cyclodextrin complex was found to be the most suitable for biotransformation, and the reaction of prenylation resulted in a 6-fold higher yield of the final product when compared with the use of the free substrate. The reaction provided as the sole product the 3'-dimethylallyl derivative isocordoin, a biologically active plant compound. The results obtained allow the development of systems based on the use of biofermentors or the use of immobilized cells in order to enhance the biotransformation yields.

PuPHOS: a synthetically useful chiral bidentate ligand for the intermolecular Pauson-Khand reaction.

PubMed

Verdaguer, Xavier; Lledó, Agustí; López-Mosquera, Cristina; Maestro, Miguel Angel; Pericàs, Miquel A; Riera, Antoni

2004-11-12

Here we describe the synthesis and use of the Pulegone-derived bidentate P,S ligands PuPHOS and CyPuPHOS in the intermolecular Pauson-Khand reaction. Ligand exchange reaction of hexacarbonyldicobalt-alkyne complexes with PuPHOS provides a diasteromeric mixture of complexes (up to 4.5:1) from which the major isomers can be conveniently separated by simple crystallization. An isomerization-crystallization sequence of the original mixture results in a dynamic resolution that allows the preparation of the pure major Co(2)(mu-TMSC(2)H)(CO)(4)-PuPHOS (15a) in a multigram scale. Pauson-Khand reaction of 15a with norbornadiene provided, for the first time, the corresponding enone 18 with up to 93% yield and 97% ee. The use of (+)-18 as a surrogate of chiral cyclopentadienone is also demonstrated. Copper-catalyzed Michael addition of a Grignard reagent followed by removal of the TMS group with TBAF were the most reliable methods to transform (+)-18 into valuable starting materials 20a-e for the enantioselective synthesis of cyclopentenoid systems.

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

PubMed

Szabó, István; Czakó, Gábor

2017-11-30

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.

High Density Hydrogen Storage System Demonstration Using NaAlH4 Based Complex Compound Hydrides

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

Daniel A. Mosher; Xia Tang; Ronald J. Brown

2007-07-27

This final report describes the motivations, activities and results of the hydrogen storage independent project "High Density Hydrogen Storage System Demonstration Using NaAlH4 Based Complex Compound Hydrides" performed by the United Technologies Research Center under the Department of Energy Hydrogen Program, contract # DE-FC36-02AL67610. The objectives of the project were to identify and address the key systems technologies associated with applying complex hydride materials, particularly ones which differ from those for conventional metal hydride based storage. This involved the design, fabrication and testing of two prototype systems based on the hydrogen storage material NaAlH4. Safety testing, catalysis studies, heat exchangermore » optimization, reaction kinetics modeling, thermochemical finite element analysis, powder densification development and material neutralization were elements included in the effort.« less

New instrumentation for the comprehension of chemical reactions under microwave and classical heating with the aid of a wide frequency band dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Chevalier, S.; Meyer, O.; Weil, R.; Fourrierlamer, A.; Petit, A.; Loupy, A.; Maurel, F.

2001-09-01

An instrumentation system for measuring wide frequency band complex permittivity of a sample submitted to a microwave irradiation has been optimized in order to allow macroscopic temperature measurements. The reaction of saponification of aromatic esters is studied using this instrumentation. We take interest in the behavior of the ionic conductivity phenomenon occurring in the reactive medium during microwave heating, and we compare it with the results obtained under classical heating. We show that the activation energy associated with ionic conductivity is lower when the reaction is performed under microwaves than when it is performed under classical heating. We thus deduce that microwaves act on the reaction advancement as a catalyst, and thus makes the reaction easier.

Pattern Formation on Networks: from Localised Activity to Turing Patterns

PubMed Central

McCullen, Nick; Wagenknecht, Thomas

2016-01-01

Networks of interactions between competing species are used to model many complex systems, such as in genetics, evolutionary biology or sociology and knowledge of the patterns of activity they can exhibit is important for understanding their behaviour. The emergence of patterns on complex networks with reaction-diffusion dynamics is studied here, where node dynamics interact via diffusion via the network edges. Through the application of a generalisation of dynamical systems analysis this work reveals a fundamental connection between small-scale modes of activity on networks and localised pattern formation seen throughout science, such as solitons, breathers and localised buckling. The connection between solutions with a single and small numbers of activated nodes and the fully developed system-scale patterns are investigated computationally using numerical continuation methods. These techniques are also used to help reveal a much larger portion of of the full number of solutions that exist in the system at different parameter values. The importance of network structure is also highlighted, with a key role being played by nodes with a certain so-called optimal degree, on which the interaction between the reaction kinetics and the network structure organise the behaviour of the system. PMID:27273339

Driving forces and the influence of the buffer composition on the complexation reaction between ibuprofen and HPCD.

PubMed

Perlovich, German L; Skar, Merete; Bauer-Brandl, Annette

2003-10-01

Cyclodextrins are often used in order to increase the aqueous solubility of drug substances by complexation. In order to investigate the complexation reaction of ibuprofen and hydroxypropyl-beta-cyclodextrin, titration calorimetry was used as a direct method. The thermodynamic parameters of the complexation process (stability constant, K(11); complexation enthalpy, deltaH(c) degrees ) were obtained in two different buffer systems (citric acid/sodium-phosphate and phosphoric acid) at various pH values. Based on these data the relative contributions of the enthalpic and entropic terms of the Gibbs energy to the complexation process have been analyzed. In both buffers the enthalpic and entropic terms are of different sign and this case corresponds to a 'nonclassical' model of hydrophobic interaction. In citric buffer, the main driving force of complexation is the entropy, which increases from 60 to 67% while the pH of the solution increases from 3.2 to 8.0. However, for the phosphoric buffer the entropic term decreases from 60 to 45%, while the pH-value of the solution increases from 5.0 to 8.2, and the driving force of the complexation process changes from entropy to enthalpy. The experimental data of the present study are compared to results of other authors and discrepancies discussed in detail.

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation.

PubMed

Chernia, Zelig; Tsori, Yoav

2018-03-14

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.

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation

NASA Astrophysics Data System (ADS)

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.

Interactions of platinum metals and their complexes in biological systems.

PubMed Central

LeRoy, A F

1975-01-01

Platinum-metal oxidation catalysts are to be introduced in exhaust systems of many 1975 model-year automobiles in the U.S. to meet Clean Air Act standards. Small quantities of finely divided catalyst have been found issuing from prototype systems; platinum and palladium compounds may be found also. Although platinum exhibits a remarkable resistance to oxidation and chemical attack, it reacts chemically under some conditions producing coordination complex compounds. Palladium reacts more readily than platinum. Some platinum-metal complexes interact with biological systems as bacteriostatic, bacteriocidal, viricidal, and immunosuppressive agents. Workers chronically exposed to platinum complexes often develop asthma-like respiratory distress and skin reactions called platinosis. Platinum complexes used alone and in combination therapy with other drugs have recently emerged as effective agents in cancer chemotherapy. Understanding toxic and favorable interactions of metal species with living organisms requires basic information on quantities and chemical characteristics of complexes at trace concentrations in biological materials. Some basic chemical kinetic and thermodynamic data are presented to characterize the chemical behavior of the complex cis-[Pt(NH3)2Cl2] used therapeutically. A brief discussion of platinum at manogram levels in biological tissue is discussed. PMID:50943

A comprehensive study of the complexation of alkali metal cations by lower rim calix[4]arene amide derivatives.

PubMed

Horvat, Gordan; Frkanec, Leo; Cindro, Nikola; Tomišić, Vladislav

2017-09-13

The complexation of alkali metal cations by lower rim N,N-dihexylacetamide (L1) and newly synthesized N-hexyl-N-methylacetamide (L2) calix[4]arene tertiary-amide derivatives was thoroughly studied at 25 °C in acetonitrile (MeCN), benzonitrile (PhCN), and methanol (MeOH) by means of direct and competitive microcalorimetric titrations, and UV and 1 H NMR spectroscopies. In addition, by measuring the ligands' solubilities, the solution (transfer) Gibbs energies of the ligands and their alkali metal complexes were obtained. The inclusion of solvent molecules in the free and complexed calixarene hydrophobic cavities was also investigated. Computational (classical molecular dynamics) investigations of the studied systems were also carried out. The obtained results were compared with those previously obtained by studying the complexation ability of an N-hexylacetamidecalix[4]arene secondary-amide derivative (L3). The stability constants of 1 : 1 complexes were determined in all solvents used (the values obtained by different methods being in excellent agreement), as were the corresponding complexation enthalpies and entropies. Almost all of the examined reactions were enthalpically controlled. The most striking exceptions were reactions of Li + with both ligands in methanol, for which the entropic contribution to the reaction Gibbs energy was substantial due the entropically favourable desolvation of the smallest lithium cation. The thermodynamic stabilities of the complexes were quite solvent dependent (the stability decreased in the solvent order: MeCN > PhCN ≫ MeOH), which could be accounted for by considering the differences in the solvation of the ligand and free and complexed alkali metal cations in the solvents used. Comparison of the stability constants of the ligand L1 and L2 complexes clearly revealed that the higher electron-donating ability of the hexyl with respect to the methyl group is of considerable importance in determining the equilibria of the complexation reactions. Additionally, the quite strong influence of intramolecular hydrogen bond formation in compound L3 (not present in ligands L1 and L2) and that of the inclusion of solvent molecules in the calixarene hydrophobic cone were shown to be of great importance in determining the thermodynamic stability of the calixarene-cation complexes. The experimental results were fully supported by those obtained by MD simulations.

Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials

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

Hoang, Tuan L.; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, CA 94550; Marian, Jaime, E-mail: jmarian@ucla.edu

2015-11-01

An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a proceduremore » for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe{sup 3+}, He{sup +} and H{sup +}) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.« less

Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials

NASA Astrophysics Data System (ADS)

Hoang, Tuan L.; Marian, Jaime; Bulatov, Vasily V.; Hosemann, Peter

2015-11-01

An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a procedure for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe3+, He+ and H+) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.

Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways

PubMed Central

Kawakami, Eiryo; Singh, Vivek K; Matsubara, Kazuko; Ishii, Takashi; Matsuoka, Yukiko; Hase, Takeshi; Kulkarni, Priya; Siddiqui, Kenaz; Kodilkar, Janhavi; Danve, Nitisha; Subramanian, Indhupriya; Katoh, Manami; Shimizu-Yoshida, Yuki; Ghosh, Samik; Jere, Abhay; Kitano, Hiroaki

2016-01-01

Cellular stress responses require exquisite coordination between intracellular signaling molecules to integrate multiple stimuli and actuate specific cellular behaviors. Deciphering the web of complex interactions underlying stress responses is a key challenge in understanding robust biological systems and has the potential to lead to the discovery of targeted therapeutics for diseases triggered by dysregulation of stress response pathways. We constructed large-scale molecular interaction maps of six major stress response pathways in Saccharomyces cerevisiae (baker’s or budding yeast). Biological findings from over 900 publications were converted into standardized graphical formats and integrated into a common framework. The maps are posted at http://www.yeast-maps.org/yeast-stress-response/ for browse and curation by the research community. On the basis of these maps, we undertook systematic analyses to unravel the underlying architecture of the networks. A series of network analyses revealed that yeast stress response pathways are organized in bow–tie structures, which have been proposed as universal sub-systems for robust biological regulation. Furthermore, we demonstrated a potential role for complexes in stabilizing the conserved core molecules of bow–tie structures. Specifically, complex-mediated reversible reactions, identified by network motif analyses, appeared to have an important role in buffering the concentration and activity of these core molecules. We propose complex-mediated reactions as a key mechanism mediating robust regulation of the yeast stress response. Thus, our comprehensive molecular interaction maps provide not only an integrated knowledge base, but also a platform for systematic network analyses to elucidate the underlying architecture in complex biological systems. PMID:28725465

A Quasi-Optical Method for Measuring the Complex Permittivity of Materials.

DTIC Science & Technology

1984-09-01

structural mechanics, flight dynamics; high-temperature thermomechanica, gas kinetics and radiation; research in environmental chemistry and...specific chemical reactions and radia- tion transport in rocket pluses, applied laser spectroscopy, laser chemistry, batery electrochemistry, space...corrosion; evaluation of materials in space environment ; materials performance In space transportation systems; anal- ysis of system vulnerability and

Interfacial mechanisms of heterogeneous Fenton reactions catalyzed by iron-based materials: A review.

PubMed

He, Jie; Yang, Xiaofang; Men, Bin; Wang, Dongsheng

2016-01-01

The heterogeneous Fenton reaction can generate highly reactive hydroxyl radicals (OH) from reactions between recyclable solid catalysts and H2O2 at acidic or even circumneutral pH. Hence, it can effectively oxidize refractory organics in water or soils and has become a promising environmentally friendly treatment technology. Due to the complex reaction system, the mechanism behind heterogeneous Fenton reactions remains unresolved but fascinating, and is crucial for understanding Fenton chemistry and the development and application of efficient heterogeneous Fenton technologies. Iron-based materials usually possess high catalytic activity, low cost, negligible toxicity and easy recovery, and are a superior type of heterogeneous Fenton catalysts. Therefore, this article reviews the fundamental but important interfacial mechanisms of heterogeneous Fenton reactions catalyzed by iron-based materials. OH, hydroperoxyl radicals/superoxide anions (HO2/O2(-)) and high-valent iron are the three main types of reactive oxygen species (ROS), with different oxidation reactivity and selectivity. Based on the mechanisms of ROS generation, the interfacial mechanisms of heterogeneous Fenton systems can be classified as the homogeneous Fenton mechanism induced by surface-leached iron, the heterogeneous catalysis mechanism, and the heterogeneous reaction-induced homogeneous mechanism. Different heterogeneous Fenton systems catalyzed by characteristic iron-based materials are comprehensively reviewed. Finally, related future research directions are also suggested. Copyright © 2015. Published by Elsevier B.V.

Restricted Hartree Fock using complex-valued orbitals: A long-known but neglected tool in electronic structure theory

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

Small, David W.; Sundstrom, Eric J.; Head-Gordon, Martin

2015-01-14

Restricted Hartree Fock using complex-valued orbitals (cRHF) is studied. We introduce an orbital pairing theorem, with which we obtain a concise connection between cRHF and real-valued RHF, and use it to uncover the close relationship between cRHF, unrestricted Hartree Fock, and generalized valence bond perfect pairing. This enables an intuition for cRHF, contrasting with the generally unintuitive nature of complex orbitals. We also describe an efficient computer implementation of cRHF and its corresponding stability analysis. By applying cRHF to the Be + H{sub 2} insertion reaction, a Woodward-Hoffmann violating reaction, and a symmetry-driven conical intersection, we demonstrate in genuine molecularmore » systems that cRHF is capable of removing certain potential energy surface singularities that plague real-valued RHF and related methods. This complements earlier work that showed this capability in a model system. We also describe how cRHF is the preferred RHF method for certain radicaloid systems like singlet oxygen and antiaromatic molecules. For singlet O{sub 2}, we show that standard methods fail even at the equilibrium geometry. An implication of this work is that, regardless of their individual efficacies, cRHF solutions to the HF equations are fairly commonplace.« less

Pattern formation in mass conserving reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Brauns, Fridtjof; Halatek, Jacob; Frey, Erwin

We present a rigorous theoretical framework able to generalize and unify pattern formation for quantitative mass conserving reaction-diffusion models. Mass redistribution controls chemical equilibria locally. Separation of diffusive mass redistribution on the level of conserved species provides a general mathematical procedure to decompose complex reaction-diffusion systems into effectively independent functional units, and to reveal the general underlying bifurcation scenarios. We apply this framework to Min protein pattern formation and identify the mechanistic roles of both involved protein species. MinD generates polarity through phase separation, whereas MinE takes the role of a control variable regulating the existence of MinD phases. Hence, polarization and not oscillations is the generic core dynamics of Min proteins in vivo. This establishes an intrinsic mechanistic link between the Min system and a broad class of intracellular pattern forming systems based on bistability and phase separation (wave-pinning). Oscillations are facilitated by MinE redistribution and can be understood mechanistically as relaxation oscillations of the polarization direction.

Divergent pathways in the reaction of Fischer carbenes and palladium.

PubMed

López-Alberca, María P; Mancheño, María J; Fernandez, Israel; Gómez-Gallego, Mar; Sierra, Miguel A; Torres, Rosario

2007-04-26

[reaction: see text] The Pd-catalyzed reaction of beta-arylaminochromium(0) carbene complexes produces by transmetalation the first isolated and X-ray structurally characterized bis-Pd(II) carbene complex, as well as other alternative reaction pathways, such as the oxidative addition-transmetalation sequence, not seen before in this chemistry.

Chemical dynamics simulations of the monohydrated OH-(H2O) + CH3I reaction. Atomic-level mechanisms and comparison with experiment

NASA Astrophysics Data System (ADS)

Xie, Jing; Otto, Rico; Wester, Roland; Hase, William L.

2015-06-01

Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH-(H2O) + CH3I reaction. The SN2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH2I-, and to a lesser extent CH2I- (H2O), becomes important. The SN2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of SN2 and proton transfer pre-reaction complexes and intermediates, including [CH3--I--OH]-. In contrast, for the unsolvated OH- + CH3I SN2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH-(H2O) + CH3IߙSN2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the SN2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H2O molecule is unimportant. The SN2 reaction is dominated by events in which H2O leaves the reactive system as CH3OH is formed or before CH3OH formation. Formation of solvated products is unimportant and participation of the (H2O)CH3OH---I- post-reaction complex for the SN2 reaction is negligible.

Towards a comprehensive understanding of emerging dynamics and function of pancreatic islets: A complex network approach. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

NASA Astrophysics Data System (ADS)

Loppini, Alessandro

2018-03-01

Complex network theory represents a comprehensive mathematical framework to investigate biological systems, ranging from sub-cellular and cellular scales up to large-scale networks describing species interactions and ecological systems. In their exhaustive and comprehensive work [1], Gosak et al. discuss several scenarios in which the network approach was able to uncover general properties and underlying mechanisms of cells organization and regulation, tissue functions and cell/tissue failure in pathology, by the study of chemical reaction networks, structural networks and functional connectivities.

Logic circuits based on molecular spider systems.

PubMed

Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

2016-08-01

Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Facile regio- and stereoselective hydrometalation of alkynes with a combination of carboxylic acids and group 10 transition metal complexes: selective hydrogenation of alkynes with formic acid.

PubMed

Shen, Ruwei; Chen, Tieqiao; Zhao, Yalei; Qiu, Renhua; Zhou, Yongbo; Yin, Shuangfeng; Wang, Xiangbo; Goto, Midori; Han, Li-Biao

2011-10-26

A facile, highly stereo- and regioselective hydrometalation of alkynes generating alkenylmetal complex is disclosed for the first time from a reaction of alkyne, carboxylic acid, and a zerovalent group 10 transition metal complex M(PEt(3))(4) (M = Ni, Pd, Pt). A mechanistic study showed that the hydrometalation does not proceed via the reaction of alkyne with a hydridometal generated by the protonation of a carboxylic acid with Pt(PEt(3))(4), but proceeds via a reaction of an alkyne coordinate metal complex with the acid. This finding clarifies the long proposed reaction mechanism that operates via the generation of an alkenylpalladium intermediate and subsequent transformation of this complex in a variety of reactions catalyzed by a combination of Brϕnsted acid and Pd(0) complex. This finding also leads to the disclosure of an unprecedented reduction of alkynes with formic acid that can selectively produce cis-, trans-alkenes and alkanes by slightly tuning the conditions.

Ligand reprogramming in dinuclear helicate complexes: a consequence of allosteric or electrostatic effects?

PubMed

Jeffery, John C; Rice, Craig R; Harding, Lindsay P; Baylies, Christian J; Riis-Johannessen, Thomas

2007-01-01

The ditopic ligand 6,6'-bis(4-methylthiazol-2-yl)-3,3'-([18]crown-6)-2,2'-bipyridine (L(1)) contains both a potentially tetradentate pyridyl-thiazole (py-tz) N-donor chain and an additional "external" crown ether binding site which spans the central 2,2'-bipyridine unit. In polar solvents (MeCN, MeNO(2)) this ligand forms complexes with Zn(II), Cd(II), Hg(II) and Cu(I) ions via coordination of the N donors to the metal ion. Reaction with both Hg(II) and Cu(I) ions results in the self-assembly of dinuclear double-stranded helicate complexes. The ligands are partitioned by rotation about the central py--py bond, such that each can coordinate to both metals as a bis-bidentate donor ligand. With Zn(II) ions a single-stranded mononuclear species is formed in which one ligand coordinates the metal ion in a planar tetradentate fashion. Reaction with Cd(II) ions gives rise to an equilibrium between both the dinuclear double-stranded helicate and the mononuclear species. These complexes can further coordinate s-block metal cations via the remote crown ether O-donor domains; a consequence of which are some remarkable changes in the binding modes of the N-donor domains. Reaction of the Hg(II)- or Cd(II)-containing helicate with either Ba(2+) or Sr(2+) ions effectively reprogrammes the ligand to form only the single-stranded heterobinuclear complexes [MM'(L(1))](4+) (M=Hg(II), Cd(II); M'=Ba(2+), Sr(2+)), where the transition and s-block cations reside in the N- and O-donor sites, respectively. In contrast, the same ions have only a minor structural impact on the Zn(II) species, which already exists as a single-stranded mononuclear complex. Similar reactions with the Cd(II) system result in a shift in equilibrium towards the single-stranded species, the extent of which depends on the size and charge of the s-block cation in question. Reaction of the dicopper(I) double-stranded helicate with Ba(2+) shows that the dinuclear structure still remains intact but the pitch length is significantly increased.

