The effect of addition of primary positive salts, complex salt, on the ionic strength and rate constant at various temperatures by reaction kinetics

NASA Astrophysics Data System (ADS)

Kurade, S. S.; Ramteke, A. A.

2018-05-01

In this work, we have investigated the rate of reaction by using ionic strength at different temperatures. The main goal of this experiment is to determine the relation between ionic strength with reaction rate, reaction time and rate constant with temperature. It is observed that the addition of positive salt indicate the increasing ionic strength with increase in run time at various temperatures. Thus the temperature affects the speed of reaction and mechanism by which chemical reaction occurs and time variable plays vital role in the progress of reaction at different temperatures.

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

PubMed

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

2018-01-01

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

Transition Manifolds of Complex Metastable Systems

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

PubMed

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

2010-11-11

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

Extreme reaction times determine fluctuation scaling in human color vision

NASA Astrophysics Data System (ADS)

Medina, José M.; Díaz, José A.

2016-11-01

In modern mental chronometry, human reaction time defines the time elapsed from stimulus presentation until a response occurs and represents a reference paradigm for investigating stochastic latency mechanisms in color vision. Here we examine the statistical properties of extreme reaction times and whether they support fluctuation scaling in the skewness-kurtosis plane. Reaction times were measured for visual stimuli across the cardinal directions of the color space. For all subjects, the results show that very large reaction times deviate from the right tail of reaction time distributions suggesting the existence of dragon-kings events. The results also indicate that extreme reaction times are correlated and shape fluctuation scaling over a wide range of stimulus conditions. The scaling exponent was higher for achromatic than isoluminant stimuli, suggesting distinct generative mechanisms. Our findings open a new perspective for studying failure modes in sensory-motor communications and in complex networks.

Electron and Ion Reactions in Molecular Solids: from astrochemistry to radiobiology

NASA Astrophysics Data System (ADS)

Huels, Michael A.

2001-05-01

Wherever ionizing radiation interacts with matter, it initiates reaction cascades involving ions, radicals, and ballistic secondary electrons; these reactions occur on fs time-scales, and may lead to substantial physical and chemical modifications of a medium. Here I present measurements of 0-80 eV electron and ion reactions in condensed films ranging from simple to complex, and astrophysical to biological in nature. Targets contain either: small molecules, hydrocarbons of increasing complexity (incl. bases, sugars, single/double stranded DNA), molecules on rare gas matrices, or mixed cryogenic films resembling astrophysical or planetary surface ices containing O2, H2O, methane, and aromatic hydrocarbons. The basic electron or ion reaction mechanisms and pathways are found to be fundamentally universal, but are modulated by the physical and chemical nature of the medium; depending on the latter, a reaction cascade may lead to different end-points, e.g. a decrease in molecular complexity via molecular fragmentations, or increases in complexity via secondary ion collision induced synthesis of larger molecules in hydrocarbon rich surface ices.

[Influence of personality traits on reaction performance in volunteers after a single administration of placebo, crotylbarbital and caffeine].

PubMed

Meyer, F P; Walther, T; Walther, H

1983-01-01

We examined the influence of single applications of placebo, caffeine (7 mg/kg), and crotylbarbital (2 mg/kg) on reaction and attention performance in 15 volunteers. A newly developed reaction-time apparatus permits the reaction time to be split for differentiation between initiation time and movement time. Moreover, simple and complex attention performance can be quantified. The volunteers were selected as to the dimensions of "introversion/extraversion" and "emotional lability/stability" by means of the Freiburg Personality Inventory. Labile volunteers responded to placebo faster than stables. Caffeine improved mainly the performance of introverted subjects. Crotylbarbital was without influence on the reaction time at the threshold dose applied.

DHA- Rich Fish Oil Improves Complex Reaction Time in Female Elite Soccer Players

PubMed Central

Guzmán, José F.; Esteve, Hector; Pablos, Carlos; Pablos, Ana; Blasco, Cristina; Villegas, José A.

2011-01-01

Omega-3 fatty acids (n-3) has shown to improve neuromotor function. This study examined the effects of docosahexaenoic acid (DHA) on complex reaction time, precision and efficiency, in female elite soccer players. 24 players from two Spanish female soccer Super League teams were randomly selected and assigned to two experimental groups, then administered, in a double-blind manner, 3.5 g·day-1 of either DHA-rich fish oil (FO =12) or olive oil (OO = 12) over 4 weeks of training. Two measurements (pre- and post-treatment) of complex reaction time and precision were taken. Participants had to press different buttons and pedals with left and right hands and feet, or stop responding, according to visual and auditory stimuli. Multivariate analysis of variance displayed an interaction between supplement administration (pre/post) and experimental group (FO/OO) on complex reaction time (FO pre = 0.713 ± 0.142 ms, FO post = 0.623 ± 0.109 ms, OO pre = 0.682 ± 1.132 ms, OO post = 0.715 ± 0.159 ms; p = 0.004) and efficiency (FO pre = 40.88 ± 17.41, FO post = 57.12 ± 11.05, OO pre = 49.52 ± 14.63, OO post = 49. 50 ± 11.01; p = 0.003). It was concluded that after 4 weeks of supplementation with FO, there was a significant improvement in the neuromotor function of female elite soccer players. Key points The results obtained from the study suggest that supplementation with DHA produced perceptual-motor benefits in female elite athletes. DHA could be a beneficial supplement in sports where decision making and reaction time efficiency are of importance. PMID:24149875

A novel approach to sports concussion assessment: Computerized multilimb reaction times and balance control testing.

PubMed

Vartiainen, Matti V; Holm, Anu; Lukander, Jani; Lukander, Kristian; Koskinen, Sanna; Bornstein, Robert; Hokkanen, Laura

2016-01-01

Mild traumatic brain injuries (MTBI) or concussions often result in problems with attention, executive functions, and motor control. For better identification of these diverse problems, novel approaches integrating tests of cognitive and motor functioning are needed. The aim was to characterize minor changes in motor and cognitive performance after sports-related concussions with a novel test battery, including balance tests and a computerized multilimb reaction time test. The cognitive demands of the battery gradually increase from a simple stimulus response to a complex task requiring executive attention. A total of 113 male ice hockey players (mean age = 24.6 years, SD = 5.7) were assessed before a season. During the season, nine concussed players were retested within 36 hours, four to six days after the concussion, and after the season. A control group of seven nonconcussed players from the same pool of players with comparable demographics were retested after the season. Performance was measured using a balance test and the Motor Cognitive Test battery (MotCoTe) with multilimb responses in simple reaction, choice reaction, inhibition, and conflict resolution conditions. The performance of the concussed group declined at the postconcussion assessment compared to both the baseline measurement and the nonconcussed controls. Significant changes were observed in the concussed group for the multilimb choice reaction and inhibition tests. Tapping and balance showed a similar trend, but no statistically significant difference in performance. In sports-related concussions, complex motor tests can be valuable additions in assessing the outcome and recovery. In the current study, using subtasks with varying cognitive demands, it was shown that while simple motor performance was largely unaffected, the more complex tasks induced impaired reaction times for the concussed subjects. The increased reaction times may reflect the disruption of complex and integrative cognitive function in concussions.

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

PubMed

Samoilov, Michael; Arkin, Adam; Ross, John

2001-03-01

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

A Nonequilibrium Rate Formula for Collective Motions of Complex Molecular Systems

NASA Astrophysics Data System (ADS)

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

2010-09-01

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

Understanding titanium-catalysed radical-radical reactions: a DFT study unravels the complex kinetics of ketone-nitrile couplings.

PubMed

Streuff, Jan; Himmel, Daniel; Younas, Sara L

2018-04-03

The computational investigation of a titanium-catalysed reductive radical-radical coupling is reported. The results match the conclusions from an earlier experimental study and enable a further interpretation of the previously observed complex reaction kinetics. Furthermore, the interplay between neutral and cationic reaction pathways in titanium(iii)-catalysed reactions is investigated for the first time. The results show that hydrochloride additives and reaction byproducts play an important role in the respective equilibria. A full reaction profile is assembled and the computed activation barrier is found to be in reasonable agreement with the experiment. The conclusions are of fundamental importance to the field of low-valent titanium catalysis and the understanding of related catalytic radical-radical coupling reactions.

Improved 18F Labeling of Peptides with a Fluoride-Aluminum-Chelate Complex

PubMed Central

McBride, William J.; D’Souza, Christopher A.; Sharkey, Robert M.; Karacay, Habibe; Rossi, Edmund A.; Chang, Chien-Hsing; Goldenberg, David M.

2010-01-01

We reported previously the feasibility to radiolabel peptides with fluorine-18 (18F) using a rapid, one-pot, method that first mixes 18F− with Al3+, and then binds the (Al18F)2+ complex to a NOTA ligand on the peptide. In this report, we examined several new NOTA ligands and determined how temperature, reaction time, and reagent concentration affected the radiolabeling yield. Four structural variations of the NOTA ligand had isolated radiolabeling yields ranging from 5.8% to 87% under similar reaction conditions. All of the Al18F NOTA complexes were stable in vitro in human serum and those that were tested in vivo also were stable. The radiolabeling reactions were performed at 100°C and the peptides could be labeled in as little as five minutes. The IMP467 peptide could be labeled up to 115 GBq/μmol (3100 Ci/mmol), with a total reaction and purification time of 30 min without chromatographic purification. PMID:20540570

Lanthanide anilido complexes: synthesis, characterization, and use as highly efficient catalysts for hydrophosphonylation of aldehydes and unactivated ketones.

PubMed

Liu, Chengwei; Qian, Qinqin; Nie, Kun; Wang, Yaorong; Shen, Qi; Yuan, Dan; Yao, Yingming

2014-06-14

Lanthanide anilido complexes stabilized by the 2,6-diisopropylanilido ligand have been synthesized and characterized, and their catalytic activity for hydrophosphonylation reaction was explored. A reaction of anhydrous LnCl3 with 5 equivalents of LiNHPh-(I)Pr2-2,6 in THF generated the heterobimetallic lanthanide-lithium anilido complexes (2,6-(I)Pr2PhNH)5LnLi2(THF)2 [Ln = Sm(1), Nd(2), Y(3)] in good isolated yields. These complexes are well characterized by elemental analysis, IR, NMR (for complex ) and single-crystal structure determination. Complexes 1 - 3 are isostructural. In these complexes, the lanthanide metal ion is five-coordinated by five nitrogen atoms from five 2,6-diisopropylanilido ligands to form a distorted trigonal bipyramidal geometry. The lithium ion is coordinated by two nitrogen atoms from two 2,6-diisopropylanilido ligands, and one oxygen atom from a THF molecule. It was found that these simple lanthanide anilido complexes are highly efficient for catalyzing hydrophosphonylation reactions of various aldehydes and unactivated ketones to generate α-hydroxyphosphonates in good to excellent yields (up to 99%) within a short time (5 min for aldehydes, 20 min for ketones). Furthermore, the mechanism of hydrophosphonylation reactions has also been elucidated via(1)H NMR monitoring of reaction.

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

PubMed

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

2008-06-16

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

Kinetic studies on the oxidation of oxyhemoglobin by biologically active iron thiosemicarbazone complexes: relevance to iron-chelator-induced methemoglobinemia.

PubMed

Basha, Maram T; Rodríguez, Carlos; Richardson, Des R; Martínez, Manuel; Bernhardt, Paul V

2014-03-01

The oxidation of oxyhemoglobin to methemoglobin has been found to be facilitated by low molecular weight iron(III) thiosemicarbazone complexes. This deleterious reaction, which produces hemoglobin protein units unable to bind dioxygen and occurs during the administration of iron chelators such as the well-known 3-aminopyridine-2-pyridinecarbaldehyde thiosemicarbazone (3-AP; Triapine), has been observed in the reaction with Fe(III) complexes of some members of the 3-AP structurally-related thiosemicarbazone ligands derived from di-2-pyridyl ketone (HDpxxT series). We have studied the kinetics of this oxidation reaction in vitro using human hemoglobin and found that the reaction proceeds with two distinct time-resolved steps. These have been associated with sequential oxidation of the two different oxyheme cofactors in the α and β protein chains. Unexpected steric and hydrogen-bonding effects on the Fe(III) complexes appear to be the responsible for the observed differences in the reaction rate across the series of HDpxxT ligand complexes used in this study.

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

NASA Astrophysics Data System (ADS)

Bligh, Mark W.; Waite, T. David

2010-10-01

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

Asymmetric intermolecular Pauson-Khand reaction of symmetrically substituted alkynes.

PubMed

Ji, Yining; Riera, Antoni; Verdaguer, Xavier

2009-10-01

The asymmetric intermolecular Pauson-Khand reaction of symmetric alkynes has been accomplished for the first time. N-Phosphino-p-tolylsulfinamide (PNSO) ligands have been identified as efficient ligands in this process. The chirality of the cobalt S-bonded sulfinyl moiety was found to direct olefin insertion into one of the two possible cobalt-carbon bonds in the alkyne complex. Reaction of symmetric alkynes allows for a simplified experimental protocol since there is no need for separation of diastereomeric complexes.

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

PubMed

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

2015-03-19

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

Individual strategy ratings improve the control for task difficulty effects in arithmetic problem solving paradigms.

PubMed

Tschentscher, Nadja; Hauk, Olaf

2015-01-01

Mental arithmetic is a powerful paradigm to study problem solving using neuroimaging methods. However, the evaluation of task complexity varies significantly across neuroimaging studies. Most studies have parameterized task complexity by objective features such as the number size. Only a few studies used subjective rating procedures. In fMRI, we provided evidence that strategy self-reports control better for task complexity across arithmetic conditions than objective features (Tschentscher and Hauk, 2014). Here, we analyzed the relative predictive value of self-reported strategies and objective features for performance in addition and multiplication tasks, by using a paradigm designed for neuroimaging research. We found a superiority of strategy ratings as predictor of performance above objective features. In a Principal Component Analysis on reaction times, the first component explained over 90 percent of variance and factor loadings reflected percentages of self-reported strategies well. In multiple regression analyses on reaction times, self-reported strategies performed equally well or better than objective features, depending on the operation type. A Receiver Operating Characteristic (ROC) analysis confirmed this result. Reaction times classified task complexity better when defined by individual ratings. This suggests that participants' strategy ratings are reliable predictors of arithmetic complexity and should be taken into account in neuroimaging research.

Individual strategy ratings improve the control for task difficulty effects in arithmetic problem solving paradigms

PubMed Central

Tschentscher, Nadja; Hauk, Olaf

2015-01-01

Mental arithmetic is a powerful paradigm to study problem solving using neuroimaging methods. However, the evaluation of task complexity varies significantly across neuroimaging studies. Most studies have parameterized task complexity by objective features such as the number size. Only a few studies used subjective rating procedures. In fMRI, we provided evidence that strategy self-reports control better for task complexity across arithmetic conditions than objective features (Tschentscher and Hauk, 2014). Here, we analyzed the relative predictive value of self-reported strategies and objective features for performance in addition and multiplication tasks, by using a paradigm designed for neuroimaging research. We found a superiority of strategy ratings as predictor of performance above objective features. In a Principal Component Analysis on reaction times, the first component explained over 90 percent of variance and factor loadings reflected percentages of self-reported strategies well. In multiple regression analyses on reaction times, self-reported strategies performed equally well or better than objective features, depending on the operation type. A Receiver Operating Characteristic (ROC) analysis confirmed this result. Reaction times classified task complexity better when defined by individual ratings. This suggests that participants’ strategy ratings are reliable predictors of arithmetic complexity and should be taken into account in neuroimaging research. PMID:26321997

Mechanistic kinetic models of enzymatic cellulose hydrolysis-A review.

PubMed

Jeoh, Tina; Cardona, Maria J; Karuna, Nardrapee; Mudinoor, Akshata R; Nill, Jennifer

2017-07-01

Bioconversion of lignocellulose forms the basis for renewable, advanced biofuels, and bioproducts. Mechanisms of hydrolysis of cellulose by cellulases have been actively studied for nearly 70 years with significant gains in understanding of the cellulolytic enzymes. Yet, a full mechanistic understanding of the hydrolysis reaction has been elusive. We present a review to highlight new insights gained since the most recent comprehensive review of cellulose hydrolysis kinetic models by Bansal et al. (2009) Biotechnol Adv 27:833-848. Recent models have taken a two-pronged approach to tackle the challenge of modeling the complex heterogeneous reaction-an enzyme-centric modeling approach centered on the molecularity of the cellulase-cellulose interactions to examine rate limiting elementary steps and a substrate-centric modeling approach aimed at capturing the limiting property of the insoluble cellulose substrate. Collectively, modeling results suggest that at the molecular-scale, how rapidly cellulases can bind productively (complexation) and release from cellulose (decomplexation) is limiting, while the overall hydrolysis rate is largely insensitive to the catalytic rate constant. The surface area of the insoluble substrate and the degrees of polymerization of the cellulose molecules in the reaction both limit initial hydrolysis rates only. Neither enzyme-centric models nor substrate-centric models can consistently capture hydrolysis time course at extended reaction times. Thus, questions of the true reaction limiting factors at extended reaction times and the role of complexation and decomplexation in rate limitation remain unresolved. Biotechnol. Bioeng. 2017;114: 1369-1385. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The fast method of Cu-porphyrin complex synthesis for potential use in positron emission tomography imaging

NASA Astrophysics Data System (ADS)

Kilian, Krzysztof; Pęgier, Maria; Pyrzyńska, Krystyna

2016-04-01

Porphyrin based photosensitizers are useful agents for photodynamic therapy and fluorescence imaging of cancer. Additionally, porphyrins are excellent metal chelators, forming stable metalo-complexes and 64Cu isotope can serve as a positron emitter (t1/2 = 12.7 h). The other advantage of 64Cu is its decay characteristics that facilitates the use of 64Cu-porphyrin complex as a therapeutic agent. Thus, 64Cu chelation with porphyrin photosensitizer may become a simple and versatile labeling strategy for clinical positron emission tomography. The present study reports a convenient method for the synthesis of Cu complex with tetrakis(4-carboxyphenyl)porphyrin (TCPP). The experimental conditions for labeling, such as the metal-to-ligand molar ratio, pH and time of reaction were optimized to achieve a high complexation efficiency in a short period of time as possible. In order to accelerate the metallation, the use of substitution reactions of cadmium or lead porphyrin and the presence of reducing agent, such as ascorbic acid, hydroxylamine and flavonoid - morin, were evaluated. The optimum conditions for the synthesis of the copper complex were borate buffer at pH 9 with the addition of 10-fold molar excess, with respect to Cu2 + ions and TCPP and ascorbic acid which resulted in reduction of the reaction time from 30 min to below 1 min.

Sulfonato-imino copper(ii) complexes: fast and general Chan-Evans-Lam coupling of amines and anilines.

PubMed

Hardouin Duparc, V; Schaper, F

2017-10-14

Sulfonato-imine copper complexes with either chloride or triflate counteranions were prepared in a one-step reaction followed by anion-exchange. They are highly active in Chan-Evans-Lam couplings under mild conditions with a variety of amines or anilines, in particular with sterically hindered substrates. No optimization of reaction conditions other than time and/or temperature is required.

Do Contributors to Intellect Explain the Moral Judgment Abilities of Gifted Youth?

ERIC Educational Resources Information Center

Derryberry, W. Pitt; Barger, Brian

2008-01-01

To assess reaction time and attributional complexity as factors contributing to the relatively high moral judgment of gifted youth, a sample of 30 gifted youth and 30 college students responded to a computerized measure of moral judgment development, which also indexed reaction time. Additionally, participants completed a measurement of…

Time-resolved vibrational spectroscopy detects protein-based intermediates in the photosynthetic oxygen-evolving cycle.

PubMed

Barry, Bridgette A; Cooper, Ian B; De Riso, Antonio; Brewer, Scott H; Vu, Dung M; Dyer, R Brian

2006-05-09

Photosynthetic oxygen production by photosystem II (PSII) is responsible for the maintenance of aerobic life on earth. The production of oxygen occurs at the PSII oxygen-evolving complex (OEC), which contains a tetranuclear manganese (Mn) cluster. Photo-induced electron transfer events in the reaction center lead to the accumulation of oxidizing equivalents on the OEC. Four sequential photooxidation reactions are required for oxygen production. The oxidizing complex cycles among five oxidation states, called the S(n) states, where n refers to the number of oxidizing equivalents stored. Oxygen release occurs during the S(3)-to-S(0) transition from an unstable intermediate, known as the S(4) state. In this report, we present data providing evidence for the production of an intermediate during each S state transition. These protein-derived intermediates are produced on the microsecond to millisecond time scale and are detected by time-resolved vibrational spectroscopy on the microsecond time scale. Our results suggest that a protein-derived conformational change or proton transfer reaction precedes Mn redox reactions during the S(2)-to-S(3) and S(3)-to-S(0) transitions.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Reformulation and solution of the master equation for multiple-well chemical reactions.

PubMed

Georgievskii, Yuri; Miller, James A; Burke, Michael P; Klippenstein, Stephen J

2013-11-21

We consider an alternative formulation of the master equation for complex-forming chemical reactions with multiple wells and bimolecular products. Within this formulation the dynamical phase space consists of only the microscopic populations of the various isomers making up the reactive complex, while the bimolecular reactants and products are treated equally as sources and sinks. This reformulation yields compact expressions for the phenomenological rate coefficients describing all chemical processes, i.e., internal isomerization reactions, bimolecular-to-bimolecular reactions, isomer-to-bimolecular reactions, and bimolecular-to-isomer reactions. The applicability of the detailed balance condition is discussed and confirmed. We also consider the situation where some of the chemical eigenvalues approach the energy relaxation time scale and show how to modify the phenomenological rate coefficients so that they retain their validity.

Synthesis and crystal structure of an oxovanadium(IV) complex with a pyrazolone ligand and its use as a heterogeneous catalyst for the oxidation of styrene under mild conditions.

PubMed

Parihar, Sanjay; Pathan, Soyeb; Jadeja, R N; Patel, Anjali; Gupta, Vivek K

2012-01-16

1-Phenyl-3-methyl-4-touloyl-5-pyrazolone (ligand) was synthesized and used to prepare an oxovanadium(IV) complex. The complex was characterized by single-crystal X-ray analysis and various spectroscopic techniques. The single-crystal X-ray analysis of the complex shows that the ligands are coordinated in a syn configuration to each other and create a distorted octahedral environment around the metal ion. A heterogeneous catalyst comprising an oxovanadium(IV) complex and hydrous zirconia was synthesized, characterized by various physicochemical techniques, and successfully used for the solvent-free oxidation of styrene. The influence of the reaction parameters (percent loading, molar ratio of the substrate to H(2)O(2), amount of catalyst, and reaction time) was studied. The catalyst was reused three times without any significant loss in the catalytic activity.

Bio-waste corn-cob cellulose supported poly(hydroxamic acid) copper complex for Huisgen reaction: Waste to wealth approach.

PubMed

Mandal, Bablu Hira; Rahman, Md Lutfor; Yusoff, Mashitah Mohd; Chong, Kwok Feng; Sarkar, Shaheen M

2017-01-20

Corn-cob cellulose supported poly(hydroxamic acid) Cu(II) complex was prepared by the surface modification of waste corn-cob cellulose through graft copolymerization and subsequent hydroximation. The complex was characterized by IR, UV, FESEM, TEM, XPS, EDX and ICP-AES analyses. The complex has been found to be an efficient catalyst for 1,3-dipolar Huisgen cycloaddition (CuAAC) of aryl/alkyl azides with a variety of alkynes as well as one-pot three-components reaction in the presence of sodium ascorbate to give the corresponding cycloaddition products in up to 96% yield and high turn over number (TON 18,600) and turn over frequency (TOF 930h -1 ) were achieved. The complex was easy to recover from the reaction mixture and reused six times without significant loss of its catalytic activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

Kayala, Matthew A; Baldi, Pierre

2012-10-22

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

The Role of Coordination Environment and pH in Tuning the Oxidation Rate of Europium(II).

PubMed

Ekanger, Levi A; Basal, Lina A; Allen, Matthew J

2017-01-23

The Eu II/III redox couple offers metal-based oxidation-sensing with magnetic resonance imaging making the study of Eu II oxidation chemistry important in the design of new probes. Accordingly, we explored oxidation reactions with a set of Eu II -containing complexes. Superoxide formation from the reaction between Eu II and dioxygen was observed using electron paramagnetic resonance spectroscopy. Additionally, oxidation kinetics of three Eu II -containing complexes with bromate and glutathione disulfide at pH values, including 5 and 7, is reported. In the reaction with bromate, the oxidation rate of two of the complexes increased by 7.3 and 6.7 times upon decreasing pH from 7 to 5, but the rate increased by 17 times for a complex containing amide functional groups over the same pH range. The oxidation rate of a fluorobenzo-functionalized cryptate was relatively slow, indicating that the ligand used to impart thermodynamic oxidative stability might also be useful for controlling oxidation kinetics. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Active control of complex, multicomponent self-assembly processes

NASA Astrophysics Data System (ADS)

Schulman, Rebecca

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

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

PubMed

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

2012-12-28

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

[Reaction time of drivers who caused road traffic accidents].

PubMed

Durić, Predrag; Filipović, Danka

2009-01-01

Human factor is the single cause of road traffic injuries in 57%, and together with other factors in more than 90% of all road traffic accidents. Human factor includes many aspects, where reaction time is very important. Thirty healthy drivers 28-40 y.o. with 50-500 km passed per week, having caused at least one road traffic accident in the last ten years were selected, provided they were not under the influence of alcohol and drugs during traffic accident. The same number of control were selected. Both cases and controls were tested to reaction time. We found statistically significant difference between car drivers who caused car accidents and those who did not in both simple and choice reaction times. Car drivers who caused road traffic accidents have longer reaction time (both simple and choice reaction time), but as the tasks were more complex, that difference was less visible. Since drivers involved in this study had introductory phase before measuring their reaction times, they faced with unpleasant sound when they made mistake, which forced them to be aware not to make a mistake in further tasks, so they showed longer reaction times. Measuring of reaction time seems to be important, and as we have showed they are different in drivers who have caused road traffic accidents and those who have do not.

On the Meaning of Cross-Cultural Differences in Simple Cognitive Measures

ERIC Educational Resources Information Center

van de Vijver, Fons J. R.

2008-01-01

A set of 5 reaction time tests of increasing cognitive complexity were administered to 35 secondary school pupils in Zimbabwe and The Netherlands at 4 consecutive school days in order to explore the existence and nature of cross-cultural differences on reaction time tests measuring basic cognitive operations. No cross-cultural differences were…

Reaction time, impulsivity, and attention in hyperactive children and controls: a video game technique.

PubMed

Mitchell, W G; Chavez, J M; Baker, S A; Guzman, B L; Azen, S P

1990-07-01

Maturation of sustained attention was studied in a group of 52 hyperactive elementary school children and 152 controls using a microcomputer-based test formatted to resemble a video game. In nonhyperactive children, both simple and complex reaction time decreased with age, as did variability of response time. Omission errors were extremely infrequent on simple reaction time and decreased with age on the more complex tasks. Commission errors had an inconsistent relationship with age. Hyperactive children were slower, more variable, and made more errors on all segments of the game than did controls. Both motor speed and calculated mental speed were slower in hyperactive children, with greater discrepancy for responses directed to the nondominant hand, suggesting that a selective right hemisphere deficit may be present in hyperactives. A summary score (number of individual game scores above the 95th percentile) of 4 or more detected 60% of hyperactive subjects with a false positive rate of 5%. Agreement with the Matching Familiar Figures Test was 75% in the hyperactive group.

Probing the type of anomalous diffusion with single-particle tracking.

PubMed

Ernst, Dominique; Köhler, Jürgen; Weiss, Matthias

2014-05-07

Many reactions in complex fluids, e.g. signaling cascades in the cytoplasm of living cells, are governed by a diffusion-driven encounter of reactants. Yet, diffusion in complex fluids often exhibits an anomalous characteristic ('subdiffusion'). Since different types of subdiffusion have distinct effects on timing and equilibria of chemical reactions, a thorough determination of the reactants' type of random walk is key to a quantitative understanding of reactions in complex fluids. Here we introduce a straightforward and simple approach for determining the type of subdiffusion from single-particle tracking data. Unlike previous approaches, our method also is sensitive to transient subdiffusion phenomena, e.g. obstructed diffusion below the percolation threshold. We validate our strategy with data from experiment and simulation.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

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

PubMed

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

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

Preparation and characterization of (10)B boric acid with high purity for nuclear industry.

PubMed

Zhang, Weijiang; Liu, Tianyu; Xu, Jiao

2016-01-01

Boric acid is often added into coolant as neutron capture agent for pressurized water reactor, whose amount is influenced by its abundance and purity. Therefore, the preparation of enriched (10)B boric acid with high purity is beneficial to nuclear industry. (10)B is also used in developing tumor-specific boronated drugs in boron neutron capture therapy. The boronated drug can be administered to patient intravenously, intratumorally, or deposited at tumor site in surgical excision. Thus, enriched (10)B boric acid is of practical significance in the field of medicine. Self-made boron trifluoride-methanol-complex solution was selected as one of the experimental reagents, and the preparation of (10)B acid was realized by one-step reaction for the complexes with water and calcium chloride. The determination of electrical conductivity in reaction process proves that the optimum reaction time was 16-20 h. Furthermore, the effect of reaction time, ratio of calcium chloride to complex as well as the amount of water on the purity and yield of boric acid was investigated. Finally, the optimum reaction time was 20 h, the optimal solid-liquid ratio (molar ratio) was 3:1, and the amount of water was 1 L of deionized water for each mol of the complex. H2O2 was added in the reaction process to remove Fe(2+). After recrystallization, IR spectra of (10)B boric acid was measured and compared with standard to verify the product of boric acid. The feasibility of the preparation method was determined by the detection of XRD of boric acid. To observe the morphology by polarizing microscope, crystal structure was obtained. The purity of the final product is 99.95 %, and the yield is 96.47 %. The ion concentration of boric acid accords with the national standard of high purity, which was determined by ICP.

The sensitivity of gas-phase models of dense interstellar clouds to changes in dissociative recombination branching ratios

NASA Technical Reports Server (NTRS)

Millar, T. J.; Defrees, D. J.; Mclean, A. D.; Herbst, E.

1988-01-01

The approach of Bates to the determination of neutral product branching ratios in ion-electron dissociative recombination reactions has been utilized in conjunction with quantum chemical techniques to redetermine branching ratios for a wide variety of important reactions of this class in dense interstellar clouds. The branching ratios have then been used in a pseudo time-dependent model calculation of the gas phase chemistry of a dark cloud resembling TMC-1 and the results compared with an analogous model containing previously used branching ratios. In general, the changes in branching ratios lead to stronger effects on calculated molecular abundances at steady state than at earlier times and often lead to reductions in the calculated abundances of complex molecules. However, at the so-called 'early time' when complex molecule synthesis is most efficient, the abundances of complex molecules are hardly affected by the newly used branching ratios.

Novel Visualization Approaches in Environmental Mineralogy

NASA Astrophysics Data System (ADS)

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

2006-05-01

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

Novel bipyridinyl oxadiazole-based metal coordination complexes: High efficient and green synthesis of 3,4-dihydropyrimidin-2(1H)-ones through the Biginelli reactions

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

Wang, Jin-Hua; Zhang, E.; Tang, Gui-Mei, E-mail: meiguit@163.com

2016-09-15

Three new metal coordination complexes, namely, [Co(BPO){sub 2}(H{sub 2}O){sub 4}](BS){sub 2}(H{sub 2}O){sub 2} (1), [Co(BPO){sub 2}(H{sub 2}O){sub 4}](ABS){sub 2}(H{sub 2}O){sub 2} (2), [Co(BPO){sub 2}(H{sub 2}O){sub 4}](MBS){sub 2}(H{sub 2}O){sub 2} (3) [BPO=2,5-di(pyridin-4-yl)-1,3,4-oxadiazole, BS=benzenesulphonate, ABS=4-aminobenzenesulphonate, MBS=4-methylbenzenesulphonate] were obtained under hydrothermal conditions. Complexes 1–3 were structurally characterized by single-crystal X-ray diffraction, powder X-ray diffraction, IR and thermogravimetric analyses (TGA). All of them display a zero-dimensional motif, in which strong intermolecular hydrogen bonding interactions (O–H···O/N) and packing interactions (C–H···π and π···π) make them achieve a three-dimensional supramolecular architecture. The primary catalytic results of these three complexes show that high efficiency for the green synthesismore » of a variety of 3,4-dihydropyrimidin-2(1H)-ones was observed under solvent free conditions through Biginelli reactions. The present catalytic protocols exhibit advantages such as excellent yield, easy isolation, eco-friendly conditions, and short reaction time. - Graphical abstract: Three new metal coordination complexes with bipyridinyl-oxadiazole were obtained under hydrothermal conditions, which display a zero-dimensional motif, and show high efficiency for the green synthesis of a variety of 3,4-dihydropyrimidin-2(1H)-ones under solvent free conditions through Biginelli reactions. The present catalytic protocols exhibit advantages such as excellent yield, easy isolation, eco-friendly conditions, and short reaction time. Display Omitted.« less

Syntheses and characterizations of two new energetic copper–amine-DNANT complexes and their effects on thermal decomposition of RDX

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

Qiu, Qianqian; Xu, Kangzhen, E-mail: xukz@nwu.edu.cn; Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon

Two novel copper complexes of dinitroacetonitrile (DNANT), Cu(NH{sub 3}){sub 4}(DNANT){sub 2} (1) and Cu(en){sub 2}(DNATN){sub 2} (2), have been synthesized for the first time through an unique reaction, and structurally characterized. The single-crystal X-ray structural analysis shows that the Cu{sup 2+} cations in the two complexes share a similar four-coordinated structure, which however does not directly involve the main energetic DNANT{sup −} anion. The differential scanning calorimetry (DSC) study reveals that the two complexes have higher thermal stability and lower sensitivity than the analogous FOX-7 complexes, and exhibit good catalytic action to the decomposition of RDX. - Graphical abstract: Cu(NH{submore » 3}){sub 4}(DNANT){sub 2} (1) and Cu(en){sub 2}(DNATN){sub 2} (2) have been first synthesized through an unique reaction. Cu{sup 2+} ion shares a similar four-coordinated structure in the two complexes. Display Omitted - Highlights: • A new reaction is unexpectedly found, and reaction process was discussed in this work. • Cu(NH{sub 3}){sub 4} (DNANT){sub 2}and Cu(en){sub 2}(DNATN){sub 2} were first synthesized through an unique reaction. • The structures and properties of the two complexes were discussed in detail, and they all present good application performances. • The adjacent amino-hydrazino group in AHDNE exhibits high reactivity. The work is another typical example for the reactivity.« less

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

PubMed Central

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

2008-01-01

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

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

PubMed

Indurkhya, Sagar; Beal, Jacob

2010-01-06

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

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

PubMed Central

Indurkhya, Sagar; Beal, Jacob

2010-01-01

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

Using Multiorder Time-Correlation Functions (TCFs) To Elucidate Biomolecular Reaction Pathways from Microsecond Single-Molecule Fluorescence Experiments.

