Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning.

PubMed

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2017-12-21

The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates. We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D.

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

PubMed Central

Chevalier, Michael W.; El-Samad, Hana

2014-01-01

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled. PMID:25481130

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

NASA Astrophysics Data System (ADS)

Chevalier, Michael W.; El-Samad, Hana

2014-12-01

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.

General chemical kinetics computer program for static and flow reactions, with application to combustion and shock-tube kinetics

NASA Technical Reports Server (NTRS)

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

1972-01-01

A general chemical kinetics program is described for complex, homogeneous ideal-gas reactions in any chemical system. Its main features are flexibility and convenience in treating many different reaction conditions. The program solves numerically the differential equations describing complex reaction in either a static system or one-dimensional inviscid flow. Applications include ignition and combustion, shock wave reactions, and general reactions in a flowing or static system. An implicit numerical solution method is used which works efficiently for the extreme conditions of a very slow or a very fast reaction. The theory is described, and the computer program and users' manual are included.

Enzymatic production of monoacylglycerols containing polyunsaturated fatty acids through an efficient glycerolysis system.

PubMed

Yang, Tiankui; Rebsdorf, Morten; Engelrud, Ulrik; Xu, Xuebing

2005-03-09

The aim of the study was to develop an efficient glycerolysis system for the enzymatic production of monoacylglycerols (MAGs) containing polyunsaturated fatty acids. Glycerolysis has been widely applied in industry for the chemical production of food MAGs under high temperature. The enzymatic glycerolysis system at 40-70 degrees C is unfortunately a multiphase system, which leads to the lower reaction efficiency. A tert-butyl alcohol system was developed after careful evaluation and more than 20-fold of the reaction efficiency from this system was obtained compared to the solvent-free system. Novozym 435 was employed as a catalyst in the glycerolysis from the screening. In the batch reaction system with tert-butyl alcohol, temperature higher than 40 degrees C was favored. The glycerol/oil ratio was best in the study with 4.5 while the solvent weight ratio from 1 to 3 had little effect. In general, 60-70% yield can be obtained at 2 h in the stirred tank reactor. The continuous glycerolysis was conducted in a packed bed reactor. MAG yield up to 70% was reached at 30-40 min residence time. The continuous glycerolysis was more sensitive to the amount of tert-butyl alcohol, and in the weight ratio to oil more than 2 was favored. The continuous process was optimized with the assistance of response surface methodology. Optimal conditions for the packed bed reactor after all considerations were recommended as glycerol/oil 4:1 (mol/mol), temperature 40 degrees C, and residence time 45 min. The operation stability study showed that there was no slight reduction of reaction performance at more than 30 days, implying a high feasibility in practical applications.

Catalytic reactive separation system for energy-efficient production of cumene

DOEpatents

Buelna, Genoveva [Nuevo Laredo, MX; Nenoff, Tina M [Albuquerque, NM

2009-07-28

The present invention relates to an atmospheric pressure, reactive separation column packed with a solid acid zeolite catalyst for producing cumene from the reaction of benzene with propylene. Use of this un-pressurized column, where simultaneous reaction and partial separation occur during cumene production, allow separation of un-reacted, excess benzene from other products as they form. This high-yielding, energy-efficient system allows for one-step processing of cumene, with reduced need for product purification. Reacting propylene and benzene in the presence of beta zeolite catalysts generated a selectivity greater than 85% for catalytic separation reactions at a reaction temperature of 115 degrees C and at ambient pressure. Simultaneously, up to 76% of un-reacted benzene was separated from the product; which could be recycled back to the reactor for re-use.

CuAAC-Based Click Chemistry in Self-Healing Polymers.

PubMed

Döhler, Diana; Michael, Philipp; Binder, Wolfgang H

2017-10-17

Click chemistry has emerged as a significant tool for materials science, organic chemistry, and bioscience. Based on the initial concept of Barry Sharpless in 2001, the copper(I)-catalyzed azide/alkyne cycloaddition (CuAAC) reaction has triggered a plethora of chemical concepts for linking molecules and building blocks under ambient conditions, forming the basis for applications in autonomous cross-linking materials. Self-healing systems on the other hand are often based on mild cross-linking chemistries that are able to react either autonomously or upon an external trigger. In the ideal case, self-healing takes place efficiently at low temperatures, independent of the substrate(s) used, by forming strong and stable networks, binding to the newly generated (cracked) interfaces to restore the original material properties. The use of the CuAAC in self-healing systems, most of all the careful design of copper-based catalysts linked to additives as well as the chemical diversity of substrates, has led to an enormous potential of applications of this singular reaction. The implementation of click-based strategies in self-healing systems therefore is highly attractive, as here chemical (and physical) concepts of molecular reactivity, molecular design, and even metal catalysis are connected to aspects of materials science. In this Account, we will show how CuAAC reactions of multivalent components can be used as a tool for self-healing materials, achieving cross-linking at low temperatures (exploiting concepts of autocatalysis or internal chelation within the bulk CuAAC and systematic optimization of the efficiency of the used Cu(I) catalysts). Encapsulation strategies to separate the click components by micro- and nanoencapsulation are required in this context. Consequently, the examples reported here describe chemical concepts to realize more efficient and faster click reactions in self-healing polymeric materials. Thus, enhanced chain diffusion in (hyper)branched polymers, autocatalysis, or internal chelation concepts enable efficient click cross-linking already at 5 °C with a simultaneously reduced amount of Cu(I) catalyst and increased reaction rates, culminating in the first reported self-healing system based on click cycloaddition reactions. Via tailor-made nanocarbon/Cu(I) catalysts we can further improve the click cross-linking reaction in view of efficiency and kinetics, leading to the generation of self-healing graphene-based epoxy nanocomposites. Additionally, we have designed special CuAAC click methods for chemical reporting and visualization systems based on the detection of ruptured capsules via a fluorogenic click reaction, which can be combined with CuAAC cross-linking reactions to obtain simultaneous stress detection and self-healing within polymeric materials. In a similar concept, we have prepared polymeric Cu(I)-biscarbene complexes to detect (mechanical) stress within self-healing polymeric materials via a triggered fluorogenic reaction, thus using a destructive force for a constructive chemical response.

Effect of Chemicals on Morphology and Luminescence of CdSe Quantum Dots.

PubMed

Zhang, Xiao; Li, Xiaoyu; Zhang, Ruili; Yang, Ping

2015-04-01

CdSe quantum dots (QDs) with several morphologies were fabricated using various reaction sys- tems. In a trioctylamine (TOA) and octadecylphosphonic acid (ODPA) system, yellow-emitting (a photoluminescence (PL) peak wavelength of 583 nm) CdSe QDs revealed rod morphology and nar- row size distribution. When ODPA was replaced by tetradecylphosphonic acid (TDPA), red-emitting CdSe rods (a PL peak wavelength of 653 nm) with broad size distribution were fabricated. This is ascribed that the short carbon chain accelerated the growth of CdSe QDs. As a result, the use of ODPA resulted in CdSe QDs with high PL efficiency (3.1%). Furthermore, cubic-like CdSe QDs were created in a stearic acid (SA) and octadecene (ODE) reaction system. The PL efficiency of the QDs is low (0.2%). When hexadecylamine (HDA) was added in such SA and ODE reaction system, spherical CdSe QDs with narrow size distribution and high PL efficiency (3.4%) were prepared.

Improvement of the efficiency of a space oxygen-hydrogen electrochemical generator

NASA Astrophysics Data System (ADS)

Glukhikh, I. N.; Shcherbakov, A. N.; Chelyaev, V. F.

2014-12-01

This paper describes the method used for cooling of an on-board oxygen-hydrogen electrochemical generator (ECG). Apart from electric power, such a unit produces water of reaction and heat; the latter is an additional load on the thermal control system of a space vehicle. This load is undesirable in long-duration space flights, when specific energy characteristics of on-board systems are the determining factors. It is suggested to partially compensate the energy consumption by the thermal control system of a space vehicle required for cooling of the electrochemical generator through evaporation of water of reaction from the generator into a vacuum (or through ice sublimation if the pressure in the ambient space is lower than that in the triple point of water.) Such method of cooling of an electrochemical generator improves specific energy parameters of an on-board electric power supply system, and, due to the presence of the negative feedback, it makes the operation of this system more stable. Estimates suggest that it is possible to compensate approximately one half of heat released from the generator through evaporation of its water of reaction at the electrical efficiency of the electrochemical generator equal to 60%. In this case, even minor increase in the efficiency of the generator would result in a considerable increase in the efficiency of the evaporative system intended for its cooling.

Highly selective transformation of ammonia nitrogen to N2 based on a novel solar-driven photoelectrocatalytic-chlorine radical reactions system.

PubMed

Ji, Youzhi; Bai, Jing; Li, Jinhua; Luo, Tao; Qiao, Li; Zeng, Qingyi; Zhou, Baoxue

2017-11-15

A highly selective method for transforming ammonia nitrogen to N 2 was proposed, based on a novel solar-driven photoelectrocatalytic-chlorine radical reactions (PEC-chlorine) system. The PEC-chlorine system was facilitated by a visible light response WO 3 nanoplate array (NPA) electrode in an ammonia solution containing chloride ions (Cl - ). Under illumination, photoholes from WO 3 promote the oxidation of Cl - to chlorine radical (Cl). This radical can selectively transform ammonia nitrogen to N 2 (79.9%) and NO 3 - (19.2%), similar to the breakpoint chlorination reaction. The ammonia nitrogen removal efficiency increased from 10.6% (PEC without Cl - ) to 99.9% with the PEC-chlorine system within 90 min operation, which can be attributed to the cyclic reactions between Cl - /Cl and the reaction intermediates (NH 2 , NHCl, etc.) that expand the degradation reactions from the surface of the electrodes to the whole solution system. Moreover, Cl is the main radical species contributing to the transformation of ammonia nitrogen to N 2 , which is confirmed by the tBuOH capture experiment. Compared to conventional breakpoint chlorination, the PEC-chlorine system is a more economical and efficient means for ammonia nitrogen degradation because of the fast removal rate, no additional chlorine cost, and its use of clean energy (since it is solar-driven). Copyright © 2017 Elsevier Ltd. All rights reserved.

The allylation reactions of aromatic aldehydes and ketones with tin dichloride in water.

PubMed

Bian, Yan-Jiang; Xue, Wei-Li; Yu, Xu-Guang

2010-01-01

The allylation reactions of aromatic aldehydes and ketones were carried out in 31-86% yield using SnCl(2)-H(2)O system under ultrasound irradiation at r.t. for 5h. The reactions in the same system gave homoallyl alcohols in 21-84% yield with stirring at r.t. for 24h. Compared with traditional stirring methods, ultrasonic irradiation is more convenient and efficient.

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.

Biological optimization systems for enhancing photosynthetic efficiency and methods of use

DOEpatents

Hunt, Ryan W.; Chinnasamy, Senthil; Das, Keshav C.; de Mattos, Erico Rolim

2012-11-06

Biological optimization systems for enhancing photosynthetic efficiency and methods of use. Specifically, methods for enhancing photosynthetic efficiency including applying pulsed light to a photosynthetic organism, using a chlorophyll fluorescence feedback control system to determine one or more photosynthetic efficiency parameters, and adjusting one or more of the photosynthetic efficiency parameters to drive the photosynthesis by the delivery of an amount of light to optimize light absorption of the photosynthetic organism while providing enough dark time between light pulses to prevent oversaturation of the chlorophyll reaction centers are disclosed.

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

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

Chevalier, Michael W., E-mail: Michael.Chevalier@ucsf.edu; El-Samad, Hana, E-mail: Hana.El-Samad@ucsf.edu

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation timesmore » of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.« less

Biomimicry Promotes the Efficiency of a 10-Step Sequential Enzymatic Reaction on Nanoparticles, Converting Glucose to Lactate.

PubMed

Mukai, Chinatsu; Gao, Lizeng; Nelson, Jacquelyn L; Lata, James P; Cohen, Roy; Wu, Lauren; Hinchman, Meleana M; Bergkvist, Magnus; Sherwood, Robert W; Zhang, Sheng; Travis, Alexander J

2017-01-02

For nanobiotechnology to achieve its potential, complex organic-inorganic systems must grow to utilize the sequential functions of multiple biological components. Critical challenges exist: immobilizing enzymes can block substrate-binding sites or prohibit conformational changes, substrate composition can interfere with activity, and multistep reactions risk diffusion of intermediates. As a result, the most complex tethered reaction reported involves only 3 enzymes. Inspired by the oriented immobilization of glycolytic enzymes on the fibrous sheath of mammalian sperm, here we show a complex reaction of 10 enzymes tethered to nanoparticles. Although individual enzyme efficiency was higher in solution, the efficacy of the 10-step pathway measured by conversion of glucose to lactate was significantly higher when tethered. To our knowledge, this is the most complex organic-inorganic system described, and it shows that tethered, multi-step biological pathways can be reconstituted in hybrid systems to carry out functions such as energy production or delivery of molecular cargo. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biomimicry promotes the efficiency of a 10-step sequential enzymatic reaction on nanoparticles, converting glucose to lactate

PubMed Central

Mukai, Chinatsu; Gao, Lizeng; Nelson, Jacquelyn L.; Lata, James P.; Cohen, Roy; Wu, Lauren; Hinchman, Meleana M.; Bergkvist, Magnus; Sherwood, Robert W.; Zhang, Sheng; Travis, Alexander J.

2016-01-01

For nanobiotechnology to achieve its potential, complex organic-inorganic systems must grow to utilize the sequential functions of multiple biological components. Critical challenges exist: immobilizing enzymes can block substrate-binding sites or prohibit conformational changes, substrate composition can interfere with activity, and multistep reactions risk diffusion of intermediates. As a result, the most complex tethered reaction reported involves only 3 enzymes. Inspired by the oriented immobilization of glycolytic enzymes on the fibrous sheath of mammalian sperm, here we show a complex reaction of 10 enzymes tethered to nanoparticles. Although individual enzyme efficiency was higher in solution, the efficacy of the 10-step pathway measured by conversion of glucose to lactate was significantly higher when tethered. To our knowledge, this is the most complex organic-inorganic system described, and it shows that tethered, multi-step biological pathways can be reconstituted in hybrid systems to carry out functions such as energy production or delivery of molecular cargo. PMID:27901298

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.

Formal modeling of a system of chemical reactions under uncertainty.

PubMed

Ghosh, Krishnendu; Schlipf, John

2014-10-01

We describe a novel formalism representing a system of chemical reactions, with imprecise rates of reactions and concentrations of chemicals, and describe a model reduction method, pruning, based on the chemical properties. We present two algorithms, midpoint approximation and interval approximation, for construction of efficient model abstractions with uncertainty in data. We evaluate computational feasibility by posing queries in computation tree logic (CTL) on a prototype of extracellular-signal-regulated kinase (ERK) pathway.

Hybrid discrete/continuum algorithms for stochastic reaction networks

DOE PAGES

Safta, Cosmin; Sargsyan, Khachik; Debusschere, Bert; ...

2014-10-22

Direct solutions of the Chemical Master Equation (CME) governing Stochastic Reaction Networks (SRNs) are generally prohibitively expensive due to excessive numbers of possible discrete states in such systems. To enhance computational efficiency we develop a hybrid approach where the evolution of states with low molecule counts is treated with the discrete CME model while that of states with large molecule counts is modeled by the continuum Fokker-Planck equation. The Fokker-Planck equation is discretized using a 2nd order finite volume approach with appropriate treatment of flux components to avoid negative probability values. The numerical construction at the interface between the discretemore » and continuum regions implements the transfer of probability reaction by reaction according to the stoichiometry of the system. As a result, the performance of this novel hybrid approach is explored for a two-species circadian model with computational efficiency gains of about one order of magnitude.« less

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Using single-chamber microbial fuel cells as renewable power sources of electro-Fenton reactors for organic pollutant treatment.

PubMed

Zhu, Xiuping; Logan, Bruce E

2013-05-15

Electro-Fenton reactions can be very effective for organic pollutant degradation, but they typically require non-sustainable electrical power to produce hydrogen peroxide. Two-chamber microbial fuel cells (MFCs) have been proposed for pollutant treatment using Fenton-based reactions, but these types of MFCs have low power densities and require expensive membranes. Here, more efficient dual reactor systems were developed using a single-chamber MFC as a low-voltage power source to simultaneously accomplish H2O2 generation and Fe(2+) release for the Fenton reaction. In tests using phenol, 75 ± 2% of the total organic carbon (TOC) was removed in the electro-Fenton reactor in one cycle (22 h), and phenol was completely degraded to simple and readily biodegradable organic acids. Compared to previously developed systems based on two-chamber MFCs, the degradation efficiency of organic pollutants was substantially improved. These results demonstrate that this system is an energy-efficient and cost-effective approach for industrial wastewater treatment of certain pollutants. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

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

PubMed Central

2017-01-01

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

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

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

Thanh, Vo Hong, E-mail: vo@cosbi.eu; Priami, Corrado, E-mail: priami@cosbi.eu; Department of Mathematics, University of Trento, Trento

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

Charge transfer mechanism in titanium-doped microporous silica for photocatalytic water-splitting applications

DOE PAGES

Sapp, Wendi; Koodali, Ranjit; Kilin, Dmitri

2016-02-29

Solar energy conversion into chemical form is possible using artificial means. One example of a highly-efficient fuel is solar energy used to split water into oxygen and hydrogen. Efficient photocatalytic water-splitting remains an open challenge for researchers across the globe. Despite significant progress, several aspects of the reaction, including the charge transfer mechanism, are not fully clear. Density functional theory combined with density matrix equations of motion were used to identify and characterize the charge transfer mechanism involved in the dissociation of water. A simulated porous silica substrate, using periodic boundary conditions, with Ti 4+ ions embedded on the innermore » pore wall was found to contain electron and hole trap states that could facilitate a chemical reaction. A trap state was located within the silica substrate that lengthened relaxation time, which may favor a chemical reaction. A chemical reaction would have to occur within the window of photoexcitation; therefore, the existence of a trapping state may encourage a chemical reaction. Furthermore, this provides evidence that the silica substrate plays an integral part in the electron/hole dynamics of the system, leading to the conclusion that both components (photoactive materials and support) of heterogeneous catalytic systems are important in optimization of catalytic efficiency.« less

Reaction wheels for kinetic energy storage

NASA Astrophysics Data System (ADS)

Studer, P. A.

1984-11-01

In contrast to all existing reaction wheel implementations, an order of magnitude increase in speed can be obtained efficiently if power to the actuators can be recovered. This allows a combined attitude control-energy storage system to be developed with structure mounted reaction wheels. The feasibility of combining reaction wheels with energy storage wwheels is demonstrated. The power required for control torques is a function of wheel speed but this energy is not dissipated; it is stored in the wheel. The I(2)R loss resulting from a given torque is shown to be constant, independent of the design speed of the motor. What remains, in order to efficiently use high speed wheels (essential for energy storage) for control purposes, is to reduce rotational losses to acceptable levels. Progress was made in permanent magnet motor design for high speed operation. Variable field motors offer more control flexibility and efficiency over a broader speed range.

Reaction wheels for kinetic energy storage

NASA Technical Reports Server (NTRS)

Studer, P. A.

1984-01-01

In contrast to all existing reaction wheel implementations, an order of magnitude increase in speed can be obtained efficiently if power to the actuators can be recovered. This allows a combined attitude control-energy storage system to be developed with structure mounted reaction wheels. The feasibility of combining reaction wheels with energy storage wwheels is demonstrated. The power required for control torques is a function of wheel speed but this energy is not dissipated; it is stored in the wheel. The I(2)R loss resulting from a given torque is shown to be constant, independent of the design speed of the motor. What remains, in order to efficiently use high speed wheels (essential for energy storage) for control purposes, is to reduce rotational losses to acceptable levels. Progress was made in permanent magnet motor design for high speed operation. Variable field motors offer more control flexibility and efficiency over a broader speed range.

Biosynthesis-inspired deracemizative production of d-luciferin by combining luciferase and thioesterase.

PubMed

Maeda, Juri; Kato, Dai-Ichiro; Okuda, Masatoshi; Takeo, Masahiro; Negoro, Seiji; Arima, Kazunari; Ito, Yuji; Niwa, Kazuki

2017-08-01

Due to the strict enantioselectivity of firefly luciferase, only d-luciferin can be used as a substrate for bioluminescence reactions. Unfortunately, luciferin racemizes easily and accumulation of nonluminous l-luciferin has negative influences on the light emitting reaction. Thus, maintaining the enantiopurity of luciferin in the reaction mixture is one of the most important demands in bioluminescence applications using firefly luciferase. In fireflies, however, l-luciferin is the biosynthetic precursor of d-luciferin, which is produced from the L-form undergoing deracemization. This deracemization consists of three successive reactions: l-enantioselective thioesterification by luciferase, in situ epimerization, and hydrolysis by thioesterase. In this work, we introduce a deracemizative luminescence system inspired by the biosynthetic pathway of d-luciferin using a combination of firefly luciferase from Luciola cruciata (LUC-G) and fatty acyl-CoA thioesterase II from Escherichia coli (TESB). The enzymatic reaction property analysis indicated the importance of the concentration balance between LUC-G and TESB for efficient d-luciferin production and light emission. Using this deracemizative luminescence system, a highly sensitive quantitative analysis method for l-cysteine was constructed. This LUC-G-TESB combination system can improve bioanalysis applications using the firefly bioluminescence reaction by efficient deracemization of D-luciferin. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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

2016-06-28

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

Citric Acid-Modified Fenton's Reaction for the Oxidation of Chlorinated Ethylenes in Soil Solution Systems

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

Seol, Yongkoo; Javandel, Iraj

Fenton's reagent, a solution of hydrogen peroxide and ferrous iron catalyst, is used for an in-situ chemical oxidation of organic contaminants. Sulfuric acid is commonly used to create an acidic condition needed for catalytic oxidation. Fenton's reaction often involves pressure buildup and precipitation of reaction products, which can cause safety hazards and diminish efficiency. We selected citric acid, a food-grade substance, as an acidifying agent to evaluate its efficiencies for organic contaminant removal in Fenton's reaction, and examined the impacts of using citric acid on the unwanted reaction products. A series of batch and column experiments were performed with varyingmore » H{sub 2}O{sub 2} concentrations to decompose selected chlorinated ethylenes. Either dissolved iron from soil or iron sulfate salt was added to provide the iron catalyst in the batch tests. Batch experiments revealed that both citric and sulfuric acid systems achieved over 90% contaminant removal rates, and the presence of iron catalyst was essential for effective decontamination. Batch tests with citric acid showed no signs of pressure accumulation and solid precipitations, however the results suggested that an excessive usage of H{sub 2}O{sub 2} relative to iron catalysts (Fe{sup 2+}/H{sub 2}O{sub 2} < 1/330) would result in lowering the efficiency of contaminant removal by iron chelations in the citric acid system. Column tests confirmed that citric acid could provide suitable acidic conditions to achieve higher than 55% contaminant removal rates.« less

Citric acid-modified Fenton's reaction for the oxidation of chlorinated ethylenes in soil solution systems.

PubMed

Seol, Yongkoo; Javandel, Iraj

2008-06-01

Fenton's reagent, a solution of hydrogen peroxide and ferrous iron catalyst, is used for an in situ chemical oxidation of organic contaminants. Sulfuric acid is commonly used to create an acidic condition needed for catalytic oxidation. Fenton's reaction often involves pressure buildup and precipitation of reaction products, which can cause safety hazards and diminish efficiency. We selected citric acid, a food-grade substance, as an acidifying agent to evaluate its efficiencies for organic contaminant removal in Fenton's reaction, and examined the impacts of using citric acid on the unwanted reaction products. A series of batch and column experiments were performed with varying H2O2 concentrations to decompose selected chlorinated ethylenes. Either dissolved iron from soil or iron sulfate salt was added to provide the iron catalyst in the batch tests. Batch experiments revealed that both citric and sulfuric acid systems achieved over 90% contaminant removal rates, and the presence of iron catalyst was essential for effective decontamination. Batch tests with citric acid showed no signs of pressure accumulation and solid precipitations, however the results suggested that an excessive usage of H2O2 relative to iron catalysts (Fe2+/H2O2<1/330) would result in lowering the efficiency of contaminant removal by iron chelation in the citric acid system. Column tests confirmed that citric acid could provide suitable acidic conditions to achieve higher than 55% contaminant removal rates.

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

Modeling and simulation of enzymatic gluconic acid production using immobilized enzyme and CSTR-PFTR circulation reaction system.

PubMed

Li, Can; Lin, Jianqun; Gao, Ling; Lin, Huibin; Lin, Jianqiang

2018-04-01

Production of gluconic acid by using immobilized enzyme and continuous stirred tank reactor-plug flow tubular reactor (CSTR-PFTR) circulation reaction system. A production system is constructed for gluconic acid production, which consists of a continuous stirred tank reactor (CSTR) for pH control and liquid storage and a plug flow tubular reactor (PFTR) filled with immobilized glucose oxidase (GOD) for gluconic acid production. Mathematical model is developed for this production system and simulation is made for the enzymatic reaction process. The pH inhibition effect on GOD is modeled by using a bell-type curve. Gluconic acid can be efficiently produced by using the reaction system and the mathematical model developed for this system can simulate and predict the process well.

Fenton-like initiation of a toluene transformation mechanism

EPA Science Inventory

In Fenton-driven oxidation treatment systems, reaction intermediates derived from parent compounds can play a significant role in the overall treatment process. Fenton-like reactions in the presence of toluene or benzene, involved a transformation mechanism that was highly effici...

Polyhedral Interpolation for Optimal Reaction Control System Jet Selection

NASA Technical Reports Server (NTRS)

Gefert, Leon P.; Wright, Theodore

2014-01-01

An efficient algorithm is described for interpolating optimal values for spacecraft Reaction Control System jet firing duty cycles. The algorithm uses the symmetrical geometry of the optimal solution to reduce the number of calculations and data storage requirements to a level that enables implementation on the small real time flight control systems used in spacecraft. The process minimizes acceleration direction errors, maximizes control authority, and minimizes fuel consumption.

A novel sodium iodide and ammonium molybdate co-catalytic system for the efficient synthesis of 2-benzimidazoles using hydrogen peroxide under ultrasound irradiation.

PubMed

Bai, Guo-Yi; Lan, Xing-Wang; Chen, Guo-Feng; Liu, Xiao-Fang; Li, Tian-Yu; Shi, Ling-Juan

2014-03-01

The reaction of aldehydes and o-phenylenediamine for the preparation of 2-benzimidazoles has been studied using hydrogen peroxide as an oxidant under ultrasound irradiation at room temperature in this paper. The combination of substoichiometric sodium iodide and ammonium molybdate as co-catalysts, together with using small amounts of hydrogen peroxide, makes this transformation very efficient and attractive under ultrasound. Thus, a mild, green and efficient method is established to carry out this reaction in high yield. Copyright © 2013 Elsevier B.V. All rights reserved.

An intermediate level of abstraction for computational systems chemistry.

PubMed

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

2017-12-28

Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, because precise information on the molecular composition, the dominant reaction chemistry and the conditions for that era are scarce. The exploration of large chemical reaction networks is a central aspect in this endeavour. While quantum chemical methods can accurately predict the structures and reactivities of small molecules, they are not efficient enough to cope with large-scale reaction systems. The formalization of chemical reactions as graph grammars provides a generative system, well grounded in category theory, at the right level of abstraction for the analysis of large and complex reaction networks. An extension of the basic formalism into the realm of integer hyperflows allows for the identification of complex reaction patterns, such as autocatalysis, in large reaction networks using optimization techniques.This article is part of the themed issue 'Reconceptualizing the origins of life'. © 2017 The Author(s).

Efficient Solar Energy Harvesting and Storage through a Robust Photocatalyst Driving Reversible Redox Reactions.

PubMed

Zhou, Yangen; Zhang, Shun; Ding, Yu; Zhang, Leyuan; Zhang, Changkun; Zhang, Xiaohong; Zhao, Yu; Yu, Guihua

2018-06-14

Simultaneous solar energy conversion and storage is receiving increasing interest for better utilization of the abundant yet intermittently available sunlight. Photoelectrodes driving nonspontaneous reversible redox reactions in solar-powered redox cells (SPRCs), which can deliver energy via the corresponding reverse reactions, present a cost-effective and promising approach for direct solar energy harvesting and storage. However, the lack of photoelectrodes having both high conversion efficiency and high durability becomes a bottleneck that hampers practical applications of SPRCs. Here, it is shown that a WO 3 -decorated BiVO 4 photoanode, without the need of extra electrocatalysts, can enable a single-photocatalyst-driven SPRC with a solar-to-output energy conversion efficiency as high as 1.25%. This SPRC presents stable performance over 20 solar energy storage/delivery cycles. The high efficiency and stability are attributed to the rapid redox reactions, the well-matched energy level, and the efficient light harvesting and charge separation of the prepared BiVO 4 . This demonstrated device system represents a potential alternative toward the development of low-cost, durable, and easy-to-implement solar energy technologies. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An efficient hybrid method for stochastic reaction-diffusion biochemical systems with delay

NASA Astrophysics Data System (ADS)

Sayyidmousavi, Alireza; Ilie, Silvana

2017-12-01

Many chemical reactions, such as gene transcription and translation in living cells, need a certain time to finish once they are initiated. Simulating stochastic models of reaction-diffusion systems with delay can be computationally expensive. In the present paper, a novel hybrid algorithm is proposed to accelerate the stochastic simulation of delayed reaction-diffusion systems. The delayed reactions may be of consuming or non-consuming delay type. The algorithm is designed for moderately stiff systems in which the events can be partitioned into slow and fast subsets according to their propensities. The proposed algorithm is applied to three benchmark problems and the results are compared with those of the delayed Inhomogeneous Stochastic Simulation Algorithm. The numerical results show that the new hybrid algorithm achieves considerable speed-up in the run time and very good accuracy.

Unravelling Site-Specific Photo-Reactions of Ethanol on Rutile TiO2(110)

PubMed Central

Hansen, Jonas Ø.; Bebensee, Regine; Martinez, Umberto; Porsgaard, Soeren; Lira, Estephania; Wei, Yinying; Lammich, Lutz; Li, Zheshen; Idriss, Hicham; Besenbacher, Flemming; Hammer, Bjørk; Wendt, Stefan

2016-01-01

Finding the active sites of catalysts and photo-catalysts is crucial for an improved fundamental understanding and the development of efficient catalytic systems. Here we have studied the photo-activated dehydrogenation of ethanol on reduced and oxidized rutile TiO2(110) in ultrahigh vacuum conditions. Utilizing scanning tunnelling microscopy, various spectroscopic techniques and theoretical calculations we found that the photo-reaction proceeds most efficiently when the reactants are adsorbed on regular Ti surface sites, whereas species that are strongly adsorbed at surface defects such as O vacancies and step edges show little reaction under reducing conditions. We propose that regular Ti surface sites are the most active sites in photo-reactions on TiO2. PMID:26915303

Highly efficient reversible addition-fragmentation chain-transfer polymerization in ethanol/water via flow chemistry

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

Ye, Piaoran; Cao, Peng -Fei; Su, Zhe

Here, utilization of a flow reactor under high pressure allows highly efficient polymer synthesis via reversible addition–fragmentation chain-transfer (RAFT) polymerization in an aqueous system. Compared with the batch reaction, the flow reactor allows the RAFT polymerization to be performed in a high-efficiency manner at the same temperature. The adjustable pressure of the system allows further elevation of the reaction temperature and hence faster polymerization. Other reaction parameters, such as flow rate and initiator concentration, were also well studied to tune the monomer conversion and the molar mass dispersity (Ð) of the obtained polymers. Gel permeation chromatography, nuclear magnetic resonance (NMR),more » and Fourier transform infrared spectroscopies (FTIR) were utilized to monitor the polymerization process. With the initiator concentration of 0.15 mmol L –1, polymerization of poly(ethylene glycol) methyl ethermethacrylate with monomer conversion of 52% at 100 °C under 73 bar can be achieved within 40 min with narrow molar mass dispersity (D) Ð (<1.25). The strategy developed here provides a method to produce well-defined polymers via RAFT polymerization with high efficiency in a continuous manner.« less

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).

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

Greene, Samuel M., E-mail: samuel.greene@chem.ox.ac.uk; Shan, Xiao, E-mail: xiao.shan@chem.ox.ac.uk; Clary, David C., E-mail: david.clary@chem.ox.ac.u

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

Clustering and optimal arrangement of enzymes in reaction-diffusion systems.

PubMed

Buchner, Alexander; Tostevin, Filipe; Gerland, Ulrich

2013-05-17

Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion model. The optimal arrangement transitions from a cluster to a distributed profile as a single parameter, which controls the probability of reaction versus diffusive loss of pathway intermediates, is varied. We introduce the concept of enzyme exposure to explain how this transition arises from the stochastic nature of molecular reactions and diffusion.

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

ERIC Educational Resources Information Center

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

2005-01-01

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

A highly efficient synthesis of the FGH ring of micrandilactone A. Application of thioureas as ligands in the Co-catalyzed Pauson-Khand reaction and Pd-catalyzed carbonylative annulation.

PubMed

Tang, Yefeng; Zhang, Yandong; Dai, Mingji; Luo, Tuoping; Deng, Lujiang; Chen, Jiahua; Yang, Zhen

2005-03-03

The functionalized FGH ring system of micrandilactone A was successfully constructed in high selectivity and good yields. The key reactions in our strategy are the Co-thiourea-catalyzed stereoselective, intramolecular Pauson-Khand reaction and Pd-thiourea-catalyzed stereoselective, intramolecular annulation. [structure: see text

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.

Structured fluids as microreactors for flavor formation by the Maillard reaction.

PubMed

Vauthey, S; Milo, C; Frossard, P; Garti, N; Leser, M E; Watzke, H J

2000-10-01

Thermal reactions of cysteine/furfural and cysteine/ribose mixtures were studied in model systems to gain more insight into the influence of structured fluids such as L(2) microemulsions and cubic phases on the generation of aroma compounds. Formation of 2-furfurylthiol from cysteine/furfural was particularly efficient in L(2) microemulsions and cubic phases compared to aqueous systems. The reaction led to the formation of two new sulfur compounds, which were identified as 2-(2-furyl)thiazolidine and, tentatively, N-(2-mercaptovinyl)-2-(2-furyl)thiazolidine. Similarly, generation of 2-furfurylthiol and 2-methyl-3-furanthiol from cysteine/ribose mixtures was strongly enhanced in structured fluids. The cubic phase was shown to be even more efficient in flavor generation than the L(2) microemulsion. It was denoted "cubic catalyst" or "cubic selective microreactor". The obtained results are interpreted in terms of a surface and curvature control of the reactions defined by the structural properties of the formed surfactant associates.

Antiproton-Induced Microfission

DTIC Science & Technology

1994-02-21

than chemical propulsion, other systems may prove even more efficient. Matter -antimatter reactions release enormous amounts of energy, mostly in the form...and matter -antimatter annihilation, to that of H2+0 2 combustion. Table 1.1 Theorectical specific energies of various reactions. System eth J/kg...For the case of hydrogen plasma, protons represent the ions. It would seem that two fluids interacting 25 would greatly complicate matters ; however

The efficiency of driving chemical reactions by a physical non-equilibrium is kinetically controlled.

PubMed

Göppel, Tobias; Palyulin, Vladimir V; Gerland, Ulrich

2016-07-27

An out-of-equilibrium physical environment can drive chemical reactions into thermodynamically unfavorable regimes. Under prebiotic conditions such a coupling between physical and chemical non-equilibria may have enabled the spontaneous emergence of primitive evolutionary processes. Here, we study the coupling efficiency within a theoretical model that is inspired by recent laboratory experiments, but focuses on generic effects arising whenever reactant and product molecules have different transport coefficients in a flow-through system. In our model, the physical non-equilibrium is represented by a drift-diffusion process, which is a valid coarse-grained description for the interplay between thermophoresis and convection, as well as for many other molecular transport processes. As a simple chemical reaction, we consider a reversible dimerization process, which is coupled to the transport process by different drift velocities for monomers and dimers. Within this minimal model, the coupling efficiency between the non-equilibrium transport process and the chemical reaction can be analyzed in all parameter regimes. The analysis shows that the efficiency depends strongly on the Damköhler number, a parameter that measures the relative timescales associated with the transport and reaction kinetics. Our model and results will be useful for a better understanding of the conditions for which non-equilibrium environments can provide a significant driving force for chemical reactions in a prebiotic setting.

FERN - a Java framework for stochastic simulation and evaluation of reaction networks.

PubMed

Erhard, Florian; Friedel, Caroline C; Zimmer, Ralf

2008-08-29

Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary. In this article, we present FERN (Framework for Evaluation of Reaction Networks), a Java framework for the efficient simulation of chemical reaction networks. FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level. To illustrate how FERN can be easily integrated into other systems biology applications, plugins to Cytoscape and CellDesigner are included. These plugins make it possible to run simulations and to observe the simulation progress in a reaction network in real-time from within the Cytoscape or CellDesigner environment. FERN addresses shortcomings of currently available stochastic simulation programs in several ways. First, it provides a broad range of efficient and accurate algorithms both for exact and approximate stochastic simulation and a simple interface for extending to new algorithms. FERN's implementations are considerably faster than the C implementations of gillespie2 or the Java implementations of ISBJava. Second, it can be used in a straightforward way both as a stand-alone program and within new systems biology applications. Finally, complex scenarios requiring intervention during the simulation progress can be modelled easily with FERN.

Innovative Strategy on Hydrogen Evolution Reaction Utilizing Activated Liquid Water

NASA Astrophysics Data System (ADS)

Hwang, Bing-Joe; Chen, Hsiao-Chien; Mai, Fu-Der; Tsai, Hui-Yen; Yang, Chih-Ping; Rick, John; Liu, Yu-Chuan

2015-11-01

Splitting water for hydrogen production using light, or electrical energy, is the most developed ‘green technique’. For increasing efficiency in hydrogen production, currently, the most exciting and thriving strategies are focused on efficient and inexpensive catalysts. Here, we report an innovative idea for efficient hydrogen evolution reaction (HER) utilizing plasmon-activated liquid water with reduced hydrogen-bonded structure by hot electron transfer. This strategy is effective for all HERs in acidic, basic and neutral systems, photocatalytic system with a g-C3N4 (graphite carbon nitride) electrode, as well as in an inert system with an ITO (indium tin oxide) electrode. Compared to deionized water, the efficiency of HER increases by 48% based on activated water ex situ on a Pt electrode. Increase in energy efficiency from activated water is 18% at a specific current yield of -20 mA in situ on a nanoscale-granulated Au electrode. Moreover, the onset potential of -0.023 V vs RHE was very close to the thermodynamic potential of the HER (0 V). The measured current density at the corresponding overpotential for HER in an acidic system was higher than any data previously reported in the literature. This approach establishes a new vista in clean green energy production.

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.

A programmable soft chemo-mechanical actuator exploiting a catalyzed photochemical water-oxidation reaction.