Edible carbohydrates from formaldehyde in a spacecraft

NASA Technical Reports Server (NTRS)

Weiss, A. H.

1975-01-01

The autocatalytic nature of the base catalyzed condensation of formaldehyde to formose sugars is eliminated by using as a cocatalyst, an aldose, or ketose having an alpha-hydrogen. This is more strongly complexed by base than is formaldehyde and the cocatalyst and sugar products accumulate as catalyst complexes instead of formaldehyde. Because of the presence of alpha-hydrogen atoms in cocatalysts and formose sugars, their removal by cross Cannizzaro reaction of complexed sugars does not occur, so the formose reaction behaves autocatalytically due to this accumulation. It is believed that a given catalytic formose complex is not a discrete complexed sugar, but rather, a scrambled dynamic mixture of sugars having weakened structures. The sugar complexes derive from a common salt-like formaldehyde complex, which, because of the absence of alpha-hydrogen, has a greater tendency to undergo Cannizzaro reaction, rather than formose condensation. Because of this, the Cannizzaro reaction can proceed without measurable formose condensation. The reverse is not possible.

Approaches to the origin of life on Earth.

PubMed

Kauffman, Stuart A

2011-11-18

I discuss briefly the history of the origin of life field, focusing on the "Miller" era of prebiotic synthesis, through the "Orgel" era seeking enzyme free template replication of single stranded RNA or similar polynucleotides, to the RNA world era with one of its foci on a ribozyme with the capacity to act as a polymerase able to copy itself. I give the history of the independent invention in 1971 by T. Ganti, M. Eigen and myself of three alternative theories of the origin of molecular replication: the Chemotron, the Hypercycle, and Collectively Autocatalytic Sets, CAS, respectively. To date, only collectively autocatalytic DNA, RNA, and peptide sets have achieved molecular reproduction of polymers. Theoretical work and experimental work on CAS both support their plausibility as models of openly evolvable protocells, if housed in dividing compartments such as dividing liposomes. My own further hypothesis beyond that of CAS in themselves, of their formation as a phase transition in complex chemical reaction systems of substrates, reactions and products, where the molecules in the system are candidates to catalyze the very same reactions, now firmly established as theorems, awaits experimental proof using combinatorial chemistry to make libraries of stochastic DNA, RNA and/or polypeptides, or other classes of molecules to test the hypothesis that molecular polymer reproduction has emerged as a true phase transition in complex chemical reaction systems. I remark that my colleague Marc Ballivet of the University of Geneva and I, may have issued the first publications discussing what became combinatorial chemistry, in published issued patents in 1987, 1989 and later, in this field.

Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noise

NASA Astrophysics Data System (ADS)

Leier, André; Marquez-Lago, Tatiana T.; Burrage, Kevin

2008-05-01

The delay stochastic simulation algorithm (DSSA) by Barrio et al. [Plos Comput. Biol. 2, 117(E) (2006)] was developed to simulate delayed processes in cell biology in the presence of intrinsic noise, that is, when there are small-to-moderate numbers of certain key molecules present in a chemical reaction system. These delayed processes can faithfully represent complex interactions and mechanisms that imply a number of spatiotemporal processes often not explicitly modeled such as transcription and translation, basic in the modeling of cell signaling pathways. However, for systems with widely varying reaction rate constants or large numbers of molecules, the simulation time steps of both the stochastic simulation algorithm (SSA) and the DSSA can become very small causing considerable computational overheads. In order to overcome the limit of small step sizes, various τ-leap strategies have been suggested for improving computational performance of the SSA. In this paper, we present a binomial τ-DSSA method that extends the τ-leap idea to the delay setting and avoids drawing insufficient numbers of reactions, a common shortcoming of existing binomial τ-leap methods that becomes evident when dealing with complex chemical interactions. The resulting inaccuracies are most evident in the delayed case, even when considering reaction products as potential reactants within the same time step in which they are produced. Moreover, we extend the framework to account for multicellular systems with different degrees of intercellular communication. We apply these ideas to two important genetic regulatory models, namely, the hes1 gene, implicated as a molecular clock, and a Her1/Her 7 model for coupled oscillating cells.

Role of Mediator and Effects of Temperature on ortho-C-N Bond Fusion Reactions of Aniline Using Ruthenium Templates: Isolation and Characterization of New Ruthenium Complexes of the in-Situ-Generated Ligands.

PubMed

Roy, Suman K; Sengupta, Debabrata; Rath, Santi Prasad; Saha, Tanushri; Samanta, Subhas; Goswami, Sreebrata

2017-05-01

In this work, ortho-C-N bond fusion reactions of aniline are followed by the use of two different ruthenium mediators. Reaction of aniline with [Ru III (terpy)Cl 3 ] (terpy = 2,2':6',2″-terpyridine) resulted in a trans bis-aniline ruthenium(II) complex [1] + which upon oxidation with H 2 O 2 produced compound [2] + of a bidentate ligand, N-phenyl-1,2-benzoquinonediimine, due to an oxidative ortho-C-N bond fusion reaction. Complex [1] + and aniline (neat) at 185 °C produced a bis-chelated ruthenium complex (3). A previously reported complex [Ru II (N-phenyl-1,2-benzoquinonediimine)(aniline) 2 (Cl) 2 ] (5) undergoes similar oxidation by air at 185 °C to produce complex [3]. A separate chemical reaction between aniline and strongly oxidizing tetra-n-propylammonium perruthenate [(n-pr) 4 N] + [RuO 4 ] - in air produced a ruthenium complex [4] of a N 4 -tetraamidophenylmacrocycle ligand via multiple ortho-C-N bond fusion reaction. Notably, the yield of this product is low (5%) at 100 °C but increases to 25% in refluxing aniline. All these complexes are characterized fully by their physicochemical characterizations and X-ray structure determination. From their structural parameters and other spectroscopic studies, complex [2] + is assigned as [Ru II (terpy)(N-phenyl-1,2-benzoquinonediimine)(Cl)] + whereas complex [4] is described as a ruthenium(VI) complex comprised of a reduced deprotonated N-phenyl-1,2-diamidobenzene and N 4 -tetraamidophenylmacrocyclic ligand. Complex [2] + exhibits one reversible oxidation at 1.32 V and one reversible reduction at -0.75 V vs Ag/AgCl reference electrode. EPR of the electrogenerated complexes has revealed that the oxidized complex is a ruthenium(III) complex with an axial EPR spectrum at g av = 2.06. The reduced complex [2], on the other hand, shows a single-line EPR signal at g av = 1.998. In contrast, complex [4] shows two successive one-electron oxidation waves at 0.5 and 0.8 V and an irreversible reduction wave at -0.9 V. EPR studies of the oxidized complexes [4] + and [4] 2+ reveal that oxidations are ligand centered. DFT calculations were employed to elucidate the electronic structures as well as the redox processes associated with the above complexes. Aerial ortho-C-N bond fusion reactions of aniline using two different mediators, viz. [Ru III (terpy)Cl 3 ] and [(n-pr) 4 N] + [RuO 4 ] - , have been followed. It is found that in the case of oxidizable Ru(III) mediator complex, C-N bond fusion is limited only to dimerization reaction whereas the high-valent Ru(VII) salt mediates multiple C-N bond fusion reactions leading to the formation of a novel tetradentate N 4 -tetraamidophenylmacrocyclic ligand. Valence ambiguity in the complexes of the resultant redox-active ligands is scrutinized.

Preparation, characterization, and thermal stability of β-cyclodextrin/soybean lecithin inclusion complex.

PubMed

Wang, Xinge; Luo, Zhigang; Xiao, Zhigang

2014-01-30

β-Cyclodextrin (β-CD), which is widely used to increase the stability, solubility, and bioavailability of guests, can form host-guest inclusion complexes with a wide variety of organic molecules. In this study the β-CD/soybean lecithin inclusion complex was prepared. The effect of reaction parameters such as reaction temperature, reaction time and the molar ratio of β-CD/soybean lecithin on inclusion ratio were studied. The inclusion ratio of the product prepared under the optimal conditions of β-CD/soybean lecithin molar ratio 2:1, reaction temperature 60°C reaction time 2h was 40.2%. The results of UV-vis, DSC, XRD and FT-IR spectrum indicated the formation of inclusion complex. The thermal stability experiment indicated that the thermal stability of soybean lecithin in inclusion complex was significantly improved compared with free soybean lecithin. Copyright © 2013 Elsevier Ltd. All rights reserved.

Developments of a new data acquisition system at ANNRI

NASA Astrophysics Data System (ADS)

Nakao, T.; Terada, K.; Kimura, A.; Nakamura, S.; Iwamoto, O.; Harada, H.; Katabuchi, T.; Igashira, M.; Hori, J.

2017-09-01

A new data acquisition system (DAQ system) has been developed at the Accurate Neutron-Nucleus Reaction Measurement Instrument (ANNRI) facility in the Japan Proton Accelerator Research Complex, Materials and Life Science Experimental Facility (J-PARC/MLF). DAQ systems for both the Ge detector system and the Li-glass detector system were tested by using a gold sample. The applicability of the time-of-flight method was checked. System performance was evaluated on the basis of digital conversion nonlinearity, energy resolution, multi-channel coincidence and dead time.

Ionic interactions in biological and physical systems: a variational treatment.

PubMed

Eisenberg, Bob

2013-01-01

Chemistry is about chemical reactions. Chemistry is about electrons changing their configurations as atoms and molecules react. Chemistry has for more than a century studied reactions as if they occurred in ideal conditions of infinitely dilute solutions. But most reactions occur in salt solutions that are not ideal. In those solutions everything (charged) interacts with everything else (charged) through the electric field, which is short and long range extending to the boundaries of the system. Mathematics has recently been developed to deal with interacting systems of this sort. The variational theory of complex fluids has spawned the theory of liquid crystals (or vice versa). In my view, ionic solutions should be viewed as complex fluids, particularly in the biological and engineering context. In both biology and electrochemistry ionic solutions are mixtures highly concentrated (to approximately 10 M) where they are most important, near electrodes, nucleic ids, proteins, active sites of enzymes, and ionic channels. Ca2+ is always involved in biological solutions because the concentration (really free energy per mole) of Ca2+ in a particular location is the signal that controls many biological functions. Such interacting systems are not simple fluids, and it is no wonder that analysis of interactions, such as the Hofmeister series, rooted in that tradition has not succeeded as one would hope. Here, we present a variational treatment of ard spheres in a frictional dielectric with the hope that such a treatment of an lectrolyte as a complex fluid will be productive. The theory automatically extends to spatially nonuniform boundary conditions and the nonequilibrium systems and flows they produce. The theory is unavoidably self-consistent since differential equations are derived (not assumed) from models of (Helmholtz free) nergy and dissipation of the electrolyte. The origin of the Hofmeister series is (in my view) an inverse problem that becomes well posed when enough data from disjoint experimental traditions are interpreted with a self-consistent theory.

Modelling chemical reactions by QM/MM calculations: the case of the tautomerization in fireflies bioluminescent systems

NASA Astrophysics Data System (ADS)

Berraud-Pache, Romain; Garcia-Iriepa, Cristina; Navizet, Isabelle

2018-04-01

In less than half a century, the hybrid QM/MM method has become one of the most used technique to model molecules embedded in a complex environment. A well-known application of the QM/MM method is for biological systems. Nowadays, one can understand how enzymatic reactions work or compute spectroscopic properties, like the wavelength of emission. Here, we have tackled the issue of modelling chemical reactions inside proteins. We have studied a bioluminescent system, fireflies, and deciphered if a keto-enol tautomerization is possible inside the protein. The two tautomers are candidates to be the emissive molecule of the bioluminescence but no outcome has been reached. One hypothesis is to consider a possible keto-enol tautomerization to treat this issue, as it has been already observed in water. A joint approach combining extensive MD simulations as well as computation of key intermediates like TS using QM/MM calculations is presented in this publication. We also emphasize the procedure and difficulties met during this approach in order to give a guide for this kind of chemical reactions using QM/MM methods.

Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems

PubMed Central

Berraud-Pache, Romain; Garcia-Iriepa, Cristina; Navizet, Isabelle

2018-01-01

In less than half a century, the hybrid QM/MM method has become one of the most used technique to model molecules embedded in a complex environment. A well-known application of the QM/MM method is for biological systems. Nowadays, one can understand how enzymatic reactions work or compute spectroscopic properties, like the wavelength of emission. Here, we have tackled the issue of modeling chemical reactions inside proteins. We have studied a bioluminescent system, fireflies, and deciphered if a keto-enol tautomerization is possible inside the protein. The two tautomers are candidates to be the emissive molecule of the bioluminescence but no outcome has been reached. One hypothesis is to consider a possible keto-enol tautomerization to treat this issue, as it has been already observed in water. A joint approach combining extensive MD simulations as well as computation of key intermediates like TS using QM/MM calculations is presented in this publication. We also emphasize the procedure and difficulties met during this approach in order to give a guide for this kind of chemical reactions using QM/MM methods. PMID:29719820

A mathematical model for the generation and control of a pH gradient in an immobilized enzyme system involving acid generation.

PubMed

Chen, G; Fournier, R L; Varanasi, S

1998-02-20

An optimal pH control technique has been developed for multistep enzymatic synthesis reactions where the optimal pH differs by several units for each step. This technique separates an acidic environment from a basic environment by the hydrolysis of urea within a thin layer of immobilized urease. With this technique, a two-step enzymatic reaction can take place simultaneously, in proximity to each other, and at their respective optimal pH. Because a reaction system involving an acid generation represents a more challenging test of this pH control technique, a number of factors that affect the generation of such a pH gradient are considered in this study. The mathematical model proposed is based on several simplifying assumptions and represents a first attempt to provide an analysis of this complex problem. The results show that, by choosing appropriate parameters, the pH control technique still can generate the desired pH gradient even if there is an acid-generating reaction in the system. Copyright 1998 John Wiley & Sons, Inc.

Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems.

PubMed

Berraud-Pache, Romain; Garcia-Iriepa, Cristina; Navizet, Isabelle

2018-01-01

In less than half a century, the hybrid QM/MM method has become one of the most used technique to model molecules embedded in a complex environment. A well-known application of the QM/MM method is for biological systems. Nowadays, one can understand how enzymatic reactions work or compute spectroscopic properties, like the wavelength of emission. Here, we have tackled the issue of modeling chemical reactions inside proteins. We have studied a bioluminescent system, fireflies, and deciphered if a keto-enol tautomerization is possible inside the protein. The two tautomers are candidates to be the emissive molecule of the bioluminescence but no outcome has been reached. One hypothesis is to consider a possible keto-enol tautomerization to treat this issue, as it has been already observed in water. A joint approach combining extensive MD simulations as well as computation of key intermediates like TS using QM/MM calculations is presented in this publication. We also emphasize the procedure and difficulties met during this approach in order to give a guide for this kind of chemical reactions using QM/MM methods.

Photochemical Reactions of (n(5)-Pentamethylcyclpentadienyl)-Dicarbonyliron-Alkyl and -Silyl Complexes: Reversible Ethylene Insertion into an Iron-Silicon Bond and Implications for the Mechanism of Transition Metal-Catalyzed Hydrosilation of Alkenes.

DTIC Science & Technology

1985-12-11

RD-R162 462 PHOTOCHEMICAL REACTIONS OF(N(S)-P NTANETNYLCVCLPENTADIENYL)-DICARRONVLIR.. (U) MASSACHUSETTS INST OF TECH CAMBRIDGE DEPT OF CHEMISTRY...34 Photochemical Reactions of (n5-Pentamethylcyclpentadienyl)- Dicarbonyliron-Alkyl and -Silyl Complexes: Reversible Ethylene Insertion into an Iron-Silicon Bond...Chemical Society) PHOTOCHEMICAL REACTIONS OF (n5-PENTAMETHYLCYCLOPENTADIENYL)- DICARBONYLIRON-ALKYL AND -SILYL COMPLEXES: REVERSIBLE ETHYLENE INSERTION INTO

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

DOE R&D Accomplishments Database

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.

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Calculating the True and Observed Rates of Complex Heterogeneous Catalytic Reactions

NASA Astrophysics Data System (ADS)

Avetisov, A. K.; Zyskin, A. G.

2018-06-01

Equations of the theory of steady-state complex reactions are considered in matrix form. A set of stage stationarity equations is given, and an algorithm is described for deriving the canonic set of stationarity equations with appropriate corrections for the existence of fast stages in a mechanism. A formula for calculating the number of key compounds is presented. The applicability of the Gibbs rule to estimating the number of independent compounds in a complex reaction is analyzed. Some matrix equations relating the rates of dependent and key substances are derived. They are used as a basis to determine the general diffusion stoichiometry relationships between temperature, the concentrations of dependent reaction participants, and the concentrations of key reaction participants in a catalyst grain. An algorithm is described for calculating heat and mass transfer in a catalyst grain with respect to arbitrary complex heterogeneous catalytic reactions.

A hybrid continuous-discrete method for stochastic reaction-diffusion processes.

PubMed

Lo, Wing-Cheong; Zheng, Likun; Nie, Qing

2016-09-01

Stochastic fluctuations in reaction-diffusion processes often have substantial effect on spatial and temporal dynamics of signal transductions in complex biological systems. One popular approach for simulating these processes is to divide the system into small spatial compartments assuming that molecules react only within the same compartment and jump between adjacent compartments driven by the diffusion. While the approach is convenient in terms of its implementation, its computational cost may become prohibitive when diffusive jumps occur significantly more frequently than reactions, as in the case of rapid diffusion. Here, we present a hybrid continuous-discrete method in which diffusion is simulated using continuous approximation while reactions are based on the Gillespie algorithm. Specifically, the diffusive jumps are approximated as continuous Gaussian random vectors with time-dependent means and covariances, allowing use of a large time step, even for rapid diffusion. By considering the correlation among diffusive jumps, the approximation is accurate for the second moment of the diffusion process. In addition, a criterion is obtained for identifying the region in which such diffusion approximation is required to enable adaptive calculations for better accuracy. Applications to a linear diffusion system and two nonlinear systems of morphogens demonstrate the effectiveness and benefits of the new hybrid method.

Conformation-dependent chemical reaction of formic acid with an oxygen atom.

PubMed

Khriachtchev, Leonid; Domanskaya, Alexandra; Marushkevich, Kseniya; Räsänen, Markku; Grigorenko, Bella; Ermilov, Alexander; Andrijchenko, Natalya; Nemukhin, Alexander

2009-07-23

Conformation dictates many physical and chemical properties of molecules. The importance of conformation in the selectivity and function of biologically active molecules is widely accepted. However, clear examples of conformation-dependent bimolecular chemical reactions are lacking. Here we consider a case of formic acid (HCOOH) that is a valuable model system containing the -COOH carboxyl functional group, similar to many biomolecules including the standard amino acids. We have found a strong case of conformation-dependent reaction between formic acid and atomic oxygen obtained in cryogenic matrices. The reaction surprisingly leads to peroxyformic acid only from the ground-state trans conformer of formic acid, and it results in the hydrogen-bonded complex for the higher-energy cis conformer.

A Stopped-Flow Apparatus with Light-Scattering Detection and Its Application to Biochemical Reactions

PubMed Central

Riesner, Detlev; Buenemann, Hans

1973-01-01

A stopped-flow apparatus utilizing light-scattering for following the progress of a reaction is described. The method is applicable to all reactions that result in a significant change of the average molecular weight. It was possible due to several modifications of a conventional stopped-flow system to obtain a sensitivity comparable to that of commercial instruments for static light-scattering measurements. Experiments on three reactions are reported: association and dissociation of mercury ligands with DNA, dissociation of the dimers of DNA-dependent RNA polymerase, and complex formation of tRNASer (yeast) with the cognate aminoacyl-tRNA synthetase. The changes in the intensities of the scattered light are calculated and compared with the measured amplitudes. PMID:4577138

DFT Studies of SN2 Dechlorination of Polychlorinated Biphenyls.