PubMed

Phelps, Carey; Israels, Brett; Marsh, Morgan C; von Hippel, Peter H; Marcus, Andrew H

2016-12-29

Recent advances in single-molecule fluorescence imaging have made it possible to perform measurements on microsecond time scales. Such experiments have the potential to reveal detailed information about the conformational changes in biological macromolecules, including the reaction pathways and dynamics of the rearrangements involved in processes, such as sequence-specific DNA "breathing" and the assembly of protein-nucleic acid complexes. Because microsecond-resolved single-molecule trajectories often involve "sparse" data, that is, they contain relatively few data points per unit time, they cannot be easily analyzed using the standard protocols that were developed for single-molecule experiments carried out with tens-of-millisecond time resolution and high "data density." Here, we describe a generalized approach, based on time-correlation functions, to obtain kinetic information from microsecond-resolved single-molecule fluorescence measurements. This approach can be used to identify short-lived intermediates that lie on reaction pathways connecting relatively long-lived reactant and product states. As a concrete illustration of the potential of this methodology for analyzing specific macromolecular systems, we accompany the theoretical presentation with the description of a specific biologically relevant example drawn from studies of reaction mechanisms of the assembly of the single-stranded DNA binding protein of the T4 bacteriophage replication complex onto a model DNA replication fork.

Generic approach to access barriers in dehydrogenation reactions

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

Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

Generic approach to access barriers in dehydrogenation reactions

DOE PAGES

Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

2018-03-08

The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

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

PubMed

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

2009-07-07

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

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

PubMed Central

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

2009-01-01

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

A new chitosan Schiff base supported Pd(II) complex for microwave-assisted synthesis of biaryls compounds

NASA Astrophysics Data System (ADS)

Baran, Talat

2017-08-01

In this study, a new heterogeneous palladium (II) catalyst that contains O-carboxymethyl chitosan Schiff base has been designed for Suzuki coupling reactions. The chemical structures of the synthesized catalyst were characterized with the FTIR, TG/DTG, ICP-OES, SEM/EDAX, 1H NMR, 13C NMR, GC/MS, XRD, and magnetic moment techniques. The reusability and catalytic behavior of heterogeneous catalyst was tested towards Suzuki reactions. As a result of the tests, excellent selectivity was obtained, and by-products of homo coupling were not seen in the spectra. The biaryls products were identified on a GC/MS. In addition, it was determined in the reusability tests that the catalysts could be used several times (seven runs). More importantly, with very low catalyst loading (6 × 10-3 mol %) in very short reaction time (5 min), chitosan Schiff base supported Pd(II) complex gave high TON and TOF values. These findings showed that Schiff base supported Pd(II) catalyst is suitable for Suzuki cross coupling reactions.

Intra-individual reaction time variability and all-cause mortality over 17 years: a community-based cohort study.

PubMed

Batterham, Philip J; Bunce, David; Mackinnon, Andrew J; Christensen, Helen

2014-01-01

very few studies have examined the association between intra-individual reaction time variability and subsequent mortality. Furthermore, the ability of simple measures of variability to predict mortality has not been compared with more complex measures. a prospective cohort study of 896 community-based Australian adults aged 70+ were interviewed up to four times from 1990 to 2002, with vital status assessed until June 2007. From this cohort, 770-790 participants were included in Cox proportional hazards regression models of survival. Vital status and time in study were used to conduct survival analyses. The mean reaction time and three measures of intra-individual reaction time variability were calculated separately across 20 trials of simple and choice reaction time tasks. Models were adjusted for a range of demographic, physical health and mental health measures. greater intra-individual simple reaction time variability, as assessed by the raw standard deviation (raw SD), coefficient of variation (CV) or the intra-individual standard deviation (ISD), was strongly associated with an increased hazard of all-cause mortality in adjusted Cox regression models. The mean reaction time had no significant association with mortality. intra-individual variability in simple reaction time appears to have a robust association with mortality over 17 years. Health professionals such as neuropsychologists may benefit in their detection of neuropathology by supplementing neuropsychiatric testing with the straightforward process of testing simple reaction time and calculating raw SD or CV.

The reaction times of drivers aged 20 to 80 during a divided attention driving.

PubMed

Svetina, Matija

2016-11-16

Many studies addressing age-related changes in driving performance focus on comparing young vs. older drivers, which might lead to the biased conclusion that driving performance decreases only after the age of 65. The main aim of the study was to show that changes in driving performance are progressive throughout the adult years. A sample of 351 drivers aged 20 to 80 was assessed for their reaction times while driving between road cones. The drivers were exposed to 2 conditions varying according to task complexity. In single task conditions, the drivers performed a full stopping maneuver at a given signal; in dual task conditions, the drivers were distracted before the signal for stopping maneuver was triggered. Reaction times were compared across conditions and age groups. The results showed that both reaction times and variability of driving performance increased progressively between the ages of 20 and 80. The increase in both reaction times and variability was greater in the complex task condition. The high-performing quarter of elderly drivers performed equally well or better than younger drivers did. The data clearly supported the claim that driving performance changes steadily across age groups: both mean reaction time and interindividual variability progressively increase with age. In addition, a significant group of older drivers was identified who did not show the expected age-related decrease in performance. The findings have important implications, suggesting that in relation to driving, aging is a progressive phenomenon and may lead to variety of driving performance; age-related studies of driving performance should put more emphasis on investigating changes across the whole driver age range rather than only comparing younger and older drivers.

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

Single-Molecule Spectroscopy and Imaging Studies of Protein Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter

2012-04-01

Enzymatic reactions and protein-protein interactions are traditionally studied at the ensemble level, despite significant static and dynamic inhomogeneities. Subtle conformational changes play a crucial role in protein functions, and these protein conformations are highly dynamic rather than being static. We applied AFM-enhanced single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of T4 lysozyme and HPPK enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation. Our new approach is applicable to a wide range of single-molecule FRET measurements for protein conformational changes under enzymatic reactions.

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

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

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

2011-06-28

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

Perturbation theory in the catalytic rate constant of the Henri-Michaelis-Menten enzymatic reaction.

PubMed

Bakalis, Evangelos; Kosmas, Marios; Papamichael, Emmanouel M

2012-11-01

The Henry-Michaelis-Menten (HMM) mechanism of enzymatic reaction is studied by means of perturbation theory in the reaction rate constant k (2) of product formation. We present analytical solutions that provide the concentrations of the enzyme (E), the substrate (S), as well as those of the enzyme-substrate complex (C), and the product (P) as functions of time. For k (2) small compared to k (-1), we properly describe the entire enzymatic activity from the beginning of the reaction up to longer times without imposing extra conditions on the initial concentrations E ( o ) and S ( o ), which can be comparable or much different.

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

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

A mathematical model for foreign body reactions in 2D.

PubMed

Su, Jianzhong; Gonzales, Humberto Perez; Todorov, Michail; Kojouharov, Hristo; Tang, Liping

2011-02-01

The foreign body reactions are commonly referred to the network of immune and inflammatory reactions of human or animals to foreign objects placed in tissues. They are basic biological processes, and are also highly relevant to bioengineering applications in implants, as fibrotic tissue formations surrounding medical implants have been found to substantially reduce the effectiveness of devices. Despite of intensive research on determining the mechanisms governing such complex responses, few mechanistic mathematical models have been developed to study such foreign body reactions. This study focuses on a kinetics-based predictive tool in order to analyze outcomes of multiple interactive complex reactions of various cells/proteins and biochemical processes and to understand transient behavior during the entire period (up to several months). A computational model in two spatial dimensions is constructed to investigate the time dynamics as well as spatial variation of foreign body reaction kinetics. The simulation results have been consistent with experimental data and the model can facilitate quantitative insights for study of foreign body reaction process in general.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

Ionization dynamics of the water trimer: A direct ab initio MD study

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto; Takada, Tomoya

2013-03-01

Ionization dynamics of the cyclic water trimer (H2O)3 have been investigated by means of direct ab initio molecular dynamics (AIMD) method. Two reaction channels, complex formation and OH dissociation, were found following the ionization of (H2O)3. In both channels, first, a proton was rapidly transferred from H2O+ to H2O (time scale is ˜15 fs after the ionization). In complex channel, an ion-radical contact pair (H3O+-OH) solvated by the third water molecule was formed as a long-lived H3O+(OH)H2O complex. In OH dissociation channel, the second proton transfer further takes place from H3O+(OH) to H2O (time scale is 50-100 fs) and the OH radical is separated from the H3O+. At the same time, the OH dissociation takes place when the excess energy is efficiently transferred into the kinetic energy of OH radical. The OH dissociation channel is significantly minor, and almost all product channels were the complex formation. The reaction mechanism was discussed on the basis of theoretical results.

Sharper Graph-Theoretical Conditions for the Stabilization of Complex Reaction Networks

PubMed Central

Knight, Daniel; Shinar, Guy; Feinberg, Martin

2015-01-01

Across the landscape of all possible chemical reaction networks there is a surprising degree of stable behavior, despite what might be substantial complexity and nonlinearity in the governing differential equations. At the same time there are reaction networks, in particular those that arise in biology, for which richer behavior is exhibited. Thus, it is of interest to understand network-structural features whose presence enforces dull, stable behavior and whose absence permits the dynamical richness that might be necessary for life. We present conditions on a network’s Species-Reaction Graph that ensure a high degree of stable behavior, so long as the kinetic rate functions satisfy certain weak and natural constraints. These graph-theoretical conditions are considerably more incisive than those reported earlier. PMID:25600138

Complications of modeling glycosylation reactions: can the anomeric conformation of a donor determine the glycopyranosyl oxacarbenium ring conformation?

PubMed

Whitfield, Dennis M

2012-07-15

That the ring conformation of glycopyranosyl oxacarbenium ions can influence the stereochemical outcome of glycosylation reactions has been postulated for some time. Some new ionization calculations show that the ultimate conformation (4)H(3) or (5)S(1) of D-glucopyranosyl oxacarbenium ions depends on the initial ϕ(H) (CH-1-C-1-S(+)-SCH(3)) conformation of anomeric thiosulfonium ions. Evidence is also presented that nucleophile:electrophile hydrogen bonded complexes, 1,6-anhydro-carbenium ions and electron rich carbon nucleophile:oxacarbenium ion complexes are all probably artifacts of neglecting counter ions or nucleophiles in the DFT calculation. All three cationic species are likely important for glycosylation reaction side reactions but not as productive species. Copyright © 2012. Published by Elsevier Ltd.

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

PubMed

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

2017-01-01

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

Parallel effects of memory set activation and search on timing and working memory capacity.

PubMed

Schweickert, Richard; Fortin, Claudette; Xi, Zhuangzhuang; Viau-Quesnel, Charles

2014-01-01

Accurately estimating a time interval is required in everyday activities such as driving or cooking. Estimating time is relatively easy, provided a person attends to it. But a brief shift of attention to another task usually interferes with timing. Most processes carried out concurrently with timing interfere with it. Curiously, some do not. Literature on a few processes suggests a general proposition, the Timing and Complex-Span Hypothesis: A process interferes with concurrent timing if and only if process performance is related to complex span. Complex-span is the number of items correctly recalled in order, when each item presented for study is followed by a brief activity. Literature on task switching, visual search, memory search, word generation and mental time travel supports the hypothesis. Previous work found that another process, activation of a memory set in long term memory, is not related to complex-span. If the Timing and Complex-Span Hypothesis is true, activation should not interfere with concurrent timing in dual-task conditions. We tested such activation in single-task memory search task conditions and in dual-task conditions where memory search was executed with concurrent timing. In Experiment 1, activating a memory set increased reaction time, with no significant effect on time production. In Experiment 2, set size and memory set activation were manipulated. Activation and set size had a puzzling interaction for time productions, perhaps due to difficult conditions, leading us to use a related but easier task in Experiment 3. In Experiment 3 increasing set size lengthened time production, but memory activation had no significant effect. Results here and in previous literature on the whole support the Timing and Complex-Span Hypotheses. Results also support a sequential organization of activation and search of memory. This organization predicts activation and set size have additive effects on reaction time and multiplicative effects on percent correct, which was found.

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

PubMed

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

2012-06-22

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

Solute-solvent complex switching dynamics of chloroform between acetone and dimethylsulfoxide-two-dimensional IR chemical exchange spectroscopy.

PubMed

Kwak, Kyungwon; Rosenfeld, Daniel E; Chung, Jean K; Fayer, Michael D

2008-11-06

Hydrogen bonds formed between C-H and various hydrogen bond acceptors play important roles in the structure of proteins and organic crystals, and the mechanisms of C-H bond cleavage reactions. Chloroform, a C-H hydrogen bond donor, can form weak hydrogen-bonded complexes with acetone and with dimethylsulfoxide (DMSO). When chloroform is dissolved in a mixed solvent consisting of acetone and DMSO, both types of hydrogen-bonded complexes exist. The two complexes, chloroform-acetone and chloroform-DMSO, are in equilibrium, and they rapidly interconvert by chloroform exchanging hydrogen bond acceptors. This fast hydrogen bond acceptor substitution reaction is probed using ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy. Deuterated chloroform is used in the experiments, and the 2D-IR spectrum of the C-D stretching mode is measured. The chemical exchange of the chloroform hydrogen bonding partners is tracked by observing the time-dependent growth of off-diagonal peaks in the 2D-IR spectra. The measured substitution rate is 1/30 ps for an acetone molecule to replace a DMSO molecule in a chloroform-DMSO complex and 1/45 ps for a DMSO molecule to replace an acetone molecule in a chloroform-acetone complex. Free chloroform exists in the mixed solvent, and it acts as a reactive intermediate in the substitution reaction, analogous to a SN1 type reaction. From the measured rates and the equilibrium concentrations of acetone and DMSO, the dissociation rates for the chloroform-DMSO and chloroform-acetone complexes are found to be 1/24 ps and 1/5.5 ps, respectively. The difference between the measured rate for the complete substitution reaction and the rate for complex dissociation corresponds to the diffusion limited rate. The estimated diffusion limited rate agrees well with the result from a Smoluchowski treatment of diffusive reactions.

Simulation of anaerobic digestion processes using stochastic algorithm.

PubMed

Palanichamy, Jegathambal; Palani, Sundarambal

2014-01-01

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

Fine-tuning the nucleophilic reactivities of boron ate complexes derived from aryl and heteroaryl boronic esters.

PubMed

Berionni, Guillaume; Leonov, Artem I; Mayer, Peter; Ofial, Armin R; Mayr, Herbert

2015-02-23

Boron ate complexes derived from thienyl and furyl boronic esters and aryllithium compounds have been isolated and characterized by X-ray crystallography. Products and mechanisms of their reactions with carbenium and iminium ions have been analyzed. Kinetics of these reactions were monitored by UV/Vis spectroscopy, and the influence of the aryl substituents, the diol ligands (pinacol, ethylene glycol, neopentyl glycol, catechol), and the counterions on the nucleophilic reactivity of the boron ate complexes were examined. A Hammett correlation confirmed the polar nature of their reactions with benzhydrylium ions, and the correlation lg k(20 °C)=sN (E+N) was employed to determine the nucleophilicities of the boron ate complexes and to compare them with those of other borates and boronates. The neopentyl and ethylene glycol derivatives were found to be 10(4) times more reactive than the pinacol and catechol derivatives. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phasic heart rate responses and cardiac cycle time in auditory choice reaction time.

PubMed

van der Molen, M W; Somsen, R J; Orlebeke, J F

1983-01-01

This study investigated the cardiovascular-behavioral interaction under short and long stimulus interval conditions. In addition, the cardiovascular-behavioral interaction was studied as affected by cardiac cycle duration. Fourteen subjects performed a choice reaction time (RT) task employing a mixed speed-accuracy tradeoff design in which reactions were paced to coincide with a signal that occurs randomly at either 200 or 500 msec after the reaction stimulus. The preparatory interval between a warning stimulus and a lead-reaction stimulus complex was also varied (2 vs. 4.5 sec). Anticipatory deceleration occurred within the 4.5 sec interval but not in the 2 sec interval. The depth of anticipatory deceleration did not discriminate between fast and slow reactions; but an earlier shift from deceleration to acceleration was associated with fast reactions. The effect of stimulus timing relative to the R-wave of the electrocardiogram was also analysed. Meaningful stimuli tended to produce cardiac slowing as previously described in the literature. Early occurring stimuli prolong the cycle of their occurrence more than late occurring stimuli. The later prolong the subsequent cycle. Cardiac cycle time effects were absent for unattended stimuli. The results of anticipatory deceleration suggested that the depth of deceleration was regulated by time-uncertainty and speed-accuracy criterion.

A GTPase reaction accompanying the rejection of Leu-tRNA2 by UUU-programmed ribosomes. Proofreading of the codon-anticodon interaction by ribosomes.

PubMed

Thompson, R C; Dix, D B; Gerson, R B; Karim, A M

1981-01-10

The characteristics of a GTPase reaction between poly(U)-programmed ribosomes, EFTu . GTP, and the near-cognate aminoacyl (aa)-tRNA, Leu-tRNA Leu 2, have been studied to assess the role of this reaction in proofreading of the codon-anticodon interaction. The reaction resembles the GTPase reaction with cognate aa-tRNAs and EFTu . GTP in its substrate requirements, in its involving EFTu . GTP . aa-tRNA ternary complexes, and in its requiring a free ribosomal A-site. The noncognate reaction differs from the cognate one in that aa-tRNA becomes stably bound to the ribosomes only 5% of the time; it therefore seems best characterized as an abortive enzymatic binding reaction. The rate of reaction is a significant fraction (4%) of that of the cognate aa-tRNA, indicating that recognition of ternary complexes by ribosomes involves a level of error greater than that of translation as a whole. The rejection of the noncognate aa-tRNA following GTP hydrolysis is therefore a vital step in the translation process and fulfills the criteria set for a proofreading reaction. Leu-tRNA Leu 2 which escapes rejection through proofreading, forms a stable complex with the ribosomal A-site, so it appears that the Leu-tRNA2 which was rejected never reached the A-site and that proofreading precedes full A-site binding.

Moderate anxiety modifies the electromyographic activity of a forearm muscle during a time-reaction task in women.

PubMed

Langlet, C; Hainaut, J P; Bolmont, B

2017-03-16

Arousal anxiety has a great impact on reaction time, physiological parameters and motor performance. Numerous studies have focused on the influence of anxiety on muscular activity during simple non ecologic task. We investigate the impact of a moderate state-anxiety (arousal stressor) on the specific component of a complex multi-joint ecologic movement during a reaction time task of auditory stimulus-response. Our objective is to know if central and peripheral voluntary motor processes were modulated in the same way by an arousal stressor. Eighteen women volunteers performed simple reaction time tasks of auditory stimulus-response. Video-recorded Stroop test with interferences was used to induced moderate state-anxiety. Electromyographic activity of the wrist extensor was recorded in order to analyse the two components of the reaction time: the premotor and motor time. In anxiogenic condition, an acceleration and an increase of muscular activity of the reaction time was obtained. This increase was due to a stronger muscle activity during the premotor time in the anxiogenic condition. Arousal anxiety has a different impact on central and peripheral voluntary motor processes. The modifications observed could be related to an increase in arousal related to a higher anxiety in order to prepare the body to act. Copyright © 2017 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Mechanism of Ferric Oxalate Photolysis

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

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

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

Mechanism of Ferric Oxalate Photolysis

DOE PAGES

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

2017-06-08

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

Carbon-hydrogen activation of cycloalkanes by cyclopentadienylcarbonylrhodium--a lifetime enigma.

PubMed

Pitts, Amanda L; Wriglesworth, Alisdair; Sun, Xue-Zhong; Calladine, James A; Zarić, Snežana D; George, Michael W; Hall, Michael B

2014-06-18

Carbon-hydrogen bond activation reactions of four cycloalkanes (C5H10, C6H12, C7H14, and C8H16) by the Cp'Rh(CO) fragments (Cp' = η(5)-C5H5 (Cp) or η(5)-C5Me5 (Cp*)) were modeled theoretically by combining density functional and coupled cluster theories, and their reaction rates were measured by fast time-resolved infrared spectroscopy. The reaction has two steps, starting with the formation of a σ-complex intermediate, followed by oxidative addition of the C-H bond by the rhodium. A range of σ-complex stabilities among the electronically unique C-H bonds in a cycloalkane were calculated and are related to the individual strengths of the C-H bond's interactions with the Rh fragment and the steric repulsion that is incurred upon forming the specific σ-complex. The unexpectedly large increase in the lifetimes of the σ-complexes from cyclohexane to cycloheptane was predicted to be due to the large range of stabilities of the different σ-complexes found for cycloheptane. The reaction lifetimes were simulated with two mechanisms, with and without migrations among the different σ-complexes, to determine if ring migrations prior to C-H activation were influencing the rate. Both mechanisms predicted similar lifetimes for cyclopentane, cyclohexane, and, to a lesser extent, cycloheptane, suggesting ring migrations do not have a large impact on the rate of C-H activation for these cycloalkanes. For cyclooctane, the inclusion of ring migrations in the reaction mechanism led to a more accurate prediction of the lifetime, indicating that ring migrations did have an effect on the rate of C-H activation for this alkane, and that migration among the σ-complexes is faster than the C-H activation for this larger cycloalkane.

Five different tests of reaction time evaluated in HIV seropositive men.

PubMed

Dunlop, O; Bjørklund, R A; Abdelnoor, M; Myrvang, B

1992-09-01

In an attempt to develop a short neuropsychological test battery five different tests of reaction time were assessed according to their ability to discriminate between HIV seropositive men and healthy controls. In all tests a patient group with clinical symptoms was slower than the control group. In the complex reaction time test, which has a large cognitive aspect, even a clinically "asymptomatic" group was slower than the control group. The movement test, a new test with a large motor component, identified most slow responders, defining approximately half of the patients with clinical symptoms and one third of the "asymptomatic" patients as such. A test battery consisting of three tests is suggested for serial assessment and screening.

An analysis of relational complexity in an air traffic control conflict detection task.

PubMed

Boag, Christine; Neal, Andrew; Loft, Shayne; Halford, Graeme S

2006-11-15

Theoretical analyses of air traffic complexity were carried out using the Method for the Analysis of Relational Complexity. Twenty-two air traffic controllers examined static air traffic displays and were required to detect and resolve conflicts. Objective measures of performance included conflict detection time and accuracy. Subjective perceptions of mental workload were assessed by a complexity-sorting task and subjective ratings of the difficulty of different aspects of the task. A metric quantifying the complexity of pair-wise relations among aircraft was able to account for a substantial portion of the variance in the perceived complexity and difficulty of conflict detection problems, as well as reaction time. Other variables that influenced performance included the mean minimum separation between aircraft pairs and the amount of time that aircraft spent in conflict.

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

PubMed

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

2017-08-04

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

DNA barcoding and real-time PCR detection of Bactrocera xanthodes (Tephritidae: Diptera) complex.

PubMed

Li, D; Waite, D W; Gunawardana, D N; McCarthy, B; Anderson, D; Flynn, A; George, S

2018-05-06

Immature fruit fly stages of the family Tephritidae are commonly intercepted on breadfruit from Pacific countries at the New Zealand border but are unable to be identified to the species level using morphological characters. Subsequent molecular identification showed that they belong to Bactrocera xanthodes, which is part of a species complex that includes Bactrocera paraxanthodes, Bactrocera neoxanthodes and an undescribed species. To establish a more reliable molecular identification system for B. xanthodes, a reference database of DNA barcode sequences for the 5'-fragment of COI gene region was constructed for B. xanthodes from Fiji, Samoa and Tonga. To better understand the species complex, B. neoxanthodes from Vanuatu and B. paraxanthodes from New Caledonia were also barcoded. Using the results of this analysis, real-time TaqMan polymerase chain reaction (PCR) assays for the detection of B. xanthodes complex and for the three individual species of the complex were developed and validated. The assay showed high specificity for the target species, with no cross-reaction observed for closely related organisms. Each of the real-time PCR assays is sensitive, detecting the target sequences at concentrations as low as ten copies µl-1 and can be used as either singleplex or multiplex formats. This real-time PCR assay for B. xanthodes has been successfully applied at the borders in New Zealand, leading to the rapid identification of intercepted Tephritidae eggs and larvae. The developed assays will be useful biosecurity tools for rapid detection of species in the B. xanthodes complex worldwide.

Vibrational Excitation of Both Products of the Reaction of CN Radicals with Acetone in Solution

PubMed Central

2015-01-01

Transient electronic and vibrational absorption spectroscopy unravel the mechanisms and dynamics of bimolecular reactions of CN radicals with acetone in deuterated chloroform solutions. The CN radicals are produced by ultrafast ultraviolet photolysis of dissolved ICN. Two reactive forms of CN radicals are distinguished by their electronic absorption bands: “free” (uncomplexed) CN radicals, and “solvated” CN radicals that are complexed with solvent molecules. The lifetimes of the free CN radicals are limited to a few picoseconds following their photolytic production because of geminate recombination to ICN and INC, complexation with CDCl3 molecules, and reaction with acetone. The acetone reaction occurs with a rate coefficient of (8.0 ± 0.5) × 1010 M–1 s–1 and transient vibrational spectra in the C=N and C=O stretching regions reveal that both the nascent HCN and 2-oxopropyl (CH3C(O)CH2) radical products are vibrationally excited. The rate coefficient for the reaction of solvated CN with acetone is 40 times slower than for free CN, with a rate coefficient of (2.0 ± 0.9) × 109 M–1 s–1 obtained from the rise in the HCN product v1(C=N stretch) IR absorption band. Evidence is also presented for CN complexes with acetone that are more strongly bound than the CN–CDCl3 complexes because of CN interactions with the carbonyl group. The rates of reactions of these more strongly associated radicals are slower still. PMID:26192334

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

PubMed Central

Takeshita, Yuki; Takakura, Kazuya; Akitsu, Takashiro

2015-01-01

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

Bradykinesia and bradyphrenia revisited: patterns of subclinical deficit in motor speed and cognitive functioning in head-injured patients with good recovery.

PubMed

Gray, C; Cantagallo, A; Della Sala, S; Basaglia, N

1998-05-01

Twenty-four patients, showing a good clinical recovery from coma-inducing injury and coping well with the activities of everyday living, were tested, at least 1 year after trauma, on motor speed and reaction time, and given a neuropsychological examination. While the patients generally performed within the normal range on the neuropsychological tests, their motor speeds and reaction times--both simple (SRT) and complex (CRT)--were significantly slower than those of matched controls. This points to a subclinical bradykinesia. The patients' motor speed scores did not correlate significantly with any of the neuropsychological tests; nor did SRT or CRT. While the difference between simple and complex reaction time was significantly greater in the patient group, the percentage difference was not significantly different between the two groups. Collectively, these results suggest that bradykinesia and bradyphrenia do not necessarily overlap. Finally, there was no significant correlation between motor performance and severity of original injury, whether the latter was measured by number and size of lesions or by duration of post-traumatic amnesia.

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

DTIC Science & Technology

2017-10-10

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

Rhythms of Mental Performance

ERIC Educational Resources Information Center

Valdez, Pablo; Reilly, Thomas; Waterhouse, Jim

2008-01-01

Cognitive performance is affected by an individual's characteristics and the environment, as well as by the nature of the task and the amount of practice at it. Mental performance tests range in complexity and include subjective estimates of mood, simple objective tests (reaction time), and measures of complex performance that require decisions to…

Complex and Simple Clinical Reaction Times Are Associated with Gait, Balance, and Major Fall Injury in Older Subjects with Diabetic Peripheral Neuropathy

PubMed Central

Richardson, James K.; Eckner, James T.; Allet, Lara; Kim, Hogene; Ashton-Miller, James

2016-01-01

Objective To identify relationships between complex and simple clinical measures of reaction time (RTclin), and indicators of balance in older subjects with and without diabetic peripheral neuropathy (DPN). Design Prospective cohort design. Complex RTclin Accuracy, Simple RTclin Latency, and their ratio were determined using a novel device in 42 subjects (age = 69.1 ± 8.3 yrs), 26 with DPN and 16 without. Dependent variables included unipedal stance time (UST), step width variability and range on an uneven surface, and major fall-related injury over 12 months. Results In the DPN subjects the ratio of Complex RTclin Accuracy:Simple RTclin Latency was strongly associated with longer UST (r/p = .653/.004), and decreased step width variability and range (r/p = −.696/.001 and −.782/<.001, respectively) on an uneven surface. Additionally, the two DPN subjects sustaining major injuries had lower Complex RTclin Accuracy:Simple: RTclin Latency than those without. Conclusions The ratio of Complex RTclin Accuracy:Simple RTclin Latency is a potent predictor of UST and frontal plane gait variability in response to perturbations, and may predict major fall injury in older subjects with DPN. These short latency neurocognitive measures may compensate for lower limb neuromuscular impairments, and provide a more comprehensive understanding of balance and fall risk. PMID:27552354

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

PubMed

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

2017-04-07

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

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.

Reaction Workup Planning: A Structured Flowchart Approach, Exemplified in Difficult Aqueous Workup of Hydrophilic Products

ERIC Educational Resources Information Center

Hill, George B.; Sweeney, Joseph B.

2015-01-01

Reaction workup can be a complex problem for those facing novel synthesis of difficult compounds for the first time. Workup problem solving by systematic thinking should be inculcated as mid-graduate-level is reached. A structured approach is proposed, building decision tree flowcharts to analyze challenges, and an exemplar flowchart is presented…

Real-time optical studies of respiratory Complex I turnover.

PubMed

Belevich, Nikolai; Belevich, Galina; Verkhovskaya, Marina

2014-12-01

Reduction of Complex l (NADH:ubiquinone oxidoreductase l) from Escherichia coli by NADH was investigated optically by means of an ultrafast stopped-flow approach. A locally designed microfluidic stopped-flow apparatus with a low volume (0.21Jl) but a long optical path (10 mm) cuvette allowed measurements in the time range from 270 ).IS to seconds. The data acquisition system collected spectra in the visible range every 50 )JS. Analysis of the obtained time-resolved spectral changes upon the reaction of Complex I with NADH revealed three kinetic components with characteristic times of <270 ).IS, 0.45-0.9 ms and 3-6 ms, reflecting reduction of different FeS clusters and FMN. The rate of the major ( T = 0.45-0.9 ms) component was slower than predicted by electron transfer theory for the reduction of all FeS clusters in the intraprotein redox chain. This delay of the reaction was explained by retention of NAD+ in the catalytic site. The fast optical changes in the time range of 0.27- 1.5 ms were not altered significantly in the presence of 1 0-fold excess of NAD+ over NADH. The data obtained on the NuoF E95Q variant of Complex I shows that the single amino acid replacement in the catalytic site caused a strong decrease of NADH binding and/or the hydride transfer from bound NADH to FMN.

Chemistry of vinylidene complexes. XXIV. A new μ-vinylidene complex containing RePt core, and platinum-bound carbonyl ligand. Spectroscopic, structural and electrochemical study

NASA Astrophysics Data System (ADS)

Verpekin, Victor V.; Vasiliev, Alexander D.; Kondrasenko, Alexander A.; Burmakina, Galina V.; Chudin, Oleg S.; Pavlenko, Nina I.; Zimonin, Dmitry V.; Rubaylo, Anatoly I.

2018-07-01

The novel heterobinuclear μ-vinylidene complex [Cp(CO)2Re(μ-C=CHPh)Pt(PPh3)(CO)] (1) was isolated from the reaction mixture of [Cp(CO)2Re(μ-C=CHPh)Fe(CO)4] and Pt(PPh3)4 for the first time. Alternative high-yield synthetic approaches to 1 were developed including the reactions of [Cp(CO)2Re(μ-C=CHPh)Pt(PPh3)2] (2) with Co2(CO)8 and Rh(acac)(CO)2. The complex was characterized by IR and 1H, 13C and 31P NMR spectroscopy, a molecular structure of 1 was determined by X-ray diffraction analysis. The electrochemical behavior of the new complex was studied by cyclic voltammetry at platinum or glassed carbon electrodes and by dc polarography at a dropping mercury electrode.