PubMed

Yuan, P; McCracken, J M; Gross, D E; Braun, P V; Moore, J S; Nuzzo, R G

2017-10-18

We describe a composite hydrogel containing an embedding coupled chemistry for light-sensitized catalytic reactions that enables chemo-mechanical actuation of poly(acrylic acid)-based gels. In these materials, a photosensitizer and catalyst-ruthenium trisbipyridine and iridium dioxide nanoparticles, respectively-are incorporated into the hydrogel where together, with visible light irradiation, they undergo a catalytic water-oxidation reaction that lowers the pH and induces a dissipative/chemically-driven strain change in the gel. To demonstrate the capacity for 3D chemo-mechanical actuation, a layer of non-pH responsive poly(2-hydroxyethyl methacrylate) is added to the photo-active composite gel to create a model bimorph actuator. Triggering and terminating the water-oxidation reaction leads to a programmatic expansion and contraction of the active layer, which induces different modes of biomimetic curling motions in the bimorph actuator in light and dark environments. The efficiency of this system is fundamentally limited by the system-level design, which provides no capacity to sustain a local pH gradient against diffusive mixing. Even so, if the initial pH of the background solution is reestablished either actively or passively between each reaction cycle, it is possible to realize multiple cycles of reversible actuation. We describe a thermodynamic analysis of this system which identifies specific features mediating efficiency losses and conceptual requirements for mesoscopic design rules for optimization of this system and for advancing soft actuation systems in general.

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.

A Hydrazone-Based Covalent Organic Framework as an Efficient and Reusable Photocatalyst for the Cross-Dehydrogenative Coupling Reaction of N-Aryltetrahydroisoquinolines.

PubMed

Liu, Wanting; Su, Qing; Ju, Pengyao; Guo, Bixuan; Zhou, Hui; Li, Guanghua; Wu, Qiaolin

2017-02-22

A hydrazone-based covalent organic framework (COF) was synthesized by condensation of 2,5-dimethoxyterephthalohydrazide with 1,3,5-triformylbenzene under solvothermal conditions. The COF material exhibits excellent porosity with a BET surface area of up to 1501 m 2  g -1 , high crystallinity, and good thermal and chemical stability. Moreover, it showed efficient photocatalytic activity towards cross-dehydrogenative coupling (CDC) reactions between tetrahydroisoquinolines and nucleophiles such as nitromethane, acetone, and phenylethyl ketone. The metal-free catalytic system also offers attractive advantages including simplicity of operation, wide substrate adaptability, ambient reaction conditions, and robust recycling capability of the catalyst, thus providing a promising platform for highly efficient and reusable photocatalysts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

CRISPR/Cas9-Assisted Transformation-Efficient Reaction (CRATER) for Near-Perfect Selective Transformation

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.; Greenberg, Daniel T.; Takahashi, Jack R.; Thompson, Kirsten A.; Maheshwari, Akshay J.; Kent, Ryan E.; McCutcheon, Griffin; Shih, Joseph D.; Calvet, Charles; Devlin, Tyler D.;

Polynomial-time quantum algorithm for the simulation of chemical dynamics

PubMed Central

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

2008-01-01

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

Comparative study of the degradation of real textile effluents by photocatalytic reactions involving UV/TiO2/H2O2 and UV/Fe2+/H2O2 systems.

PubMed

Garcia, J C; Oliveira, J L; Silva, A E C; Oliveira, C C; Nozaki, J; de Souza, N E

2007-08-17

This work investigated the treatability of real textile effluents using several systems involving advanced oxidation processes (AOPs) such as UV/H2O2, UV/TiO2, UV/TiO2/H2O2, and UV/Fe2+/H2O2. The efficiency of each technique was evaluated according to the reduction levels observed in the UV absorbance of the effluents, COD, and organic nitrogen reduction, as well as mineralization as indicated by the formation of ammonium, nitrate, and sulfate ions. The results indicate the association of TiO2 and H2O2 as the most efficient treatment for removing organic pollutants from textile effluents. In spite of their efficiency, Fenton reactions based treatment proved to be slower and exhibited more complicated kinetics than the ones using TiO2, which are pseudo-first-order reactions. Decolorization was fast and effective in all the experiments despite the fact that only H2O2 was used.

Efficient reactive Brownian dynamics

DOE PAGES

Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

2018-01-21

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently processmore » reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.« less

Efficient reactive Brownian dynamics

NASA Astrophysics Data System (ADS)

Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

2018-01-01

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.

Efficient reactive Brownian dynamics

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

Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently processmore » reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.« less

A simple but highly efficient multi-formyl phenol-amine system for fluorescence detection of peroxide explosive vapour.

PubMed

Xu, Wei; Fu, Yanyan; Gao, Yixun; Yao, Junjun; Fan, Tianchi; Zhu, Defeng; He, Qingguo; Cao, Huimin; Cheng, Jiangong

2015-07-11

A simple, highly stable, sensitive and selective fluorescent system for peroxide explosives was developed via an aromatic aldehyde oxidation reaction. The high efficiency arises from its higher HOMO level and multiple H-bonding. The sensitivity is obtained to be 0.1 ppt for H2O2 and 0.2 ppb for TATP.

Palladium-Catalyzed Telomerization of Butadiene with Polyols: From Mono to Polysaccharides

NASA Astrophysics Data System (ADS)

Bouquillon, Sandrine; Muzart, Jacques; Pinel, Catherine; Rataboul, Franck

The telomerization of butadiene with alcohols is an elegant way to synthesize ethers with minimal environmental impact since this reaction is 100% atom efficient. Besides telomerization of butadiene with methanol and water that is industrially developed, the modification of polyols is still under development. Recently, a series of new substrates has been involved in this reaction, including diols, pure or crude glycerol, protected or unprotected monosaccharides, as well as polysaccharides. This opens up the formation of new products having specific physicochemical properties. We will describe recent advances in this field, focusing on the reaction of renewable products and more specifically on saccharides. The efficient catalytic systems as well as the optimized reaction conditions will be described and some physicochemical properties of the products will be reported.

Computational singular perturbation analysis of stochastic chemical systems with stiffness

NASA Astrophysics Data System (ADS)

Wang, Lijin; Han, Xiaoying; Cao, Yanzhao; Najm, Habib N.

2017-04-01

Computational singular perturbation (CSP) is a useful method for analysis, reduction, and time integration of stiff ordinary differential equation systems. It has found dominant utility, in particular, in chemical reaction systems with a large range of time scales at continuum and deterministic level. On the other hand, CSP is not directly applicable to chemical reaction systems at micro or meso-scale, where stochasticity plays an non-negligible role and thus has to be taken into account. In this work we develop a novel stochastic computational singular perturbation (SCSP) analysis and time integration framework, and associated algorithm, that can be used to not only construct accurately and efficiently the numerical solutions to stiff stochastic chemical reaction systems, but also analyze the dynamics of the reduced stochastic reaction systems. The algorithm is illustrated by an application to a benchmark stochastic differential equation model, and numerical experiments are carried out to demonstrate the effectiveness of the construction.

A Review of Study on Thermal Energy Transport System by Synthesis and Decomposition Reactions of Methanol

NASA Astrophysics Data System (ADS)

Liu, Qiusheng; Yabe, Akira; Kajiyama, Shiro; Fukuda, Katsuya

The study on thermal energy transport system by synthesis and decomposition reactions of methanol was reviewed. To promote energy conservation and global environment protection, a two-step liquid-phase methanol synthesis process, which starts with carbonylation of methanol to methyl formate, then followed by the hydrogenolysis of the formate, was studied to recover wasted or unused discharged heat from industrial sources for the thermal energy demands of residential and commercial areas by chemical reactions. The research and development of the system were focused on the following three points. (1) Development of low-temperature decomposition and synthetic catalysts, (2) Development of liquid phase reactor (heat exchanger accompanying chemical reaction), (3) Simulation of the energy transport efficiency of entire system which contains heat recovery and supply sections. As the result of the development of catalyst, promising catalysts which agree with the development purposes for the methyl formate decomposition reaction and the synthetic reaction are being developed though some studies remain for the methanol decomposition and synthetic reactions. In the fundamental development of liquid phase reactor, the solubilities of CO and H2 gases in methanol and methyl formate were measured by the method of total pressure decrease due to absorption under pressures up to 1500kPa and temperatures up to 140°C. The diffusivity of CO gas in methanol was determined by measuring the diameter and solution time of single CO bubbles in methanol. The chemical reaction rate of methanol synthesis by hydrogenolysis of methyl formate was measured using a plate-type of Raney copper catalyst in a reactor with rectangular channel and in an autoclave reactor. The reaction characteristics were investigated by carrying out the experiments at various temperatures, flow rates and at various catalyst development conditions. We focused on the effect of Raney copper catalyst thickness on the liquid-phase chemical reaction by varying the development time of the catalyst. Investigation results of the catalyst such as surface area, pore radius, lattice size, and photographs of scanning electron microscope (SEM) were also given. In the simulation of energy transport efficiency of this system, by simulating the energy transfer system using two-step liquid phase methanol decomposition and synthetic reactions, and comparing with the technology so far, it can be expected that an innovative energy transfer system is possible to realize.

Efficient asymmetric hydrolysis of styrene oxide catalyzed by Mung bean epoxide hydrolases in ionic liquid-based biphasic systems.

PubMed

Chen, Wen-Jing; Lou, Wen-Yong; Zong, Min-Hua

2012-07-01

The asymmetric hydrolysis of styrene oxide to (R)-1-phenyl-1,2-ethanediol using Mung bean epoxide hydrolases was, for the first time, successfully conducted in an ionic liquid (IL)-containing biphasic system. Compared to aqueous monophasic system, IL-based biphasic systems could not only dissolve the substrate, but also effectively inhibit the non-enzymatic hydrolysis, and therefore markedly improve the reaction efficiency. Of all the tested ILs, the best results were observed in the biphasic system containing C(4)MIM·PF(6), which exhibited good biocompatibility with the enzyme and was an excellent solvent for the substrate. In the C(4)MIM·PF(6)/buffer biphasic system, it was found that the optimal volume ratio of IL to buffer, reaction temperature, buffer pH and substrate concentration were 1/6, 35°C, 6.5 and 100 mM, respectively, under which the initial reaction rate, the yield and the product e.e. were 18.4 mM/h, 49.4% and 97.0%. The biocatalytic process was shown to be feasible on a 500-mL preparative scale. Copyright © 2011 Elsevier Ltd. All rights reserved.

p-Aminophenol degradation by ozonation combined with sonolysis: operating conditions influence and mechanism.

PubMed

He, Zhiqiao; Song, Shuang; Ying, Haiping; Xu, Lejin; Chen, Jianmeng

2007-07-01

The degradation of p-aminophenol (PAP) in aqueous solution by sonolysis, by ozonation, and by a combination of both was investigated in laboratory-scale experiments. Operation parameters such as pH, temperature, ultrasonic energy density and ozone dose were optimized with regard to the efficiency of PAP removal. The concentration of PAP during the reaction was detected by high-pressure liquid chromatography. The concentrations of ammonium ions and nitrate ions were monitored during the degradation. Intermediate products such as 4-iminocyclohexa-2,5-dien-1-one, phenol, but-2-enedioic acid, and acetic acid were detected by gas chromatography coupled with mass spectrometry. The degradation rate of PAP was higher in the combined system than in the linear combination of separate experiments. The degradation efficiency was decreased rapidly when n-butanol was added to the combined reaction system, which showed that some radical reaction might proceed during the laboratory experiments.

Powering Lithium-Sulfur Battery Performance by Propelling Polysulfide Redox at Sulfiphilic Hosts.

PubMed

Yuan, Zhe; Peng, Hong-Jie; Hou, Ting-Zheng; Huang, Jia-Qi; Chen, Cheng-Meng; Wang, Dai-Wei; Cheng, Xin-Bing; Wei, Fei; Zhang, Qiang

2016-01-13

Lithium-sulfur (Li-S) battery system is endowed with tremendous energy density, resulting from the complex sulfur electrochemistry involving multielectron redox reactions and phase transformations. Originated from the slow redox kinetics of polysulfide intermediates, the flood of polysulfides in the batteries during cycling induced low sulfur utilization, severe polarization, low energy efficiency, deteriorated polysulfide shuttle, and short cycling life. Herein, sulfiphilic cobalt disulfide (CoS2) was incorporated into carbon/sulfur cathodes, introducing strong interaction between lithium polysulfides and CoS2 under working conditions. The interfaces between CoS2 and electrolyte served as strong adsorption and activation sites for polar polysulfides and therefore accelerated redox reactions of polysulfides. The high polysulfide reactivity not only guaranteed effective polarization mitigation and promoted energy efficiency by 10% but also promised high discharge capacity and stable cycling performance during 2000 cycles. A slow capacity decay rate of 0.034%/cycle at 2.0 C and a high initial capacity of 1368 mAh g(-1) at 0.5 C were achieved. Since the propelling redox reaction is not limited to Li-S system, we foresee the reported strategy herein can be applied in other high-power devices through the systems with controllable redox reactions.

Synergetic Effect of Ultrasound, the Heterogeneous Fenton Reaction and Photocatalysis by TiO2 Loaded on Nickel Foam on the Degradation of Pollutants

PubMed Central

Qiu, Shan; Xu, Shanwen; Li, Guangming; Yang, Jixian

2016-01-01

The synergistic effect of ultrasound, the heterogeneous Fenton reaction and photocatalysis was studied using a nickel foam (NF)-supporting TiO2 system and rhodamine B (RhB) as a target. The NF-supporting TiO2 system was prepared by depositing TiO2 on the skeleton of NF repeatedly and then calcining it. To optimize the conditions and parameters, the catalytic activity was tested in four systems (ultrasound alone (US), nickel foam (NF), US/NF and NF/US/H2O2). The optimal conditions were fixed at 0.1 g/mL NF, initial 5.00 mg/L RhB, 300 W ultrasonic power, pH = 3 and 5.00 mg/L H2O2. The effects of the dissolution of nickel from NF and quenching of the Fenton reaction were studied on degradation efficiency. When the heterogeneous Fenton reaction is combined with TiO2-photocatalysis, the pollutant removal efficiency is enhanced significantly. Through this synergistic effect, 22% and 80% acetochlor was degraded within 10 min and 80 min, respectively. PMID:28773580

Integrated solar thermochemical reaction system for steam methane reforming

DOE PAGES

Zheng, Feng; Diver, Rich; Caldwell, Dustin D.; ...

2015-06-05

Solar-aided upgrade of the energy content of fossil fuels, such as natural gas, can provide a near-term transition path towards a future solar-fuel economy and reduce carbon dioxide emission from fossil fuel consumption. Both steam and dry reforming a methane-containing fuel stream have been studied with concentrated solar power as the energy input to drive the highly endothermic reactions but the concept has not been demonstrated at a commercial scale. Under a current project with the U.S. Department of Energy, PNNL is developing an integrated solar thermochemical reaction system that combines solar concentrators with micro- and meso-channel reactors and heatmore » exchangers to accomplish more than 20% solar augment of methane higher heating value. The objective of our three-year project is to develop and prepare for commercialization such solar reforming system with a high enough efficiency to serve as the frontend of a conventional natural gas (or biogas) combined cycle power plant, producing power with a levelized cost of electricity less than 6¢/kWh, without subsidies, by the year 2020. In this paper, we present results from the first year of our project that demonstrated a solar-to-chemical energy conversion efficiency as high as 69% with a prototype reaction system.« less

Development of a ruthenium/phosphite catalyst system for domino hydroformylation-reduction of olefins with carbon dioxide.

PubMed

Liu, Qiang; Wu, Lipeng; Fleischer, Ivana; Selent, Detlef; Franke, Robert; Jackstell, Ralf; Beller, Matthias

2014-06-02

An efficient domino ruthenium-catalyzed reverse water-gas-shift (RWGS)-hydroformylation-reduction reaction of olefins to alcohols is reported. Key to success is the use of specific bulky phosphite ligands and triruthenium dodecacarbonyl as the catalyst. Compared to the known ruthenium/chloride system, the new catalyst allows for a more efficient hydrohydroxymethylation of terminal and internal olefins with carbon dioxide at lower temperature. Unwanted hydrogenation of the substrate is prevented. Preliminary mechanism investigations uncovered the homogeneous nature of the active catalyst and the influence of the ligand and additive in individual steps of the reaction sequence. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Contemporary screening approaches to reaction discovery and development.

PubMed

Collins, Karl D; Gensch, Tobias; Glorius, Frank

2014-10-01

New organic reactivity has often been discovered by happenstance. Several recent research efforts have attempted to leverage this to discover new reactions. In this Review, we attempt to unify reported approaches to reaction discovery on the basis of the practical and strategic principles applied. We concentrate on approaches to reaction discovery as opposed to reaction development, though conceptually groundbreaking approaches to identifying efficient catalyst systems are also considered. Finally, we provide a critical overview of the utility and application of the reported methods from the perspective of a synthetic chemist, and consider the future of high-throughput screening in reaction discovery.

Utilization of Stop-flow Micro-tubing Reactors for the Development of Organic Transformations.

PubMed

Toh, Ren Wei; Li, Jie Sheng; Wu, Jie

2018-01-04

A new reaction screening technology for organic synthesis was recently demonstrated by combining elements from both continuous micro-flow and conventional batch reactors, coined stop-flow micro-tubing (SFMT) reactors. In SFMT, chemical reactions that require high pressure can be screened in parallel through a safer and convenient way. Cross-contamination, which is a common problem in reaction screening for continuous flow reactors, is avoided in SFMT. Moreover, the commercially available light-permeable micro-tubing can be incorporated into SFMT, serving as an excellent choice for light-mediated reactions due to a more effective uniform light exposure, compared to batch reactors. Overall, the SFMT reactor system is similar to continuous flow reactors and more superior than batch reactors for reactions that incorporate gas reagents and/or require light-illumination, which enables a simple but highly efficient reaction screening system. Furthermore, any successfully developed reaction in the SFMT reactor system can be conveniently translated to continuous-flow synthesis for large scale production.

ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

PubMed

Fooshee, David; Andronico, Alessio; Baldi, Pierre

2013-11-25

Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu .

Control of Nitrogen Dioxide in Stack Emission by Reaction with Ammonia

NASA Technical Reports Server (NTRS)

Metzler, A. J.; Stevenson, E. F.

1970-01-01

The development of an acid base gas-phase reaction system which utilizes anhydrous ammonia as the reactant to remove nitrogen dioxide from hydrazine-nitrogen tetroxide rocket combustion exhaust is reported. This reaction reduced NO2 levels in exhaust emissions so that the resulting stack emission is completely white instead of the earlier observed typical reddish-brown coloration. Preliminary analyses indicate the importance of reaction time and ammonia concentration on removal efficiency and elimination of the health hazard to individuals with respiratory problems.

Binomial leap methods for simulating stochastic chemical kinetics.

PubMed

Tian, Tianhai; Burrage, Kevin

2004-12-01

This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on the tau-leap and midpoint tau-leap methods of Gillespie [D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001)], binomial random variables are used in these leap methods rather than Poisson random variables. The motivation for this approach is to improve the efficiency of the Poisson leap methods by using larger stepsizes. Unlike Poisson random variables whose range of sample values is from zero to infinity, binomial random variables have a finite range of sample values. This probabilistic property has been used to restrict possible reaction numbers and to avoid negative molecular numbers in stochastic simulations when larger stepsize is used. In this approach a binomial random variable is defined for a single reaction channel in order to keep the reaction number of this channel below the numbers of molecules that undergo this reaction channel. A sampling technique is also designed for the total reaction number of a reactant species that undergoes two or more reaction channels. Samples for the total reaction number are not greater than the molecular number of this species. In addition, probability properties of the binomial random variables provide stepsize conditions for restricting reaction numbers in a chosen time interval. These stepsize conditions are important properties of robust leap control strategies. Numerical results indicate that the proposed binomial leap methods can be applied to a wide range of chemical reaction systems with very good accuracy and significant improvement on efficiency over existing approaches. (c) 2004 American Institute of Physics.

Transdermal thiol-acrylate polyethylene glycol hydrogel synthesis using near infrared light

NASA Astrophysics Data System (ADS)

Chung, Solchan; Lee, Hwangjae; Kim, Hyung-Seok; Kim, Min-Gon; Lee, Luke P.; Lee, Jae Young

2016-07-01

Light-induced polymerization has been widely applied for hydrogel synthesis, which conventionally involves the use of ultraviolet or visible light to activate a photoinitiator for polymerization. However, with these light sources, transdermal gelation is not efficient and feasible due to their substantial interactions with biological systems, and thus a high power is required. In this study, we used biocompatible and tissue-penetrating near infrared (NIR) light to remotely trigger a thiol-acrylate reaction for efficient in vivo gelation with good controllability. Our gelation system includes gold nanorods as a photothermal agent, a thermal initiator, diacrylate polyethylene glycol (PEG), and thiolated PEG. Irradiation with a low-power NIR laser (0.3 W cm-2) could induce gelation via a mixed-mode reaction with a small increase in temperature (~5 °C) under the optimized conditions. We also achieved successful transdermal gelation via the NIR-assisted photothermal thiol-acryl reactions. This new type of NIR-assisted thiol-acrylate polymerization provides new opportunities for in situ hydrogel formation for injectable hydrogels and delivery of drugs/cells for various biomedical applications.Light-induced polymerization has been widely applied for hydrogel synthesis, which conventionally involves the use of ultraviolet or visible light to activate a photoinitiator for polymerization. However, with these light sources, transdermal gelation is not efficient and feasible due to their substantial interactions with biological systems, and thus a high power is required. In this study, we used biocompatible and tissue-penetrating near infrared (NIR) light to remotely trigger a thiol-acrylate reaction for efficient in vivo gelation with good controllability. Our gelation system includes gold nanorods as a photothermal agent, a thermal initiator, diacrylate polyethylene glycol (PEG), and thiolated PEG. Irradiation with a low-power NIR laser (0.3 W cm-2) could induce gelation via a mixed-mode reaction with a small increase in temperature (~5 °C) under the optimized conditions. We also achieved successful transdermal gelation via the NIR-assisted photothermal thiol-acryl reactions. This new type of NIR-assisted thiol-acrylate polymerization provides new opportunities for in situ hydrogel formation for injectable hydrogels and delivery of drugs/cells for various biomedical applications. Electronic supplementary information (ESI) available: FE-SEM image of thiol-acrylate hydrogels; UV/Vis spectra of Ellman's assay; the temperature increase during transdermal photothermal hydrogelation. See DOI: 10.1039/c6nr01956k

Towards Versatile and Sustainable Hydrogen Production through Electrocatalytic Water Splitting: Electrolyte Engineering

PubMed Central

Shinagawa, Tatsuya

2017-01-01

Abstract Recent advances in power generation from renewable resources necessitate conversion of electricity to chemicals and fuels in an efficient manner. Electrocatalytic water splitting is one of the most powerful and widespread technologies. The development of highly efficient, inexpensive, flexible, and versatile water electrolysis devices is desired. This review discusses the significance and impact of the electrolyte on electrocatalytic performance. Depending on the circumstances under which the water splitting reaction is conducted, the required solution conditions, such as the identity and molarity of ions, may significantly differ. Quantitative understanding of such electrolyte properties on electrolysis performance is effective to facilitate the development of efficient electrocatalytic systems. The electrolyte can directly participate in reaction schemes (kinetics), affect electrode stability, and/or indirectly impact the performance by influencing the concentration overpotential (mass transport). This review aims to guide fine‐tuning of the electrolyte properties, or electrolyte engineering, for (photo)electrochemical water splitting reactions. PMID:27984671

Carbon Nanomaterials in Direct Liquid Fuel Cells.

PubMed

Du, Huayun; Zhao, Cindy Xinxin; Lin, Jing; Guo, Jiang; Wang, Bin; Hu, Zhen; Shao, Qian; Pan, Duo; Wujcik, Evan K; Guo, Zhanhu

2018-04-19

Fuel cells have attracted more attentions due to many advantages they can provide, including high energy efficiency and low environmental burden. To form a stable, low cost and efficient catalyst, we presented here the state of the art of electrocatalyst fabrication approaches, involving carbon nanotubes and their multifunctional nanocomposites incorporated with noble metals, such as Pt, Pd, Au, their binary and ternary systems. Both fuel oxidation reactions and oxygen reduction reactions were emphasized with comprehensive examples and future prospects. © 2018 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical Continuous Time Random Walks

NASA Astrophysics Data System (ADS)

Aquino, T.; Dentz, M.

2017-12-01

Traditional methods for modeling solute transport through heterogeneous media employ Eulerian schemes to solve for solute concentration. More recently, Lagrangian methods have removed the need for spatial discretization through the use of Monte Carlo implementations of Langevin equations for solute particle motions. While there have been recent advances in modeling chemically reactive transport with recourse to Lagrangian methods, these remain less developed than their Eulerian counterparts, and many open problems such as efficient convergence and reconstruction of the concentration field remain. We explore a different avenue and consider the question: In heterogeneous chemically reactive systems, is it possible to describe the evolution of macroscopic reactant concentrations without explicitly resolving the spatial transport? Traditional Kinetic Monte Carlo methods, such as the Gillespie algorithm, model chemical reactions as random walks in particle number space, without the introduction of spatial coordinates. The inter-reaction times are exponentially distributed under the assumption that the system is well mixed. In real systems, transport limitations lead to incomplete mixing and decreased reaction efficiency. We introduce an arbitrary inter-reaction time distribution, which may account for the impact of incomplete mixing. This process defines an inhomogeneous continuous time random walk in particle number space, from which we derive a generalized chemical Master equation and formulate a generalized Gillespie algorithm. We then determine the modified chemical rate laws for different inter-reaction time distributions. We trace Michaelis-Menten-type kinetics back to finite-mean delay times, and predict time-nonlocal macroscopic reaction kinetics as a consequence of broadly distributed delays. Non-Markovian kinetics exhibit weak ergodicity breaking and show key features of reactions under local non-equilibrium.

Palladium Nanoparticle-Loaded Cellulose Paper: A Highly Efficient, Robust, and Recyclable Self-Assembled Composite Catalytic System.

PubMed

Zheng, Guangchao; Kaefer, Katharina; Mourdikoudis, Stefanos; Polavarapu, Lakshminarayana; Vaz, Belén; Cartmell, Samantha E; Bouleghlimat, Azzedine; Buurma, Niklaas J; Yate, Luis; de Lera, Ángel R; Liz-Marzán, Luis M; Pastoriza-Santos, Isabel; Pérez-Juste, Jorge

2015-01-15

We present a novel strategy based on the immobilization of palladium nanoparticles (Pd NPs) on filter paper for development of a catalytic system with high efficiency and recyclability. Oleylamine-capped Pd nanoparticles, dispersed in an organic solvent, strongly adsorb on cellulose filter paper, which shows a great ability to wick fluids due to its microfiber structure. Strong van der Waals forces and hydrophobic interactions between the particles and the substrate lead to nanoparticle immobilization, with no desorption upon further immersion in any solvent. The prepared Pd NP-loaded paper substrates were tested for several model reactions such as the oxidative homocoupling of arylboronic acids, the Suzuki cross-coupling reaction, and nitro-to-amine reduction, and they display efficient catalytic activity and excellent recyclability and reusability. This approach of using NP-loaded paper substrates as reusable catalysts is expected to open doors for new types of catalytic support for practical applications.

An efficient copper-catalyzed synthesis of anilines by employing aqueous ammonia.

PubMed

Zeng, Xin; Huang, Wenming; Qiu, Yatao; Jiang, Sheng

2011-12-21

Under the catalysis of CuI/2-carboxylic acid-quinoline-N-oxide, the cross coupling reactions between aryl iodides or bromides and aqueous ammonia proceed very well to afford N-unprotected aniline derivatives in excellent yields. This inexpensive catalytic system shows great functional group tolerance and excellent reaction selectivity.

Improving the electrocatalytic performance of carbon nanotubes for VO2+/VO2+ redox reaction by KOH activation

NASA Astrophysics Data System (ADS)

Dai, Lei; Jiang, Yingqiao; Meng, Wei; Zhou, Huizhu; Wang, Ling; He, Zhangxing

2017-04-01

In this paper, carbon nanotubes (CNTs) was activated by KOH treatment at high temperature and investigated as catalyst for VO2+/VO2+ redox reaction for vanadium redox flow battery (VRFB). X-ray photoelectron spectroscopy results suggest that the oxygen-containing groups can be introduced on CNTs by KOH activation. The mass transfer of vanadium ions can be accelerated by chemical etching by KOH activation and improved wettability due to the introduction of hydrophilic groups. The electrochemical properties of VO2+/VO2+ redox reaction can be enhanced by introduced oxygen-containing groups as active sites. The sample treated at 900 °C with KOH/CNTs mass ratio of 3:1 (CNTs-3) exhibits the highest electrocatalytic activity for VO2+/VO2+ redox reaction. The cell using CNTs-3 as positive catalyst demonstrates the smallest electrochemical polarization, the highest capacity and efficiency among the samples. Using KOH-activated CNTs-3 can increase the average energy efficiency of the cell by 4.4%. This work suggests that KOH-activated CNTs is a low-cost, efficient and promising catalyst for VO2+/VO2+ redox reaction for VRFB system.

Graphene Facilitated Removal of Labetalol in Laccase-ABTS System: Reaction Efficiency, Pathways and Mechanism

PubMed Central

Dong, Shipeng; Xiao, Huifang; Huang, Qingguo; Zhang, Jian; Mao, Liang; Gao, Shixiang

2016-01-01

The widespread occurrence of the beta-blocker labetalol causes environmental health concern. Enzymatic reactions are highly efficient and specific offering biochemical transformation of trace contaminants with short reaction time and little to none energy consumption. Our experiments indicate that labetalol can be effectively transformed by laccase-catalyzed reaction using 2, 2-Azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as a mediator, while no significant removal of labetalol can be achieved in the absence of ABTS. A total of three products were identified. It is interesting that the presence of graphene greatly increased the reaction rate while not changed the products. In the presence of 100 μg/L graphene, the pseudo-first-order reaction rate constant was increased ~50 times. We found that the enhancement of graphene is probably attributed to the formation and releasing of ABTS2+ which has a much greater reactivity towards labetalol when graphene is present. This study provides fundamental information for laccase-ABTS mediated labetalol reactions and the effect of graphene, which could eventually lead to development of novel methods to control beta-blocker contamination. PMID:26891761

A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems

PubMed Central

Lo, Wing-Cheong; Chen, Long; Wang, Ming; Nie, Qing

2012-01-01

An inhomogeneous steady state pattern of nonlinear reaction-diffusion equations with no-flux boundary conditions is usually computed by solving the corresponding time-dependent reaction-diffusion equations using temporal schemes. Nonlinear solvers (e.g., Newton’s method) take less CPU time in direct computation for the steady state; however, their convergence is sensitive to the initial guess, often leading to divergence or convergence to spatially homogeneous solution. Systematically numerical exploration of spatial patterns of reaction-diffusion equations under different parameter regimes requires that the numerical method be efficient and robust to initial condition or initial guess, with better likelihood of convergence to an inhomogeneous pattern. Here, a new approach that combines the advantages of temporal schemes in robustness and Newton’s method in fast convergence in solving steady states of reaction-diffusion equations is proposed. In particular, an adaptive implicit Euler with inexact solver (AIIE) method is found to be much more efficient than temporal schemes and more robust in convergence than typical nonlinear solvers (e.g., Newton’s method) in finding the inhomogeneous pattern. Application of this new approach to two reaction-diffusion equations in one, two, and three spatial dimensions, along with direct comparisons to several other existing methods, demonstrates that AIIE is a more desirable method for searching inhomogeneous spatial patterns of reaction-diffusion equations in a large parameter space. PMID:22773849

Miscible viscous fingering involving production of gel by chemical reactions

NASA Astrophysics Data System (ADS)

Nagatsu, Yuichiro; Hoshino, Kenichi

2015-11-01

We have experimentally investigated miscible viscous fingering with chemical reactions producing gel. Here, two systems were employed. In one system, sodium polyacrylate (SPA) solution and aluminum ion (Al3 +) solution were used as the more and less viscous liquids, respectively. In another system, SPA solution and ferric ion (Fe3 +) solution were used as the more and less viscous liquids, respectively. In the case of Al3 +, displacement efficiency was smaller than that in the non-reactive case, whereas in the case of Fe3 +, the displacement efficiency was larger. We consider that the difference in change of the patterns in the two systems will be caused by the difference in the properties of the gels. Therefore, we have measured the rheological properties of the gels by means of a rheometer. We discuss relationship between the VF patterns and the rheological measurement.

Sequential allylic substitution/Pauson-Khand reaction: a strategy to bicyclic fused cyclopentenones from MBH-acetates of acetylenic aldehydes.

PubMed

Raji Reddy, Chada; Kumaraswamy, Paridala; Singarapu, Kiran K

2014-09-05

An efficient approach for the construction of novel bicyclic fused cyclopentenones starting from Morita-Baylis-Hillman (MBH) acetates of acetylenic aldehydes with flexible scaffold diversity has been achieved using a two-step reaction sequence involving allylic substitution and the Pauson-Khand reaction. This strategy provided a facile access to various bicyclic cyclopentenones fused with either a carbocyclic or a heterocyclic ring system in good yield.

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics.

PubMed

Strehl, Robert; Ilie, Silvana

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.

Generation and reactions of oxiranyllithiums by use of a flow microreactor system.

PubMed

Nagaki, Aiichiro; Takizawa, Eiji; Yoshida, Jun-ichi

2010-12-17

A flow microreactor system consisting of micromixers and microtubes provides an effective reactor for the generation and reactions of aryloxiranyllithiums without decomposition by virtue of short residence time and efficient temperature control. The deprotonation of styrene oxides with sBuLi can be conducted by using the flow microreactor system at -78 or -68 °C (whereas much lower temperatures (< -100 °C) are needed for the same reactions conducted under macrobatch conditions). The resulting α-aryloxiranyllithiums were allowed to react with electrophiles in the flow microreactor system at the same temperature. The sequential introduction of various electrophiles onto 2,3-diphenyloxiranes was also achieved by using an integrated flow microreactor, which serves as a powerful system for the stereoselective synthesis of tetrasubstituted epoxides.

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.

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

NASA Astrophysics Data System (ADS)

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

2014-10-01

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

New high-efficiency ion-trap mobility detection system for narcotics

NASA Astrophysics Data System (ADS)

McGann, William J.

1997-02-01

A new patented Ion Trap Mobility Spectrometer design is presented. Conventional IMS designs typically operate below 0.1 percent efficiency. This is due primarily to electric field driven, sample ion discharge on a shutter grid. Since 99.9 percent of the sample ions generated in the reaction region are lost int his discharge process, the sensitivity of conventional systems is limited. The new design provides greater detection efficiency than conventional designs through the use of an 'ion trap' concept. The paper describes the plasma and sample ion dynamics in the reaction region of the new detector and discusses the advantages of utilizing a 'field-free' space to generate sample ions with high efficiency. Fast electronic switching is described which is used to perturb the field-free space and pulse the sample ions into the drift region for separation and subsequent detection using pseudo real-time software for analysis and display of the data. One application for this new detector is now being developed, a portable, hand-held system with switching capability for the detection of drugs and explosives. Preliminary ion spectra and sensitivity data are presented for cocaine and heroin using a hand sniffer configuration.

[Characteristics and mechanism of sodium removal by the synergistic action of flue gas and waste solid].

PubMed

Yi, Yuan-Rong; Han, Min-Fang

2012-07-01

The carbon dioxide (CO2) in flue gas was used to remove the sodium in the red mud (RM) , a kind of alkaline solid waste generated during alumina production. The reaction characteristics and mechanism of sodium removal by the synergistic action of CO2 and RM were studied with different medium pH, reaction time and temperature. It was demonstrated that the remove of sodium by RM was actually the result of the synergistic action of sodium-based solid waste in RM with the CO2-H2O and OH(-)-CO2 systems. The sodium removal efficiency was correlated with pH, reaction temperature and time. The characteristics of RM before and after sodium removal were analyzed using X-ray diffractometer (XRD) and scanning electron microscope (SEM), and the results showed that the alkaline materials in the red mud reacted with CO2 and the sodium content in solid phases decreased significantly after reaction. The sodium removal efficiency could reach up to 70% with scientific procedure. The results of this research will offer an efficient way for low-cost sodium removal.

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.

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.

Methanol Fuel Cell

NASA Technical Reports Server (NTRS)

Voecks, G. E.

1985-01-01

In proposed fuel-cell system, methanol converted to hydrogen in two places. External fuel processor converts only part of methanol. Remaining methanol converted in fuel cell itself, in reaction at anode. As result, size of fuel processor reduced, system efficiency increased, and cost lowered.

Efficiency of a hybrid-type plasma-assisted fuel reformation system

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

Matveev, I.B.; Serbin, S.I.; Lux, S.M.

2008-12-15

The major advantages of a new plasma-assisted fuel reformation system are its cost effectiveness and technical efficiency. Applied Plasma Technologies has proposed its new highly efficient hybrid-type plasma-assisted system for organic fuel combustion and gasification. The system operates as a multimode multipurpose reactor in a wide range of plasma feedstock gases and turndown ratios. This system also has convenient and simultaneous feeding of several reagents in the reaction zone such as liquid fuels, coal, steam, and air. A special methodology has been developed for such a system in terms of heat balance evaluation and optimization. This methodology considers all existingmore » and possible energy streams, which could influence the system's efficiency. The developed hybrid-type plasma system could be suitable for combustion applications, mobile and autonomous small- to mid-size liquid fuel and coal gasification modules, hydrogen-rich gas generators, waste-processing facilities, and plasma chemical reactors.« less

Computational singular perturbation analysis of stochastic chemical systems with stiffness

DOE PAGES

Wang, Lijin; Han, Xiaoying; Cao, Yanzhao; ...

2017-01-25

Computational singular perturbation (CSP) is a useful method for analysis, reduction, and time integration of stiff ordinary differential equation systems. It has found dominant utility, in particular, in chemical reaction systems with a large range of time scales at continuum and deterministic level. On the other hand, CSP is not directly applicable to chemical reaction systems at micro or meso-scale, where stochasticity plays an non-negligible role and thus has to be taken into account. In this work we develop a novel stochastic computational singular perturbation (SCSP) analysis and time integration framework, and associated algorithm, that can be used to notmore » only construct accurately and efficiently the numerical solutions to stiff stochastic chemical reaction systems, but also analyze the dynamics of the reduced stochastic reaction systems. Furthermore, the algorithm is illustrated by an application to a benchmark stochastic differential equation model, and numerical experiments are carried out to demonstrate the effectiveness of the construction.« less

Practical Synthesis of Amides via Copper/ABNO-Catalyzed Aerobic Oxidative Coupling of Alcohols and Amines.

PubMed

Zultanski, Susan L; Zhao, Jingyi; Stahl, Shannon S

2016-05-25

A modular Cu/ABNO catalyst system has been identified that enables efficient aerobic oxidative coupling of alcohols and amines to amides. All four permutations of benzylic/aliphatic alcohols and primary/secondary amines are viable in this reaction, enabling broad access to secondary and tertiary amides. The reactions exhibit excellent functional group compatibility and are complete within 30 min-3 h at rt. All components of the catalyst system are commercially available.

Modelling biochemical reaction systems by stochastic differential equations with reflection.

PubMed

Niu, Yuanling; Burrage, Kevin; Chen, Luonan

2016-05-07

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

Toward a microfluidic-based rapid amylase assay system.