PubMed

Krzemińska, Agnieszka; Paneth, Piotr

2016-06-21

Nucleophilic dechlorination of all 209 PCBs congeners by ethylene glycol anion has been studied theoretically at the DFT level. The obtained Gibbs free energies of activation are in the range 7-22 kcal/mol. The reaction Gibbs free energies indicate that all reactions are virtually irreversible. Due to geometric constrains these reactions undergo rather untypical attack with attacking oxygen atom being nearly perpendicular to the attacked C-Cl bond. The most prone to substitution are chlorine atoms that occupy ortho- (2, 2', 6, 6') positions. These results provide extensive information on the PEG/KOH dependent PCBs degradation. They can also be used in further developments of reaction class transition state theory (RC-TST) for description of complex reactive systems encountered for example in combustion processes.

Electron transfer reaction of oxo(salen)chromium(V) ion with anilines.

PubMed

Premsingh, Sundarsingh; Venkataramanan, Natarajan Sathiyamoorthy; Rajagopal, Seenivasan; Mirza, Shama P; Vairamani, Mariappanadar; Rao, P Sambasiva; Velavan, K

2004-09-06

The kinetics of oxidation of 16 meta-, ortho-, and para-substituted anilines with nine oxo(salen)chromium(V) ions have been studied by spectrophotometric, ESIMS, and EPR techniques. During the course of the reaction, two new peaks with lambda(max) at 470 and 730 nm appear in the absorption spectrum, and these peaks are due to the formation of emeraldine forms of oligomers of aniline supported by the ESIMS peaks with m/z values 274 and 365 (for the trimer and tetramer of aniline). The rate of the reaction is highly sensitive to the change of substituents in the aryl moiety of aniline and in the salen ligand of chromium(V) complexes. Application of the Hammett equation to analyze kinetic data yields a rho value of -3.8 for the substituent variation in aniline and +2.2 for the substituent variation in the salen ligand of the metal complex. On the basis of the spectral, kinetic, and product analysis studies, a mechanism involving an electron transfer from the nitrogen of aniline to the metal complex in the rate controlling step has been proposed. The Marcus equation has been successfully applied to this system, and the calculated values are compliant with the measured values.

Kinetics of reduction of plutonium(VI) and neptunium(VI) by sulfide in neutral and alkaline solutions

USGS Publications Warehouse

Nash, K.L.; Cleveland, J.M.; Sullivan, J.C.; Woods, M.

1986-01-01

The rate of reduction of plutonium(VI) and neptunium(VI) by bisulfide ion in neutral and mildly alkaline solutions has been investigated by the stopped-flow technique. The reduction of both of these ions to the pentavalent oxidation state appears to occur in an intramolecular reaction involving an unusual actinide(VI)-hydroxide-bisulfide complex. For plutonium the rate of reduction is 27.4 (??4.1) s-1 at 25??C with ??H* = +33.2 (??1.0) kJ/mol and ??S* = -106 (??4) J/(mol K). The apparent stability constant for the transient complex is 4.66 (??0.94) ?? 103 M-1 at 25??C with associated thermodynamic parameters of ??Hc = +27.7 (??0.4) kJ/mol and ??Sc = +163 (??2) J/(mol K). The corresponding rate and stability constants are determined for the neptunium system at 25??C (k3 = 139 (??30) s-1, Kc. = 1.31 (??0.32) ?? 103 M-1), but equivalent parameters cannot be determined at reduced temperatures. The reaction rate is decreased by bicarbonate ion. At pH > 10.5, a second reaction mechanism, also involving a sulfide complex, is indicated. ?? 1986 American Chemical Society.

Stability and Unimolecular Reactivity of Palladate(II) Complexes [Ln PdR3 ]- (L=Phosphine, R=Organyl, n=0 and 1).

PubMed

Kolter, Marlene; Koszinowski, Konrad

2016-10-24

The reduction of Pd II precatalysts to catalytically active Pd 0 species is a key step in many palladium-mediated cross-coupling reactions. Besides phosphines, the stoichiometrically used organometallic reagents can afford this reduction, but do so in a poorly understood way. To elucidate the mechanism of this reaction, we have treated solutions of Pd(OAc) 2 and a phosphine ligand L in tetrahydrofuran with RMgCl (R=Ph, Bn, Bu) as well as other organometallic reagents. Analysis of these model systems by electrospray- ionization mass spectrometry found palladate(II) complexes [L n PdR 3 ] - (n=0 and 1), thus pointing to the occurrence of transmetallation reactions. Upon gas-phase fragmentation, the [L n PdR 3 ] - anions preferentially underwent a reductive elimination to yield Pd 0 species. The sequence of the transmetallation and reductive elimination, thus, constitutes a feasible mechanism for the reduction of the Pd(OAc) 2 precatalyst. Other species of interest observed include the Pd IV complex [PdBn 5 ] - , which did not fragment via a reductive elimination but lost BnH instead. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Complexity reduction of rate-equations models for two-choice decision-making.

PubMed

Carrillo, José Antonio; Cordier, Stéphane; Deco, Gustavo; Mancini, Simona

2013-01-01

We are concerned with the complexity reduction of a stochastic system of differential equations governing the dynamics of a neuronal circuit describing a decision-making task. This reduction is based on the slow-fast behavior of the problem and holds on the whole phase space and not only locally around the spontaneous state. Macroscopic quantities, such as performance and reaction times, computed applying this reduction are in agreement with previous works in which the complexity reduction is locally performed at the spontaneous point by means of a Taylor expansion.

Radiochemical study of reactions of alkyl cations with amines. I. Reactions of methyl and sec-butyl cations with diethylamine

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

Ignat`ev, I.S.; Kochina, T.A.; Nefedov, V.D.

1995-08-10

Ion-molecular gas-phase reactions of free methyl and sec-butyl cations with diethylamine were studied. These reactions proceed via two competing pathways involving formation of a condensation complex or a proton-transfer complex, the latter process predominating. 32 refs., 1 tab.

Methodology for extracting local constants from petroleum cracking flows

DOEpatents

Chang, Shen-Lin; Lottes, Steven A.; Zhou, Chenn Q.

2000-01-01

A methodology provides for the extraction of local chemical kinetic model constants for use in a reacting flow computational fluid dynamics (CFD) computer code with chemical kinetic computations to optimize the operating conditions or design of the system, including retrofit design improvements to existing systems. The coupled CFD and kinetic computer code are used in combination with data obtained from a matrix of experimental tests to extract the kinetic constants. Local fluid dynamic effects are implicitly included in the extracted local kinetic constants for each particular application system to which the methodology is applied. The extracted local kinetic model constants work well over a fairly broad range of operating conditions for specific and complex reaction sets in specific and complex reactor systems. While disclosed in terms of use in a Fluid Catalytic Cracking (FCC) riser, the inventive methodology has application in virtually any reaction set to extract constants for any particular application and reaction set formulation. The methodology includes the step of: (1) selecting the test data sets for various conditions; (2) establishing the general trend of the parametric effect on the measured product yields; (3) calculating product yields for the selected test conditions using coupled computational fluid dynamics and chemical kinetics; (4) adjusting the local kinetic constants to match calculated product yields with experimental data; and (5) validating the determined set of local kinetic constants by comparing the calculated results with experimental data from additional test runs at different operating conditions.

Step-by-Step Simulation of Radiation of Radiation Chemistry Using Green Functions for Diffusion-Influenced Reactions

NASA Technical Reports Server (NTRS)

Plante, Ianik; Cucinotta, Francis A.

2011-01-01

The irradiation of biological systems leads to the formation of radiolytic species such as H(raised dot), (raised dot)OH, H2, H2O2, e(sup -)(sub aq), etc.[1]. These species react with neighboring molecules, which result in damage in biological molecules such as DNA. Radiation chemistry is there for every important to understand the radiobiological consequences of radiation[2]. In this work, we discuss an approach based on the exact Green Functions for diffusion-influenced reactions which may be used to simulate radiation chemistry and eventually extended to study more complex systems, including DNA.

A Systems Approach towards an Intelligent and Self-Controlling Platform for Integrated Continuous Reaction Sequences**

PubMed Central

Ingham, Richard J; Battilocchio, Claudio; Fitzpatrick, Daniel E; Sliwinski, Eric; Hawkins, Joel M; Ley, Steven V

2015-01-01

Performing reactions in flow can offer major advantages over batch methods. However, laboratory flow chemistry processes are currently often limited to single steps or short sequences due to the complexity involved with operating a multi-step process. Using new modular components for downstream processing, coupled with control technologies, more advanced multi-step flow sequences can be realized. These tools are applied to the synthesis of 2-aminoadamantane-2-carboxylic acid. A system comprising three chemistry steps and three workup steps was developed, having sufficient autonomy and self-regulation to be managed by a single operator. PMID:25377747

Microfluidic Technology: Uncovering the Mechanisms of Nanocrystal Nucleation and Growth.

PubMed

Lignos, Ioannis; Maceiczyk, Richard; deMello, Andrew J

2017-05-16

The controlled and reproducible formation of colloidal semiconductor nanocrystals (or quantum dots) is of central importance in nanoscale science and technology. The tunable size- and shape-dependent properties of such materials make them ideal candidates for the development of efficient and low-cost displays, solar cells, light-emitting devices, and catalysts. The formidable difficulties associated with the macroscale preparation of semiconductor nanocrystals (possessing bespoke optical and chemical properties) result from the fact that underlying reaction mechanisms are complex and that the reactive environment is difficult to control. Automated microfluidic reactors coupled with monitoring systems and optimization algorithms aim to elucidate complex reaction mechanisms that govern both nucleation and growth of nanocrystals. Such platforms are ideally suited for the efficient optimization of reaction parameters, assuring the reproducible synthesis of nanocrystals with user-defined properties. This Account aims to inform the nanomaterials community about how microfluidic technologies can supplement flask experimentation for the ensemble investigation of formation mechanisms and design of semiconductor nanocrystals. We present selected studies outlining the preparation of quantum dots using microfluidic systems with integrated analytics. Such microfluidic reaction systems leverage the ability to extract real-time information regarding optical, structural, and compositional characteristics of quantum dots during nucleation and growth stages. The Account further highlights our recent research activities focused on the development and application of droplet-based microfluidics with integrated optical detection systems for the efficient and rapid screening of reaction conditions and a better understanding of the mechanisms of quantum dot synthesis. We describe the features and operation of fully automated microfluidic reactors and their subsequent application to high-throughput parametric screening of metal chalcogenides (CdSe, PbS, PbSe, CdSeTe), ternary and core/shell heavy metal-free quantum dots (CuInS 2 , CuInS 2 /ZnS), and all-inorganic perovskite nanocrystals (CsPbX 3 , X = Cl, Br, I) syntheses. Critically, concurrent absorption and photoluminescence measurements on millisecond to second time scales allow the extraction of basic parameters governing nanocrystal formation. Moreover, experimental data obtained from such microfluidic platforms can be directly supported by theoretical models of nucleation and growth. To this end, we also describe the use of metamodeling algorithms able to accurately predict optimized conditions of CdSe synthesis using a minimal number of sample parameters. Importantly, we discuss future challenges that must be addressed before microfluidic technologies are in a position to be widely adopted for the on-demand formation of nanocrystals. From a technology perspective, these challenges include the development of novel engineering platforms for the formation of complex architectures, the integration of monitoring systems able to harvest photophysical and structural information, the incorporation of continuous purification systems, and the application of optimization algorithms to multicomponent quantum dot systems.

Linear pi-Acceptor-Templated Dynamic Clipping to Macrobicycles and[2]Rotaxanes

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

Klivansky, Liana M.; Koshkakaryan, Gayane; Cao, Dennis

2009-04-30

Functional rotaxanes are one of the representative nanoscale molecular machines that have found applications in many areas, including molecular electronics, nanoelectromechanical systems (NEMS), photo controllable smart surfaces, and nanovalves. With the advent of molecular recognition and self-assembly, such molecular compounds can now be obtained efficiently through template-directed synthesis. One of the common strategies of making [2]rotaxanes involves the clipping of a macrocycle around a preformed dumbbell-shaped template in a [1+1] or [2+2] manner. While early examples were based on irreversible kinetic pathway through covalent bond formation, recent advances on reversible dynamic covalent chemistry (DCC) has attracted great attention to thismore » field. By virtue of thermodynamically controlled equilibria, DCC has provided highly efficient and versatile synthetic routes in the selection of specific products from a complex system. Among the several reversible reactions in the category of DCC reactions, the imine formation has proven to be very versatile in macrocyclization to give complex interlocked molecular compounds. Cryptands are three dimensional bicyclic hosts with preorganized cavities capable of inclusion of ions and small molecules. Replacing the nitrogen bridgeheads in common cryptands with aromatic ring systems gives cyclophane-based macrobicycles. The introduction of aromatic ring systems into a preorganized cage-like geometry facilitates ion-{pi} interactions and {pi}-{pi} interactions, resulting in novel metal sandwiches, fluoride receptors, and host-guest complexes. In particular, the seminal work by Gibson, Huang and coworkers on cryptand complexation with paraquat and diquat guests have resulted in the efficient synthesis of mechanically interlocked rotaxanes. The synthesis of cyclophane-based macrobicycles, however, was mostly realized through multiple reaction steps and in high-dilution conditions, which often suffered from low yield and tedious workup. Thus, a one-step, five-component [2+3] clipping reaction that can give the desired macrobicycle is highly desirable. We are motivated by a {pi}-guest templating protocol, because not only {pi}-{pi} interactions can contribute to the formation of macrobicycles, but also the resulting host-guest system holds great promise as a forerunner in the construction of interlocked molecules. (Scheme 1c) Very simple precursors, namely 1,3,5-benzenetrialdehyde (1) and 2,2{prime}-(ethylenedioxy)diethylamine (2) were chosen as the components for desired macrobicycle. (Scheme 2) The formation of six imine bonds would connect the five components to give a macrobicycle while extending the conjugation in the C{sub 3}-symmetric aromatic 'ceiling' and 'floor', which is suitable for enhancing the {pi}-{pi} interactions with a complementary aromatic template. Meanwhile, the ethylene glycol 'pillars' can provide sufficient flexibility, proper spacing, and polar binding sites to assist guest encapsulation. Initial screening of ?-templates engaged several C{sub 3} symmetric aromatic compounds in order to match the symmetry of the desired macrobicycle, which only resulted in nonspecific mixtures. It was found instead that linear bipyridinium (BPY) containing guests effectively templated the [2+3] clipping reaction. Based on this protocol, a [2]rotaxane was successfully assembled as the single product from the six-component reaction.« less

Electron-transfer reactions of cobalt(III) complexes. 1. The kinetic investigation of the reduction of various surfactant cobalt(III) complexes by iron(II) in surface active ionic liquids

NASA Astrophysics Data System (ADS)

Nagaraj, Karuppiah; Senthil Murugan, Krishnan; Thangamuniyandi, Pilavadi; Sakthinathan, Subramanian

2015-05-01

The kinetics of outer sphere electron transfer reaction of surfactant cobalt(III) complex ions, cis-[Co(en)2(C12H25NH2)2]3+ (1), cis-[Co(dp)2(C12H25NH2)2]3+ (2), cis-[Co(trien)(C12H25NH2)2]3+ (3), cis-[Co(bpy)2(C12H25NH2)2]3+ (4) and cis-[Co(phen)2(C12H25NH2)2]3+ (5) (en: ethylenediamine, dp: diaminopropane, trien : triethylenetetramine, bpy: 2,2‧-bipyridyl, phen: 1,10-phenanthroline and C12H25NH2 : dodecylamine) have been interrogated by Fe2+ ion in ionic liquid (1-butyl-3-methylimidazoliumbromide) medium at different temperatures (298, 303, 308, 313, 318 and 323 K) by the spectrophotometry method under pseudo first order conditions using an excess of the reductant. Experimentally the reactions were found to be of second order and the electron transfer as outer sphere. The second order rate constant for the electron transfer reaction in ionic liquids was found to increase with increase in the concentration of all these surfactant cobalt(III) complexes. Among these complexes (from en to phen ligand), complex containing the phenanthroline ligand rate is higher compared to other complexes. By assuming the outer sphere mechanism, the results have been explained based on the presence of aggregated structures containing cobalt(III) complexes at the surface of ionic liquids formed by the surfactant cobalt(III) complexes in the reaction medium. The activation parameters (enthalpy of activation ΔH‡ and entropy of activation ΔS‡) of the reaction have been calculated which substantiate the kinetics of the reaction.

Reductive Elimination from Phosphine-Ligated Alkylpalladium(II) Amido Complexes To Form sp3 Carbon-Nitrogen Bonds.

PubMed

Peacock, D Matthew; Jiang, Quan; Hanley, Patrick S; Cundari, Thomas R; Hartwig, John F

2018-04-11

We report the formation of phosphine-ligated alkylpalladium(II) amido complexes that undergo reductive elimination to form alkyl-nitrogen bonds and a combined experimental and computational investigation of the factors controlling the rates of these reactions. The free-energy barriers to reductive elimination from t-Bu 3 P-ligated complexes were significantly lower (ca. 3 kcal/mol) than those previously reported from NHC-ligated complexes. The rates of reactions from complexes containing a series of electronically and sterically varied anilido ligands showed that the reductive elimination is slower from complexes of less electron-rich or more sterically hindered anilido ligands than from those containing more electron-rich and less hindered anilido ligands. Reductive elimination of alkylamines also occurred from complexes bearing bidentate P,O ligands. The rates of reactions of these four-coordinate complexes were slower than those for reactions of the three-coordinate, t-Bu 3 P-ligated complexes. The calculated pathway for reductive elimination from rigid, 2-methoxyarylphosphine-ligated complexes does not involve initial dissociation of the oxygen. Instead, reductive elimination is calculated to occur directly from the four-coordinate complex in concert with a lengthening of the Pd-O bond. To investigate this effect experimentally, a four-coordinate Pd(II) anilido complex containing a flexible, aliphatic linker between the P and O atoms was synthesized. Reductive elimination from this complex was faster than that from the analogous complex containing the more rigid, aryl linker. The flexible linker enables full dissociation of the ether ligand during reductive elimination, leading to the faster reaction of this complex.

Dissociation kinetics of open-chain and macrocyclic gadolinium(III)-aminopolycarboxylate complexes related to magnetic resonance imaging: catalytic effect of endogenous ligands.

PubMed

Baranyai, Zsolt; Pálinkás, Zoltán; Uggeri, Fulvio; Maiocchi, Alessandro; Aime, Silvio; Brücher, Ernő

2012-12-14

The kinetics of the metal exchange reactions between open-chain Gd(DTPA)(2-) and Gd(DTPA-BMA), macrocyclic Gd(DOTA)(-) and Gd(HP-DO3A) complexes, and Cu(2+)  ions were investigated in the presence of endogenous citrate, phosphate, carbonate and histidinate ligands in the pH range 6-8 in NaCl (0.15 M) at 25 °C. The rates of the exchange reactions of Gd(DTPA)(2-) and Gd(DTPA-BMA) are independent of the Cu(2+) concentration in the presence of citrate and the reactions occur via the dissociation of Gd(3+)  complexes catalyzed by the citrate ions. The HCO(3)(-)/CO(3)(2-) and H(2)PO(4)(-) ions also catalyze the dissociation of complexes. The rates of the dissociation of Gd(DTPA-BMA), catalyzed by the endogenous ligands, are about two orders of magnitude higher than those of the Gd(DTPA)(2-). In fact near to physiological conditions the bicarbonate and carbonate ions show the largest catalytic effect, that significantly increase the dissociation rate of Gd(DTPA-BMA) and make the higher pH values (when the carbonate ion concentration is higher) a risk-factor for the dissociation of complexes in body fluids. The exchange reactions of Gd(DOTA)(-) and Gd(HP-DO3A) with Cu(2+) occur through the proton assisted dissociation of complexes in the pH range 3.5-5 and the endogenous ligands do not affect the dissociation rates of complexes. More insights into the interaction scheme between Gd(DTPA-BMA) and Gd(DTPA)(2-) and endogenous ligands have been obtained by acquiring the (13)C NMR spectra of the corresponding diamagnetic Y(III)-complexes, indicating the increase of the rates of the intramolecular rearrangements in the presence of carbonate and citrate ions. The herein reported results may have implications in the understanding of the etiology of nephrogenic systemic fibrosis, a rare disease that has been associated to the administration of Gd-containing agents to patients with impaired renal function. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interactions of diamines with adenosine-5'-triphosphate (ATP) in the systems including copper(II) ions.