Theoretical study on atmospheric reactions of fluoranthene and pyrene with N2O5/NO3/NO2

NASA Astrophysics Data System (ADS)

Wang, Youfeng; Yang, Bo; Shu, Jinian; Li, Nana; Zhang, Peng; Sun, Wanqi

2015-08-01

It is complex to assign the products obtained from the gas-phase reactions of PAHs with NO3/NO2 and N2O5. For this purpose, theoretical calculations are performed. Results show that 2-nitrofluoranthene and 2-nitropyrene are the dominant products for reactions of fluoranthene and pyrene with NO3/NO2, while 3-nitrofluoranthene and 1-nitropyrene are the major nitration products of N2O5. SN2 reaction mechanisms are elucidated and homolytic mechanisms are calculated for the first time. Rate constants for reactions of fluoranthene and pyrene with N2O5 are deduced for the first time, which are 2.50 × 10-27 and 2.16 × 10-24 cm3 molecule-1 s-1, respectively at 298 K.

Pd(II) and Pt(II) complexes of α-keto stabilized sulfur ylide: Synthesis, structural, theoretical and catalytic activity studies

NASA Astrophysics Data System (ADS)

Sabounchei, Seyyed Javad; Hashemi, Ali; Sedghi, Asieh; Bayat, Mehdi; Akhlaghi Bagherjeri, Fateme; Gable, Robert W.

2017-05-01

Reaction of dimethyl sulfide with 2, 3‧-dibromoacetophenone led to formation of sulfonium salt [Me2SCH2C(O)C6H4-m-Br]Br (1). The resulted sulfonium salt was treated with NaOH and gave the α-keto stabilized sulfur ylide Me2SC(H)C(O)C6H4-m-Br (2). This ligand was reacted with [MCl2(cod)] (M = Pd, Pt; cod = 1,5-cyclooctadiene) to form the new cis- and trans-[MCl2(ylide)2] (M = Pd (cis- and trans-3), Pt (cis- and trans-4)) complexes. Characterization of the obtained compounds was performed by elemental analysis, IR, 1H and 13C NMR. Recrystallization of dichlorobis(ylide) palladium(II) and platinum(II) complexes from DMSO solution yielded the crystalline products, which X-ray diffraction data revealed that the both compounds were crystallized as cis-[MCl2(ylide)(DMSO)] (M = Pd (5), Pt (6)) complexes. Also, a theoretical study on structure and nature of the Msbnd C bonding between the Y ligand (ylide) and [MCl2·DMSO] fragments in [YMCl2·DMSO] (M = Pd, Pt) complexes has been reported via NBO and energy-decomposition analysis (EDA). Furthermore, the palladium catalyzed Suzuki-Miyaura reaction of various aryl chlorides with arylboronic acids was performed. The results showed that the Pd(II) complexes cis- and trans-3 catalyzed efficiently coupling reactions at low catalyst loading and short reaction time.

Catalyst activation, deactivation, and degradation in palladium-mediated Negishi cross-coupling reactions.

PubMed

Böck, Katharina; Feil, Julia E; Karaghiosoff, Konstantin; Koszinowski, Konrad

2015-03-27

Pd-mediated Negishi cross-coupling reactions were studied by a combination of kinetic measurements, electrospray-ionization (ESI) mass spectrometry, (31)P NMR and UV/Vis spectroscopy. The kinetic measurements point to a rate-determining oxidative addition. Surprisingly, this step seems to involve not only the Pd catalyst and the aryl halide substrate, but also the organozinc reagent. In this context, the ESI-mass spectrometric observation of heterobimetallic Pd-Zn complexes [L2 PdZnR](+) (L=S-PHOS, R=Bu, Ph, Bn) is particularly revealing. The inferred presence of these and related neutral complexes with a direct Pd-Zn interaction in solution explains how the organozinc reagent can modulate the reactivity of the Pd catalyst. Previous theoretical calculations by González-Pérez et al. (Organometallics- 2012, 31, 2053) suggest that the complexation by the organozinc reagent lowers the activity of the Pd catalyst. Presumably, a similar effect also causes the rate decrease observed upon addition of ZnBr2 . In contrast, added LiBr apparently counteracts the formation of Pd-Zn complexes and restores the high activity of the Pd catalyst. At longer reaction times, deactivation processes due to degradation of the S-PHOS ligand and aggregation of the Pd catalyst come into play, thus further contributing to the appreciable complexity of the title reaction. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed Central

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

2017-01-01

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

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

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

Sasai, Hiroaki; Arai, Takayoshi; Shibasaki, Masakatsu

1994-02-23

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

Development of a Paradigm to Assess Nutritive and Biochemical Substances in Humans: A Preliminary Report on the Effects of Tyrosine upon Altitude- and Cold-Induced Stress Responses

DTIC Science & Technology

1987-03-01

3/4 hours. Performance tests evaluated simple and choice reaction time to visual stimuli, vigilance, and processing of symbolic, numerical, verbal...minimize the adverse consequences of these stressors. Tyrosine enhanced performance (e.g. complex information processing , vigilance, and reaction time... processes inherent in many real-world tasks. For example, Map Compass requires association of Wsi PL AFCm uA O-SV CHETCLtISS) direction and degree

Scale-Dependent Rates of Uranyl Surface Complexation Reaction in Sediments

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

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

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

Syntheses, structural analyses and redox kinetics of four-coordinate [CuL2]2+ and five-coordinate [CuL2(solvent)]2+ complexes (L = 6,6'-dimethyl-2,2'-bipyridine or 2,9-dimethyl-1,10-phenanthroline): completely gated reduction reaction of [Cu(dmp)2]2+ in nitromethane.

PubMed

Itoh, Sumitaka; Kishikawa, Nobuyuki; Suzuki, Takayoshi; Takagi, Hideo D

2005-03-21

[Cu(2,9-dimethyl-1,10-phenanthroline)(2)](2+) and [Cu(6,6'-dimethyl-2,2'-bipyridine)(2)](2+/+) complexes with no coordinated solvent molecule were synthesized and the crystal structures were analyzed: the coordination geometry around the Cu(i) center was in the D(2d) symmetry while a D(2) structure was observed for the four-coordinate Cu(ii) complexes. Coordination of a water or an acetonitrile molecule was found in the trigonal plane of the five-coordinate Cu(ii) complex in the Tbp(trigonal bipyramidal) structure. Spectrophotometric analyses revealed that the D(2) structure of the Cu(ii) complex was retained in nitromethane, although a five-coordinate Tbp species (green in color), was readily formed upon dissolution of the solid (reddish brown) in acetonitrile. The electron self-exchange reaction between D(2d)-Cu(I) and D(2)-Cu(II), observed by the NMR method, was very rapid with k(ex)=(1.1 +/- 0.2) x 10(5) kg mol(-1) s(-1) at 25 degrees C (DeltaH*= 15.6 +/- 1.3 kJ mol(-1) and DeltaS*=-96 +/- 4 J mol(-1) K(-1)), which was more than 10 times larger than that reported for the self-exchange reaction between D(2d)-Cu(I) and Tbp-Cu(II) in acetonitrile. The cross reduction reactions of D(2)-Cu(ii) by ferrocene and decamethylferrocene in nitromethane exhibited a completely gated behavior, while the oxidation reaction of D(2d)-Cu(i) by [Ni(1,4,7-triazacyclononane)(2)](3+) in nitromethane estimated an identically large self-exchange rate constant to that directly obtained by the NMR method. The electron self-exchange rate constant estimated from the oxidation cross reaction in 50% v/v acetonitrile-nitromethane mixture was 10 times smaller than that observed in pure nitromethane. On the basis of the Principle of the Least Motion (PLM) and the Symmetry Rules, it was concluded that gated behaviors observed for the reduction reactions of the five-coordinate Cu(ii)-polypyridine complexes are related to the high-energy C(2v)--> D(2d) conformational change around Cu(ii), and that the electron self-exchange reactions of the Cu(ii)/(i) couples are always adiabatic through the C(2v) structures for both Cu(ii) and Cu(i) since the conformational changes between D(2d), D(2) and C(2v) structures for Cu(i) as well as the conformational change between Tbp and C(2v) structures for Cu(ii) are symmetry-allowed. The completely gated behavior observed for the reduction reactions of D(2)-Cu(ii) species in nitromethane was attributed to the very slow conformational change from the ground-state D(2) to the entatic D(2d) structure that is symmetry-forbidden for d(9) metal complexes: the very slow back reaction, the forbidden conformational change from entatic D(2d) to the ground-state D(2) structure, ensures that the rate of the reduction reaction is independent of the concentration of the reducing reagent.

Detecting changes in dynamic and complex acoustic environments

PubMed Central

Boubenec, Yves; Lawlor, Jennifer; Górska, Urszula; Shamma, Shihab; Englitz, Bernhard

2017-01-01

Natural sounds such as wind or rain, are characterized by the statistical occurrence of their constituents. Despite their complexity, listeners readily detect changes in these contexts. We here address the neural basis of statistical decision-making using a combination of psychophysics, EEG and modelling. In a texture-based, change-detection paradigm, human performance and reaction times improved with longer pre-change exposure, consistent with improved estimation of baseline statistics. Change-locked and decision-related EEG responses were found in a centro-parietal scalp location, whose slope depended on change size, consistent with sensory evidence accumulation. The potential's amplitude scaled with the duration of pre-change exposure, suggesting a time-dependent decision threshold. Auditory cortex-related potentials showed no response to the change. A dual timescale, statistical estimation model accounted for subjects' performance. Furthermore, a decision-augmented auditory cortex model accounted for performance and reaction times, suggesting that the primary cortical representation requires little post-processing to enable change-detection in complex acoustic environments. DOI: http://dx.doi.org/10.7554/eLife.24910.001 PMID:28262095

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

PubMed

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

2016-05-18

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

EEG Patterns Related to Cognitive Tasks of Varying Complexity.

ERIC Educational Resources Information Center

Dunn, Denise A.; And Others

A study was conducted that attempted to show changes in electroencephalographic (EEG) patterns (identified using topographic EEG mapping) when children were required to perform the relatively simple task of button pressing during an eyes-open baseline session of low cognitive demand and a complex reaction time (RT) task of high cognitive demand.…

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

PubMed

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

2015-11-16

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

Amine-selective bioconjugation using arene diazonium salts.

PubMed

Diethelm, Stefan; Schafroth, Michael A; Carreira, Erick M

2014-08-01

A novel bioconjugation strategy is presented that relies on the coupling of diazonium terephthalates with amines in proteins. The diazonium captures the amine while the vicinal ester locks it through cyclization, ensuring no reversibility. The reaction is highly efficient and proceeds under mild conditions and short reaction times. Densely functionalized, complex natural products were directly coupled to proteins using low concentrations of coupling partners.

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

PubMed

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

2005-12-09

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

Biomaterials for 4D stem cell culture

PubMed Central

Hilderbrand, Amber M.; Ovadia, Elisa M.; Rehmann, Matthew S.; Kharkar, Prathamesh M.; Guo, Chen; Kloxin, April M.

2017-01-01

Stem cells reside in complex three-dimensional (3D) environments within the body that change with time, promoting various cellular functions and processes such as migration and differentiation. These complex changes in the surrounding environment dictate cell fate yet, until recently, have been challenging to mimic within cell culture systems. Hydrogel-based biomaterials are well suited to mimic aspects of these in vivo environments, owing to their high water content, soft tissue-like elasticity, and often-tunable biochemical content. Further, hydrogels can be engineered to achieve changes in matrix properties over time to better mimic dynamic native microenvironments for probing and directing stem cell function and fate. This review will focus on techniques to form hydrogel-based biomaterials and modify their properties in time during cell culture using select addition reactions, cleavage reactions, or non-covalent interactions. Recent applications of these techniques for the culture of stem cells in four dimensions (i.e., in three dimensions with changes over time) also will be discussed for studying essential stem cell processes. PMID:28717344

Simulating complex atomistic processes: On-the-fly kinetic Monte Carlo scheme with selective active volumes

NASA Astrophysics Data System (ADS)

Xu, Haixuan; Osetsky, Yury N.; Stoller, Roger E.

2011-10-01

An accelerated atomistic kinetic Monte Carlo (KMC) approach for evolving complex atomistic structures has been developed. The method incorporates on-the-fly calculations of transition states (TSs) with a scheme for defining active volumes (AVs) in an off-lattice (relaxed) system. In contrast to conventional KMC models that require all reactions to be predetermined, this approach is self-evolving and any physically relevant motion or reaction may occur. Application of this self-evolving atomistic kinetic Monte Carlo (SEAK-MC) approach is illustrated by predicting the evolution of a complex defect configuration obtained in a molecular dynamics (MD) simulation of a displacement cascade in Fe. Over much longer times, it was shown that interstitial clusters interacting with other defects may change their structure, e.g., from glissile to sessile configuration. The direct comparison with MD modeling confirms the atomistic fidelity of the approach, while the longer time simulation demonstrates the unique capability of the model.

Direct Observation of Photoinduced Charge Separation in Ruthenium Complex/Ni(OH) 2 Nanoparticle Hybrid

DOE PAGES

Tang, Yu; Pattengale, Brian A.; Ludwig, John M.; ...

2015-12-17

We report that Ni(OH) 2 have emerged as important functional materials for solar fuel conversion because of their potential as cost-effective bifunctional catalysts for both hydrogen and oxygen evolution reactions. However, their roles as photocatalysts in the photoinduced charge separation (CS) reactions remain unexplored. In this paper, we investigate the CS dynamics of a newly designed hybrid catalyst by integrating a Ru complex with Ni(OH) 2 nanoparticles (NPs). Using time resolved X-ray absorption spectroscopy (XTA), we directly observed the formation of the reduced Ni metal site (~60 ps), unambiguously demonstrating CS process in the hybrid through ultrafast electron transfer frommore » Ru complex to Ni(OH) 2 NPs. Compared to the ultrafast CS process, the charge recombination in the hybrid is ultraslow (>>50 ns). These results not only suggest the possibility of developing Ni(OH) 2 as solar fuel catalysts, but also represent the first time direct observation of efficient CS in a hybrid catalyst using XTA.« less

Porous polycarbene-bearing membrane actuator for ultrasensitive weak-acid detection and real-time chemical reaction monitoring.

PubMed

Sun, Jian-Ke; Zhang, Weiyi; Guterman, Ryan; Lin, Hui-Juan; Yuan, Jiayin

2018-04-30

Soft actuators with integration of ultrasensitivity and capability of simultaneous interaction with multiple stimuli through an entire event ask for a high level of structure complexity, adaptability, and/or multi-responsiveness, which is a great challenge. Here, we develop a porous polycarbene-bearing membrane actuator built up from ionic complexation between a poly(ionic liquid) and trimesic acid (TA). The actuator features two concurrent structure gradients, i.e., an electrostatic complexation (EC) degree and a density distribution of a carbene-NH 3 adduct (CNA) along the membrane cross-section. The membrane actuator performs the highest sensitivity among the state-of-the-art soft proton actuators toward acetic acid at 10 -6  mol L -1 (M) level in aqueous media. Through competing actuation of the two gradients, it is capable of monitoring an entire process of proton-involved chemical reactions that comprise multiple stimuli and operational steps. The present achievement constitutes a significant step toward real-life application of soft actuators in chemical sensing and reaction technology.

Preparation of Lanthanide-Polymer Composite Material via Click Chemistry.

PubMed

Chen, Bin; Wen, Guian; Wu, Jiajie; Feng, Jiachun

2015-10-01

Covalently attaching lanthanide complexes to the polymer backbone can effectively reduce the clustering of lanthanides and thus become an important strategy to fully unleash their potential. In this Communication, a metal-free click reaction is used for the first time to link a lanthanide complex to the polymer matrix. A diene-bearing copolymer with anthracenylmethyl methacrylate as a monomer and a dienophile-bearing lanthanide complex with 5-maleimido-1,10-phenanthroline as the second ligand are synthesized and coupled together through a Diels-Alder cycloaddition (DA). A comparative investigation demonstrates that the composite material prepared by DA click reaction shows the highest quantum yields in the same lanthanide concentration as compared to materials prepared by widely used "directly doping" and "in situ coordinating lanthanide ions with macromolecular ligand" approaches. This work suggests that the "metal-free" DA click reaction can be a promising tool in the synthesis of high efficient lanthanide functionalized polymeric materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Discovery of a Significant Acetone•Hydroperoxy Adduct Chaperone Effect and Its Impact on the Determination of Room Temperature Rate Constants for Acetonylperoxy/Hydroperoxy Self-Reactions and Cross Reaction Via Infrared Kinetic Spectroscopy.

NASA Astrophysics Data System (ADS)

Grieman, F. J.; Hui, A. O.; Okumura, M.; Sander, S. P.

2017-12-01

In order to model the upper troposphere/lower stratosphere in regions containing acetone properly, the kinetics of the acetonylperoxy/hydroperoxy self-reactions and cross reaction have been studied over a wide temperature range using Infrared Kinetic Spectroscopy. We report here the determination of different rate constants for the acetonylperoxy chemistry that we obtained at 298 K compared to currently accepted values. A considerable increase in the observed HO2 self-reaction rate constant due to rate enhancement via the chaperone effect from the reaction between HO2 and the (CH3)2CO•HO2 hydrogen-bonded adduct, even at room temperature, was discovered that was previously ignored. Correct determination of the acetonylperoxy and hydroperoxy kinetics must include this dependence of the HO2 self-reaction rate on acetone concentration. Via excimer laser flash photolysis to create the radical reactants, HO2 absorption was monitored in the infrared by diode laser wavelength modulation detection simultaneously with CH3C(O)CH2O2absorption monitored in the ultraviolet at 300 nm as a function of time. Resulting decay curves were fit concurrently first over a short time scale to obtain the rate constants minimizing subsequent product reactions. Modeling/fitting with a complete reaction scheme was then performed to refine the rate constants and test their veracity. Experiments were carried out over a variety of concentrations of acetone and methanol. Although no effect due to methanol concentration was found at room temperature, the rate constant for the hydroperoxy self-reaction was found to increase linearly with acetone concentration which is interpreted as the adduct being formed and resulting in a chaperone mechanism that enhances the self-reaction rate: (CH3)2CO·HO2 + HO2 → H2O2 + O2 + (CH3)2CO Including this effect, the resulting room temperature rate constants for the cross reaction and the acetonylperoxy self-reaction were found to be 2-3 times smaller than previously reported. This complex formation/chaperone mechanism is similar to that found for methanol, but different in that it occurs at room temperature. No precursor concentration dependence was found for the acetonylperoxy radical reactions. The equilibrium constant for the complex formation will also be presented.

New Sensitive Kinetic Spectrophotometric Methods for Determination of Omeprazole in Dosage Forms

PubMed Central

Mahmoud, Ashraf M.

2009-01-01

New rapid, sensitive, and accurate kinetic spectrophotometric methods were developed, for the first time, to determine omeprazole (OMZ) in its dosage forms. The methods were based on the formation of charge-transfer complexes with both iodine and 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ). The variables that affected the reactions were carefully studied and optimized. The formed complexes and the site of interaction were examined by UV/VIS, IR, and 1H-NMR techniques, and computational molecular modeling. Under optimum conditions, the stoichiometry of the reactions between OMZ and the acceptors was found to be 1 : 1. The order of the reactions and the specific rate constants were determined. The thermodynamics of the complexes were computed and the mechanism of the reactions was postulated. The initial rate and fixed time methods were utilized for the determination of OMZ concentrations. The linear ranges for the proposed methods were 0.10–3.00 and 0.50–25.00 μg mL−1 with the lowest LOD of 0.03 and 0.14 μg mL−1 for iodine and DDQ, respectively. Analytical performance of the methods was statistically validated; RSD was <1.25% for the precision and <1.95% for the accuracy. The proposed methods were successfully applied to the analysis of OMZ in its dosage forms; the recovery was 98.91–100.32% ± 0.94–1.84, and was found to be comparable with that of reference method. PMID:20140076

Basic quantitative polymerase chain reaction using real-time fluorescence measurements.

PubMed

Ares, Manuel

2014-10-01

This protocol uses quantitative polymerase chain reaction (qPCR) to measure the number of DNA molecules containing a specific contiguous sequence in a sample of interest (e.g., genomic DNA or cDNA generated by reverse transcription). The sample is subjected to fluorescence-based PCR amplification and, theoretically, during each cycle, two new duplex DNA molecules are produced for each duplex DNA molecule present in the sample. The progress of the reaction during PCR is evaluated by measuring the fluorescence of dsDNA-dye complexes in real time. In the early cycles, DNA duplication is not detected because inadequate amounts of DNA are made. At a certain threshold cycle, DNA-dye complexes double each cycle for 8-10 cycles, until the DNA concentration becomes so high and the primer concentration so low that the reassociation of the product strands blocks efficient synthesis of new DNA and the reaction plateaus. There are two types of measurements: (1) the relative change of the target sequence compared to a reference sequence and (2) the determination of molecule number in the starting sample. The first requires a reference sequence, and the second requires a sample of the target sequence with known numbers of the molecules of sequence to generate a standard curve. By identifying the threshold cycle at which a sample first begins to accumulate DNA-dye complexes exponentially, an estimation of the numbers of starting molecules in the sample can be extrapolated. © 2014 Cold Spring Harbor Laboratory Press.

Reactions and mass spectra of complex particles using Aerosol CIMS

NASA Astrophysics Data System (ADS)

Hearn, John D.; Smith, Geoffrey D.

2006-12-01

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

Coding the Assembly of Polyoxotungstates with a Programmable Reaction System.

PubMed

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

2017-05-01

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

Coding the Assembly of Polyoxotungstates with a Programmable Reaction System

PubMed Central

2017-01-01

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

Simulations of isoprene: Ozone reactions for a general circulation/chemical transport model

NASA Technical Reports Server (NTRS)

Makar, P. A.; Mcconnell, J. C.

1994-01-01

A parameterized reaction mechanism has been created to examine the interactions between isoprene and other tropospheric gas-phase chemicals. Tests of the parameterization have shown that its results match those of a more complex reaction set to a high degree of accuracy. Comparisons between test runs have shown that the presence of isoprene at the start of a six day interval can enhance later ozone concentrations by as much as twenty-nine percent. The test cases used no input fluxes beyond the initial time, implying that a single input of a biogenic hydrocarbon to an airmass can alter its ozone chemistry over a time scale on the order of a week.

On the ortho-positronium quenching reactions promoted by Fe(II), Fe(III), Co(III), Ni(II), Zn(II) and Cd(II) cyanocomplexes

NASA Astrophysics Data System (ADS)

Fantola Lazzarini, Anna L.; Lazzarini, Ennio

The o-Ps quenching reactions promoted in aqueous solutions by the following six cyanocomplexes: [Fe(CN) 6] 4-; [Co(CN) 6] 3-; [Zn(CN) 4] 2-; [Cd(CN) 6] 2-; [Fe(CN) 6] 3-; [Ni(CN) 4] 2- were investigated. The first four reactions probably consist in o-Ps addition across the CN bond, their rate constants at room temperature, Tr, being ⩽(0.04±0.02) × 10 9 M -1 s -1, i.e. almost at the limit of experimental errors. The rate constant of the fifth reaction, in o-Ps oxydation, at Tr is (20.3±0.4) × 10 9 M -1 s -1. The [Ni(CN) 4] 2-k value at Tr, is (0.27±0.01) × 10 9 M -1 s -1, i.e. 100 times less than the rate constants of o-Ps oxydation, but 10 times larger than those of the o-Ps addition across the CN bond. The [Ni(CN) 4] 2- reaction probably results in formation of the following positronido complex: [Ni(CN) 4Ps] 2-. However, it is worth noting that the existence of such a complex is only indirectly deduced. In fact it arises from comparison of the [Ni(CN) 4] 2- rate constant with those of the Fe(II), Zn(II), Cd(II), and Co(III) cyanocomplexes, which, like the Ni(II) cyanocomplex, do not promote o-Ps oxydation or spin exchange reactions.

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

PubMed

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

2017-10-28

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

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

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

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

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

2015-07-16

We have developed a multi-scale approach (Burke, M. P.; Klippenstein, S. J.; Harding, L. B. Proc. Combust. Inst. 2013, 34, 547–555.) to kinetic model formulation that directly incorporates elementary kinetic theories as a means to provide reliable, physics-based extrapolation to unexplored conditions. Here, we extend and generalize the multi-scale modeling strategy to treat systems of considerable complexity – involving multi-well reactions, potentially missing reactions, non-statistical product branching ratios, and non-Boltzmann (i.e. non-thermal) reactant distributions. The methodology is demonstrated here for a subsystem of low-temperature propane oxidation, as a representative system for low-temperature fuel oxidation. A multi-scale model is assembled andmore » informed by a wide variety of targets that include ab initio calculations of molecular properties, rate constant measurements of isolated reactions, and complex systems measurements. Active model parameters are chosen to accommodate both “parametric” and “structural” uncertainties. Theoretical parameters (e.g. barrier heights) are included as active model parameters to account for parametric uncertainties in the theoretical treatment; experimental parameters (e.g. initial temperatures) are included to account for parametric uncertainties in the physical models of the experiments. RMG software is used to assess potential structural uncertainties due to missing reactions. Additionally, branching ratios among product channels are included as active model parameters to account for structural uncertainties related to difficulties in modeling sequences of multiple chemically activated steps. The approach is demonstrated here for interpreting time-resolved measurements of OH, HO2, n-propyl, i-propyl, propene, oxetane, and methyloxirane from photolysis-initiated low-temperature oxidation of propane at pressures from 4 to 60 Torr and temperatures from 300 to 700 K. In particular, the multi-scale informed model provides a consistent quantitative explanation of both ab initio calculations and time-resolved species measurements. The present results show that interpretations of OH measurements are significantly more complicated than previously thought – in addition to barrier heights for key transition states considered previously, OH profiles also depend on additional theoretical parameters for R + O2 reactions, secondary reactions, QOOH + O2 reactions, and treatment of non-Boltzmann reaction sequences. Extraction of physically rigorous information from those measurements may require more sophisticated treatment of all of those model aspects, as well as additional experimental data under more conditions, to discriminate among possible interpretations and ensure model reliability. Keywords: Optimization, Uncertainty quantification, Chemical mechanism, Low-Temperature Oxidation, Non-Boltzmann« less

Numerical simulation of two-dimensional flow over a heated carbon surface with coupled heterogeneous and homogeneous reactions

NASA Astrophysics Data System (ADS)

Johnson, Ryan Federick; Chelliah, Harsha Kumar

2017-01-01

For a range of flow and chemical timescales, numerical simulations of two-dimensional laminar flow over a reacting carbon surface were performed to understand further the complex coupling between heterogeneous and homogeneous reactions. An open-source computational package (OpenFOAM®) was used with previously developed lumped heterogeneous reaction models for carbon surfaces and a detailed homogeneous reaction model for CO oxidation. The influence of finite-rate chemical kinetics was explored by varying the surface temperatures from 1800 to 2600 K, while flow residence time effects were explored by varying the free-stream velocity up to 50 m/s. The reacting boundary layer structure dependence on the residence time was analysed by extracting the ratio of chemical source and species diffusion terms. The important contributions of radical species reactions on overall carbon removal rate, which is often neglected in multi-dimensional simulations, are highlighted. The results provide a framework for future development and validation of lumped heterogeneous reaction models based on multi-dimensional reacting flow configurations.

Synthesis and structures of bis-ligated zinc complexes supported by tridentate ketoimines that initiate L-lactide polymerization.

PubMed

Gerling, Kimberly A; Rezayee, Nomaan M; Rheingold, Arnold L; Green, David B; Fritsch, Joseph M

2014-11-21

Eight bis-ligated, homoleptic, zinc complexes were synthesized through the reaction of NNO Schiff base ketoimines bearing varying substituents with diethyl zinc in an inert atmosphere glovebox at room temperature and isolated in 62-95% yield. The complexes were characterized with (1)H, (13)C, and (19)F nuclear magnetic resonance spectroscopy, absorbance spectroscopy, high resolution mass spectrometry, elemental analysis, and single crystal X-ray crystallography. The complexes were shown to adopt distorted octahedral coordination geometry around zinc. The (1)H and (19)F NMR spectra of complexes 1-7 showed stable zinc coordination at 300 K while the effect of steric encumbrance and two trifluoromethyl groups in complex 8 was investigated with variable temperature NMR. The bis-ligated zinc complexes were effective initiators for the ring opening polymerization of L-lactide into poly-L-lactic acid (PLLA). With [L-lac]/[Zn complex] = 50, the bis-ligated zinc complexes yielded percentage conversion of 14-98% with polymerization times varying from 15-1440 min, where the longest reaction times were required when two trifluoromethyl groups were present. The addition of 4-fluorophenol co-catalyst resulted in up to a 5-fold increase in the percentage conversion in toluene solution and up to a 14-fold increase in bulk melt polymerization with reductions in the poly-dispersity index values for the isolated PLLA. Addition of 4-fluorophenol to complex 1 was studied with (1)H and (19)F NMR and appeared to yield an in situ generated zinc alkoxide complex.

Process for making surfactant capped nanocrystals

DOEpatents

Alivisatos, A Paul; Rockenberger, Joerg

2002-01-01

Disclosed is a process for making surfactant capped nanocrystals of transition metal oxides. The process comprises reacting a metal cupferron complex of the formula M Cup, wherein M is a transition metal, and Cup is a cupferron, with a coordinating surfactant, the reaction being conducted at a temperature ranging from about 250 to about 300 C., for a period of time sufficient to complete the reaction.

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

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

Schmehl, Russell H.

2016-03-02

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

[Study on the interaction of hemoglobin and Cu(II)-ARS complex].

PubMed

Wu, Xiao-Hua; Miao, Ji-Gen; Miao, Yu-Qing; Chen, Jian-Rong

2007-06-01

The reaction of hemoglobin (Hb) with copper(II)-Alizarin red S (ARS) complex was studied in H3PO4-KH2PO4 buffer solution (pH 4. 2) by ultraviolet-visible spectrophotometry. The results show that the interaction of Hb and Cu(II)-ARS complex produces red ionic association complex with its maximum absorption peak at 537 nm. At the maximum absorption, the composition of the complex was determined to be n(Hb) : n(Cu(II)) : n(ARS) =1 : 4 : 8, and the apparent molar absorptivity was 1.52 x 10(5) L x mol(-1) x cm(-1). The concentration of Hb is linear with the absorbency in the range of 1.0 x 10(-7)-2.0 x 10(-6) mol x L(-1) and the regression equation was established as A = 0.026 9 + 151 675c (mol x L(-1)) with the coefficient r = 0.997 2. The effects of solution acidity, reagent amount, reaction time, temperature, ionic strength and the added surfactant were examined on the formation of the Hb-Cu(II)-ARS complex. A preliminary investigation was carried out to elucidate the reaction mechanism, and it could be concluded that the Hb and Cu(II)-ARS complex are combined mainly by electrostatic attraction. Further investigation was also undertaken to find out the effects of common amino acids and metallic ions on the formation of Hb-Cu(II)-ARS complex.

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

Kinetic Profiling of Catalytic Organic Reactions as a Mechanistic Tool.

PubMed

Blackmond, Donna G

2015-09-02

The use of modern kinetic tools to obtain virtually continuous reaction progress data over the course of a catalytic reaction opens up a vista that provides mechanistic insights into both simple and complex catalytic networks. Reaction profiles offer a rate/concentration scan that tells the story of a batch reaction time course in a qualitative "fingerprinting" manner as well as in quantitative detail. Reaction progress experiments may be mathematically designed to elucidate catalytic rate laws from only a fraction of the number of experiments required in classical kinetic measurements. The information gained from kinetic profiles provides clues to direct further mechanistic analysis by other approaches. Examples from a variety of catalytic reactions spanning two decades of the author's work help to delineate nuances on a central mechanistic theme.

Matrix isolation infrared spectra of O2 and N2 insertion reactions with atomic uranium

NASA Astrophysics Data System (ADS)

Hunt, Rodney D.; Toth, L. Mac; Yustein, Jason T.; Andrews, Lester

1993-10-01

Laser ablation of refractory metals can be an effective source of vapor for matrix isolation IR studies. This combination of techniques was used for the first time to study the mechanisms of U vapor reactions with atmospheric components. U atoms and O2 were codeposited with excess Ar at 12 K. The dominant codeposition products were UO2 and UO3. In contrast, the UO yield was always small because UO2 is formed by an insertion mechanism. This mechanism was verified in the 16O2/18O2 experiments which failed to produce 16OU18O. The effects of UV photolysis and matrix annealings were also examined. The U atoms and O2 reaction requires little or no activation energy since UO2 was formed from cold reagents. New charge-transfer species, (UO2+2)(O2-2) and (UO+2)(O-2), and a weak complex, UO3-O2, were primarily produced under conditions which favored further O2 reactions. Similar U atom and N2 experiments produced only linear NUN which is also produced by an insertion mechanism. This U reaction represents the first time that atom was observed breaking and inserting into the triple bond of N2. Photolysis dramatically increased the NUN yield by 3-fold. Matrix annealings produced weak UN2-N2 and UN2-2N2 complexes.

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

PubMed

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

2008-08-15

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

Solar photolysis of water

NASA Technical Reports Server (NTRS)

Ryason, P. R. (Inventor)

1978-01-01

A cyclic process is described for the solar photolysis of water, including a first stage in which water is reduced in the presence of a Eu(+2) photooxidizable reagent producing hydrogen and spent oxidized Eu(+3) reagent. The spent reagent Eu(+3) is reduced by means of a transition metal ligand complex reductant, RuL(+3) in a photoexcited state, such as a ruthenium pyridyl complex. Due to competing reactions between the photolysis and regeneration products, the photooxidation reaction must be separated from the regeneration in space and time by supporting the reagent and/or the reductant on solid supports and utilizing pH, wavelength and flow control to maximize hydrogen and oxygen production.