PubMed

Holmes, Richard J; Summersgil, Philip; Ryan, Timothy; Brown, Bernard J Treves; Mockbil, Amal; Grieve, Bruce D; Fielden, Peter R

2009-08-01

This article describes work into a prototype system for the assay of amylase, using microfludic technologies. The new system has a significantly shorter cycle time than the current laboratory methods, which generally use microtitre plates, yet is capable of generating significantly superior results. As such, we have shown that sensitivity is enhanced by a factor of 10 in the standard assay trials, and by a factor of 2 in the real-sample lab trials. In both assays, the use of a microreactor system reduced the reaction time by a factor of 6.2, from 20 min incubation to 3.2 min. Basing the conclusion on the Megazyme Cerealpha Standard Method, and using the Cerealpha units as a measure of assay efficiency, the typical response for the microfluidic assay was shown to be 1.0 x 10(-3) CU/mL (standard deviation [SD] 2.5 x 10(-4) CU/mL), compared to 2.56 x 10(-4) CU/mL (SD 5.94 x 10(-5) CU/mL) for the standard macroassay. It is believed that this improvement in the reaction schematics is due to the inherent advantages of microfluidic devices such as superior mixing, higher thermal efficiency, and enhanced reaction kinetics.

On the enhanced sampling over energy barriers in molecular dynamics simulations.

PubMed

Gao, Yi Qin; Yang, Lijiang

2006-09-21

We present here calculations of free energies of multidimensional systems using an efficient sampling method. The method uses a transformed potential energy surface, which allows an efficient sampling of both low and high energy spaces and accelerates transitions over barriers. It allows efficient sampling of the configuration space over and only over the desired energy range(s). It does not require predetermined or selected reaction coordinate(s). We apply this method to study the dynamics of slow barrier crossing processes in a disaccharide and a dipeptide system.

Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing.

PubMed

Mora-Castilla, Sergio; To, Cuong; Vaezeslami, Soheila; Morey, Robert; Srinivasan, Srimeenakshi; Dumdie, Jennifer N; Cook-Andersen, Heidi; Jenkins, Joby; Laurent, Louise C

2016-08-01

As the cost of next-generation sequencing has decreased, library preparation costs have become a more significant proportion of the total cost, especially for high-throughput applications such as single-cell RNA profiling. Here, we have applied novel technologies to scale down reaction volumes for library preparation. Our system consisted of in vitro differentiated human embryonic stem cells representing two stages of pancreatic differentiation, for which we prepared multiple biological and technical replicates. We used the Fluidigm (San Francisco, CA) C1 single-cell Autoprep System for single-cell complementary DNA (cDNA) generation and an enzyme-based tagmentation system (Nextera XT; Illumina, San Diego, CA) with a nanoliter liquid handler (mosquito HTS; TTP Labtech, Royston, UK) for library preparation, reducing the reaction volume down to 2 µL and using as little as 20 pg of input cDNA. The resulting sequencing data were bioinformatically analyzed and correlated among the different library reaction volumes. Our results showed that decreasing the reaction volume did not interfere with the quality or the reproducibility of the sequencing data, and the transcriptional data from the scaled-down libraries allowed us to distinguish between single cells. Thus, we have developed a process to enable efficient and cost-effective high-throughput single-cell transcriptome sequencing. © 2016 Society for Laboratory Automation and Screening.

Plasmon-Enhanced Multi-Carrier Photocatalysis.

PubMed

Shaik, Firdoz; Peer, Imanuel; Jain, Prashant K; Amirav, Lilac

2018-06-22

Conversion of solar energy into liquid fuel often relies on multi-electron redox processes that include highly reactive intermediates, with back reaction routes that hinder the overall efficiency of the process. Here we reveal that these undesirable reaction pathways can be minimized, rendering the photocatalytic reactions more efficient, when charge carriers are harvested from a multi-excitonic state of a semiconductor photocatalyst. A plasmonic antenna, comprised of Au nanoprisms, was employed to accomplish feasible levels of multiple carrier excitations in semiconductor nanocrystal-based photocatalytic systems (CdSe@CdS core-shell quantum dots and CdSe@CdS seeded nanorods). The antenna's near-field amplifies the otherwise inherently weak two-photon absorption in the semiconductor. The two-electron photoreduction of Pt and Pd metal precursors served as model reactions. In the presence of the plasmonic antenna, these photocatalyzed two-electron reactions exhibited enhanced yields and kinetics. This work uniquely relies on a non-linear enhancement that has potential for large amplification of photocatalytic activity in the presence of a plasmonic near-field.

Visible-light-driven chemoselective hydrogenation of nitroarenes to anilines in water via graphitic carbon nitride metal-free photocatalysis.

PubMed

Xiao, Gang; Li, Peifeng; Zhao, Yilin; Xu, Shengnan; Su, Haijia

2018-05-20

Green and efficient procedures are highly required for the chemoselective hydrogenation of functionalized nitroarenes to industrially important anilines. Here, we show that visible-light-driven, chemoselective hydrogenation of functionalized nitroarenes bearing the sensitive groups to anilines can be achieved in good to excellent yields (82-100%) in water under relatively mild conditions, catalyzed by low-cost and recyclable graphitic carbon nitride. It is also applicable in gram-scale reaction with 86% yield of aniline. Mechanism study reveals that visible light induced electrons are responsible for the hydrogenation reactions and thermal energy can also promote the photocatalytic activity. Kinetics study shows that this reaction possibly occurs via one-step hydrogenation or stepwise condensation route. Wide applications can be expected using this green, efficient, and highly selective photocatalysis system in reduction reactions for fine chemical synthesis. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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

PubMed Central

Yang, Jin; Hlavacek, William S.

2011-01-01

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

Using Equation-Free Computation to Accelerate Network-Free Stochastic Simulation of Chemical Kinetics.

PubMed

Lin, Yen Ting; Chylek, Lily A; Lemons, Nathan W; Hlavacek, William S

2018-06-21

The chemical kinetics of many complex systems can be concisely represented by reaction rules, which can be used to generate reaction events via a kinetic Monte Carlo method that has been termed network-free simulation. Here, we demonstrate accelerated network-free simulation through a novel approach to equation-free computation. In this process, variables are introduced that approximately capture system state. Derivatives of these variables are estimated using short bursts of exact stochastic simulation and finite differencing. The variables are then projected forward in time via a numerical integration scheme, after which a new exact stochastic simulation is initialized and the whole process repeats. The projection step increases efficiency by bypassing the firing of numerous individual reaction events. As we show, the projected variables may be defined as populations of building blocks of chemical species. The maximal number of connected molecules included in these building blocks determines the degree of approximation. Equation-free acceleration of network-free simulation is found to be both accurate and efficient.

Metallic nanocatalysts for electrochemical CO2 reduction in aqueous solutions.

PubMed

Wang, Yuanxing; Niu, Cailing; Wang, Dunwei

2018-05-16

How to effectively and efficiently reduce carbon dioxide (CO 2 ) to value-added chemicals represent a frontier in catalysis research. Due to the high activation energy needs and the endothermic nature of CO 2 reduction, the reactions are difficult to carry out. When H 2 O is present, hydrogen evolution reactions (HER) often compete favorably with CO 2 reduction reactions. For these reactions, catalysts are of critical importance to CO 2 reduction. In this article, we review the various metal nanocatalysts for electrochemical CO 2 reduction (ECR) reactions. In recognition of the importance of H 2 O to CO 2 reduction, we focus our discussions on systems in aqueous solutions. Nanostructured metal catalysts are chosen for the discussions because they represent the most effective catalysts for ECR. After a brief introduction of the fundamental principles of ECR, we devote the rest of the article on the discussions of various types of nanostructured metallic catalysts, which are categorized by their compositions and working mechanisms. Lastly, strategies for improving reaction efficiency and selectivity are discussed. Copyright © 2018 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.

A general moment expansion method for stochastic kinetic models

NASA Astrophysics Data System (ADS)

Ale, Angelique; Kirk, Paul; Stumpf, Michael P. H.

2013-05-01

Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities and which allows expansion up to any number of moments. For some chemical reaction systems, more than two moments are necessary to describe the dynamic properties of the system, which the linear noise approximation is unable to provide. Moreover, also for systems for which the mean does not have a strong dependence on higher order moments, moment approximation methods give information about higher order moments of the underlying probability distribution. We demonstrate the method using a dimerisation reaction, Michaelis-Menten kinetics and a model of an oscillating p53 system. We show that for the dimerisation reaction and Michaelis-Menten enzyme kinetics system higher order moments have limited influence on the estimation of the mean, while for the p53 system, the solution for the mean can require several moments to converge to the average obtained from many stochastic simulations. We also find that agreement between lower order moments does not guarantee that higher moments will agree. Compared to stochastic simulations, our approach is numerically highly efficient at capturing the behaviour of stochastic systems in terms of the average and higher moments, and we provide expressions for the computational cost for different system sizes and orders of approximation. We show how the moment expansion method can be employed to efficiently quantify parameter sensitivity. Finally we investigate the effects of using too few moments on parameter estimation, and provide guidance on how to estimate if the distribution can be accurately approximated using only a few moments.

Towards Self-Replicating Chemical Systems Based on Cytidylic and Guanylic Acids

NASA Technical Reports Server (NTRS)

Kanavarioti, Anastassia; Bernasconi, Claude F.

1997-01-01

This project is aimed towards a better understanding of template-directed reactions and, based on this, towards the development of efficient non-enzymatic RNA replicating systems. These systems could serve as models for the prebiotic synthesis of an RNA world. The major objectives of this project were: (a) To elucidate the mechanistic aspects of template-directed (TD) chemistry, (b) to identify the conditions, environmental and other, that favor "organized chemistry" and stereo selective polymerization of nucleotides and (c) to search and, hopefully, find catalysts that will improve the efficiency of these reactions. Enhanced efficiency is expected to facilitate the road towards a self-replicating chemical system based on all four nucleic acid bases. During the first nine months of the granting period from January 1997 to October 1997, we have made substantial progress towards the first two objectives. During this period our activities were directed towards (1) synthesizing activated nucleotides to be used as substrates, (2) using these substrates in order to determine the effect of the leaving group (imidazole (Im), 2-methylimidazole (2-MeIm), and 2,4-dimethylimidazole (2,4-diMeIm)) in the product distribution, (3) developing techniques for analysis of mixtures by LC/MS, (4) creating a protocol in order to obtain kinetic parameters of the dimerization reaction and (5) analyzing kinetic data obtained with the poly(C)/2-MeImpG system. With the exception of item (5), the experimental work for the projects (1) - (4) is still in progress. A list of publications and manuscripts resulted from this research is enclosed.

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

PubMed

Salis, Howard; Kaznessis, Yiannis N

2005-12-01

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

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

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

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

Strehl, Robert; Ilie, Silvana, E-mail: silvana@ryerson.ca

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated onmore » three benchmarking systems, with special focus on approximation accuracy and efficiency.« less

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.

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

PubMed

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

2014-03-11

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

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

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

Thanh, Vo Hong, E-mail: vo@cosbi.eu; Priami, Corrado, E-mail: priami@cosbi.eu; Department of Mathematics, University of Trento

2014-10-07

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

Comparison of exciplex generation under optical and X-ray excitation

NASA Astrophysics Data System (ADS)

Kipriyanov, A. A.; Melnikov, A. R.; Stass, D. V.; Doktorov, A. B.

2017-09-01

Exciplex generation under optical and X-ray excitation in identical conditions is experimentally compared using a specially chosen model donor-acceptor system, anthracene (electron acceptor) and N,N-dimethylaniline (electron donor) in non-polar solution, and the results are analyzed and interpreted based on analytically calculated luminescence quantum yields. Calculations are performed on the basis of kinetic equations for multistage schemes of bulk exciplex production reaction under optical excitation and combination of bulk and geminate reactions of radical ion pairs under X-ray excitation. These results explain the earlier experimentally found difference in the ratio of the quantum yields of exciplexes and excited electron acceptors (exciplex generation efficiency) and the corresponding change in the exciplex generation efficiency under X-irradiation as compared to the reaction under optical excitation.

Comparison of exciplex generation under optical and X-ray excitation.

PubMed

Kipriyanov, A A; Melnikov, A R; Stass, D V; Doktorov, A B

2017-09-07

Exciplex generation under optical and X-ray excitation in identical conditions is experimentally compared using a specially chosen model donor-acceptor system, anthracene (electron acceptor) and N,N-dimethylaniline (electron donor) in non-polar solution, and the results are analyzed and interpreted based on analytically calculated luminescence quantum yields. Calculations are performed on the basis of kinetic equations for multistage schemes of bulk exciplex production reaction under optical excitation and combination of bulk and geminate reactions of radical ion pairs under X-ray excitation. These results explain the earlier experimentally found difference in the ratio of the quantum yields of exciplexes and excited electron acceptors (exciplex generation efficiency) and the corresponding change in the exciplex generation efficiency under X-irradiation as compared to the reaction under optical excitation.

Real-Time PCR Quantification Using A Variable Reaction Efficiency Model

PubMed Central

Platts, Adrian E.; Johnson, Graham D.; Linnemann, Amelia K.; Krawetz, Stephen A.

2008-01-01

Quantitative real-time PCR remains a cornerstone technique in gene expression analysis and sequence characterization. Despite the importance of the approach to experimental biology the confident assignment of reaction efficiency to the early cycles of real-time PCR reactions remains problematic. Considerable noise may be generated where few cycles in the amplification are available to estimate peak efficiency. An alternate approach that uses data from beyond the log-linear amplification phase is explored with the aim of reducing noise and adding confidence to efficiency estimates. PCR reaction efficiency is regressed to estimate the per-cycle profile of an asymptotically departed peak efficiency, even when this is not closely approximated in the measurable cycles. The process can be repeated over replicates to develop a robust estimate of peak reaction efficiency. This leads to an estimate of the maximum reaction efficiency that may be considered primer-design specific. Using a series of biological scenarios we demonstrate that this approach can provide an accurate estimate of initial template concentration. PMID:18570886

Towards Versatile and Sustainable Hydrogen Production through Electrocatalytic Water Splitting: Electrolyte Engineering.

PubMed

Shinagawa, Tatsuya; Takanabe, Kazuhiro

2017-04-10

Recent advances in power generation from renewable resources necessitate conversion of electricity to chemicals and fuels in an efficient manner. Electrocatalytic water splitting is one of the most powerful and widespread technologies. The development of highly efficient, inexpensive, flexible, and versatile water electrolysis devices is desired. This review discusses the significance and impact of the electrolyte on electrocatalytic performance. Depending on the circumstances under which the water splitting reaction is conducted, the required solution conditions, such as the identity and molarity of ions, may significantly differ. Quantitative understanding of such electrolyte properties on electrolysis performance is effective to facilitate the development of efficient electrocatalytic systems. The electrolyte can directly participate in reaction schemes (kinetics), affect electrode stability, and/or indirectly impact the performance by influencing the concentration overpotential (mass transport). This review aims to guide fine-tuning of the electrolyte properties, or electrolyte engineering, for (photo)electrochemical water splitting reactions. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Efficient conversion of 3He(n,tp) and 10B(n, α7Li) reaction energies into far-ultraviolet radiation by noble gas excimers

NASA Astrophysics Data System (ADS)

Hughes, Patrick P.; Coplan, Michael A.; Thompson, Alan K.; Vest, Robert E.; Clark, Charles W.

2011-03-01

Previous work showed that the 3He(n , tp) reaction in a cell of 3He at atmospheric pressure generated tens of far-ultraviolet (FUV) photons per reacted neutron. Here we report amplification of that signal by factors of 1000 when noble gases are added to the cell. Calibrated filter-detector measurements show that this large signal is due to noble-gas excimer emissions, and that the nuclear reaction energy is converted to FUV radiation with efficiencies of up to 30 % . Our results have been placed on an absolute scale through calibrations at the NIST SURF III Synchrotron and Center for Neutron Research. We have also seen large neutron-induced FUV signals when the 3He gas in our system is replaced with a 10B film target; an experiment on substituting 3He with BF3 is underway. Our results suggest possibilities for high-efficiency, non-3He neutron detectors as an alternative to existing proportional counters.

Modeling the oxidation kinetics of sono-activated persulfate's process on the degradation of humic acid.

PubMed

Songlin, Wang; Ning, Zhou; Si, Wu; Qi, Zhang; Zhi, Yang

2015-03-01

Ultrasound degradation of humic acid has been investigated in the presence of persulfate anions at ultrasonic frequency of 40 kHz. The effects of persulfate anion concentration, ultrasonic power input, humic acid concentration, reaction time, solution pH and temperature on humic acid removal efficiency were studied. It is found that up to 90% humic acid removal efficiency was achieved after 2 h reaction. In this system, sulfate radicals (SO₄⁻·) were considered to be the mainly oxidant to mineralize humic acid while persulfate anion can hardly react with humic acid directly. A novel kinetic model based on sulfate radicals (SO₄⁻·) oxidation was established to describe the humic acid mineralization process mathematically and chemically in sono-activated persulfate system. According to the new model, ultrasound power, persulfate dosage, solution pH and reaction temperature have great influence on humic acid degradation. Different initial concentration of persulfate anions and humic acid, ultrasonic power, initial pH and reaction temperature have been discussed to valid the effectiveness of the model, and the simulated data showed new model had good agreement with the experiments data.

Second-Order Biomimicry: In Situ Oxidative Self-Processing Converts Copper(I)/Diamine Precursor into a Highly Active Aerobic Oxidation Catalyst.

PubMed

McCann, Scott D; Lumb, Jean-Philip; Arndtsen, Bruce A; Stahl, Shannon S

2017-04-26

A homogeneous Cu-based catalyst system consisting of [Cu(MeCN) 4 ]PF 6 , N , N '-di- tert -butylethylenediamine (DBED), and p -( N , N -dimethylamino)pyridine (DMAP) mediates efficient aerobic oxidation of alcohols. Mechanistic study of this reaction shows that the catalyst undergoes an in situ oxidative self-processing step, resulting in conversion of DBED into a nitroxyl that serves as an efficient cocatalyst for aerobic alcohol oxidation. Insights into this behavior are gained from kinetic studies, which reveal an induction period at the beginning of the reaction that correlates with the oxidative self-processing step, EPR spectroscopic analysis of the catalytic reaction mixture, which shows the buildup of the organic nitroxyl species during steady state turnover, and independent synthesis of oxygenated DBED derivatives, which are shown to serve as effective cocatalysts and eliminate the induction period in the reaction. The overall mechanism bears considerable resemblance to enzymatic reactivity. Most notable is the "oxygenase"-type self-processing step that mirrors generation of catalytic cofactors in enzymes via post-translational modification of amino acid side chains. This higher-order function within a synthetic catalyst system presents new opportunities for the discovery and development of biomimetic catalysts.

Actinometric measurement of solar ultraviolet and development of a weighted solar UV integral. [photochemical reaction rate determination

NASA Technical Reports Server (NTRS)

Gupta, A.; Coulbert, C.

1978-01-01

An actinometer has been developed to measure outdoor irradiance in the range 295-400 nm. Actinometric measurements of radiation are based on determination of photochemical reaction rates for reactions of known quantum efficiency. Actinometers have the advantage of providing irradiance data over surfaces of difficult accessibility; in addition, actinometrically determined irradiance data are wavelength weighted and therefore provide a useful means of assessing the degradation rates of polymers employed in solar energy systems.

Systemic reactions during maintenance immunotherapy with honey bee venom.

PubMed

Bousquet, J; Ménardo, J L; Velasquez, G; Michel, F B

1988-07-01

Immunotherapy with hymenoptera venoms is safe and effective in most patients but treatment failures have been reported. Five patients experienced systemic symptoms of anaphylaxis when they were in maintenance immunotherapy with honey bee venom. In one case, the patient presented a severe life-threatening reaction when stung by a honey bee. Three others had the development of new clinical sensitivity suggesting a re-sensitization. This occurred in the fifth patient after a severe viral infection. By means of a rush protocol and monthly doses of 200 to 400 micrograms of honey bee venom, the patients were subsequently protected efficiently. In most cases these reactions might have been predicted since patients experienced large local reactions prior to the systemic reactions when allergens were injected. Further, in four cases there was an increased skin test reactivity or raised serum honey bee venom IgE levels or both. In all patients, the levels of serum honey bee venom IgG was under 200 U/mL (IgG Pharmacia RAST).

Limits to solar power conversion efficiency with applications to quantum and thermal systems

NASA Technical Reports Server (NTRS)

Byvik, C. E.; Buoncristiani, A. M.; Smith, B. T.

1983-01-01

An analytical framework is presented that permits examination of the limit to the efficiency of various solar power conversion devices. Thermodynamic limits to solar power efficiency are determined for both quantum and thermal systems, and the results are applied to a variety of devices currently considered for use in space systems. The power conversion efficiency for single-threshold energy quantum systems receiving unconcentrated air mass zero solar radiation is limited to 31 percent. This limit applies to photovoltaic cells directly converting solar radiation, or indirectly, as in the case of a thermophotovoltaic system. Photoelectrochemical cells rely on an additional chemical reaction at the semiconductor-electrolyte interface, which introduces additional second-law demands and a reduction of the solar conversion efficiency. Photochemical systems exhibit even lower possible efficiencies because of their relatively narrow absorption bands. Solar-powered thermal engines in contact with an ambient reservoir at 300 K and operating at maximum power have a peak conversion efficiency of 64 percent, and this occurs for a thermal reservoir at a temperature of 2900 K. The power conversion efficiency of a solar-powered liquid metal magnetohydrodydnamic generator, a solar-powered steam turbine electric generator, and an alkali metal thermoelectric converter is discussed.

Study of the reaction of atomic oxygen with aerosols

NASA Technical Reports Server (NTRS)

Akers, F. I.; Wightman, J. P.

1975-01-01

The rate of disappearance of atomic oxygen was measured at several pressures in a fast flow pyrex reactor system with its walls treated with (NH4)2SO4 (s), H2SO4 (l), and NH4CL (s). Atomic oxygen, P-3 was generated by dissociation of pure, low pressure oxygen in a microwave discharge. Concentrations of atomic oxygen were measured at several stations in the reactor system using chemiluminescent titration with NO2. Recombination efficiencies calculated from experimentally determined wall recombination rate constants are in good agreement with reported values for clean Pyrex and an H2SO4 coated wall. The recombination efficiency for (NH4)2SO4, results in a slightly lower value than for H2S04. A rapid exothermic reaction between atomic oxygen and the NH4Cl wall coating prevented recombination efficiency determination for this coating. The results show that the technique is highly useful for wall recombination measurements and as a means of extrapolating to the case of free stream aerosol-gas interactions.

Synthesis and characterization of hydrolysed starch-g-poly(methacrylic acid) composite.

PubMed

Zahran, Magdy K; Ahmed, Enas M; El-Rafie, Mohamed H

2016-06-01

A novel method for the synthesis of starch-g-poly(methacrylic acid) composite was adopted by graft polymerization of hydrolysed starch (HS) and methacrylic acid (MAA) in aqueous medium using an efficient sodium perborate (SPB)-thiourea (TU) redox initiation system. The parameters influencing the redox system efficiency and thence the polymerization method were considered. These parameters comprehended the concentrations of MAA, SPB, TU and SPB/TU molar ratio as well as the polymerization temperature. The polymerization reaction was scrutinized through calculation of the MAA total conversion percent (TC%). The resultant poly(MAA-HS) composite was assessed by evaluating the polymer criteria (the graft yield, GY%; the grafting efficiency, GE%; the homopolymer, HP%; and the total conversion). The comportment of the apparent viscosity of the cooked poly(MAA)-starch composite paste, obtained under diverse polymerization conditions, was examined. Tentative mechanisms, which depict all occasions that happen amid the entire course of the polymerization reaction, have been proffered. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Improved strategies for electrochemical 1,4-NAD(P)H2 regeneration: A new era of bioreactors for industrial biocatalysis.

PubMed

Morrison, Clifford S; Armiger, William B; Dodds, David R; Dordick, Jonathan S; Koffas, Mattheos A G

Industrial enzymatic reactions requiring 1,4-NAD(P)H 2 to perform redox transformations often require convoluted coupled enzyme regeneration systems to regenerate 1,4-NAD(P)H 2 from NAD(P) and recycle the cofactor for as many turnovers as possible. Renewed interest in recycling the cofactor via electrochemical means is motivated by the low cost of performing electrochemical reactions, easy monitoring of the reaction progress, and straightforward product recovery. However, electrochemical cofactor regeneration methods invariably produce adventitious reduced cofactor side products which result in unproductive loss of input NAD(P). We review various literature strategies for mitigating adventitious product formation by electrochemical cofactor regeneration systems, and offer insight as to how a successful electrochemical bioreactor system could be constructed to engineer efficient 1,4-NAD(P)H 2 -dependent enzyme reactions of interest to the industrial biocatalysis community. Copyright © 2017 Elsevier Inc. All rights reserved.

Improved measurement of ozone and carbonyls using a dual-bed sampling cartridge containing trans-1,2-bis(2-pyridyl)ethylene and 2,4-dinitrophenylhydrazine-impregnated silica.

PubMed

Uchiyama, Shigehisa; Naito, Suekazu; Matsumoto, Mariko; Inaba, Yohei; Kunugita, Naoki

2009-08-01

We have previously developed a new method using trans-1,2-bis-(4-pyridyl)ethylene (4-BPE) and 2,4-dinitrophenylhydrazine (DNPH) for the simultaneous determination of ozone and carbonyls in air using a two-bed cartridge system. In this method, 4-BPE was used to capture ozone. However, the method suffered from long reaction times in the eluate, low solubility of the DNPH derivative, and a strong dependence on atmospheric moisture. These problems could be overcome by using trans-1,2-bis-(2-pyridyl)ethylene (2-BPE) in place of 4-BPE. The efficiency of the reaction of ozone with 2-BPE to form pyridine-2-aldehyde (2PA) is higher than the corresponding reaction with 4-BPE. Under the optimized elution conditions, the reaction times of 2PA and 4PA with DNPH are within 15 and 120 min, respectively. In the elution from the sampling cartridge, 2PA formed from 2-BPE and ozone is easier to dissolve in the elution solvent. A stronger influence of humidity was observed in ozone recovery by the 4-BPE/DNPH method. 2-BPE exhibits a maximum reaction efficiency of 84% at 32% relative humidity (RH), while 4-BPE attains a maximum reaction efficiency of 82% at 49% RH. Humidity has much less influence on the reaction of 2-BPE with ozone. Above 18% RH, the reaction efficiency of 2-BPE with ozone is in the range 80-84%. Thus, 2-BPE is the more useful reagent for ozone analysis. The concentrations of ozone and carbonyls by the improved 2-BPE/DNPH method corresponded with the mean value by an ozone auto analyzer in an air monitoring station and a DNPH cartridge coupled with a KI-ozone scrubbing cartridge.

A general method for the catalytic nazarov cyclization of heteroaromatic compounds.

PubMed

Malona, John A; Colbourne, Jessica M; Frontier, Alison J

2006-11-23

A general, catalytic method for efficient Nazarov cyclization of systems containing heteroaromatic components has been developed. Scandium triflate was identified as the most reactive promoter, and it was found that addition of lithium perchlorate was necessary for synthetically useful catalytic cyclizations. The method was used to synthesize a range of cyclopentanone-fused heteroaromatic systems in 36-97% yield, and the reactivity trends observed demonstrate the impact of polarization on cyclization efficiency. [reaction: see text].

On Study of Application of Micro-reactor in Chemistry and Chemical Field

NASA Astrophysics Data System (ADS)

Zhang, Yunshen

2018-02-01

Serving as a micro-scale chemical reaction system, micro-reactor is characterized by high heat transfer efficiency and mass transfer, strictly controlled reaction time and good safety performance; compared with the traditional mixing reactor, it can effectively shorten reaction time by virtue of these advantages and greatly enhance the chemical reaction conversion rate. However, problems still exist in the process where micro-reactor is used for production in chemistry and chemical field, and relevant researchers are required to optimize and perfect the performance of micro-reactor. This paper analyzes specific application of micro-reactor in chemistry and chemical field.

Rhodium/Silver-Cocatalyzed Transannulation of N-Sulfonyl-1,2,3-triazoles with Vinyl Azides: Divergent Synthesis of Pyrroles and 2 H-Pyrazines.

PubMed

Zhang, Lin; Sun, Ge; Bi, Xihe

2016-11-07

The first cyclization reaction between vinyl azides and N-sulfonyl-1,2,3-triazoles is reported. A Rh/Ag binary metal catalyst system proved to be necessary for the successful cyclization. By varying the structure of vinyl azides, such reaction allows the divergent synthesis of pyrroles and 2H-pyrazines. The cyclization reactions feature a broad substrate scope, good functional group tolerance, high reaction efficiency, and good to high product yields. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Removal of high concentration p-nitrophenol in aqueous solution by zero valent iron with ultrasonic irradiation (US-ZVI).

PubMed

Lai, Bo; Chen, Zhaoyu; Zhou, Yuexi; Yang, Ping; Wang, Juling; Chen, Zhiqiang

2013-04-15

In this study, the US-ZVI system was used to produce the strong reductants including H and nascent Fe(2+) ions to eliminate the toxicity of the high concentration p-nitrophenol (PNP) wastewater. The effect of the reactor structure, initial pH, ZVI dosage, ultrasonic power and initial PNP concentration on the removal efficiency of PNP from water was investigated intensively. The results show that a higher removal rate can be obtained by using a conical structure reactor, and the lower initial pH can aid the acceleration of PNP removal rate by using US-ZVI system. Furthermore, the removal efficiencies of PNP increased obviously with the increase of initial ZVI concentration from 0 to 15 gL(-1). Also, the treatment capacity of ZVI was enhanced remarkably by the ultrasonic irradiation, and the US-ZVI system can maintain high treatment efficiency for the high concentration PNP wastewater (500-10,000 mgL(-1)). Meanwhile, the high removal efficiency of PNP was mainly resulted from the synergistic reaction of ZVI and US. At last, the main degradation product (i.e., p-aminophenol) was detected by gas chromatography-mass spectrum (GC-MS). Thus, the reaction pathway of PNP in the US-ZVI system is proposed as a reducing process by the H and nascent Fe(2+) ions. Copyright © 2013 Elsevier B.V. All rights reserved.

Roles of different initial Maillard intermediates and pathways in meat flavor formation for cysteine-xylose-glycine model reaction systems.

PubMed

Hou, Li; Xie, Jianchun; Zhao, Jian; Zhao, Mengyao; Fan, Mengdie; Xiao, Qunfei; Liang, Jingjing; Chen, Feng

2017-10-01

To explore initial Maillard reaction pathways and mechanisms for maximal formation of meaty flavors in heated cysteine-xylose-glycine systems, model reactions with synthesized initial Maillard intermediates, Gly-Amadori, TTCA (2-threityl-thiazolidine-4-carboxylic acids) and Cys-Amadori, were investigated. Relative relativities were characterized by spectrophotometrically monitoring the development of colorless degradation intermediates and browning reaction products. Aroma compounds formed were determined by solid-phase microextraction combined with GC-MS and GC-olfactometry. Gly-Amadori showed the fastest reaction followed by Cys-Amadori then TTCA. Free glycine accelerated reaction of TTCA, whereas cysteine inhibited that of Gly-Amadori due to association forming relatively stable thiazolidines. Cys-Amadori/Gly had the highest reactivity in development of both meaty flavors and brown products. TTCA/Gly favored yielding meaty flavors, whereas Gly-Amadori/Cys favored generation of brown products. Conclusively, initial formation of TTCA and pathway involving TTCA with glycine were more applicable to efficiently produce processed-meat flavorings in a cysteine-xylose-glycine system. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of a new method for measurement of neutron detector efficiency up to 20 MeV

DOE PAGES

Kornilov, N. V.; Grimes, S. M.; Massey, T. N.; ...

2014-09-03

A new approach to neutron detector efficiency has been taken. A neutron detector has been calibrated with a 252Cf source at low energy. The calibration can be extended to energies above 8 MeV based on the 252Cf results. The techniques uses the fact that the cross section for a symmetric reaction with nucleus of atomic number A yielding a final nucleus with atomic number (2A-1) and a neutron A + A → (2A – 1) + n. This reaction must be symmetric about 90° in the center-of-mass system. Furthermore, the laboratory energies for the neutrons at the paired energies differmore » substantially. Thus, an efficiency known at one of the two angles can be used to determine the efficiency to higher energies or, for a negative Q, to lower neutron energies.« less

Organocatalytic upgrading of furfural and 5-hydroxymethyl furfural to C10 and C12 furoins with quantitative yield and atom-efficiency.

PubMed

Zang, Hongjun; Chen, Eugene Y X

2015-03-30

There is increasing interest in the upgrading of C5 furfural (FF) and C6 5-hydroxymethyl furfural (HMF) into C10 and C12 furoins as higher energy-density intermediates for renewable chemicals, materials, and biofuels. This work utilizes the organocatalytic approach, using the in situ generated N,S-heterocyclic carbene catalyst derived from thiazolium ionic liquids (ILs), to achieve highly efficient self-coupling reactions of FF and HMF. Specifically, variations of the thiazolium IL structure have led to the most active and efficient catalyst system of the current series, which is derived from a new thiazolium IL carrying the electron-donating acetate group at the 5-ring position. For FF coupling by this IL (0.1 mol %, 60 °C, 1 h), when combined with Et3N, furoin was obtained in >99% yield. A 97% yield of the C12 furoin was also achieved from the HMF coupling by this catalyst system (10 mol % loading, 120 °C, 3 h). On the other hand, the thiazolium IL bearing the electron-withdrawing group at the 5-ring position is the least active and efficient catalyst. The mechanistic aspects of the coupling reaction by the thiazolium catalyst system have also been examined and a mechanism has been proposed.

REDOX electrochemical energy storage

NASA Technical Reports Server (NTRS)

Thaller, L. H.

1980-01-01

Reservoirs of chemical solutions can store electrical energy with high efficiency. Reactant solutions are stored outside conversion section where charging and discharging reactions take place. Conversion unit consists of stacks of cells connected together in parallel hydraulically, and in series electrically. Stacks resemble fuel cell batteries. System is 99% ampere-hour efficient, 75% watt hour efficient, and has long projected lifetime. Applications include storage buffering for remote solar or wind power systems, and industrial load leveling. Cost estimates are $325/kW of power requirement plus $51/kWh storage capacity. Mass production would reduce cost by about factor of two.

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.

Hybrid ODE/SSA methods and the cell cycle model

NASA Astrophysics Data System (ADS)

Wang, S.; Chen, M.; Cao, Y.

2017-07-01

Stochastic effect in cellular systems has been an important topic in systems biology. Stochastic modeling and simulation methods are important tools to study stochastic effect. Given the low efficiency of stochastic simulation algorithms, the hybrid method, which combines an ordinary differential equation (ODE) system with a stochastic chemically reacting system, shows its unique advantages in the modeling and simulation of biochemical systems. The efficiency of hybrid method is usually limited by reactions in the stochastic subsystem, which are modeled and simulated using Gillespie's framework and frequently interrupt the integration of the ODE subsystem. In this paper we develop an efficient implementation approach for the hybrid method coupled with traditional ODE solvers. We also compare the efficiency of hybrid methods with three widely used ODE solvers RADAU5, DASSL, and DLSODAR. Numerical experiments with three biochemical models are presented. A detailed discussion is presented for the performances of three ODE solvers.

Novel duplex vapor-electrochemical method for silicon solar cells. [reaction of fluorine and silicon compounds with sodium

NASA Technical Reports Server (NTRS)

Nanis, L.; Sanjurjo, A.; Sancier, K. M.; Bartlett, R.; Westphal, S.

1979-01-01

The dependence of the SiF4 Na reaction initiation time and of the efficiency of the reaction on Na particle size and reaction temperature were studied. Close to 100 percent utilization of Na was obtained, and formation of byproduct fluoro-silicate was decreased to below 10 percent. A SiF4 Na reactor was built to scale up the reaction by a factor of about four and is now being tested. A scaled up melting system was built and successfully used to separate Si from kilogram quantities of SiF4 NaF mixtures. Support studies of the volatilization of NaF performed in a smaller melting system indicated minimal loss of NaF as vapor at 1410 C. The wetting of graphite was also investigated to determine the constituents of the NaF phase which promote good wetting.

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

Ozonation of Canadian Athabasca asphaltene

NASA Astrophysics Data System (ADS)

Cha, Zhixiong

Application of ozonation in the petrochemical industry for heavy hydrocarbon upgrading has not been sufficiently explored. Among heavy hydrocarbons, asphaltenes are the heaviest and the most difficult fractions for analysis and treatment. Therefore, ozonation of asphaltenes presents an interesting application in the petrochemical industry. Commercial application of ozonation in the petrochemical industry has three obstacles: availability of an ozone-resistant and environmentally friendly solvent, the precipitation of ozonation intermediates during reaction, and recovery of the solvent and separation of the ozonation products. Preliminary ozonation of Athabasca oil sands asphaltene in nonparticipating solvents encountered serious precipitation of the ozonation intermediates. The precipitated intermediates could be polymeric ozonides and intermolecular ozonides or polymeric peroxides. Because the inhomogeneous reaction medium caused low ozone efficiency, various participating solvents such as methanol and acetic acid were added to form more soluble hydroperoxides. The mass balance results showed that on average, one asphaltene molecule reacted with 12 ozone molecules through the electrophilic reaction and the subsequent decomposition of ozonation intermediates generated acetone extractable products. GC/MS analysis of these compounds indicated that the free radical reactions could be important for generation of volatile products. The extensively ozonated asphaltene in the presence of participating solvents were refluxed with methanol to generate more volatile products. GC/MS analysis of the methanol-esterified ozonation products indicated that most volatile products were aliphatic carboxylic acid esters generated through cleavage of substituents. Reaction kinetics study showed that asphaltene ozonation was initially a diffusion rate-controlled reaction and later developed to a chemical reaction rate-controlled reaction after depletion of the reactive aromatic sites. Two new solvent systems, a self-sustaining ozonation system and a cyclohexane/acetone/water or a cyclohexane/acetone/methanol system, were studied to overcome the drawback of using halogenated solvents. The self-sustaining ozonation process employed the final ozonation products as the reaction solvent. Compared to the self-sustaining ozonation, the cyclohexane solvent system showed higher ozone efficiency; however, it required dynamic adjustment of the solvent system during ozonation. An extensively ozonated asphaltene's weight would be doubled. Distillation of the products separated about 45% volatile products having biodiesel-style chemical structures. Compared to distillation, more than 90% of the ozonation products were extractable by acetone. The remaining acetone-insoluble part was further classified by dichloromethane and other solvents of different polarities. The separated ozonation products were good fuel additives or materials for other products.

Parametric Evaluation of an Innovative Ultra-Violet PhotocatalyticOxidation (UVPCO) Air Cleaning Technology for Indoor Applications

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

Hodgson, Alfred T.; Sullivan, Douglas P.; Fisk, William J.