PubMed

Bregier-Jarzebowska, R; Gasowska, A; Hoffmann, S K; Lomozik, L

2016-09-01

Interactions were studied in the systems ATP/tn and ATP/Put (tn=1,3-diaminopropane, Put=putrescine) whereas the complexation reactions in ternary systems Cu(II)/ATP/tn and Cu(II)/ATP/Put. Results of the potentiometric and spectroscopic studies evidenced the formation of adducts of the type (ATP)H x (PA), where PA=diamine. The thermodynamic stability of the complexes and the mode of interactions were determined. On the basis of analysis of changes in the positions of NMR signals, in the pH range of (ATP)H 3 (Put) formation, the preferred centres of the interaction between ATP and Put are the endocyclic nitrogen atoms from the nucleotide. On the other hand, the shorter diamine tn in the entire pH range reacts with the phosphate groups from ATP. The positive centres of noncovalent interactions are the protonated NH x + groups from amines. In both complexes Cu(ATP)H 2 (tn) and Cu(ATP)H 3 (Put) formed in ternary systems at pH<6.5, the amines are in the outer sphere of coordination with the noncovalent interaction with anchoring Cu(ATP). Only the phosphate groups from the nucleotide take part in metalation. At higher pH in the range of Cu(ATP)(PA) complex formation, significant differences in the reactions of the two amines appear. The shorter one (tn) binds Cu(II) ions with two nitrogen atoms, while putrescine coordinates in the monofunctional mode, which is undoubtedly related to the differences in lengths of methylene chain. This explains the considerable differences in the stability of Cu(ATP)(tn) and Cu(ATP)(Put). In both complexes the nucleotide is coordinated through phosphate groups. As a result of noncovalent interactions ATP forms molecular complexes with 1,3-diaminopropane and 1,4-diaminobutane (putrescine). Significant differences in the mode of interactions between the two diamines were observed in ATP/diamine binary systems and in ternary systems Cu(II)/ATP/diamine, at high pH. Copyright © 2016 Elsevier Inc. All rights reserved.

Double channel emission from a redox active single component quantum dot complex.

PubMed

Bhandari, Satyapriya; Roy, Shilaj; Pramanik, Sabyasachi; Chattopadhyay, Arun

2015-01-13

Herein we report the generation and control of double channel emission from a single component system following a facile complexation reaction between a Mn(2+) doped ZnS colloidal quantum dot (Qdot) and an organic ligand (8-hydroxy quinoline; HQ). The double channel emission of the complexed quantum dot-called the quantum dot complex (QDC)-originates from two independent pathways: one from the complex (ZnQ2) formed on the surface of the Qdot and the other from the dopant Mn(2+) ions of the Qdot. Importantly, reaction of ZnQ2·2H2O with the Qdot resulted in the same QDC formation. The emission at 500 nm with an excitation maximum at 364 nm is assigned to the surface complex involving ZnQ2 and a dangling sulfide bond. On the other hand, the emission at 588 nm-with an excitation maximum at 330 nm-which is redox tunable, is ascribed to Mn(2+) dopant. The ZnQ2 complex while present in QDC has superior thermal stability in comparison to the bare complex. Interestingly, while the emission of Mn(2+) was quenched by an electron quencher (benzoquinone), that due to the surface complex remained unaffected. Further, excitation wavelength dependent tunability in chromaticity color coordinates makes the QDC a potential candidate for fabricating a light emitting device of desired color output.

[Jellyfish sting injuries].

PubMed

Mebs, D

2014-10-01

Jellyfish are distributed worldwide; they cause local skin injuries upon contact which are often followed by systemic signs of envenoming. Which jellyfish species are of medical importance, which skin reactions and systemic symptoms occur, which first-aid measures and treatment options exist? Review of the medical literature and discussion of first-aid and therapeutic options. Jellyfish capable of causing skin injuries occur in almost all oceans. Several jellyfish species may cause severe, potentially lethal, systemic symptoms; they include the Portuguese man-of-war (Physalia physalis) and box jellyfish (Chironex fleckeri, Carukia barnesi, Chiropsalmus quadrigatus). Among the injuries and envenoming symptoms caused by marine organisms, jellyfish dermatitis should not be underestimated. Skin reactions may not only a dermatological problem, but also be accompanied by complex systemic toxic symptoms which are a challenge for internists.

Construction of new biopolymer (chitosan)-based pincer-type Pd(II) complex and its catalytic application in Suzuki cross coupling reactions

NASA Astrophysics Data System (ADS)

Baran, Talat; Menteş, Ayfer

2017-04-01

In this paper we described the fabrication, characterization and application of a new biopolymer (chitosan)-based pincer-type Pd(II) catalyst in Suzuki cross coupling reactions using a non-toxic, cheap, eco-friendly and practical method. The catalytic activity tests showed remarkable product yields as well as TON (19800) and TOF (330000) values with a small catalyst loading. In addition, the catalyst indicated good recyclability in the Suzuki C-C reaction. This biopolymer supported catalyst can be used with various catalyst systems due to its unique properties, such as being inert, green in nature, low cost and chemically durable.

Controlled droplet microfluidic systems for multistep chemical and biological assays.

PubMed

Kaminski, T S; Garstecki, P

2017-10-16

Droplet microfluidics is a relatively new and rapidly evolving field of science focused on studying the hydrodynamics and properties of biphasic flows at the microscale, and on the development of systems for practical applications in chemistry, biology and materials science. Microdroplets present several unique characteristics of interest to a broader research community. The main distinguishing features include (i) large numbers of isolated compartments of tiny volumes that are ideal for single cell or single molecule assays, (ii) rapid mixing and negligible thermal inertia that all provide excellent control over reaction conditions, and (iii) the presence of two immiscible liquids and the interface between them that enables new or exotic processes (the synthesis of new functional materials and structures that are otherwise difficult to obtain, studies of the functions and properties of lipid and polymer membranes and execution of reactions at liquid-liquid interfaces). The most frequent application of droplet microfluidics relies on the generation of large numbers of compartments either for ultrahigh throughput screens or for the synthesis of functional materials composed of millions of droplets or particles. Droplet microfluidics has already evolved into a complex field. In this review we focus on 'controlled droplet microfluidics' - a portfolio of techniques that provide convenient platforms for multistep complex reaction protocols and that take advantage of automated and passive methods of fluid handling on a chip. 'Controlled droplet microfluidics' can be regarded as a group of methods capable of addressing and manipulating droplets in series. The functionality and complexity of controlled droplet microfluidic systems can be positioned between digital microfluidics (DMF) addressing each droplet individually using 2D arrays of electrodes and ultrahigh throughput droplet microfluidics focused on the generation of hundreds of thousands or even millions of picoliter droplets that cannot be individually addressed by their location on a chip.

Alkyne Benzannulation Reactions for the Synthesis of Novel Aromatic Architectures.

PubMed

Hein, Samuel J; Lehnherr, Dan; Arslan, Hasan; J Uribe-Romo, Fernando; Dichtel, William R

2017-11-21

Aromatic compounds and polymers are integrated into organic field effect transistors, light-emitting diodes, photovoltaic devices, and redox-flow batteries. These compounds and materials feature increasingly complex designs, and substituents influence energy levels, bandgaps, solution conformation, and crystal packing, all of which impact performance. However, many polycyclic aromatic hydrocarbons of interest are difficult to prepare because their substitution patterns lie outside the scope of current synthetic methods, as strategies for functionalizing benzene are often unselective when applied to naphthalene or larger systems. For example, cross-coupling and nucleophilic aromatic substitution reactions rely on prefunctionalized arenes, and even directed metalation methods most often modify positions near Lewis basic sites. Similarly, electrophilic aromatic substitutions access single regioisomers under substrate control. Cycloadditions provide a convergent route to densely functionalized aromatic compounds that compliment the above methods. After surveying cycloaddition reactions that might be used to modify the conjugated backbone of poly(phenylene ethynylene)s, we discovered that the Asao-Yamamoto benzannulation reaction is notably efficient. Although this reaction had been reported a decade earlier, its scope and usefulness for synthesizing complex aromatic systems had been under-recognized. This benzannulation reaction combines substituted 2-(phenylethynyl)benzaldehydes and substituted alkynes to form 2,3-substituted naphthalenes. The reaction tolerates a variety of sterically congested alkynes, making it well-suited for accessing poly- and oligo(ortho-arylene)s and contorted hexabenzocoronenes. In many cases in which asymmetric benzaldehyde and alkyne cycloaddition partners are used, the reaction is regiospecific based on the electronic character of the alkyne substrate. Recognizing these desirable features, we broadened the substrate scope to include silyl- and halogen-substituted alkynes. Through a combined experimental and computational approach, we have elucidated mechanistic insight and key principles that govern the regioselectivity outcome of the benzannulation of structurally diverse alkynes. We have applied these methods to prepare sterically hindered, shape-persistent aromatic systems, heterocyclic aromatic compounds, functionalized 2-aryne precursors, polyheterohalogenated naphthalenes, ortho-arylene foldamers, and graphene nanoribbons. As a result of these new synthetic avenues, aromatic structures with interesting properties were uncovered such as ambipolar charge transport in field effect transistors based on our graphene nanoribbons, conformational aspects of ortho-arylene architectures resulting from intramolecular π-stacking, and modulation of frontier molecular orbitals via protonation of heteroatom containing aromatic systems. Given the availability of many substituted 2-(phenylethynyl)benzaldehydes and the regioselectivity of the benzannulation reaction, naphthalenes can be prepared with control of the substitution pattern at seven of the eight substitutable positions. Researchers in a range of fields are likely to benefit directly from newly accessible molecular and polymeric systems derived from polyfunctionalized naphthalenes.

The Copper-nicotinamide complex: sustainable applications in coupling and cycloaddition reactions

EPA Science Inventory

Crystalline copper (II)-nicotinamide complex, synthesized via simple mixing of copper chloride and nicotinamide solution at room temperature, catalyzes the C-S, C-N bond forming and cycloaddition reactions under a variety of sustainable reaction conditions.

Study of the intensification of solar photo-Fenton degradation of carbamazepine with ferrioxalate complexes and ultrasound.

PubMed

Expósito, A J; Monteagudo, J M; Durán, A; San Martín, I; González, L

2018-01-15

The intensification of the solar photo-Fenton system with ferrioxalate photoactive complexes and ultrasound applied to the mineralization of 15mg/L carbamazepine aqueous solution (CBZ) was evaluated. The experiments were carried out in a solar compound parabolic collector (CPC) pilot plant reactor coupled to an ultrasonic processor. The dynamic behavior of hydroxyl radicals generated under the different studied reaction systems was discussed. The initial concentrations of hydrogen peroxide and ferrous/oxalic acid and pH were found to be the most significant variables (32.79%, 25.98% and 26.04%, respectively). Under the selected optimal conditions ([H 2 O 2 ] 0 =150mg/L; [Fe 2+ ] 0 =2.5mg/L/[(COOH) 2 ] 0 =12.1mg/L; pH=5) CBZ was fully degraded after 5min and 80% of TOC was removed using a solar photo-Fenton system intensified with ferrioxalate (SPFF). However, no improvement in the mineralization using SPFF process combined with ultrasound was observed. More mild pH conditions could be used in the SPFF system if compared to the traditional photo-Fenton (pH 3) acidic systems. Finally, a possible reaction pathway for the mineralization of CBZ by the SPFF system was proposed and therein discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Mathematical methods to analysis of topology, functional variability and evolution of metabolic systems based on different decomposition concepts.

PubMed

Mrabet, Yassine; Semmar, Nabil

2010-05-01

Complexity of metabolic systems can be undertaken at different scales (metabolites, metabolic pathways, metabolic network map, biological population) and under different aspects (structural, functional, evolutive). To analyse such a complexity, metabolic systems need to be decomposed into different components according to different concepts. Four concepts are presented here consisting in considering metabolic systems as sets of metabolites, chemical reactions, metabolic pathways or successive processes. From a metabolomic dataset, such decompositions are performed using different mathematical methods including correlation, stiochiometric, ordination, classification, combinatorial and kinetic analyses. Correlation analysis detects and quantifies affinities/oppositions between metabolites. Stoichiometric analysis aims to identify the organisation of a metabolic network into different metabolic pathways on the hand, and to quantify/optimize the metabolic flux distribution through the different chemical reactions of the system. Ordination and classification analyses help to identify different metabolic trends and their associated metabolites in order to highlight chemical polymorphism representing different variability poles of the metabolic system. Then, metabolic processes/correlations responsible for such a polymorphism can be extracted in silico by combining metabolic profiles representative of different metabolic trends according to a weighting bootstrap approach. Finally evolution of metabolic processes in time can be analysed by different kinetic/dynamic modelling approaches.

Aeromedical Factors in Aviator Fatigue, Crew Work/Rest Schedules and Extended Flight Operations: An Annotated Bibliography.

DTIC Science & Technology

1981-01-01

complex is a common psychological reaction to stress, which causes a chronic overactivity of the higher brain centers and the vagal-parasympathetic...continuous military operations in which other complex man-machine systems were being used. In addition, we found great interest in multidisciplinary...2. Adams, J. T. 1967. Fatigue in helicopter aircrews in combat. In: Aeromedical aspects of helicopter operations in the tac- tical situation

LSENS, The NASA Lewis Kinetics and Sensitivity Analysis Code

NASA Technical Reports Server (NTRS)

Radhakrishnan, K.

2000-01-01

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

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

DOE PAGES

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

2009-01-01

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

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

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

The equilibrium constant of complex formation in solution: A study utilizing a dielectric constant method

NASA Astrophysics Data System (ADS)

Loh, C. W.

1980-03-01

A method was developed for determining equilibrium constants, heat of reaction, and change in free energy and entropy during a 1:1 complex formation in solutions. The measurements were carried out on ternary systems containing two interacting solutes in an inert solvent. The procedures was applied to the investigation of hydrogen bond complex formations in two mixtures systems, phenol and pyridine in carbon tetrachloride, and 4, 5, 6, 7-tetrachloro-2-trifluoromethylbenzimidazole (TTFB) and alkyl acetate in styrene. The first mixture system was studied in order to compare the results with those obtained by other methods. Results for the second mixture system indicated strong association between molecules of TTFB and alkyl acetate and suggested that the blocking of valinomycin-mediated bilayer membrane conductance by substituted benzimidazoles was due to competition for a limited number of adsorption sites on the membrane surface.

Observation of hydroxymethyl hydroperoxide in a reaction system containing CH{sub 2}OO and water vapor through pure rotational spectroscopy

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

Nakajima, Masakazu; Endo, Yasuki, E-mail: endo@bunshi.c.u-tokyo.ac.jp

Pure rotational transitions of hydroxymethyl hydroperoxide (HMHP) were observed in the discharged plasma of a CH{sub 2}I{sub 2}/O{sub 2}/water gas mixture, where the water complex with the simplest Criegee intermediate CH{sub 2}OO has been identified [M. Nakajima and Y. Endo, J. Chem. Phys. 140, 134302 (2014)]. Isotope experiments using heavy water support that the currently observed HMHP molecule was produced by the reaction of CH{sub 2}OO with water vapor. The observed species was identified as the most stable conformer with the help of quantum chemical calculations. We also clarified that productions of formic acid and dioxirane are promoted by themore » existence of water vapor in the discharged reaction system.« less

Ultrasensitivity by Molecular Titration in Spatially Propagating Enzymatic Reactions

PubMed Central

Semenov, Sergey N.; Markvoort, Albert J.; Gevers, Wouter B.L.; Piruska, Aigars; de Greef, Tom F.A.; Huck, Wilhelm T.S.

2013-01-01

Delineating design principles of biological systems by reconstitution of purified components offers a platform to gauge the influence of critical physicochemical parameters on minimal biological systems of reduced complexity. Here we unravel the effect of strong reversible inhibitors on the spatiotemporal propagation of enzymatic reactions in a confined environment in vitro. We use micropatterned, enzyme-laden agarose gels which are stamped on polyacrylamide films containing immobilized substrates and reversible inhibitors. Quantitative fluorescence imaging combined with detailed numerical simulations of the reaction-diffusion process reveal that a shallow gradient of enzyme is converted into a steep product gradient by addition of strong inhibitors, consistent with a mathematical model of molecular titration. The results confirm that ultrasensitive and threshold effects at the molecular level can convert a graded input signal to a steep spatial response at macroscopic length scales. PMID:23972857

Bimetallic redox synergy in oxidative palladium catalysis.

PubMed

Powers, David C; Ritter, Tobias

2012-06-19

Polynuclear transition metal complexes, which are embedded in the active sites of many metalloenzymes, are responsible for effecting a diverse array of oxidation reactions in nature. The range of chemical transformations remains unparalleled in the laboratory. With few noteworthy exceptions, chemists have primarily focused on mononuclear transition metal complexes in developing homogeneous catalysis. Our group is interested in the development of carbon-heteroatom bond-forming reactions, with a particular focus on identifying reactions that can be applied to the synthesis of complex molecules. In this context, we have hypothesized that bimetallic redox chemistry, in which two metals participate synergistically, may lower the activation barriers to redox transformations relevant to catalysis. In this Account, we discuss redox chemistry of binuclear Pd complexes and examine the role of binuclear intermediates in Pd-catalyzed oxidation reactions. Stoichiometric organometallic studies of the oxidation of binuclear Pd(II) complexes to binuclear Pd(III) complexes and subsequent C-X reductive elimination from the resulting binuclear Pd(III) complexes have confirmed the viability of C-X bond-forming reactions mediated by binuclear Pd(III) complexes. Metal-metal bond formation, which proceeds concurrently with oxidation of binuclear Pd(II) complexes, can lower the activation barrier for oxidation. We also discuss experimental and theoretical work that suggests that C-X reductive elimination is also facilitated by redox cooperation of both metals during reductive elimination. The effect of ligand modification on the structure and reactivity of binuclear Pd(III) complexes will be presented in light of the impact that ligand structure can exert on the structure and reactivity of binuclear Pd(III) complexes. Historically, oxidation reactions similar to those discussed here have been proposed to proceed via mononuclear Pd(IV) intermediates, and the hypothesis of mononuclear Pd(II/IV) catalysis has guided the successful development of many reactions. Herein we discuss differences between monometallic Pd(IV) and bimetallic Pd(III) redox catalysis. We address whether appreciation of the relevance of bimetallic Pd(III) redox catalysis is of academic interest exclusively, serving to provide a more nuanced description of catalysis, or if the new insight regarding bimetallic Pd(III) chemistry can be a platform to enable future reaction development. To this end, we describe an example in which the hypothesis of bimetallic redox chemistry guided reaction development, leading to the discovery of reactivity distinct from monometallic catalysts.

Computational methods for diffusion-influenced biochemical reactions.

PubMed

Dobrzynski, Maciej; Rodríguez, Jordi Vidal; Kaandorp, Jaap A; Blom, Joke G

2007-08-01

We compare stochastic computational methods accounting for space and discrete nature of reactants in biochemical systems. Implementations based on Brownian dynamics (BD) and the reaction-diffusion master equation are applied to a simplified gene expression model and to a signal transduction pathway in Escherichia coli. In the regime where the number of molecules is small and reactions are diffusion-limited predicted fluctuations in the product number vary between the methods, while the average is the same. Computational approaches at the level of the reaction-diffusion master equation compute the same fluctuations as the reference result obtained from the particle-based method if the size of the sub-volumes is comparable to the diameter of reactants. Using numerical simulations of reversible binding of a pair of molecules we argue that the disagreement in predicted fluctuations is due to different modeling of inter-arrival times between reaction events. Simulations for a more complex biological study show that the different approaches lead to different results due to modeling issues. Finally, we present the physical assumptions behind the mesoscopic models for the reaction-diffusion systems. Input files for the simulations and the source code of GMP can be found under the following address: http://www.cwi.nl/projects/sic/bioinformatics2007/

Hybrid stochastic simulations of intracellular reaction-diffusion systems.

PubMed

Kalantzis, Georgios

2009-06-01

With the observation that stochasticity is important in biological systems, chemical kinetics have begun to receive wider interest. While the use of Monte Carlo discrete event simulations most accurately capture the variability of molecular species, they become computationally costly for complex reaction-diffusion systems with large populations of molecules. On the other hand, continuous time models are computationally efficient but they fail to capture any variability in the molecular species. In this study a hybrid stochastic approach is introduced for simulating reaction-diffusion systems. We developed an adaptive partitioning strategy in which processes with high frequency are simulated with deterministic rate-based equations, and those with low frequency using the exact stochastic algorithm of Gillespie. Therefore the stochastic behavior of cellular pathways is preserved while being able to apply it to large populations of molecules. We describe our method and demonstrate its accuracy and efficiency compared with the Gillespie algorithm for two different systems. First, a model of intracellular viral kinetics with two steady states and second, a compartmental model of the postsynaptic spine head for studying the dynamics of Ca+2 and NMDA receptors.