The effects of deanol on cognitive performance and electrophysiology in elderly humans.

PubMed

Marsh, G R; Linnoila, M

1979-01-01

Deanol (900 mg/day for 21 days) had no effect on learning a list of words when tested at weekly intervals. Tests of simple and complex reaction time and a test of continuous serial decoding of digits showed no enhancement with the drug. Several components of evoked potentials recorded from several scalp sites did show enhanced amplitude under drug treatment. These changes were not accompanied by changes in the EEG spectrum as are seen with some other psychoactive drugs. Deanol seems to be an ineffective treatment for the normal slowing of cognitive function seen in the normal elderly person or those elderly with only minimal cognitive decline and free of symptoms of dementia. Contrary to earlier reports, elderly persons were found to be able to benefit from warning signals in a complex reaction time task.

The influence of reaction time on hydrogen sulphide removal from air by means of Fe(III)-EDTA/Fiban catalysts

NASA Astrophysics Data System (ADS)

Wasag, H.; Cel, W.; Chomczynska, M.; Kujawska, J.

2018-05-01

The paper deals with a new method of hydrogen sulphide removal from air by its filtration and selective catalytic oxidation with the use of fibrous carriers of Fe(III)-EDTA complex. The basis of these filtering materials includes fibrous ion exchangers with the complex immobilized on their functional groups. It has been established that the degree of catalytic hydrogen sulphide decomposition depends on the reaction time. Thus, the required degree of hydrogen sulphide removal from air could be easily controlled by applying appropriate thickness of the filtering layer under a given filtering velocity. It allows applying very thin filtering layers of the Fe(III)-EDTA/Fiban AK-22 or Fiban A-6 catalysts. The obtained results of the research confirm the applicability of these materials for deep air purification from hydrogen sulphide.

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

NASA Astrophysics Data System (ADS)

Gurevich, Svetlana V.

2013-05-01

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

Electron transfer reactions of excited dyes with metal complexes. Progress report, May 1, 1976--January 31, 1977. [Fe(III)--thionine reaction

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

Lichtin, N.N.

1977-02-01

A study was initiated of the factors which determine quantum efficiency of transfer of reducing equivalents between excited dye molecules and metal complexes in their ground state and composition and dynamics of formation and decay of related photostationary states. A ruby laser capable of delivering a 3.6 J, 19 nsec flash was acquired and assembly of an apparatus for laser flash photolysis begun. At the same time, conventional flash photolysis was used to pursue investigation of the dependence upon solvent, anions, pH, and ionic strength of the kinetics of the spontaneous dark reaction of Fe(H/sub 2/O)/sup 3 +//sub 6/ withmore » leucothionine and with semithionine, reactions which contribute to the composition and dynamics of formation and decay of the photostationary state of the iron-thionine photoredox reaction. Results are consistent with formation of an intermediate complex between leucothionine and Fe(III), K/sub A/ = 380 M/sup -1/ and k(elec. transfer) = 0.88 s/sup -1/ at approximately 22/sup 0/ in water solution at pH2, with sulfate as anion and ..mu.. = .05 - .1 M. Under similar conditions in 50 v/v percent aqueous CH/sub 3/CN, K/sub A/ = 780 M/sup -1/, k(elec. transfer) = 0.55 s/sup -1/. In both solvents, sulfate produces a large positive salt effect. Intermediacy of a complex was not established for the faster reaction of Fe(III) with semithionine under similar conditions: K/sub A/ . k(elec. transfer) approximately 3.5 x 10/sup 5/ M/sup -1/s/sup -1/ in H/sub 2/O, approximately 1.0 x 10/sup 4/ in 50 v/v percent aqueous CH/sub 3/CN.« less

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

NASA Astrophysics Data System (ADS)

Martin, Daniel R.; Matyushov, Dmitry V.

2015-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2009-08-01

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

Are Experienced Hearing Aid Users Faster at Grasping the Meaning of a Sentence Than Inexperienced Users? An Eye-Tracking Study

PubMed Central

Kollmeier, Birger; Neher, Tobias

2016-01-01

This study assessed the effects of hearing aid (HA) experience on how quickly a participant can grasp the meaning of an acoustic sentence-in-noise stimulus presented together with two similar pictures that either correctly (target) or incorrectly (competitor) depict the meaning conveyed by the sentence. Using an eye tracker, the time taken by the participant to start fixating the target (the processing time) was measured for two levels of linguistic complexity (low vs. high) and three HA conditions: clinical linear amplification (National Acoustic Laboratories-Revised), single-microphone noise reduction with National Acoustic Laboratories-Revised, and linear amplification ensuring a sensation level of ≥ 15 dB up to at least 4 kHz for the speech material used here. Timed button presses to the target stimuli after the end of the sentences (offline reaction times) were also collected. Groups of experienced (eHA) and inexperienced (iHA) HA users matched in terms of age, hearing loss, and working memory capacity took part (N = 15 each). For the offline reaction times, no effects were found. In contrast, processing times increased with linguistic complexity. Furthermore, for all HA conditions, processing times were longer (poorer) for the iHA group than for the eHA group, despite comparable speech recognition performance. Taken together, these results indicate that processing times are more sensitive to speech processing-related factors than offline reaction times. Furthermore, they support the idea that HA experience positively impacts the ability to process noisy speech quickly, irrespective of the precise gain characteristics. PMID:27595793

(1)H NMR-based DS determination of barley starch sulfates prepared in 1-allyl-3-methylimidazolium chloride.

PubMed

Kärkkäinen, Johanna; Wik, Tiia-Riikka; Niemelä, Matti; Lappalainen, Katja; Joensuu, Päivi; Lajunen, Marja

2016-01-20

The use of natural resources in a development of products and materials is currently increasing. Starch is one of the investigated resources due to its bioavailability, biodegradability, safety and affordability. In this study, native barley starch was sulfated using a SO3-pyridine complex. The reaction was carried out for the first time using 1-allyl-3-methylimidazolium chloride ionic liquid, an excellent solvent for the starch modification. Reaction conditions (temperature, time and amount of the reagent) were studied using an experimental design. Starch sulfates with the degree of substitution (DS) 1.37 were obtained when the reaction was carried out at 40 °C for 75 min with 4:1 molar ratio of SO3-pyridine complex:anhydroglucose unit. The determination of DS was based on (1)H NMR instead of elemental analysis, which showed overestimated DS values in this study. Starch sulfates were analyzed with FTIR and HPLC, which showed that products contained small and large sulfated molecules. Copyright © 2015 Elsevier Ltd. All rights reserved.

Real time monitoring of accelerated chemical reactions by ultrasonication-assisted spray ionization mass spectrometry.

PubMed

Lin, Shu-Hsuan; Lo, Ta-Ju; Kuo, Fang-Yin; Chen, Yu-Chie

2014-01-01

Ultrasonication has been used to accelerate chemical reactions. It would be ideal if ultrasonication-assisted chemical reactions could be monitored by suitable detection tools such as mass spectrometry in real time. It would be helpful to clarify reaction intermediates/products and to have a better understanding of reaction mechanism. In this work, we developed a system for ultrasonication-assisted spray ionization mass spectrometry (UASI-MS) with an ~1.7 MHz ultrasonic transducer to monitor chemical reactions in real time. We demonstrated that simply depositing a sample solution on the MHz-based ultrasonic transducer, which was placed in front of the orifice of a mass spectrometer, the analyte signals can be readily detected by the mass spectrometer. Singly and multiply charged ions from small and large molecules, respectively, can be observed in the UASI mass spectra. Furthermore, the ultrasonic transducer used in the UASI setup accelerates the chemical reactions while being monitored via UASI-MS. The feasibility of using this approach for real-time acceleration/monitoring of chemical reactions was demonstrated. The reactions of Girard T reagent and hydroxylamine with steroids were used as the model reactions. Upon the deposition of reactant solutions on the ultrasonic transducer, the intermediate/product ions are readily generated and instantaneously monitored using MS within 1 s. Additionally, we also showed the possibility of using this reactive UASI-MS approach to assist the confirmation of trace steroids from complex urine samples by monitoring the generation of the product ions. Copyright © 2014 John Wiley & Sons, Ltd.

Catalytic Activity of μ-Carbido-Dimeric Iron(IV) Octapropylporphyrazinate in the 3,5,7,2',4'-Pentahydroxyflavone Oxidation Reaction with tert-Butyl Hydroperoxide

NASA Astrophysics Data System (ADS)

Tyurin, D. V.; Zaitseva, S. V.; Kudrik, E. V.

2018-05-01

It is found for the first time that μ-carbido-dimeric iron(IV) octapropylporphyrazinate displays catalytic activity in the oxidation reaction of natural flavonol morin with tert-butyl hydroperoxide, with the catalyst being stable under conditions of the reaction. The kinetics of this reaction are studied. It is shown the reaction proceeds via tentative formation of a complex between the catalyst and the oxidant, followed by O‒O bond homolytic cleavage. The kinetics of the reaction is described in the coordinates of the Michaelis-Menten equation. A linear dependence of the apparent reaction rate constant on the concentration of the catalyst is observed, testifying to its participation in the limiting reaction step. The equilibrium constants and rates of interaction are found. A mechanism is proposed for the reaction on the basis of the experimental data.

Hydrogen-bond formation between isoindolo[2,1-a]indol-6-one and aliphatic alcohols in n-hexane.

PubMed

Demeter, Attila; Bérces, Tibor

2005-03-17

The spectroscopic, kinetic, and equilibrium properties of isoindolo[2,1-a]indol-6-one (I) were studied in n-hexane in the presence and absence of alcohols (X). Hydrogen-bonded-complex formation was found to occur between the alcohol and the ground state as well as the excited state of the I molecule. The spectra of I and its singly complexed derivative (IX) are similar; however, that of IX is red shifted. The extent of red shift increases with the hydrogen-bonding ability of the alcohol. Equilibrium constant measurements were made to determine the hydrogen-bond basicity (beta(2)(H)) for I and the singlet excited (1)I. The beta(2)(H) value for (1)I is found to be about twice that of the ground-state I. Time-resolved fluorescence decay measurements indicate that the reaction of singlet excited I with fluorinated alcohols is diffusion controlled, while the rate of complexation with nonfluorinated (weaker hydrogen bonding) aliphatic alcohols depends on the Gibbs energy change in the complexation reaction. The quantitative correlation between the rate coefficient of complexation of (1)I with alcohols and the Gibbs energy change in the complexation process allowed us to estimate the rate coefficient for the complexation of the ground-state I with alcohols. The formation of the singlet excited hydrogen-bonded complex is irreversible; (1)IX disappears in a first order and an alcohol induced second order reaction. The first order decay is predominantly due to internal conversion to the ground state, the rate of which depends on the ionization energy of the complexing alcohol.

Dembo polymerase chain reaction technique for detection of bovine abortion, diarrhea, and respiratory disease complex infectious agents in potential vectors and reservoirs.

PubMed

Rahpaya, Sayed Samim; Tsuchiaka, Shinobu; Kishimoto, Mai; Oba, Mami; Katayama, Yukie; Nunomura, Yuka; Kokawa, Saki; Kimura, Takashi; Kobayashi, Atsushi; Kirino, Yumi; Okabayashi, Tamaki; Nonaka, Nariaki; Mekata, Hirohisa; Aoki, Hiroshi; Shiokawa, Mai; Umetsu, Moeko; Morita, Tatsushi; Hasebe, Ayako; Otsu, Keiko; Asai, Tetsuo; Yamaguchi, Tomohiro; Makino, Shinji; Murata, Yoshiteru; Abi, Ahmad Jan; Omatsu, Tsutomu; Mizutani, Tetsuya

2018-05-31

Bovine abortion, diarrhea, and respiratory disease complexes, caused by infectious agents, result in high and significant economic losses for the cattle industry. These pathogens are likely transmitted by various vectors and reservoirs including insects, birds, and rodents. However, experimental data supporting this possibility are scarce. We collected 117 samples and screened them for 44 bovine abortive, diarrheal, and respiratory disease complex pathogens by using Dembo polymerase chain reaction (PCR), which is based on TaqMan real-time PCR. Fifty-seven samples were positive for at least one pathogen, including bovine viral diarrhea virus, bovine enterovirus, Salmonella enterica ser. Dublin, Salmonella enterica ser. Typhimurium, and Neospora caninum ; some samples were positive for multiple pathogens. Bovine viral diarrhea virus and bovine enterovirus were the most frequently detected pathogens, especially in flies, suggesting an important role of flies in the transmission of these viruses. Additionally, we detected the N. caninum genome from a cockroach sample for the first time. Our data suggest that insects (particularly flies), birds, and rodents are potential vectors and reservoirs of abortion, diarrhea, and respiratory infectious agents, and that they may transmit more than one pathogen at the same time.

Time-resolved and steady-state fluorescence studies of excited-state proton-transfer reactions of proflavine

NASA Astrophysics Data System (ADS)

De Silvestri, S.; Laporta, P.

1984-01-01

Time-resolved and steady-state fluorescence studies of proflavine in aqueous solution are presented. The observation of a monoexponential fluorescence decay with a time constant decreasing with increasing pH and the presence of an anomalous red-shift in the fluorescence spectrum as a function of pH indicate the existence of a complex proton-transfer mechanism in the excited state. A reaction scheme is proposed and the corresponding proton-transfer rates are evaluated. An excited-state pK value of 12.85 is obtained for the equilibrium between the cationic form of proflavine and the same form dissociated at an amino group.

Reliability and Criterion Validity of a Novel Clinical Test of Simple and Complex Reaction Time in Athletes1

PubMed Central

Eckner, James T.; Richardson, James K.; Kim, Hogene; Joshi, Monica S.; Oh, Youkeun K.; Ashton-Miller, James A.

2015-01-01

Summary Slowed reaction time (RT) represents both a risk factor for and a consequence of sport concussion. The purpose of this study was to determine the reliability and criterion validity of a novel clinical test of simple and complex RT, called RTclin, in contact sport athletes. Both tasks were adapted from the well-known ruler drop test of RT and involve manually grasping a falling vertical shaft upon its release, with the complex task employing a go/no-go paradigm based on a slight cue. In 46 healthy contact sport athletes (24 males; M = 16.3 yr., SD = 5.0; 22 women: M age= 15.0 yr., SD = 4.0) whose sports included soccer, ice hockey, American football, martial arts, wrestling, and lacrosse, the latency and accuracy of simple and complex RTclin had acceptable test-retest and inter-rater reliabilities and correlated with a computerized criterion standard, the Axon Computerized Cognitive Assessment Tool. Medium to large effect sizes were found. The novel RTclin tests have acceptable reliability and criterion validity for clinical use and hold promise as concussion assessment tools. PMID:26106803

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

PubMed Central

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

2009-01-01

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

Observation of oscillatory surface reactions of riboflavin, trolox, and singlet oxygen using single carbon nanotube fluorescence spectroscopy.

PubMed

Sen, Fatih; Boghossian, Ardemis A; Sen, Selda; Ulissi, Zachary W; Zhang, Jingqing; Strano, Michael S

2012-12-21

Single-molecule fluorescent microscopy allows semiconducting single-walled carbon nanotubes (SWCNTs) to detect the adsorption and desorption of single adsorbate molecules as a stochastic modulation of emission intensity. In this study, we identify and assign the signature of the complex decomposition and reaction pathways of riboflavin in the presence of the free radical scavenger Trolox using DNA-wrapped SWCNT sensors dispersed onto an aminopropyltriethoxysilane (APTES) coated surface. SWCNT emission is quenched by riboflavin-induced reactive oxygen species (ROS), but increases upon the adsorption of Trolox, which functions as a reductive brightening agent. Riboflavin has two parallel reaction pathways, a Trolox oxidizer and a photosensitizer for singlet oxygen and superoxide generation. The resulting reaction network can be detected in real time in the vicinity of a single SWCNT and can be completely described using elementary reactions and kinetic rate constants measured independently. The reaction mechanism results in an oscillatory fluorescence response from each SWCNT, allowing for the simultaneous detection of multiple reactants. A series-parallel kinetic model is shown to describe the critical points of these oscillations, with partition coefficients on the order of 10(-6)-10(-4) for the reactive oxygen and excited state species. These results highlight the potential for SWCNTs to characterize complex reaction networks at the nanometer scale.

Gamma-resonance investigation of the kinetics of the reduction of (. cap alpha. -benzil dioximato-1)(. cap alpha. -benzil dioximato-2)di(pyridine)iron(III)

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

Turte, K.I.; Bulgak, I.I.; Stukan, R.A.

1986-07-01

(..cap alpha..-Benzil dioximato-1)(..cap alpha..-benzil dioximato-2)di(pyridine)iron(III) in the form of the diacetone solvate (II) is spontaneously converted at room temperature into (..cap alpha..-benzil dioximato-1)(..cap alpha..-benzil dioximato-2)di(pyridine)iron(II) (III). The quantitative composition of a sample containing complexes II and III has been determined as a function of the temperature and the time by gamma-resonance spectroscopy, which made it possible to investigate the kinetics of this reaction. The changes obtained in the percentage of complex II in the sample as a function of time at a given temperature was treated with the use of the Kolmogorov-Erofeev equation for a topochemical reaction of the typemore » A/sub s/ ..-->.. B/sub s/ + C/sub g/. The rate constants of the reaction at various temperatures and the activation energy *E have been determined. In the temperature range from 293 to 304/sup 0/K *E = 25.6 kcal/mole. The possibilities of gamma-resonance spectroscopy in the investigation of topochemical reactions associated with changes in the oxidation state of iron ions have been demonstrated.« less

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

NASA Technical Reports Server (NTRS)

Sarani, Sam

2010-01-01

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

Stochastic simulation and analysis of biomolecular reaction networks

PubMed Central

Frazier, John M; Chushak, Yaroslav; Foy, Brent

2009-01-01

Background In recent years, several stochastic simulation algorithms have been developed to generate Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks. However, the effects of various stochastic simulation and data analysis conditions on the observed dynamics of complex biomolecular reaction networks have not recieved much attention. In order to investigate these issues, we employed a a software package developed in out group, called Biomolecular Network Simulator (BNS), to simulate and analyze the behavior of such systems. The behavior of a hypothetical two gene in vitro transcription-translation reaction network is investigated using the Gillespie exact stochastic algorithm to illustrate some of the factors that influence the analysis and interpretation of these data. Results Specific issues affecting the analysis and interpretation of simulation data are investigated, including: (1) the effect of time interval on data presentation and time-weighted averaging of molecule numbers, (2) effect of time averaging interval on reaction rate analysis, (3) effect of number of simulations on precision of model predictions, and (4) implications of stochastic simulations on optimization procedures. Conclusion The two main factors affecting the analysis of stochastic simulations are: (1) the selection of time intervals to compute or average state variables and (2) the number of simulations generated to evaluate the system behavior. PMID:19534796

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

PubMed Central

Alexanian, Erik J.; Hartwig, John F.

2010-01-01

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

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

NASA Astrophysics Data System (ADS)

Danielson, Thomas; Savara, Aditya; Hin, Celine

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

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

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

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

2015-07-15

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

Thin liquid films with time-dependent chemical reactions sheared by an ambient gas flow

NASA Astrophysics Data System (ADS)

Bender, Achim; Stephan, Peter; Gambaryan-Roisman, Tatiana

2017-08-01

Chemical reactions in thin liquid films are found in many industrial applications, e.g., in combustion chambers of internal combustion engines where a fuel film can develop on pistons or cylinder walls. The reactions within the film and the turbulent outer gas flow influence film stability and lead to film breakup, which in turn can lead to deposit formation. In this work we examine the evolution and stability of a thin liquid film in the presence of a first-order chemical reaction and under the influence of a turbulent gas flow. Long-wave theory with a double perturbation analysis is used to reduce the complexity of the problem and obtain an evolution equation for the film thickness. The chemical reaction is assumed to be slow compared to film evolution and the amount of reactant in the film is limited, which means that the reaction rate decreases with time as the reactant is consumed. A linear stability analysis is performed to identify the influence of reaction parameters, material properties, and environmental conditions on the film stability limits. Results indicate that exothermic reactions have a stabilizing effect whereas endothermic reactions destabilize the film and can lead to rupture. It is shown that an initially unstable film can become stable with time as the reaction rate decreases. The shearing of the film by the external gas flow leads to the appearance of traveling waves. The shear stress magnitude has a nonmonotonic influence on film stability.

Effect of α-stable sorptive waiting times on microbial transport in microflow cells

NASA Astrophysics Data System (ADS)

Bonilla, F. Alejandro; Cushman, John H.

2002-09-01

The interaction of bacteria in the fluid phase with pore walls of a porous material involves a wide range of effective reaction times which obey a diversity of substrate-bacteria adhesion conditions, and adhesive mechanisms. For a transported species, this heterogeneity in sorption conditions occurs both in time and space. Modern experimental methods allow one to measure adhesive reaction times of individual bacteria. This detailed information may be incorporated into nonequilibrium transport-sorption models that capture the heterogeneity in reaction times caused by varying chemical conditions. We have carried out particle (Brownian dynamic) simulations of adhesive, self-motile bacteria convected between two infinite plates as a model for a microflow cell. The adhesive heterogeneity is included by introducing adhesive reaction time (understood as time spent at a solid boundary once the particle collides against it) as a random variable that can be infinite (irreversible sorption) or vary over a wide range of values. This is made possible by treating this reaction time random variable as having an α-stable probability distribution whose properties (e.g., infinite moments and long tails) are distinctive from the standard exponential distribution commonly used to model reversible sorption. In addition, the α-stable distribution is renormalizable and hence upscalable to complex porous media. Simulations are performed in a pressure-driven microflow cell. Bacteria motility (driven by an effective Brownian force) acts as a dispersive component in the convective field. Upon collision with the pore wall, bacteria attachment or detachment occurs. The time bacteria spend at the wall varies over a wide range of time scales. This model has the advantage of being parsimonious, that is, involving very few parameters to model complex irreversible or reversible adhesion in heterogeneous environments. It is shown that, as in Taylor dispersion, the ratio of the channel half width b to the Brownian bacteria motility coefficient (D0 or dispersion coefficient) tb=b2/D0 controls the different adhesion regimes along with the value of α. Universal scalings (with respect to dimensionless time t*=t/tb) for the mean position, =V*efftθ*, and mean-square displacement, <ΔX2>=D*efftγ* exist for long-time dispersion and the coefficients were obtained. The model can account for a great many sorptive processes including reversible and irreversible sorption, and sub- and superdispersive regimes with just a few parameters.

Poststimulation time interval-dependent effects of motor cortex anodal tDCS on reaction-time task performance.

PubMed

Molero-Chamizo, Andrés; Alameda Bailén, José R; Garrido Béjar, Tamara; García López, Macarena; Jaén Rodríguez, Inmaculada; Gutiérrez Lérida, Carolina; Pérez Panal, Silvia; González Ángel, Gloria; Lemus Corchero, Laura; Ruiz Vega, María J; Nitsche, Michael A; Rivera-Urbina, Guadalupe N

2018-02-01

Anodal transcranial direct current stimulation (tDCS) induces long-term potentiation-like plasticity, which is associated with long-lasting effects on different cognitive, emotional, and motor performances. Specifically, tDCS applied over the motor cortex is considered to improve reaction time in simple and complex tasks. The timing of tDCS relative to task performance could determine the efficacy of tDCS to modulate performance. The aim of this study was to compare the effects of a single session of anodal tDCS (1.5 mA, for 15 min) applied over the left primary motor cortex (M1) versus sham stimulation on performance of a go/no-go simple reaction-time task carried out at three different time points after tDCS-namely, 0, 30, or 60 min after stimulation. Performance zero min after anodal tDCS was improved during the whole course of the task. Performance 30 min after anodal tDCS was improved only in the last block of the reaction-time task. Performance 60 min after anodal tDCS was not significantly different throughout the entire task. These findings suggest that the motor cortex excitability changes induced by tDCS can improve motor responses, and these effects critically depend on the time interval between stimulation and task performance.

Detection of Reaction Intermediates in Mg2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography.

PubMed

Samara, Nadine L; Gao, Yang; Wu, Jinjun; Yang, Wei

2017-01-01

Structures of enzyme-substrate/product complexes have been studied for over four decades but have been limited to either before or after a chemical reaction. Recently using in crystallo catalysis combined with X-ray diffraction, we have discovered that many enzymatic reactions in nucleic acid metabolism require additional metal ion cofactors that are not present in the substrate or product state. By controlling metal ions essential for catalysis, the in crystallo approach has revealed unprecedented details of reaction intermediates. Here we present protocols used for successful studies of Mg 2+ -dependent DNA polymerases and ribonucleases that are applicable to analyses of a variety of metal ion-dependent reactions. © 2017 Elsevier Inc. All rights reserved.

Homogeneous and Supported Niobium Catalysts as Lewis Acid and Radical Catalysts

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

Wayne Tikkanen

2006-12-31

The synthesis of tetrachlorotetraphenylcyclopentadienyl group 5 metal complexes has been accomplished through two routes, one a salt metathesis with lithiumtetraphenylcyclopentadiende and the other, reaction with trimethyltintetraphenylcyclopentadiene. The reactants and products have been characterized by {sup 1}H and {sup 13}C({sup 1}H) NMR spectroscopy. The niobium complex promotes the silylcyanation of butyraldehyde. The grafting of metal complexes to silica gel surfaces has been accomplished using tetrakisdimethylamidozirconium as the metal precursor. The most homogeneous binding as determined by CP-MAS {sup 13}C NMR and infrared spectroscopy was obtained with drying at 500 C at 3 mtorr vacuum. The remaining amido groups can be replacedmore » by reaction with alcohols to generate surface bound metal alkoxides. These bound catalysts promote silylcyanation of aryl aldehydes and can be reused three times with no loss of activity.« less

Optical properties, excitation energy and primary charge transfer in photosystem II: theory meets experiment.

PubMed

Renger, Thomas; Schlodder, Eberhard

2011-01-01

In this review we discuss structure-function relationships of the core complex of photosystem II, as uncovered from analysis of optical spectra of the complex and its subunits. Based on descriptions of optical difference spectra including site directed mutagenesis we propose a revision of the multimer model of the symmetrically arranged reaction center pigments, described by an asymmetric exciton Hamiltonian. Evidence is provided for the location of the triplet state, the identity of the primary electron donor, the localization of the cation and the secondary electron transfer pathway in the reaction center. We also discuss the stationary and time-dependent optical properties of the CP43 and CP47 subunits and the excitation energy transfer and trapping-by-charge-transfer kinetics in the core complex. Copyright © 2011 Elsevier B.V. All rights reserved.

Chess players' eye movements reveal rapid recognition of complex visual patterns: Evidence from a chess-related visual search task.

PubMed

Sheridan, Heather; Reingold, Eyal M

2017-03-01

To explore the perceptual component of chess expertise, we monitored the eye movements of expert and novice chess players during a chess-related visual search task that tested anecdotal reports that a key differentiator of chess skill is the ability to visualize the complex moves of the knight piece. Specifically, chess players viewed an array of four minimized chessboards, and they rapidly searched for the target board that allowed a knight piece to reach a target square in three moves. On each trial, there was only one target board (i.e., the "Yes" board), and for the remaining "lure" boards, the knight's path was blocked on either the first move (the "Easy No" board) or the second move (i.e., "the Difficult No" board). As evidence that chess experts can rapidly differentiate complex chess-related visual patterns, the experts (but not the novices) showed longer first-fixation durations on the "Yes" board relative to the "Difficult No" board. Moreover, as hypothesized, the task strongly differentiated chess skill: Reaction times were more than four times faster for the experts relative to novices, and reaction times were correlated with within-group measures of expertise (i.e., official chess ratings, number of hours of practice). These results indicate that a key component of chess expertise is the ability to rapidly recognize complex visual patterns.

Structural brain aging and speech production: a surface-based brain morphometry study.

PubMed

Tremblay, Pascale; Deschamps, Isabelle

2016-07-01

While there has been a growing number of studies examining the neurofunctional correlates of speech production over the past decade, the neurostructural correlates of this immensely important human behaviour remain less well understood, despite the fact that previous studies have established links between brain structure and behaviour, including speech and language. In the present study, we thus examined, for the first time, the relationship between surface-based cortical thickness (CT) and three different behavioural indexes of sublexical speech production: response duration, reaction times and articulatory accuracy, in healthy young and older adults during the production of simple and complex meaningless sequences of syllables (e.g., /pa-pa-pa/ vs. /pa-ta-ka/). The results show that each behavioural speech measure was sensitive to the complexity of the sequences, as indicated by slower reaction times, longer response durations and decreased articulatory accuracy in both groups for the complex sequences. Older adults produced longer speech responses, particularly during the production of complex sequence. Unique age-independent and age-dependent relationships between brain structure and each of these behavioural measures were found in several cortical and subcortical regions known for their involvement in speech production, including the bilateral anterior insula, the left primary motor area, the rostral supramarginal gyrus, the right inferior frontal sulcus, the bilateral putamen and caudate, and in some region less typically associated with speech production, such as the posterior cingulate cortex.

Formation of singlet oxygen by decomposition of protein hydroperoxide in photosystem II.

PubMed

Pathak, Vinay; Prasad, Ankush; Pospíšil, Pavel

2017-01-01

Singlet oxygen (1O2) is formed by triplet-triplet energy transfer from triplet chlorophyll to O2 via Type II photosensitization reaction in photosystem II (PSII). Formation of triplet chlorophyll is associated with the change in spin state of the excited electron and recombination of triplet radical pair in the PSII antenna complex and reaction center, respectively. Here, we have provided evidence for the formation of 1O2 by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. Protein hydroperoxide is formed by protein oxidation initiated by highly oxidizing chlorophyll cation radical and hydroxyl radical formed by Type I photosensitization reaction. Under highly oxidizing conditions, protein hydroperoxide is oxidized to protein peroxyl radical which either cyclizes to dioxetane or recombines with another protein peroxyl radical to tetroxide. These highly unstable intermediates decompose to triplet carbonyls which transfer energy to O2 forming 1O2. Data presented in this study show for the first time that 1O2 is formed by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex.

Formation of singlet oxygen by decomposition of protein hydroperoxide in photosystem II

PubMed Central

Pathak, Vinay; Prasad, Ankush

2017-01-01

Singlet oxygen (1O2) is formed by triplet-triplet energy transfer from triplet chlorophyll to O2 via Type II photosensitization reaction in photosystem II (PSII). Formation of triplet chlorophyll is associated with the change in spin state of the excited electron and recombination of triplet radical pair in the PSII antenna complex and reaction center, respectively. Here, we have provided evidence for the formation of 1O2 by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. Protein hydroperoxide is formed by protein oxidation initiated by highly oxidizing chlorophyll cation radical and hydroxyl radical formed by Type I photosensitization reaction. Under highly oxidizing conditions, protein hydroperoxide is oxidized to protein peroxyl radical which either cyclizes to dioxetane or recombines with another protein peroxyl radical to tetroxide. These highly unstable intermediates decompose to triplet carbonyls which transfer energy to O2 forming 1O2. Data presented in this study show for the first time that 1O2 is formed by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. PMID:28732060

Dual phase multiplex polymerase chain reaction

DOEpatents

Pemov, Alexander [Charlottesville, VA; Bavykin, Sergei [Darien, IL

2008-10-07

Highly specific and sensitive methods were developed for multiplex amplification of nucleic acids on supports such as microarrays. Based on a specific primer design, methods include five types of amplification that proceed in a reaction chamber simultaneously. These relate to four types of multiplex amplification of a target DNA on a solid support, directed by forward and reverse complex primers immobilized to the support and a fifth type--pseudo-monoplex polymerase chain reaction (PCR) of multiple targets in solution, directed by a single pair of unbound universal primers. The addition of the universal primers in the reaction mixture increases the yield over the traditional "bridge" amplification on a solid support by approximately ten times. Methods that provide multitarget amplification and detection of as little as 0.45-4.5.times.10.sup.-12 g (equivalent to 10.sup.2-10.sup.3 genomes) of a bacterial genomic DNA are disclosed.

Rapid and direct synthesis of complex perovskite oxides through a highly energetic planetary milling

PubMed Central

Lee, Gyoung-Ja; Park, Eun-Kwang; Yang, Sun-A; Park, Jin-Ju; Bu, Sang-Don; Lee, Min-Ku

2017-01-01

The search for a new and facile synthetic route that is simple, economical and environmentally safe is one of the most challenging issues related to the synthesis of functional complex oxides. Herein, we report the expeditious synthesis of single-phase perovskite oxides by a high-rate mechanochemical reaction, which is generally difficult through conventional milling methods. With the help of a highly energetic planetary ball mill, lead-free piezoelectric perovskite oxides of (Bi, Na)TiO3, (K, Na)NbO3 and their modified complex compositions were directly synthesized with low contamination. The reaction time necessary to fully convert the micron-sized reactant powder mixture into a single-phase perovskite structure was markedly short at only 30–40 min regardless of the chemical composition. The cumulative kinetic energy required to overtake the activation period necessary for predominant formation of perovskite products was ca. 387 kJ/g for (Bi, Na)TiO3 and ca. 580 kJ/g for (K, Na)NbO3. The mechanochemically derived powders, when sintered, showed piezoelectric performance capabilities comparable to those of powders obtained by conventional solid-state reaction processes. The observed mechanochemical synthetic route may lead to the realization of a rapid, one-step preparation method by which to create other promising functional oxides without time-consuming homogenization and high-temperature calcination powder procedures. PMID:28387324

Aqueous photochemical reactions of chloride, bromide, and iodide ions in a diode-array spectrophotometer. Autoinhibition in the photolysis of iodide ions.