2005-10-31

An innovative Ultra-Violet Photocatalytic Oxidation (UVPCO) air cleaning technology employing a semitransparent catalyst coated on a semitransparent polymer substrate was evaluated to determine its effectiveness for treating mixtures of volatile organic compounds (VOCs) representative of indoor environments at low, indoor-relevant concentration levels. The experimental UVPCO contained four 30 by 30-cm honeycomb monoliths irradiated with nine UVA lamps arranged in three banks. A parametric evaluation of the effects of monolith thickness, air flow rate through the device, UV power, and reactant concentrations in inlet air was conducted for the purpose of suggesting design improvements. The UVPCO was challenged with three mixturesmore » of VOCs. A synthetic office mixture contained 27 VOCs commonly measured in office buildings. A building product mixture was created by combining sources including painted wallboard, composite wood products, carpet systems, and vinyl flooring. The third mixture contained formaldehyde and acetaldehyde. Steady state concentrations were produced in a classroom laboratory or a 20-m{sup 3} chamber. Air was drawn through the UVPCO, and single-pass conversion efficiencies were measured from replicate samples collected upstream and downstream of the reactor. Thirteen experiments were conducted in total. In this UVPCO employing a semitransparent monolith design, an increase in monolith thickness is expected to result in general increases in both reaction efficiencies and absolute reaction rates for VOCs oxidized by photocatalysis. The thickness of individual monolith panels was varied between 1.2 and 5 cm (5 to 20 cm total thickness) in experiments with the office mixture. VOC reaction efficiencies and rates increased with monolith thickness. However, the analysis of the relationship was confounded by high reaction efficiencies in all configurations for a number of compounds. These reaction efficiencies approached or exceeded 90% for alcohols, glycol ethers, and other individual compounds including d-limonene, 1,2,4-trimethylbenzene, and decamethylcyclopentasiloxane. This result implies a reaction efficiency of about 30% per irradiated monolith face, which is in agreement with the maximum efficiency for the system predicted with a simulation model. In these and other experiments, the performance of the system for highly reactive VOCs appeared to be limited by mass transport of reactants to the catalyst surface rather than by photocatalytic activity. Increasing the air flow rate through the UVPCO device decreases the residence time of the air in the monoliths and improves mass transfer to the catalyst surface. The effect of gas velocity was examined in four pairs of experiments in which the air flow rate was varied from approximately 175 m{sup 3}/h to either 300 or 600 m{sup 3}/h. Increased gas velocity caused a decrease in reaction efficiency for nearly all reactive VOCs. For all of the more reactive VOCs, the decrease in performance was less, and often substantially less, than predicted based solely on residence time, again likely due to mass transfer limitations at the low flow rate. The results demonstrate that the UVPCO is capable of achieving high conversion efficiencies for reactive VOCs at air flow rates above the base experimental rate of 175 m{sup 3}/h. The effect of UV power was examined in a series of experiments with the building product mixture in which the number of lamps was varied between nine and three. For the most reactive VOCs in the mixture, the effects of UV power were surprisingly small. Thus, even with only one lamp in each section, there appears to be sufficient photocatalytic activity to decompose most of the mass of reactive VOCs that reach the catalyst surface. For some less reactive VOCs, the trend of decreasing efficiency with decreasing UV intensity was in general agreement with simulation model predictions.« less

Remediation of trichloroethylene-contaminated groundwater by three modifier-coated microscale zero-valent iron.

PubMed

Han, Jun; Xin, Jia; Zheng, Xilai; Kolditz, Olaf; Shao, Haibing

2016-07-01

Building a microscale zero-valent iron (mZVI) reaction zone is a promising in situ remediation technology for restoring groundwater contaminated by trichloroethylene (TCE). In order to determine a suitable modifier that could not only overcome gravity sedimentation of mZVI but also improve its remediation efficiency for TCE, the three biopolymers xanthan gum (XG), guargum (GG), and carboxymethyl cellulose (CMC) were employed to coat mZVI for surface modification. The suspension stability of the modified mZVI and its TCE removal efficiency were systematically investigated. The result indicated that XG as a shear-thinning fluid showed the most remarkable efficiency of preventing mZVI from gravity sedimentation and enhancing the TCE removal efficiency by mZVI. In a 480-h experiment, the presence of XG (3 g L(-1)) increased the TCE removal efficiency by 31.85 %, whereas GG (3 g L(-1)) and CMC (3 g L(-1)) merely increased by 15.61 and 9.69 % respectively. The pH value, Eh value, and concentration of ferrous ion as functions of the reaction time were recorded in all the reaction systems, which indicated that XG worked best in buffering the pH value of the solution and inhibiting surface passivation of mZVI.

A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks

PubMed Central

Khammash, Mustafa

2014-01-01

Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology, epidemiology, immunology, systems biology and synthetic biology. It is now well-established that, for small population sizes, stochastic models for biochemical reaction networks are necessary to capture randomness in the interactions. The tools for analyzing such models, however, still lag far behind their deterministic counterparts. In this paper, we bridge this gap by developing a constructive framework for examining the long-term behavior and stability properties of the reaction dynamics in a stochastic setting. In particular, we address the problems of determining ergodicity of the reaction dynamics, which is analogous to having a globally attracting fixed point for deterministic dynamics. We also examine when the statistical moments of the underlying process remain bounded with time and when they converge to their steady state values. The framework we develop relies on a blend of ideas from probability theory, linear algebra and optimization theory. We demonstrate that the stability properties of a wide class of biological networks can be assessed from our sufficient theoretical conditions that can be recast as efficient and scalable linear programs, well-known for their tractability. It is notably shown that the computational complexity is often linear in the number of species. We illustrate the validity, the efficiency and the wide applicability of our results on several reaction networks arising in biochemistry, systems biology, epidemiology and ecology. The biological implications of the results as well as an example of a non-ergodic biological network are also discussed. PMID:24968191

One-pot synthesis of keto thioethers by palladium/gold-catalyzed click and pinacol reactions.

PubMed

Cadu, Alban; Watile, Rahul A; Biswas, Srijit; Orthaber, Andreas; Sjöberg, Per J R; Samec, Joseph S M

2014-11-07

An atom-efficient synthesis of keto thioethers was devised via tandem gold/palladium catalysis. The reaction proceeds through a regioselective thiol attack at the β-position of the alcohol, followed by an alkyl, aryl, or benzyl 1,2-shift. Both acyclic and cyclic systems were studied, in the latter case leading to the ring expansion of cyclic substrates.

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

Sugar analog synthesis by in vitro biocatalytic cascade: A comparison of alternative enzyme complements for dihydroxyacetone phosphate production as a precursor to rare chiral sugar synthesis

PubMed Central

French, Nigel G.; Scoble, Judith A.; Williams, Charlotte C.; Churches, Quentin I.; Frazer, Andrew R.; Taylor, Matthew C.; Coia, Greg; Simpson, Gregory; Turner, Nicholas J.; Scott, Colin

2017-01-01

Carbon-carbon bond formation is one of the most challenging reactions in synthetic organic chemistry, and aldol reactions catalysed by dihydroxyacetone phosphate-dependent aldolases provide a powerful biocatalytic tool for combining C-C bond formation with the generation of two new stereo-centres, with access to all four possible stereoisomers of a compound. Dihydroxyacetone phosphate (DHAP) is unstable so the provision of DHAP for DHAP-dependent aldolases in biocatalytic processes remains complicated. Our research has investigated the efficiency of several different enzymatic cascades for the conversion of glycerol to DHAP, including characterising new candidate enzymes for some of the reaction steps. The most efficient cascade for DHAP production, comprising a one-pot four-enzyme reaction with glycerol kinase, acetate kinase, glycerophosphate oxidase and catalase, was coupled with a DHAP-dependent fructose-1,6-biphosphate aldolase enzyme to demonstrate the production of several rare chiral sugars. The limitation of batch biocatalysis for these reactions and the potential for improvement using kinetic modelling and flow biocatalysis systems is discussed. PMID:29112947

Sugar analog synthesis by in vitro biocatalytic cascade: A comparison of alternative enzyme complements for dihydroxyacetone phosphate production as a precursor to rare chiral sugar synthesis.

PubMed

Hartley, Carol J; French, Nigel G; Scoble, Judith A; Williams, Charlotte C; Churches, Quentin I; Frazer, Andrew R; Taylor, Matthew C; Coia, Greg; Simpson, Gregory; Turner, Nicholas J; Scott, Colin

2017-01-01

Carbon-carbon bond formation is one of the most challenging reactions in synthetic organic chemistry, and aldol reactions catalysed by dihydroxyacetone phosphate-dependent aldolases provide a powerful biocatalytic tool for combining C-C bond formation with the generation of two new stereo-centres, with access to all four possible stereoisomers of a compound. Dihydroxyacetone phosphate (DHAP) is unstable so the provision of DHAP for DHAP-dependent aldolases in biocatalytic processes remains complicated. Our research has investigated the efficiency of several different enzymatic cascades for the conversion of glycerol to DHAP, including characterising new candidate enzymes for some of the reaction steps. The most efficient cascade for DHAP production, comprising a one-pot four-enzyme reaction with glycerol kinase, acetate kinase, glycerophosphate oxidase and catalase, was coupled with a DHAP-dependent fructose-1,6-biphosphate aldolase enzyme to demonstrate the production of several rare chiral sugars. The limitation of batch biocatalysis for these reactions and the potential for improvement using kinetic modelling and flow biocatalysis systems is discussed.

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.

Toward efficiency in heterogeneous multispecies reactive transport modeling: A particle-tracking solution for first-order network reactions

NASA Astrophysics Data System (ADS)

Henri, Christopher; Fernàndez-Garcia, Daniel

2015-04-01

Modeling multi-species reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterwards. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the effect of biochemical reactions.

Toward efficiency in heterogeneous multispecies reactive transport modeling: A particle-tracking solution for first-order network reactions

NASA Astrophysics Data System (ADS)

Henri, Christopher V.; Fernàndez-Garcia, Daniel

2014-09-01

Modeling multispecies reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterward. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the effect of biochemical reactions.

Fundamental Researches on the High-speed and High-efficiency Steelmaking Reaction

NASA Astrophysics Data System (ADS)

Kitamura, Shin-ya; Shibata, Hiroyuki; Maruoka, Nobuhiro

2012-06-01

Traditionally, steelmaking reactions have been analyzed by thermodynamics. Recently, software packages that can be used to calculate the equilibrium conditions have improved greatly. In some cases, information obtained in this software is useful for analyzing the steelmaking reaction. On the other hand, in industrial operation, steelmaking reactions, i.e., decarburization, dephosphorization, desulfurization or nitrogen removal, do not reach the equilibrium condition. Therefore, the kinetic model is very important for gaining a theoretical understanding of the steelmaking reaction. In this paper, the following recent research activities were shown; 1) mass transfer of impurities between solid oxide and liquid slag, 2) simulation model of hot metal dephosphorization by multiphase slag, 3) evaluation of reaction rate at bath surface in gas-liquid reaction system and 4) condition for forming of metal emulsion by bottom bubbling.

The Eschenmoser coupling reaction under continuous-flow conditions

PubMed Central

Singh, Sukhdeep; Köhler, J Michael; Schober, Andreas

2011-01-01

Summary The Eschenmoser coupling is a useful carbon–carbon bond forming reaction which has been used in various different synthesis strategies. The reaction proceeds smoothly if S-alkylated ternary thioamides or thiolactames are used. In the case of S-alkylated secondary thioamides or thiolactames, the Eschenmoser coupling needs prolonged reaction times and elevated temperatures to deliver valuable yields. We have used a flow chemistry system to promote the Eschenmoser coupling under enhanced reaction conditions in order to convert the demanding precursors such as S-alkylated secondary thioamides and thiolactames in an efficient way. Under pressurized reaction conditions at about 220 °C, the desired Eschenmoser coupling products were obtained within 70 s residence time. The reaction kinetics was investigated and 15 examples of different building block combinations are given. PMID:21915222

Self-Cleaning Boudouard Reactor for Full Oxygen Recovery from CO2 Project

NASA Technical Reports Server (NTRS)

Zeitlin, Nancy; Muscatello, Anthony

2015-01-01

Oxygen recovery from respiratory CO2 is an important aspect of human spaceflight. Methods exist to sequester the CO2, but production of oxygen needs further development. The current ISS Carbon Dioxide Reduction System (CRS) uses the Sabatier reaction to produce water (and ultimately breathing air). Oxygen recovery is limited to 50% because half of the hydrogen used in the Sabatier reactor is lost as methane, which is vented overboard. The Bosch reaction is the only real alternative to the Sabatier reaction, but in the last reaction in the cycle (Boudouard) the resulting carbon buildup will eventually foul the nickel or iron catalyst, reducing reactor life and increasing consumables. To minimize this fouling, find a use for this waste product, and increase efficiency, we propose testing various self-cleaning catalyst designs in an existing MSFC Boudouard reaction test bed and to determine which one is the most reliable in conversion and lack of fouling. Challenges include mechanical reliability of the cleaning method and maintaining high conversion efficiency with lower catalyst surface area. The above chemical reactions are well understood, but planned implementations are novel (TRL 2) and haven't been investigated at any level.

Temperature-programmed natural convection for micromixing and biochemical reaction in a single microfluidic chamber.

PubMed

Kim, Sung-Jin; Wang, Fang; Burns, Mark A; Kurabayashi, Katsuo

2009-06-01

Micromixing is a crucial step for biochemical reactions in microfluidic networks. A critical challenge is that the system containing micromixers needs numerous pumps, chambers, and channels not only for the micromixing but also for the biochemical reactions and detections. Thus, a simple and compatible design of the micromixer element for the system is essential. Here, we propose a simple, yet effective, scheme that enables micromixing and a biochemical reaction in a single microfluidic chamber without using any pumps. We accomplish this process by using natural convection in conjunction with alternating heating of two heaters for efficient micromixing, and by regulating capillarity for sample transport. As a model application, we demonstrate micromixing and subsequent polymerase chain reaction (PCR) for an influenza viral DNA fragment. This process is achieved in a platform of a microfluidic cartridge and a microfabricated heating-instrument with a fast thermal response. Our results will significantly simplify micromixing and a subsequent biochemical reaction that involves reagent heating in microfluidic networks.

Sensing Size through Clustering in Non-Equilibrium Membranes and the Control of Membrane-Bound Enzymatic Reactions

PubMed Central

Vagne, Quentin; Turner, Matthew S.; Sens, Pierre

2015-01-01

The formation of dynamical clusters of proteins is ubiquitous in cellular membranes and is in part regulated by the recycling of membrane components. We show, using stochastic simulations and analytic modeling, that the out-of-equilibrium cluster size distribution of membrane components undergoing continuous recycling is strongly influenced by lateral confinement. This result has significant implications for the clustering of plasma membrane proteins whose mobility is hindered by cytoskeletal “corrals” and for protein clustering in cellular organelles of limited size that generically support material fluxes. We show how the confinement size can be sensed through its effect on the size distribution of clusters of membrane heterogeneities and propose that this could be regulated to control the efficiency of membrane-bound reactions. To illustrate this, we study a chain of enzymatic reactions sensitive to membrane protein clustering. The reaction efficiency is found to be a non-monotonic function of the system size, and can be optimal for sizes comparable to those of cellular organelles. PMID:26656912

Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics.

PubMed

Bauler, Patricia; Huber, Gary; Leyh, Thomas; McCammon, J Andrew

2010-05-06

Nature often colocalizes successive steps in a metabolic pathway. Such organization is predicted to increase the effective concentration of pathway intermediates near their recipient active sites and to enhance catalytic efficiency. Here, the pathway of a two-step reaction is modeled using a simple spherical approximation for the enzymes and substrate particles. Brownian dynamics are used to simulate the trajectory of a substrate particle as it diffuses between the active site zones of two different enzyme spheres. The results approximate distances for the most effective reaction pathways, indicating that the most effective reaction pathway is one in which the active sites are closely aligned. However, when the active sites are too close, the ability of the substrate to react with the first enzyme was hindered, suggesting that even the most efficient orientations can be improved for a system that is allowed to rotate or change orientation to optimize the likelihood of reaction at both sites.

Heterobimetallic Pd-Sn catalysis: Michael addition reaction with C-, N-, O-, and S-nucleophiles and in situ diagnostics.

PubMed

Das, Debjit; Pratihar, Sanjay; Roy, Sujit

2013-03-15

An efficient Michael addition reaction of differently substituted enones with carbon, sulfur, oxygen, and nitrogen nucleophiles has been achieved by a new heterobimetallic "Pd-Sn" catalyst system. The nature of the catalytically relevant species and their interactions with the enone moiety has been examined by spectroscopy. The effect of ligand and the coordination mode of enone with "Pd-Sn" heterobimetallic system have been investigated by kinetics and DFT studies. A straightforward application of this methodology is shown in the synthesis of 1,4-oxathiepane core.

Improved removal performance and mechanism investigation of papermaking wastewater treatment using manganese enhanced Fenton reaction.

PubMed

Wang, Yingcai; Wang, Can; Shi, Shuai; Fang, Shuai

2018-06-01

The effects of Mn(II) on Fenton system to treat papermaking wastewater and the mechanism of Mn(II) enhanced Fenton reaction were investigated in this study. The chemical oxygen demand (COD) removal efficiency was enhanced in the presence of Mn(II), which increased by 19% compared with that of the Fenton system alone. The pseudo-first order reaction kinetic rate constant of Mn(II)/Fenton system was 2.11 times higher than that of Fenton system. 67%-81% COD were removed with the increasing Mn(II) concentration from 0 to 0.8 g/L. COD removal efficiency was also enhanced in a wider pH range (3-7), which indicated the operation parameters of Fenton technology could be broadened to a milder condition. The study of the mechanism showed that Mn(II) participated in the oxidation and coagulation stages in Fenton system. In the oxidation stage, Mn(II) promotes the production of HO 2 •/ O 2 • - , then HO 2 •/ O 2 • - reacts with Fe(III) to accelerate the formation of Fe(II), and finally accelerates the production of HO•. Meantime MnMnO 3 and Fe(OH) 3 forms in the coagulation stage, facilitating the removal of suspended substances and a large amount of COD, which enhances the overall COD removal of papermaking wastewater. This study provided a detailed mechanism to improve practical applications of Fenton technology.

Parallel replica dynamics with a heterogeneous distribution of barriers: Application to n-hexadecane pyrolysis

NASA Astrophysics Data System (ADS)

Kum, Oyeon; Dickson, Brad M.; Stuart, Steven J.; Uberuaga, Blas P.; Voter, Arthur F.

2004-11-01

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100-2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energetic basins. This algorithm allows efficient parallelization of small systems even when using more processors than particles (in contrast to more traditional parallelization algorithms), and even when there are frequent conformational transitions (in contrast to previous implementations of the parallel replica algorithm). The parallel efficiency for pyrolysis initiation reactions was over 90% on 61 processors for this 50-atom system. The parallel replica dynamics technique results in reaction probabilities that are statistically indistinguishable from those obtained from direct molecular dynamics, under conditions where both are feasible, but allows simulations at temperatures as much as 1000 K lower than direct molecular dynamics simulations. The rate of initiation displayed Arrhenius behavior over the entire temperature range, with an activation energy and frequency factor of Ea=79.7 kcal/mol and log A/s-1=14.8, respectively, in reasonable agreement with experiment and empirical kinetic models. Several interesting unimolecular reaction mechanisms were observed in simulations of the chain propagation reactions above 2000 K, which are not included in most coarse-grained kinetic models. More studies are needed in order to determine whether these mechanisms are experimentally relevant, or specific to the potential energy surface used.

Bicarbonate-induced activation of H₂O₂ for metal-free oxidative desulfurization.

PubMed

Bokare, Alok D; Choi, Wonyong

2016-03-05

Efficient oxidative desulfurization (ODS) of model oil containing dibenzothiophene (DBT) and aromatic thiophenic derivatives has been achieved at room temperature using hydrogen peroxide activation by inorganic bicarbonate (HCO3(-)). Using in-situ formation of peroxymonocarbonate as oxidant, the transformation of main model substrate DBT to corresponding DBT-sulfone was easily accomplished in biphasic reaction conditions. In the presence of water-acetonitrile polar phase, increasing the water content upto 50% decreased the extraction capacity more than 3 times, but ∼ 90% DBT oxidation was still achieved. The oxidizing capacity of bicarbonate catalyst was maintained during repeated ODS cycles, but DBT removal efficiency was critically dependent on the extraction capacity of the polar phase. Under heterogeneous reaction conditions, bicarbonate-modified ion-exchange resin achieved similar ODS activity compared to the homogeneous catalytic system. Additionally, the efficient formation of peroxymonocarbonate using gaseous CO2 precursor in alkaline conditions was also utilized for DBT oxidation. The present study proposes the NaHCO3/H2O2 catalytic system as an efficient and cheap metal-free alternative for the oxidative removal of aromatic sulfur compounds from fuel oil. Copyright © 2015 Elsevier B.V. All rights reserved.

New, high-efficiency ion trap mobility detection system for narcotics and explosives

NASA Astrophysics Data System (ADS)

McGann, William J.; Bradley, V.; Borsody, A.; Lepine, S.

1994-10-01

A new patented Ion Trap Mobility Spectrometer (ITMS) design is presented. Conventional IMS designs typically operate below 0.1% efficiency. This is due primarily to electric field driven, sample ion discharge on a shutter grid. Since 99.9% of the sample ions generated in the reaction region are lost in this discharge process, the sensitivity of conventional systems is limited. The new design provides greater detection efficiency than conventional designs through the use of an `ion trap' concept. The paper describes the plasma and sample ion dynamics in the reaction region of the new detector and discusses the advantages of utilizing a `field-free' space to generate sample ions with high efficiency. Fast electronic switching is described which is used to perturb the field-free space and pulse the sample ions into the drift region for separation and subsequent detection using pseudo real-time software for analysis and display of the data. Many applications for this new detector are now being considered including the detection of narcotics and explosives. Preliminary ion spectra, reduced mobility data and sensitivity data are presented for fifteen narcotics, including cocaine, THC and LSD are reported.

New high-efficiency ion trap mobility detection system for narcotics and explosives

NASA Astrophysics Data System (ADS)

McGann, William J.; Jenkins, Anthony; Ribiero, K.; Napoli, J.

1994-03-01

A new patented ion trap mobility spectrometer design is presented. Conventional IMS designs typically operate below 0.1% efficiency. This is due primarily to electrical-field-driven, sample ion discharge on a shutter grid. Since 99.9% of the sample ions generated in the reaction region are lost in this discharge process, the sensitivity of conventional systems is limited. The new design provides greater detection efficiency than conventional designs through the use of an `ion trap' concept. The paper describes the plasma and sample ion dynamics in the reaction region of the new detector and discusses the advantages of utilizing a `field-free' space to generate sample ions with high efficiency. Fast electronic switching is described which is used to perturb the field-free space and pulse the sample ions into the drift region for separation and subsequent detection using pseudo real-time software for analysis and display of the data. Many applications for this new detector are now being considered including the detection of narcotics and explosives. Preliminary ion spectra, reduced mobility data and sensitivity data are presented for fifteen narcotics, including cocaine, THC, and LSD are reported.

Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions.

PubMed

Salis, Howard; Kaznessis, Yiannis

2005-02-01

The dynamical solution of a well-mixed, nonlinear stochastic chemical kinetic system, described by the Master equation, may be exactly computed using the stochastic simulation algorithm. However, because the computational cost scales with the number of reaction occurrences, systems with one or more "fast" reactions become costly to simulate. This paper describes a hybrid stochastic method that partitions the system into subsets of fast and slow reactions, approximates the fast reactions as a continuous Markov process, using a chemical Langevin equation, and accurately describes the slow dynamics using the integral form of the "Next Reaction" variant of the stochastic simulation algorithm. The key innovation of this method is its mechanism of efficiently monitoring the occurrences of slow, discrete events while simultaneously simulating the dynamics of a continuous, stochastic or deterministic process. In addition, by introducing an approximation in which multiple slow reactions may occur within a time step of the numerical integration of the chemical Langevin equation, the hybrid stochastic method performs much faster with only a marginal decrease in accuracy. Multiple examples, including a biological pulse generator and a large-scale system benchmark, are simulated using the exact and proposed hybrid methods as well as, for comparison, a previous hybrid stochastic method. Probability distributions of the solutions are compared and the weak errors of the first two moments are computed. In general, these hybrid methods may be applied to the simulation of the dynamics of a system described by stochastic differential, ordinary differential, and Master equations.

INFORMATION RETRIEVAL EXPERIMENT. FINAL REPORT.

ERIC Educational Resources Information Center

SELYE, HANS

THIS REPORT IS A BRIEF REVIEW OF RESULTS OF AN EXPERIMENT TO DETERMINE THE INFORMATION RETRIEVAL EFFICIENCY OF A MANUAL SPECIALIZED INFORMATION SYSTEM BASED ON 700,000 DOCUMENTS IN THE FIELDS OF ENDOCRINOLOGY, STRESS, MAST CELLS, AND ANAPHYLACTOID REACTIONS. THE SYSTEM RECEIVES 30,000 PUBLICATIONS ANNUALLY. DETAILED INFORMATION IS REPRESENTED BY…

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

Evaluation and linking of effective parameters in particle-based models and continuum models for mixing-limited bimolecular reactions

NASA Astrophysics Data System (ADS)

Zhang, Yong; Papelis, Charalambos; Sun, Pengtao; Yu, Zhongbo

2013-08-01

Particle-based models and continuum models have been developed to quantify mixing-limited bimolecular reactions for decades. Effective model parameters control reaction kinetics, but the relationship between the particle-based model parameter (such as the interaction radius R) and the continuum model parameter (i.e., the effective rate coefficient Kf) remains obscure. This study attempts to evaluate and link R and Kf for the second-order bimolecular reaction in both the bulk and the sharp-concentration-gradient (SCG) systems. First, in the bulk system, the agent-based method reveals that R remains constant for irreversible reactions and decreases nonlinearly in time for a reversible reaction, while mathematical analysis shows that Kf transitions from an exponential to a power-law function. Qualitative link between R and Kf can then be built for the irreversible reaction with equal initial reactant concentrations. Second, in the SCG system with a reaction interface, numerical experiments show that when R and Kf decline as t-1/2 (for example, to account for the reactant front expansion), the two models capture the transient power-law growth of product mass, and their effective parameters have the same functional form. Finally, revisiting of laboratory experiments further shows that the best fit factor in R and Kf is on the same order, and both models can efficiently describe chemical kinetics observed in the SCG system. Effective model parameters used to describe reaction kinetics therefore may be linked directly, where the exact linkage may depend on the chemical and physical properties of the system.

Ferrocene-catalyzed heterogeneous Fenton-like degradation mechanisms and pathways of antibiotics under simulated sunlight: A case study of sulfamethoxazole.

PubMed

Li, Yingjie; Zhang, Biaojun; Liu, Xiangliang; Zhao, Qun; Zhang, Heming; Zhang, Yuechao; Ning, Ping; Tian, Senlin

2018-07-05

Readily-available and efficient catalyst is essential for activating oxidants to produce reactive species for deeply remediating water bodies contaminated by antibiotics. In this study, Ferrocene (Fc) was introduced to establish a heterogeneous photo-Fenton system for the degradation of sulfonamide antibiotics, taking sulfamethoxazole as a representative. Results showed that the removal of sulfamethoxazole was effective in Fc-catalyzed photo-Fenton system. Electron spin resonance and radical scavenging experiments verified that there was a photoindued electron transfer process from Fc to H 2 O 2 and dissolved oxygen resulting in the formation of OH that was primarily responsible for the degradation of sulfamethoxazole. The reactions of OH with substructure model compounds of sulfamethoxazole unveiled that aniline moiety was the preferable reaction site of sulfamethoxazole, which was verified by the formation of hydroxylated product and the dimer of sulfamethoxazole in Fc-catalyzed photo-Fenton system. This heterogeneous photo-Fenton system displayed an effective degradation efficiency even in a complex water matrices, and Fc represented a long-term stability by using the catalyst for multiple cycles. These results demonstrate that Fc-catalyzed photo-Fenton oxidation may be an efficient approach for remediation of wastewater containing antibiotics. Copyright © 2018. Published by Elsevier B.V.

Enzymatic synthesis of esculin ester in ionic liquids buffered with organic solvents.

PubMed

Hu, Yifan; Guo, Zheng; Lue, Bena-Marie; Xu, Xuebing

2009-05-13

The enzymatic esterification of esculin catalyzed by Candida antarctica lipase B (Novozym 435) was carried out in ionic liquid (IL)-organic solvent mixed systems in comparison with individual systems. The reaction behaviors in IL-organic solvents were systemically evaluated using acetone as a model solvent. With organic solvents as media, the esterification rates of esculin depended mainly on its solubility in solvents; for the reactions in ILs, the reaction rates were generally low, and the anion part of the IL played a critical role in enzyme activity. Therefore, the esterification of esculin in IL-acetone mixtures made it possible to improve the solubility of esculin while the effects of ILs on lipase activity were minimized. Following the benignity of ILs to lipase activity, the anions of ILs were ranked in the order as [Tf(2)N](-) > [PF(6)](-) > [BF(4)](-) > [CF(3)SO(3)](-) > [C(4)F(9)SO(3)](-) > [TAF](-) > [MDEGSO(4)](-) > [OctSO(4)](-) > [ES](-) = [DMP](-) = [OTs](- )= Cl(-). The reaction behaviors differed in different systems and largely depended on the properties of the ILs and organic solvents. In general, improvements were observed in terms of both solubility and reaction efficiency. The knowledge acquired in this work gives a better understanding of multiple interactions in IL-organic solvent systems, which provide guidance for system design and optimization.

Second-Order Biomimicry: In Situ Oxidative Self-Processing Converts Copper(I)/Diamine Precursor into a Highly Active Aerobic Oxidation Catalyst

PubMed Central

2017-01-01

A homogeneous Cu-based catalyst system consisting of [Cu(MeCN)4]PF6, N,N′-di-tert-butylethylenediamine (DBED), and p-(N,N-dimethylamino)pyridine (DMAP) mediates efficient aerobic oxidation of alcohols. Mechanistic study of this reaction shows that the catalyst undergoes an in situ oxidative self-processing step, resulting in conversion of DBED into a nitroxyl that serves as an efficient cocatalyst for aerobic alcohol oxidation. Insights into this behavior are gained from kinetic studies, which reveal an induction period at the beginning of the reaction that correlates with the oxidative self-processing step, EPR spectroscopic analysis of the catalytic reaction mixture, which shows the buildup of the organic nitroxyl species during steady state turnover, and independent synthesis of oxygenated DBED derivatives, which are shown to serve as effective cocatalysts and eliminate the induction period in the reaction. The overall mechanism bears considerable resemblance to enzymatic reactivity. Most notable is the “oxygenase”-type self-processing step that mirrors generation of catalytic cofactors in enzymes via post-translational modification of amino acid side chains. This higher-order function within a synthetic catalyst system presents new opportunities for the discovery and development of biomimetic catalysts. PMID:28470049

Metal-organic cooperative catalysis in C-H and C-C bond activation and its concurrent recovery.

PubMed

Park, Young Jun; Park, Jung-Woo; Jun, Chul-Ho

2008-02-01

The development of an efficient catalytic activation (cleavage) system for C-H and C-C bonds is an important challenge in organic synthesis, because these bonds comprise a variety of organic molecules such as natural products, petroleum oils, and polymers on the earth. Among many elegant approaches utilizing transition metals to activate C-H and C-C bonds facilely, chelation-assisted protocols based on the coordinating ability of an organic moiety have attracted great attention, though they have often suffered from the need for an intact coordinating group in a substrate. In this Account, we describe our entire efforts to activate C-H or C-C bonds adjacent to carbonyl groups by employing a new concept of metal-organic cooperative catalysis (MOCC), which enables the temporal installation of a 2-aminopyridyl group into common aldehydes or ketones in a catalytic way. Consequently, a series of new catalytic reactions such as alcohol hydroacylation, oxo-ester synthesis, C-C triple bond cleavage, hydrative dimerization of alkynes, and skeletal rearrangements of cyclic ketones was realized through MOCC. In particular, in the quest for an optimized MOCC system composed of a Wilkinson's catalyst (Ph 3P) 3RhCl and an organic catalyst (2-amino-3-picoline), surprising efficiency enhancements could be achieved when benzoic acid and aniline were introduced as promoters for the aldimine formation process. Furthermore, a notable accomplishment of C-C bond activation has been made using 2-amino-3-picoline as a temporary chelating auxiliary in the reactions of unstrained ketones with various terminal olefins and Wilkinson's catalyst. In the case of seven-membered cyclic ketones, an interesting ring contraction to five- or six-membered ones takes place through skeletal rearrangements initiated by the C-C bond activation of MOCC. On the other hand, the fundamental advances of these catalytic systems into recyclable processes could be achieved by immobilizing both metal and organic components using a hydrogen-bonded self-assembled system as a catalyst support. This catalyst-recovery system provides a homogeneous phase at high temperature during the reaction and a heterogeneous phase at room temperature after the reaction. The product could be separated conveniently from the self-assembly support system by decanting the upper layer. The immobilized catalysts of both 2-aminopyridine and rhodium metal species sustained high catalytic activity for up to the eight catalytic reactions. In conclusion, the successful incorporation of an organocatalytic cycle into a transition metal catalyzed reaction led us to find MOCC for C-H and C-C bond activation. In addition, the hydrogen-bonded self-assembled support has been developed for an efficient and effective recovery system of homogeneous catalysts and could be successful in immobilizing both metal and organic catalysts.

Solvent-assisted multistage nonequilibrium electron transfer in rigid supramolecular systems: Diabatic free energy surfaces and algorithms for numerical simulations

NASA Astrophysics Data System (ADS)

Feskov, Serguei V.; Ivanov, Anatoly I.

2018-03-01

An approach to the construction of diabatic free energy surfaces (FESs) for ultrafast electron transfer (ET) in a supramolecule with an arbitrary number of electron localization centers (redox sites) is developed, supposing that the reorganization energies for the charge transfers and shifts between all these centers are known. Dimensionality of the coordinate space required for the description of multistage ET in this supramolecular system is shown to be equal to N - 1, where N is the number of the molecular centers involved in the reaction. The proposed algorithm of FES construction employs metric properties of the coordinate space, namely, relation between the solvent reorganization energy and the distance between the two FES minima. In this space, the ET reaction coordinate zn n' associated with electron transfer between the nth and n'th centers is calculated through the projection to the direction, connecting the FES minima. The energy-gap reaction coordinates zn n' corresponding to different ET processes are not in general orthogonal so that ET between two molecular centers can create nonequilibrium distribution, not only along its own reaction coordinate but along other reaction coordinates too. This results in the influence of the preceding ET steps on the kinetics of the ensuing ET. It is important for the ensuing reaction to be ultrafast to proceed in parallel with relaxation along the ET reaction coordinates. Efficient algorithms for numerical simulation of multistage ET within the stochastic point-transition model are developed. The algorithms are based on the Brownian simulation technique with the recrossing-event detection procedure. The main advantages of the numerical method are (i) its computational complexity is linear with respect to the number of electronic states involved and (ii) calculations can be naturally parallelized up to the level of individual trajectories. The efficiency of the proposed approach is demonstrated for a model supramolecular system involving four redox centers.

Self-assembled nanospheres with multiple endohedral binding sites pre-organize catalysts and substrates for highly efficient reactions

NASA Astrophysics Data System (ADS)

Wang, Qi-Qiang; Gonell, Sergio; Leenders, Stefan H. A. M.; Dürr, Maximilian; Ivanović-Burmazović, Ivana; Reek, Joost N. H.

2016-03-01

Tuning reagent and catalyst concentrations is crucial in the development of efficient catalytic transformations. In enzyme-catalysed reactions the substrate is bound—often by multiple non-covalent interactions—in a well-defined pocket close to the active site of the enzyme; this pre-organization facilitates highly efficient transformations. Here we report an artificial system that co-encapsulates multiple catalysts and substrates within the confined space defined by an M12L24 nanosphere that contains 24 endohedral guanidinium-binding sites. Cooperative binding means that sulfonate guests are bound much more strongly than carboxylates. This difference has been used to fix gold-based catalysts firmly, with the remaining binding sites left to pre-organize substrates. This strategy was applied to a Au(I)-catalysed cyclization of acetylenic acid to enol lactone in which the pre-organization resulted in much higher reaction rates. We also found that the encapsulated sulfonate-containing Au(I) catalysts did not convert neutral (acid) substrates, and so could have potential in the development of substrate-selective catalysis and base-triggered on/off switching of catalysis.

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).

Two palladium-catalyzed domino reactions from one set of substrates/reagents: efficient synthesis of substituted indenes and cis-stilbenoid hydrocarbons from the same internal alkynes and hindered Grignard reagents.

PubMed

Dong, Cheng-Guo; Yeung, Pik; Hu, Qiao-Sheng

2007-01-18

Two types of domino reactions from the same internal alkynes and hindered Grignard reagents based on carbopalladation, Pd-catalyzed cross-coupling reaction, and a C-H activation strategy are described. The realization of these domino reactions relied on the control of the use of the ligand and the reaction temperature. Our study provides efficient access to useful polysubstituted indenes and cis-substituted stilbenes and may offer a new means of development of tandem/domino reactions in a more efficient way. [reaction: see text].

A novel liquid organic hydrogen carrier system based on catalytic peptide formation and hydrogenation

PubMed Central

Hu, Peng; Fogler, Eran; Diskin-Posner, Yael; Iron, Mark A.; Milstein, David

2015-01-01

Hydrogen is an efficient green fuel, but its low energy density when stored under high pressure or cryogenically, and safety issues, presents significant disadvantages; hence finding efficient and safe hydrogen carriers is a major challenge. Of special interest are liquid organic hydrogen carriers (LOHCs), which can be readily loaded and unloaded with considerable amounts of hydrogen. However, disadvantages include high hydrogen pressure requirements, high reaction temperatures for both hydrogenation and dehydrogenation steps, which require different catalysts, and high LOHC cost. Here we present a readily reversible LOHC system based on catalytic peptide formation and hydrogenation, using an inexpensive, safe and abundant organic compound with high potential capacity to store and release hydrogen, applying the same catalyst for loading and unloading hydrogen under relatively mild conditions. Mechanistic insight of the catalytic reaction is provided. We believe that these findings may lead to the development of an inexpensive, safe and clean liquid hydrogen carrier system. PMID:25882348

Preliminary assessment of the velocity pump reaction turbine as a geothermal total-flow expander

NASA Astrophysics Data System (ADS)

Demuth, O. J.

1984-06-01

The velocity pump reaction turbine (VPRT) was evaluated as a total flow expander in a geothermal-electric conversion cycle. Values of geofluid effectiveness of VPRT systems were estimated for conditions consisting of: a 360(F) geothermal resource, 60 F wet-bulb ambient temperature, zero and 0.003 mass concentrations of dissolved noncondensible gas in the geofluid, 100 and 120 F condensing temperatures, and engine efficiencies ranging from 0.4 to 1.0. Achievable engine efficiencies were estimated to range from 0.77, with plant geofluid effectiveness values ranging as high as 9.5 watt hr-lbm geofluid for the 360 F resource temperature. This value is competitive with magnitudes of geofluid effectiveness projected for advanced binary plants, and is on the order of 40% higher than estimates for dual-flash steam and other total flow systems reviewed. Because of its potentially high performance and relative simplicity, the VPRT system appears to warrant further investigation toward its use in a well-head geothermal plant.

A general model for techno-economic analysis of CSP plants with thermochemical energy storage systems

NASA Astrophysics Data System (ADS)

Peng, Xinyue; Maravelias, Christos T.; Root, Thatcher W.

2017-06-01

Thermochemical energy storage (TCES), with high energy density and wide operating temperature range, presents a potential solution for CSP plant energy storage. We develop a general optimization based process model for CSP plants employing a wide range of TCES systems which allows us to assess the plant economic feasibility and energy efficiency. The proposed model is applied to a 100 MW CSP plant employing ammonia or methane TCES systems. The methane TCES system with underground gas storage appears to be the most promising option, achieving a 14% LCOE reduction over the current two-tank molten-salt CSP plants. For general TCES systems, gas storage is identified as the main cost driver, while the main energy driver is the compressor electricity consumption. The impacts of separation and different reaction parameters are also analyzed. This study demonstrates that the realization of TCES systems for CSP plants is contingent upon low storage cost and a reversible reaction with proper reaction properties.