A Self-Perpetuating Catalyst for the Production of Complex Organic Molecules in Protostellar Nebulae

NASA Technical Reports Server (NTRS)

Nuth, Joseph A.; Johnson, N. M.

2010-01-01

The formation of abundant carbonaceous material in meteorites is a long standing problem and an important factor in the debate on the potential for the origin of life in other stellar systems. Many mechanisms may contribute to the total organic content in protostellar nebulae, ranging from organics formed via ion-molecule and atom-molecule reactions in the cold dark clouds from which such nebulae collapse, to similar ion-molecule and atom-molecule reactions in the dark regions of the nebula far from the proto star, to gas phase reactions in sub-nebulae around growing giant planets and in the nebulae themselves. The Fischer-Tropsch-type (FTT) catalytic reduction of CO by hydrogen was once the preferred model for production of organic materials in the primitive solar nebula. The Haber-Bosch catalytic reduction of N2 by hydrogen was thought to produce the reduced nitrogen found in meteorites. However, the clean iron metal surfaces that catalyze these reactions are easily poisoned via reaction with any number of molecules, including the very same complex organics that they produce and both reactions work more efficiently in the hot regions of the nebula. We have demonstrated that many grain surfaces can catalyze both FTT and HB-type reactions, including amorphous iron and magnesium silicates, pure silica smokes as well as several minerals. Although none work as well as pure iron grains, and all produce a wide range of organic products rather than just pure methane, these materials are not truly catalysts.

Carbon Dioxide Transformation in Imidazolium Salts: Hydroaminomethylation Catalyzed by Ru-Complexes.

PubMed

Ali, Meher; Gual, Aitor; Ebeling, Gunter; Dupont, Jairton

2016-08-23

The catalytic species generated by dissolving Ru3 (CO)12 in the ionic liquids 1-n-butyl-3-methyl-imidazolium chloride or 1-n-butyl-2,3-dimethyl-imidazolium chloride are efficient multifunctional catalysts for: (a) reverse water-gas shift, (b) hydroformylation of alkenes, and (c) reductive amination of aldehydes. Thus the reaction of alkenes with primary or secondary amines (alkene/amine, 1:1) under CO2 /H2 (1:1) affords the hydroaminomethylations products in high alkene conversions (up to 99 %) and selectivities (up to 96 %). The reaction proceeds under relatively mild reaction conditions (120 °C, 60 bar=6 MPa) and affords selectively secondary and tertiary amines. The presence of amine strongly reduces the alkene hydrogenation competitive pathway usually observed in the hydroformylation of terminal alkenes by Ru complexes. The catalytic system is also highly active for the reductive amination of aldehydes and ketones yielding amines in high yields (>90 %). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A bioinspired redox relay that mimics radical interactions of the Tyr-His pairs of photosystem II

NASA Astrophysics Data System (ADS)

Megiatto, Jackson D., Jr.; Méndez-Hernández, Dalvin D.; Tejeda-Ferrari, Marely E.; Teillout, Anne-Lucie; Llansola-Portolés, Manuel J.; Kodis, Gerdenis; Poluektov, Oleg G.; Rajh, Tijana; Mujica, Vladimiro; Groy, Thomas L.; Gust, Devens; Moore, Thomas A.; Moore, Ana L.

2014-05-01

In water-oxidizing photosynthetic organisms, light absorption generates a powerfully oxidizing chlorophyll complex (P680•+) in the photosystem II reaction centre. This is reduced via an electron transfer pathway from the manganese-containing water-oxidizing catalyst, which includes an electron transfer relay comprising a tyrosine (Tyr)-histidine (His) pair that features a hydrogen bond between a phenol group and an imidazole group. By rapidly reducing P680•+, the relay is thought to mitigate recombination reactions, thereby ensuring a high quantum yield of water oxidation. Here, we show that an artificial reaction centre that features a benzimidazole-phenol model of the Tyr-His pair mimics both the short-internal hydrogen bond in photosystem II and, using electron paramagnetic resonance spectroscopy, the thermal relaxation that accompanies proton-coupled electron transfer. Although this artificial system is much less complex than the natural one, theory suggests that it captures the essential features that are important in the function of the relay.

Group transfer and electron transfer reactions of organometallic complexes

NASA Astrophysics Data System (ADS)

Atwood, Jim D.

During 1994, despite the disruptions, the authors have made progress in several aspects of their research on electron transfer reactions between organometallic complexes. This summary covers three areas that are relatively complete: (1) reactions between metal carbonyl anions and metal carbonyl halides, (2) reactions of hydrido- and alkyl-containing anions (RFe(CO)4(-) and RW(CO)5(-) with metal carbonyl cations; and (3) reactions of a seventeen-electron complex (Cp* Cr(CO)3*) with metal carbonyl derivatives. Two areas of examination that have just begun (possible carbene transfer and the possible role of metal carbonyl anions in carbon-hydrogen bond activation) will also be described.

What does systems biology mean for drug development?

PubMed

Schrattenholz, André; Soskić, Vukić

2008-01-01

The complexity and flexibility of cellular architectures is increasingly recognized by impressive progress on the side of molecular analytics, i.e. proteomics, genomics and metabolomics. One of the messages from systems biology is that the number of molecular species in cellular networks is orders of magnitude bigger than anticipated by genomic analysis, in particular by fast posttranslational modifications of proteins. The requirements to manage external signals, integrate spatiotemporal signal transduction inside an organism and at the same time optimizing networks of biochemical and chemical reactions result in chemically extremely fine tuned molecular entities. Chemical side reactions of enzymatic activity, like e.g. random oxidative damage of proteins by free radicals during aging constantly introduce epigenetic alterations of protein targets. These events gradually and on an individual stochastic scale, keep modifying activities of these targets, and their affinities and selectivities towards biological and pharmacological ligands. One further message is that many of the key reactions in living systems are essentially based on interactions of low affinities and even low selectivities. This principle is responsible for the enormous flexibility and redundancy of cellular circuitries. So, in complex disorders like cancer or neurodegenerative diseases, which are rooted in relatively subtle and multimodal dysfunction of important physiologic pathways, drug discovery programs based on the concept of high affinity/high specificity compounds ("one-target, one-disease"), which still dominate the pharmaceutical industry increasingly turn out to be unsuccessful. Despite improvements in rational drug design and high throughput screening methods, the number of novel, single-target drugs fell much behind expectations during the past decade and the treatment of "complex diseases" remains a most pressing medical need. Currently a change of paradigm can be observed with regard to a new focus on agents that modulate multiple targets simultaneously. Targeting cellular function as a system rather than on the level of the single protein molecule significantly increases the size of the drugable proteome and is expected to introduce novel classes of multi-target drugs with fewer adverse effects and toxicity. Multiple target approaches have recently been used to design medications against atherosclerosis, cancer, depression, psychosis and neurodegenerative diseases. A focussed approach towards "systemic" drugs will certainly require the development of novel computational and mathematical concepts for appropriate modelling of complex data and extraction of "screenable" information from biological systems essentially ruled by deterministic chaotic processes on a background of individual stochasticity.

A hybrid approach to simulation of electron transfer in complex molecular systems

PubMed Central

Kubař, Tomáš; Elstner, Marcus

2013-01-01

Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors. PMID:23883952

Wave Phenomena in Reaction-Diffusion Systems

NASA Astrophysics Data System (ADS)

Steinbock, Oliver; Engel, Harald

2013-12-01

Pattern formation in excitable and oscillatory reaction-diffusion systems provides intriguing examples for the emergence of macroscopic order from molecular reaction events and Brownian motion. Here we review recent results on several aspects of excitation waves including anomalous dispersion, vortex pinning, and three-dimensional scroll waves. Anomalies in the speed-wavelength dependence of pulse trains include nonmonotonic behavior, bistability, and velocity gaps. We further report on the hysteresis effects during the pinning-depinning transition of twodimensional spiral waves. The pinning of three-dimensional scroll waves shows even richer dynamic complexity, partly due to the possibility of geometric and topological mismatches between the unexcitable, pinning heterogeneities and the one-dimensional rotation backbone of the vortex. As examples we present results on the pinning of scroll rings to spherical, C-shaped, and genus-2-type heterogeneities. We also review the main results of several experimental studies employing the Belousov-Zhabotinsky reaction and briefly discuss the biomedical relevance of this research especially in the context of cardiology.

Copper-free Sonogashira cross-coupling for functionalization of alkyne-encoded proteins in aqueous medium and in bacterial cells.

PubMed

Li, Nan; Lim, Reyna K V; Edwardraja, Selvakumar; Lin, Qing

2011-10-05

Bioorthogonal reactions suitable for functionalization of genetically or metabolically encoded alkynes, for example, copper-catalyzed azide-alkyne cycloaddition reaction ("click chemistry"), have provided chemical tools to study biomolecular dynamics and function in living systems. Despite its prominence in organic synthesis, copper-free Sonogashira cross-coupling reaction suitable for biological applications has not been reported. In this work, we report the discovery of a robust aminopyrimidine-palladium(II) complex for copper-free Sonogashira cross-coupling that enables selective functionalization of a homopropargylglycine (HPG)-encoded ubiquitin protein in aqueous medium. A wide range of aromatic groups including fluorophores and fluorinated aromatic compounds can be readily introduced into the HPG-containing ubiquitin under mild conditions with good to excellent yields. The suitability of this reaction for functionalization of HPG-encoded ubiquitin in Escherichia coli was also demonstrated. The high efficiency of this new catalytic system should greatly enhance the utility of Sonogashira cross-coupling in bioorthogonal chemistry.

Re-evaluation of the origin and evolution of > 4.2 Ga zircons from the Jack Hills metasedimentary rocks

NASA Astrophysics Data System (ADS)

Nemchin, A. A.; Pidgeon, R. T.; Whitehouse, M. J.

2006-04-01

New data are presented on internal structures, U-Pb systematics and oxygen isotope compositions of eight detrital zircons with ages greater than 4.2 Ga, from the Jack Hills metasedimentary belt, Australia. Cathodoluminescence imaging, ion-microprobe U-Pb and oxygen isotope results show evidence for an extensive period of complex zircon growth, secondary reaction and U-Pb isotopic disturbance from 4.36 to 3.90 Ga. In addition many of the zircons have discordant U-Pb systems and excess common Pb indicating a superimposed, relatively recent, reaction between radiation damaged zircon and low temperature fluids. The significance of oxygen isotope compositions for zircons with complex internal structures and U-Pb systems is complicated by uncertainty in the origin of the grains and the unknown effect of later reactions. However, a minority of grains with sharp oscillatory zoning, uniform and concordant U-Pb systems, igneous Th-U ratios and low common Pb contents, are interpreted as undisturbed primary magmatic zircons. The oldest identified, oscillatory zoned, magmatic grain, with an age 4363 ± 20 Ma, is one of a few reported magmatic grains with this age, which is interpreted as the oldest reliable age for Hadean magmatic zircons. Mantle δ18O values are reported for these zircons. Younger oscillatory zoned zircon, including oscillatory zoned cores in complex grains, have δ18O values lower than 6.5‰, which are within the range of ion microprobe analysed δ18O values for zircons in high temperature equilibrium with the normal mantle rocks of 5.3 ± 0.6‰ (2 standard deviations). These values are also within the range of δ18O values found in lunar zircons. The absence of heavy oxygen in the grains that can be interpreted as primary magmatic zircons and the complex history over the period from 4.36 to 3.9 Ga, seen in all other Jack Hills zircons and reflected in the internal structures and U-Pb isotopic systems, questions the model for the early Earth involving long intervals of relatively temperate conditions from 4.4 to 4.0 Ga that were conducive to oceans and possibly life.

MODELING MONOMETHYLMERCURY AND TRIBUTYLTIN SPECIATION WITH EPA'S GEOCHEMICAL SPECIATION MODEL MINTEQA2

EPA Science Inventory

Given the complexity of the various, simultaneous (and competing) equilibrium reactions governing the speciation of ionic species in aquatic systems, EPA has developed and distributed the geochemical speciation model MINTEQA2 (Brown and Allison, 1987, Allison et al., 1991; Hydrog...

Programmable chemical controllers made from DNA.

PubMed

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2013-10-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.

Programmable chemical controllers made from DNA

NASA Astrophysics Data System (ADS)

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2013-10-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.

Programmable chemical controllers made from DNA

PubMed Central

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2014-01-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language', and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents. PMID:24077029

Solar chemistry of metal complexes

NASA Astrophysics Data System (ADS)

Gray, H. B.; Maverick, A. W.

1981-12-01

Electronic excited states of certain transition metal complexes undergo oxidation-reduction reactions that store chemical energy. Such reactions have been extensively explored for mononuclear complexes. Two classes of polynuclear species exhibit similar properties, and these complexes are now being studied as possible homogeneous sensitizer-catalysts for hydrogen production from aqueous solutions.

A molecular orbital study of a model of the Mg2+ coordination complex of the self splicing reaction of ribosomal RNA

NASA Technical Reports Server (NTRS)

McCourt, M.; Shibata, M.; McIver, J. W.; Rein, R.

1988-01-01

Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.

Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

PubMed

Sankar, Punnaivanam; Aghila, Gnanasekaran

2007-01-01

The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

Temperature Dependence of the NO + O3 Reaction Rate from 195 to 369 K,

DTIC Science & Technology

1982-01-01

variety of complex reactive systems . Some of these systems are interesting for their illumin- ation of fundamental chemical processes, while others...attract attention for the roles they play in naturally occurring phenomena. Tropospheric and stratospheric chemistry are two systems in the latter...technique 03 is the excess reagent and the NO concentration is followed. This is the first such thermal study of this type on this system , and it is the

Heterogeneous photocatalytic degradation of gallic acid under different experimental conditions.

PubMed

Quici, Natalia; Litter, Marta I

2009-07-01

UV/TiO(2)-heterogeneous photocatalysis was tested as a process to degrade gallic acid (Gal) in oxygenated solutions at pH 3. In the absence of oxidants other than oxygen, decay followed a zero order rate at different concentrations and was slow at concentrations higher than 0.5 mM. Addition of Fe(3+), H(2)O(2) and the combination Fe(3+)/H(2)O(2) improved Gal degradation. In the absence of H(2)O(2), an optimal Fe : Gal molar ratio of 0.33 : 1 was found for the photocatalytic decay, beyond which addition of Fe(3+) was detrimental and even worse in comparison with the system in the absence of Fe(3+). TiO(2) addition was beneficial compared with the same system in the absence of the photocatalyst if Fe(3+) was added at low concentration (0.33 : 1 Fe : Gal molar ratio), while at high concentration (1 : 1 Fe : Gal molar ratio) TiO(2) did not exert any significant effect. H(2)O(2) addition (1 : 0.33 Gal : H(2)O(2) molar ratio, absence of Fe(iii)) also enhanced the heterogeneous photocatalytic reaction. Simultaneous addition of Fe(3+) and H(2)O(2) was more effective than the addition of the separate oxidants. This system was compared with Fenton and photo-Fenton systems. At low H(2)O(2) concentration (0.33 : 1 : 0.2 Fe : Gal : H(2)O(2) molar ratio), the presence of TiO(2) also enhanced the reaction. The influence of the thermal charge transfer reaction between Gal and Fe(iii), which leads to an important Gal depletion in the dark with formation of quinones, was analysed. The mechanisms taking place in these complex systems are proposed, paying particular attention to the important charge transfer reaction of the Fe(iii)-Gal complex operative in dark conditions.

Can a Reaction's Environment Program its Outcome, and Does it Matter?

NASA Astrophysics Data System (ADS)

Surman, A. J.; Rodriguez-Garcia, M.; Abul-Haija, Y.; Cooper, G. J. T.; Donkers, K.; Planchat i Barbarà, J. M.; Kube, J.; Mullin, M.; Hezwani, M.; Cronin, L.

2017-07-01

Where most eschew reactions producing complex mixtures (‘tar') and prefer to plan ‘clean' syntheses, we embrace complexity. We show that environments can steer ‘messy' reactions, and ask if this can yield significant difference in structure and function.

Lanthanide anilido complexes: synthesis, characterization, and use as highly efficient catalysts for hydrophosphonylation of aldehydes and unactivated ketones.

PubMed

Liu, Chengwei; Qian, Qinqin; Nie, Kun; Wang, Yaorong; Shen, Qi; Yuan, Dan; Yao, Yingming

2014-06-14

Lanthanide anilido complexes stabilized by the 2,6-diisopropylanilido ligand have been synthesized and characterized, and their catalytic activity for hydrophosphonylation reaction was explored. A reaction of anhydrous LnCl3 with 5 equivalents of LiNHPh-(I)Pr2-2,6 in THF generated the heterobimetallic lanthanide-lithium anilido complexes (2,6-(I)Pr2PhNH)5LnLi2(THF)2 [Ln = Sm(1), Nd(2), Y(3)] in good isolated yields. These complexes are well characterized by elemental analysis, IR, NMR (for complex ) and single-crystal structure determination. Complexes 1 - 3 are isostructural. In these complexes, the lanthanide metal ion is five-coordinated by five nitrogen atoms from five 2,6-diisopropylanilido ligands to form a distorted trigonal bipyramidal geometry. The lithium ion is coordinated by two nitrogen atoms from two 2,6-diisopropylanilido ligands, and one oxygen atom from a THF molecule. It was found that these simple lanthanide anilido complexes are highly efficient for catalyzing hydrophosphonylation reactions of various aldehydes and unactivated ketones to generate α-hydroxyphosphonates in good to excellent yields (up to 99%) within a short time (5 min for aldehydes, 20 min for ketones). Furthermore, the mechanism of hydrophosphonylation reactions has also been elucidated via(1)H NMR monitoring of reaction.

Blood coagulation reactions on nanoscale membrane surfaces

NASA Astrophysics Data System (ADS)

Pureza, Vincent S.

Blood coagulation requires the assembly of several membrane-bound protein complexes composed of regulatory and catalytic subunits. The biomembranes involved in these reactions not only provide a platform for these procoagulant proteins, but can also affect their function. Increased exposure of acidic phospholipids on the outer leaflet of the plasma membrane can dramatically modulate the catalytic efficiencies of such membrane-bound enzymes. Under physiologic conditions, however, these phospholipids spontaneously cluster into a patchwork of membrane microdomains upon which membrane binding proteins may preferentially assemble. As a result, the membrane composition surrounding these proteins is largely unknown. Through the development and use of a nanometer-scale bilayer system that provides rigorous control of the phospholipid membrane environment, I investigated the role of phosphatidylserine, an acidic phospholipid, in the direct vicinity (within nanometers) of two critical membrane-bound procoagulant protein complexes and their respective natural substrates. Here, I present how the assembly and function of the tissue factor˙factor VIIa and factor Va˙factor Xa complexes, the first and final cofactor˙enzyme complexes of the blood clotting cascade, respectively, are mediated by changes in their immediate phospholipid environments.

Electronic structural changes of Mn in the oxygen-evolving complex of photosystem II during the catalytic cycle.

PubMed

Glatzel, Pieter; Schroeder, Henning; Pushkar, Yulia; Boron, Thaddeus; Mukherjee, Shreya; Christou, George; Pecoraro, Vincent L; Messinger, Johannes; Yachandra, Vittal K; Bergmann, Uwe; Yano, Junko

2013-05-20

The oxygen-evolving complex (OEC) in photosystem II (PS II) was studied in the S0 through S3 states using 1s2p resonant inelastic X-ray scattering spectroscopy. The spectral changes of the OEC during the S-state transitions are subtle, indicating that the electrons are strongly delocalized throughout the cluster. The result suggests that, in addition to the Mn ions, ligands are also playing an important role in the redox reactions. A series of Mn(IV) coordination complexes were compared, particularly with the PS II S3 state spectrum to understand its oxidation state. We find strong variations of the electronic structure within the series of Mn(IV) model systems. The spectrum of the S3 state best resembles those of the Mn(IV) complexes Mn3(IV)Ca2 and saplnMn2(IV)(OH)2. The current result emphasizes that the assignment of formal oxidation states alone is not sufficient for understanding the detailed electronic structural changes that govern the catalytic reaction in the OEC.

Self-Consistency of the Theory of Elementary Stage Rates of Reversible Processes and the Equilibrium Distribution of Reaction Mixture Components

NASA Astrophysics Data System (ADS)

Tovbin, Yu. K.