PubMed

Kalmár, József; Dóka, Éva; Lente, Gábor; Fábián, István

2014-03-28

The aqueous photoreactions of three halide ions (chloride, bromide and iodide) were studied using a diode array spectrophotometer to drive and detect the process at the same time. The concentration and pH dependences of the halogen formation rates were studied in detail. The experimental data were interpreted by improving earlier models where the cage complex of a halogen atom and an electron has a central role. The triiodide ion was shown to exert a strong inhibiting effect on the reaction sequence leading to its own formation. An assumed chemical reaction between the triiodide ion and the cage complex interpreted the strong autoinhibition effect. It is shown that there is a real danger of unwanted interference from the photoreactions of halide ions when halide salts are used as supporting electrolytes in spectrophotometric experiments using a relatively high intensity UV light source.

A novel copper complex supported on magnetic reduced graphene oxide: an efficient and green nanocatalyst for the synthesis of 1-amidoalkyl-2-naphthol derivatives

NASA Astrophysics Data System (ADS)

Kooti, M.; Karimi, M.; Nasiri, E.

2018-02-01

A new Cu(II) complex supported on magnetic reduced graphene oxide was prepared and characterized by various techniques, such as FT-IR, XRD, SEM, EDX, TEM, TGA, BET, ICP, and VSM. The synthesized nanocomposite, which has size distribution of 25-30 nm, was employed as catalyst in one-pot synthesis of 1-amidoalkyl-2-naphthols via three-component condensation reaction of amides, aromatic aldehydes, and 2-naphthol, under solvent-free conditions. The introduced catalysis procedure for the synthesis of 1-amidoalkyl-2-naphthol derivatives offers several advantages namely, short reaction times, high yields, facile recyclability, and cost effectiveness. [Figure not available: see fulltext.

Econophysics — complex correlations and trend switchings in financial time series

NASA Astrophysics Data System (ADS)

Preis, T.

2011-03-01

This article focuses on the analysis of financial time series and their correlations. A method is used for quantifying pattern based correlations of a time series. With this methodology, evidence is found that typical behavioral patterns of financial market participants manifest over short time scales, i.e., that reactions to given price patterns are not entirely random, but that similar price patterns also cause similar reactions. Based on the investigation of the complex correlations in financial time series, the question arises, which properties change when switching from a positive trend to a negative trend. An empirical quantification by rescaling provides the result that new price extrema coincide with a significant increase in transaction volume and a significant decrease in the length of corresponding time intervals between transactions. These findings are independent of the time scale over 9 orders of magnitude, and they exhibit characteristics which one can also find in other complex systems in nature (and in physical systems in particular). These properties are independent of the markets analyzed. Trends that exist only for a few seconds show the same characteristics as trends on time scales of several months. Thus, it is possible to study financial bubbles and their collapses in more detail, because trend switching processes occur with higher frequency on small time scales. In addition, a Monte Carlo based simulation of financial markets is analyzed and extended in order to reproduce empirical features and to gain insight into their causes. These causes include both financial market microstructure and the risk aversion of market participants.

Catalytic asymmetric Meerwein-Ponndorf-Verley reduction of glyoxylates induced by a chiral N,N'-dioxide/Y(OTf)3 complex.

PubMed

Wu, Wangbin; Zou, Sijia; Lin, Lili; Ji, Jie; Zhang, Yuheng; Ma, Baiwei; Liu, Xiaohua; Feng, Xiaoming

2017-03-18

An asymmetric Meerwein-Ponndorf-Verley (MPV) reduction of glyoxylates was for the first time accomplished via an N,N'-dioxide/Y(OTf) 3 complex with aluminium alkoxide and molecular sieves (MSs) as crucial additives. A variety of optically active α-hydroxyesters were obtained with excellent results. A possible reaction mechanism was proposed based on the experiments.

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

NASA Astrophysics Data System (ADS)

Fellner, Klemens; Tang, Bao Quoc

2018-06-01

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

Determination of redox reaction rates and orders by in situ liquid cell electron microscopy of Pd and Au solution growth.

PubMed

Sutter, Eli A; Sutter, Peter W

2014-12-03

In-situ liquid cell transmission and scanning transmission electron microscopy (TEM/STEM) experiments are important, as they provide direct insight into processes in liquids, such as solution growth of nanoparticles, among others. In liquid cell TEM/STEM redox reaction experiments, the hydrated electrons e(-)aq created by the electron beam are responsible for the reduction of metal-ion complexes. Here we investigate the rate equation of redox reactions involving reduction by e(-)aq generated by the electron beam during in situ liquid TEM/STEM. Specifically we consider the growth of Pd on Au seeds in aqueous solutions containing Pd-chloro complexes. From the quantification of the rate of Pd deposition at different electron beam currents and as a function of distance from a stationary, nanometer-sized exciting beam, we determine that the reaction is first order with respect to the concentration of hydrated electrons, [e(-)aq]. By comparing Pd- and Au-deposition, we further demonstrate that measurements of the local deposition rate on nanoparticles in the solution via real-time imaging can be used to measure not only [e(-)aq] but also the rate of reduction of a metal-ion complex to zerovalent metal atoms in solution.

Determination of redox reaction rates and orders by in situ liquid cell electron microscopy of Pd and Au solution growth

DOE PAGES

Sutter, Eli A.; Sutter, Peter W.

2014-11-19

In-situ liquid cell transmission and scanning transmission electron microscopy (TEM/STEM) experiments are important as they provide direct insight into processes in liquids, such as solution growth of nanoparticles among others. In liquid cell TEM/STEM redox reaction experiments the hydrated electrons e⁻ aq created by the electron beam are responsible for the reduction of metal-ion complexes. Here we investigate the rate equation of redox reactions involving reduction by e⁻ aq generated by the electron beam during in-situ liquid TEM/STEM. Specifically we consider the growth of Pd on Au seeds in aqueous solutions containing Pd-chloro complexes. From the quantification of the ratemore » of Pd deposition at different electron beam currents and as a function of distance from a stationary, nanometer-sized exciting beam, we determine that the reaction is first order with respect to the concentration of hydrated electrons, [e⁻ aq]. In addition, by comparing Pd- and Au-deposition, we further demonstrate that measurements of the local deposition rate on nanoparticles in the solution via real-time imaging can be used to measure not only [e⁻ aq] but also the rate of reduction of a metal-ion complex to zero-valent metal atoms in solution.« less

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

NASA Astrophysics Data System (ADS)

Liu, Xinfang; Zhang, Songlin; Ding, Yuqiang

2012-06-01

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

Development of an on-site rapid real-time polymerase chain reaction system and the characterization of suitable DNA polymerases for TaqMan probe technology.

PubMed

Furutani, Shunsuke; Naruishi, Nahoko; Hagihara, Yoshihisa; Nagai, Hidenori

2016-08-01

On-site quantitative analyses of microorganisms (including viruses) by the polymerase chain reaction (PCR) system are significantly influencing medical and biological research. We have developed a remarkably rapid and portable real-time PCR system that is based on microfluidic approaches. Real-time PCR using TaqMan probes consists of a complex reaction. Therefore, in a rapid real-time PCR, the optimum DNA polymerase must be estimated by using actual real-time PCR conditions. In this study, we compared the performance of three DNA polymerases in actual PCR conditions using our rapid real-time PCR system. Although KAPA2G Fast HS DNA Polymerase has the highest enzymatic activity among them, SpeedSTAR HS DNA Polymerase exhibited better performance to rapidly increase the fluorescence signal in an actual real-time PCR using TaqMan probes. Furthermore, we achieved rapid detection of Escherichia coli in 7 min by using SpeedSTAR HS DNA Polymerase with the same sensitivity as that of a conventional thermal cycler.

Dramatic Influence of an Anionic Donor on the Oxygen-Atom Transfer Reactivity of a MnV–Oxo Complex

PubMed Central

Neu, Heather M; Quesne, Matthew G; Yang, Tzuhsiung; Prokop-Prigge, Katharine A; Lancaster, Kyle M; Donohoe, James; DeBeer, Serena; de Visser, Sam P; Goldberg, David P

2014-01-01

Addition of an anionic donor to an MnV(O) porphyrinoid complex causes a dramatic increase in 2-electron oxygen-atom-transfer (OAT) chemistry. The 6-coordinate [MnV(O)(TBP8Cz)(CN)]− was generated from addition of Bu4N+CN− to the 5-coordinate MnV(O) precursor. The cyanide-ligated complex was characterized for the first time by Mn K-edge X-ray absorption spectroscopy (XAS) and gives Mn–O=1.53 Å, Mn–CN=2.21 Å. In combination with computational studies these distances were shown to correlate with a singlet ground state. Reaction of the CN− complex with thioethers results in OAT to give the corresponding sulfoxide and a 2e−-reduced MnIII(CN)− complex. Kinetic measurements reveal a dramatic rate enhancement for OAT of approximately 24 000-fold versus the same reaction for the parent 5-coordinate complex. An Eyring analysis gives ΔH≠=14 kcal mol−1, ΔS≠=−10 cal mol−1 K−1. Computational studies fully support the structures, spin states, and relative reactivity of the 5- and 6-coordinate MnV(O) complexes. PMID:25256417

Ynamides in Ring Forming Transformations

PubMed Central

WANG, XIAO-NA; YEOM, HYUN-SUK; FANG, LI-CHAO; HE, SHUZHONG; MA, ZHI-XIONG; KEDROWSKI, BRANT L.; HSUNG, RICHARD P.

2013-01-01

Conspectus The ynamide functional group activates carbon-carbon triple bonds through an attached nitrogen atom that bears an electron-withdrawing group. As a result, the alkyne has both electrophilic and nucleophilic properties. Through the selection of the electron-withdrawing group attached to nitrogen chemists can modulate the electronic properties and reactivity of ynamides, making these groups versatile synthetic building blocks. The reactions of ynamides also lead directly to nitrogen-containing products, which provides access to important structural motifs found in natural products and molecules of medicinal interest. Therefore, researchers have invested increasing time and research in the chemistry of ynamides in recent years. This Account surveys and assesses new organic transformations involving ynamides developed in our laboratory and in others around the world. We showcase the synthetic power of ynamides for rapid assembly of complex molecular structures. Among the recent reports of ynamide transformations, ring-forming reactions provide a powerful tool for generating molecular complexity quickly. In addition to their synthetic utility, such reactions are mechanistically interesting. Therefore, we focus primarily on the cyclization chemistry of ynamides. This Account highlights ynamide reactions that are useful in the rapid synthesis of cyclic and polycyclic structural manifolds. We discuss the mechanisms active in the ring formations and describe representative examples that demonstrate the scope of these reactions and provide mechanistic insights. In this discussion we feature examples of ynamide reactions involving radical cyclizations, ring-closing metathesis, transition metal and non-transition metal mediated cyclizations, cycloaddition reactions, and rearrangements. The transformations presented rapidly introduce structural complexity and include nitrogen within, or in close proximity to, a newly formed ring (or rings). Thus, ynamides have emerged as powerful synthons for nitrogen-containing heterocycles and nitrogen-substituted rings, and we hope this Account will promote continued interest in the chemistry of ynamides. PMID:24164363

Very early reaction intermediates detected by microsecond time scale kinetics of cytochrome cd1-catalyzed reduction of nitrite.

PubMed

Sam, Katharine A; Strampraad, Marc J F; de Vries, Simon; Ferguson, Stuart J

2008-10-10

Paracoccus pantotrophus cytochrome cd(1) is a nitrite reductase found in the periplasm of many denitrifying bacteria. It catalyzes the reduction of nitrite to nitric oxide during the denitrification part of the biological nitrogen cycle. Previous studies of early millisecond intermediates in the nitrite reduction reaction have shown, by comparison with pH 7.0, that at the optimum pH, approximately pH 6, the earliest intermediates were lost in the dead time of the instrument. Access to early time points (approximately 100 micros) through use of an ultra-rapid mixing device has identified a spectroscopically novel intermediate, assigned as the Michaelis complex, formed from reaction of fully reduced enzyme with nitrite. Spectroscopic observation of the subsequent transformation of this species has provided data that demand reappraisal of the general belief that the two subunits of the enzyme function independently.

STRUCTURAL DYNAMICS OF METAL PARTITIONING TO MINERAL SURFACES

EPA Science Inventory

The conceptual understanding of surface complexation reactions that control trace element partitioning to mineral surfaces is limited by the assumption that the solid reactant possesses a finite, time-invariant population of surface functional groups. This assumption has limited...

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

DOE PAGES

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

2014-07-12

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

Wet air oxidation as a pretreatment option for selective biodegradability enhancement and biogas generation potential from complex effluent.

PubMed

Padoley, K V; Tembhekar, P D; Saratchandra, T; Pandit, A B; Pandey, R A; Mudliar, S N

2012-09-01

This study looks at the possibility of wet air oxidation (WAO) based pretreatment of complex effluent to selectively enhance the biodegradability (without substantial COD destruction) and facilitate biogas generation potential. A lab-scale wet air oxidation reactor with biomethanated distillery wastewater (B-DWW) as a model complex effluent (COD 40,000 mg L(-1)) was used to demonstrate the proof-of-concept. The studies were conducted using a designed set of experiments and reaction temperature (150-200°C), air pressure (6-12 bar) and reaction time (15-120 min) were the main process variables of concern for WAO process optimization. WAO pretreatment of B-DWW enhanced the biodegradability of the complex wastewater by the virtue of enhancing its biodegradability index (BI) from 0.2 to 0.88, which indicate favorable Biochemical Methane Potential (BMP) for biogas generation. The kinetics of COD destruction and BI enhancement has also been reported. Copyright © 2012 Elsevier Ltd. All rights reserved.

The Semireduced Mechanism for Nitric Oxide Reduction by Non-Heme Diiron Complexes: Modeling Flavodiiron Nitric Oxide Reductases.

PubMed

White, Corey J; Speelman, Amy L; Kupper, Claudia; Demeshko, Serhiy; Meyer, Franc; Shanahan, James P; Alp, E Ercan; Hu, Michael; Zhao, Jiyong; Lehnert, Nicolai

2018-02-21

Flavodiiron nitric oxide reductases (FNORs) are a subclass of flavodiiron proteins (FDPs) capable of preferential binding and subsequent reduction of NO to N 2 O. FNORs are found in certain pathogenic bacteria, equipping them with resistance to nitrosative stress, generated as a part of the immune defense in humans, and allowing them to proliferate. Here, we report the spectroscopic characterization and detailed reactivity studies of the diiron dinitrosyl model complex [Fe 2 (BPMP)(OPr)(NO) 2 ](OTf) 2 for the FNOR active site that is capable of reducing NO to N 2 O [Zheng et al., J. Am. Chem. Soc. 2013, 135, 4902-4905]. Using UV-vis spectroscopy, cyclic voltammetry, and spectro-electrochemistry, we show that one reductive equivalent is in fact sufficient for the quantitative generation of N 2 O, following a semireduced reaction mechanism. This reaction is very efficient and produces N 2 O with a first-order rate constant k > 10 2 s -1 . Further isotope labeling studies confirm an intramolecular N-N coupling mechanism, consistent with the rapid time scale of the reduction and a very low barrier for N-N bond formation. Accordingly, the reaction proceeds at -80 °C, allowing for the direct observation of the mixed-valent product of the reaction. At higher temperatures, the initial reaction product is unstable and decays, ultimately generating the diferrous complex [Fe 2 (BPMP)(OPr) 2 ](OTf) and an unidentified ferric product. These results combined offer deep insight into the mechanism of NO reduction by the relevant model complex [Fe 2 (BPMP)(OPr)(NO) 2 ] 2+ and provide direct evidence that the semireduced mechanism would constitute a highly efficient pathway to accomplish NO reduction to N 2 O in FNORs and in synthetic catalysts.

Characterising Complex Enzyme Reaction Data

PubMed Central

Rahman, Syed Asad; Thornton, Janet M.

2016-01-01

The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC) number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG). Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution. PMID:26840640

The relationship between psychological distress and baseline sports-related concussion testing.

PubMed

Bailey, Christopher M; Samples, Hillary L; Broshek, Donna K; Freeman, Jason R; Barth, Jeffrey T

2010-07-01

This study examined the effect of psychological distress on neurocognitive performance measured during baseline concussion testing. Archival data were utilized to examine correlations between personality testing and computerized baseline concussion testing. Significantly correlated personality measures were entered into linear regression analyses, predicting baseline concussion testing performance. Suicidal ideation was examined categorically. Athletes underwent testing and screening at a university athletic training facility. Participants included 47 collegiate football players 17 to 19 years old, the majority of whom were in their first year of college. Participants were administered the Concussion Resolution Index (CRI), an internet-based neurocognitive test designed to monitor and manage both at-risk and concussed athletes. Participants took the Personality Assessment Inventory (PAI), a self-administered inventory designed to measure clinical syndromes, treatment considerations, and interpersonal style. Scales and subscales from the PAI were utilized to determine the influence psychological distress had on the CRI indices: simple reaction time, complex reaction time, and processing speed. Analyses revealed several significant correlations among aspects of somatic concern, depression, anxiety, substance abuse, and suicidal ideation and CRI performance, each with at least a moderate effect. When entered into a linear regression, the block of combined psychological symptoms accounted for a significant amount of baseline CRI performance, with moderate to large effects (r = 0.23-0.30). When examined categorically, participants with suicidal ideation showed significantly slower simple reaction time and complex reaction time, with a similar trend on processing speed. Given the possibility of obscured concussion deficits after injury, implications for premature return to play, and the need to target psychological distress outright, these findings heighten the clinical importance of screening for psychological distress during baseline and post-injury concussion evaluations.

Synthesis and characterization of a new Inonotus obliquus polysaccharide-iron(III) complex.

PubMed

Wang, Jia; Chen, Haixia; Wang, Yanwei; Xing, Lisha

2015-04-01

A new Inonotus obliquus polysaccharide-iron(III) complex (IOPS-iron) was synthesized and characterized. The preparation conditions of IOPS-iron(III) were optimized and the physicochemical properties were characterized by physicochemical methods, scanning electron microscopy (SEM), electron paramagnetic resonance (EPR) spectroscopy, fourier transform infrared (FTIR) spectroscopy, circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy, respectively. The highest iron content of IOPS-iron(III) complex (19.40%) was obtained at the conditions: the ratio of IOPS and FeCl3 • 6H2O was 3:5 (w/w), the pH value of alkali solution was 10, the reaction temperature was 30 °C and the reaction time was 6h. The iron(III) was shown to be bound through the binding sites of the polysaccharide IOPS and it could form spatially separated iron centers on the polysaccharide backbone. IOPS-iron(III) complex was found to have good digestive availability and antioxidant activities in the in vitro assays, which suggested the IOPS-iron(III) complex might be used as a new iron supplement candidate. Copyright © 2015 Elsevier B.V. All rights reserved.

Effect of adsorbed metals ions on the transport of Zn- and Ni-EDTA complexes in a sand and gravel aquifer

USGS Publications Warehouse

Kent, D.B.; Davis, J.A.; Anderson, L.C.D.; Rea, B.A.; Coston, J.A.

2002-01-01

Adsorption, complexation, and dissolution reactions strongly influenced the transport of metal ions complexed with ethylenediaminetetraacetic acid (EDTA) in a predominantly quartz-sand aquifer during two tracer tests conducted under mildly reducing conditions at pH 5.8 to 6.1. In tracer test M89, EDTA complexes of zinc (Zn) and nickel (Ni), along with excess free EDTA, were injected such that the lower portion of the tracer cloud traveled through a region with adsorbed manganese (Mn) and the upper portion of the tracer cloud traveled through a region with adsorbed Zn. In tracer test S89, Ni- and Zn-EDTA complexes, along with excess EDTA complexed with calcium (Ca), were injected into a region with adsorbed Mn. The only discernable chemical reaction between Ni-EDTA and the sediments was a small degree of reversible adsorption leading to minor retardation. In the absence of adsorbed Zn, the injected Zn was displaced from EDTA complexes by iron(III) [Fe(III)] dissolved from the sediments. Displacement of Zn by Fe(III) on EDTA became increasingly thermodynamically favorable with decreasing total EDTA concentration. The reaction was slow compared to the time-scale of transport. Free EDTA rapidly dissolved aluminum (Al) from the sediments, which was subsequently displaced slowly by Fe. In the portion of tracer cloud M89 that traveled through the region contaminated with adsorbed Zn, little displacement of Zn complexed with EDTA was observed, and Al was rapidly displaced from EDTA by Zn desorbed from the sediments, in agreement with equilibrium calculations. In tracer test S89, desorption of Mn dominated over the more thermodynamically favorable dissolution of Al oxyhydroxides. Comparison with results from M89 suggests that dissolution of Al oxyhydroxides in coatings on these sediment grains by Ca-EDTA was rate-limited whereas that by free EDTA reached equilibrium on the time-scale of transport. Rates of desorption are much faster than rates of dissolution of Fe oxyhydroxides from sediment-grain surfaces and, therefore, adsorbed metal ions can strongly influence the speciation of ligands like EDTA in soils and sediments, especially over small temporal and spatial scales. Copyright ?? 2002 Elsevier Science Ltd.

New strategies for the synthesis of naphthoquinones employing Cu(II) complexes: Crystal structures and cytotoxicity

NASA Astrophysics Data System (ADS)

Azeredo, Nathália F. B.; Souza, Fabrícia P.; Demidoff, Felipe C.; Netto, Chaquip D.; Resende, Jackson A. L. C.; Franco, Roberto W. A.; Colepicolo, Pio; Ferreira, Ana M. C.; Fernandes, Christiane

2018-01-01

The syntheses, physico-chemical characterization and cytotoxicity toward three human cell lines (standard and resistant sarcoma cells, and fibroblast) of a new copper(II) complex [Cu(HBPA)(L1)Cl]·3H2O 2 are reported. Complex 2 was obtained through the reaction between the ligand stilbene-quinone (HL1) and Cu[HBPA]Cl21, where HBPA = 2-hydroxybenzyl-2pyridylmethylamine. The synthesis of HL1 was performed in high yield through Heck reaction on PEG-400. X-ray diffraction and solution studies (UV-Vis, EPR, ESI(+)-MS and ESI(+)-MS/MS) were performed for complex 2, in which the copper(II) center is coordinated to the quinone in its deprotonated form, to the ligand HBPA and to a chloro ligand. Similar reaction employing CuCl2·2H2O, instead of Cu[HBPA]Cl21 and HL1, has resulted in the obtainment of a furano-o-naphtoquinone (L2) with 99% selectivity, suggesting a new methodology to cyclize the ligand HL1. In order to obtain the analogous para-isomer (L3), and to evaluate the isomerism influence on cytotoxicity activity, a cyclization reaction of HL1 with NBS (N-bromosuccinimide) was also performed, which resulted in the obtainment of L2 (8%) and L3 (13%). X-ray diffraction studies were performed for L2 and complex 2, and the description of their structure elucidated. Results from MTT assay revealed that complex 2 is more active against sarcoma cell lines (MES-SA/Dx5 and MES-SA) than both the free ligand HL1 and complex 1, reducing cell viability to less than 50 μmol L-1. L2 was the most active in the series, presenting cytotoxicity against resistant MES-SA/Dx5 and its standard MES-SA cell line, respectively, three and ten times higher than the current drug doxorubicin.

Effects of pallidal deep brain stimulation and levodopa treatment on reaction-time performance in Parkinson's disease.

PubMed

Schubert, T; Volkmann, J; Müller, U; Sturm, V; Voges, J; Freund, H-J; Von Cramon, D Y

2002-05-01

Basal ganglia-thalamocortical circuits play an important role in movement preparation and execution. Tracer, single-cell, and lesion studies in monkeys suggest the existence of topologically segregated motor and nonmotor basal ganglia cortical circuits. In this study we used deep brain stimulation (DBS) of the posteroventrolateral globus pallidus internus (GPi) in patients with Parkinson's disease to elucidate the function of the GPi in human sensorimotor behavior. This question was investigated by comparing the influence of DBS on patients' performance in various reaction-time tasks that differed with respect to cognitive but not motor requirements. As a main result, DBS improved performance on the different tasks independently of the complexity of the involved cognitive processing functions. Furthermore, the observed effects did not depend on the modality of the processed information. These results suggest that the functional state of the posteroventrolateral GPi selectively affects the motor stage in simple sensorimotor acts, because this stage was the only stage involved in all investigated tasks. In addition to DBS, we manipulated the levodopa medication state of the PD patients. In contrast to DBS, levodopa effects on reaction times were less consistent. Levodopa improved reaction times in choice reaction tasks significantly, while affecting reaction times in a simple reaction task to a lesser extent. Error analysis revealed that the medication-dependent reaction-time improvement in the choice reaction tasks was accompanied by an increase in errors, suggesting a shift of the speed-accuracy criteria of the patients. A similar pattern of results was not observed for the DBS effects. Taken together, our data are in agreement with recent findings in monkeys that indicate a topological organization of the GPi in which motor functions are localized in posterolateral regions apart from cognitive regions. Furthermore, our data show a way to uncover the subcortical-cortical circuitry serving human sensorimotor behavior.

Extending atomistic scale chemistry to mesoscale model of condensed-phase deflagration

NASA Astrophysics Data System (ADS)

Joshi, Kaushik; Chaudhuri, Santanu

2017-01-01

Predictive simulations connecting chemistry that follow the shock or thermal initiation of energetic materials to subsequent deflagration or detonation events is currently outside the realm of possibilities. Molecular dynamics and first-principles based dynamics have made progress in understanding reactions in picosecond to nanosecond time scale. Results from thermal ignition of different phases of RDX show a complex reaction network and emergence of a deterministic behavior for critical temperature before ignition and hot spot growth rates. The kinetics observed is dependent on the hot spot temperature, system size and thermal conductivity. For cases where ignition is observed, the incubation period is dominated by intermolecular and intramolecular hydrogen transfer reactions. The gradual temperature and pressure increase in the incubation period is accompanied by accumulation of heavier polyradicals. The challenge of connecting such chemistry in mesoscale simulations remain in reducing the complexity of chemistry. The hot spot growth kinetics in RDX grains and interfaces is an important challenge for reactive simulations aiming to fill in the gaps in our knowledge in the nanoseconds to microseconds time scale. The results discussed indicate that the mesoscale chemistry may include large polyradical molecules in dense reactive mix reaching an instability point at certain temperatures and pressures.

Sex differences in mental rotation with polygons of different complexity: Do men utilize holistic processes whereas women prefer piecemeal ones?

PubMed

Heil, Martin; Jansen-Osmann, Petra

2008-05-01

Sex differences in mental rotation were investigated as a function of stimulus complexity with a sample size of N = 72. Replicating earlier findings with polygons, mental rotation was faster for males than for females, and reaction time increased with more complex polygons. Additionally, sex differences increased for complex polygons. Most importantly, however, mental rotation speed decreased with increasing complexity for women but did not change for men. Thus, the sex effects reflect a difference in strategy, with women mentally rotating the polygons in an analytic, piecemeal fashion and men using a holistic mode of mental rotation.

Measurement of the {sup 12}C({alpha},{gamma}){sup 16}O reaction at TRIAC

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

Makii, H.; Miyatake, H.; Wakabayashi, Y.

2012-11-12

We have measured the {gamma}-ray angular distribution of the {sup 12}C({alpha},{gamma}){sup 16}O reaction at TRIAC (Tokai Radioactive Ion Accelerator Complex) to accurately determine the E1 and E2 cross sections. In this experiment, we used high efficiency anti-Compton NaI(T1) spectrometers to detect a {gamma}-ray from the reaction with large S/N ratio, intense pulsed {alpha}-beams to discriminate true event from background events due to neutrons from {sup 13}C({alpha},n){sup 16}O reaction with a time-of-flight (TOF) method. We succeeded in removing a background events due to neutrons and clearly detected {gamma}-ray from the {sup 12}C({alpha}{gamma}){sup 16}O reaction with high statistics.

The effects of on-street parking and road environment visual complexity on travel speed and reaction time.

PubMed

Edquist, Jessica; Rudin-Brown, Christina M; Lenné, Michael G

2012-03-01

On-street parking is associated with elevated crash risk. It is not known how drivers' mental workload and behaviour in the presence of on-street parking contributes to, or fails to reduce, this increased crash risk. On-street parking tends to co-exist with visually complex streetscapes that may affect workload and crash risk in their own right. The present paper reports results from a driving simulator study examining the effects of on-street parking and road environment visual complexity on driver behaviour and surrogate measures of crash risk. Twenty-nine participants drove a simulated urban commercial and arterial route. Compared to sections with no parking bays or empty parking bays, in the presence of occupied parking bays drivers lowered their speed and shifted their lateral position towards roadway centre to compensate for the higher mental workload they reported experiencing. However, this compensation was not sufficient to reduce drivers' reaction time on a safety-relevant peripheral detection task or to an unexpected pedestrian hazard. Compared to the urban road environments, the less visually complex arterial road environment was associated with speeds that were closer to the posted limit, lower speed variability and lower workload ratings. These results support theoretical positions that proffer workload as a mediating variable of speed choice. However, drivers in this study did not modify their speed sufficiently to maintain safe hazard response times in complex environments with on-street parking. This inadequate speed compensation is likely to affect real world crash risk. Copyright © 2011 Elsevier Ltd. All rights reserved.

Kinetics of natural oxidant demand by permanganate in aquifer solids.

PubMed

Urynowicz, Michael A; Balu, Balamurali; Udayasankar, Umamaheshwari

2008-02-19

During in situ chemical oxidation with permanganate, natural organic matter and other reduced species in the subsurface compete with the target compounds for the available oxidant and can exert a significant natural oxidant demand. This competition between target and nontarget compounds can have a significant impact on the permeation, dispersal, and persistence of permanganate in the subsurface. The kinetics of natural oxidant demand by permanganate was investigated using a composite sample made up of aquifer material collected from three different sites. The study found that although the depletion of organic carbon increased with increased permanganate dosage and increased reaction period, the mass ratio of MnO(4)(-):OC (wt/wt) was relatively constant over time (11.4+/-0.9). The reaction order and rate with respect to permanganate were found to decrease with time suggesting a continuum of reactions with the slower reactions becoming more controlling with time. However, the data also suggests that this continuum of reactions can be simplified into short- and long-term kinetic expressions representing fast and slow reactions. An independent first-order kinetic model with separate fast and slow reaction rate constants was used to successfully describe the complete kinetic expression of natural oxidant demand. The kinetic parameters used in the model are easily determined and can be used to better understand the complex kinetics of natural oxidant demand.

Ferrocenyl-substituted dinuclear Cu(II) complex: Synthesis, spectroscopy, electrochemistry, DFT calculations and catecholase activity

NASA Astrophysics Data System (ADS)

Emirik, Mustafa; Karaoğlu, Kaan; Serbest, Kerim; Menteşe, Emre; Yilmaz, Ismail

2016-02-01

A new ferrocenyl-substituted heterocyclic hydrazide ligand and its Cu(II) complex were prepared. The DFT calculations were performed to determine the electronic and molecular structures of the title compounds. The electronic spectra were calculated by using time-dependent DFT method, and the transitions were correlated with the molecular orbitals of the compounds. The bands assignments of IR spectra were achieved in the light of the theoretical vibrational spectral data and total energy distribution values calculated at DFT/B3LYP/6-311++G(d,p) level. The redox behaviors of the ferrocene derivatives were investigated by cyclic voltammetry. The compounds show reversible redox couple assignable to Fc+/Fc couple. The copper(II) complex behaves as an effective catalyst towards oxidation of 3,5-di-tert-butylcatechol to its corresponding quinone derivative in DMF saturated with O2. The reaction follows Michaelis-Menten enzymatic reaction kinetics with turnover numbers 2.32 × 103.

A Ni(iii) complex stabilized by silica nanoparticles as an efficient nanoheterogeneous catalyst for oxidative C-H fluoroalkylation.

PubMed

Khrizanforov, Mikhail N; Fedorenko, Svetlana V; Strekalova, Sofia O; Kholin, Kirill V; Mustafina, Asiya R; Zhilkin, Mikhail Ye; Khrizanforova, Vera V; Osin, Yuri N; Salnikov, Vadim V; Gryaznova, Tatyana V; Budnikova, Yulia H

2016-07-26

We have developed Ni(III)-doped silica nanoparticles ([(bpy)xNi(III)]@SiO2) as a recyclable, low-leaching, and efficient oxidative functionalization nanocatalyst for aromatic C-H bonds. The catalyst is obtained by doping the complex [(bpy)3Ni(II)] on silica nanoparticles along with its subsequent electrooxidation to [(bpy)xNi(III)] without an additional oxidant. The coupling reaction of arenes with perfluoroheptanoic acid occurs with 100% conversion of reactants in a single step at room temperature under nanoheterogeneous conditions. The catalyst content is only 1% with respect to the substrates under electrochemical regeneration conditions. The catalyst can be easily separated from the reaction mixture and reused a minimum of five times. The results emphasize immobilization on the silica support and the electrochemical regeneration of Ni(III) complexes as a facile route for developing an efficient nanocatalyst for oxidative functionalization.

Monitoring of protease catalyzed reactions by quantitative MALDI MS using metal labeling.

PubMed

Gregorius, Barbara; Jakoby, Thomas; Schaumlöffel, Dirk; Tholey, Andreas

2013-05-21

Quantitative mass spectrometry is a powerful tool for the determination of enzyme activities as it does not require labeled substrates and simultaneously allows for the identification of reaction products. However, major restrictions are the limited number of samples which can be measured in parallel due to the need for isotope labeled internal standards. Here we describe the use of metal labeling of peptides for the setup of multiplexed enzyme activity assays. After proteolytic reaction, using the protease trypsin, remaining substrates and peptide products formed in the reaction were labeled with metal chelators complexing rare earth metal ions. Labeled peptides were quantified with high accuracy and over a wide dynamic range (at least 2 orders of magnitude) using MALDI MS in case of simple peptide mixtures or by LC-MALDI MS for complex substrate mixtures and used for the monitoring of time-dependent product formation and substrate consumption. Due to multiplexing capabilities and accuracy, the presented approach will be useful for the determination of enzyme activities with a wide range of biochemical and biotechnological applications.