Organocatalytic Upgrading of Furfural and 5-Hydroxymethyl Furfural to C10 and C12 Furoins with Quantitative Yield and Atom-Efficiency

PubMed Central

Zang, Hongjun; Chen, Eugene Y. X.

2015-01-01

There is increasing interest in the upgrading of C5 furfural (FF) and C6 5-hydroxymethyl furfural (HMF) into C10 and C12 furoins as higher energy-density intermediates for renewable chemicals, materials, and biofuels. This work utilizes the organocatalytic approach, using the in situ generated N,S-heterocyclic carbene catalyst derived from thiazolium ionic liquids (ILs), to achieve highly efficient self-coupling reactions of FF and HMF. Specifically, variations of the thiazolium IL structure have led to the most active and efficient catalyst system of the current series, which is derived from a new thiazolium IL carrying the electron-donating acetate group at the 5-ring position. For FF coupling by this IL (0.1 mol %, 60 °C, 1 h), when combined with Et3N, furoin was obtained in >99% yield. A 97% yield of the C12 furoin was also achieved from the HMF coupling by this catalyst system (10 mol % loading, 120 °C, 3 h). On the other hand, the thiazolium IL bearing the electron-withdrawing group at the 5-ring position is the least active and efficient catalyst. The mechanistic aspects of the coupling reaction by the thiazolium catalyst system have also been examined and a mechanism has been proposed. PMID:25830482

Correlation of Hydrogen-Atom Abstraction Reaction Efficiencies for Aryl Radicals with their Vertical Electron Affinities and the Vertical Ionization Energies of the Hydrogen Atom Donors

PubMed Central

Jing, Linhong; Nash, John J.

2009-01-01

The factors that control the reactivities of aryl radicals toward hydrogen-atom donors were studied by using a dual-cell Fourier-transform ion cyclotron resonance mass spectrometer (FT – ICR). Hydrogen-atom abstraction reaction efficiencies for two substrates, cyclohexane and isopropanol, were measured for twenty-three structurally different, positively-charged aryl radicals, which included dehydrobenzenes, dehydronaphthalenes, dehydropyridines, and dehydro(iso)quinolines. A logarithmic correlation was found between the hydrogen-atom abstraction reaction efficiencies and the (calculated) vertical electron affinities (EA) of the aryl radicals. Transition state energies calculated for three of the aryl radicals with isopropanol were found to correlate linearly with their (calculated) EAs. No correlation was found between the hydrogen-atom abstraction reaction efficiencies and the (calculated) enthalpy changes for the reactions. Measurement of the reaction efficiencies for the reactions of several different hydrogen-atom donors with a few selected aryl radicals revealed a logarithmic correlation between the hydrogen-atom abstraction reaction efficiencies and the vertical ionization energies (IE) of the hydrogen-atom donors, but not the lowest homolytic X – H (X = heavy atom) bond dissociation energies of the hydrogen-atom donors. Examination of the hydrogen-atom abstraction reactions of twenty-nine different aryl radicals and eighteen different hydrogen-atom donors showed that the reaction efficiency increases (logarithmically) as the difference between the IE of the hydrogen-atom donor and the EA of the aryl radical decreases. This dependence is likely to result from the increasing polarization, and concomitant stabilization, of the transition state as the energy difference between the neutral and ionic reactants decreases. Thus, the hydrogen-atom abstraction reaction efficiency for an aryl radical can be “tuned” by structural changes that influence either the vertical EA of the aryl radical or the vertical IE of the hydrogen atom donor. PMID:19061320

An efficient graph theory based method to identify every minimal reaction set in a metabolic network

PubMed Central

2014-01-01

Background Development of cells with minimal metabolic functionality is gaining importance due to their efficiency in producing chemicals and fuels. Existing computational methods to identify minimal reaction sets in metabolic networks are computationally expensive. Further, they identify only one of the several possible minimal reaction sets. Results In this paper, we propose an efficient graph theory based recursive optimization approach to identify all minimal reaction sets. Graph theoretical insights offer systematic methods to not only reduce the number of variables in math programming and increase its computational efficiency, but also provide efficient ways to find multiple optimal solutions. The efficacy of the proposed approach is demonstrated using case studies from Escherichia coli and Saccharomyces cerevisiae. In case study 1, the proposed method identified three minimal reaction sets each containing 38 reactions in Escherichia coli central metabolic network with 77 reactions. Analysis of these three minimal reaction sets revealed that one of them is more suitable for developing minimal metabolism cell compared to other two due to practically achievable internal flux distribution. In case study 2, the proposed method identified 256 minimal reaction sets from the Saccharomyces cerevisiae genome scale metabolic network with 620 reactions. The proposed method required only 4.5 hours to identify all the 256 minimal reaction sets and has shown a significant reduction (approximately 80%) in the solution time when compared to the existing methods for finding minimal reaction set. Conclusions Identification of all minimal reactions sets in metabolic networks is essential since different minimal reaction sets have different properties that effect the bioprocess development. The proposed method correctly identified all minimal reaction sets in a both the case studies. The proposed method is computationally efficient compared to other methods for finding minimal reaction sets and useful to employ with genome-scale metabolic networks. PMID:24594118

A direct method for unfolding the resolution function from measurements of neutron induced reactions

NASA Astrophysics Data System (ADS)

Žugec, P.; Colonna, N.; Sabate-Gilarte, M.; Vlachoudis, V.; Massimi, C.; Lerendegui-Marco, J.; Stamatopoulos, A.; Bacak, M.; Warren, S. G.; n TOF Collaboration

2017-12-01

The paper explores the numerical stability and the computational efficiency of a direct method for unfolding the resolution function from the measurements of the neutron induced reactions. A detailed resolution function formalism is laid out, followed by an overview of challenges present in a practical implementation of the method. A special matrix storage scheme is developed in order to facilitate both the memory management of the resolution function matrix, and to increase the computational efficiency of the matrix multiplication and decomposition procedures. Due to its admirable computational properties, a Cholesky decomposition is at the heart of the unfolding procedure. With the smallest but necessary modification of the matrix to be decomposed, the method is successfully applied to system of 105 × 105. However, the amplification of the uncertainties during the direct inversion procedures limits the applicability of the method to high-precision measurements of neutron induced reactions.

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

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

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

2012-01-01

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

Two Palladium-Catalyzed Domino Reactions from One Set of Substrates/Reagents: Efficient Synthesis of Substituted Indenes and cis-Stilbenoid Hydrocarbons from the Same Internal Alkynes and Hindered Grignard Reagents

PubMed Central

Dong, Cheng-Guo; Yeung, Pik; Hu, Qiao-Sheng

2008-01-01

Two types of domino reactions from the same internal alkynes and hindered Grignard reagents based on carbopalladation, Pd-catalyzed cross-coupling reaction and C-H activation strategy are described. The realization of these domino reactions relied on the control of the use of the ligand and the reaction temperature. Our study provides an efficient access to useful polysubstituted indenes and cis-substituted stilbenes, and may offer new means to the development of tandem/domino reactions in a more efficient way. PMID:17217305

[An increase in efficiency of adaptations and a weakening of organism protective reactions in the process of biological evolution].

PubMed

Ivanov, K P

2014-01-01

The main direction of evolution of living organisms is development of the central nervous system and sense organ, an increase of energy exchange development of homoiothermia, development of the more and more complex forms of behavior, an increase in energy expenditure in connection with an increase of the organism activity, and development of adaptation to the habitat. Such fundamental processes were subjected and have been subjected to numerous studies and discussions. However, in different animals there exist different species peculiarities of evolution of physiological functions, from which finally formed are fundamental evolutionary processes. We studied some of these specific processes by dividing them into two categories. The first category is "Increase of efficiency of adaptation" in development of biological evolution. By this term we mean development of amazing by perfection specific physiological mechanisms of adaptive character. The second category is "Weakening of protective organism reactions". By this we understand disturbance of protective mechanisms of the organism immune system, discoordination of movement of leukocytes along microvessels, the absence of efficient collateral circulation in brain and in heart, etc.

Analysis of the Efficiency of Surfactant-Mediated Stabilization Reactions of EGaIn Nanodroplets.

PubMed

Finkenauer, Lauren R; Lu, Qingyun; Hakem, Ilhem F; Majidi, Carmel; Bockstaller, Michael R

2017-09-26

A methodology based on light scattering and spectrophotometry was developed to evaluate the effect of organic surfactants on the size and yield of eutectic gallium/indium (EGaIn) nanodroplets formed in organic solvents by ultrasonication. The process was subsequently applied to systematically evaluate the role of headgroup chemistry as well as polar/apolar interactions of aliphatic surfactant systems on the efficiency of nanodroplet formation. Ethanol was found to be the most effective solvent medium in promoting the formation and stabilization of EGaIn nanodroplets. For the case of thiol-based surfactants in ethanol, the yield of nanodroplet formation increased with the number of carbon atoms in the aliphatic part. In the case of the most effective surfactant system-octadecanethiol-the nanodroplet yield increased by about 370% as compared to pristine ethanol. The rather low overall efficiency of the reaction process along with the incompatibility of surfactant-stabilized EGaIn nanodroplets in nonpolar organic solvents suggests that the stabilization mechanism differs from the established self-assembled monolayer formation process that has been widely observed in nanoparticle formation.

Thermal and Electrical Recharging of Sodium/Sulfur Cells

NASA Technical Reports Server (NTRS)

Richter, Robert

1987-01-01

Efficiency as high as 60 percent achieved. Proposed thermal and electrical recharging scheme expected to increase overall energy efficiency of battery of sodium/sulfur cells (beta cells). Takes advantage of peculiarity in chemical kinetics of recharge portion of operating cycle to give thermal assist to electrically driven chemical reactions. Future application include portable power supplies and energy storage in commercial power systems during offpeak periods.

Optimization of enzymatic esterification of dihydrocaffeic acid with hexanol in ionic liquid using response surface methodology.

PubMed

Gholivand, Somayeh; Lasekan, Ola; Tan, Chin Ping; Abas, Faridah; Wei, Leong Sze

2017-05-26

Developing an efficient lipophilization reaction system for phenolic derivatives could enhance their applications in food processing. Low solubility of phenolic acids reduces the efficiency of phenolic derivatives in most benign enzyme solvents. The conversion of phenolic acids through esterification alters their solubility and enhances their use as food antioxidant additives as well as their application in cosmetics. This study has shown that lipase-catalyzed esterification of dihydrocaffeic acid with hexanol in ionic liquid (1-butyl-3-methylimidazoliumbis (trifluoromethylsulfonyl) imide) was the best approach for esterification reaction. In order to achieve the maximum yield, the process was optimized by response surface methodology (RSM) based on a five-level and four independent variables such as: dosage of enzyme; hexanol/dihydrocaffeic acid mole ratio; temperature and reaction time. The optimum esterification condition (Y = 84.4%) was predicted to be obtained at temperature of 39.4 °C, time of 77.5 h dosage of enzyme at 41.6% and hexanol/dihydrocaffeic acid mole ratio of 2.1. Finally, this study has produced an efficient enzymatic esterification method for the preparation of hexyl dihydrocaffeate in vitro using a lipase in an ionic liquid system. Concentration of hexanol was the most significant (p < 0.05) independent variable that influenced the yield of hexyl dihydrocaffeate. Graphical abstract Synthesis of different Hexyl dihydrocaffeates in ionic liquid.

Morphological evolution of copper nanoparticles: Microemulsion reactor system versus batch reactor system

NASA Astrophysics Data System (ADS)

Xia, Ming; Tang, Zengmin; Kim, Woo-Sik; Yu, Taekyung; Park, Bum Jun

2017-07-01

In the synthesis of nanoparticles, the reaction rate is important to determine the morphology of nanoparticles. We investigated morphology evolution of Cu nanoparticles in this two different reactors, microemulsion reactor and batch reactor. In comparison with the batch reactor system, the enhanced mass and heat transfers in the emulsion system likely led to the relatively short nucleation time and the highly homogeneous environment in the reaction mixture, resulting in suppressing one or two dimensional growth of the nanoparticles. We believe that this work can offer a good model system to quantitatively understand the crystal growth mechanism that depends strongly on the local monomer concentration, the efficiency of heat transfer, and the relative contribution of the counter ions (Br- and Cl-) as capping agents.

A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.

PubMed

Huang, Ming; Dissanayake, Thakshila; Kuechler, Erich; Radak, Brian K; Lee, Tai-Sung; Giese, Timothy J; York, Darrin M

2017-09-12

The computational efficiency of approximate quantum mechanical methods allows their use for the construction of multidimensional reaction free energy profiles. It has recently been demonstrated that quantum models based on the neglect of diatomic differential overlap (NNDO) approximation have difficulty modeling deoxyribose and ribose sugar ring puckers and thus limit their predictive value in the study of RNA and DNA systems. A method has been introduced in our previous work to improve the description of the sugar puckering conformational landscape that uses a multidimensional B-spline correction map (BMAP correction) for systems involving intrinsically coupled torsion angles. This method greatly improved the adiabatic potential energy surface profiles of DNA and RNA sugar rings relative to high-level ab initio methods even for highly problematic NDDO-based models. In the present work, a BMAP correction is developed, implemented, and tested in molecular dynamics simulations using the AM1/d-PhoT semiempirical Hamiltonian for biological phosphoryl transfer reactions. Results are presented for gas-phase adiabatic potential energy surfaces of RNA transesterification model reactions and condensed-phase QM/MM free energy surfaces for nonenzymatic and RNase A-catalyzed transesterification reactions. The results show that the BMAP correction is stable, efficient, and leads to improvement in both the potential energy and free energy profiles for the reactions studied, as compared with ab initio and experimental reference data. Exploration of the effect of the size of the quantum mechanical region indicates the best agreement with experimental reaction barriers occurs when the full CpA dinucleotide substrate is treated quantum mechanically with the sugar pucker correction.

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

Fisk, William J.; Destaillats, H.; Apte, M.G.

Heating, ventilating, and cooling classrooms in California consume substantial electrical energy. Indoor air quality (IAQ) in classrooms affects studenthealth and performance. In addition to airborne pollutants that are emitted directly by indoor sources and those generated outdoors, secondary pollutants can be formed indoors by chemical reaction of ozone with other chemicals and materials. Filters are used in nearly all classroom heating, ventilation and air?conditioning (HVAC) systems to maintain energy-efficient HVAC performance and improve indoor air quality; however, recent evidence indicates that ozone reactions with filters may, in fact, be a source of secondary pollutants. This project quantitatively evaluated ozone depositionmore » in HVAC filters and byproduct formation, and provided a preliminary assessment of the extent towhich filter systems are degrading indoor air quality. The preliminary information obtained will contribute to the design of subsequent research efforts and the identification of energy efficient solutions that improve indoor air quality in classrooms and the health and performance of students.« less

Parametric and energy consumption optimization of Basic Red 2 removal by electrocoagulation/egg shell adsorption coupling using response surface methodology in a batch system.

PubMed

de Carvalho, Helder Pereira; Huang, Jiguo; Zhao, Meixia; Liu, Gang; Yang, Xinyu; Dong, Lili; Liu, Xingjuan

2016-01-01

In this study, response surface methodology (RSM) model was applied for optimization of Basic Red 2 (BR2) removal using electrocoagulation/eggshell (ES) coupling process in a batch system. Central composite design was used to evaluate the effects and interactions of process parameters including current density, reaction time, initial pH and ES dosage on the BR2 removal efficiency and energy consumption. The analysis of variance revealed high R(2) values (≥85%) indicating that the predictions of RSM models are adequately applicable for both responses. The optimum conditions when the dye removal efficiency of 93.18% and energy consumption of 0.840 kWh/kg were observed were 11.40 mA/cm(2) current density, 5 min and 3 s reaction time, 6.5 initial pH and 10.91 g/L ES dosage.

Interfacial reaction dependent performance of hollow carbon nanosphere - sulfur composite as a cathode for Li-S battery

DOE PAGES

Zheng, Jianming; Yan, Pengfei; Gu, Meng; ...

2015-05-26

Lithium-sulfur (Li-S) battery is a promising energy storage system due to its high energy density, cost effectiveness and environmental friendliness of sulfur. However, there are still a number of challenges, such as low Coulombic efficiency and poor long-term cycling stability, impeding the commercialization of Li-S battery. The electrochemical performance of Li-S battery is closely related with the interfacial reactions occurring between hosting substrate and active sulfur species which are poorly conducting at fully oxidized and reduced states. Here, we correlate the relationship between the performance and interfacial reactions in the Li-S battery system, using a hollow carbon nanosphere (HCNS) withmore » highly graphitic character as hosting substrate for sulfur. With an appropriate amount of sulfur loading, HCNS/S composite exhibits excellent electrochemical performance because of the fast interfacial reactions between HCNS and the polysulfides. However, further increase of sulfur loading leads to increased formation of highly resistive insoluble reaction products (Li 2S 2/Li 2S) which limits the reversibility of the interfacial reactions and results in poor electrochemical performance. In conclusion, these findings demonstrate the importance of the interfacial reaction reversibility in the whole electrode system on achieving high capacity and long cycle life of sulfur cathode for Li-S batteries.« less

Glucose Synthesis in a Protein-Based Artificial Photosynthesis System.

PubMed

Lu, Hao; Yuan, Wenqiao; Zhou, Jack; Chong, Parkson Lee-Gau

2015-09-01

The objective of this study was to understand glucose synthesis of a protein-based artificial photosynthesis system affected by operating conditions, including the concentrations of reactants, reaction temperature, and illumination. Results from non-vesicle-based glyceraldehyde-3-phosphate (GAP) and glucose synthesis showed that the initial concentrations of ribulose-1,5-bisphosphate (RuBP) and adenosine triphosphate (ATP), lighting source, and temperature significantly affected glucose synthesis. Higher initial concentrations of RuBP and ATP significantly enhanced GAP synthesis, which was linearly correlated to glucose synthesis, confirming the proper functions of all catalyzing enzymes in the system. White fluorescent light inhibited artificial photosynthesis and reduced glucose synthesis by 79.2 % compared to in the dark. The reaction temperature of 40 °C was optimum, whereas lower or higher temperature reduced glucose synthesis. Glucose synthesis in the vesicle-based artificial photosynthesis system reconstituted with bacteriorhodopsin, F 0 F 1 ATP synthase, and polydimethylsiloxane-methyloxazoline-polydimethylsiloxane triblock copolymer was successfully demonstrated. This system efficiently utilized light-induced ATP to drive glucose synthesis, and 5.2 μg ml(-1) glucose was synthesized in 0.78-ml reaction buffer in 7 h. Light-dependent reactions were found to be the bottleneck of the studied artificial photosynthesis system.

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

PubMed

Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

2011-04-15

The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

Semi-implicit integration factor methods on sparse grids for high-dimensional systems

NASA Astrophysics Data System (ADS)

Wang, Dongyong; Chen, Weitao; Nie, Qing

2015-07-01

Numerical methods for partial differential equations in high-dimensional spaces are often limited by the curse of dimensionality. Though the sparse grid technique, based on a one-dimensional hierarchical basis through tensor products, is popular for handling challenges such as those associated with spatial discretization, the stability conditions on time step size due to temporal discretization, such as those associated with high-order derivatives in space and stiff reactions, remain. Here, we incorporate the sparse grids with the implicit integration factor method (IIF) that is advantageous in terms of stability conditions for systems containing stiff reactions and diffusions. We combine IIF, in which the reaction is treated implicitly and the diffusion is treated explicitly and exactly, with various sparse grid techniques based on the finite element and finite difference methods and a multi-level combination approach. The overall method is found to be efficient in terms of both storage and computational time for solving a wide range of PDEs in high dimensions. In particular, the IIF with the sparse grid combination technique is flexible and effective in solving systems that may include cross-derivatives and non-constant diffusion coefficients. Extensive numerical simulations in both linear and nonlinear systems in high dimensions, along with applications of diffusive logistic equations and Fokker-Planck equations, demonstrate the accuracy, efficiency, and robustness of the new methods, indicating potential broad applications of the sparse grid-based integration factor method.

From Förster resonance energy transfer to coherent resonance energy transfer and back

NASA Astrophysics Data System (ADS)

Clegg, Robert M.; Sener, Melih; Govindjee, .

2010-02-01

Photosynthesis converts solar energy into chemical energy. It provides food and oxygen; and, in the future, it could directly provide bioenergy or renewable energy sources, such as bio-alcohol or hydrogen. To exploit such a highly efficient capture of energy requires an understanding of the fundamental physics. The process is initiated by photon absorption, followed by highly efficient and extremely rapid transfer and trapping of the excitation energy. We first review early fluorescence experiments on in vivo energy transfer, which were undertaken to understand the mechanism of such efficient energy capture. A historical synopsis is given of experiments and interpretations by others that dealt with the question of how energy is transferred from the original location of photon absorption in the photosynthetic antenna system into the reaction centers, where it is converted into useful chemical energy. We conclude by examining the physical basis of some current models concerning the roles of coherent excitons and incoherent hopping in the exceptionally efficient transfer of energy into the reaction center.

Highly improved voltage efficiency of seawater battery by use of chloride ion capturing electrode

NASA Astrophysics Data System (ADS)

Kim, Kyoungho; Hwang, Soo Min; Park, Jeong-Sun; Han, Jinhyup; Kim, Junsoo; Kim, Youngsik

2016-05-01

Cost-effective and eco-friendly battery system with high energy density is highly desirable. Herein, we report a seawater battery with a high voltage efficiency, in which a chloride ion-capturing electrode (CICE) consisting of Ag foil is utilized as the cathode. The use of Ag as the cathode leads to a sharp decrease in the voltage gaps between charge and discharge curves, based on reversible redox reaction of Ag/AgCl (at ∼2.9 V vs. Na+/Na) in a seawater catholyte during cycling. The Ag/AgCl reaction proves to be highly reversible during battery cycling. The battery employing the Ag electrode shows excellent cycling performance with a high Coulombic efficiency (98.6-98.7%) and a highly improved voltage efficiency (90.3% compared to 73% for carbonaceous cathode) during 20 cycles (total 500 h). These findings demonstrate that seawater batteries using a CICE could be used as next-generation batteries for large-scale stationary energy storage plants.

Less haste, less waste: on recycling and its limits in strand displacement systems

PubMed Central

Condon, Anne; Hu, Alan J.; Maňuch, Ján; Thachuk, Chris

2012-01-01

We study the potential for molecule recycling in chemical reaction systems and their DNA strand displacement realizations. Recycling happens when a product of one reaction is a reactant in a later reaction. Recycling has the benefits of reducing consumption, or waste, of molecules and of avoiding fuel depletion. We present a binary counter that recycles molecules efficiently while incurring just a moderate slowdown compared with alternative counters that do not recycle strands. This counter is an n-bit binary reflecting Gray code counter that advances through 2n states. In the strand displacement realization of this counter, the waste—total number of nucleotides of the DNA strands consumed—is polynomial in n, the number of bits of the counter, while the waste of alternative counters grows exponentially in n. We also show that our n-bit counter fails to work correctly when many (Θ(n)) copies of the species that represent the bits of the counter are present initially. The proof applies more generally to show that in chemical reaction systems where all but one reactant of each reaction are catalysts, computations longer than a polynomial function of the size of the system are not possible when there are polynomially many copies of the system present. PMID:22649584

Development of Remendable Polymer Composites using a Thermoreversible Reaction

NASA Astrophysics Data System (ADS)

Peterson, Amy Michelle

2011-12-01

Materials that can repair cracks and recover from mechanical failure are desirable. Because remendable materials both repair and prevent the propagation of cracks on the micro scale, they offer the potential for increased durability, safety, and cost efficiency for many applications. The focus of this work was to understand the kinetic and physical parameters that control thermoreversible Diels-Alder bond formation in different types of healable polymeric systems. Three healing systems were developed based on the thermoreversible Diets-Alder reaction of furan and maleimide. In one, crack healing of a thermoset was induced by thermally reversible cross-linking of a secondary phase. In another, a furan-functionalized epoxy-amine thermoset were healed with a bismaleimide solution at room temperature and minimal pressure, with significant load recovery possible multiple times. The third system allowed for interfacial healing of glass fiber-reinforced epoxy-amine composites via compatible functionalization of glass fibers and the polymer network. The Diels-Alder reaction was characterized in all systems as well as highly mobile small molecule solutions. It was found that mobility, coupled with kinetics, dictate the extent of reaction and consequent strength recovery.

Investigation and kinetic evaluation of the reactions of hydroxymethylfurfural with amino and thiol groups of amino acids.

PubMed

Hamzalıoğlu, Aytül; Gökmen, Vural

2018-02-01

In this study, reactions of hydroxymethylfurfural (HMF) with selected amino acids (arginine, cysteine and lysine) were investigated in HMF-amino acid (high moisture) and Coffee-amino acid (low moisture) model systems at 5, 25 and 50°C. The results revealed that HMF reacted efficiently and effectively with amino acids in both high and low moisture model systems. High-resolution mass spectrometry (HRMS) analyses of the reaction mixtures confirmed the formations of Michael adduct and Schiff base of HMF with amino acids. Calculated pseudo-first order reaction rate constants were in the following order; k Cysteine >k Arginine >k Lysine for high moisture model systems. Comparing to these rate constants, the k Cysteine decreased whereas, k Arginine and k Lysine increased under the low moisture conditions of Coffee-amino acid model systems. The temperature dependence of the rate constants was found to obey the Arrhenius law in a temperature range of 5-50°C under both low and high moisture conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Infrared Chemiluminescence Studies of Ion-Molecule Reactions in a Flowing Afterglow.

DTIC Science & Technology

1982-01-01

reaction rate constants and branching ratios have been addressed in drift tubes and flow drift systems, and the translational energy distribution of atomic...composed of about 40 thin cylindrical sections of flow tube , separated by mylar spacers and connected by precision resistors. In the region of LIF... tube radius (Albritton, 1967). For proper operation of a drift tube , ionic species of only one polarity can be present. Efficient separation of

Numerical Simulation of Pulse Detonation Rocket-Induced MHD Ejector (PDRIME) Concepts for Advanced Propulsion Systems

DTIC Science & Technology

2012-02-28

Coupling in Detonation Waves: 1D Dynamics”, Paper 89, 23rd International Colloquium on the Dynamics of Explosions and Reactive ...and temperature, and can be modeled as a constant volume reaction , which is more efficient than a constant pressure reaction . After the detonation ... kinetics , and flow processes using high order numerical methods. A fifth-order WENO (weighted essentially non -oscillatory12,13) scheme was used

Exquisite Enzyme-Fenton Biomimetic Catalysts for Hydroxyl Radical Production by Mimicking an Enzyme Cascade.

PubMed

Zhang, Qi; Chen, Shuo; Wang, Hua; Yu, Hongtao

2018-03-14

Hydrogen peroxide (H 2 O 2 ) is a key reactant in the Fenton process. As a byproduct of enzymatic reaction, H 2 O 2 can be obtained via catalytical oxidation of glucose using glucose oxidase in the presence of O 2 . Another oxidation product (gluconic acid) can suitably adjust the microenvironmental pH contributing to the Fe 3+ /Fe 2+ cycle in the Fenton reaction. Enzymes are extremely efficient at catalyzing a variety of reactions with high catalytic activity, substrate specificity, and yields in living organisms. Inspired by the multiple functions of natural multienzyme systems, an exquisite nanozyme-modified α-FeOOH/porous carbon (PC) biomimetic catalyst constructed by in situ growth of glucose oxidase-mimicking Au nanoparticles and crystallization of adsorbed ferric ions within carboxyl into hierarchically PC is developed as an efficient enzyme-Fenton catalyst. The products (H 2 O 2 , ∼4.07 mmol·L -1 ) of the first enzymatic reaction are immediately used as substrates for the second Fenton-like reaction to generate the valuable • OH (∼96.84 μmol·L -1 ), thus mimicking an enzyme cascade pathway. α-FeOOH nanocrystals, attached by C-O-Fe bondings, are encapsulated into the mesoporous PC frameworks, facilitating the electron transfer between α-FeOOH and the PC support and greatly suppressing iron leaching. This study paves a new avenue for designing biomimetic enzyme-based Fenton catalysts mimicking a natural system for • OH production.

Renewable Wood Pulp Paper Reactor with Hierarchical Micro/Nanopores for Continuous-Flow Nanocatalysis.

PubMed

Koga, Hirotaka; Namba, Naoko; Takahashi, Tsukasa; Nogi, Masaya; Nishina, Yuta

2017-06-22

Continuous-flow nanocatalysis based on metal nanoparticle catalyst-anchored flow reactors has recently provided an excellent platform for effective chemical manufacturing. However, there has been limited progress in porous structure design and recycling systems for metal nanoparticle-anchored flow reactors to create more efficient and sustainable catalytic processes. In this study, traditional paper is used for a highly efficient, recyclable, and even renewable flow reactor by tailoring the ultrastructures of wood pulp. The "paper reactor" offers hierarchically interconnected micro- and nanoscale pores, which can act as convective-flow and rapid-diffusion channels, respectively, for efficient access of reactants to metal nanoparticle catalysts. In continuous-flow, aqueous, room-temperature catalytic reduction of 4-nitrophenol to 4-aminophenol, a gold nanoparticle (AuNP)-anchored paper reactor with hierarchical micro/nanopores provided higher reaction efficiency than state-of-the-art AuNP-anchored flow reactors. Inspired by traditional paper materials, successful recycling and renewal of AuNP-anchored paper reactors were also demonstrated while high reaction efficiency was maintained. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Renewable Wood Pulp Paper Reactor with Hierarchical Micro/Nanopores for Continuous‐Flow Nanocatalysis

PubMed Central

Namba, Naoko; Takahashi, Tsukasa; Nogi, Masaya; Nishina, Yuta

2017-01-01

Abstract Continuous‐flow nanocatalysis based on metal nanoparticle catalyst‐anchored flow reactors has recently provided an excellent platform for effective chemical manufacturing. However, there has been limited progress in porous structure design and recycling systems for metal nanoparticle‐anchored flow reactors to create more efficient and sustainable catalytic processes. In this study, traditional paper is used for a highly efficient, recyclable, and even renewable flow reactor by tailoring the ultrastructures of wood pulp. The “paper reactor” offers hierarchically interconnected micro‐ and nanoscale pores, which can act as convective‐flow and rapid‐diffusion channels, respectively, for efficient access of reactants to metal nanoparticle catalysts. In continuous‐flow, aqueous, room‐temperature catalytic reduction of 4‐nitrophenol to 4‐aminophenol, a gold nanoparticle (AuNP)‐anchored paper reactor with hierarchical micro/nanopores provided higher reaction efficiency than state‐of‐the‐art AuNP‐anchored flow reactors. Inspired by traditional paper materials, successful recycling and renewal of AuNP‐anchored paper reactors were also demonstrated while high reaction efficiency was maintained. PMID:28394501

Advanced degradation of brominated epoxy resin and simultaneous transformation of glass fiber from waste printed circuit boards by improved supercritical water oxidation processes.

PubMed

Liu, Kang; Zhang, Zhiyuan; Zhang, Fu-Shen

2016-10-01

This work investigated various supercritical water oxidation (SCWO) systems, i.e. SCWO1 (only water), SCWO2 (water+H2O2) and SCWO3 (water+H2O2/NaOH), for waste printed circuit boards (PCBs) detoxification and recycling. Response surface methodology (RSM) was applied to optimize the operating conditions of the optimal SCWO3 systems. The optimal reaction conditions for debromination were found to be the NaOH of 0.21g, the H2O2 volume of 9.04mL, the time of 39.7min, maximum debromination efficiency of 95.14%. Variance analysis indicated that the factors influencing debromination efficiency was in the sequence of NaOH>H2O2>time. Mechanism studies indicated that the dissociated ions from NaOH in supercritical water promoted the debromination of brominated epoxy resins (BERs) through an elimination reaction and nucleophilic substitution. HO2, produced by H2O2 could induce the oxidation of phenol ring to open (intermediates of BERs), which were thoroughly degraded to form hydrocarbons, CO2, H2O and NaBr. In addition, the alkali-silica reaction between OH(-) and SiO2 induced the phase transformation of glass fibers, which were simultaneously converted into anorthite and albite. Waste PCBs in H2O2/NaOH improved SCWO system were fully degraded into useful products and simultaneously transformed into functional materials. These findings are helpful for efficient recycling of waste PCBs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Essential chemistry for biochemists

PubMed Central

Jonsson, Amanda L.; Roberts, Mark A.J.; Kiappes, J.L.; Scott, Kathryn A.

2017-01-01

Within every living organism, countless reactions occur every second. These reactions typically occur more rapidly and with greater efficiency than would be possible under the same conditions in the chemical laboratory, and while using only the subset of elements that are readily available in nature. Despite these apparent differences between life and the laboratory, biological reactions are governed by the same rules as any other chemical reaction. Thus, a firm understanding of the fundamentals of chemistry is invaluable in biochemistry. There are entire textbooks devoted to the application of chemical principles in biological systems and so it is not possible to cover all of the relevant topics in depth in this short article. The aim is instead to provide a brief overview of those areas in chemistry that are most relevant to biochemistry. We summarize the basic principles, give examples of how these principles are applied in biological systems and suggest further reading on individual topics. PMID:28951470

Liposome-chaperoned cell-free synthesis for the design of proteoliposomes: Implications for therapeutic delivery.

PubMed

Lu, Mei; Zhao, Xiaoyun; Xing, Haonan; Xun, Zhe; Yang, Tianzhi; Cai, Cuifang; Wang, Dongkai; Ding, Pingtian

2018-04-03

Cell-free (CF) protein synthesis has emerged as a powerful technique platform for efficient protein production in vitro. Liposomes have been widely studied as therapeutic carriers due to their biocompatibility, biodegradability, low toxicity, flexible surface manipulation, easy preparation, and higher cargo encapsulation capability. However, rapid immune clearance, insufficient targeting capacity, and poor cytoplasmic delivery efficiency substantially restrict their clinical application. The incorporation of functional membrane proteins (MPs) or peptides allows the transfer of biological properties to liposomes and imparts them with improved circulation, increased targeting, and efficient intracellular delivery. Liposome-chaperoned CF synthesis enables production of proteoliposomes in one-step reaction, which not only substantially simplifies the production procedure but also keeps protein functionality intact. Building off these observations, proteoliposomes with integrated MPs represent an excellent candidate for therapeutic delivery. In this review, we describe recent advances in CF synthesis with emphasis on detailing key factors for improving CF expression efficiency. Furthermore, we provide insights into strategies for rational design of proteoliposomal nanodelivery systems via CF synthesis. Liposome-chaperoned CF synthesis has emerged as a powerful approach for the design of recombinant proteoliposomes in one-step reaction. The incorporation of bioactive MPs or peptides into liposomes via CF synthesis can facilitate the development of proteoliposomal nanodelivery systems with improved circulation, increased targeting, and enhanced cellular delivery capacity. Moreover, by adapting lessons learned from natural delivery vehicles, novel bio-inspired proteoliposomes with enhanced delivery properties could be produced in CF systems. In this review, we first give an overview of CF synthesis with focus on enhancing protein expression in liposome-chaperoned CF systems. Furthermore, we intend to provide insight into harnessing CF-synthesized proteoliposomes for efficient therapeutic delivery. Copyright © 2018. Published by Elsevier Ltd.

A proposed simulation method for directed self-assembly of nanographene

NASA Astrophysics Data System (ADS)

Geraets, J. A.; Baldwin, J. P. C.; Twarock, R.; Hancock, Y.

2017-09-01

A methodology for predictive kinetic self-assembly modeling of bottom-up chemical synthesis of nanographene is proposed. The method maintains physical transparency in using a novel array format to efficiently store molecule information and by using array operations to determine reaction possibilities. Within a minimal model approach, the parameter space for the bond activation energies (i.e. molecule functionalization) at fixed reaction temperature and initial molecule concentrations is explored. Directed self-assembly of nanographene from functionalized tetrabenzanthracene and benzene is studied with regions in the activation energy phase-space showing length-to-width ratio tunability. The degree of defects and reaction reproducibility in the simulations is also determined, with the rate of functionalized benzene addition providing additional control of the dimension and quality of the nanographene. Comparison of the reaction energetics to available density functional theory data suggests the synthesis may be experimentally tenable using aryl-halide cross-coupling and noble metal surface-assisted catalysis. With full access to the intermediate reaction network and with dynamic coupling to density functional theory-informed tight-binding simulation, the method is proposed as a computationally efficient means towards detailed simulation-driven design of new nanographene systems.

Electrochemical synthesis of azanucleoside derivatives using a lithium perchlorate-nitromethane system.

PubMed

Kim, Shokaku; Shoji, Takao; Kitano, Yoshikazu; Chiba, Kazuhiro

2013-07-25

We have developed a highly efficient synthetic method for azanucleosides using a lithium perchlorate-nitromethane reaction medium, allowing direct and exclusive installation of various nucleophiles, including protected nucleobases into prolinol derivatives at the preferred 5-position.

Single, simultaneous and sequential applications of ultrasonic frequencies for the elimination of ibuprofen in water.

PubMed

Ziylan-Yavas, Asu; Ince, Nilsun H

2018-01-01

The study is about the assessment of single and multi-frequency operations for the overall degradation of a widely consumed analgesic pharmaceutical-ibuprofen (IBP). The selected frequencies were in the range of 20-1130kHz emissions coming from probes, baths and piezo-electric transducers attached to plate-type devices. Multi-frequency operations were applied either simultaneously as "duals", or sequentially at fixed time intervals; and the total reaction time in all operations was 30-min. The work also covers evaluation of the effect of zero-valent iron (ZVI) on the efficiency of the degradation process and the performance of the reaction systems. It was found that low-frequency probe type devices especially at 20kHz were ineffective when applied singly and without ZVI, and relatively more effective in combined-frequency operations in the presence of ZVI. The power efficiencies of the reactors and/or reaction systems showed that 20-kHz probe was considerably more energy intensive than all others, and was therefore not used in multi-frequency operations. The most efficient reactor in terms of power consumption was the bath (200kHz), which however provided insufficient mineralization of the test chemical. The highest percentage of TOC decay (37%) was obtained in a dual-frequency operation (40/572kHz) with ZVI, in which the energy consumption was neither low nor exceptionally too high. A sequential operation (40+200kHz) in that respect was more efficient, because it required much less energy for a similar TOC decay performance (30%). In general, the degradation of IBP increased with increased power consumption, which in turn reduced the sonochemical yield. The study also showed that advanced Fenton reactions with ZVI were faster in the presence of ultrasound, and the metal was very effective in improving the performance of low-frequency operations. Copyright © 2017 Elsevier B.V. All rights reserved.

Recent advances in isoxazole chemistry

NASA Astrophysics Data System (ADS)

Galenko, A. V.; Khlebnikov, A. F.; Novikov, M. S.; Pakalnis, V. V.; Rostovskii, N. V.

2015-04-01

The preparation methods and reactions of isoxazoles are described and systematized on the basis of analysis of the literature published from 2005 to present. In the discussion of synthesis, major attention is focused on the most efficient approaches: condensation of hydroxylamine with 1,3-dielectrophiles and reactions of nitrile oxides with alkenes and alkynes. Five-membered ring opening reactions leading to acyclic functionalized or other heterocyclic compounds are considered. The transformations of isoxazole derivatives that occur without ring cleavage to form fused heterocyclic systems, as well as reactions that lead to the introduction of C-substituents into isoxazoles, are considered. Data on the biological activity of some isoxazole derivatives are reported. The bibliography includes 439 references.