2018-06-01

An analysis is presented of one of the key concepts of physical chemistry of condensed phases: the theory self-consistency in describing the rates of elementary stages of reversible processes and the equilibrium distribution of components in a reaction mixture. It posits that by equating the rates of forward and backward reactions, we must obtain the same equation for the equilibrium distribution of reaction mixture components, which follows directly from deducing the equation in equilibrium theory. Ideal reaction systems always have this property, since the theory is of a one-particle character. Problems arise in considering interparticle interactions responsible for the nonideal behavior of real systems. The Eyring and Temkin approaches to describing nonideal reaction systems are compared. Conditions for the self-consistency of the theory for mono- and bimolecular processes in different types of interparticle potentials, the degree of deviation from the equilibrium state, allowing for the internal motions of molecules in condensed phases, and the electronic polarization of the reagent environment are considered within the lattice gas model. The inapplicability of the concept of an activated complex coefficient for reaching self-consistency is demonstrated. It is also shown that one-particle approximations for considering intermolecular interactions do not provide a theory of self-consistency for condensed phases. We must at a minimum consider short-range order correlations.

Representing Operational Modes for Situation Awareness

NASA Astrophysics Data System (ADS)

Kirchhübel, Denis; Lind, Morten; Ravn, Ole

2017-01-01

Operating complex plants is an increasingly demanding task for human operators. Diagnosis of and reaction to on-line events requires the interpretation of real time data. Vast amounts of sensor data as well as operational knowledge about the state and design of the plant are necessary to deduct reasonable reactions to abnormal situations. Intelligent computational support tools can make the operator’s task easier, but they require knowledge about the overall system in form of some model. While tools used for fault-tolerant control design based on physical principles and relations are valuable tools for designing robust systems, the models become too complex when considering the interactions on a plant-wide level. The alarm systems meant to support human operators in the diagnosis of the plant-wide situation on the other hand fail regularly in situations where these interactions of systems lead to many related alarms overloading the operator with alarm floods. Functional modelling can provide a middle way to reduce the complexity of plant-wide models by abstracting from physical details to more general functions and behaviours. Based on functional models the propagation of failures through the interconnected systems can be inferred and alarm floods can potentially be reduced to their root-cause. However, the desired behaviour of a complex system changes due to operating procedures that require more than one physical and functional configuration. In this paper a consistent representation of possible configurations is deduced from the analysis of an exemplary start-up procedure by functional models. The proposed interpretation of the modelling concepts simplifies the functional modelling of distinct modes. The analysis further reveals relevant links between the quantitative sensor data and the qualitative perspective of the diagnostics tool based on functional models. This will form the basis for the ongoing development of a novel real-time diagnostics system based on the on-line adaptation of the underlying MFM model.

Mi2, an auto-antigen for dermatomyositis, is an ATP-dependent nucleosome remodeling factor.

PubMed

Wang, H B; Zhang, Y

2001-06-15

Dynamic changes in chromatin structure play an important role in transcription regulation. Recent studies have revealed two mechanisms that alter chromatin structure. One involves ATP-dependent chromatin remodeling, and the other involves acetylation of the core histone tails. We have previously purified and characterized a multi-subunit protein complex, NuRD, which possesses both nucleosome remodeling and histone deacetylase activities. Despite extensive biochemical characterization of the complex, little is known about the functions of its individual components. In this study, we focused on Mi2, a component of the NuRD complex. We found that, similar to the native NuRD complex, recombinant Mi2 is a DNA-dependent, nucleosome-stimulated ATPase. Kinetic analysis of the ATP hydrolysis reaction indicated that the differential stimulation of the Mi2 ATPase by DNA and nucleosomes were primarily due to their differential effects on the turnover number of the reaction. Furthermore, we demonstrated that recombinant Mi2 is an efficient nucleosome remodeling factor when compared to that of the native NuRD complex. Our results define the biochemical function of Mi2 and set the stage for understanding the mechanism of nucleosome remodeling in a defined reconstituted system.

Mi2, an auto-antigen for dermatomyositis, is an ATP-dependent nucleosome remodeling factor

PubMed Central

Wang, Heng-Bin; Zhang, Yi

2001-01-01

Dynamic changes in chromatin structure play an important role in transcription regulation. Recent studies have revealed two mechanisms that alter chromatin structure. One involves ATP-dependent chromatin remodeling, and the other involves acetylation of the core histone tails. We have previously purified and characterized a multi-subunit protein complex, NuRD, which possesses both nucleosome remodeling and histone deacetylase activities. Despite extensive biochemical characterization of the complex, little is known about the functions of its individual components. In this study, we focused on Mi2, a component of the NuRD complex. We found that, similar to the native NuRD complex, recombinant Mi2 is a DNA-dependent, nucleosome-stimulated ATPase. Kinetic analysis of the ATP hydrolysis reaction indicated that the differential stimulation of the Mi2 ATPase by DNA and nucleosomes were primarily due to their differential effects on the turnover number of the reaction. Furthermore, we demonstrated that recombinant Mi2 is an efficient nucleosome remodeling factor when compared to that of the native NuRD complex. Our results define the biochemical function of Mi2 and set the stage for understanding the mechanism of nucleosome remodeling in a defined reconstituted system. PMID:11410659

Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy

PubMed Central

Greco, Todd M.; Guise, Amanda J.; Cristea, Ileana M.

2016-01-01

In biological systems, proteins catalyze the fundamental reactions that underlie all cellular functions, including metabolic processes and cell survival and death pathways. These biochemical reactions are rarely accomplished alone. Rather, they involve a concerted effect from many proteins that may operate in a directed signaling pathway and/or may physically associate in a complex to achieve a specific enzymatic activity. Therefore, defining the composition and regulation of protein complexes is critical for understanding cellular functions. In this chapter, we describe an approach that uses quantitative mass spectrometry (MS) to assess the specificity and the relative stability of protein interactions. Isolation of protein complexes from mammalian cells is performed by rapid immunoaffinity purification, and followed by in-solution digestion and high-resolution mass spectrometry analysis. We employ complementary quantitative MS workflows to assess the specificity of protein interactions using label-free MS and statistical analysis, and the relative stability of the interactions using a metabolic labeling technique. For each candidate protein interaction, scores from the two workflows can be correlated to minimize nonspecific background and profile protein complex composition and relative stability. PMID:26867737

The Determination of Molecular Quantities from Measurements on Macroscopic Systems.V. Existence and Properties of 1:1 and 2:1-Electron-Donor-Acceptor Complexes of Hexamethylbenzene with Tetracyanoethylene

NASA Astrophysics Data System (ADS)

Liptay, Wolfgang; Rehm, Torsten; Wehning, Detlev; Schanne, Lothar; Baumann, Wolfram; Lang, Werner

1982-12-01

The formation of electron-donor-acceptor complexes of hexamethylbenzene (HMB) with tetracyanoethylene (TCNE) was investigated by measurements of the optical absorptions, the densities, the permittivities and the electro-optical absorptions of solutions in CCl4. The careful evaluation of data based on some previously reported models, has shown that the assumption of the formation of the 1: 1 and the 2 : 1 complex agrees with all experimental data, but that the assumption of the formation of only the 1: 1 complex is contradictory to experimental facts even if the activity effects on the equilibrium constant and of the solvent dependences of observed molar quantities are taken into account. The evaluation leads to the molar optical absorption coefficients and the molar volumes of both complexes and to their electric dipole moments in the electronic ground state and the considered excited state. According to these results the complexes are of the sandwich type HMB-TCNE and HMB-TCNE-HMB. In spite of the fact that the 2: 1 complex owns a center of symmetry, at least approximately, there is a rather large electric dipole moment in its excited state. Furthermore, values for the equilibrium constants and for the standard reaction enthalpies of both complex formation reactions are estimated from experimental data.

Cleavage reaction of HDV ribozymes in the presence of Mg2+ is accompanied by a conformational change.

PubMed

Tanaka, Yoichiro; Tagaya, Mitsuhiro; Hori, Tamaki; Sakamoto, Taiichi; Kurihara, Yasuyuki; Katahira, Masato; Uesugi, Seiichi

2002-06-01

Hepatitis delta virus (HDV) ribozymes cleave RNA in the presence of divalent metal ions. We have previously elucidated the solution conformation of a minimized trans-acting HDV ribozyme and obtained evidence by NMR study that an Mg2+ ion binds to a site close to the cleavage site. We examined two ribozyme systems: a pre-cleavage complex with a non-cleavable substrate analogue (mS8) and a post-cleavage complex with a 3' cleavage product (P7). Upon titration with MgCl2, the complex with P7 showed a profound spectral change, while that with mS8 showed broadening of the signals. Analysis of the NOESY spectra of the P7 complex at high Mg2+ concentration revealed that a G:U pair is formed within the L3 loop, and the P1 and P4 stems are stabilized with respect to those of the pre-cleavage complex. The present analysis indicates that the cleavage reaction of the HDV ribozyme produces a big conformational change. Furthermore, presence of the 5'-terminal cytidine residue prevents this conformational change and its absence stabilizes the product-ribozyme complex in the presence of Mg2+. The structure of the Mg2+-bound P7 complex is similar to the crystal structure found for a product-ribozyme complex but is different from the pre-cleavage structure.

Molybdenum compounds in organic synthesis

NASA Astrophysics Data System (ADS)

Khusnutdinov, R. I.; Oshnyakova, T. M.; Dzhemilev, U. M.

2017-02-01

The review presents the first analysis and systematic discussion of data published in the last 35-40 years on the use of molybdenum compounds and complexes in organic synthesis and catalysis of various ion coordination and radical reactions. Detailed account is given of the key trends in the use of molybdenum complexes as catalysts of alkene epoxidation and oxyketonation, oxidation of sulfur, nitrogen and phosphorus compounds, hydrosilylation of 1,3-dienes, ketones and aldehydes, hydrostannylation of acetylenes and hydrogermylation of norbornadienes. Considerable attention is paid to the description of new reactions and in situ generation of highly reactive hypohalites, ROX and HOX, induced by molybdenum complexes and the use of hypohalites in oxidative transformations. Data on the application of molybdenum complexes in well-known reactions are discussed, including Kharasch and Pauson-Khand reactions, allylic alkylation of C-nucleophiles, aminocarbonylation of halo derivatives and oligomerization of cyclic dienes, trienes, alkynes and 1,3-dienes. The last Section of the review considers 'unusual' organic reactions involving molybdenum compounds and complexes. The bibliography includes 257 references.

Copper(II) complexes with uridine, uridine 5'-monophosphate, spermidine, or spermine in aqueous solution.

PubMed

Lomozik, Lechoslaw; Jastrzab, Renata

2003-01-15

Molecular complexes of the types (Urd)H(x)(PA) and (UMP)H(x)(PA) are formed in the uridine (Urd) or uridine 5'-monophosphate (UMP) plus spermidine or spermine systems, as shown by the results of equilibrium and spectral studies. Overall stability constants of the adducts and equilibrium constants of their formation have been determined. An increase in the efficiency of the reaction between the bioligands is observed with increasing length of the polyamine. The pH range of adduct formation is found to coincide with that in which the polyamine is protonated while uridine or its monophosphate is deprotonated. The -NH(x)(+) groups from PA and the N(3) atom of the purine base as well as phosphate groups from the nucleotides have been identified as the significant centres of non-covalent interactions. Compared to cytidine, the pH range of Urd adduct formation is shifted significantly higher due to differences in the protonation constants of the endocyclic N(3) donor atoms of particular nucleosides. Overall stability constants of the Cu(II) complexes with uridine and uridine 5'-monophosphate in ternary systems with spermidine or spermine have been determined. It has been found from spectral data that in the Cu(II) ternary complexes with nucleosides and polyamines the reaction of metallation involves mainly N(3) atoms from the pyrimidine bases, as well as the amine groups of PA. This unexpected type of interaction has been evidenced in the coordination mode of the complexes forming in the Cu-UMP systems including spermidine or spermine. Results of spectral and equilibrium studies indicate that the phosphate groups taking part in metallation are at the same time involved in non-covalent interaction with the protonated polyamine.

Single-Cell RT-PCR in Microfluidic Droplets with Integrated Chemical Lysis.

PubMed

Kim, Samuel C; Clark, Iain C; Shahi, Payam; Abate, Adam R

2018-01-16

Droplet microfluidics can identify and sort cells using digital reverse transcription polymerase chain reaction (RT-PCR) signals from individual cells. However, current methods require multiple microfabricated devices for enzymatic cell lysis and PCR reagent addition, making the process complex and prone to failure. Here, we describe a new approach that integrates all components into a single device. The method enables controlled exposure of isolated single cells to a high pH buffer, which lyses cells and inactivates reaction inhibitors but can be instantly neutralized with RT-PCR buffer. Using our chemical lysis approach, we distinguish individual cells' gene expression with data quality equivalent to more complex two-step workflows. Our system accepts cells and produces droplets ready for amplification, making single-cell droplet RT-PCR faster and more reliable.

Thermal stability of bioactive enzymatic papers.

PubMed

Khan, Mohidus Samad; Li, Xu; Shen, Wei; Garnier, Gil

2010-01-01

The thermal stability of two enzymes adsorbed on paper, alkaline phosphatase (ALP) and horseradish peroxidase (HRP), was measured using a colorimetric technique quantifying the intensity of the product complex. The enzymes adsorbed on paper retained their functionality and selectivity. Adsorption on paper increased the enzyme thermal stability by 2-3 orders of magnitude compared to the same enzyme in solution. ALP and HRP enzymatic papers had half-lives of 533 h and 239 h at 23 degrees C, respectively. The thermal degradation of adsorbed enzyme was found to follow two sequential first-order reactions, indication of a reaction system. A complex pattern of enzyme was printed on paper using a thermal inkjet printer. Paper and inkjet printing are ideal material and process to manufacture low-cost-high volume bioactive surfaces.

Thermodynamically consistent model calibration in chemical kinetics

PubMed Central

2011-01-01

Background The dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. Constructing biochemical reaction systems from experimental observations often leads to parameter values that do not satisfy the necessary thermodynamic constraints. This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function. Results We introduce a thermodynamically consistent model calibration (TCMC) method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. The proposed method formulates the model calibration problem as a constrained optimization problem that takes thermodynamic constraints (and, if desired, additional non-thermodynamic constraints) into account. By calculating thermodynamically feasible values for the kinetic parameters of a well-known model of the EGF/ERK signaling cascade, we demonstrate the qualitative and quantitative significance of imposing thermodynamic constraints on these parameters and the effectiveness of our method for accomplishing this important task. MATLAB software, using the Systems Biology Toolbox 2.1, can be accessed from http://www.cis.jhu.edu/~goutsias/CSS lab/software.html. An SBML file containing the thermodynamically feasible EGF/ERK signaling cascade model can be found in the BioModels database. Conclusions TCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new models. Furthermore, TCMC can provide dimensionality reduction, better estimation performance, and lower computational complexity, and can help to alleviate the problem of data overfitting. PMID:21548948

Evaluating cis-2,6-Dimethylpiperidide (cis-DMP) as a Base Component in Lithium-Mediated Zincation Chemistry

PubMed Central

Armstrong, David R; Garden, Jennifer A; Kennedy, Alan R; Leenhouts, Sarah M; Mulvey, Robert E; O'Keefe, Philip; O'Hara, Charles T; Steven, Alan

2013-01-01

Most recent advances in metallation chemistry have centred on the bulky secondary amide 2,2,6,6-tetramethylpiperidide (TMP) within mixed metal, often ate, compositions. However, the precursor amine TMP(H) is rather expensive so a cheaper substitute would be welcome. Thus this study was aimed towards developing cheaper non-TMP based mixed-metal bases and, as cis-2,6-dimethylpiperidide (cis-DMP) was chosen as the alternative amide, developing cis-DMP zincate chemistry which has received meagre attention compared to that of its methyl-rich counterpart TMP. A new lithium diethylzincate, [(TMEDA)LiZn(cis-DMP)Et2] (TMEDA=N,N,N′,N′-tetramethylethylenediamine) has been synthesised by co-complexation of Li(cis-DMP), Et2Zn and TMEDA, and characterised by NMR (including DOSY) spectroscopy and X-ray crystallography, which revealed a dinuclear contact ion pair arrangement. By using N,N-diisopropylbenzamide as a test aromatic substrate, the deprotonative reactivity of [(TMEDA)LiZn(cis-DMP)Et2] has been probed and contrasted with that of the known but previously uninvestigated di-tert-butylzincate, [(TMEDA)LiZn(cis-DMP)tBu2]. The former was found to be the superior base (for example, producing the ortho-deuteriated product in respective yields of 78 % and 48 % following D2O quenching of zincated benzamide intermediates). An 88 % yield of 2-iodo-N,N-diisopropylbenzamide was obtained on reaction of two equivalents of the diethylzincate with the benzamide followed by iodination. Comparisons are also drawn using 1,1,1,3,3,3-hexamethyldisilazide (HMDS), diisopropylamide and TMP as the amide component in the lithium amide, Et2Zn and TMEDA system. Under certain conditions, the cis-DMP base system was found to give improved results in comparison to HMDS and diisopropylamide (DA), and comparable results to a TMP system. Two novel complexes isolated from reactions of the di-tert-butylzincate and crystallographically characterised, namely the pre-metallation complex [{(iPr)2N(Ph)C=O}LiZn(cis-DMP)tBu2] and the post-metallation complex [(TMEDA)Li(cis-DMP){2-[1-C(=O)N(iPr)2]C6H4}Zn(tBu)], shed valuable light on the structures and mechanisms involved in these alkali-metal-mediated zincation reactions. Aspects of these reactions are also modelled by DFT calculations. PMID:23955639

Improved neutron activation prediction code system development

NASA Technical Reports Server (NTRS)

Saqui, R. M.

1971-01-01

Two integrated neutron activation prediction code systems have been developed by modifying and integrating existing computer programs to perform the necessary computations to determine neutron induced activation gamma ray doses and dose rates in complex geometries. Each of the two systems is comprised of three computational modules. The first program module computes the spatial and energy distribution of the neutron flux from an input source and prepares input data for the second program which performs the reaction rate, decay chain and activation gamma source calculations. A third module then accepts input prepared by the second program to compute the cumulative gamma doses and/or dose rates at specified detector locations in complex, three-dimensional geometries.

Group 4 Metalloporphyrin diolato Complexes and Catalytic Application of Metalloporphyrins and Related Transition Metal Complexes

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

Du, Guodong

In this work, the first examples of group 4 metalloporphyrin 1,2-diolato complexes were synthesized through a number of strategies. In general, treatment of imido metalloporphyrin complexes, (TTP)M=NR, (M = Ti, Zr, Hf), with vicinal diols led to the formation of a series of diolato complexes. Alternatively, the chelating pinacolate complexes could be prepared by metathesis of (TTP)MCl 2 (M = Ti, Hf) with disodium pinacolate. These complexes were found to undergo C-C cleavage reactions to produce organic carbonyl compounds. For titanium porphyrins, treatment of a titanium(II) alkyne adduct, (TTP)Ti(η 2-PhC≡CPh), with aromatic aldehydes or aryl ketones resulted in reductive couplingmore » of the carbonyl groups to produce the corresponding diolato complexes. Aliphatic aldehydes or ketones were not reactive towards (TTP)Ti(η 2-PhC≡CPh). However, these carbonyl compounds could be incorporated into a diolato complex on reaction with a reactive precursor, (TTP)Ti[O(Ph) 2C(Ph) 2O] to provide unsymmetrical diolato complexes via cross coupling reactions. In addition, an enediolato complex (TTP)Ti(OCPhCPhO) was obtained from the reaction of (TTP)Ti(η 2-PhC≡CPh) with benzoin. Titanium porphyrin diolato complexes were found to be intermediates in the (TTP)Ti=O-catalyzed cleavage reactions of vicinal diols, in which atmospheric oxygen was the oxidant. Furthermore, (TTP)Ti=O was capable of catalyzing the oxidation of benzyl alcohol and α-hydroxy ketones to benzaldehyde and α-diketones, respectively. Other high valent metalloporphyrin complexes also can catalyze the oxidative diol cleavage and the benzyl alcohol oxidation reactions with dioxygen. A comparison of Ti(IV) and Sn(IV) porphyrin chemistry was undertaken. While chelated diolato complexes were invariably obtained for titanium porphyrins on treatment with 1,2-diols, the reaction of vicinal diols with tin porphyrins gave a number of products, including mono-, bis-alkoxo, and chelating diolato complexes, depending on the identity of diols and the stoichiometry employed. It was also found that tin porphyrin complexes promoted the oxidative cleavage of vicinal diols and the oxidation of α-ketols to α-diketones with dioxygen. In extending the chemistry of metalloporphyrins and analogous complexes, a series of chiral tetraaza macrocyclic ligands and metal complexes were designed and synthesized. Examination of iron(II) complexes showed that they were efficient catalysts for the cyclopropanation of styrene by diazo reagents. Good yields and high diastereoselectivity were obtained with modest enantioselectivity. A rationalization of the stereoselectivity was presented on the basis of structural factors in a carbene intermediate.« less

A Comparison of Analytical and Numerical Methods for Modeling Dissolution and Other Reactions in Transport Limited Systems

NASA Astrophysics Data System (ADS)

Hochstetler, D. L.; Kitanidis, P. K.