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

PubMed

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

2004-11-12

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

COMPLEX RUTHENIUM ACIDO-NITROS COMPOUNDS (in Russian)

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

Zvyagintsev, O.E.; Starostin, S.M.

1961-06-01

The chemical nature of the water in the complex ruthenium acidonitroso compounds is studied by measuring certain acid properties, reactions, and behaviors of the compounds in aqueous solution. The dependence of molecular electrical conductivity on time and dilution, variations of specific electroconductivity, the optical density, and the light absorption of the compounds at 200 to 800 m mu wave range were investigated and the dissociation constants were calculated. (R.V.J.)

Development of a test for recording both visual and auditory reaction times, potentially useful for future studies in patients on opioids therapy

PubMed Central

Miceli, Luca; Bednarova, Rym; Rizzardo, Alessandro; Samogin, Valentina; Della Rocca, Giorgio

2015-01-01

Objective Italian Road Law limits driving while undergoing treatment with certain kinds of medication. Here, we report the results of a test, run as a smartphone application (app), assessing auditory and visual reflexes in a sample of 300 drivers. The scope of the test is to provide both the police force and medication-taking drivers with a tool that can evaluate the individual’s capacity to drive safely. Methods The test is run as an app for Apple iOS and Android mobile operating systems and facilitates four different reaction times to be assessed: simple visual and auditory reaction times and complex visual and auditory reaction times. Reference deciles were created for the test results obtained from a sample of 300 Italian subjects. Results lying within the first three deciles were considered as incompatible with safe driving capabilities. Results Performance is both age-related (r>0.5) and sex-related (female reaction times were significantly slower than those recorded for male subjects, P<0.05). Only 21% of the subjects were able to perform all four tests correctly. Conclusion We developed and fine-tuned a test called Safedrive that measures visual and auditory reaction times through a smartphone mobile device; the scope of the test is two-fold: to provide a clinical tool for the assessment of the driving capacity of individuals taking pain relief medication; to promote the sense of social responsibility in drivers who are on medication and provide these individuals with a means of testing their own capacity to drive safely. PMID:25709406

Development of a test for recording both visual and auditory reaction times, potentially useful for future studies in patients on opioids therapy.

PubMed

Miceli, Luca; Bednarova, Rym; Rizzardo, Alessandro; Samogin, Valentina; Della Rocca, Giorgio

2015-01-01

Italian Road Law limits driving while undergoing treatment with certain kinds of medication. Here, we report the results of a test, run as a smartphone application (app), assessing auditory and visual reflexes in a sample of 300 drivers. The scope of the test is to provide both the police force and medication-taking drivers with a tool that can evaluate the individual's capacity to drive safely. The test is run as an app for Apple iOS and Android mobile operating systems and facilitates four different reaction times to be assessed: simple visual and auditory reaction times and complex visual and auditory reaction times. Reference deciles were created for the test results obtained from a sample of 300 Italian subjects. Results lying within the first three deciles were considered as incompatible with safe driving capabilities. Performance is both age-related (r>0.5) and sex-related (female reaction times were significantly slower than those recorded for male subjects, P<0.05). Only 21% of the subjects were able to perform all four tests correctly. We developed and fine-tuned a test called Safedrive that measures visual and auditory reaction times through a smartphone mobile device; the scope of the test is two-fold: to provide a clinical tool for the assessment of the driving capacity of individuals taking pain relief medication; to promote the sense of social responsibility in drivers who are on medication and provide these individuals with a means of testing their own capacity to drive safely.

Exploiting single photon vacuum ultraviolet photoionization to unravel the synthesis of complex organic molecules in interstellar ices

NASA Astrophysics Data System (ADS)

Abplanalp, Matthew J.; Förstel, Marko; Kaiser, Ralf I.

2016-01-01

Complex organic molecules (COM) such as aldehydes, ketones, carboxylic acids, esters, and amides are ubiquitous in the interstellar medium, but traditional gas phase astrochemical models cannot explain their formation routes. By systematically exploiting on line and in situ vacuum ultraviolet photoionization coupled with reflectron time of flight mass spectrometry (PI-ReTOF-MS) and combining these data with infrared spectroscopy (FTIR), we reveal that complex organic molecules can be synthesized within interstellar ices that are condensed on interstellar grains via non-equilibrium reactions involving suprathermal hydrogen atoms at temperatures as low as 5 K. By probing for the first time specific structural isomers without their degradation (fragment-free), the incorporation of tunable vacuum ultraviolet photoionization allows for a much greater understanding of reaction mechanisms that exist in interstellar ices compared to traditional methods, thus eliminating the significant gap between observational and laboratory data that existed for the last decades. With the commission of the Atacama Large Millimeter/Submillimeter Array (ALMA), the number of detections of more complex organic molecules in space will continue to grow ⿿ including biorelevant molecules connected to the Origins of Life theme ⿿ and an understanding of these data will rely on future advances in sophisticated physical chemistry laboratory experiments.

SCScore: Synthetic Complexity Learned from a Reaction Corpus.

PubMed

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

2018-02-26

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

Kinetics and mechanism of olefin catalytic hydroalumination by organoaluminum compounds

NASA Astrophysics Data System (ADS)

Koledina, K. F.; Gubaidullin, I. M.

2016-05-01

The complex reaction mechanism of α-olefin catalytic hydroalumination by alkylalanes is investigated via mathematical modeling that involves plotting the kinetic models for the individual reactions that make up a complex system and a separate study of their principles. Kinetic parameters of olefin catalytic hydroalumination are estimated. Activation energies of the possible steps of the schemes of complex reaction mechanisms are compared and possible reaction pathways are determined.

Kinetic studies of the reaction of the hydroxymethyl radical with NO and NO sub 2

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

Nesbitt, F.L.; Payne, W.A.; Stief, L.J.

1989-06-29

The absolute rate constant for the reaction CD{sub 2}OH + NO has been measured from 230 to 373 K in a discharge-flow system. The decay of the CD{sub 2}OH radical was monitored in excess NO by collision-free sampling mass spectrometry. At 298 K, k{sub 1} = (2.2 {plus minus} 0.4) {times} 10{sup {minus}12} cm{sup 3}s{sup {minus}1} (2{sigma}) independent of pressure from 0.5 to 1.5 Torr. For the 230-298 K interval, an activation energy of 1.2 kcal/mol is obtained, but k{sub 1} does not appear to change within experimental error on going from 298 to 373 K. The absolute rate constantmore » at 298 K has also been measured for the reaction CH{sub 2}OH + NO{sub 2} by the same technique. The result is k{sub 2} = (8.3 {plus minus} 4.1) {times} 10{sup {minus}12} cm{sup 3} s{sup {minus}1} (2{sigma}). Qualitative detection was made of D{sub 2}CO and H{sub 2}CO as products of these reactions, but no evidence was obtained for the expected accompanying products HNO and HNO{sub 2} nor for the CD{sub 2}OHNO and CH{sub 2}OHNO{sub 2} adducts. It is suggested, partially by analogy with the CH{sub 2}OH + O{sub 2} reaction, that the reaction mechanism in both cases involves initial formation of a vibrationally excited complex that, depending on reaction conditions, can dissociate back to reactants or, after isomerization, dissociate to products. Collisional stabilization of the addition complex may be feasible, but they have no evidence for this under the low-pressure condition of their experiments. The rate constants for reaction of CH{sub 2}OH with O{sub 2}, NO, and NO{sub 2} are briefly compared.« less

UV-Photochemistry of the Disulfide Bond: Evolution of Early Photoproducts from Picosecond X-ray Absorption Spectroscopy at the Sulfur K-Edge.

PubMed

Ochmann, Miguel; Hussain, Abid; von Ahnen, Inga; Cordones, Amy A; Hong, Kiryong; Lee, Jae Hyuk; Ma, Rory; Adamczyk, Katrin; Kim, Tae Kyu; Schoenlein, Robert W; Vendrell, Oriol; Huse, Nils

2018-05-30

We have investigated dimethyl disulfide as the basic moiety for understanding the photochemistry of disulfide bonds, which are central to a broad range of biochemical processes. Picosecond time-resolved X-ray absorption spectroscopy at the sulfur K-edge provides unique element-specific insight into the photochemistry of the disulfide bond initiated by 267 nm femtosecond pulses. We observe a broad but distinct transient induced absorption spectrum which recovers on at least two time scales in the nanosecond range. We employed RASSCF electronic structure calculations to simulate the sulfur-1s transitions of multiple possible chemical species, and identified the methylthiyl and methylperthiyl radicals as the primary reaction products. In addition, we identify disulfur and the CH 2 S thione as the secondary reaction products of the perthiyl radical that are most likely to explain the observed spectral and kinetic signatures of our experiment. Our study underscores the importance of elemental specificity and the potential of time-resolved X-ray spectroscopy to identify short-lived reaction products in complex reaction schemes that underlie the rich photochemistry of disulfide systems.

Logic circuits based on molecular spider systems.

PubMed

Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

2016-08-01

Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

[Changes in the work capacity of the operators of command-measuring systems during daily duty].

PubMed

Novikov, V S; Lustin, S I; Blaginin, A A; Kozlov, V P

1997-06-01

Through 12 hours of work the operators of command-measuring complexes had initial signs of exhaustion, showed them-self by decrease of health state, activity, mood, increase of latent period of simple sensorimotor reaction. These changes of a functional condition had no effect on quality of fulfillment of target problems. At the end of daily duty exhaustion, described by deterioration of health state, increase of operators' anxiousness, rapid pulse, reduction of time of delay of breath, increase of time of instability of sensorimotor reactions, amount of faulty actions, reduction of speed of mental processes and distribution of attention were developed.

The informativity of sound modulates crossmodal facilitation of visual discrimination: a fMRI study.

PubMed

Li, Qi; Yu, Hongtao; Li, Xiujun; Sun, Hongzan; Yang, Jingjing; Li, Chunlin

2017-01-18

Many studies have investigated behavioral crossmodal facilitation when a visual stimulus is accompanied by a concurrent task-irrelevant sound. Lippert and colleagues reported that a concurrent task-irrelevant sound reduced the uncertainty of the timing of the visual display and improved perceptional responses (informative sound). However, the neural mechanism by which the informativity of sound affected crossmodal facilitation of visual discrimination remained unclear. In this study, we used event-related functional MRI to investigate the neural mechanisms underlying the role of informativity of sound in crossmodal facilitation of visual discrimination. Significantly faster reaction times were observed when there was an informative relationship between auditory and visual stimuli. The functional MRI results showed sound informativity-induced activation enhancement including the left fusiform gyrus and the right lateral occipital complex. Further correlation analysis showed that the right lateral occipital complex was significantly correlated with the behavioral benefit in reaction times. This suggests that this region was modulated by the informative relationship within audiovisual stimuli that was learnt during the experiment, resulting in late-stage multisensory integration and enhanced behavioral responses.

First Evidence of Vibrationally Driven Bimolecular Reactions in Solution: Reactions of Br Atoms with Dimethylsulfoxide and Methanol.

PubMed

Shin, Jae Yoon; Shaloski, Michael A; Crim, F Fleming; Case, Amanda S

2017-03-23

We present evidence for vibrational enhancement of the rate of bimolecular reactions of Br atoms with dimethylsulfoxide (DMSO) and methanol (CH 3 OH) in the condensed phase. The abstraction of a hydrogen atom from either of these solvents by a Br atom is highly endoergic: 3269 cm -1 for DMSO and 1416 or 4414 cm -1 for CH 3 OH, depending on the hydrogen atom abstracted. Thus, there is no thermal abstraction reaction at room temperature. Broadband electronic transient absorption shows that following photolysis of bromine precursors Br atoms form van der Waals complexes with the solvent molecules in about 5 ps and this Br • -solvent complex undergoes recombination. To explore the influence of vibrational energy on the abstraction reactions, we introduce a near-infrared (NIR) pump pulse following the photolysis pulse to excite the first overtone of the C-H (or O-H) stretch of the solvent molecules. Using single-wavelength detection, we observe a loss of the Br • -solvent complex that requires the presence of both photolysis and NIR pump pulses. Moreover, the magnitude of this loss depends on the NIR wavelength. Although this loss of reactive Br supports the notion of vibrationally driven chemistry, it is not concrete evidence of the hydrogen-abstraction reaction. To verify that the loss of reactive Br results from the vibrationally driven bimolecular reaction, we examine the pH dependence of the solution (as a measure of the formation of the HBr product) following long-time irradiation of the sample with both photolysis and NIR pump beams. We observe that when the NIR beam is on-resonance, the hydronium ion concentration increases fourfold as compared to that when it is off-resonance, suggesting the formation of HBr via a vibrationally driven hydrogen-abstraction reaction in solution.

Cortical Specializations Underlying Fast Computations

PubMed Central

Volgushev, Maxim

2016-01-01

The time course of behaviorally relevant environmental events sets temporal constraints on neuronal processing. How does the mammalian brain make use of the increasingly complex networks of the neocortex, while making decisions and executing behavioral reactions within a reasonable time? The key parameter determining the speed of computations in neuronal networks is a time interval that neuronal ensembles need to process changes at their input and communicate results of this processing to downstream neurons. Theoretical analysis identified basic requirements for fast processing: use of neuronal populations for encoding, background activity, and fast onset dynamics of action potentials in neurons. Experimental evidence shows that populations of neocortical neurons fulfil these requirements. Indeed, they can change firing rate in response to input perturbations very quickly, within 1 to 3 ms, and encode high-frequency components of the input by phase-locking their spiking to frequencies up to 300 to 1000 Hz. This implies that time unit of computations by cortical ensembles is only few, 1 to 3 ms, which is considerably faster than the membrane time constant of individual neurons. The ability of cortical neuronal ensembles to communicate on a millisecond time scale allows for complex, multiple-step processing and precise coordination of neuronal activity in parallel processing streams, while keeping the speed of behavioral reactions within environmentally set temporal constraints. PMID:25689988

A New Method to Develop Human Dental Pulp Cells and Platelet-rich Fibrin Complex.

PubMed

He, Xuan; Chen, Wen-Xia; Ban, Guifei; Wei, Wei; Zhou, Jun; Chen, Wen-Jin; Li, Xian-Yu

2016-11-01

Platelet-rich fibrin (PRF) has been used as a scaffold material in various tissue regeneration studies. In the previous methods to combine seed cells with PRF, the structure of PRF was damaged, and the manipulation time in vitro was also increased. The objective of this in vitro study was to explore an appropriate method to develop a PRF-human dental pulp cell (hDPC) complex to maintain PRF structure integrity and to find out the most efficient part of PRF. The PRF-hDPC complex was developed at 3 different time points during PRF preparation: (1) the before centrifugation (BC) group, the hDPC suspension was added to the venous blood before blood centrifugation; (2) the immediately after centrifugation (IAC) group, the hDPC suspension was added immediately after blood centrifugation; (3) the after centrifugation (AC) group, the hDPC suspension was added 10 minutes after blood centrifugation; and (4) the control group, PRF without hDPC suspension. The prepared PRF-hDPC complexes were cultured for 7 days. The samples were fixed for histologic, immunohistochemistry, and scanning electron microscopic evaluation. Real-time polymerase chain reaction was performed to evaluate messenger RNA expression of alkaline phosphatase and dentin sialophosphoprotein. Enzyme-linked immunosorbent assay quantification for growth factors was performed within the different parts of the PRF. Histologic, immunohistochemistry, and scanning electron microscopic results revealed that hDPCs were only found in the BC group and exhibited favorable proliferation. Real-time polymerase chain reaction revealed that alkaline phosphatase and dentin sialophosphoprotein expression increased in the cultured PRF-hDPC complex. The lower part of the PRF released the maximum quantity of growth factors. Our new method to develop a PRF-hDPCs complex maintained PRF structure integrity. The hDPCs were distributed in the buffy coat, which might be the most efficient part of PRF. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Complexity reduction of rate-equations models for two-choice decision-making.

PubMed

Carrillo, José Antonio; Cordier, Stéphane; Deco, Gustavo; Mancini, Simona

2013-01-01

We are concerned with the complexity reduction of a stochastic system of differential equations governing the dynamics of a neuronal circuit describing a decision-making task. This reduction is based on the slow-fast behavior of the problem and holds on the whole phase space and not only locally around the spontaneous state. Macroscopic quantities, such as performance and reaction times, computed applying this reduction are in agreement with previous works in which the complexity reduction is locally performed at the spontaneous point by means of a Taylor expansion.

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.

Single-Molecule Probing the Energy Landscape of Enzymatic Reaction and Non-Covalent Interactions

NASA Astrophysics Data System (ADS)

Lu, H. Peter; Hu, Dehong; Chen, Yu; Vorpagel, Erich R.

2002-03-01

We have applied single-molecule spectroscopy under physiological conditions to study the mechanisms and dynamics of T4 lysozyme enzymatic reactions, characterizing mode-specific protein conformational dynamics. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time. The overall reaction rates were found to vary widely from molecule-to-molecule, and the initial non-specific binding of the enzyme to the substrate was seen to dominate this inhomogeneity. The reaction steps subsequent to the initial binding were found to have homogeneous rates. Molecular dynamics simulation has been applied to elucidate the mechanism and intermediate states of the single-molecule enzymatic reaction. Combining the analysis of single-molecule experimental trajectories, MD simulation trajectories, and statistical modeling, we have revealed the nature of multiple intermediate states involved in the active enzyme-substrate complex formation and the associated conformational change mechanism and dynamics.

Cross-linked chitosan aerogel modified with Au: Synthesis, characterization and catalytic application.

PubMed

Keshipour, Sajjad; Mirmasoudi, Seyyedeh Sahra

2018-09-15

Dimercaprol as the chelating agent of Au(III) was loaded on chitosan aerogel. Dimercaprol supported on chitosan aerogel efficiently was complexed with Au(III). The new organometallic compound showed good catalytic activity in the oxidation reaction of some aliphatic alcohols, benzyl alcohol, and ethylbenzene. High conversions and excellent selectivities were obtained in the solvent-free oxidation reactions under mild reaction conditions. Also, turnover numbers were calculated for the oxidation reactions with 203, 134, 308, 282, 392, and 153 for 1-pentanol, 1-octanol, 2-propanol, 2-butanol, benzyl alcohol, and ethylbenzene, respectively. The organometallic compound is applicable as a heterogeneous Au(III) catalyst with high chemical stabilityand recyclability up to 6 times. Copyright © 2018 Elsevier Ltd. All rights reserved.

Zwitterion formation in titan ice analogs: reaction between HC3N and NH3.

PubMed

Couturier-Tamburelli, Isabelle; Sessouma, Bintou; Chiavassa, Thierry; Piétri, Nathalie

2012-11-08

A zwitterion is formed in the laboratory at low temperatures in the solid phase from the thermal reaction of HC(3)N and NH(3). We report for the first time its infrared spectrum. We study its reaction using Fourier transform infrared spectroscopy. Its reaction rate is estimated to be k(T) = 2.9 × 10(5) exp(-2.3 ± 0.1 (kJ mol(-1))/RT). Calculations using density functional theory (B3LYP/6-31g**) are used to characterize all the species (complexes, zwitterions, and transition states) and are in good agreement with the infrared spectra. The structure of the zwitterion is determined planar and it is characterized by a N-C bond around 1.5 Å.

Timed picture naming in seven languages

PubMed Central

BATES, ELIZABETH; D’AMICO, SIMONA; JACOBSEN, THOMAS; SZÉKELY, ANNA; ANDONOVA, ELENA; DEVESCOVI, ANTONELLA; HERRON, DAN; LU, CHING CHING; PECHMANN, THOMAS; PLÉH, CSABA; WICHA, NICOLE; FEDERMEIER, KARA; GERDJIKOVA, IRINI; GUTIERREZ, GABRIEL; HUNG, DAISY; HSU, JEANNE; IYER, GOWRI; KOHNERT, KATHERINE; MEHOTCHEVA, TEODORA; OROZCO-FIGUEROA, ARACELI; TZENG, ANGELA; TZENG, OVID

2012-01-01

Timed picture naming was compared in seven languages that vary along dimensions known to affect lexical access. Analyses over items focused on factors that determine cross-language universals and cross-language disparities. With regard to universals, number of alternative names had large effects on reaction time within and across languages after target–name agreement was controlled, suggesting inhibitory effects from lexical competitors. For all the languages, word frequency and goodness of depiction had large effects, but objective picture complexity did not. Effects of word structure variables (length, syllable structure, compounding, and initial frication) varied markedly over languages. Strong cross-language correlations were found in naming latencies, frequency, and length. Other-language frequency effects were observed (e.g., Chinese frequencies predicting Spanish reaction times) even after within-language effects were controlled (e.g., Spanish frequencies predicting Spanish reaction times). These surprising cross-language correlations challenge widely held assumptions about the lexical locus of length and frequency effects, suggesting instead that they may (at least in part) reflect familiarity and accessibility at a conceptual level that is shared over languages. PMID:12921412

Excellently guarded materials against UV and oxygen in the surfactant molecular complex crystal matrix

NASA Astrophysics Data System (ADS)

Ichikawa, Haruyo; Iimura, Nahoko; Hirata, Hirotaka

2000-07-01

Crystalline surfactant molecular complexes (SCMs) generated between quaternary ammonium cationic surfactants such as CTAB and various additives disclose their excellent protective properties from UV light and oxygen to complex additive materials, which are occluded in the complex crystal matrix. The effects of UV and oxygen were followed by the absorption decay of additive chromophores in comparing that of naked additive specimens with that of those in the complexed state. From the decay profiles, the rate constants and the half-life times were estimated under the assumptions in which the photo and oxidation processes were dominated in accordance with the first-ordered reaction. The results afford us promising prospects in extending the shelf-life of every material, above all medicinal drug, with the consequence that these obtained values evidently demonstrate the remarkably suppressed rate and extremely elongated half-life times.

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

Chen, L. X.; Zhang, X.; Lockard, J. V.

Transient molecular structures along chemical reaction pathways are important for predicting molecular reactivity, understanding reaction mechanisms, as well as controlling reaction pathways. During the past decade, X-ray transient absorption spectroscopy (XTA, or LITR-XAS, laser-initiated X-ray absorption spectroscopy), analogous to the commonly used optical transient absorption spectroscopy, has been developed. XTA uses a laser pulse to trigger a fundamental chemical process, and an X-ray pulse(s) to probe transient structures as a function of the time delay between the pump and probe pulses. Using X-ray pulses with high photon flux from synchrotron sources, transient electronic and molecular structures of metal complexes havemore » been studied in disordered media from homogeneous solutions to heterogeneous solution-solid interfaces. Several examples from the studies at the Advanced Photon Source in Argonne National Laboratory are summarized, including excited-state metalloporphyrins, metal-to-ligand charge transfer (MLCT) states of transition metal complexes, and charge transfer states of metal complexes at the interface with semiconductor nanoparticles. Recent developments of the method are briefly described followed by a future prospective of XTA. It is envisioned that concurrent developments in X-ray free-electron lasers and synchrotron X-ray facilities as well as other table-top laser-driven femtosecond X-ray sources will make many breakthroughs and realise dreams of visualizing molecular movies and snapshots, which ultimately enable chemical reaction pathways to be controlled.« less

Criticality and Induction Time of Hot Spots in Detonating Heterogeneous Explosives

NASA Astrophysics Data System (ADS)

Hill, Larry

2017-06-01

Detonation reaction in physically heterogeneous explosives is-to an extent that depends on multiple material attributes-likewise heterogeneous. Like all heterogeneous reaction, detonation heterogeneous reaction begins at nucleation sites, which, in this case, comprise localized regions of higher-than-average temperature-so-called hot spots. Burning grows at, and then spreads from these nucleation sites, via reactive-thermal (R-T) waves, to consume the interstitial material. Not all hot spots are consequential, but only those that are 1) supercritical, and 2) sufficiently so as to form R-T waves before being consumed by those already emanating from neighboring sites. I explore aspects of these two effects by deriving simple formulae for hot spot criticality and the induction time of supercritical hot spots. These results serve to illustrate the non-intuitive, yet mathematically simplifying, effects of extreme dependence of reaction rate upon temperature. They can play a role in the development of better reactive burn models, for which we seek to homogenize the essentials of heterogeneous detonation reaction without introducing spurious complexity. Work supported by the US Dept. of Energy.

Scramjet Combustor Simulations Using Reduced Chemical Kinetics for Practical Fuels

DTIC Science & Technology

2003-12-01

the aerospace industry in reducing prototype and testing costs and the time needed to bring products to market . Accurate simulation of chemical...JP-8 kinetics and soot models into the UNICORN CFD code (Montgomery et al., 2003a) NSF Phase I and II SBIRs for development of a computer-assisted...divided by diameter QSS quasi-steady state REI Reaction Engineering International UNICORN UNsteady Ignition and COmbustion with ReactioNs VULCAN Viscous Upwind aLgorithm for Complex flow ANalysis

General Synthesis of Alkenyl Sulfides by Palladium-Catalyzed Thioetherification of Alkenyl Halides and Tosylates.

PubMed

Velasco, Noelia; Virumbrales, Cintia; Sanz, Roberto; Suárez-Pantiga, Samuel; Fernández-Rodríguez, Manuel A

2018-05-08

The cross-coupling reaction of alkenyl bromides with thiols catalyzed by palladium complexes derived from inexpensive dppf ligand is reported. These reactions occur under low catalyst loading and in high yields and display wide scope, including the coupling of bulky thiols and trisubstituted bromoolefins, and functional group tolerance. In addition, the thioetherification of less reactive chloroalkenes and, for the first time, alkenyl tosylates was accomplished using a catalyst generated from CyPF tBu alkylbisphosphine ligand.

A kinetic study of jack-bean urease denaturation by a new dithiocarbamate bismuth compound

NASA Astrophysics Data System (ADS)

Menezes, D. C.; Borges, E.; Torres, M. F.; Braga, J. P.

2012-10-01

A kinetic study concerning enzymatic inhibitory effect of a new bismuth dithiocarbamate complex on jack-bean urease is reported. A neural network approach is used to solve the ill-posed inverse problem arising from numerical treatment of the subject. A reaction mechanism for the urease denaturation process is proposed and the rate constants, relaxation time constants, equilibrium constants, activation Gibbs free energies for each reaction step and Gibbs free energies for the transition species are determined.

Time-controlled synthesis mechanism analysis of kesterite-phased Cu2ZnSnS4 nanorods via colloidal route

NASA Astrophysics Data System (ADS)

Jain, Shefali; Singh, Dinesh; Vijayan, N.; Sharma, Shailesh Narain

2018-05-01

In this work, stable Cu2ZnSnS4 (CZTS) nanocrystals (NCs) in pure kesterite phase were synthesized by a facile one-pot rapid injection technique (colloidal route). Time-dependent reaction mechanism for the synthesis of CZTS nanoparticles is explained. When TOP-S (Tri-octyl phosphine-sulphur) was injected in the CuZnSn-complex with TOPO (Tri-octyl phosphine oxide) as capping ligand, orthorhombic phase Cu2-X S nanoparticles of spherical shape were found at nucleation sites. With an advancement in the reaction time, Sn got infused in Cu2-X S to form Cu2SnS3 and its shape got deformed. Further increase in reaction time infuses Zn to form Cu2ZnSnS4 with the gradual vanishing of Cu2-X S and Cu2SnS3 phases and finally, the rod-shaped CZTS Np's were obtained. This factor of reaction time, which influence the morphology and size were studied in detail. The structural and optical properties of the pure kesterite phase CZTS nanorods were also analysed. The band gap of the rod-like CZTS is determined to be around 1.43 eV, which is an optimum value for solar photoelectric conversion.

Reaction front dynamics under shear flow for arbitrary Damköhler numbers

NASA Astrophysics Data System (ADS)

Bandopadhyay, Aditya; Méheust, Yves; Le Borgne, Tanguy

2016-04-01

Reaction fronts where two reactive fluids displace one another play an important role in a range of applications, including contaminant plume transport and reaction, soil and aquifer remediation, CO2 sequestration, geothermal dipoles and the development of hotspots of reaction in mixing zones. The background flow induces enhanced mixing, and therefore reaction, through interfacial shear. Hence the coupling of fluid flow with chemical reactions is pivotal in understanding and quantifying effective reaction kinetics in reaction fronts. While this problem has been addressed in the limit of fast reactions (e.g. de Simoni 2005, Le Borgne 2014), in natural systems reactions can span a large range of Damköhler numbers since their characteristic reaction times vary over a large range of typical values. Here the coupling of shear flow and reversible chemical reactions is studied for a reaction front with initially separated reactants at arbitrary Damköhler numbers. Approximate analytical expressions for the global production rate are derived based on a reactive lamella approach. We observe three distinct regimes, each of them characterized by different scalings of the global production rate and width of the reactive zone. We describe the dependency of these scalings and the associated characteristic transition times as a function of Damköhler and Péclet numbers. These results are validated against 2D numerical simulations. The study is expected to shed light on the inherently complex cases of reactive mixing with varying reaction rates under the influence of an imposed flow. de Simoni et al. (2005) Water Resour. Res., 41, W11410 Le Borgne et al. (2014) GRL, 41(22), 7898

Spectrophotometric Determination of 6-Propyl-2-Thiouracil in Pharmaceutical Formulations Based on Prussian Blue Complex Formation: An Undergraduate Instrumental Analysis Laboratory Experiment

ERIC Educational Resources Information Center

Zakrzewski, Robert; Skowron, Monika; Ciesielski, Witold; Rembisz, Zaneta

2016-01-01

The laboratory experiment challenges students to determine 6-propyl-2-thiouracil (PTU) based on Prussian blue complex formation. Prussian blue is formed by ferricyanide and Fe(II) ions which are generated in situ from Fe(III) ions reduced by PTU. The absorbance of this product was measured at a wavelength of 840 nm, after a reaction time of 30…

Simulation of the mobility of metal - EDTA complexes in groundwater: The influence of contaminant metals

USGS Publications Warehouse

Friedly, J.C.; Kent, D.B.; Davis, J.A.

2002-01-01

Reactive transport simulations were conducted to model chemical reactions between metal - EDTA (ethylenediaminetetraacetic acid) complexes during transport in a mildly acidic quartz - sand aquifer. Simulations were compared with the results of small-scale tracer tests wherein nickel-, zinc-, and calcium - EDTA complexes and free EDTA were injected into three distinct chemical zones of a plume of sewage-contaminated groundwater. One zone had a large mass of adsorbed, sewage-derived zinc; one zone had a large mass of adsorbed manganese resulting from mildly reducing conditions created bythe sewage plume; and one zone had significantly less adsorbed manganese and negligible zinc background. The chemical model assumed that the dissolution of iron(III) from metal - hydroxypolymer coatings on the aquifer sediments by the metal - EDTA complexes was kinetically restricted. All other reactions, including metal - EDTA complexation, zinc and manganese adsorption, and aluminum hydroxide dissolution were assumed to reach equilibrium on the time scale of transport; equilibrium constants were either taken from the literature or determined independently in the laboratory. A single iron(III) dissolution rate constant was used to fit the breakthrough curves observed in the zone with negligible zinc background. Simulation results agreed well with the experimental data in all three zones, which included temporal moments derived from breakthrough curves at different distances downgradient from the injections and spatial moments calculated from synoptic samplings conducted at different times. Results show that the tracer cloud was near equilibrium with respect to Fe in the sediment after 11 m of transport in the Zn-contaminated region but remained far from equilibrium in the other two zones. Sensitivity studies showed that the relative rate of iron(III) dissolution by the different metal - EDTA complexes was less important than the fact that these reactions are rate controlled. Results suggest that the published solubility for ferrihydrite reasonably approximates the Fe solubility of the hydroxypolymer coatings on the sediments. Aluminum may be somewhat more soluble than represented by the equilibrium constant for gibbsite, and its dissolution may be rate controlled when reacting with Ca - EDTA complexes.

Inside out: Speed-dependent barriers to reactive mixing

NASA Astrophysics Data System (ADS)

Kelley, Douglas; Nevins, Thomas

2015-11-01

Reactive mixing occurs wherever fluid flow and chemical or biological growth interact over time and space. Those interactions often lead to steep gradients in reactant and product concentration, arranged in complex spatial structures that can cause wide variation in the global reaction rate and concentrations. By simultaneously measuring fluid velocity and reaction front locations in laboratory experiments with the Belousov-Zhabotinsky reaction, we find that the barriers defining those structures vary dramatically with speed. In particular, we find that increasing flow speed causes reacted regions to move from vortex edges to vortex cores, thus turning the barriers ``inside out''. This observation has implications for reactive mixing of phytoplankton in global oceans.

Low-Cost Robotic Assessment of Visuo-Motor Deficits in Alzheimer's Disease.

PubMed

Bartoli, Eleonora; Caso, Francesca; Magnani, Giuseppe; Baud-Bovy, Gabriel

2017-07-01

A low-cost robotic interface was used to assess the visuo-motor performance of patients with Alzheimer's disease (AD). Twenty AD patients and twenty age-matched controls participated in this work. The battery of tests included simple reaction times, position tracking, and stabilization tasks performed with both hands. The regularity, velocity, visual and haptic feedback were manipulated to vary movement complexity. Reaction times and movement tracking error were analyzed. Results show a marked group effect on a subset of conditions, in particular when the patients could not rely on the visual feedback of hand movement. The visuo-motor performance correlated with the measures of global cognitive functioning and with different memory-related abilities. Our results support the hypothesis that the ability to recall and use visuo-spatial associations might underlie the impairment in complex motor behavior that has been reported in AD patients. Importantly, the patients had preserved learning effects across sessions, which might relate to visuo-motor deficits being less evident in every-day life and clinical assessments. This robotic assessment, lasting less than 1 h, provides detailed information about the integrity of visuo-motor abilities. The data can aid the understanding of the complex pattern of deficits that characterizes this pervasive disease.