Study of the 20,22Ne+20,22Ne and 10,12,13,14,15C+12C Fusion Reactions with MUSIC

NASA Astrophysics Data System (ADS)

Avila, M. L.; Rehm, K. E.; Almaraz-Calderon, S.; Carnelli, P. F. F.; DiGiovine, B.; Esbensen, H.; Hoffman, C. R.; Jiang, C. L.; Kay, B. P.; Lai, J.; Nusair, O.; Pardo, R. C.; Santiago-Gonzalez, D.; Talwar, R.; Ugalde, C.

2016-05-01

A highly efficient MUlti-Sampling Ionization Chamber (MUSIC) detector has been developed for measurements of fusion reactions. A study of fusion cross sections in the 10,12,13,14,15C+12C and 20,22Ne+20,22Ne systems has been performed at ATLAS. Experimental results and comparison with theoretical predictions are presented. Furthermore, results of direct measurements of the 17O(α, n)20Ne, 23Ne(α, p)26Mg and 23Ne(α, n)26Al reactions will be discussed.

A numerical study of mixing enhancement in supersonic reacting flow fields. [in scramjets

NASA Technical Reports Server (NTRS)

Drummond, J. Philip; Mukunda, H. S.

1988-01-01

NASA Langley has intensively investigated the components of ramjet and scramjet systems for endoatmospheric, airbreathing hypersonic propulsion; attention is presently given to the optimization of scramjet combustor fuel-air mixing and reaction characteristics. A supersonic, spatially developing and reacting mixing layer has been found to serve as an excellent physical model for the mixing and reaction process. Attention is presently given to techniques that have been applied to the enhancement of the mixing processes and the overall combustion efficiency of the mixing layer. A fuel injector configuration has been computationally designed which significantly increases mixing and reaction rates.

Rapid Catalyst Screening by a Continuous-Flow Microreactor Interfaced with Ultra High Pressure Liquid Chromatography

PubMed Central

Fang, Hui; Xiao, Qing; Wu, Fanghui; Floreancig, Paul E.; Weber, Stephen G.

2010-01-01

A high-throughput screening system for homogeneous catalyst discovery has been developed by integrating a continuous-flow capillary-based microreactor with ultra-high pressure liquid chromatography (UHPLC) for fast online analysis. Reactions are conducted in distinct and stable zones in a flow stream that allows for time and temperature regulation. UHPLC detection at high temperature allows high throughput online determination of substrate, product, and byproduct concentrations. We evaluated the efficacies of a series of soluble acid catalysts for an intramolecular Friedel-Crafts addition into an acyliminium ion intermediate within one day and with minimal material investment. The effects of catalyst loading, reaction time, and reaction temperature were also screened. This system exhibited high reproducibility for high-throughput catalyst screening and allowed several acid catalysts for the reaction to be identified. Major side products from the reactions were determined through off-line mass spectrometric detection. Er(OTf)3, the catalyst that showed optimal efficiency in the screening, was shown to be effective at promoting the cyclization reaction on a preparative scale. PMID:20666502

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

PubMed Central

2012-01-01

Background 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. Results 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. Conclusion 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/ PMID:22574658

Cu-catalyzed formal methylative and hydrogenative carboxylation of alkynes with carbon dioxide: efficient synthesis of α,β-unsaturated carboxylic acids.

PubMed

Takimoto, Masanori; Hou, Zhaomin

2013-08-19

The sequential hydroalumination or methylalumination of various alkynes catalyzed by different catalyst systems, such those based on Sc, Zr, and Ni complexes, and the subsequent carboxylation of the resulting alkenylaluminum species with CO2 catalyzed by an N-heterocyclic carbene (NHC)-copper catalyst have been examined in detail. The regio- and stereoselectivity of the overall reaction relied largely on the hydroalumination or methylalumination reactions, which significantly depended on the catalyst and alkyne substrates. The subsequent Cu-catalyzed carboxylation proceeded with retention of the stereoconfiguration of the alkenylaluminum species. All the reactions could be carried out in one-pot to afford efficiently a variety of α,β-unsaturated carboxylic acids with well-controlled configurations, which are difficult to construct by previously reported methods. This protocol could be practically useful and attractive because of its high regio- and stereoselectivity, simple one-pot reaction operation, and the use of CO2 as a starting material. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling

NASA Astrophysics Data System (ADS)

Núñez, M.; Robie, T.; Vlachos, D. G.

2017-10-01

Kinetic Monte Carlo (KMC) simulation provides insights into catalytic reactions unobtainable with either experiments or mean-field microkinetic models. Sensitivity analysis of KMC models assesses the robustness of the predictions to parametric perturbations and identifies rate determining steps in a chemical reaction network. Stiffness in the chemical reaction network, a ubiquitous feature, demands lengthy run times for KMC models and renders efficient sensitivity analysis based on the likelihood ratio method unusable. We address the challenge of efficiently conducting KMC simulations and performing accurate sensitivity analysis in systems with unknown time scales by employing two acceleration techniques: rate constant rescaling and parallel processing. We develop statistical criteria that ensure sufficient sampling of non-equilibrium steady state conditions. Our approach provides the twofold benefit of accelerating the simulation itself and enabling likelihood ratio sensitivity analysis, which provides further speedup relative to finite difference sensitivity analysis. As a result, the likelihood ratio method can be applied to real chemistry. We apply our methodology to the water-gas shift reaction on Pt(111).

Low to high temperature energy conversion system

NASA Technical Reports Server (NTRS)

Miller, C. G. (Inventor)

1977-01-01

A method for converting heat energy from low temperature heat sources to higher temperature was developed. It consists of a decomposition chamber in which ammonia is decomposed into hydrogen and nitrogen by absorbing heat of decomposition from a low temperature energy source. A recombination reaction then takes place which increases the temperature of a fluid significantly. The system is of use for the efficient operation of compact or low capital investment turbine driven electrical generators, or in other applications, to enable chemical reactions that have a critical lower temperature to be used. The system also recovers heat energy from low temperature heat sources, such as solar collectors or geothermal sources, and converts it to high temperatures.

Computation of Kinetics for the Hydrogen/Oxygen System Using the Thermodynamic Method

NASA Technical Reports Server (NTRS)

Marek, C. John

1996-01-01

A new method for predicting chemical rate constants using thermodynamics has been applied to the hydrogen/oxygen system. This method is based on using the gradient of the Gibbs free energy and a single proportionality constant D to determine the kinetic rate constants. Using this method the rate constants for any gas phase reaction can be computed from thermodynamic properties. A modified reaction set for the H/O system is determined. A11 of the third body efficiencies M are taken to be unity. Good agreement was obtained between the thermodynamic method and the experimental shock tube data. In addition, the hydrogen bromide experimental data presented in previous work is recomputed with M's of unity.

[Degradation of 2, 4-dichlorophenol in aqueous solution by ZVI/EDDS/air system].

PubMed

Sun, Qian; Zhou, Hai-Yan; Cao, Meng-Hua; Wu, Lin-Na; Wang, Lin-Ling; Chen, Jing; Lu, Xiao-Hua

2012-11-01

A new oxidation system of Fenton-like system (ZVI/EDDS/Air) has been developed to degrade 2,4-chlorophenols (2,4-DCP) in aqueous solution. The influences of initial conditions, i. e., EDDS concentration, iron dosage, aeration rate, 2,4-DCP concentration and pH as well as reaction temperature on the degradation of 2,4-DCP were studied. The results demonstrated that this ZVI/EDDS/Air system was able to effectively degrade 2,4-DCP in aqueous solution, and the degradation of 2,4-DCP conforms to the pseudo-first-order reaction kinetics equation. Removal of above 99% 2,4-DCP was achieved in ZVI/EDDS/Air system at room temperature and pressure after 1 h reaction when the initial conditions were 2,4-DCP 100 mg x L(-1), EDDS 0.80 mmo x L(-1), ZVI 20 g x L(-1), aeration rate 2 L x (min x L)(-1). Compared with ZVI/EDTA/Air system, ZVI/EDDS/Air system showed higher efficiency in the degradation of 2,4-DCP at ambient circumstance and was more environmentally benign.

Functional Cellular Mimics for the Spatiotemporal Control of Multiple Enzymatic Cascade Reactions.

PubMed

Liu, Xiaoling; Formanek, Petr; Voit, Brigitte; Appelhans, Dietmar

2017-12-18

Next-generation therapeutic approaches are expected to rely on the engineering of biomimetic cellular systems that can mimic specific cellular functions. Herein, we demonstrate a highly effective route for constructing structural and functional eukaryotic cell mimics by loading pH-sensitive polymersomes as membrane-associated and free-floating organelle mimics inside the multifunctional cell membrane. Metabolism mimicry has been validated by performing successive enzymatic cascade reactions spatially separated at specific sites of cell mimics in the presence and absence of extracellular organelle mimics. These enzymatic reactions take place in a highly controllable, reproducible, efficient, and successive manner. Our biomimetic approach to material design for establishing functional principles brings considerable enrichment to the fields of biomedicine, biocatalysis, biotechnology, and systems biology. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Can Drosophila melanogaster represent a model system for the detection of reproductive adverse drug reactions?

PubMed

Avanesian, Agnesa; Semnani, Sahar; Jafari, Mahtab

2009-08-01

Once a molecule is identified as a potential drug, the detection of adverse drug reactions is one of the key components of its development and the FDA approval process. We propose using Drosophila melanogaster to screen for reproductive adverse drug reactions in the early stages of drug development. Compared with other non-mammalian models, D. melanogaster has many similarities to the mammalian reproductive system, including putative sex hormones and conserved proteins involved in genitourinary development. Furthermore, the D. melanogaster model would present significant advantages in time efficiency and cost-effectiveness compared with mammalian models. We present data on methotrexate (MTX) reproductive adverse events in multiple animal models, including fruit flies, as proof-of-concept for the use of the D. melanogaster model.

A dual-catalysis approach to enantioselective [2 + 2] photocycloadditions using visible light.

PubMed

Du, Juana; Skubi, Kazimer L; Schultz, Danielle M; Yoon, Tehshik P

2014-04-25

In contrast to the wealth of catalytic systems that are available to control the stereochemistry of thermally promoted cycloadditions, few similarly effective methods exist for the stereocontrol of photochemical cycloadditions. A major unsolved challenge in the design of enantioselective catalytic photocycloaddition reactions has been the difficulty of controlling racemic background reactions that occur by direct photoexcitation of substrates while unbound to catalyst. Here, we describe a strategy for eliminating the racemic background reaction in asymmetric [2 + 2] photocycloadditions of α,β-unsaturated ketones to the corresponding cyclobutanes by using a dual-catalyst system consisting of a visible light-absorbing transition-metal photocatalyst and a stereocontrolling Lewis acid cocatalyst. The independence of these two catalysts enables broader scope, greater stereochemical flexibility, and better efficiency than previously reported methods for enantioselective photochemical cycloadditions.

Towards Self-Replicating Chemical Systems Based on Cytidylic and Guanylic Acids

NASA Technical Reports Server (NTRS)

Kanavarioti, Anastassia

1999-01-01

This project was aimed towards a better understanding of template-directed reactions and, based on this, towards the development of efficient non-enzymatic RNA replicating systems. These systems could serve as models for the prebiotic synthesis of an RNA world. The major objectives of this project are: (a) To elucidate the mechanistic aspects of template-directed (TD) chemistry and (b) to identify active boundary regions, or conditions, environmental and other, that favor "organized chemistry" and stereo-selective polymerization of nucleotides. "Organized chemistry" may lead to enhanced polymerization efficiency which in turn is expected to facilitate the road towards a self-replicating chemical system based on all four nucleic acid bases.

Transport in Physical Space: The Example of Pedestrians, Cars, and Molecular Motors

NASA Astrophysics Data System (ADS)

Appert-Rolland, Cécile; Klein, Sarah; Ebbinghaus, Maximilian; Santen, Ludger

Transport systems in physical space exhibit various phenomena which may have some counterparts in socio- or econo-systems. We review here several of them. In highway vehicular traffic, the introduction of a reaction time leads to metastability and hysteresis. Pattern formation occurs in pedestrian flows. At a microscopic scale, we can learn from molecular pedestrians that transporting an object by opposite teams can be more efficient in a crowded environment and allow for an easy control of the system. Besides, we will show that the interplay between transport and the dynamics of the underlying network can sometimes lead to positive effects in terms of efficiency of transport.

Heat-pump cool storage in a clathrate of freon

NASA Astrophysics Data System (ADS)

Tomlinson, J. J.

Presented are the analytical description and assessment of a unique heat pump/storage system in which the conventional evaporator of the vapor compression cycle is replaced by a highly efficient direct contract crystallizer. The thermal storage technique requires the formation of a refrigerant gas hydrate (a clathrate) and exploits an enthalpy of reaction comparable to the heat of fusion of ice. Additional system operational benefits include cool storage at the favorable temperatures of 4 to 7 C (40 to 45 F), and highly efficient heat transfer ates afforded by he direct contact mechanism. In addition, the experimental approach underway at ORNL to study such a system is discussed.

Dynamic dielectric properties of a wood liquefaction system using polyethylene glycol and glycerol

Treesearch

Mengchao Zhou; Thomas L. Eberhardt; Bo Cai; Chung-Yun Hse; Hui Pan

2017-01-01

Microwave-assisted liquefaction has shown potential for rapid thermal processing of lignocellulosic biomass. The efficiency of microwave heating depends largely on the dielectric properties of the materials being heated. The objective of this study was to investigate the dynamic interactions between microwave energy and the reaction system during the liquefaction of a...

Supercritical water oxidation of products of human metabolism

NASA Technical Reports Server (NTRS)

Tester, Jefferson W.; Orge A. achelling, Richard K. ADTHOMASSON; Orge A. achelling, Richard K. ADTHOMASSON

1986-01-01

Although the efficient destruction of organic material was demonstrated in the supercritical water oxidation process, the reaction kinetics and mechanisms are unknown. The kinetics and mechanisms of carbon monoxide and ammonia oxidation in and reaction with supercritical water were studied experimentally. Experimental oxidation of urine and feces in a microprocessor controlled system was performed. A minaturized supercritical water oxidation process for space applications was design, including preliminary mass and energy balances, power, space and weight requirements.

Heat recirculating cooler for fluid stream pollutant removal

DOEpatents

Richards, George A.; Berry, David A.

2008-10-28

A process by which heat is removed from a reactant fluid to reach the operating temperature of a known pollutant removal method and said heat is recirculated to raise the temperature of the product fluid. The process can be utilized whenever an intermediate step reaction requires a lower reaction temperature than the prior and next steps. The benefits of a heat-recirculating cooler include the ability to use known pollutant removal methods and increased thermal efficiency of the system.

Fission Systems for Mars Exploration

NASA Technical Reports Server (NTRS)

Houts, Michael G.; Kim, T.; Dorney, D. J.; Swint, Marion Shayne

2012-01-01

Fission systems are used extensively on earth, and 34 such systems have flown in space. The energy density of fission is over 10 million times that of chemical reactions, giving fission the potential to eliminate energy density constraints for many space missions. Potential safety and operational concerns with fission systems are well understood, and strategies exist for affordably developing such systems. By enabling a power-rich environment and highly efficient propulsion, fission systems could enable affordable, sustainable exploration of Mars.

Strategies for Efficient Charge Separation and Transfer in Artificial Photosynthesis of Solar Fuels.

PubMed

Xu, Yuxing; Li, Ailong; Yao, Tingting; Ma, Changtong; Zhang, Xianwen; Shah, Jafar Hussain; Han, Hongxian

2017-11-23

Converting sunlight to solar fuels by artificial photosynthesis is an innovative science and technology for renewable energy. Light harvesting, photogenerated charge separation and transfer (CST), and catalytic reactions are the three primary steps in the processes involved in the conversion of solar energy to chemical energy (SE-CE). Among the processes, CST is the key "energy pump and delivery" step in determining the overall solar-energy conversion efficiency. Efficient CST is always high priority in designing and assembling artificial photosynthesis systems for solar-fuel production. This Review not only introduces the fundamental strategies for CST but also the combinatory application of these strategies to five types of the most-investigated semiconductor-based artificial photosynthesis systems: particulate, Z-scheme, hybrid, photoelectrochemical, and photovoltaics-assisted systems. We show that artificial photosynthesis systems with high SE-CE efficiency can be rationally designed and constructed through combinatory application of these strategies, setting a promising blueprint for the future of solar fuels. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems

PubMed Central

Hummer, Gerhard

2015-01-01

We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green's function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions. PMID:26005592

Simultaneous removal of SO2 and NOx from flue gas by wet scrubbing using a urea solution.

PubMed

Li, Ge; Wang, Baodong; Xu, Wayne Qiang; Li, Yonglong; Han, Yifan; Sun, Qi

2018-03-27

Nitrogen oxides (NO x ) and sulfur dioxide (SO 2 ) are major air pollutants, so simultaneously removing them from gases emitted during fossil fuel combustion in stationary systems is important. Wet denitrification using urea is used for a wide range of systems. Additives have strong effects on wet denitrification using urea, and different mechanisms are involved and different effects found using different additives. In this study, the effects of different additives, initial urea concentrations, reaction temperatures, initial pH values, gas flow rates, and reaction times on the simultaneous desulfurization and denitrification efficiencies achieved using wet denitrification using urea were studied in single factor experiment. The optimum reaction conditions for desulfurization and denitrification were found. Desulfurization and denitrification efficiencies of 97.5% and 96.3%, respectively, were achieved at a KMnO 4 concentration 5 mmol/L, a reaction temperature of 70°C, initial urea solution pH 8, a urea concentration of 9%, and a gas flow rate of 40 L/h. The concentrations of the desulfurization and denitrification reaction products in the solution were determined. NO x was mainly transformed into N 2 , and the [Formula: see text] and [Formula: see text] concentrations in the solution became very low. The reactions involved in SO 2 and NO x removal using urea were analyzed from the thermodynamic viewpoint. Increasing the temperature was not conducive to the reactions but increased the rate constant, so an optimum temperature was determined. The simultaneous desulfurization and denitrification kinetics were calculated. The urea consumption and [Formula: see text], [Formula: see text], and [Formula: see text] generation reactions were all zero order. The [Formula: see text] generation rate was greater than the [Formula: see text] generation rate. The simultaneous desulfurization and denitrification process and mechanism were studied. The results provide reference data for performing flue gas desulfurization and denitrification in factories.

Comparative study on antibody immobilization strategies for efficient circulating tumor cell capture.

PubMed

Ates, Hatice Ceren; Ozgur, Ebru; Kulah, Haluk

2018-03-23

Methods for isolation and quantification of circulating tumor cells (CTCs) are attracting more attention every day, as the data for their unprecedented clinical utility continue to grow. However, the challenge is that CTCs are extremely rare (as low as 1 in a billion of blood cells) and a highly sensitive and specific technology is required to isolate CTCs from blood cells. Methods utilizing microfluidic systems for immunoaffinity-based CTC capture are preferred, especially when purity is the prime requirement. However, antibody immobilization strategy significantly affects the efficiency of such systems. In this study, two covalent and two bioaffinity antibody immobilization methods were assessed with respect to their CTC capture efficiency and selectivity, using an anti-epithelial cell adhesion molecule (EpCAM) as the capture antibody. Surface functionalization was realized on plain SiO 2 surfaces, as well as in microfluidic channels. Surfaces functionalized with different antibody immobilization methods are physically and chemically characterized at each step of functionalization. MCF-7 breast cancer and CCRF-CEM acute lymphoblastic leukemia cell lines were used as EpCAM positive and negative cell models, respectively, to assess CTC capture efficiency and selectivity. Comparisons reveal that bioaffinity based antibody immobilization involving streptavidin attachment with glutaraldehyde linker gave the highest cell capture efficiency. On the other hand, a covalent antibody immobilization method involving direct antibody binding by N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC)-N-hydroxysuccinimide (NHS) reaction was found to be more time and cost efficient with a similar cell capture efficiency. All methods provided very high selectivity for CTCs with EpCAM expression. It was also demonstrated that antibody immobilization via EDC-NHS reaction in a microfluidic channel leads to high capture efficiency and selectivity.

Highly efficient hydrogen storage system based on ammonium bicarbonate/formate redox equilibrium over palladium nanocatalysts.

PubMed

Su, Ji; Yang, Lisha; Lu, Mi; Lin, Hongfei

2015-03-01

A highly efficient, reversible hydrogen storage-evolution process has been developed based on the ammonium bicarbonate/formate redox equilibrium over the same carbon-supported palladium nanocatalyst. This heterogeneously catalyzed hydrogen storage system is comparable to the counterpart homogeneous systems and has shown fast reaction kinetics of both the hydrogenation of ammonium bicarbonate and the dehydrogenation of ammonium formate under mild operating conditions. By adjusting temperature and pressure, the extent of hydrogen storage and evolution can be well controlled in the same catalytic system. Moreover, the hydrogen storage system based on aqueous-phase ammonium formate is advantageous owing to its high volumetric energy density. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improvement of ethanol productivity and energy efficiency by degradation of inhibitors using recombinant Zymomonas mobilis (pHW20a-fdh).

PubMed

Dong, Hong-Wei; Fan, Li-Qiang; Luo, Zichen; Zhong, Jian-Jiang; Ryu, Dewey D Y; Bao, Jie

2013-09-01

Toxic compounds, such as formic acid, furfural, and hydroxymethylfurfural (HMF) generated during pretreatment of corn stover (CS) at high temperature and low pH, inhibit growth of Zymomonas mobilis and lower the conversion efficiency of CS to biofuel and other products. The inhibition of toxic compounds is considered as one of the major technical barriers in the lignocellulose bioconversion. In order to detoxify and/or degrade these toxic compounds by the model ethanologenic strain Z. mobilis itself in situ the fermentation medium, we constructed a recombinant Z. mobilis ZM4 (pHW20a-fdh) strain that is capable of degrading toxic inhibitor, formate. This is accomplished by cloning heterologous formate dehydrogenase gene (fdh) from Saccharomyces cerevisiae and by coupling this reaction of NADH regeneration reaction system with furfural and HMF degradation in the recombinant Z. mobilis strain. The NADH regeneration reaction also improved both the energy efficiency and cell physiological activity of the recombinant organism, which were definitely confirmed by the improved cell growth, ethanol yield, and ethanol productivity during fermentation with CS hydrolysate. Copyright © 2013 Wiley Periodicals, Inc.

Efficient treatment of phenolic wastewater with high salinity using a novel integrated system of magnetically immobilized cells coupling with electrodes.

PubMed

Jiang, Bei; Shi, Shengnan; Song, Lun; Tan, Liang; Li, Meidi; Liu, Jiaxin; Xue, Lanlan

2016-10-01

A novel integrated system in which magnetically immobilized cells coupled with a pair of stainless iron meshes-graphite plate electrodes has been designed and operated to enhance the treatment performance of phenolic wastewater under high salinity. With NaCl concentration increased, phenol, o-cresol, m-cresol, p-cresol and COD removal rates by integrated system increased significantly, which were obviously higher than the sum of removal rates by single magnetically immobilized cells and electrode reaction. This integrated system exhibited higher removal rates for all the compounds than that by single magnetically immobilized cells during six cycles for reuse, and it still performed better, even when the voltage was cut off. These results indicated that there was a coupling effect between biodegradation and electrode reaction. The investigation of phenol hydroxylase activity and cells concentration confirmed that electrode reaction played an important role in this coupling effect. Copyright © 2016 Elsevier Ltd. All rights reserved.

Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting.

PubMed

Hellander, Andreas; Lawson, Michael J; Drawert, Brian; Petzold, Linda

2014-06-01

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity.

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.

Centrifugal Microfluidic System for Nucleic Acid Amplification and Detection.

PubMed

Miao, Baogang; Peng, Niancai; Li, Lei; Li, Zheng; Hu, Fei; Zhang, Zengming; Wang, Chaohui

2015-11-04

We report here the development of a rapid PCR microfluidic system comprising a double-shaft turntable and centrifugal-based disc that rapidly drives the PCR mixture between chambers set at different temperatures, and the bidirectional flow improved the space utilization of the disc. Three heating resistors and thermistors maintained uniform, specific temperatures for the denaturation, annealing, and extension steps of the PCR. Infrared imaging showed that there was little thermal interference between reaction chambers; the system enabled the cycle number and reaction time of each step to be independently adjusted. To validate the function and efficiency of the centrifugal microfluidic system, a 350-base pair target gene from the hepatitis B virus was amplified and quantitated by fluorescence detection. By optimizing the cycling parameters, the reaction time was reduced to 32 min as compared to 120 min for a commercial PCR machine. DNA samples with concentrations ranging from 10 to 10⁶ copies/mL could be quantitatively analyzed using this system. This centrifugal-based microfluidic platform is a useful system and possesses industrialization potential that can be used for portable diagnostics.

Centrifugal Microfluidic System for Nucleic Acid Amplification and Detection

PubMed Central

Miao, Baogang; Peng, Niancai; Li, Lei; Li, Zheng; Hu, Fei; Zhang, Zengming; Wang, Chaohui

2015-01-01

We report here the development of a rapid PCR microfluidic system comprising a double-shaft turntable and centrifugal-based disc that rapidly drives the PCR mixture between chambers set at different temperatures, and the bidirectional flow improved the space utilization of the disc. Three heating resistors and thermistors maintained uniform, specific temperatures for the denaturation, annealing, and extension steps of the PCR. Infrared imaging showed that there was little thermal interference between reaction chambers; the system enabled the cycle number and reaction time of each step to be independently adjusted. To validate the function and efficiency of the centrifugal microfluidic system, a 350-base pair target gene from the hepatitis B virus was amplified and quantitated by fluorescence detection. By optimizing the cycling parameters, the reaction time was reduced to 32 min as compared to 120 min for a commercial PCR machine. DNA samples with concentrations ranging from 10 to 106 copies/mL could be quantitatively analyzed using this system. This centrifugal-based microfluidic platform is a useful system and possesses industrialization potential that can be used for portable diagnostics. PMID:26556354

Fusion cross sections measurements with MUSIC

NASA Astrophysics Data System (ADS)

Carnelli, P. F. F.; Fernández Niello, J. O.; Almaraz-Calderon, S.; Rehm, K. E.; Albers, M.; Digiovine, B.; Esbensen, H.; Henderson, D.; Jiang, C. L.; Nusair, O.; Palchan-Hazan, T.; Pardo, R. C.; Ugalde, C.; Paul, M.; Alcorta, M.; Bertone, P. F.; Lai, J.; Marley, S. T.

2014-09-01

The interaction between exotic nuclei plays an important role for understanding the reaction mechanism of the fusion processes as well as for the energy production in stars. With the advent of radioactive beams new frontiers for fusion reaction studies have become accessible. We have performed the first measurements of the total fusion cross sections in the systems 10 , 14 , 15C + 12C using a newly developed active target-detector system (MUSIC). Comparison of the obtained cross sections with theoretical predictions show a good agreement in the energy region accessible with existing radioactive beams. This type of comparison allows us to calibrate the calculations for cases that cannot be studied in the laboratory with the current experimental capabilities. The high efficiency of this active detector system will allow future measurements with even more neutron-rich isotopes. The interaction between exotic nuclei plays an important role for understanding the reaction mechanism of the fusion processes as well as for the energy production in stars. With the advent of radioactive beams new frontiers for fusion reaction studies have become accessible. We have performed the first measurements of the total fusion cross sections in the systems 10 , 14 , 15C + 12C using a newly developed active target-detector system (MUSIC). Comparison of the obtained cross sections with theoretical predictions show a good agreement in the energy region accessible with existing radioactive beams. This type of comparison allows us to calibrate the calculations for cases that cannot be studied in the laboratory with the current experimental capabilities. The high efficiency of this active detector system will allow future measurements with even more neutron-rich isotopes. This work is supported by the U.S. DOE Office of Nuclear Physics under Contract No. DE-AC02-06CH11357 and the Universidad Nacional de San Martin, Argentina, Grant SJ10/39.

Nuclear-Pumped Lasers. [efficient conversion of energy liberated in nuclear reactions to coherent radiation

NASA Technical Reports Server (NTRS)

1979-01-01

The state of the art in nuclear pumped lasers is reviewed. Nuclear pumped laser modeling, nuclear volume and foil excitation of laser plasmas, proton beam simulations, nuclear flashlamp excitation, and reactor laser systems studies are covered.

Performance and cost of energy transport and storage systems for dish applications using reversible chemical reactions

NASA Technical Reports Server (NTRS)

Schredder, J. M.; Fujita, T.

1984-01-01

The use of reversible chemical reactions for energy transport and storage for parabolic dish networks is considered. Performance and cost characteristics are estimated for systems using three reactions (sulfur-trioxide decomposition, steam reforming of methane, and carbon-dioxide reforming of methane). Systems are considered with and without storage, and in several energy-delivery configurations that give different profiles of energy delivered versus temperature. Cost estimates are derived assuming the use of metal components and of advanced ceramics. (The latter reduces the costs by three- to five-fold). The process that led to the selection of the three reactions is described, and the effects of varying temperatures, pressures, and heat exchanger sizes are addressed. A state-of-the-art survey was performed as part of this study. As a result of this survey, it appears that formidable technical risks exist for any attempt to implement the systems analyzed in this study, especially in the area of reactor design and performance. The behavior of all components and complete systems under thermal energy transients is very poorly understood. This study indicates that thermochemical storage systems that store reactants as liquids have efficiencies below 60%, which is in agreement with the findings of earlier investigators.

Enzymatic reactivity of glucose oxidase confined in nanochannels.

PubMed

Yu, Jiachao; Zhang, Yuanjian; Liu, Songqin

2014-05-15

The construction of nanodevices coupled with an integrated real-time detection system for evaluation of the function of biomolecules in biological processes, and enzymatic reaction kinetics occurring at the confined space or interface is a significant challenge. In this work, a nanochannel-enzyme system in which the enzymatic reaction could be investigated with an electrochemical method was constructed. The model system was established by covalently linking glucose oxidase (GOD) onto the inner wall of the nanochannels of the porous anodic alumina (PAA) membrane. An Au disc was attached at the end of the nanochannels of the PAA membrane as the working electrode for detection of H2O2 product of enzymatic reaction. The effects of ionic strength, amount of immobilized enzyme and pore diameter of the nanochannels on the enzymatic reaction kinetics were illustrated. The GOD confined in nanochannels showed high stability and reactivity. Upon addition of glucose to the nanochannel-enzyme system, the current response had a calibration range span from 0.005 to 2 mM of glucose concentration. The apparent Michaelis-Menten constant (K(m)(app)) of GOD confined in nanochannel was 0.4 mM. The presented work provided a platform for real-time monitoring of the enzyme reaction kinetics confined in nanospaces. Such a nanochannel-enzyme system could also help design future biosensors and enzyme reactors with high sensitivity and efficiency. Copyright © 2013 Elsevier B.V. All rights reserved.

Highly efficient catalytic systems based on Pd-coated microbeads

NASA Astrophysics Data System (ADS)

Lim, Jin Hyun; Cho, Ahyoung; Lee, Seung Hwan; Park, Bumkyo; Kang, Dong Woo; Koo, Chong Min; Yu, Taekyung; Park, Bum Jun

2018-01-01

The efficiency of two prototype catalysis systems using palladium (Pd)-coated microparticles was investigated with regard to the recovery and recyclability of the catalytic particles. One such system was the interface-adsorption method, in which polymer particles coated with Pd nanoparticles strongly and irreversibly attach to the oil-water interface. Due to the irreversible adsorption of the catalytic particles to the interface, particle loss was completely prevented while mixing the aqueous solution and while collecting the products. The other system was based on the magnetic field-associated particle recovery method. The use of polymeric microparticles containing Pd nanoparticles and magnetite nanoparticles accelerated the sedimentation of the particles in the aqueous phase by applying a strong magnetic field, consequently suppressing drainage of the particles from the reactor along the product stream. Upon multiple runs of the catalytic reactions, it was found that conversion does not change significantly, demonstrating the excellent recyclability and performance efficiency in the catalytic processes.

Thermally multiplexed polymerase chain reaction.

PubMed

Phaneuf, Christopher R; Pak, Nikita; Saunders, D Curtis; Holst, Gregory L; Birjiniuk, Joav; Nagpal, Nikita; Culpepper, Stephen; Popler, Emily; Shane, Andi L; Jerris, Robert; Forest, Craig R

2015-07-01

Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously-each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel.

Microarray-integrated optoelectrofluidic immunoassay system

PubMed Central

Han, Dongsik

2016-01-01

A microarray-based analytical platform has been utilized as a powerful tool in biological assay fields. However, an analyte depletion problem due to the slow mass transport based on molecular diffusion causes low reaction efficiency, resulting in a limitation for practical applications. This paper presents a novel method to improve the efficiency of microarray-based immunoassay via an optically induced electrokinetic phenomenon by integrating an optoelectrofluidic device with a conventional glass slide-based microarray format. A sample droplet was loaded between the microarray slide and the optoelectrofluidic device on which a photoconductive layer was deposited. Under the application of an AC voltage, optically induced AC electroosmotic flows caused by a microarray-patterned light actively enhanced the mass transport of target molecules at the multiple assay spots of the microarray simultaneously, which reduced tedious reaction time from more than 30 min to 10 min. Based on this enhancing effect, a heterogeneous immunoassay with a tiny volume of sample (5 μl) was successfully performed in the microarray-integrated optoelectrofluidic system using immunoglobulin G (IgG) and anti-IgG, resulting in improved efficiency compared to the static environment. Furthermore, the application of multiplex assays was also demonstrated by multiple protein detection. PMID:27190571

Microarray-integrated optoelectrofluidic immunoassay system.

PubMed

Han, Dongsik; Park, Je-Kyun

2016-05-01

A microarray-based analytical platform has been utilized as a powerful tool in biological assay fields. However, an analyte depletion problem due to the slow mass transport based on molecular diffusion causes low reaction efficiency, resulting in a limitation for practical applications. This paper presents a novel method to improve the efficiency of microarray-based immunoassay via an optically induced electrokinetic phenomenon by integrating an optoelectrofluidic device with a conventional glass slide-based microarray format. A sample droplet was loaded between the microarray slide and the optoelectrofluidic device on which a photoconductive layer was deposited. Under the application of an AC voltage, optically induced AC electroosmotic flows caused by a microarray-patterned light actively enhanced the mass transport of target molecules at the multiple assay spots of the microarray simultaneously, which reduced tedious reaction time from more than 30 min to 10 min. Based on this enhancing effect, a heterogeneous immunoassay with a tiny volume of sample (5 μl) was successfully performed in the microarray-integrated optoelectrofluidic system using immunoglobulin G (IgG) and anti-IgG, resulting in improved efficiency compared to the static environment. Furthermore, the application of multiplex assays was also demonstrated by multiple protein detection.

Electrocatalysts for Hydrogen Evolution in Alkaline Electrolytes: Mechanisms, Challenges, and Prospective Solutions.

PubMed

Mahmood, Nasir; Yao, Yunduo; Zhang, Jing-Wen; Pan, Lun; Zhang, Xiangwen; Zou, Ji-Jun

2018-02-01

Hydrogen evolution reaction (HER) in alkaline medium is currently a point of focus for sustainable development of hydrogen as an alternative clean fuel for various energy systems, but suffers from sluggish reaction kinetics due to additional water dissociation step. So, the state-of-the-art catalysts performing well in acidic media lose considerable catalytic performance in alkaline media. This review summarizes the recent developments to overcome the kinetics issues of alkaline HER, synthesis of materials with modified morphologies, and electronic structures to tune the active sites and their applications as efficient catalysts for HER. It first explains the fundamentals and electrochemistry of HER and then outlines the requirements for an efficient and stable catalyst in alkaline medium. The challenges with alkaline HER and limitation with the electrocatalysts along with prospective solutions are then highlighted. It further describes the synthesis methods of advanced nanostructures based on carbon, noble, and inexpensive metals and their heterogeneous structures. These heterogeneous structures provide some ideal systems for analyzing the role of structure and synergy on alkaline HER catalysis. At the end, it provides the concluding remarks and future perspectives that can be helpful for tuning the catalysts active-sites with improved electrochemical efficiencies in future.

Electrocatalysts for Hydrogen Evolution in Alkaline Electrolytes: Mechanisms, Challenges, and Prospective Solutions

PubMed Central

Mahmood, Nasir; Yao, Yunduo; Zhang, Jing‐Wen; Pan, Lun; Zhang, Xiangwen

2017-01-01

Abstract Hydrogen evolution reaction (HER) in alkaline medium is currently a point of focus for sustainable development of hydrogen as an alternative clean fuel for various energy systems, but suffers from sluggish reaction kinetics due to additional water dissociation step. So, the state‐of‐the‐art catalysts performing well in acidic media lose considerable catalytic performance in alkaline media. This review summarizes the recent developments to overcome the kinetics issues of alkaline HER, synthesis of materials with modified morphologies, and electronic structures to tune the active sites and their applications as efficient catalysts for HER. It first explains the fundamentals and electrochemistry of HER and then outlines the requirements for an efficient and stable catalyst in alkaline medium. The challenges with alkaline HER and limitation with the electrocatalysts along with prospective solutions are then highlighted. It further describes the synthesis methods of advanced nanostructures based on carbon, noble, and inexpensive metals and their heterogeneous structures. These heterogeneous structures provide some ideal systems for analyzing the role of structure and synergy on alkaline HER catalysis. At the end, it provides the concluding remarks and future perspectives that can be helpful for tuning the catalysts active‐sites with improved electrochemical efficiencies in future. PMID:29610722

FAD C(4a)-hydroxide stabilized in a naturally fused styrene monooxygenase

PubMed Central

Schlömann, Michael; van Berkel, Willem J.H.; Gassner, George T.

2013-01-01

StyA2B represents a new class of styrene monooxygenases that integrates flavin-reductase and styrene-epoxidase activities into a single polypeptide. This naturally-occurring fusion protein offers new avenues for studying and engineering biotechnologically relevant enantioselective biochemical epoxidation reactions. Stopped-flow kinetic studies of StyA2B reported here identify reaction intermediates similar to those reported for the separate reductase and epoxidase components of related two-component systems. Our studies identify substrate epoxidation and elimination of water from the FAD C(4a)-hydroxide as rate-limiting steps in the styrene epoxidation reaction. Efforts directed at accelerating these reaction steps are expected to greatly increase catalytic efficiency and the value of StyA2B as biocatalyst. PMID:24157359

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

Pressure and temperature dependence kinetics study of the NO + BrO yielding NO2 + Br reaction - Implications for stratospheric bromine photochemistry

NASA Technical Reports Server (NTRS)

Watson, R. T.; Sander, S. P.; Yung, Y. L.

1979-01-01

The reactivity of NO with BrO radicals over a wide range of pressure (100-700 torr) and temperature (224-398 K) is investigated using the flash photolysis-ultraviolet absorption technique. The flash photolysis system consists of a high-pressure xenon arc light source, a reaction cell/gas filter/flash lamp combination, and a 216.5 half-meter monochromator/polychromator/spectrography for wavelength selectivity. The details of the reaction and its corresponding Arrhenius expression are identified. The results are compared with previous measurements, and atmospheric implications of the reaction are discussed. The NO + BrO yielding NO2 + Br reaction is shown to be important in controlling the concentration ratios of BrO/Br and BrO/HBr in the stratosphere, but this reaction does not affect the catalytic efficiency of BrOx in ozone destruction.