2009-12-01

Modeling the transport of reactive species is a computationally demanding problem, especially in complex subsurface media, where it is crucial to improve understanding of geochemical processes and the fate of groundwater contaminants. In most of these systems, reactions are inherently fast and actual rates of transformations are limited by the slower physical transport mechanisms. There have been efforts to reformulate multi-component reactive transport problems into systems that are simpler and less demanding to solve. These reformulations include defining conservative species and decoupling of reactive transport equations so that fewer of them must be solved, leaving mostly conservative equations for transport [e.g., De Simoni et al., 2005; De Simoni et al., 2007; Kräutle and Knabner, 2007; Molins et al., 2004]. Complex and computationally cumbersome numerical codes used to solve such problems have also caused De Simoni et al. [2005] to develop more manageable analytical solutions. Furthermore, this work evaluates reaction rates and has reaffirmed that the mixing rate,▽TuD▽u, where u is a solute concentration and D is the dispersion tensor, as defined by Kitanidis [1994], is an important and sometimes dominant factor in determining reaction rates. Thus, mixing of solutions is often reaction-limiting. We will present results from analytical and computational modeling of multi-component reactive-transport problems. The results have applications to dissolution of solid boundaries (e.g., calcite), dissolution of non-aqueous phase liquids (NAPLs) in separate phases, and mixing of saltwater and freshwater (e.g. saltwater intrusion in coastal carbonate aquifers). We quantify reaction rates, compare numerical and analytical results, and analyze under what circumstances which approach is most effective for a given problem. References: DeSimoni, M., et al. (2005), A procedure for the solution of multicomponent reactive transport problems, Water Resources Research, 41(W11410). DeSimoni, M., et al. (2007), A mixing ratios-based formulation for multicomponent reactive transport, Water Resources Research, 43(W07419). Kitanidis, P. (1994), The Concept of the Dilution Index, Water Resources Research, 30(7), 2011-2026. Kräutle, S., and P. Knabner (2007), A reduction scheme for coupled multicomponent transport-reaction problems in porous media: Generalization to problems with heterogeneous equilibrium reactions Water Resources Research, 43. Molins, S., et al. (2004), A formulation for decoupling components in reactive transport porblems, Water Resources Research, 40, 13.

Sputtering, Plasma Chemistry, and RF Sheath Effects in Low-Temperature and Fusion Plasma Modeling

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Kruger, Scott E.; McGugan, James M.; Pankin, Alexei Y.; Roark, Christine M.; Smithe, David N.; Stoltz, Peter H.

2016-09-01

A new sheath boundary condition has been implemented in VSim, a plasma modeling code which makes use of both PIC/MCC and fluid FDTD representations. It enables physics effects associated with DC and RF sheath formation - local sheath potential evolution, heat/particle fluxes, and sputtering effects on complex plasma-facing components - to be included in macroscopic-scale plasma simulations that need not resolve sheath scale lengths. We model these effects in typical ICRF antenna operation scenarios on the Alcator C-Mod fusion device, and present comparisons of our simulation results with experimental data together with detailed 3D animations of antenna operation. Complex low-temperature plasma chemistry modeling in VSim is facilitated by MUNCHKIN, a standalone python/C++/SQL code that identifies possible reaction paths for a given set of input species, solves 1D rate equations for the ensuing system's chemical evolution, and generates VSim input blocks with appropriate cross-sections/reaction rates. These features, as well as principal path analysis (to reduce the number of simulated chemical reactions while retaining accuracy) and reaction rate calculations from user-specified distribution functions, will also be demonstrated. Supported by the U.S. Department of Energy's SBIR program, Award DE-SC0009501.

Electron and Ion Reactions in Molecular Solids: from astrochemistry to radiobiology

NASA Astrophysics Data System (ADS)

Huels, Michael A.

2001-05-01

Wherever ionizing radiation interacts with matter, it initiates reaction cascades involving ions, radicals, and ballistic secondary electrons; these reactions occur on fs time-scales, and may lead to substantial physical and chemical modifications of a medium. Here I present measurements of 0-80 eV electron and ion reactions in condensed films ranging from simple to complex, and astrophysical to biological in nature. Targets contain either: small molecules, hydrocarbons of increasing complexity (incl. bases, sugars, single/double stranded DNA), molecules on rare gas matrices, or mixed cryogenic films resembling astrophysical or planetary surface ices containing O2, H2O, methane, and aromatic hydrocarbons. The basic electron or ion reaction mechanisms and pathways are found to be fundamentally universal, but are modulated by the physical and chemical nature of the medium; depending on the latter, a reaction cascade may lead to different end-points, e.g. a decrease in molecular complexity via molecular fragmentations, or increases in complexity via secondary ion collision induced synthesis of larger molecules in hydrocarbon rich surface ices.

Predictive Modeling in Actinide Chemistry and Catalysis

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

Yang, Ping

2016-05-16

These are slides from a presentation on predictive modeling in actinide chemistry and catalysis. The following topics are covered in these slides: Structures, bonding, and reactivity (bonding can be quantified by optical probes and theory, and electronic structures and reaction mechanisms of actinide complexes); Magnetic resonance properties (transition metal catalysts with multi-nuclear centers, and NMR/EPR parameters); Moving to more complex systems (surface chemistry of nanomaterials, and interactions of ligands with nanoparticles); Path forward and conclusions.

Integrated Analysis of Genetic and Proteomic Data Identifies Biomarkers Associated with Adverse Events Following Smallpox Vaccination

EPA Science Inventory

Complex clinical outcomes, such as adverse reaction to vaccination, arise from the concerted interactions among the myriad components of a biological system. Therefore, comprehensive etiological models can be developed only through the integrated study of multiple types of experi...

Intramolecular Aza-Diels-Alder Reactions of ortho-Quinone Methide Imines: Rapid, Catalytic, and Enantioselective Assembly of Benzannulated Quinolizidines.

PubMed

Kretzschmar, Martin; Hofmann, Fabian; Moock, Daniel; Schneider, Christoph

2018-04-16

Aza-Diels-Alder reactions (ADARs) are powerful processes that furnish N-heterocycles in a straightforward fashion. Intramolecular variants offer the additional possibility of generating bi- and polycyclic systems with high stereoselectivity. We report herein a novel Brønsted acid catalyzed process in which ortho-quinone methide imines tethered to the dienophile via the N substituent react in an intramolecular ADAR to form complex quinolizidines and oxazinoquinolines in a one-step process. The reactions proceed under very mild conditions, with very good yields and good to very good diastereo- and enantioselectivities. Furthermore, the process was extended to a domino reaction that efficiently combines substrate synthesis, ortho-quinone methide imine formation, and ADAR. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Periodic changes in the oxidation states of the center ion in the cobalt-histidine complex induced by the BrO3- - SO32- pH-oscillator

NASA Astrophysics Data System (ADS)

Kurin-Csörgei, Krisztina; Poros, Eszter; Csepiova, Julianna; Orbán, Miklós

2018-05-01

The coupling of acid-base type pH-dependent equilibria to pH-oscillators expanded significantly the number and type of species which can participate in oscillatory chemical processes. Here, we report a new version of oscillatory phenomena that can appear in coupled oscillators. Oscillations in the oxidation states of the center ion bound in a chelate complex were generated in a combined system, when the participants of the oscillator as dynamical unit and the components of the complex formation interacted with each other through redox reaction. It was demonstrated, when the BrO3- - SO32- pH-oscillator and the Co2+ - histidine complex were mixed in a continuous stirred tank reactor, periodic changes in the pH were accompanied with periodic transitions in the oxidation number of the cobalt ion between +2 and +3. The oscillatory build up and removal of the Co(III)-complex were followed by recording the light absorption at the wavelength characteristic for this species with simultaneous monitoring the pH-oscillations. The dual role of the SO32- ion in the explanation of this observation was pointed out. Its partial and consecutive total oxidations by BrO3- give rise to and maintain sustained pH-oscillations in the combined system and its presence induces the rapid conversion of the Co2+ to a highly inert Co(III)-histidine chelate when the system jumps to and remains in the high pH-state. The oscillatory cycle is completed when the Co(III)-complex is washed out from the reactor and the reagents are replenished by the flow during the time the system spends in the acidic range of pH. The idea, to couple a core oscillator to an equilibrium through a redox reaction that takes place between the constituents of the oscillator and the target species of the linked subsystem, may be generally used to bring about forced oscillations in many other combined chemical systems.

Tetramer model of leukoemeraldine-emeraldine electrochemistry in the presence of trihalogenoacetic acids. DFT approach.

PubMed

Barbosa, Nuno Almeida; Grzeszczuk, Maria; Wieczorek, Robert

2015-01-15

First results of the application of the DFT computational approach to the reversible electrochemistry of polyaniline are presented. A tetrameric chain was used as the simplest model of the polyaniline polymer species. The system under theoretical investigation involved six tetramer species, two electrons, and two protons, taking part in 14 elementary reactions. Moreover, the tetramer species were interacting with two trihalogenoacetic acid molecules. Trifluoroacetic, trichloroacetic, and tribromoacetic acids were found to impact the redox transformation of polyaniline as shown by cyclic voltammetry. The theoretical approach was considered as a powerful tool for investigating the main factors of importance for the experimental behavior. The DFT method provided molecular structures, interaction energies, and equilibrium energies of all of the tetramer-acid complexes. Differences between the energies of the isolated tetramer species and their complexes with acids are discussed in terms of the elementary reactions, that is, ionization potentials and electron affinities, equilibrium constants, electrode potentials, and reorganization energies. The DFT results indicate a high impact of the acid on the reorganization energy of a particular elementary electron-transfer reaction. The ECEC oxidation path was predicted by the calculations. The model of the reacting system must be extended to octamer species and/or dimeric oligomer species to better approximate the real polymer situation.

Photocatalytic CO2 reduction with high turnover frequency and selectivity of formic acid formation using Ru(II) multinuclear complexes.

PubMed

Tamaki, Yusuke; Morimoto, Tatsuki; Koike, Kazuhide; Ishitani, Osamu

2012-09-25

Previously undescribed supramolecules constructed with various ratios of two kinds of Ru(II) complexes-a photosensitizer and a catalyst-were synthesized. These complexes can photocatalyze the reduction of CO(2) to formic acid with high selectivity and durability using a wide range of wavelengths of visible light and NADH model compounds as electron donors in a mixed solution of dimethylformamide-triethanolamine. Using a higher ratio of the photosensitizer unit to the catalyst unit led to a higher yield of formic acid. In particular, of the reported photocatalysts, a trinuclear complex with two photosensitizer units and one catalyst unit photocatalyzed CO(2) reduction (Φ(HCOOH) = 0.061, TON(HCOOH) = 671) with the fastest reaction rate (TOF(HCOOH) = 11.6 min(-1)). On the other hand, photocatalyses of a mixed system containing two kinds of model mononuclear Ru(II) complexes, and supramolecules with a higher ratio of the catalyst unit were much less efficient, and black oligomers and polymers were produced from the Ru complexes during photocatalytic reactions, which reduced the yield of formic acid. The photocatalytic formation of formic acid using the supramolecules described herein proceeds via two sequential processes: the photochemical reduction of the photosensitizer unit by NADH model compounds and intramolecular electron transfer to the catalyst unit.

The compositional and evolutionary logic of metabolism

NASA Astrophysics Data System (ADS)

Braakman, Rogier; Smith, Eric

2013-02-01

Metabolism is built on a foundation of organic chemistry, and employs structures and interactions at many scales. Despite these sources of complexity, metabolism also displays striking and robust regularities in the forms of modularity and hierarchy, which may be described compactly in terms of relatively few principles of composition. These regularities render metabolic architecture comprehensible as a system, and also suggests the order in which layers of that system came into existence. In addition metabolism also serves as a foundational layer in other hierarchies, up to at least the levels of cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, motivates us to interpret metabolism as a source of causation or constraint on many forms of organization in the biosphere. Many of the forms of modularity and hierarchy exhibited by metabolism are readily interpreted as stages in the emergence of catalytic control by living systems over organic chemistry, sometimes recapitulating or incorporating geochemical mechanisms. We identify as modules, either subsets of chemicals and reactions, or subsets of functions, that are re-used in many contexts with a conserved internal structure. At the small molecule substrate level, module boundaries are often associated with the most complex reaction mechanisms, catalyzed by highly conserved enzymes. Cofactors form a biosynthetically and functionally distinctive control layer over the small-molecule substrate. The most complex members among the cofactors are often associated with the reactions at module boundaries in the substrate networks, while simpler cofactors participate in widely generalized reactions. The highly tuned chemical structures of cofactors (sometimes exploiting distinctive properties of the elements of the periodic table) thereby act as ‘keys’ that incorporate classes of organic reactions within biochemistry. Module boundaries provide the interfaces where change is concentrated, when we catalogue extant diversity of metabolic phenotypes. The same modules that organize the compositional diversity of metabolism are argued, with many explicit examples, to have governed long-term evolution. Early evolution of core metabolism, and especially of carbon-fixation, appears to have required very few innovations, and to have used few rules of composition of conserved modules, to produce adaptations to simple chemical or energetic differences of environment without diverse solutions and without historical contingency. We demonstrate these features of metabolism at each of several levels of hierarchy, beginning with the small-molecule metabolic substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.

The hexadehydro-Diels-Alder reaction.

PubMed

Hoye, Thomas R; Baire, Beeraiah; Niu, Dawen; Willoughby, Patrick H; Woods, Brian P

2012-10-11

Arynes (aromatic systems containing, formally, a carbon-carbon triple bond) are among the most versatile of all reactive intermediates in organic chemistry. They can be 'trapped' to give products that are used as pharmaceuticals, agrochemicals, dyes, polymers and other fine chemicals. Here we explore a strategy that unites the de novo generation of benzynes-through a hexadehydro-Diels-Alder reaction-with their in situ elaboration into structurally complex benzenoid products. In the hexadehydro-Diels-Alder reaction, a 1,3-diyne is engaged in a [4+2] cycloisomerization with a 'diynophile' to produce the highly reactive benzyne intermediate. The reaction conditions for this simple, thermal transformation are notable for being free of metals and reagents. The subsequent and highly efficient trapping reactions increase the power of the overall process. Finally, we provide examples of how this de novo benzyne generation approach allows new modes of intrinsic reactivity to be revealed.

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

Alvarez-Ramirez, J.; Aguilar, R.; Lopez-Isunza, F.

FCC processes involve complex interactive dynamics which are difficult to operate and control as well as poorly known reaction kinetics. This work concerns the synthesis of temperature controllers for FCC units. The problem is addressed first for the case where perfect knowledge of the reaction kinetics is assumed, leading to an input-output linearizing state feedback. However, in most industrial FCC units, perfect knowledge of reaction kinetics and composition measurements is not available. To address the problem of robustness against uncertainties in the reaction kinetics, an adaptive model-based nonlinear controller with simplified reaction models is presented. The adaptive strategy makes usemore » of estimates of uncertainties derived from calorimetric (energy) balances. The resulting controller is similar in form to standard input-output linearizing controllers and can be tuned analogously. Alternatively, the controller can be tuned using a single gain parameter and is computationally efficient. The performance of the closed-loop system and the controller design procedure are shown with simulations.« less

Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis.

PubMed

Wang, Harris H; Huang, Po-Yi; Xu, George; Haas, Wilhelm; Marblestone, Adam; Li, Jun; Gygi, Steven P; Forster, Anthony C; Jewett, Michael C; Church, George M

2012-02-17

Protein pathways are dynamic and highly coordinated spatially and temporally, capable of performing a diverse range of complex chemistries and enzymatic reactions with precision and at high efficiency. Biotechnology aims to harvest these natural systems to construct more advanced in vitro reactions, capable of new chemistries and operating at high yield. Here, we present an efficient Multiplex Automated Genome Engineering (MAGE) strategy to simultaneously modify and co-purify large protein complexes and pathways from the model organism Escherichia coli to reconstitute functional synthetic proteomes in vitro. By application of over 110 MAGE cycles, we successfully inserted hexa-histidine sequences into 38 essential genes in vivo that encode for the entire translation machinery. Streamlined co-purification and reconstitution of the translation protein complex enabled protein synthesis in vitro. Our approach can be applied to a growing area of applications in in vitro one-pot multienzyme catalysis (MEC) to manipulate or enhance in vitro pathways such as natural product or carbohydrate biosynthesis.

Simulating complex atomistic processes: On-the-fly kinetic Monte Carlo scheme with selective active volumes

NASA Astrophysics Data System (ADS)

Xu, Haixuan; Osetsky, Yury N.; Stoller, Roger E.

2011-10-01

An accelerated atomistic kinetic Monte Carlo (KMC) approach for evolving complex atomistic structures has been developed. The method incorporates on-the-fly calculations of transition states (TSs) with a scheme for defining active volumes (AVs) in an off-lattice (relaxed) system. In contrast to conventional KMC models that require all reactions to be predetermined, this approach is self-evolving and any physically relevant motion or reaction may occur. Application of this self-evolving atomistic kinetic Monte Carlo (SEAK-MC) approach is illustrated by predicting the evolution of a complex defect configuration obtained in a molecular dynamics (MD) simulation of a displacement cascade in Fe. Over much longer times, it was shown that interstitial clusters interacting with other defects may change their structure, e.g., from glissile to sessile configuration. The direct comparison with MD modeling confirms the atomistic fidelity of the approach, while the longer time simulation demonstrates the unique capability of the model.

Redox and complexation chemistry of the CrVI/CrV-D-glucaric acid system.

PubMed

Mangiameli, María Florencia; González, Juan Carlos; Bellú, Sebastián; Bertoni, Fernando; Sala, Luis F

2014-06-28

When an excess of uronic acid over Cr(VI) is used, the oxidation of D-glucaric acid (Glucar) by Cr(VI) yields D-arabinaric acid, CO2 and Cr(III)-Glucar complex as final redox products. The redox reaction involves the formation of intermediate Cr(IV) and Cr(V) species. The reaction rate increases with [H(+)] and [substrate]. The experimental results indicated that Cr(IV) and Cr(V) are very reactive intermediates since their disappearance rates are much faster than Cr(VI). Cr(IV) and Cr(V) intermediates are involved in fast steps and do not accumulate in the redox reaction of the mixture Cr(VI)-Glucar. Kinetic studies show that the redox reaction between Glucar and Cr(VI) proceeds through a mechanism combining one- and two-electron pathways: Cr(VI) → Cr(IV) → Cr(II) and Cr(VI) → Cr(IV) → Cr(III). After the redox reaction, results show a slow hydrolysis of the Cr(III)-Glucar complex into [Cr(OH2)6](3+). The proposed mechanism is supported by the observation of free radicals, CrO2(2+) (superoxo-Cr(III) ion) and oxo-Cr(V)-Glucar species as reaction intermediates. The continuous-wave electron paramagnetic resonance, CW-EPR, spectra show that five-coordinate oxo-Cr(V) bischelates are formed at pH ≤ 4 with the aldaric acid bound to oxo-Cr(V) through the carboxylate and the α-OH group. A different oxo-Cr(V) species with Glucar was detected at pH 6.0. The high g(iso) value for the last species suggests a mixed coordination species, a five-coordinated oxo-Cr(V) bischelate with one molecule of Glucar acting as a bi-dentate ligand, using the 2-hydroxycarboxylate group, and a second molecule of Glucar with any vic-diolate sites. At pH 7.5 only a very weak EPR signal was observed, which may point to instability of these complexes. This behaviour contrasts with oxo-Cr(V)-uronic species, and must thus be related to the Glucar acyclic structure. In vitro, our studies on the chemistry of oxo-Cr(V)-Glucar complexes can provide information on the nature of the species that are likely to be stabilized in vivo.

Visible-Light-Driven Oxidation of Organic Substrates with Dioxygen Mediated by a [Ru(bpy)3 ](2+) /Laccase System.

PubMed

Schneider, Ludovic; Mekmouche, Yasmina; Rousselot-Pailley, Pierre; Simaan, A Jalila; Robert, Viviane; Réglier, Marius; Aukauloo, Ally; Tron, Thierry

2015-09-21

Oxidation reactions are highly important chemical transformations that still require harsh reaction conditions and stoichiometric amounts of chemical oxidants that are often toxic. To circumvent these issues, olefins oxidation is achieved in mild conditions upon irradiation of an aqueous solution of the complex [Ru(bpy)3 ](2+) and the enzyme laccase. Epoxide formation is coupled to the light-driven reduction of O2 by [Ru(bpy)3 ](2+) /laccase system. The reactivity can be explained by dioxygen acting both as an oxidative agent and as renewable electron acceptor, avoiding the use of a sacrificial electron acceptor. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems.