Divergent pathways in the reaction of Fischer carbenes and palladium.

PubMed

López-Alberca, María P; Mancheño, María J; Fernandez, Israel; Gómez-Gallego, Mar; Sierra, Miguel A; Torres, Rosario

2007-04-26

[reaction: see text] The Pd-catalyzed reaction of beta-arylaminochromium(0) carbene complexes produces by transmetalation the first isolated and X-ray structurally characterized bis-Pd(II) carbene complex, as well as other alternative reaction pathways, such as the oxidative addition-transmetalation sequence, not seen before in this chemistry.

Modeling competitive substitution in a polyelectrolyte complex

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

Peng, B.; Muthukumar, M., E-mail: muthu@polysci.umass.edu

2015-12-28

We have simulated the invasion of a polyelectrolyte complex made of a polycation chain and a polyanion chain, by another longer polyanion chain, using the coarse-grained united atom model for the chains and the Langevin dynamics methodology. Our simulations reveal many intricate details of the substitution reaction in terms of conformational changes of the chains and competition between the invading chain and the chain being displaced for the common complementary chain. We show that the invading chain is required to be sufficiently longer than the chain being displaced for effecting the substitution. Yet, having the invading chain to be longermore » than a certain threshold value does not reduce the substitution time much further. While most of the simulations were carried out in salt-free conditions, we show that presence of salt facilitates the substitution reaction and reduces the substitution time. Analysis of our data shows that the dominant driving force for the substitution process involving polyelectrolytes lies in the release of counterions during the substitution.« less

Edible carbohydrates from formaldehyde in a spacecraft

NASA Technical Reports Server (NTRS)

Weiss, A. H.

1975-01-01

The autocatalytic nature of the base catalyzed condensation of formaldehyde to formose sugars is eliminated by using as a cocatalyst, an aldose, or ketose having an alpha-hydrogen. This is more strongly complexed by base than is formaldehyde and the cocatalyst and sugar products accumulate as catalyst complexes instead of formaldehyde. Because of the presence of alpha-hydrogen atoms in cocatalysts and formose sugars, their removal by cross Cannizzaro reaction of complexed sugars does not occur, so the formose reaction behaves autocatalytically due to this accumulation. It is believed that a given catalytic formose complex is not a discrete complexed sugar, but rather, a scrambled dynamic mixture of sugars having weakened structures. The sugar complexes derive from a common salt-like formaldehyde complex, which, because of the absence of alpha-hydrogen, has a greater tendency to undergo Cannizzaro reaction, rather than formose condensation. Because of this, the Cannizzaro reaction can proceed without measurable formose condensation. The reverse is not possible.

A multi-species reactive transport model to estimate biogeochemical rates based on single-well push-pull test data

NASA Astrophysics Data System (ADS)

Phanikumar, Mantha S.; McGuire, Jennifer T.

2010-08-01

Push-pull tests are a popular technique to investigate various aquifer properties and microbial reaction kinetics in situ. Most previous studies have interpreted push-pull test data using approximate analytical solutions to estimate (generally first-order) reaction rate coefficients. Though useful, these analytical solutions may not be able to describe important complexities in rate data. This paper reports the development of a multi-species, radial coordinate numerical model (PPTEST) that includes the effects of sorption, reaction lag time and arbitrary reaction order kinetics to estimate rates in the presence of mixing interfaces such as those created between injected "push" water and native aquifer water. The model has the ability to describe an arbitrary number of species and user-defined reaction rate expressions including Monod/Michelis-Menten kinetics. The FORTRAN code uses a finite-difference numerical model based on the advection-dispersion-reaction equation and was developed to describe the radial flow and transport during a push-pull test. The accuracy of the numerical solutions was assessed by comparing numerical results with analytical solutions and field data available in the literature. The model described the observed breakthrough data for tracers (chloride and iodide-131) and reactive components (sulfate and strontium-85) well and was found to be useful for testing hypotheses related to the complex set of processes operating near mixing interfaces.

Step-by-Step Simulation of Radiation Chemistry Using Green Functions for Diffusion-Influenced Reactions

NASA Technical Reports Server (NTRS)

Plante, Ianik; Cucinotta, Francis A.

2011-01-01

Radiolytic species are formed approximately 1 ps after the passage of ionizing radiation through matter. After their formation, they diffuse and chemically react with other radiolytic species and neighboring biological molecules, leading to various oxidative damage. Therefore, the simulation of radiation chemistry is of considerable importance to understand how radiolytic species damage biological molecules [1]. The step-by-step simulation of chemical reactions is difficult, because the radiolytic species are distributed non-homogeneously in the medium. Consequently, computational approaches based on Green functions for diffusion-influenced reactions should be used [2]. Recently, Green functions for more complex type of reactions have been published [3-4]. We have developed exact random variate generators of these Green functions [5], which will allow us to use them in radiation chemistry codes. Moreover, simulating chemistry using the Green functions is which is computationally very demanding, because the probabilities of reactions between each pair of particles should be evaluated at each timestep [2]. This kind of problem is well adapted for General Purpose Graphic Processing Units (GPGPU), which can handle a large number of similar calculations simultaneously. These new developments will allow us to include more complex reactions in chemistry codes, and to improve the calculation time. This code should be of importance to link radiation track structure simulations and DNA damage models.

Role of Mediator and Effects of Temperature on ortho-C-N Bond Fusion Reactions of Aniline Using Ruthenium Templates: Isolation and Characterization of New Ruthenium Complexes of the in-Situ-Generated Ligands.

PubMed

Roy, Suman K; Sengupta, Debabrata; Rath, Santi Prasad; Saha, Tanushri; Samanta, Subhas; Goswami, Sreebrata

2017-05-01

In this work, ortho-C-N bond fusion reactions of aniline are followed by the use of two different ruthenium mediators. Reaction of aniline with [Ru III (terpy)Cl 3 ] (terpy = 2,2':6',2″-terpyridine) resulted in a trans bis-aniline ruthenium(II) complex [1] + which upon oxidation with H 2 O 2 produced compound [2] + of a bidentate ligand, N-phenyl-1,2-benzoquinonediimine, due to an oxidative ortho-C-N bond fusion reaction. Complex [1] + and aniline (neat) at 185 °C produced a bis-chelated ruthenium complex (3). A previously reported complex [Ru II (N-phenyl-1,2-benzoquinonediimine)(aniline) 2 (Cl) 2 ] (5) undergoes similar oxidation by air at 185 °C to produce complex [3]. A separate chemical reaction between aniline and strongly oxidizing tetra-n-propylammonium perruthenate [(n-pr) 4 N] + [RuO 4 ] - in air produced a ruthenium complex [4] of a N 4 -tetraamidophenylmacrocycle ligand via multiple ortho-C-N bond fusion reaction. Notably, the yield of this product is low (5%) at 100 °C but increases to 25% in refluxing aniline. All these complexes are characterized fully by their physicochemical characterizations and X-ray structure determination. From their structural parameters and other spectroscopic studies, complex [2] + is assigned as [Ru II (terpy)(N-phenyl-1,2-benzoquinonediimine)(Cl)] + whereas complex [4] is described as a ruthenium(VI) complex comprised of a reduced deprotonated N-phenyl-1,2-diamidobenzene and N 4 -tetraamidophenylmacrocyclic ligand. Complex [2] + exhibits one reversible oxidation at 1.32 V and one reversible reduction at -0.75 V vs Ag/AgCl reference electrode. EPR of the electrogenerated complexes has revealed that the oxidized complex is a ruthenium(III) complex with an axial EPR spectrum at g av = 2.06. The reduced complex [2], on the other hand, shows a single-line EPR signal at g av = 1.998. In contrast, complex [4] shows two successive one-electron oxidation waves at 0.5 and 0.8 V and an irreversible reduction wave at -0.9 V. EPR studies of the oxidized complexes [4] + and [4] 2+ reveal that oxidations are ligand centered. DFT calculations were employed to elucidate the electronic structures as well as the redox processes associated with the above complexes. Aerial ortho-C-N bond fusion reactions of aniline using two different mediators, viz. [Ru III (terpy)Cl 3 ] and [(n-pr) 4 N] + [RuO 4 ] - , have been followed. It is found that in the case of oxidizable Ru(III) mediator complex, C-N bond fusion is limited only to dimerization reaction whereas the high-valent Ru(VII) salt mediates multiple C-N bond fusion reactions leading to the formation of a novel tetradentate N 4 -tetraamidophenylmacrocyclic ligand. Valence ambiguity in the complexes of the resultant redox-active ligands is scrutinized.

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

PubMed

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

2017-03-09

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

Reaction intermediates in the catalytic Gif-type oxidation from nuclear inelastic scattering

NASA Astrophysics Data System (ADS)

Rajagopalan, S.; Asthalter, T.; Rabe, V.; Laschat, S.

2016-12-01

Nuclear inelastic scattering (NIS) of synchrotron radiation, also known as nuclear resonant vibrational spectroscopy (NRVS), has been shown to provide valuable insights into metal-centered vibrations at Mössbauer-active nuclei. We present a study of the iron-centered vibrational density of states (VDOS) during the first step of the Gif-type oxidation of cyclohexene with a novel trinuclear Fe3(μ 3-O) complex as catalyst precursor. The experiments were carried out on shock-frozen solutions for different combinations of reactants: Fe3(μ 3-O) in pyridine solution, Fe3(μ 3-O) plus Zn/acetic acid in pyridine without and with addition of either oxygen or cyclohexene, and Fe3(μ 3-O)/Zn/acetic acid/pyridine/cyclohexene (reaction mixture) for reaction times of 1 min, 5 min, and 30 min. The projected VDOS of the Fe atoms was calculated on the basis of pseudopotential density functional calculations. Two possible reaction intermediates were identified as [Fe(III)(C5H5N)2(O2CCH3)2]+ and Fe(II)(C5H5N)4(O2CCH3)2, yielding evidence that NIS (NRVS) allows to identify the presence of iron-centered intermediates also in complex reaction mixtures.

Photochemical Reactions of (n(5)-Pentamethylcyclpentadienyl)-Dicarbonyliron-Alkyl and -Silyl Complexes: Reversible Ethylene Insertion into an Iron-Silicon Bond and Implications for the Mechanism of Transition Metal-Catalyzed Hydrosilation of Alkenes.

DTIC Science & Technology

1985-12-11

RD-R162 462 PHOTOCHEMICAL REACTIONS OF(N(S)-P NTANETNYLCVCLPENTADIENYL)-DICARRONVLIR.. (U) MASSACHUSETTS INST OF TECH CAMBRIDGE DEPT OF CHEMISTRY...34 Photochemical Reactions of (n5-Pentamethylcyclpentadienyl)- Dicarbonyliron-Alkyl and -Silyl Complexes: Reversible Ethylene Insertion into an Iron-Silicon Bond...Chemical Society) PHOTOCHEMICAL REACTIONS OF (n5-PENTAMETHYLCYCLOPENTADIENYL)- DICARBONYLIRON-ALKYL AND -SILYL COMPLEXES: REVERSIBLE ETHYLENE INSERTION INTO

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.

On the theory of time dilation in chemical kinetics

NASA Astrophysics Data System (ADS)

Baig, Mirza Wasif

2017-10-01

The rates of chemical reactions are not absolute but their magnitude depends upon the relative speeds of the moving observers. This has been proved by unifying basic theories of chemical kinetics, which are transition state theory, collision theory, RRKM and Marcus theory, with the special theory of relativity. Boltzmann constant and energy spacing between permitted quantum levels of molecules are quantum mechanically proved to be Lorentz variant. The relativistic statistical thermodynamics has been developed to explain quasi-equilibrium existing between reactants and activated complex. The newly formulated Lorentz transformation of the rate constant from Arrhenius equation, of the collision frequency and of the Eyring and Marcus equations renders the rate of reaction to be Lorentz variant. For a moving observer moving at fractions of the speed of light along the reaction coordinate, the transition state possess less kinetic energy to sweep translation over it. This results in the slower transformation of reactants into products and in a stretched time frame for the chemical reaction to complete. Lorentz transformation of the half-life equation explains time dilation of the half-life period of chemical reactions and proves special theory of relativity and presents theory in accord with each other. To demonstrate the effectiveness of the present theory, the enzymatic reaction of methylamine dehydrogenase and radioactive disintegration of Astatine into Bismuth are considered as numerical examples.

Dynamics and control of gold-encapped gallium arsenide nanowires imaged by 4D electron microscopy

PubMed Central

Chen, Bin; Fu, Xuewen; Tang, Jau; Lysevych, Mykhaylo; Tan, Hark Hoe; Jagadish, Chennupati; Zewail, Ahmed H.

2017-01-01

Eutectic-related reaction is a special chemical/physical reaction involving multiple phases, solid and liquid. Visualization of a phase reaction of composite nanomaterials with high spatial and temporal resolution provides a key understanding of alloy growth with important industrial applications. However, it has been a rather challenging task. Here, we report the direct imaging and control of the phase reaction dynamics of a single, as-grown free-standing gallium arsenide nanowire encapped with a gold nanoparticle, free from environmental confinement or disturbance, using four-dimensional (4D) electron microscopy. The nondestructive preparation of as-grown free-standing nanowires without supporting films allows us to study their anisotropic properties in their native environment with better statistical character. A laser heating pulse initiates the eutectic-related reaction at a temperature much lower than the melting points of the composite materials, followed by a precisely time-delayed electron pulse to visualize the irreversible transient states of nucleation, growth, and solidification of the complex. Combined with theoretical modeling, useful thermodynamic parameters of the newly formed alloy phases and their crystal structures could be determined. This technique of dynamical control aided by 4D imaging of phase reaction processes on the nanometer-ultrafast time scale opens new venues for engineering various reactions in a wide variety of other systems. PMID:29158393

Dynamic reservoir-condition microtomography of reactive transport in complex carbonates: Effect of initial pore structure and initial brine pH

NASA Astrophysics Data System (ADS)

Menke, H. P.; Bijeljic, B.; Blunt, M. J.

2017-05-01

We study the impact of brine acidity and initial pore structure on the dynamics of fluid/solid reaction at high Péclet numbers and low Damköhler numbers. A laboratory μ-CT scanner was used to image the dissolution of Ketton, Estaillades, and Portland limestones in the presence of CO2-acidified brine at reservoir conditions (10 MPa and 50 °C) at two injected acid strengths for a period of 4 h. Each sample was scanned between 6 and 10 times at ∼4 μm resolution and multiple effluent samples were extracted. The images were used as inputs into flow simulations, and analysed for dynamic changes in porosity, permeability, and reaction rate. Additionally, the effluent samples were used to verify the image-measured porosity changes. We find that initial brine acidity and pore structure determine the type of dissolution. Dissolution is either uniform where the porosity increases evenly both spatially and temporally, or occurs as channelling where the porosity increase is concentrated in preferential flow paths. Ketton, which has a relatively homogeneous pore structure, dissolved uniformly at pH = 3.6 but showed more channelized flow at pH = 3.1. In Estaillades and Portland, increasingly complex carbonates, channelized flow was observed at both acidities with the channel forming faster at lower pH. It was found that the effluent pH, which is higher than that injected, is a reasonably good indicator of effective reaction rate during uniform dissolution, but a poor indicator during channelling. The overall effective reaction rate was up to 18 times lower than the batch reaction rate measured on a flat surface at the effluent pH, with the lowest reaction rates in the samples with the most channelized flow, confirming that transport limitations are the dominant mechanism in determining reaction dynamics at the fluid/solid boundary.

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

DOE R&D Accomplishments Database

Marcus, R. A.

1964-01-01

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

Evidence for Carbonate Surface Complexation during Forsterite Carbonation in Wet Supercritical Carbon Dioxide

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

Loring, John S.; Chen, Jeffrey; Benezeth, Pascale

Continental flood basalts are attractive formations for geologic sequestration of carbon dioxide because of their reactive divalent-cation containing silicates, such as forsterite (Mg2SiO4), suitable for long-term trapping of CO2 mineralized as metal carbonates. The goal of this study was to investigate at a molecular level the carbonation products formed during the reaction of forsterite with supercritical CO2 (scCO2) as a function of the concentration of H2O adsorbed to the forsterite surface. Experiments were performed at 50 °C and 90 bar using an in situ IR titration capability, and post-reaction samples were examined by ex situ techniques, including SEM, XPS, FIB-TEM,more » TGA-MS, and MAS-NMR. Carbonation products and reaction extents varied greatly with adsorbed H2O. We show for the first time evidence of Mg-carbonate surface complexation under wet scCO2 conditions. Carbonate is found to be coordinated to Mg at the forsterite surface in a predominately bidentate fashion at adsorbed H2O concentrations below 27 µmol/m2. Above this concentration and up to 76 µmol/m2, monodentate coordinated complexes become dominant. Beyond a threshold adsorbed H2O concentration of 76 µmol/m2, crystalline carbonates continuously precipitate as magnesite, and the particles that form are hundreds of times larger than the estimated thicknesses of the adsorbed water films of about 7 to 15 Å. At an applied level, the implication of these results is that mineral trapping in scCO2 dominated fluids will be insignificant and limited to surface complexation unless adsorbed H2O concentrations are high enough to promote crystalline carbonate formation. At a fundamental level, the surface complexes and their dependence on adsorbed H2O concentration give insights regarding forsterite dissolution processes and magnesite nucleation and growth.« less

Evidence for Carbonate Surface Complexation during Forsterite Carbonation in Wet Supercritical Carbon Dioxide

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

Loring, John S.; Chen, Jeffrey; Benezeth Ep Gisquet, Pascale

Continental flood basalts are attractive formations for geologic sequestration of carbon dioxide because of their reactive divalent-cation containing silicates, such as forsterite (Mg2SiO4), suitable for long-term trapping of CO2 mineralized as metal carbonates. The goal of this study was to investigate at a molecular level the carbonation products formed during the reaction of forsterite with supercritical CO2 (scCO2) as a function of the concentration of H2O adsorbed to the forsterite surface. Experiments were performed at 50 °C and 90 bar using an in situ IR titration capability, and post-reaction samples were examined by ex situ techniques, including SEM, XPS, FIB-TEM,more » TGA-MS, and MAS-NMR. Carbonation products and reaction extents varied greatly with adsorbed H2O. We show for the first time evidence of Mg-carbonate surface complexation under wet scCO2 conditions. Carbonate is found to be coordinated to Mg at the forsterite surface in a predominately bidentate fashion at adsorbed H2O concentrations below 27 µmol/m2. Above this concentration and up to 76 µmol/m2, monodentate coordinated complexes become dominant. Beyond a threshold adsorbed H2O concentration of 76 µmol/m2, crystalline carbonates continuously precipitate as magnesite, and the particles that form are hundreds of times larger than the estimated thicknesses of the adsorbed water films of about 7 to 15 Å. At an applied level, these results suggest that mineral carbonation in scCO2 dominated fluids near the wellbore and adjacent to caprocks will be insignificant and limited to surface complexation, unless adsorbed H2O concentrations are high enough to promote crystalline carbonate formation. At a fundamental level, the surface complexes and their dependence on adsorbed H2O concentration give insights regarding forsterite dissolution processes and magnesite nucleation and growth.« less

Calculating the True and Observed Rates of Complex Heterogeneous Catalytic Reactions

NASA Astrophysics Data System (ADS)

Avetisov, A. K.; Zyskin, A. G.

2018-06-01

Equations of the theory of steady-state complex reactions are considered in matrix form. A set of stage stationarity equations is given, and an algorithm is described for deriving the canonic set of stationarity equations with appropriate corrections for the existence of fast stages in a mechanism. A formula for calculating the number of key compounds is presented. The applicability of the Gibbs rule to estimating the number of independent compounds in a complex reaction is analyzed. Some matrix equations relating the rates of dependent and key substances are derived. They are used as a basis to determine the general diffusion stoichiometry relationships between temperature, the concentrations of dependent reaction participants, and the concentrations of key reaction participants in a catalyst grain. An algorithm is described for calculating heat and mass transfer in a catalyst grain with respect to arbitrary complex heterogeneous catalytic reactions.

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

PubMed

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

2013-11-01

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

Structural evidence for the sorption of Ni(II) atoms on the edges of montmorillonite clay minerals: a polarized X-ray absorption fine structure study

NASA Astrophysics Data System (ADS)

Dähn, Rainer; Scheidegger, André M.; Manceau, Alain; Schlegel, Michel L.; Baeyens, Bart; Bradbury, Michael H.; Chateigner, Daniel

The nature of surface complexes formed on Ni uptake onto montmorillonite (a dioctahedral smectite) has been investigated over an extended time period by polarized extended X-ray absorption fine structure (P-EXAFS) spectroscopy. Self-supporting films of Ni-sorbed montmorillonite were prepared by contacting Ni and montmorillonite at pH 7.2, high ionic strength (0.3 M NaClO 4), and low Ni concentration ([Ni] initial = 19.9 μM) for 14- and 360-d reaction time. The resulting Ni concentration on the clay varied from 4 to 7 μmol/g. Quantitative texture analysis indicates that the montmorillonite particles were well orientated with respect to the plane of the film. The full width at half maximum of the orientation distribution of the c* axes of individual clay platelets about the normal to the film plane was 44.3° (14-d reaction time) and 47.1° (360-d reaction time). These values were used to correct the coordination numbers determined by P-EXAFS for texture effects. Ni K-edge P-EXAFS spectra were recorded at angles between the incident beam and the film normal equal to 10, 35, 55, and 80°. Spectral analysis led to the identification of three nearest cationic subshells containing 2.0 ± 0.5 Al at 3.0 Å and 2.0 ± 0.5 Si at 3.12 Å and 4.0 ± 0.5 Si at 3.26 Å. These distances are characteristic of edge-sharing linkages between Al and Ni octahedra and of corner-sharing linkages between Ni octahedra and Si tetrahedra, as in clay structures. The angular dependence of the Ni-Al and Ni-Si contributions indicates that Ni-Al pairs are oriented parallel to the film plane, whereas Ni-Si pairs are not. The study reveals the formation of Ni inner-sphere mononuclear surface complexes located at the edges of montmorillonite platelets and thus that heavy metals binding to edge sites is a possible sorption mechanism for dioctahedral smectites. Data analysis further suggests that either the number of neighboring Al atoms slightly increases from 1.6 to 2 or that the structural order of the observed surface complexes increases from 0.01 Å 2 to 0.005 Å 2 with increasing reaction time. On the basis of the low Ni-Al coordination numbers, it appears that over an extended reaction time period of 1 yr the diffusion of Ni atoms in the octahedral layer is not the major uptake mechanism of Ni onto montmorillonite.

Diffusion-controlled reactions modeling in Geant4-DNA

NASA Astrophysics Data System (ADS)

Karamitros, M.; Luan, S.; Bernal, M. A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H. N.; Stepan, V.; Incerti, S.

2014-10-01

Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k-d tree data structure for quickly locating, for a given molecule, its closest reactants. The performance advantage is presented in terms of complexity, and the accuracy of the new algorithm is demonstrated by simulating radiation chemistry in the context of the Geant4-DNA project. Application The time-dependent radiolytic yields of the main chemical species formed after irradiation are computed for incident protons at different energies (from 50 MeV to 500 keV). Both the time-evolution and energy dependency of the yields are discussed. The evolution, at one microsecond, of the yields of hydroxyls and solvated electrons with respect to the linear energy transfer is compared to theoretical and experimental data. According to our results, at high linear energy transfer, modeling radiation chemistry in the trading compartment representation might be adopted.

Radiochemical study of reactions of alkyl cations with amines. I. Reactions of methyl and sec-butyl cations with diethylamine

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

Ignat`ev, I.S.; Kochina, T.A.; Nefedov, V.D.

1995-08-10

Ion-molecular gas-phase reactions of free methyl and sec-butyl cations with diethylamine were studied. These reactions proceed via two competing pathways involving formation of a condensation complex or a proton-transfer complex, the latter process predominating. 32 refs., 1 tab.

Reaction of atomic hydrogen with formic acid.

PubMed

Cao, Qian; Berski, Slawomir; Latajka, Zdzislaw; Räsänen, Markku; Khriachtchev, Leonid

2014-04-07

We study the reaction of atomic hydrogen with formic acid and characterize the radical products using IR spectroscopy in a Kr matrix and quantum chemical calculations. The reaction first leads to the formation of an intermediate radical trans-H2COOH, which converts to the more stable radical trans-cis-HC(OH)2via hydrogen atom tunneling on a timescale of hours at 4.3 K. These open-shell species are observed for the first time as well as a reaction between atomic hydrogen and formic acid. The structural assignment is aided by extensive deuteration experiments and ab initio calculations at the UMP2 and UCCSD(T) levels of theory. The simplest geminal diol radical trans-cis-HC(OH)2 identified in the present work as the final product of the reaction should be very reactive, and further reaction channels are of particular interest. These reactions and species may constitute new channels for the initiation and propagation of more complex organic species in the interstellar clouds.

Cognitive demand of human sensorimotor performance during an extended space mission: a dual-task study.

PubMed

Bock, Otmar; Weigelt, Cornelia; Bloomberg, Jacob J

2010-09-01

Two previous single-case studies found that the dual-task costs of manual tracking plus memory search increased during a space mission, and concluded that sensorimotor deficits during spaceflight may be related to cognitive overload. Since dual-task costs were insensitive to the difficulty of memory search, the authors argued that the overload may reflect stress-related problems of multitasking, rather than a scarcity of specific cognitive resources. Here we expand the available database and compare different types of concurrent task. Three subjects were repeatedly tested before, during, and after an extended mission on the International Space Station (ISS). They performed an unstable tracking task and four reaction-time tasks, both separately and concurrently. Inflight data could only be obtained during later parts of the mission. The tracking error increased from pre- to in flight by a factor of about 2, both under single- and dual-task conditions. The dual-task costs with a reaction-time task requiring rhythm production was 2.4 times higher than with a reaction-time task requiring visuo-spatial transformations, and 8 times higher than with a regular choice reaction-time task. Long-term sensorimotor deficits during spaceflight may reflect not only stress, but also a scarcity of resources related to complex motor programming; possibly those resources are tied up by sensorimotor adaptation to the space environment.

Electron-transfer reactions of cobalt(III) complexes. 1. The kinetic investigation of the reduction of various surfactant cobalt(III) complexes by iron(II) in surface active ionic liquids

NASA Astrophysics Data System (ADS)

Nagaraj, Karuppiah; Senthil Murugan, Krishnan; Thangamuniyandi, Pilavadi; Sakthinathan, Subramanian

2015-05-01

The kinetics of outer sphere electron transfer reaction of surfactant cobalt(III) complex ions, cis-[Co(en)2(C12H25NH2)2]3+ (1), cis-[Co(dp)2(C12H25NH2)2]3+ (2), cis-[Co(trien)(C12H25NH2)2]3+ (3), cis-[Co(bpy)2(C12H25NH2)2]3+ (4) and cis-[Co(phen)2(C12H25NH2)2]3+ (5) (en: ethylenediamine, dp: diaminopropane, trien : triethylenetetramine, bpy: 2,2‧-bipyridyl, phen: 1,10-phenanthroline and C12H25NH2 : dodecylamine) have been interrogated by Fe2+ ion in ionic liquid (1-butyl-3-methylimidazoliumbromide) medium at different temperatures (298, 303, 308, 313, 318 and 323 K) by the spectrophotometry method under pseudo first order conditions using an excess of the reductant. Experimentally the reactions were found to be of second order and the electron transfer as outer sphere. The second order rate constant for the electron transfer reaction in ionic liquids was found to increase with increase in the concentration of all these surfactant cobalt(III) complexes. Among these complexes (from en to phen ligand), complex containing the phenanthroline ligand rate is higher compared to other complexes. By assuming the outer sphere mechanism, the results have been explained based on the presence of aggregated structures containing cobalt(III) complexes at the surface of ionic liquids formed by the surfactant cobalt(III) complexes in the reaction medium. The activation parameters (enthalpy of activation ΔH‡ and entropy of activation ΔS‡) of the reaction have been calculated which substantiate the kinetics of the reaction.

Reductive Elimination from Phosphine-Ligated Alkylpalladium(II) Amido Complexes To Form sp3 Carbon-Nitrogen Bonds.

PubMed

Peacock, D Matthew; Jiang, Quan; Hanley, Patrick S; Cundari, Thomas R; Hartwig, John F

2018-04-11

We report the formation of phosphine-ligated alkylpalladium(II) amido complexes that undergo reductive elimination to form alkyl-nitrogen bonds and a combined experimental and computational investigation of the factors controlling the rates of these reactions. The free-energy barriers to reductive elimination from t-Bu 3 P-ligated complexes were significantly lower (ca. 3 kcal/mol) than those previously reported from NHC-ligated complexes. The rates of reactions from complexes containing a series of electronically and sterically varied anilido ligands showed that the reductive elimination is slower from complexes of less electron-rich or more sterically hindered anilido ligands than from those containing more electron-rich and less hindered anilido ligands. Reductive elimination of alkylamines also occurred from complexes bearing bidentate P,O ligands. The rates of reactions of these four-coordinate complexes were slower than those for reactions of the three-coordinate, t-Bu 3 P-ligated complexes. The calculated pathway for reductive elimination from rigid, 2-methoxyarylphosphine-ligated complexes does not involve initial dissociation of the oxygen. Instead, reductive elimination is calculated to occur directly from the four-coordinate complex in concert with a lengthening of the Pd-O bond. To investigate this effect experimentally, a four-coordinate Pd(II) anilido complex containing a flexible, aliphatic linker between the P and O atoms was synthesized. Reductive elimination from this complex was faster than that from the analogous complex containing the more rigid, aryl linker. The flexible linker enables full dissociation of the ether ligand during reductive elimination, leading to the faster reaction of this complex.

Nanoscale Reaction Vessels Designed for Synthesis of Copper-Drug Complexes Suitable for Preclinical Development

PubMed Central

Wehbe, Mohamed; Anantha, Malathi; Backstrom, Ian; Leung, Ada; Chen, Kent; Malhotra, Armaan; Edwards, Katarina; Bally, Marcel B.

2016-01-01

The development of copper-drug complexes (CDCs) is hindered due to their very poor aqueous solubility. Diethyldithiocarbamate (DDC) is the primary metabolite of disulfiram, an approved drug for alcoholism that is being repurposed for cancer. The anticancer activity of DDC is dependent on complexation with copper to form copper bis-diethyldithiocarbamate (Cu(DDC)2), a highly insoluble complex that has not been possible to develop for indications requiring parenteral administration. We have resolved this issue by synthesizing Cu(DDC)2 inside liposomes. DDC crosses the liposomal lipid bilayer, reacting with the entrapped copper; a reaction that can be observed through a colour change as the solution goes from a light blue to dark brown. This method is successfully applied to other CDCs including the anti-parasitic drug clioquinol, the natural product quercetin and the novel targeted agent CX-5461. Our method provides a simple, transformative solution enabling, for the first time, the development of CDCs as viable candidate anticancer drugs; drugs that would represent a brand new class of therapeutics for cancer patients. PMID:27055237

Nanoscale Reaction Vessels Designed for Synthesis of Copper-Drug Complexes Suitable for Preclinical Development.

PubMed

Wehbe, Mohamed; Anantha, Malathi; Backstrom, Ian; Leung, Ada; Chen, Kent; Malhotra, Armaan; Edwards, Katarina; Bally, Marcel B

2016-01-01

The development of copper-drug complexes (CDCs) is hindered due to their very poor aqueous solubility. Diethyldithiocarbamate (DDC) is the primary metabolite of disulfiram, an approved drug for alcoholism that is being repurposed for cancer. The anticancer activity of DDC is dependent on complexation with copper to form copper bis-diethyldithiocarbamate (Cu(DDC)2), a highly insoluble complex that has not been possible to develop for indications requiring parenteral administration. We have resolved this issue by synthesizing Cu(DDC)2 inside liposomes. DDC crosses the liposomal lipid bilayer, reacting with the entrapped copper; a reaction that can be observed through a colour change as the solution goes from a light blue to dark brown. This method is successfully applied to other CDCs including the anti-parasitic drug clioquinol, the natural product quercetin and the novel targeted agent CX-5461. Our method provides a simple, transformative solution enabling, for the first time, the development of CDCs as viable candidate anticancer drugs; drugs that would represent a brand new class of therapeutics for cancer patients.

Synthesis and characterization of water-soluble hydroxybutenyl cyclomaltooligosaccharides (cyclodextrins).

PubMed

Buchanan, Charles M; Alderson, Susan R; Cleven, Curtis D; Dixon, Daniel W; Ivanyi, Robert; Lambert, Juanelle L; Lowman, Douglas W; Offerman, Rick J; Szejtli, Jozsef; Szente, Lajos

2002-03-15

We have examined the synthesis of hydroxybutenyl cyclomaltooligosaccharides (cyclodextrins) and the ability of these cyclodextrin ethers to form guest-host complexes with guest molecules. The hydroxybutenyl cyclodextrin ethers were prepared by a base-catalyzed reaction of 3,4-epoxy-1-butene with the parent cyclodextrins in an aqueous medium. Reaction byproducts were removed by nanofiltration before the hydroxybutenyl cyclodextrins were isolated by co-evaporation of water-EtOH. Hydroxybutenyl cyclodextrins containing no unsubstituted parent cyclodextrin typically have a degree of substitution of 2-4 and a molar substitution of 4-7. These hydroxybutenyl cyclodextrins are randomly substituted, amorphous solids. The hydroxybutenyl cyclodextrin ethers were found to be highly water soluble. Complexes of HBen-beta-CD with glibenclamide and ibuprofen were prepared and isolated. In both cases, the guest content of the complexes was large, and a significant increase in the solubility of the free drug was observed. Dissolution of the complexes in pH 1.4 water was very rapid, and significant increases in the solubility of the free drugs were observed. Significantly, after reaching equilibrium concentration, a decrease in the drug concentration over time was not observed.