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.

Practical Aerobic Oxidations of Alcohols and Amines with Homogeneous Cu/TEMPO and Related Catalyst Systems

PubMed Central

Ryland, Bradford L.; Stahl, Shannon S.

2014-01-01

Alcohol and amine oxidations are common reactions in laboratory and industrial synthesis of organic molecules. Aerobic oxidation methods have long been sought for these transformations, but few practical methods exist that offer advantages over traditional oxidation methods. Recently developed homogeneous Cu/TEMPO (TEMPO = 2,2,6,6-tetramethylpiperidinyl-N-oxyl) and related catalyst systems appear to fill this void. The reactions exhibit high levels of chemoselectivity and broad functional-group tolerance, and they often operate efficiently at room temperature with ambient air as the oxidant. These advances, together with their historical context and recent applications, are highlighted in this minireview. PMID:25044821

Material-Efficient Microfluidic Platform for Exploratory Studies of Visible-Light Photoredox Catalysis.

PubMed

Coley, Connor W; Abolhasani, Milad; Lin, Hongkun; Jensen, Klavs F

2017-08-07

We present an automated microfluidic platform for in-flow studies of visible-light photoredox catalysis in liquid or gas-liquid reactions at the 15 μL scale. An oscillatory flow strategy enables a flexible residence time while preserving the mixing and heat transfer advantages of flow systems. The adjustable photon flux made possible with the platform is characterized using actinometry. Case studies of oxidative hydroxylation of phenylboronic acids and dimerization of thiophenol demonstrate the capabilities and advantages of the system. Reaction conditions identified through droplet screening translate directly to continuous synthesis with minor platform modifications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand.

PubMed

Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

2014-12-12

The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins' active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes. Copyright © 2014 Elsevier Inc. All rights reserved.

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

Experimental and modeling studies of small molecule chemistry in expanding spherical flames

NASA Astrophysics Data System (ADS)

Santner, Jeffrey

Accurate models of flame chemistry are required in order to predict emissions and flame properties, such that clean, efficient engines can be designed more easily. There are three primary methods used to improve such combustion chemistry models - theoretical reaction rate calculations, elementary reaction rate experiments, and combustion system experiments. This work contributes to model improvement through the third method - measurements and analysis of the laminar burning velocity at constraining conditions. Modern combustion systems operate at high pressure with strong exhaust gas dilution in order to improve efficiency and reduce emissions. Additionally, flames under these conditions are sensitized to elementary reaction rates such that measurements constrain modeling efforts. Measurement conditions of the present work operate within this intersection between applications and fundamental science. Experiments utilize a new pressure-release, heated spherical combustion chamber with a variety of fuels (high hydrogen content fuels, formaldehyde (via 1,3,5-trioxane), and C2 fuels) at pressures from 0.5--25 atm, often with dilution by water vapor or carbon dioxide to flame temperatures below 2000 K. The constraining ability of these measurements depends on their uncertainty. Thus, the present work includes a novel analytical estimate of the effects of thermal radiative heat loss on burning velocity measurements in spherical flames. For 1,3,5-trioxane experiments, global measurements are sufficiently sensitive to elementary reaction rates that optimization techniques are employed to indirectly measure the reaction rates of HCO consumption. Besides the influence of flame chemistry on propagation, this work also explores the chemistry involved in production of nitric oxide, a harmful pollutant, within flames. We find significant differences among available chemistry models, both in mechanistic structure and quantitative reaction rates. There is a lack of well-defined measurements of nitric oxide formation at high temperatures, contributing to disagreement between chemical models. This work accomplishes several goals. It identifies disagreements in pollutant formation chemistry. It creates a novel database of burning velocity measurements at relevant, sensitive conditions. It presents a simple, conservative estimate of radiation-induced measurement uncertainty in spherical flames. Finally, it utilizes systems-level flame experiments to indirectly measure elementary reaction rates.

Event-based text mining for biology and functional genomics

PubMed Central

Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B.

2015-01-01

The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of ‘events’, i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. PMID:24907365

Nonthermal microwave effects revisited: on the importance of internal temperature monitoring and agitation in microwave chemistry.

PubMed

Herrero, M Antonia; Kremsner, Jennifer M; Kappe, C Oliver

2008-01-04

The concept of nonthermal microwave effects has received considerable attention in recent years and is the subject of intense debate in the scientific community. Nonthermal microwave effects have been postulated to result from a direct stabilizing interaction of the electric field with specific (polar) molecules in the reaction medium that is not related to a macroscopic temperature effect. In order to probe the existence of nonthermal microwave effects, four synthetic transformations (Diels-Alder cycloaddition, alkylation of triphenylphosphine and 1,2,4-triazole, direct amide bond formation) were reevaluated under both microwave dielectric heating and conventional thermal heating. In all four cases, previous studies have claimed the existence of nonthermal microwave effects in these reactions. Experimentally, significant differences in conversion and/or product distribution comparing the conventionally and microwave-heated experiments performed at the same measured reaction temperature were found. The current reevaluation of these reactions was performed in a dedicated reactor setup that allowed accurate internal reaction temperature measurements using a multiple fiber-optic probe system. Using this technology, the importance of efficient stirring and internal temperature measurement in microwave-heated reactions was made evident. Inefficient agitation leads to temperature gradients within the reaction mixture due to field inhomogeneities in the microwave cavity. Using external infrared temperature sensors in some cases results in significant inaccuracies in the temperature measurement. Applying the fiber-optic probe temperature monitoring device, a critical reevaluation of all four reactions has provided no evidence for the existence of nonthermal microwave effects. Ensuring efficient agitation of the reaction mixture via magnetic stirring, no significant differences in terms of conversion and selectivity between experiments performed under microwave or oil bath conditions at the same internally measured reaction temperatures were experienced. The observed effects were purely thermal and not related to the microwave field.

Hydroacylation of 2-vinyl benzaldehyde systems: an efficient method for the synthesis of chiral 3-substituted indanones.

PubMed

Kundu, Kousik; McCullagh, James V; Morehead, Andrew T

2005-11-23

Asymmetric rhodium-catalyzed hydroacylation has been utilized in the synthesis of 3-substituted indanones with high conversions and enantioselectivity. The hydroacylation reaction of 2-vinyl benzaldehyde had been previously reported to give a low yield of indanone and an unidentified product. We have identified this compound as a dimer of the starting material. Substitution at the alpha-position of the 2-vinyl benzaldehyde substrates blocks the competitive dimerization reaction and allows the reaction to proceed with yields generally greater than 90%. Utilization of BINAP as a chiral ligand results in good chemical yields and enantioselectivity greater than 95% in most cases.

On-line Analysis of Catalytic Reaction Products Using a High-Pressure Tandem Micro-reactor GC/MS.

PubMed

Watanabe, Atsushi; Kim, Young-Min; Hosaka, Akihiko; Watanabe, Chuichi; Teramae, Norio; Ohtani, Hajime; Kim, Seungdo; Park, Young-Kwon; Wang, Kaige; Freeman, Robert R

2017-01-01

When a GC/MS system is coupled with a pressurized reactor, the separation efficiency and the retention time are directly affected by the reactor pressure. To keep the GC column flow rate constant irrespective of the reaction pressure, a restrictor capillary tube and an open split interface are attached between the GC injection port and the head of a GC separation column. The capability of the attached modules is demonstrated for the on-line GC/MS analysis of catalytic reaction products of a bio-oil model sample (guaiacol), produced under a pressure of 1 to 3 MPa.

Gallium (III) triflate catalyzed efficient Strecker reaction of ketones and their fluorinated analogs

PubMed Central

Prakash, G. K. Surya; Mathew, Thomas; Panja, Chiradeep; Alconcel, Steevens; Vaghoo, Habiba; Do, Clement; Olah, George A.

2007-01-01

The synthesis of α-aminonitriles and their fluorinated analogs has been carried out in high yield and purity by the Strecker reaction from the corresponding ketones and amines with trimethylsilyl cyanide using gallium triflate in dichloromethane. Monofluoro-, difluro-, or trifluoromethyl groups can be incorporated into the α-aminonitrile product by varying the nature of the fluorinated ketones. Study with various fluorinated and nonfluorinated ketones reveals that the choice of proper catalyst and the solvent system (suitable metal triflates as a catalyst and dichloromethane as a solvent) plays the key role in the direct Strecker reactions of ketones. PMID:17360416

Mechanistic details for cobalt catalyzed photochemical hydrogen production in aqueous solution: Efficiencies of the photochemical and non-photochemical steps

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

Shan, Bing; Baine, Teera; Ma, Xuan Anh N.

2013-04-17

The use of sunlight to drive chemical reactions that lead to the reduction of water to produce hydrogen is a potential avenue of solar energy utilization. There are many individual steps that take place in this process. This paper reports the investigation of a particular system that involves light absorbing molecules, electron donating agents and a catalyst for water reduction to hydrogen. We evaluated the efficiency of the light induced formation of a strong electron donor, the use of this donor to reduce the catalyst and finally the efficiency of the catalyst to produce hydrogen from water. From this, themore » sources of loss of efficiency could be clearly identified and used in the design of better systems to produce hydrogen from water.« less

Evaluation of Bosch-Based Systems Using Non-Traditional Catalysts at Reduced Temperatures

NASA Technical Reports Server (NTRS)

Abney, Morgan B.; Mansell, J. Matthew

2011-01-01

Oxygen and water resupply make open loop atmosphere revitalization (AR) systems unfavorable for long-term missions beyond low Earth orbit. Crucial to closing the AR loop are carbon dioxide reduction systems with low mass and volume, minimal power requirements, and minimal consumables. For this purpose, NASA is exploring using Bosch-based systems. The Bosch process is favorable over state-of-the-art Sabatier-based processes due to complete loop closure. However, traditional operation of the Bosch required high reaction temperatures, high recycle rates, and significant consumables in the form of catalyst resupply due to carbon fouling. A number of configurations have been proposed for next-generation Bosch systems. First, alternative catalysts (catalysts other than steel wool) can be used in a traditional single-stage Bosch reactor to improve reaction kinetics and increase carbon packing density. Second, the Bosch reactor may be split into separate stages wherein the first reactor stage is dedicated to carbon monoxide and water formation via the reverse water-gas shift reaction and the second reactor stage is dedicated to carbon formation. A series system will enable maximum efficiency of both steps of the Bosch reaction, resulting in optimized operation and maximum carbon formation rate. This paper details the results of testing of both single-stage and two-stage Bosch systems with alternative catalysts at reduced temperatures. These results are compared to a traditional Bosch system operated with a steel wool catalyst.

Cyanide oxidation by singlet oxygen generated via reaction between H2O2 from cathodic reduction and OCl(-) from anodic oxidation.

PubMed

Tian, Shichao; Li, Yibing; Zeng, Huabin; Guan, Wei; Wang, Yan; Zhao, Xu

2016-11-15

Cyanide is widely present in electroplating wastewater or metallurgical effluents. In the present study, the electrochemical destruction of cyanide with various anode and cathode compositions under alkaline conditions was investigated. The results indicated that the electrochemical system using RuO2/Ti as anode and activated carbon fiber (ACF) as cathode in the presence of sodium chloride was efficient for the cyanide removal. In this system, in situ generation of HClO by anodic oxidation of Cl(-) at RuO2/Ti anode occurred with the H2O2 generation by O2 reduction at ACF cathode. As confirmed by the electron spin resonance technique, the reaction between HClO and H2O2 led to the generation of singlet oxygen, which was responsible for the cyanide removal. Further experiment indicated that the cyanide removal efficiency increased with the increase of the current density or the sodium chloride concentration. Cyanate was identified as main product in the system. Besides, the system exhibited good stability for the cyanide removal, which was beneficial to its practical application. Copyright © 2016. Published by Elsevier Inc.

Coupling of exothermic and endothermic hydrogen storage materials

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

Brooks, Kriston P.; Bowden, Mark E.; Karkamkar, Abhijeet J.

2016-08-01

Chemical hydrogen storage (CHS) materials are a high-storage-density alternative to the gaseous compressed hydrogen currently used to provide hydrogen for fuel cell vehicles. One of the challenges of CHS materials is addressing the thermodynamic and kinetic barriers required to break the chemical bonds and release the hydrogen. Coupling CHS reactions that are endothermic and exothermic during the dehydrogenation can improve the system on-board energy efficiency and thermal control, making such materials viable. Acceptable coupling between reactions requires both thermodynamic and kinetics considerations. Models were developed to predict the reaction enthalpy and rate required to achieve high conversions for both reactionsmore » based on experimental measurements. These modeling results show that the efficiency of coupling of an exothermic and endothermic reaction is more sensitive the magnitude of the ratio of the exothermic and endothermic enthalpies than the ratio of the rates of the two steps. The modeling shows further that a slower rate of the endothermic step is desirable to permit sufficient heating of the reactor by the exothermic step. We look at two examples of a sequential and parallel reaction scheme and provide some of the first insight into the required temperature range to maximize the H2 release from 1,2-BN cyclohexane and indoline.« less

Systems analysis of the CO2 concentrating mechanism in cyanobacteria

PubMed Central

Mangan, Niall M; Brenner, Michael P

2014-01-01

Cyanobacteria are photosynthetic bacteria with a unique CO2 concentrating mechanism (CCM), enhancing carbon fixation. Understanding the CCM requires a systems level perspective of how molecular components work together to enhance CO2 fixation. We present a mathematical model of the cyanobacterial CCM, giving the parameter regime (expression levels, catalytic rates, permeability of carboxysome shell) for efficient carbon fixation. Efficiency requires saturating the RuBisCO reaction, staying below saturation for carbonic anhydrase, and avoiding wasteful oxygenation reactions. We find selectivity at the carboxysome shell is not necessary; there is an optimal non-specific carboxysome shell permeability. We compare the efficacy of facilitated CO2 uptake, CO2 scavenging, and HCO3− transport with varying external pH. At the optimal carboxysome permeability, contributions from CO2 scavenging at the cell membrane are small. We examine the cumulative benefits of CCM spatial organization strategies: enzyme co-localization and compartmentalization. DOI: http://dx.doi.org/10.7554/eLife.02043.001 PMID:24842993

Utilizing a CdTe quantum dots-enzyme hybrid system for the determination of both phenolic compounds and hydrogen peroxide.

PubMed

Yuan, Jipei; Guo, Weiwei; Wang, Erkang

2008-02-15

In this paper, we attempt to construct a simple and sensitive detection method for both phenolic compounds and hydrogen peroxide, with the successful combination of the unique property of quantum dots and the specificity of enzymatic reactions. In the presence of H2O2 and horseradish peroxidase, phenolic compounds can quench quantum dots' photoluminescence efficiently, and the extent of quenching is severalfold to more than 100-fold increase. Quinone intermediates produced from the enzymatic catalyzed oxidation of phenolic compounds were believed to play the main role in the photoluminescence quenching. Using a quantum dots-enzyme system, the detection limits for phenolic compounds and hydrogen peroxide were detected to be approximately 10(-7) mol L(-1). The coupling of efficient quenching of quantum dot photoluminescence by quinone and the effective enzymatic reactions make this a simple and sensitive method for phenolic compound detection and great potential in the development of H2O2 biosensors for various analytes.

Computational Fluid Dynamics–Discrete Element Method (CFD-DEM) Study of Mass-Transfer Mechanisms in Riser Flow

PubMed Central

2017-01-01

We report a computational fluid dynamics–discrete element method (CFD-DEM) simulation study on the interplay between mass transfer and a heterogeneous catalyzed chemical reaction in cocurrent gas-particle flows as encountered in risers. Slip velocity, axial gas dispersion, gas bypassing, and particle mixing phenomena have been evaluated under riser flow conditions to study the complex system behavior in detail. The most important factors are found to be directly related to particle cluster formation. Low air-to-solids flux ratios lead to more heterogeneous systems, where the cluster formation is more pronounced and mass transfer more influenced. Falling clusters can be partially circumvented by the gas phase, which therefore does not fully interact with the cluster particles, leading to poor gas–solid contact efficiencies. Cluster gas–solid contact efficiencies are quantified at several gas superficial velocities, reaction rates, and dilution factors in order to gain more insight regarding the influence of clustering phenomena on the performance of riser reactors. PMID:28553011

Computational Fluid Dynamics-Discrete Element Method (CFD-DEM) Study of Mass-Transfer Mechanisms in Riser Flow.

PubMed

Carlos Varas, Álvaro E; Peters, E A J F; Kuipers, J A M

2017-05-17

We report a computational fluid dynamics-discrete element method (CFD-DEM) simulation study on the interplay between mass transfer and a heterogeneous catalyzed chemical reaction in cocurrent gas-particle flows as encountered in risers. Slip velocity, axial gas dispersion, gas bypassing, and particle mixing phenomena have been evaluated under riser flow conditions to study the complex system behavior in detail. The most important factors are found to be directly related to particle cluster formation. Low air-to-solids flux ratios lead to more heterogeneous systems, where the cluster formation is more pronounced and mass transfer more influenced. Falling clusters can be partially circumvented by the gas phase, which therefore does not fully interact with the cluster particles, leading to poor gas-solid contact efficiencies. Cluster gas-solid contact efficiencies are quantified at several gas superficial velocities, reaction rates, and dilution factors in order to gain more insight regarding the influence of clustering phenomena on the performance of riser reactors.

Detection of Singlet Oxygen Formation inside Photoactive Biohybrid Composite Material.

PubMed

Hajdu, Kata; Ur Rehman, Ateeq; Vass, Imre; Nagy, László

2017-12-26

Photosynthetic reaction center proteins (RCs) are the most efficient light energy converter systems in nature. The first steps of the primary charge separation in photosynthesis take place in these proteins. Due to their unique properties, combining RCs with nano-structures promising applications can be predicted in optoelectronic systems. In the present work RCs purified from Rhodobacter sphaeroides purple bacteria were immobilized on multiwalled carbon nanotubes (CNTs). Carboxyl-and amine-functionalised CNTs were used, so different binding procedures, physical sorption and chemical sorption as well, could be applied as immobilization techniques. Light-induced singlet oxygen production was measured in the prepared photoactive biocomposites in water-based suspension by histidine mediated chemical trapping. Carbon nanotubes were applied under different conditions in order to understand their role in the equilibration of singlet oxygen concentration in the suspension. CNTs acted as effective quenchers of ¹O₂ either by physical (resonance) energy transfer or by chemical (oxidation) reaction and their efficiency showed dependence on the diffusion distance of ¹O₂.

Chemical and thermal stability of N-heterocyclic ionic liquids in catalytic C-H activation reactions.

PubMed

Chen, Guanyi; Kang, Shujuan; Ma, Qisheng; Chen, Weiqun; Tang, Yongchun

2014-11-01

(1)H-NMR spectrum analyses are applied to study the chemical and thermal stability of selected N-heterocyclic ionic liquids within the reaction system that can highly efficiently activate a C-H bond of methane and convert it into the C-O bond in methanol. Our results indicate that under such reaction conditions involving using a powerful Pt-based catalyst and strong acidic solvent, the aromatic ring of an imidazolium cation becomes unstable generating an ammonium ion (NH(4)(+)). Our results also suggest that the instability of the imidazolium ring is more chemically (participation in reactions) than thermally based. Modifications of the aromatic ring structure such as pyrazolium and triazolium cations can increase the chemical/thermal stability of ionic liquids under these reaction conditions. Copyright © 2014 John Wiley & Sons, Ltd.

A Dual-Catalysis Approach to Enantioselective [2+2] Photocycloadditions Using Visible Light

PubMed Central

Du, Juana; Skubi, Kazimer L.; Schultz, Danielle M.; Yoon, Tehshik P.

2015-01-01

In contrast to the wealth of catalytic systems that are available to control the stereochemistry of thermally promoted cycloadditions, few similarly effective methods exist for the stereocontrol of photochemical cycloadditions. A major unsolved challenge in the design of enantioselective catalytic photocycloaddition reactions has been the difficulty of controlling racemic background reactions that occur by direct photoexcitation of substrates while unbound to catalyst. Here we describe a strategy for eliminating the racemic background reaction in asymmetric [2+2] photocycloadditions of α,β-unsaturated ketones to the corresponding cyclobutanes by employing a dual-catalyst system consisting of a visible light-absorbing transition metal photocatalyst and a stereocontrolling Lewis acid co-catalyst. The independence of these two catalysts enables broader scope, greater stereochemical flexibility, and better efficiency than previously reported methods for enantioselective photochemical cycloadditions. PMID:24763585

Interrogating the catalytic mechanism of nanoparticle mediated Stille coupling reactions employing bio-inspired Pd nanocatalysts.

PubMed

Pacardo, Dennis B; Slocik, Joseph M; Kirk, Kyle C; Naik, Rajesh R; Knecht, Marc R

2011-05-01

To address issues concerning the global environmental and energy state, new catalytic technologies must be developed that translate ambient and efficient conditions to heavily used reactions. To achieve this, the structure/function relationship between model catalysts and individual reactions must be critically discerned to identify structural motifs responsible for the reactivity. This is especially true for nanoparticle-based systems where this level of information remains limited. Here we present evidence indicating that peptide-capped Pd nanoparticles drive Stille C-C coupling reactions via Pd atom leaching. Through a series of reaction studies, the materials are shown to be optimized for reactivity under ambient conditions where increases in temperature or catalyst concentration deactivate reactivity due to the leaching process. A quartz crystal microbalance analysis demonstrates that Pd leaching occurs during the initial oxidative addition step at the nanoparticle surface by aryl halides. Together, this suggests that peptide-based materials may be optimally suited for use as model systems to isolate structural motifs responsible for the generation of catalytically reactive materials under ambient synthetic conditions. © The Royal Society of Chemistry 2011

Interrogating the catalytic mechanism of nanoparticle mediated Stille coupling reactions employing bio-inspired Pd nanocatalysts

NASA Astrophysics Data System (ADS)

Pacardo, Dennis B.; Slocik, Joseph M.; Kirk, Kyle C.; Naik, Rajesh R.; Knecht, Marc R.

2011-05-01

To address issues concerning the global environmental and energy state, new catalytic technologies must be developed that translate ambient and efficient conditions to heavily used reactions. To achieve this, the structure/function relationship between model catalysts and individual reactions must be critically discerned to identify structural motifs responsible for the reactivity. This is especially true for nanoparticle-based systems where this level of information remains limited. Here we present evidence indicating that peptide-capped Pd nanoparticles drive Stille C-C coupling reactions via Pd atom leaching. Through a series of reaction studies, the materials are shown to be optimized for reactivity under ambient conditions where increases in temperature or catalyst concentration deactivate reactivity due to the leaching process. A quartz crystal microbalance analysis demonstrates that Pd leaching occurs during the initial oxidative addition step at the nanoparticle surface by aryl halides. Together, this suggests that peptide-based materials may be optimally suited for use as model systems to isolate structural motifs responsible for the generation of catalytically reactive materials under ambient synthetic conditions.

Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology

PubMed Central

Amemiya, Takahiro; Honma, Masashi; Kariya, Yoshiaki; Ghosh, Samik; Kitano, Hiroaki; Kurachi, Yoshihisa; Fujita, Ken-ichi; Sasaki, Yasutsuna; Homma, Yukio; Abernethy, Darrel R; Kume, Haruki; Suzuki, Hiroshi

2015-01-01

Background/Objectives: Targeted kinase inhibitors are an important class of agents in anticancer therapeutics, but their limited tolerability hampers their clinical performance. Identification of the molecular mechanisms underlying the development of adverse reactions will be helpful in establishing a rational method for the management of clinically adverse reactions. Here, we selected sunitinib as a model and demonstrated that the molecular mechanisms underlying the adverse reactions associated with kinase inhibitors can efficiently be identified using a systems toxicological approach. Methods: First, toxicological target candidates were short-listed by comparing the human kinase occupancy profiles of sunitinib and sorafenib, and the molecular mechanisms underlying adverse reactions were predicted by sequential simulations using publicly available mathematical models. Next, to evaluate the probability of these predictions, a clinical observation study was conducted in six patients treated with sunitinib. Finally, mouse experiments were performed for detailed confirmation of the hypothesized molecular mechanisms and to evaluate the efficacy of a proposed countermeasure against adverse reactions to sunitinib. Results: In silico simulations indicated the possibility that sunitinib-mediated off-target inhibition of phosphorylase kinase leads to the generation of oxidative stress in various tissues. Clinical observations of patients and mouse experiments confirmed the validity of this prediction. The simulation further suggested that concomitant use of an antioxidant may prevent sunitinib-mediated adverse reactions, which was confirmed in mouse experiments. Conclusions: A systems toxicological approach successfully predicted the molecular mechanisms underlying clinically adverse reactions associated with sunitinib and was used to plan a rational method for the management of these adverse reactions. PMID:28725458

Surveillance of contrast-media-induced hypersensitivity reactions using signals from an electronic medical recording system.

PubMed

Kim, Min-Hye; Park, Chang-Han; Kim, Duk-In; Kim, Kyung-Mook; Kim, Hui-Kyu; Lim, Kyu-Hyoung; Song, Woo-Jung; Lee, Sang-Min; Kim, Sae-Hoon; Kwon, Hyouk-Soo; Park, Heung-Woo; Yoon, Chang-Jin; Cho, Sang-Heon; Min, Kyung-Up; Kim, You-Young; Chang, Yoon-Seok

2012-03-01

Contrast-media (CM) hypersensitivity is a well-known adverse drug reaction. Surveillance of adverse drug reactions usually depends on spontaneous reports. However, the rate of spontaneous reports is low. Recent progress in information technology enables the electronic search on signals of adverse drug reactions from electronic medical recording (EMR) systems. To analyze the incidence and clinical characteristics of CM hypersensitivity using an EMR-based surveillance system. The surveillance system used signals from standardized terms within the international classification of nursing practice terms that can indicate symptoms of CM hypersensitivity and from the order codes for procedures that used contrast media, antihistamine, and epinephrine. The search strategy was validated by allergists comparing the electronic search strategy versus manually reviewing medical charts over one month. The main study covered for one year period. Detection rate of the electronic search method was 0.9% (7/759), while that of the manual search method was 0.8% (6/759). EMR-based electronic search method was highly efficient: reduced the charts that needed to be reviewed by 96% (28/759). The sensitivity of electronic screening was 66.7%, specificity was 99.6%, and the negative predictive value was 99.7%. CM hypersensitivity reactions were noted in 266 among 12,483 cases (2.1%). Urticaria was the most frequent symptom (74.4%). CT was the most frequent procedure (3.6%) that induced CM hypersensitivity. A surveillance system using EMR may be a useful tool in the study of drug hypersensitivity epidemiology and may be used in an adverse drug reaction alarm system and as a clinical, decision making support system. Copyright © 2012 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Quantum Dynamics Study of the Potential Energy Minima Effect on Energy Efficiency for the F- + CH3Cl → FCH3 + Cl- Reaction.

PubMed

Li, Yida; Wang, Yuping; Wang, Dunyou

2017-04-13

The Polanyi rules on the energy efficiency on reactivity are summarized solely from the locations of barriers on the potential energy surfaces. Here, our quantum dynamics study for the F - + CH 3 Cl → FCH 3 + Cl - reaction shows that the two potential energy minima in the entrance channel on the potential energy surface play an essential role in energy efficiency on reactivity. The reactivity of this reaction is dominated by the low collision energies where two distinctive reaction mechanisms involve the two minima in the entrance channel. Overall, the Cl-CH 3 stretching motion and C-H 3 umbrella motion both are more efficient than the translational motion in promoting this reaction. Although this reaction has a negative energy barrier, our study shows that it is the minima in the entrance channel, together with the energy barrier relative to these minima, that determine the energy efficacy on reactivity.

Wet air co-oxidation of decabromodiphenyl ether (BDE209) and tetrahydrofuran.

PubMed

Zhao, Hongxia; Zhang, Feifang; Qu, Baocheng; Xue, Xingya; Liang, Xinmiao

2009-09-30

The wet air co-oxidation (WACO) of a major commercial polybrominated diphenyl ether flame retardant congener, decabromodiphenyl ether (BDE209), was investigated using tetrahydrofuran (THF) as an initiator in a stainless autoclave at temperature range of 120-170 degrees C and 0.5MPa oxygen pressure. Compared to the single oxidation of BDE209 under the same conditions, the addition of THF in the reaction system greatly improved the removal efficiency of BDE209. The effect of temperature on the reaction was studied. The removals of BDE209 and Br increased with increasing temperature. In addition, the effect of NaNO(2) as the catalyst on the WACO was also investigated and the results showed that the addition of NaNO(2) could improve the Br removal efficiency.

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.

Environmentally benign Friedel-Crafts benzylation over nano-TiO2/SO4 2-

NASA Astrophysics Data System (ADS)

Devi, Kalathiparambil RPS; Sreeja, Puthenveetil B.; Sugunan, Sankaran

2013-05-01

During the past decade, much attention has been paid to the replacement of homogeneous catalysts by solid acid catalysts. Friedel-Crafts benzylation of toluene with benzyl chloride (BC) in liquid phase was carried out over highly active, nano-crystalline sulfated titania systems. These catalysts were prepared using the sol gel method. Modification was done by loading 3% of transition metal oxides over sulfated titania. Reaction parameters such as catalyst mass, molar ratio, temperature, and time have been studied. More than 80% conversion of benzyl chloride and 100% selectivity are shown by all the catalysts under optimum conditions. Catalytic activity is correlated with Lewis acidity obtained from perylene adsorption studies. The reaction appears to proceed by an electrophile, which involves the reaction of BC with the acidic titania catalyst. The catalyst was regenerated and reused up to four reaction cycles with equal efficiency as in the first run. The prepared systems are environmentally friendly and are easy to handle.

Green synthesis of isopropyl myristate in novel single phase medium Part II: Packed bed reactor (PBR) studies.

PubMed

Vadgama, Rajeshkumar N; Odaneth, Annamma A; Lali, Arvind M

2015-12-01

Isopropyl myristate is a useful functional molecule responding to the requirements of numerous fields of application in cosmetic, pharmaceutical and food industry. In the present work, lipase-catalyzed production of isopropyl myristate by esterification of myristic acid with isopropyl alcohol (molar ratio of 1:15) in the homogenous reaction medium was performed on a bench-scale packed bed reactors, in order to obtain suitable reaction performance data for upscaling. An immobilized lipase B from Candida antartica was used as the biocatalyst based on our previous study. The process intensification resulted in a clean and green synthesis process comprising a series of packed bed reactors of immobilized enzyme and water dehydrant. In addition, use of the single phase reaction system facilitates efficient recovery of the product with no effluent generated and recyclability of unreacted substrates. The single phase reaction system coupled with a continuous operating bioreactor ensures a stable operational life for the enzyme.

Investigation on energy conversion technology using biochemical reaction elements, 2

NASA Astrophysics Data System (ADS)

1994-03-01

For measures taken for resource/energy and environmental issues, a study is made on utilization of microbial biochemical reaction. As a reaction system using chemical energy, cited is production of petroleum substitution substances and food/feed by CO2 fixation using hydrogen energy and hydrogen bacteria. As to photo energy utilization, regarded as promising are CO2 fixation using photo energy and microalgae, and production of hydrogen and useful carbon compound using photosynthetic organisms. As living organism/electric energy interconversion, cited is the culture of chemoautotrophic bacteria which fix CO2 using electric energy. For enhancing its conversion efficiency, it is important to develop a technology of gene manipulation of the bacteria and a system to use functional biochemical elements adaptable to the electrode reaction. With regard to utilization of the microorganism metabolic function, the paper presents emission of soluble nitrogen in the hydrosphere into the atmosphere using denitrifying bacteria, removal of phosphorus, reduction in environmental pollution caused by heavy metal dilute solutions, and recovery as resources, etc.

A study of the rate-controlled constrained-equilibrium dimension reduction method and its different implementations

NASA Astrophysics Data System (ADS)

Hiremath, Varun; Pope, Stephen B.

2013-04-01

The Rate-Controlled Constrained-Equilibrium (RCCE) method is a thermodynamic based dimension reduction method which enables representation of chemistry involving n s species in terms of fewer n r constraints. Here we focus on the application of the RCCE method to Lagrangian particle probability density function based computations. In these computations, at every reaction fractional step, given the initial particle composition (represented using RCCE), we need to compute the reaction mapping, i.e. the particle composition at the end of the time step. In this work we study three different implementations of RCCE for computing this reaction mapping, and compare their relative accuracy and efficiency. These implementations include: (1) RCCE/TIFS (Trajectory In Full Space): this involves solving a system of n s rate-equations for all the species in the full composition space to obtain the reaction mapping. The other two implementations obtain the reaction mapping by solving a reduced system of n r rate-equations obtained by projecting the n s rate-equations for species evaluated in the full space onto the constrained subspace. These implementations include (2) RCCE: this is the classical implementation of RCCE which uses a direct projection of the rate-equations for species onto the constrained subspace; and (3) RCCE/RAMP (Reaction-mixing Attracting Manifold Projector): this is a new implementation introduced here which uses an alternative projector obtained using the RAMP approach. We test these three implementations of RCCE for methane/air premixed combustion in the partially-stirred reactor with chemistry represented using the n s=31 species GRI-Mech 1.2 mechanism with n r=13 to 19 constraints. We show that: (a) the classical RCCE implementation involves an inaccurate projector which yields large errors (over 50%) in the reaction mapping; (b) both RCCE/RAMP and RCCE/TIFS approaches yield significantly lower errors (less than 2%); and (c) overall the RCCE/TIFS approach is the most accurate, efficient (by orders of magnitude) and robust implementation.

Mesoporous TiO2 Yolk-Shell Microspheres for Dye-sensitized Solar Cells with a High Efficiency Exceeding 11%

PubMed Central

Li, Zhao-Qian; Chen, Wang-Chao; Guo, Fu-Ling; Mo, Li-E; Hu, Lin-Hua; Dai, Song-Yuan

2015-01-01

Yolk-shell TiO2 microspheres were synthesized via a one-pot template-free solvothermal method building on the aldol condensation reaction of acetylacetone. This unique structure shows superior light scattering ability resulting in power conversion efficiency as high as 11%. This work provided a new synthesis system for TiO2 microspheres from solid to hollow and a novel material platform for high performance solar cells. PMID:26384004

Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP

PubMed Central

Khorosheva, Eugenia M.; Karymov, Mikhail A.; Selck, David A.; Ismagilov, Rustem F.

2016-01-01

In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions. PMID:26358811

Enhanced analysis of real-time PCR data by using a variable efficiency model: FPK-PCR

PubMed Central

Lievens, Antoon; Van Aelst, S.; Van den Bulcke, M.; Goetghebeur, E.

2012-01-01

Current methodology in real-time Polymerase chain reaction (PCR) analysis performs well provided PCR efficiency remains constant over reactions. Yet, small changes in efficiency can lead to large quantification errors. Particularly in biological samples, the possible presence of inhibitors forms a challenge. We present a new approach to single reaction efficiency calculation, called Full Process Kinetics-PCR (FPK-PCR). It combines a kinetically more realistic model with flexible adaptation to the full range of data. By reconstructing the entire chain of cycle efficiencies, rather than restricting the focus on a ‘window of application’, one extracts additional information and loses a level of arbitrariness. The maximal efficiency estimates returned by the model are comparable in accuracy and precision to both the golden standard of serial dilution and other single reaction efficiency methods. The cycle-to-cycle changes in efficiency, as described by the FPK-PCR procedure, stay considerably closer to the data than those from other S-shaped models. The assessment of individual cycle efficiencies returns more information than other single efficiency methods. It allows in-depth interpretation of real-time PCR data and reconstruction of the fluorescence data, providing quality control. Finally, by implementing a global efficiency model, reproducibility is improved as the selection of a window of application is avoided. PMID:22102586

Precision synthesis of functional materials via RAFT polymerization and click-type chemical reactions

NASA Astrophysics Data System (ADS)

Flores, Joel Diez

2011-12-01

The need to tailor polymeric architectures with specific physico-chemical properties via the simplest, cleanest, and most efficient synthetic route possible has become the ultimate goal in polymer synthesis. Recent progress in macromolecular science, such as the discoveries of controlled/"living" free radical polymerization (CRP) methods, has brought about synthetic capabilities to prepare (co)polymers with advanced topologies, predetermined molecular weights, narrow molecular weight distributions, and precisely located functional groups. In addition, the establishment of click chemistry has redefined the selected few highly efficient chemical reactions that become highly useful in post-polymerization modification strategies. Hence, the ability to make well-defined topologies afforded by controlled polymerization techniques and the facile incorporation of functionalities along the chain via click-type reactions have yielded complex architectures, allowing the investigation of physical phenomena which otherwise could not be studied with systems prepared via conventional methods. The overarching theme of the research work described in this dissertation is the fusion of the excellent attributes of reversible addition-fragmentation chain transfer (RAFT) polymerization method, which is one of the CRP techniques, and click-type chemical reactions in the precision of synthesis of advanced functional materials. Chapter IV is divided into three sections. In Section I, the direct RAFT homopolymerization of 2-(acryloyloxy)ethyl isocyanate (AOI) and subsequent post-polymerization modifications are described. The polymerization conditions were optimized in terms of the choice of RAFT chain transfer agent (CTA), polymerization temperature and the reaction medium. Direct RAFT polymerization of AOI requires a neutral CTA, and relatively low reaction temperature to yield AOI homopolymers with low polydispersities. Efficient side-chain functionalization of PAOI homopolymers was achieved via reaction with model amine, thiol and alcohol compounds yielding urea, thiourethane and urethane derivatives, respectively. Reactions with amines and thiols (in the presence of base) were rapid, quantitative and efficient. However, the reaction with alcohols catalyzed by dibutyltin dilaurate (DBTDL) was relatively slow but proceeded to completion. Selective reaction pathways for the addition of difunctional ethanolamine and mercaptoethanol were also investigated. A related strategy is described in Section II wherein a hydroxyl-containing diblock copolymer precursor was transformed into a library of functional copolymers via two sequential post-polymerization modification reactions. A diblock copolymer scaffold, poly[(N,N-dimethylacrylamide)-b-( N-(2-hydroxyethyl)acrylamide] (PDMA-b-PHEA) was first prepared. The hydroxyl groups of the HEA block were then reacted with 2-(acryloyloxy)ethylisocyanate (AOI) and allylisocyanate (AI) resulting in acrylate- and allyl-functionalized copolymer precursors, respectively. The efficiencies of Michael-type and free radical thiol addition reactions were investigated using selected thiols having alkyl, aryl, hydroxyl, carboxylic acid, amine and amino acid functionalities. The steps of RAFT polymerization, isocyanate-hydroxyl coupling and thiol-ene addition are accomplished under mild conditions, thus offering facile and modular routes to synthesize functional copolymers. The synthesis and solution studies of pH- and salt-responsive triblock copolymer are described in Section III. This system is capable of forming self-locked micellar structures which may be controlled by changing solution pH as well as ionic strength. A triblock copolymer containing a permanently hydrophilic poly(N,N-dimethylacrylamide) (PDMA) outer block, a salt-sensitive zwitterionic poly(3[2-(N-methylacrylamido)ethyl dimethylammonio]propanesulfonate) (PMAEDAPS) middle block and a pH-responsive 3-acrylamido-3-methylbutanoic acid (PAMBA) core block was synthesized using aqueous RAFT polymerization. A facile formation of "self-locking" shell cross-linked micelles is achieved by changing solution pH and salt concentration. The reversible "self-locking" is attained from the interactions of zwitterionic groups in the middle block that constitutes the shell of the micelles. The structure slowly dissociates into unimers in 2-3 days at pH above the pKa of the PAMBA block.