PubMed

Smith, Robert W; van Rosmalen, Rik P; Martins Dos Santos, Vitor A P; Fleck, Christian

2018-06-19

Models of metabolism are often used in biotechnology and pharmaceutical research to identify drug targets or increase the direct production of valuable compounds. Due to the complexity of large metabolic systems, a number of conclusions have been drawn using mathematical methods with simplifying assumptions. For example, constraint-based models describe changes of internal concentrations that occur much quicker than alterations in cell physiology. Thus, metabolite concentrations and reaction fluxes are fixed to constant values. This greatly reduces the mathematical complexity, while providing a reasonably good description of the system in steady state. However, without a large number of constraints, many different flux sets can describe the optimal model and we obtain no information on how metabolite levels dynamically change. Thus, to accurately determine what is taking place within the cell, finer quality data and more detailed models need to be constructed. In this paper we present a computational framework, DMPy, that uses a network scheme as input to automatically search for kinetic rates and produce a mathematical model that describes temporal changes of metabolite fluxes. The parameter search utilises several online databases to find measured reaction parameters. From this, we take advantage of previous modelling efforts, such as Parameter Balancing, to produce an initial mathematical model of a metabolic pathway. We analyse the effect of parameter uncertainty on model dynamics and test how recent flux-based model reduction techniques alter system properties. To our knowledge this is the first time such analysis has been performed on large models of metabolism. Our results highlight that good estimates of at least 80% of the reaction rates are required to accurately model metabolic systems. Furthermore, reducing the size of the model by grouping reactions together based on fluxes alters the resulting system dynamics. The presented pipeline automates the modelling process for large metabolic networks. From this, users can simulate their pathway of interest and obtain a better understanding of how altering conditions influences cellular dynamics. By testing the effects of different parameterisations we are also able to provide suggestions to help construct more accurate models of complete metabolic systems in the future.

A complex reaction time study (Sternberg) in space flight

NASA Technical Reports Server (NTRS)

Thornton, W.; Uri, John; Moore, Tom

1993-01-01

Simple and complex (Sternberg) reaction time studies were flown on three and seven day Shuttle flights in 1985. Three subjects did selftesting with an onboard handheld calculator without difficulty. There was little change in simple reaction time. One subject demonstrated a decrease in the processing rate during space motion sickness while a second exhibited an increase in complex reaction time without a change in processing rate during a period of high work load. The population was too small to demonstrate significant changes. This study demonstrates the ease and practicality of such measurements and indicates the potential value of such studies in space.

Noble reaction features of bromoborane in oxidative addition of B-Br σ-bond to [M(PMe3)2] (M=Pt or Pd): theoretical study.

PubMed

Zeng, Guixiang; Sakaki, Shigeyoshi

2011-06-06

Through detailed calculations by density functional theory and second-order Møller-Plesset perturbation theory (MP2) to fourth-order Møller-Plesset perturbation theory including single, double, and quadruple excitations [MP4(SDQ)] methods, we investigated the oxidative addition of the B-Br bond of dibromo(trimethylsiloxy)borane [Br(2)B(OSiMe(3))] to Pt(0) and Pd(0) complexes [M(PMe(3))(2)] (M = Pt or Pd) directly yielding a trans bromoboryl complex trans-[MBr{BBr(OSiMe(3))}(PMe(3))(2)]. Two reaction pathways are found for this reaction: One is a nucleophilic attack pathway which directly leads to the trans product, and the other is a stepwise reaction pathway which occurs through successive cis oxidative addition of the B-Br bond to [M(PMe(3))(2)] and thermal cis-trans isomerization. In the Pt system, the former course occurs with a much smaller energy barrier (E(a) = 5.8 kcal/mol) than the latter one (E(a) = 20.7 kcal/mol), where the DFT-calculated E(a) value is presented hereafter. In the Pd system, only the latter course is found in which the rate-determining steps is the cis-trans isomerization with the E(a) of 15.1 kcal/mol. Interestingly, the thermal cis-trans isomerization occurs on the singlet potential energy surface against our expectation. This unexpected result is understood in terms of the strong donation ability of the boryl group. Detailed analyses of electronic processes in all these reaction steps as well as remarkable characteristic features of [Br(2)B(OSiMe(3))] are also provided. © 2011 American Chemical Society

Chemical and electrochemical behavior of the Cr(3)/Cr(2) half cell in the NASA Redox Energy Storage System

NASA Technical Reports Server (NTRS)

Johnson, D. A.; Reid, M. A.

1982-01-01

The Cr(III) complexes in the NASA Redox Energy Storage System were isolated and identified as Cr(H2O)6(+3) and Cr(H2O)5Cl(+2) by ion exchange chromatography and visible spectrophotometry. The cell reactions during charge-discharge cycles were followed by means of visible spectrophotometry. The spectral bands were resolved into component peaks and concentrations calculated using Beer's Law. During the charge mode Cr(H2O)5Cl(+2) is reduced to Cr(H2O)5Cl(+) and during the discharge mode Cr(H2O)5Cl(+) is oxidized back to Cr(H2O)5Cl(+2). Both electrode reactions occur via a chloride-bridge inner-sphere reaction pathway. Hysteresis effects can be explained by the slow attainment of equilibrium between Cr(H2O)6(+3) and Cr(H2O)5Cl(+2).

Carotene Degradation and Isomerization during Thermal Processing: A Review on the Kinetic Aspects.

PubMed

Colle, Ines J P; Lemmens, Lien; Knockaert, Griet; Van Loey, Ann; Hendrickx, Marc

2016-08-17

Kinetic models are important tools for process design and optimization to balance desired and undesired reactions taking place in complex food systems during food processing and preservation. This review covers the state of the art on kinetic models available to describe heat-induced conversion of carotenoids, in particular lycopene and β-carotene. First, relevant properties of these carotenoids are discussed. Second, some general aspects of kinetic modeling are introduced, including both empirical single-response modeling and mechanism-based multi-response modeling. The merits of multi-response modeling to simultaneously describe carotene degradation and isomerization are demonstrated. The future challenge in this research field lies in the extension of the current multi-response models to better approach the real reaction pathway and in the integration of kinetic models with mass transfer models in case of reaction in multi-phase food systems.

Electronic and Vibrational Coherence in Charge-Transfer Reactions

NASA Astrophysics Data System (ADS)

Scherer, Norbert

1996-03-01

The ultrafast dynamics associated with optically-induced intervalence charge-transfer reactions in solution and protein environments are reported. These studies include the Fe^(II)-Fe^(III) MMCT complex Prussian blue and the mixed valence dimer (CN)_5Ru^(II)CNRuRu^(III)(NH_3)_5. The protein systems include blue copper proteins and the bacterial photosynthetic reaction center. The experimental approaches include photon echo, wavelength-resolved pump-probe and anisotropy measurements performed with 12-16fs duration optical pulses. Complicated time-domain waveforms reflect the several different p[rocesses and time scales for relaxation of coherences (both electronic and vibrational) and populations within these systems. The photon echo and anisotropy results probe electronic coherence and dephasing prior to back electron transfer. Wavelength-resolved pump-probe results reveal vibrational modes coupled to the CT-coordinate as well as formation of new product states or vibrational cooling in the ground state following back electron transfer.

ON THE REACTION OF COMPONENETS IN MeNO$sub 3$-UO$sub 2$(NO$sub 3$)$sub 2$- H$sub 2$O TYPE SYSTEMS (in Russian)

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

Yakimov, M.A.; Nosova, N.F.; Degtyarev, A.Ya.

1963-01-01

Solubility in ternary systems TlNO/sub 3/--UO/sub 2/(NO/sub 3/)/sub 2/-- H/sub 2/ O and CsNO/sub 3/--UO/sub 2/(NO/sub 3/)/sub 2/--H/sub 2/O at 0 to 25 c- C was studi ed by the isothermal method. The first system did not form solid phase compounds; the second system formed two compounds Cs/sub 2/UO/ sub 2/(NO/sub 3/)/sub 4/ and CsUO/sub 2/(NO/sub 3/)/sub 3/ at 25 c- and of water vapor pressure over the systems at 25 c- showed that water activity in the ternary systems at certain concentrations does not exceed the water activity in binary uranyl nitratewater system (at identical uranyl nitrate concentrations) confirmingmore » the observed complex formation in the solution. The mechanism of complex formation was analyzed and expanded for alkali metal - metal salt-complexing agent water systems. (R.V.J.)« less

Development of an on-site rapid real-time polymerase chain reaction system and the characterization of suitable DNA polymerases for TaqMan probe technology.

PubMed

Furutani, Shunsuke; Naruishi, Nahoko; Hagihara, Yoshihisa; Nagai, Hidenori

2016-08-01

On-site quantitative analyses of microorganisms (including viruses) by the polymerase chain reaction (PCR) system are significantly influencing medical and biological research. We have developed a remarkably rapid and portable real-time PCR system that is based on microfluidic approaches. Real-time PCR using TaqMan probes consists of a complex reaction. Therefore, in a rapid real-time PCR, the optimum DNA polymerase must be estimated by using actual real-time PCR conditions. In this study, we compared the performance of three DNA polymerases in actual PCR conditions using our rapid real-time PCR system. Although KAPA2G Fast HS DNA Polymerase has the highest enzymatic activity among them, SpeedSTAR HS DNA Polymerase exhibited better performance to rapidly increase the fluorescence signal in an actual real-time PCR using TaqMan probes. Furthermore, we achieved rapid detection of Escherichia coli in 7 min by using SpeedSTAR HS DNA Polymerase with the same sensitivity as that of a conventional thermal cycler.

A surface complexation and ion exchange model of Pb and Cd competitive sorption on natural soils

NASA Astrophysics Data System (ADS)

Serrano, Susana; O'Day, Peggy A.; Vlassopoulos, Dimitri; García-González, Maria Teresa; Garrido, Fernando

2009-02-01

The bioavailability and fate of heavy metals in the environment are often controlled by sorption reactions on the reactive surfaces of soil minerals. We have developed a non-electrostatic equilibrium model (NEM) with both surface complexation and ion exchange reactions to describe the sorption of Pb and Cd in single- and binary-metal systems over a range of pH and metal concentration. Mineralogical and exchange properties of three different acidic soils were used to constrain surface reactions in the model and to estimate surface densities for sorption sites, rather than treating them as adjustable parameters. Soil heterogeneity was modeled with >FeOH and >SOH functional groups, representing Fe- and Al-oxyhydroxide minerals and phyllosilicate clay mineral edge sites, and two ion exchange sites (X - and Y -), representing clay mineral exchange. An optimization process was carried out using the entire experimental sorption data set to determine the binding constants for Pb and Cd surface complexation and ion exchange reactions. Modeling results showed that the adsorption of Pb and Cd was distributed between ion exchange sites at low pH values and specific adsorption sites at higher pH values, mainly associated with >FeOH sites. Modeling results confirmed the greater tendency of Cd to be retained on exchange sites compared to Pb, which had a higher affinity than Cd for specific adsorption on >FeOH sites. Lead retention on >FeOH occurred at lower pH than for Cd, suggesting that Pb sorbs to surface hydroxyl groups at pH values at which Cd interacts only with exchange sites. The results from the binary system (both Pb and Cd present) showed that Cd retained in >FeOH sites decreased significantly in the presence of Pb, while the occupancy of Pb in these sites did not change in the presence of Cd. As a consequence of this competition, Cd was shifted to ion exchange sites, where it competes with Pb and possibly Ca (from the background electrolyte). Sorption on >SOH functional groups increased with increasing pH but was small compared to >FeOH sites, with little difference between single- and binary-metal systems. Model reactions and conditional sorption constants for Pb and Cd sorption were tested on a fourth soil that was not used for model optimization. The same reactions and constants were used successfully without adjustment by estimating surface site concentrations from soil mineralogy. The model formulation developed in this study is applicable to acidic mineral soils with low organic matter content. Extension of the model to soils of different composition may require selection of surface reactions that account for differences in clay and oxide mineral composition and organic matter content.

A graphical method to evaluate predominant geochemical processes occurring in groundwater systems for radiocarbon dating

USGS Publications Warehouse

Han, Liang-Feng; Plummer, Niel; Aggarwal, Pradeep

2012-01-01

A graphical method is described for identifying geochemical reactions needed in the interpretation of radiocarbon age in groundwater systems. Graphs are constructed by plotting the measured 14C, δ13C, and concentration of dissolved inorganic carbon and are interpreted according to specific criteria to recognize water samples that are consistent with a wide range of processes, including geochemical reactions, carbon isotopic exchange, 14C decay, and mixing of waters. The graphs are used to provide a qualitative estimate of radiocarbon age, to deduce the hydrochemical complexity of a groundwater system, and to compare samples from different groundwater systems. Graphs of chemical and isotopic data from a series of previously-published groundwater studies are used to demonstrate the utility of the approach. Ultimately, the information derived from the graphs is used to improve geochemical models for adjustment of radiocarbon ages in groundwater systems.

Past and future detector arrays for complete event reconstruction in heavy-ion reactions

NASA Astrophysics Data System (ADS)

Cardella, G.; Acosta, L.; Auditore, L.; Boiano, C.; Castoldi, A.; D'Andrea, M.; De Filippo, E.; Dell'Aquila, D.; De Luca, S.; Fichera, F.; Giudice, N.; Gnoffo, B.; Grimaldi, A.; Guazzoni, C.; Lanzalone, G.; Librizzi, F.; Lombardo, I.; Maiolino, C.; Maffesanti, S.; Martorana, N. S.; Norella, S.; Pagano, A.; Pagano, E. V.; Papa, M.; Parsani, T.; Passaro, G.; Pirrone, S.; Politi, G.; Previdi, F.; Quattrocchi, L.; Rizzo, F.; Russotto, P.; Saccà, G.; Salemi, G.; Sciliberto, D.; Trifirò, A.; Trimarchi, M.; Vigilante, M.

2017-11-01

Complex and more and more complete detector arrays have been developed in the last two decades, or are in advanced design stage, in different laboratories. Such arrays are necessary to fully characterize nuclear reactions induced by stable and exotic beams. The need for contemporary detection of charged particles, and/or γ -rays, and/or neutrons, has been stressed in many fields of nuclear structure and reaction dynamics, with particular attention to the improvement of both high angular and energy resolution. Some examples of detection systems adapted to various energy ranges is discussed. Emphasis is given to the possible update of relatively old 4π detectors with new electronics and new detection methods.

FTIR Study of Comustion Species in Several Regions of a Candle Flame

NASA Astrophysics Data System (ADS)

White, Allen R.

2013-06-01

The complex chemical structure of the fuel in a candle flame, parafin, is broken down into smaller hydrocarbons in the dark region just above the candle wick during combustion. This creates fuel-rich, fuel-lean, hydrocarbon reaction, and combustion product regions in the flame during combustion that are spectroscopically rich, particularly in the infrared. IR emissions were measured for each reaction region via collection optics focused into an FTIR and used to identify IR active species present in that region and, when possible, temperature of the sampling region. The results of the measurements are useful for combustion reaction modeling as well as for future validation of mass spectroscopy sampling systems.

Micro/nanofabricated environments for synthetic biology.

PubMed

Collier, C Patrick; Simpson, Michael L

2011-08-01

A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints. Copyright © 2011 Elsevier Ltd. All rights reserved.

Oxidation kinetics and soot formation

NASA Technical Reports Server (NTRS)

Glassman, I.; Brezinsky, K.

1983-01-01

The research objective is to clarify the role of aromaticity in the soot nucleation process by determining the relative importance of phenyl radical/molecular oxygen and benzene/atomic oxygen reactions in the complex combustion of aromatic compounds. Three sets of chemical flow reactor experiments have been designed to determine the relative importance of the phenyl radical/molecular oxygen and benzene/atomic oxygen reactions. The essential elements of these experiments are 1) the use of cresols and anisole formed during the high temperature oxidation of toluene as chemical reaction indicators; 2) the in situ photolysis of molecular oxygen to provide an oxygen atom perturbation in the reacting aromatic system; and 3) the high temperature pyrolysis of phenol, the cresols and possibly anisole.

Experimental and theoretical investigation of homogeneous gaseous reaction of CO2(g) + nH2O(g) + nNH3(g) → products (n = 1, 2).

PubMed

Li, Zhuangjie; Zhang, Baoquan

2012-09-13

Decreasing CO2 emissions into the atmosphere is key for reducing global warming. To facilitate the CO2 emission reduction efforts, our laboratory conducted experimental and theoretical investigations of the homogeneous gaseous reaction of CO2(g) + nH2O(g) + nNH3(g) → (NH4)HCO3(s)/(NH4)2CO3(s) (n = 1 and 2) using Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy and ab initio molecular orbital theory. Our FTIR-ATR experimental results indicate that (NH4)2CO3(s) and (NH4)HCO3(s) are formed as aerosol particulate matter when carbon dioxide reacts with ammonia and water in the gaseous phase at room temperature. Ab initio study of this chemical system suggested that the reaction may proceed through formation of NH3·H2O(g), NH3·CO2(g), and CO2·H2O(g) complexes. Subsequent complexes, NH3·H2O·CO2 and (NH3)2·H2O·CO2, can be formed by adding gaseous reactants to the NH3·H2O(g), NH3·CO2(g), and CO2·H2O(g) complexes, respectively. The NH3·H2O·CO2 and (NH3)2·H2O·CO2 complexes can then be rearranged to produce (NH4)HCO3 and (NH4)2CO3 as final products via a transition state, and the NH3 molecule acts as a medium accepting and donating hydrogen atoms in the rearrangement process. Our computational results also reveal that the presence of an additional water molecule can reduce the activation energy of the rearrangement process. The high activation energy predicted in the present work suggests that the reaction is kinetically not favored, and our experimental observation of (NH4)HCO3(s) and (NH4)2CO3(s) may be attributed to the high concentrations of reactants increasing the reaction rate of the title reactions in the reactor.

Mechanistically Driven Development of Iridium Catalysts for Asymmetric Allylic Substitution

PubMed Central

Hartwig, John F.; Stanley, Levi M.

2010-01-01

Conspectus Enantioselective allylic substitution reactions comprise some of the most versatile methods for preparing enantiomerically enriched materials. These reactions form products that contain multiple functionalities by creating carbon–nitrogen, carbon–oxygen, carbon–carbon, and carbon–sulfur bonds. For many years, the development of catalysts for allylic substitution focused on palladium complexes. However, studies of complexes of other metals have revealed selectivities that often complement those of palladium systems. Most striking is the observation that reactions with unsymmetrical allylic electrophiles that typically occur with palladium catalysts at the less hindered site of an allylic electrophile occur at the more hindered site with catalysts based on other metals. In this Account, we describe an iridium precursor and a phosphoramidite ligand that catalyze reactions with a particularly broad scope of nucleophiles. The active form of this iridium catalyst is not generated by the simple binding of the phosphoramidite ligand to the metal precursor. Instead, the initial phosphoramidite and iridium precursor react in the presence of base to form a metallacyclic species that is the active catalyst. This species is generated either in situ or separately in isolated form by reactions with added base. The identification of the structure of the active catalyst led to the development of simplified catalysts as well as the most active form of the catalyst now available, which is stabilized by a loosely bound ethylene. Most recently, this structure was used to prepare intermediates containing allyl ligands, the structures of which provide a model for the enantioselectivities discussed here. Initial studies from our laboratory on the scope of iridium-catalyzed allylic substitution showed that reactions of primary and secondary amines, including alkylamines, benzylamines, and allylamines, and reactions of phenoxides and alkoxides occurred in high yields, with high branched-to-linear ratios and high enantioselectivities. Parallel mechanistic studies had revealed the metallacyclic structure of the active catalyst, and subsequent experiments with the purposefully formed metallacycle increased the reaction scope dramatically. Aromatic amines, azoles, ammonia, and amides and carbamates as ammonia equivalents all reacted with high selectivities and yields. Moreover, weakly basic enolates (such as silyl enol ethers) and enolate equivalents (such as enamines) also reacted, and other research groups have used this catalyst to conduct reactions of stabilized carbon nucleophiles in the absence of additional base. One hallmark of the reactions catalyzed by this iridium system is the invariably high enantioselectivity, which reflects a high stereoselectivity for formation of the allyl intermediate. Enantioselectivity typically exceeds 95%, regioselectivity for formation of branched over linear products is usually near 20:1, and yields generally exceed 75% and are often greater than 90%. Thus, the development of iridium catalysts for enantioselective allylic substitution shows how studies of reaction mechanism can lead to a particularly active and a remarkably general system for an enantioselective process. In this case, a readily accessible catalyst effects allylic substitution, with high enantioselectivity and regioselectivity complementary to that of the venerable palladium systems. PMID:20873839