Simultaneous removal of Cr(VI) and 4-chlorophenol through photocatalysis by a novel anatase/titanate nanosheet composite: Synergetic promotion effect and autosynchronous doping.

PubMed

Liu, Wen; Sun, Weiling; Borthwick, Alistair G L; Wang, Ting; Li, Fan; Guan, Yidong

2016-11-05

Clean-up of wastewaters with coexisting heavy metals and organic contaminants is a huge issue worldwide. In this study, a novel anatase/titanate nanosheet composite material (labeled as TNS) synthesized through a one-step hydrothermal reaction was demonstrated to achieve the goal of simultaneous removal of Cr(VI) and 4-cholophenol (4-CP) from water. TEM and XRD analyses indicated the TNS was a nano-composite of anatase and titanate, with anatase acting as the primary photocatalysis center and titanate as the main adsorption site. Enhanced photocatalytic removal of co-existent Cr(VI) and 4-CP was observed in binary systems, with apparent rate constants (k1) for photocatalytic reactions of Cr(VI) and 4-CP about 3.1 and 2.6 times of that for single systems. In addition, over 99% of Cr(VI) and 4-CP was removed within 120min through photocatalysis by TNS at pH 7 in the binary system. Mechanisms for enhanced photocatalytic efficiency in the binary system are identified as: (1) a synergetic effect on the photo-reduction of Cr(VI) and photo-oxidation of 4-CP due to efficient separation of electron-hole pairs, and (2) autosynchronous doping because of reduced Cr(III) adsorption onto TNS. Furthermore, TNS could be efficiently reused after a simple acid-base treatment. Copyright © 2016 Elsevier B.V. All rights reserved.

Optimum rocket propulsion for energy-limited transfer

NASA Technical Reports Server (NTRS)

Zuppero, Anthony; Landis, Geoffrey A.

1991-01-01

In order to effect large-scale return of extraterrestrial resources to Earth orbit, it is desirable to optimize the propulsion system to maximize the mass of payload returned per unit energy expended. This optimization problem is different from the conventional rocket propulsion optimization. A rocket propulsion system consists of an energy source plus reaction mass. In a conventional chemical rocket, the energy source and the reaction mass are the same. For the transportation system required, however, the best system performance is achieved if the reaction mass used is from a locally available source. In general, the energy source and the reaction mass will be separate. One such rocket system is the nuclear thermal rocket, in which the energy source is a reactor and the reaction mass a fluid which is heated by the reactor and exhausted. Another energy-limited rocket system is the hydrogen/oxygen rocket where H2/O2 fuel is produced by electrolysis of water using a solar array or a nuclear reactor. The problem is to choose the optimum specific impulse (or equivalently exhaust velocity) to minimize the amount of energy required to produce a given mission delta-v in the payload. The somewhat surprising result is that the optimum specific impulse is not the maximum possible value, but is proportional to the mission delta-v. In general terms, at the beginning of the mission it is optimum to use a very low specific impulse and expend a lot of reaction mass, since this is the most energy efficient way to transfer momentum. However, as the mission progresses, it becomes important to minimize the amount of reaction mass expelled, since energy is wasted moving the reaction mass. Thus, the optimum specific impulse will increase with the mission delta-v. Optimum I(sub sp) is derived for maximum payload return per energy expended for both the case of fixed and variable I(sub sp) engines. Sample missions analyzed include return of water payloads from the moons of Mars and of Saturn.

An efficient system for the asymmetric acylation of (R,S)-3-n-butylphthalide catalyzed by novozyme 435.

PubMed

Li, Cuiqin; He, Laping; Qiu, Baoquan; Gao, Bing

2010-01-01

Novozyme 435 could be a highly efficient catalyst in the asymmetric acylation of (R,S)-3-n-butylphthalide in tetrahydrofuran-hexane solvents. The effect of various reaction parameters such as agitation velocity, water content, mixed media, temperature, concentration of Novozyme 435, molar ratio of acetic anhydride to (R,S)-3-n-butylphthalide, reaction time, enantiomeric excess of substrate (ee(S)), enantiomeric excess of product (ee(P)), and enantioselective ratio (E) were studied. Tetrahydrofuran markedly improved (R,S)-3-n-butylphthalide conversion, enantiomeric excess of remaining 3-n-butylphthalide, and enantiomeric ratio. The optimum media were 50% (v/v) tetrahydrofuran and 50% (v/v) hexane. Other ideal reaction conditions were an agitation velocity of 150 rpm, 0.4% (v/v) water content, temperature of 30 °C, 8 mg/mL dosage of Novozyme 435, 8:1 (0.4 mmol: 0.05 mmol) molar ratio of acetic anhydride to (R,S)-3-n-butylphthalide, and a reaction time of 48 hr. Under the optimum conditions, 96.4% ee(S) and 49.3% conversion of (R,S)-3-n-butylphthalide were achieved. In addition, enantiomeric excess of the product was above 98.0%.

A simple and cost-effective molecular diagnostic system and DNA probes synthesized by light emitting diode photolithography

NASA Astrophysics Data System (ADS)

Oleksandrov, Sergiy; Kwon, Jung Ho; Lee, Ki-chang; Sujin-Ku; Paek, Mun Cheol

2014-09-01

This work introduces a novel chip to be used in the future as a simple and cost-effective method for creating DNA arrays using light emission diode (LED) photolithography. The DNA chip platform contains 24 independent reaction sites, which allows for the testing of a corresponding amount of patients' samples in hospital. An array of commercial UV LEDs and lens systems was combined with a microfluidic flow system to provide patterning of 24 individual reaction sites, each with 64 independent probes. Using the LED array instead of conventional laser exposure systems or micro-mirror systems significantly reduces the cost of equipment. The microfluidic system together with microfluidic flow cells drastically reduces the amount of used reagents, which is important due to the high cost of commercial reagents. The DNA synthesis efficiency was verified by fluorescence labeling and conventional hybridization.

O-Allylation of phenols with allylic acetates in aqueous media using a magnetically separable catalytic system

EPA Science Inventory

Allylic ethers were synthesized in water using magnetically recoverable heterogeneous Pd catalyst via O-allylation of phenols with allylic acetates under ambient conditions. Aqueous reaction medium, easy recovery of the catalyst using an external magnet, efficient recycling, and ...

A Hybrid of the Chemical Master Equation and the Gillespie Algorithm for Efficient Stochastic Simulations of Sub-Networks.

PubMed

Albert, Jaroslav

2016-01-01

Modeling stochastic behavior of chemical reaction networks is an important endeavor in many aspects of chemistry and systems biology. The chemical master equation (CME) and the Gillespie algorithm (GA) are the two most fundamental approaches to such modeling; however, each of them has its own limitations: the GA may require long computing times, while the CME may demand unrealistic memory storage capacity. We propose a method that combines the CME and the GA that allows one to simulate stochastically a part of a reaction network. First, a reaction network is divided into two parts. The first part is simulated via the GA, while the solution of the CME for the second part is fed into the GA in order to update its propensities. The advantage of this method is that it avoids the need to solve the CME or stochastically simulate the entire network, which makes it highly efficient. One of its drawbacks, however, is that most of the information about the second part of the network is lost in the process. Therefore, this method is most useful when only partial information about a reaction network is needed. We tested this method against the GA on two systems of interest in biology--the gene switch and the Griffith model of a genetic oscillator--and have shown it to be highly accurate. Comparing this method to four different stochastic algorithms revealed it to be at least an order of magnitude faster than the fastest among them.

An adaptive multi-level simulation algorithm for stochastic biological systems

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

Lester, C., E-mail: lesterc@maths.ox.ac.uk; Giles, M. B.; Baker, R. E.

2015-01-14

Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Montemore » Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10(1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.« less

Rare earth separations by selective borate crystallization

PubMed Central

Yin, Xuemiao; Wang, Yaxing; Bai, Xiaojing; Wang, Yumin; Chen, Lanhua; Xiao, Chengliang; Diwu, Juan; Du, Shiyu; Chai, Zhifang; Albrecht-Schmitt, Thomas E.; Wang, Shuao

2017-01-01

Lanthanides possess similar chemical properties rendering their separation from one another a challenge of fundamental chemical and global importance given their incorporation into many advanced technologies. New separation strategies combining green chemistry with low cost and high efficiency remain highly desirable. We demonstrate that the subtle bonding differences among trivalent lanthanides can be amplified during the crystallization of borates, providing chemical recognition of specific lanthanides that originates from Ln3+ coordination alterations, borate polymerization diversity and soft ligand coordination selectivity. Six distinct phases are obtained under identical reaction conditions across lanthanide series, further leading to an efficient and cost-effective separation strategy via selective crystallization. As proof of concept, Nd/Sm and Nd/Dy are used as binary models to demonstrate solid/aqueous and solid/solid separation processes. Controlling the reaction kinetics gives rise to enhanced separation efficiency of Nd/Sm system and a one-step quantitative separation of Nd/Dy with the aid of selective density-based flotation. PMID:28290448

Economic photoprotection in photosystem II that retains a complete light-harvesting system with slow energy traps

NASA Astrophysics Data System (ADS)

Belgio, Erica; Kapitonova, Ekaterina; Chmeliov, Jevgenij; Duffy, Christopher D. P.; Ungerer, Petra; Valkunas, Leonas; Ruban, Alexander V.

2014-07-01

The light-harvesting antenna of higher plant photosystem II has an intrinsic capability for self-defence against intense sunlight. The thermal dissipation of excess energy can be measured as the non-photochemical quenching of chlorophyll fluorescence. It has recently been proposed that the transition between the light-harvesting and self-defensive modes is associated with a reorganization of light-harvesting complexes. Here we show that despite structural changes, the photosystem II cross-section does not decrease. Our study reveals that the efficiency of energy trapping by the non-photochemical quencher(s) is lower than the efficiency of energy capture by the reaction centres. Consequently, the photoprotective mechanism works effectively for closed rather than open centres. This type of defence preserves the exceptional efficiency of electron transport in a broad range of light intensities, simultaneously ensuring high photosynthetic productivity and, under hazardous light conditions, sufficient photoprotection for both the reaction centre and the light-harvesting pigments of the antenna.

Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks.

PubMed

Rathinam, Muruhan; Sheppard, Patrick W; Khammash, Mustafa

2010-01-21

Parametric sensitivity of biochemical networks is an indispensable tool for studying system robustness properties, estimating network parameters, and identifying targets for drug therapy. For discrete stochastic representations of biochemical networks where Monte Carlo methods are commonly used, sensitivity analysis can be particularly challenging, as accurate finite difference computations of sensitivity require a large number of simulations for both nominal and perturbed values of the parameters. In this paper we introduce the common random number (CRN) method in conjunction with Gillespie's stochastic simulation algorithm, which exploits positive correlations obtained by using CRNs for nominal and perturbed parameters. We also propose a new method called the common reaction path (CRP) method, which uses CRNs together with the random time change representation of discrete state Markov processes due to Kurtz to estimate the sensitivity via a finite difference approximation applied to coupled reaction paths that emerge naturally in this representation. While both methods reduce the variance of the estimator significantly compared to independent random number finite difference implementations, numerical evidence suggests that the CRP method achieves a greater variance reduction. We also provide some theoretical basis for the superior performance of CRP. The improved accuracy of these methods allows for much more efficient sensitivity estimation. In two example systems reported in this work, speedup factors greater than 300 and 10,000 are demonstrated.

Artificial photosynthetic antennas and reaction centers

DOE PAGES

Llansola-Portoles, Manuel J.; Gust, Devens; Moore, Thomas A.; ...

2017-03-01

Presently, the world is experiencing an unprecedented crisis associated with the CO2 produced by the use of fossil fuels to power our economies. As evidenced by the increasing levels in the atmosphere, the reduction of CO2 to biomass by photosynthesis cannot keep pace with production with the result that nature has lost control of the global carbon cycle. In order to restore control of the global carbon cycle to solar-driven processes, highly efficient artificial photosynthesis can augment photosynthesis in specific ways and places. The increased efficiency of artificial photosynthesis can provide both renewable carbon-based fuels and lower net atmospheric levelsmore » of CO2, which will preserve land and support the ecosystem services upon which all life on Earth depends. The development of artificial photosynthetic antennas and reaction centers contributes to the understanding of natural photosynthesis and to the knowledge base necessary for the development of future scalable technologies. This review focuses on the design and study of molecular and hybrid molecular-semiconductor nanoparticle based systems, all of which are inspired by functions found in photosynthesis and some of which are inspired by components of photosynthesis. In addition to constructs illustrating energy transfer, photoinduced electron transfer, charge shift reactions and proton coupled electron transfer, our review covers systems that produce proton motive force.« less

Artificial photosynthetic antennas and reaction centers

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

Llansola-Portoles, Manuel J.; Gust, Devens; Moore, Thomas A.

Presently, the world is experiencing an unprecedented crisis associated with the CO2 produced by the use of fossil fuels to power our economies. As evidenced by the increasing levels in the atmosphere, the reduction of CO2 to biomass by photosynthesis cannot keep pace with production with the result that nature has lost control of the global carbon cycle. In order to restore control of the global carbon cycle to solar-driven processes, highly efficient artificial photosynthesis can augment photosynthesis in specific ways and places. The increased efficiency of artificial photosynthesis can provide both renewable carbon-based fuels and lower net atmospheric levelsmore » of CO2, which will preserve land and support the ecosystem services upon which all life on Earth depends. The development of artificial photosynthetic antennas and reaction centers contributes to the understanding of natural photosynthesis and to the knowledge base necessary for the development of future scalable technologies. This review focuses on the design and study of molecular and hybrid molecular-semiconductor nanoparticle based systems, all of which are inspired by functions found in photosynthesis and some of which are inspired by components of photosynthesis. In addition to constructs illustrating energy transfer, photoinduced electron transfer, charge shift reactions and proton coupled electron transfer, our review covers systems that produce proton motive force.« less

Design of SECAR a recoil mass separator for astrophysical capture reactions with radioactive beams

NASA Astrophysics Data System (ADS)

Berg, G. P. A.; Couder, M.; Moran, M. T.; Smith, K.; Wiescher, M.; Schatz, H.; Hager, U.; Wrede, C.; Montes, F.; Perdikakis, G.; Wu, X.; Zeller, A.; Smith, M. S.; Bardayan, D. W.; Chipps, K. A.; Pain, S. D.; Blackmon, J.; Greife, U.; Rehm, K. E.; Janssens, R. V. F.

2018-01-01

A recoil mass separator SECAR has been designed for the purpose of studying low-energy (p , γ) and (α , γ) reactions in inverse kinematics with radioactive beams for masses up to about A = 65. Their reaction rates are of importance for our understanding of the energy production and nucleosynthesis during explosive hydrogen and helium burning. The radiative capture reactions take place in a windowless hydrogen or He gas target at the entrance of the separator, which consists of four Sections. The first Section selects the charge state of the recoils. The second and third Sections contain Wien Filters providing high mass resolving power to separate efficiently the intense beam from the few reaction products. In the following fourth Section, the reaction products are guided into a detector system capable of position, angle and time-of-flight measurements. In order to accept the complete kinematic cone of recoil particles including multiple scattering in the target in the center of mass energy range of 0.2 MeV to 3.0 MeV, the system must have a large polar angle acceptance of ± 25 mrad. This requires a careful minimization of higher order aberrations. The present system will be installed at the NSCL ReA3 accelerator and will be used with the much higher beam intensities of the FRIB facility when it becomes available.

Design of SECAR a recoil mass separator for astrophysical capture reactions with radioactive beams

DOE PAGES

Berg, G. P. A.; Couder, M.; Moran, M. T.; ...

2017-09-25

A recoil mass separator SECAR has been designed for the purpose of studying low-energy (p,γ) and (α,γ) reactions in inverse kinematics with radioactive beams for masses up to about A = 65. Their reaction rates are of importance for our understanding of the energy production and nucleosynthesis during explosive hydrogen and helium burning. The radiative capture reactions take place in a windowless hydrogen or He gas target at the entrance of the separator, which consists of four Sections. The first Section selects the charge state of the recoils. The second and third Sections contain Wien Filters providing high mass resolvingmore » power to separate efficiently the intense beam from the few reaction products. In the following fourth Section, the reaction products are guided into a detector system capable of position, angle and time-of-flight measurements. In order to accept the complete kinematic cone of recoil particles including multiple scattering in the target in the center of mass energy range of 0.2 MeV to 3.0 MeV, the system must have a large polar angle acceptance of ± 25 mrad. This requires a careful minimization of higher order aberrations. Furthermore, the present system will be installed at the NSCL ReA3 accelerator and will be used with the much higher beam intensities of the FRIB facility when it becomes available.« less

Oxidative trifluoromethylation and trifluoromethylthiolation reactions using (trifluoromethyl)trimethylsilane as a nucleophilic CF3 source.

PubMed

Chu, Lingling; Qing, Feng-Ling

2014-05-20

The trifluoromethyl group is widely prevalent in many pharmaceuticals and agrochemicals because its incorporation into drug candidates could enhance chemical and metabolic stability, improve lipophilicity and bioavailability, and increase the protein bind affinity. Consequently, extensive attention has been devoted toward the development of efficient and versatile methods for introducing the CF3 group into various organic molecules. Direct trifluoromethylation reaction has become one of the most efficient and important approaches for constructing carbon-CF3 bonds. Traditionally, the nucleophilic trifluoromethylation reaction involves an electrophile and the CF3 anion, while the electrophilic trifluoromethylation reaction involves a nucleophile and the CF3 cation. In 2010, we proposed the concept of oxidative trifluoromethylation: the reaction of nucleophilic substrates and nucleophilic trifluoromethylation reagents in the presence of oxidants. In this Account, we describe our recent studies of oxidative trifluoromethylation reactions of various nucleophiles with CF3SiMe3 in the presence of oxidants. We have focused most of our efforts on constructing carbon-CF3 bonds via direct trifluoromethylation of various C-H bonds. We have demonstrated copper-mediated or -catalyzed or metal-free oxidative C-H trifluoromethylation of terminal alkynes, tertiary amines, arenes and heteroarenes, and terminal alkenes. Besides various C-H bonds, aryl boronic acids proved to be viable nucleophilic coupling partners for copper-mediated or -catalyzed cross-coupling reactions with CF3SiMe3. To further expand the reaction scope, we also applied H-phosphonates to the oxidative trifluoromethylation system to construct P-CF3 bonds. Most recently, we developed silver-catalyzed hydrotrifluoromethylation of unactivated olefins. These studies explore boronic acids, C-H bonds, and P-H bonds as novel nucleophiles in transition-metal-mediated or -catalyzed cross-coupling reactions with CF3SiMe3, opening new viewpoints for future trifluoromethylation reactions. Furthermore, we also achieved the oxidative trifluoromethylthiolation reactions of aryl boronic acids and terminal alkynes to construct carbon-SCF3 bonds by using CF3SiMe3 and elemental sulfur as the nucleophilic trifluoromethylthiolating reagent. These oxidative trifluoromethylation and trifluoromethylthiolation reactions tolerate a wide range of functional groups, affording a diverse array of CF3- and CF3S-containing compounds with high efficiencies, and provide elegant and complementary alternatives to classical trifluoromethylation and trifluoromethylthiolation reactions. Because of the importance of the CF3 and SCF3 moieties in pharmaceuticals and agrochemicals, these reactions would have potential applications in the life science fields.

Oxidative Dehydrogenation on Nanocarbon: Insights into the Reaction Mechanism and Kinetics via in Situ Experimental Methods.

PubMed

Qi, Wei; Yan, Pengqiang; Su, Dang Sheng

2018-03-20

Sustainable and environmentally benign catalytic processes are vital for the future to supply the world population with clean energy and industrial products. The replacement of conventional metal or metal oxide catalysts with earth abundant and renewable nonmetallic materials has attracted considerable research interests in the field of catalysis and material science. The stable and efficient catalytic performance of nanocarbon materials was discovered at the end of last century, and these materials are considered as potential alternatives for conventional metal-based catalysts. With its rapid development in the past 20 years, the research field of carbon catalysis has been experiencing a smooth transition from the discovery of novel nanocarbon materials or related new reaction systems to the atomistic-level mechanistic understanding on the catalytic process and the subsequent rational design of the practical catalytic reaction systems. In this Account, we summarize the recent progress in the kinetic and mechanistic studies on nanocarbon catalyzed alkane oxidative dehydrogenation (ODH) reactions. The paper attempts to extract general concepts and basic regularities for carbon catalytic process directing us on the way for rational design of novel efficient metal-free catalysts. The nature of the active sites for ODH reactions has been revealed through microcalorimetric analysis, ambient pressure X-ray photoelectron spectroscopy (XPS) measurement, and in situ chemical titration strategies. The detailed kinetic analysis and in situ catalyst structure characterization suggests that carbon catalyzed ODH reactions involve the redox cycles of the ketonic carbonyl-hydroxyl pairs, and the key physicochemical parameters (activation energy, reaction order, and rate/equilibrium constants, etc.) of the carbon catalytic systems are proposed and compared with conventional transition metal oxide catalysts. The proposal of the intrinsic catalytic activity (TOF) provides the possibility for the fair comparisons of different nanocarbon catalysts and the consequent structure-function relation regularity. Surface modification and heteroatom doping are proved as the most effective strategies to adjust the catalytic property (activity and product selectivity etc.) of the nanocarbon catalysts. Nanocarbon is actually a proper candidate platform helping us to understand the classical catalytic reaction mechanism better, since there is no lattice oxygen and all the catalytic process happens on nanocarbon surface. This Account also exhibits the importance of the in situ structural characterizations for heterogeneous nanocarbon catalysis. The research strategy and methods proposed for carbon catalysts may also shed light on other complicated catalytic systems or fields concerning the applications of nonmetallic materials, such as energy storage and environment protection etc.

Photosensitized H2 Production Using a Zinc Porphyrin-Substituted Protein, Platinum Nanoparticles, and Ascorbate with No Electron Relay: Participation of Good's Buffers.

PubMed

Clark, Emily R; Kurtz, Donald M

2017-04-17

Development of efficient light-driven splitting of water, 2H 2 O → 2H 2 + O 2 , often attempts to optimize photosensitization of the reductive and oxidative half-reactions individually. Numerous homogeneous and heterogeneous systems have been developed for photochemical stimulation of the reductive half reaction, 2H + + 2e - → H 2 . These systems generally consist of various combinations of a H + reduction catalyst, a photosensitizer (PS), and a "sacrificial" electron donor. Zinc(II)-porphyrins (ZnPs) have frequently been used as PSs for H 2 generation, but they are subject to various self-quenching processes in aqueous solutions. Colloidal platinum in nanoparticle form (Pt NP) is a classical H + reduction catalyst using ZnP photosensitizers, but efficient photosensitized H 2 generation requires an electron relay molecule between ZnP and Pt NP. The present report describes an aqueous system for visible (white) light-sensitized generation of H 2 using a protein-embedded Zn(II)-protoporphyrin IX as PS and Pt NP as H + reduction catalyst without an added electron relay. This system operated efficiently in piperazino- and morpholino-alkylsulfonic acid (Good's buffers), which served as sacrificial electron donors. The system also required ascorbate at relatively modest concentrations, which stabilized the Zn(II)-protoporphyrin IX against photodegradation. In the absence of an electron relay molecule, the photosensitized H 2 generation must involve formation of at least a transient complex between a protein-embedded Zn(II)-protoporphyrin IX species and Pt NP.

Efficient treatment of aniline containing wastewater in bipolar membrane microbial electrolysis cell-Fenton system.

PubMed

Li, Xiaohu; Jin, Xiangdan; Zhao, Nannan; Angelidaki, Irini; Zhang, Yifeng

2017-08-01

Aniline-containing wastewater can cause significant environmental problems and threaten the humans's life. However, rapid degradation of aniline with cost-efficient methods remains a challenge. In this work, a novel microbial electrolysis cell with bipolar membrane was integrated with Fenton reaction (MEC-Fenton) for efficient treatment of real wastewater containing a high concentration (4460 ± 52 mg L -1 ) of aniline. In this system, H 2 O 2 was in situ electro-synthesized from O 2 reduction on the graphite cathode and was simultaneously used as source of OH for the oxidation of aniline wastewater under an acidic condition maintained by the bipolar membrane. The aniline was effectively degraded following first-order kinetics at a rate constant of 0.0166 h -1 under an applied voltage of 0.5 V. Meanwhile, a total organic carbon (TOC) removal efficiency of 93.1 ± 1.2% was obtained, revealing efficient mineralization of aniline. The applicability of bipolar membrane MEC-Fenton system was successfully demonstrated with actual aniline wastewater. Moreover, energy balance showed that the system could be a promising technology for removal of biorefractory organic pollutants from wastewaters. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fenton-like reaction: a possible way to efficiently remove illicit drugs and pharmaceuticals from wastewater.

PubMed

Mackuľak, Tomáš; Mosný, Michal; Grabic, Roman; Golovko, Oksana; Koba, Olga; Birošová, Lucia

2015-03-01

We analyzed 13 psychoactive pharmaceuticals, illicit drugs and their metabolites in wastewater treatment plant influent and effluent and the possibility of their degradation by biological and chemical processes. Tramadol (413-853 ng/L) and methamphetamine (460-682 ng/L) were the most concentrated compounds in the wastewater in winter and summer, respectively. A significant decrease in the concentration of tramadol in wastewater was measured during the summer. The lowest efficiency was observed for tramadol, venlafaxine, citalopram and oxazepam (∼ 10%) and the highest efficiency was observed for amphetamine and THC-COOH (∼ 80%). The efficiency of compound degradation via the Fenton reaction, a modified Fenton reaction and different degradation (by algae, wood-rotting fungi and enzymes at influent versus effluent) was determined. The Fenton reaction and its modification were efficient at eliminating these substances in comparison with the tested biological processes. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Interfacial contributions of H2O2 decomposition-induced reaction current on mesoporous Pt/TiO2 systems

NASA Astrophysics Data System (ADS)

Ray, Nathan J.; Styrov, Vladislav V.; Karpov, Eduard G.

2017-12-01

We report on conversion of energy released due to chemical reactions into current for the decomposition of aqueous hydrogen peroxide solution on single phases Pt and TiO2, in addition to Pt and TiO2 simultaneously. We observe that H2O2 decomposition-induced current on TiO2 drastically overshadows the current generated by H2O2 decomposition on Pt. Photo-effects avoided, H2O2 decomposition was found to yield a conversion efficiency of 10-3 electrons generated per H2O2 molecule. Further understanding of chemical reaction-induced current shows promise as a metric with which the surface reaction may be monitored and could be greatly extended into the field of analytical chemistry.

Production of furfural from xylose, xylan and corncob in gamma-valerolactone using FeCl3·6H2O as catalyst.

PubMed

Zhang, Luxin; Yu, Hongbing; Wang, Pan; Li, Yong

2014-01-01

An efficient and simple one-pot monophasic reaction system with small carbon footprint for converting xylose, xylan and corncob into furfural was developed in gamma-valerolactone (GVL, an ideal sustainable solvent derived from lignocelluloses) by using FeCl3·6H2O as catalyst. Good yields of furfural from xylose were obtained, and the system was shown to work for xylan and corncob as well. A surprisingly high furfural yield of 79.6% from untreated corncob was achieved at 458 K for 100 min. Contrary to what was generally believed, the addition of water, reduced the rate of the reactions, but showed positive effect on preventing the furfural from degradation in GVL. Besides, the C6 sugars (glucose and cellulose) afforded 11.4-24.5% furfural yields when employing this catalytic approach. The reaction system proposed in this manuscript showed great potential for optimizing the catalytic process in furfural production. Copyright © 2013 Elsevier Ltd. All rights reserved.

Oxidative C-H/C-H Cross-Coupling Reactions between N-Acylanilines and Benzamides Enabled by a Cp*-Free RhCl3/TFA Catalytic System.

PubMed

You, Jingsong; Shi, Yang; Zhang, Luoqiang; Lan, Jingbo; Zhang, Min; Zhou, Fulin; Wei, Wenlong

2018-06-03

Using the dual chelation-assisted strategy, a completely regiocontrolled oxidative C-H/C-H cross-coupling reaction between an N-acylaniline and a benzamide has been accomplished for the first time, which enables a step-economical and highly efficient pathway to 2-amino-2'-carboxybiaryl scaffolds from readily available substrates. A Cp*-free RhCl3/TFA catalytic system has been developed to replace the generally used [Cp*RhCl2]2/AgSbF6 (Cp* = pentamethyl cyclopentadienyl) in oxidative C-H/C-H cross-coupling reactions between two (hetero)arenes. The RhCl3/TFA system avoids the use of expensive Cp* ligand and AgSbF6. As an illustrative example, the protocol developed herein greatly streamlines access to naturally occurring benzo[c]phenanthridine alkaloid oxynitidine in an excellent overall yield. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

NiMn layered double hydroxide nanosheets/NiCo2O4 nanowires with surface rich high valence state metal oxide as an efficient electrocatalyst for oxygen evolution reaction

NASA Astrophysics Data System (ADS)

Yang, Liting; Chen, Lin; Yang, Dawen; Yu, Xu; Xue, Huaiguo; Feng, Ligang

2018-07-01

High valence transition metal oxide is significant for anode catalyst of proton membrane water electrolysis technique. Herein, we demonstrate NiMn layered double hydroxide nanosheets/NiCo2O4 nanowires hierarchical nanocomposite catalyst with surface rich high valence metal oxide as an efficient catalyst for oxygen evolution reaction. A low overpotential of 310 mV is needed to drive a 10 mA cm-2 with a Tafel slope of 99 mV dec-1, and a remarkable stability during 8 h is demonstrated in a chronoamperometry test. Theoretical calculation displays the change in the rate-determining step on the nanocomposite electrode in comparison to NiCo2O4 nanowires alone. It is found high valence Ni and Mn oxide in the catalyst system can efficiently facilitate the charge transport across the electrode/electrolyte interface. The enhanced electrical conductivity, more accessible active sites and synergistic effects between NiMn layered double hydroxide nanosheets and NiCo2O4 nanowires can account for the excellent oxygen evolution reaction. The catalytic performance is comparable to most of the best non-noble catalysts and IrO2 noble catalyst, indicating the promising applications in water-splitting technology. It is an important step in the development of hierarchical nanocomposites by surface valence state tuning as an alternative to noble metals for oxygen evolution reaction.

Effective degradation of primary color direct azo dyes using Fe0 aggregates-activated persulfate process.

PubMed

Liu, Na; Ding, Feng; Weng, Chih-Huang; Hwang, Chi-Chin; Lin, Yao-Tung

2018-01-15

The present study examined the oxidation power of a Fe 0 aggregates/persulfate (PS/Fe 0 ) system for the degradation of the wastewater containing mixed primary direct dyes (i.e., Sirius ® Gelb S-2G, Sirius ® Red F3B, and Sirius ® Turkis GL01). Results indicated that decolorization efficiency was determined by operating parameters of the PS/Fe 0 system and the structural complexity of dye molecules. System efficiency increased with increasing persulfate and Fe 0 dosages. Faster decolorization was observed in experiments conducted at pH < 10. The process obeyed a first-order kinetics. Slow heterogeneous reactions were observed at high initial pH (>10.5) and low PS concentration (<2 × 10 -3  M). Inhibitory effect occurred in systems containing salts Na 2 SO 4 , NaCl, Na 2 CO 3 , and Na 2 HPO 4 at 1 × 10 -2  M. The effect was suppressed when reaction temperature was raised to 55 °C. Heat enhanced not only decolorization efficiency, but also COD removal. Complete decolorization of a mixed dye containing ADMI (the American Dye Manufacture Institute) 15105 was achieved within10 min in the PS/Fe 0 /55 °C system with an initial pH of 6.0 and dosages of 5 × 10 -3  M Na 2 S 2 O 8 and 0.5 g/L Fe 0 . Low molecular weight intermediates including organic acids were identified. Due to a relatively low activation energy (4.68 kcaL/mol), the PS/Fe 0 system exhibited higher efficiency at higher temperature. This study demonstrated that Fe 0 -activated PS is a promising process for the treatment of textile wastewaters containing mixed azo direct dyes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Laccase from Pycnoporus cinnabarinus and phenolic compounds: can the efficiency of an enzyme mediator for delignifying kenaf pulp be predicted?

PubMed

Andreu, Glòria; Vidal, Teresa

2013-03-01

In this work, kenaf pulp was delignified by using laccase in combination with various redox mediators and the efficiency of the different laccase–mediator systems assessed in terms of the changes in pulp properties after bleaching. The oxidative ability of the individual mediators used (acetosyringone, syringaldehyde, p-coumaric acid, vanillin and actovanillone) and the laccase–mediator systems was determined by monitoring the oxidation–reduction potential (ORP) during process. The results confirmed the production of phenoxy radicals of variable reactivity and stressed the significant role of lignin structure in the enzymatic process. Although changes in ORP were correlated with the oxidative ability of the mediators, pulp properties as determined after the bleaching stage were also influenced by condensation and grafting reactions. As shown here, ORP measurements provide a first estimation of the delignification efficiency of a laccase–mediator system. Copyright © 2013 Elsevier Ltd. All rights reserved.

Inflight performance of the Ulysses reaction control system

NASA Technical Reports Server (NTRS)

McGarry, Andrew; Berry, William; Parker, David

1997-01-01

The Ulysses spacecraft has been exploring the heliosphere since October 1990 in a six-year polar orbit. Despite varying operational demands, the pressure-fed monopropellant hydrazine reaction control system (RCS) has experienced few problems. The observed anomalies, having minimal operational impact, include plume impingement effects, electrical power overload effects and hydrazine gas generation effects. These anomalies are presented and discussed, with emphasis on the first observation of gas in the hydrazine propellant. The relatively low gas generation rate is attributed to: the use of high purity hydrazine; the configuration of the spin-stabilized spacecraft; the extensive use of titanium alloys; and the efficiency of the thermal control of the propellant tank which maintains a temperature of 21 C.

Computer program for prediction of fuel consumption statistical data for an upper stage three-axes stabilized on-off control system

NASA Technical Reports Server (NTRS)

1982-01-01

A FORTRAN coded computer program and method to predict the reaction control fuel consumption statistics for a three axis stabilized rocket vehicle upper stage is described. A Monte Carlo approach is used which is more efficient by using closed form estimates of impulses. The effects of rocket motor thrust misalignment, static unbalance, aerodynamic disturbances, and deviations in trajectory, mass properties and control system characteristics are included. This routine can be applied to many types of on-off reaction controlled vehicles. The pseudorandom number generation and statistical analyses subroutines including the output histograms can be used for other Monte Carlo analyses problems.

Efficient Hydrogen-Dependent Carbon Dioxide Reduction by Escherichia coli.

PubMed

Roger, Magali; Brown, Fraser; Gabrielli, William; Sargent, Frank

2018-01-08

Hydrogen-dependent reduction of carbon dioxide to formic acid offers a promising route to greenhouse gas sequestration, carbon abatement technologies, hydrogen transport and storage, and the sustainable generation of renewable chemical feedstocks [1]. The most common approach to performing direct hydrogenation of CO 2 to formate is to use chemical catalysts in homogeneous or heterogeneous reactions [2]. An alternative approach is to use the ability of living organisms to perform this reaction biologically. However, although CO 2 fixation pathways are widely distributed in nature, only a few enzymes have been described that have the ability to perform the direct hydrogenation of CO 2 [3-5]. The formate hydrogenlyase (FHL) enzyme from Escherichia coli normally oxidizes formic acid to carbon dioxide and couples that reaction directly to the reduction of protons to molecular hydrogen [6]. In this work, the reverse reaction of FHL is unlocked. It is established that FHL can operate as a highly efficient hydrogen-dependent carbon dioxide reductase when gaseous CO 2 and H 2 are placed under pressure (up to 10 bar). Using intact whole cells, the pressurized system was observed to rapidly convert 100% of gaseous CO 2 to formic acid, and >500 mM formate was observed to accumulate in solution. Harnessing the reverse reaction has the potential to allow the versatile E. coli system to be employed as an exciting new carbon capture technology or as a cell factory dedicated to formic acid production, which is a commodity in itself as well as a feedstock for the synthesis of other valued chemicals. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

First Principles Dynamics and Coarse-Grained Characterization of Photoisomerization in Complex Environments

ERIC Educational Resources Information Center

Virshup, Aaron Michael

2009-01-01

Photoisomerization of conjugated systems is a common pathway for photomechanical energy conversion in biological chromophores. Such reactions are mediated by conical intersections (CIs)--points of degeneracy between different potential energy surfaces, which efficiently funnel population between electronic states. There are many examples of a…

Minimizing Polysulfide Shuttle Effect in Lithium-Ion Sulfur Batteries by Anode Surface Passivation.

PubMed

Liu, Jian; Lu, Dongping; Zheng, Jianming; Yan, Pengfei; Wang, Biqiong; Sun, Xueliang; Shao, Yuyan; Wang, Chongmin; Xiao, Jie; Zhang, Ji-Guang; Liu, Jun

2018-06-25

Lithium-ion sulfur batteries use nonlithium materials as the anode for extended cycle life. However, polysulfide shuttle reactions still occur on the nonmetal anodes (such as graphite and Si), and result in undesirable low Coulombic efficiency. In this work, we used Al 2 O 3 layers coated by atomic layer deposition (ALD) technique to suppress the shuttle reactions. With the optimal thickness of 2 nm Al 2 O 3 coated on graphite anode, the Coulombic efficiency of the sulfur cathode was improved from 84% to 96% in the first cycle, and from 94% to 97% in the subsequent cycles. As a result, the discharge capacity of the sulfur cathode was increased to 550 mAh g -1 in the 100th cycle, as compared with 440 mAh g -1 when the pristine graphite anode was used. The Al 2 O 3 passivation layer minimizes the formation of insoluble sulfide (Li 2 S 2 , Li 2 S) on the surface of graphite anode and improves the efficiency and capacity retention of the graphite-sulfur batteries. The surface passivation strategy could also be used in other sulfur based battery systems (with Li, Si, and Sn anodes), to minimize side reactions and enable high-performance sulfur batteries.

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

Chemically Amplified Bilevel Resist Based on Condensation of Siloxanes

NASA Astrophysics Data System (ADS)

Sakata, Miwa; Ito, Toshio; Yamashita, Yoshio

1991-11-01

This paper deals with a negative bilevel resist which is based on the acid-catalyzed condensation reaction of poly(siloxane)s. The resist systems consist of photoacid generators and poly(siloxane). Ph3S+OTf- reveals an efficient activity for silanol condensation and the system has a high sensitivity of 0.31 mJ/cm2. Tetrafunctional silane plays the role of crosslinker in this system. Sensitivity improvement of low-sensitivity systems such as benzoin p-toluenesulfonate/poly(siloxane) can be achieved by this method.

Competing reaction processes on a lattice as a paradigm for catalyst deactivation

NASA Astrophysics Data System (ADS)

Abad, E.; Kozak, J. J.

2015-02-01

We mobilize both a generating function approach and the theory of finite Markov processes to compute the probability of irreversible absorption of a randomly diffusing species on a lattice with competing reaction centers. We consider an N-site lattice populated by a single deep trap, and N -1 partially absorbing traps (absorption probability 0