Programming Chemical Reaction Networks Using Intramolecular Conformational Motions of DNA.

PubMed

Lai, Wei; Ren, Lei; Tang, Qian; Qu, Xiangmeng; Li, Jiang; Wang, Lihua; Li, Li; Fan, Chunhai; Pei, Hao

2018-06-22

The programmable regulation of chemical reaction networks (CRNs) represents a major challenge toward the development of complex molecular devices performing sophisticated motions and functions. Nevertheless, regulation of artificial CRNs is generally energy- and time-intensive as compared to natural regulation. Inspired by allosteric regulation in biological CRNs, we herein develop an intramolecular conformational motion strategy (InCMS) for programmable regulation of DNA CRNs. We design a DNA switch as the regulatory element to program the distance between the toehold and branch migration domain. The presence of multiple conformational transitions leads to wide-range kinetic regulation spanning over 4 orders of magnitude. Furthermore, the process of energy-cost-free strand exchange accompanied by conformational change discriminates single base mismatches. Our strategy thus provides a simple yet effective approach for dynamic programming of complex CRNs.

Complex Cure Kinetics of the Tertiary Amine activated Reaction in DGEBA Epoxy Hardened with Diethanolamine

NASA Astrophysics Data System (ADS)

Ancipink, Windy; McCoy, John; Clarkson, Caitlyn; Kropka, Jamie; Celina, Mathias; Giron, Nicholas; Hailesilassie, Lebelo; Fredj, Narjes

The curing of a diglycidyl ether of bisphenol-A (DGEBA) epoxy with diethanolamine (DEA) involves a well understood fast amine-epoxide reaction followed by a more complicated slower hydroxyl-epoxide reaction. The time scale of these two reactions are well separated and can be studied independently from one another. The initial amine-epoxide reaction results in a tertiary amine adduct which is a product of the direct reaction of a secondary amine from the DEA reacting with a single DGEBA epoxide. The second hydroxyl-epoxide reaction results in a highly crosslinked glassy epoxy resin. The deviation in the mechanisms between high and low temperatures are discerned through the use of differential scanning calorimetry (DSC), infrared spectroscopy (IR), and isothermal microcalorimetry (IMC) data. Observations of reaction rates at temperatures ranging from 30° C to 110° C have led to the determination that the hydroxyl-epoxide reaction is temperature sensitive. The hydroxyl-epoxide reaction occurs through two different mechanisms: at low temperatures, the reaction is catalyzed by the tertiary amine adduct; at higher temperatures, the reaction does not appear to be catalyzed. Sandia National Laboratories, Albuquerque, NM.

Spatiotemporal evolution of dehydration reactions in subduction zones (Invited)

NASA Astrophysics Data System (ADS)

Padron-Navarta, J.

2013-12-01

Large-scale deep water cycling takes place through subduction zones in the Earth, making our planet unique in the solar system. This idiosyncrasy is the result of a precise but unknown balance between in-gassing and out-gassing fluxes of volatiles. Water is incorporated into hydrous minerals during seafloor alteration of the oceanic lithosphere. The cycling of volatiles is triggered by dehydration of these minerals that release fluids from the subducting slab to the mantle wedge and eventually to the crust or to the deep mantle. Whereas the loci of such reactions are reasonably well established, the mechanisms of fluid migration during dehydration reactions are still barely known. One of the challenges is that dehydration reactions are dynamic features evolving in time and space. Experimental data on low-temperature dehydration reactions (i.e. gypsum) and numerical models applied to middle-crust conditions point to a complex spatiotemporal evolution of the dehydration process. The extrapolation of these inferences to subduction settings has not yet been explored but it is essential to understand the dynamism of these settings. Here I propose an alternative approach to tackle this problem through the textural study of high-pressure terrains that experienced dehydration reactions. Spatiotemporal evolution of dehydration reactions should be recorded during mineral nucleation and growth through variations in time and space of the reaction rate. Insights on the fluid migration mechanism could be inferred therefore by noting changes in the texture of prograde assemblages. The dehydration of antigorite in serpentinite is a perfect candidate to test this approach as it releases a significant amount of fluid and produces a concomitant porosity. Unusual alternation of equilibrium and disequilibrium textures observed in Cerro del Almirez (Betic Cordillera, S Spain)[1, 2] attest for a complex fluid migration pattern for one of the most relevant reactions in subduction zones. This opens the possibility to correlate textural features recorded in high-pressure terrains with the physical fingerprint of dehydration reactions such as fluid flow rates and eventually seismicity or tremor. References [1] Padrón-Navarta, J. A., Tommasi, A., Garrido, C. J., López Sánchez-Vizcaíno, V., Gómez-Pugnaire, M. T., Jabaloy, A. & Vauchez, A. (2010). Fluid transfer into the wedge controlled by high-pressure hydrofracturing in the cold top-slab mantle. Earth and Planetary Science Letters 297, 271-286. [2] Padrón-Navarta, J. A., López Sánchez-Vizcaíno, V., Garrido, C. J. & Gómez-Pugnaire, M. T. (2011). Metamorphic Record of High-pressure Dehydration of Antigorite Serpentinite to Chlorite Harzburgite in a Subduction Setting (Cerro del Almirez, Nevado-Filábride Complex, Southern Spain). Journal of Petrology 52, 2047-2078.

Effects of age and the use of hands-free cellular phones on driving behavior and task performance.

PubMed

Liu, Yung-Ching; Ou, Yang-Kun

2011-12-01

This study used a driving simulator to investigate the effect of using a Bluetooth hands-free cellular phone earpiece on the driving behavior of two age groups. Forty-eight participants (24 aged 20-26 and 24 aged 65-73) were examined to assess their performance on the following divided-attention tasks under 2 driving load conditions (high and low): (1) attempting to maintain the speed limit and (2) using a cellular phone while driving. The length of the call conversation (long vs. short) and the conversational content (complex vs. simple) were manipulated as within-subject independent variables. The driving behavior of the participants, their task reaction times and accuracy, and subjective ratings were collected as dependent variables. The results indicate that under low driving loads, short talk times, and simple conversational content, the driving behavior of the participants showed low variance in the vehicle's mean speed. In contrast, complex conversation had a significantly negative impact on driving behavior. Notably, under a low driving load, motorists' driving behaviors, measured in lateral acceleration, caused significantly smaller variance in complex conversations compared to no call and simple conversations. The use of a hands-free cellular phone affected the performance (acceleration, lane deviation, reaction time, and accuracy) of older drivers significantly more than younger drivers. While performing divided attention tasks, the accuracy of the older drivers was 66.3 percent and that of the younger drivers was 96.3 percent. Although this study did not find a clear impact of cellular phone use on the driving behavior of younger drivers, their divided-attention task reaction times and accuracy were better under no-call than calling conditions. This study indicates that the use of hands-free cellular phones could significantly affect the safety of driving among the older and present risks, although lesser, for younger drivers.

The Copper-nicotinamide complex: sustainable applications in coupling and cycloaddition reactions

EPA Science Inventory

Crystalline copper (II)-nicotinamide complex, synthesized via simple mixing of copper chloride and nicotinamide solution at room temperature, catalyzes the C-S, C-N bond forming and cycloaddition reactions under a variety of sustainable reaction conditions.

Redox and fungicidal properties of phthalocyanine metal complexes as related to active oxygen.

PubMed

Vol'pin, M E; Novodarova, G N; Krainova NYu; Lapikova, V P; Aver'yanov, A A

2000-10-01

Some chemical and fungicidal effects of 20 phthalocyanines of Co, Fe, Cu, and Al were studied. Under dark conditions, these complexes reduced nitroblue tetrazolium in the presence of KCN, accelerated the autoxidation of ascorbate or hydroquinone and decomposed hydrogen peroxide. In the later reaction, hydroxyl radical was generated as evidenced with the deoxyribose assay. The inhibition by superoxide dismutase and catalase of catalyzed autoxidation of ascorbate suggests the participation of superoxide anion-radical and hydrogen peroxide in the reaction. Most complexes were toxic to the fungus Magnaporthe grisea which causes blast disease of rice. The toxicity was enhanced by light being diminished by antioxidant reagents sequestering active oxygen species. Some complexes (including nontoxic ones), after 1-day contact with a leaf surface of the disease-susceptible rice cultivar, induced the fungitoxicity of leaf diffusate. This toxicity was also light-activated and sensitive to antioxidant reagents. Several complexes, when added to inocula, decreased 2-3 times the frequency of the compatible symptoms of the blast. It is suggested that in planta, the dark redox activity of phthalocyanines along with their photosensitization promote the generation of active oxygen, which damages the parasite and, therefore, favors disease resistance.

Synthesis of triple-stranded complexes using bis(dipyrromethene) ligands.

PubMed

Zhang, Zhan; Dolphin, David

2010-12-20

The reaction of an α-free, β,β'-linked bis(dipyrromethene) ligand with Fe(3+) or Co(3+) led to noninterconvertible triple-stranded helicates and mesocates. In the present context, a stable α-free ligand 2 has been developed and complexation of ligands 1 and 2 with diamagnetic Co(3+), Ga(3+), and In(3+) has been studied. The triple-stranded M(2)1(3) (M = Ga, In) and M(2)2(3) (M = Co, Ga, In) complexes were characterized using matrix-assisted laser desorption ionization time-of-flight spectrometry, (1)H NMR and UV-vis spectroscopy, and X-ray crystallography. Again, the (1)H NMR analysis showed that both the triple-stranded helicates and mesocates were generated in this metal-directed assembly. Consistent with our previous finding on coordinatively inert Co(3+) complexes, variable-temperature NMR spectroscopy indicated that the triple-stranded helicate and mesocate of labile In(3+) did not interconvert in solution, either. However, the diastereoselectivity of the M(2)2(3) complexes was found to improve with an increase in the reaction temperature. Taken together, this study complements the coordination chemistry of poly(dipyrromethene) ligands and provides further insight into the formation of helicates versus mesocates.

Mirror Me: Imitative Responses in Adults with Autism

ERIC Educational Resources Information Center

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

2016-01-01

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

Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates.

PubMed Central

Walter, N G; Burke, J M

1997-01-01

Current methods for evaluating the kinetics of ribozyme-catalyzed reactions rely primarily on the use of radiolabeled RNA substrates, and so require tedious electrophoretic separation and quantitation of reaction products for each data point in any experiment. Here, we report the use of fluorescent substrates for real-time analysis of the time course of reactions of the hairpin ribozyme. Fluorescence of 3' fluorescein-labeled substrates was quenched upon binding to the hairpin ribozyme or its isolated substrate-binding strand (SBS), under conditions of ribozyme or SBS excess. This decrease was accompanied by an increase in anisotropy, and resulted from a base-specific quenching by a guanosine residue added to the 5' end of the SBS, close to fluorescein in the complex. Fluorescence quenching was used to determine rate constants for substrate binding (1.4 x 10(8) M(-1) min(-1)), cleavage (0.15 min(-1)), and substrate dissociation (0.010 min(-1)) by a structurally well-defined ribozyme at 25 degrees C in 50 mM Tris-HCI, pH 7.5, 12 mM MgCl2. These rates are in excellent agreement with those obtained using traditional radioisotopic methods. Measurements of dissociation rates provided physical support for interdomain interactions within the substrate-ribozyme complex. We estimate that 2.1 kcal/mol of additional substrate binding energy is provided by the B domain of the ribozyme. Part of this free energy apparently stems from coaxial stacking of helices in the hinge region between domains, and it is plausible that the remainder might be contributed by direct interactions with loop B. The fluorescence quenching and dequenching methods described here should be readily adaptable to studying a wide variety of RNA interactions and reactions using ribozymes and other model systems. PMID:9085846

Bimetallic redox synergy in oxidative palladium catalysis.

PubMed

Powers, David C; Ritter, Tobias

2012-06-19

Polynuclear transition metal complexes, which are embedded in the active sites of many metalloenzymes, are responsible for effecting a diverse array of oxidation reactions in nature. The range of chemical transformations remains unparalleled in the laboratory. With few noteworthy exceptions, chemists have primarily focused on mononuclear transition metal complexes in developing homogeneous catalysis. Our group is interested in the development of carbon-heteroatom bond-forming reactions, with a particular focus on identifying reactions that can be applied to the synthesis of complex molecules. In this context, we have hypothesized that bimetallic redox chemistry, in which two metals participate synergistically, may lower the activation barriers to redox transformations relevant to catalysis. In this Account, we discuss redox chemistry of binuclear Pd complexes and examine the role of binuclear intermediates in Pd-catalyzed oxidation reactions. Stoichiometric organometallic studies of the oxidation of binuclear Pd(II) complexes to binuclear Pd(III) complexes and subsequent C-X reductive elimination from the resulting binuclear Pd(III) complexes have confirmed the viability of C-X bond-forming reactions mediated by binuclear Pd(III) complexes. Metal-metal bond formation, which proceeds concurrently with oxidation of binuclear Pd(II) complexes, can lower the activation barrier for oxidation. We also discuss experimental and theoretical work that suggests that C-X reductive elimination is also facilitated by redox cooperation of both metals during reductive elimination. The effect of ligand modification on the structure and reactivity of binuclear Pd(III) complexes will be presented in light of the impact that ligand structure can exert on the structure and reactivity of binuclear Pd(III) complexes. Historically, oxidation reactions similar to those discussed here have been proposed to proceed via mononuclear Pd(IV) intermediates, and the hypothesis of mononuclear Pd(II/IV) catalysis has guided the successful development of many reactions. Herein we discuss differences between monometallic Pd(IV) and bimetallic Pd(III) redox catalysis. We address whether appreciation of the relevance of bimetallic Pd(III) redox catalysis is of academic interest exclusively, serving to provide a more nuanced description of catalysis, or if the new insight regarding bimetallic Pd(III) chemistry can be a platform to enable future reaction development. To this end, we describe an example in which the hypothesis of bimetallic redox chemistry guided reaction development, leading to the discovery of reactivity distinct from monometallic catalysts.

[Temporal changes in conscious and unconscious trace phenomena in six to seven-year-old children].

PubMed

Fedotchev, A I

1975-01-01

Development in time of unconscious trace reactions as well as a change in the time of reproduction of verbal material in natural conditions was studied by the conditioned reflex to time method on 107 school children aged from six to seven years and on 35 subjects of the same age from a kindergarten. It has been found that in schoolchildren the transfer of trace reactions to long-term storage is completed faster, and their voluntary acts in the course of conscious reproduction of an interstimuli intervals are more adequate than in the kindergarten children of the same age. The trace phenomena formed in natural conditions and in the laboratory experiment develop in time in a similar way. The change in time of conscious trace phenomena is of a more complex nature than of the unconscious phenomena. The practical significance of the data obtained is noted.

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

PubMed

Parida, Laxmi; Zhou, Ruhong

2005-06-01

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

Group transfer and electron transfer reactions of organometallic complexes

NASA Astrophysics Data System (ADS)

Atwood, Jim D.

During 1994, despite the disruptions, the authors have made progress in several aspects of their research on electron transfer reactions between organometallic complexes. This summary covers three areas that are relatively complete: (1) reactions between metal carbonyl anions and metal carbonyl halides, (2) reactions of hydrido- and alkyl-containing anions (RFe(CO)4(-) and RW(CO)5(-) with metal carbonyl cations; and (3) reactions of a seventeen-electron complex (Cp* Cr(CO)3*) with metal carbonyl derivatives. Two areas of examination that have just begun (possible carbene transfer and the possible role of metal carbonyl anions in carbon-hydrogen bond activation) will also be described.

Evidence for global processing of complex visual displays

NASA Technical Reports Server (NTRS)

Munson, Robert C.; Horst, Richard L.

1986-01-01

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

Ultrafast studies of organometallic photochemistry: The mechanism of carbon-hydrogen bond activation in solution

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

Bromberg, S.E.

1998-05-01

When certain organometallic compounds are photoexcited in room temperature alkane solution, they are able to break or activate the C-H bonds of the solvent. Understanding this potentially practical reaction requires a detailed knowledge of the entire reaction mechanism. Because of the dynamic nature of chemical reactions, time-resolved spectroscopy is commonly employed to follow the important events that take place as reactants are converted to products. For the organometallic reactions examined here, the electronic/structural characteristics of the chemical systems along with the time scales for the key steps in the reaction make ultrafast UV/Vis and IR spectroscopy along with nanosecond Step-Scanmore » FTIR spectroscopy the ideal techniques to use for this study. An initial study of the photophysics of (non-activating) model metal carbonyls centering on the photodissociation of M(CO){sub 6} (M = Cr, W, Mo) was carried out in alkane solutions using ultrafast IR spectroscopy. Next, picosecond UV/vis studies of the C-H bond activation reaction of Cp{sup *}M(CO){sub 2} (M = Rh, Ir), conducted in room temperature alkane solution, are described in an effort to investigate the origin of the low quantum yield for bond cleavage ({approximately}1%). To monitor the chemistry that takes place in the reaction after CO is lost, a system with higher quantum yield is required. The reaction of Tp{sup *}Rh(CO){sub 2} (Tp{sup *} = HB-Pz{sub 3}{sup *}, Pz{sup *} = 3,5-dimethylpyrazolyl) in alkanes has a quantum yield of {approximately}30%, making time resolved spectroscopic measurements possible. From ultrafast IR experiments, two subsequently formed intermediates were observed. The nature of these intermediates are discussed and the first comprehensive reaction mechanism for a photochemical C-H activating organometallic complex is presented.« less

The mechanism of hydrothermal hydrolysis for glycyrrhizic acid into glycyrrhetinic acid and glycyrrhetinic acid 3-O-mono-β-D-glucuronide in subcritical water.

PubMed

Fan, Rui; Li, Nan; Xu, Honggao; Xiang, Jun; Wang, Lei; Gao, Yanxiang

2016-01-01

To improve the bioactivity and sweetness properties of glycyrrhizic acid (GL), the hydrothermal hydrolysis of GL into glycyrrhetinic acid (GA) and glycyrrhetinic acid 3-O-mono-β-D-glucuronide (GAMG) in subcritical water was investigated. The effects of temperature, time and their interaction on the conversion ratios were analyzed and the reactions were elaborated with kinetics and thermodynamics. The results showed that GL hydrothermal hydrolysis was significantly (P < 0.05) affected by reaction time and temperature, as well as their interaction, and could be fitted into first-order kinetics. The thermodynamic analysis indicated that the hydrolysis of GL was endergonic and non-spontaneous. The hydrolytic pathways were composed of complex consecutive and parallel reactions. It was concluded that subcritical water may be a potential medium for producing GAMG and GA. Copyright © 2015 Elsevier Ltd. All rights reserved.

Electronic and Vibrational Coherence in Charge-Transfer Reactions

NASA Astrophysics Data System (ADS)

Scherer, Norbert

1996-03-01

The ultrafast dynamics associated with optically-induced intervalence charge-transfer reactions in solution and protein environments are reported. These studies include the Fe^(II)-Fe^(III) MMCT complex Prussian blue and the mixed valence dimer (CN)_5Ru^(II)CNRuRu^(III)(NH_3)_5. The protein systems include blue copper proteins and the bacterial photosynthetic reaction center. The experimental approaches include photon echo, wavelength-resolved pump-probe and anisotropy measurements performed with 12-16fs duration optical pulses. Complicated time-domain waveforms reflect the several different p[rocesses and time scales for relaxation of coherences (both electronic and vibrational) and populations within these systems. The photon echo and anisotropy results probe electronic coherence and dephasing prior to back electron transfer. Wavelength-resolved pump-probe results reveal vibrational modes coupled to the CT-coordinate as well as formation of new product states or vibrational cooling in the ground state following back electron transfer.

The Standardized Field Sobriety Tests (SFST) and measures of cognitive functioning.

PubMed

Downey, Luke A; Hayley, Amie C; Porath-Waller, Amy J; Boorman, Martin; Stough, Con

2016-01-01

The Standardized Field Sobriety Tests (SFST) are utilised widely to assess fitness to drive when law enforcement suspects a driver's ability to drive is impaired, whether by drugs or alcohol. The SFST ostensibly achieve this through assessment of the level of drivers' cognitive and psychomotor impairment, although no studies have explicitly assessed the relatedness of cognitive ability and performance on the SFST. The current study aimed to assess the relationship between the three components of the SFST with a well validated computerised cognitive battery. A sub-set of 61 placebo condition participants comprised the sample, with 33 females and 28 males (mean age 25.45 years). Correlations between the individual SFST subscales 'Horizontal Gaze Nystagmus' (HGN), the 'One Leg Stand' (OLS) and the 'Walk and Turn' test (WAT) and Cognitive Drug Research (CDR) sub-scales of 'Quality of Working Memory', 'Power of Attention' and 'Continuity of Attention' were analysed using point-biserial correlation. Sixty participants were included for analyses. A weak-moderate positive (five subscales) and a moderate-strong negative (two subscales) association was noted between seven of the nine individual CDR subscales and the SFST subscale of the WAT test (all p<0.05). Individually, a moderate positive association was noted between the sub-scale 'Nystagmus lack of smooth pursuit' and 'digit vigilance reaction time' and 'choice reaction time; reaction time' (both p<0.05) and 'Nystagmus head move and/or jerk' and 'simple reaction time' (p<0.001). When assessed as a partially composite factor, a comparable association was also noted between the composite score of the SFST subscale 'Nystagmus head move and/or jerk' and both (a) simple and (b) digit vigilance reaction time (both p<0.05). No association was noted between any of the individual cognitive variables and the SFST subscale 'OLS', or between composite cognitive scores 'Quality of Working Memory', 'Power of Attention' and 'Continuity of Attention' and total SFST scores. Variation in some aspects of cognitive performance was found to be moderately and positively correlated with some individual aspects of the SFST; particularly among tasks which assess reaction time. Impairment of these cognitive processes can also contribute to the completion of complex tasks such as driving or the SFST. Complex behavioural tasks such as driving are often severely impaired due to intoxication, and thus in a practical sense, the SFST can still be considered a useful screening tool to identify drug or alcohol impaired drivers. Copyright © 2015 Elsevier Ltd. All rights reserved.

Solar chemistry of metal complexes

NASA Astrophysics Data System (ADS)

Gray, H. B.; Maverick, A. W.

1981-12-01

Electronic excited states of certain transition metal complexes undergo oxidation-reduction reactions that store chemical energy. Such reactions have been extensively explored for mononuclear complexes. Two classes of polynuclear species exhibit similar properties, and these complexes are now being studied as possible homogeneous sensitizer-catalysts for hydrogen production from aqueous solutions.

A molecular orbital study of a model of the Mg2+ coordination complex of the self splicing reaction of ribosomal RNA

NASA Technical Reports Server (NTRS)

McCourt, M.; Shibata, M.; McIver, J. W.; Rein, R.

1988-01-01

Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.

Ephemeral collision complexes mediate chemically termolecular transformations that affect system chemistry [Ephemeral collision complexes induce chemically termolecular transformations that affect global chemistry

DOE PAGES

Burke, Michael P.; Klippenstein, Stephen J.

2017-08-14

Termolecular association reactions involve ephemeral collision complexes—formed from the collision of two molecules—that collide with a third and chemically inert ‘bath gas’ molecule that simply transfers energy to/from the complex. These collision complexes are generally not thought to react chemically on collision with a third molecule in the gas-phase systems of combustion and planetary atmospheres. Such ‘chemically termolecular’ reactions, in which all three molecules are involved in bond making and/or breaking, were hypothesized long ago in studies establishing radical chain branching mechanisms, but were later concluded to be unimportant. Here, with data from ab initio master equation and kinetic-transport simulations,more » we reveal that reactions of H+O 2 collision complexes with other radicals constitute major kinetic pathways under common combustion situations. These reactions are also found to influence flame propagation speeds, a common measure of global reactivity. As a result, analogous chemically termolecular reactions mediated by ephemeral collision complexes are probably of significance in various combustion and planetary environments.« less

Ephemeral collision complexes mediate chemically termolecular transformations that affect system chemistry [Ephemeral collision complexes induce chemically termolecular transformations that affect global chemistry

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

Burke, Michael P.; Klippenstein, Stephen J.

Termolecular association reactions involve ephemeral collision complexes—formed from the collision of two molecules—that collide with a third and chemically inert ‘bath gas’ molecule that simply transfers energy to/from the complex. These collision complexes are generally not thought to react chemically on collision with a third molecule in the gas-phase systems of combustion and planetary atmospheres. Such ‘chemically termolecular’ reactions, in which all three molecules are involved in bond making and/or breaking, were hypothesized long ago in studies establishing radical chain branching mechanisms, but were later concluded to be unimportant. Here, with data from ab initio master equation and kinetic-transport simulations,more » we reveal that reactions of H+O 2 collision complexes with other radicals constitute major kinetic pathways under common combustion situations. These reactions are also found to influence flame propagation speeds, a common measure of global reactivity. As a result, analogous chemically termolecular reactions mediated by ephemeral collision complexes are probably of significance in various combustion and planetary environments.« less

New La(III) complex immobilized on 3-aminopropyl-functionalized silica as an efficient and reusable catalyst for hydrolysis of phosphate ester bonds.

PubMed

Muxel, Alfredo A; Neves, Ademir; Camargo, Maryene A; Bortoluzzi, Adailton J; Szpoganicz, Bruno; Castellano, Eduardo E; Castilho, Nathalia; Bortolotto, Tiago; Terenzi, Hernán

2014-03-17

Described herein is the synthesis, structure, and monoesterase and diesterase activities of a new mononuclear [La(III)(L(1))(NO3)2] (1) complex (H2L(1) = 2-bis[{(2-pyridylmethyl)-aminomethyl}-6-[N-(2-pyridylmethyl) aminomethyl)])-4-methyl-6-formylphenol) in the hydrolysis of 2,4-bis(dinitrophenyl)phosphate (2,4-BDNPP). When covalently linked to 3-aminopropyl-functionalized silica, 1 undergoes disproportionation to form a dinuclear species (APS-1), whose catalytic efficiency is increased when compared to the homogeneous reaction due to second coordination sphere effects which increase the substrate to complex association constant. The anchored catalyst APS-1 can be recovered and reused for subsequent hydrolysis reactions (five times) with only a slight loss in activity. In the presence of DNA, we suggest that 1 is also converted into the dinuclear active species as observed with APS-1, and both were shown to be efficient in DNA cleavage.

Complex for monitoring visual acuity and its application for evaluation of human psycho-physiological state

NASA Astrophysics Data System (ADS)

Sorokoumov, P. S.; Khabibullin, T. R.; Tolstaya, A. M.

2017-01-01

The existing psychological theories associate the movement of a human eye with its reactions to external change: what we see, hear and feel. By analyzing the glance, we can compare the external human response (which shows the behavior of a person), and the natural reaction (that they actually feels). This article describes the complex for detection of visual activity and its application for evaluation of the psycho-physiological state of a person. The glasses with a camera capture all the movements of the human eye in real time. The data recorded by the camera are transmitted to the computer for processing implemented with the help of the software developed by the authors. The result is given in an informative and an understandable report, which can be used for further analysis. The complex shows a high efficiency and stable operation and can be used both, for the pedagogic personnel recruitment and for testing students during the educational process.

Modelling of polymer photodegradation for solar cell modules

NASA Technical Reports Server (NTRS)

Guillet, J. E.

1982-01-01

A computer program which simulates the complex processes of photooxidation which take place in a polymer upon prolonged exposure outdoors causing it to fail in photovoltaic and other applications. The method calculates from an input data set of elementary reactions and rates the concentration profiles of all species over time.

A New Approach To Selectively Identify And Quantify Perfluorochemicals In Complex Matrices Using Ion Trap Time-Of-Flight Mass Spectrometry

EPA Science Inventory

Most of the published studies focusing on the environmental and biological distribution of perfluorinated alkyl compounds (PFCs) have used triple quadrupole mass spectrometers for compound identification and quantitation. Multiple-reaction-monitoring (MRM) is a sensitive mass sp...

Can a Reaction's Environment Program its Outcome, and Does it Matter?

NASA Astrophysics Data System (ADS)

Surman, A. J.; Rodriguez-Garcia, M.; Abul-Haija, Y.; Cooper, G. J. T.; Donkers, K.; Planchat i Barbarà, J. M.; Kube, J.; Mullin, M.; Hezwani, M.; Cronin, L.

2017-07-01

Where most eschew reactions producing complex mixtures (‘tar') and prefer to plan ‘clean' syntheses, we embrace complexity. We show that environments can steer ‘messy' reactions, and ask if this can yield significant difference in structure and function.

Micro/nanofabricated environments for synthetic biology.

PubMed

Collier, C Patrick; Simpson, Michael L

2011-08-01

A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints. Copyright © 2011 Elsevier Ltd. All rights reserved.

A polymer supported Cu(I) catalyst for the 'click reaction' in aqueous media.

PubMed

Ul Islam, Rafique; Taher, Abu; Choudhary, Meenakshi; Witcomb, Michael J; Mallick, Kaushik

2015-01-21

Polymer stabilized monovalent copper has been synthesized using an in situ chemical transformation route and was characterized by means of different microscopic, optical and surface characterization techniques, which offered information about the chemical structure of the polymer and the morphology of the complex. The supramolecular material, Cu(i)-poly(2-aminobenzoic acid), denoted Cu(i)-pABA, showed catalytic activity for the cycloaddition reaction between terminal alkynes and azides to synthesize 1,2,3-triazoles with excellent yields. The catalyst was recovered from the reaction mixture and recycled several times without an appreciable loss of catalytic activity. The whole strategy was done under ambient conditions and in the presence of water as a solvent.

Molybdenum compounds in organic synthesis

NASA Astrophysics Data System (ADS)

Khusnutdinov, R. I.; Oshnyakova, T. M.; Dzhemilev, U. M.

2017-02-01

The review presents the first analysis and systematic discussion of data published in the last 35-40 years on the use of molybdenum compounds and complexes in organic synthesis and catalysis of various ion coordination and radical reactions. Detailed account is given of the key trends in the use of molybdenum complexes as catalysts of alkene epoxidation and oxyketonation, oxidation of sulfur, nitrogen and phosphorus compounds, hydrosilylation of 1,3-dienes, ketones and aldehydes, hydrostannylation of acetylenes and hydrogermylation of norbornadienes. Considerable attention is paid to the description of new reactions and in situ generation of highly reactive hypohalites, ROX and HOX, induced by molybdenum complexes and the use of hypohalites in oxidative transformations. Data on the application of molybdenum complexes in well-known reactions are discussed, including Kharasch and Pauson-Khand reactions, allylic alkylation of C-nucleophiles, aminocarbonylation of halo derivatives and oligomerization of cyclic dienes, trienes, alkynes and 1,3-dienes. The last Section of the review considers 'unusual' organic reactions involving molybdenum compounds and complexes. The bibliography includes 257 references.

Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damköhler numbers

NASA Astrophysics Data System (ADS)

Bandopadhyay, Aditya; Le Borgne, Tanguy; Méheust, Yves; Dentz, Marco

2017-02-01

Mixing fronts, where fluids of different chemical compositions mix with each other, are known to represent hotspots of chemical reaction in hydrological systems. These fronts are typically subjected to velocity gradients, ranging from the pore scale due to no slip boundary conditions at fluid solid interfaces, to the catchment scale due to permeability variations and complex geometry of the Darcy velocity streamlines. A common trait of these processes is that the mixing interface is strained by shear. Depending on the Péclet number Pe , which represents the ratio of the characteristic diffusion time to the characteristic shear time, and the Damköhler number Da , which represents the ratio of the characteristic diffusion time to the characteristic reaction time, the local reaction rates can be strongly impacted by the dynamics of the mixing interface. So far, this impact has been characterized mostly either in kinetics-limited or in mixing-limited conditions, that is, for either low or high Da. Here the coupling of shear flow and chemical reactivity is investigated for arbitrary Damköhler numbers, for a bimolecular reaction and an initial interface with separated reactants. Approximate analytical expressions for the global production rate and reactive mixing scale are derived based on a reactive lamella approach that allows for a general coupling between stretching enhanced mixing and chemical reactions. While for Pe < Da , reaction kinetics and stretching effects are decoupled, a scenario which we name "weak stretching", for Pe > Da , we uncover a "strong stretching" scenario where new scaling laws emerge from the interplay between reaction kinetics, diffusion, and stretching. The analytical results are validated against numerical simulations. These findings shed light on the effect of flow heterogeneity on the enhancement of chemical reaction and the creation of spatially localized hotspots of reactivity for a broad range of systems ranging from kinetic limited to mixing limited situations.

Influence of erythropoietin on cognitive performance during experimental hypoglycemia in patients with type 1 diabetes mellitus: a randomized cross-over trial.

PubMed

Kristensen, Peter Lommer; Pedersen-Bjergaard, Ulrik; Kjær, Troels Wesenberg; Olsen, Niels Vidiendal; Dela, Flemming; Holst, Jens Juul; Faber, Jens; Tarnow, Lise; Thorsteinsson, Birger

2013-01-01

The incidence of severe hypoglycemia in type 1 diabetes has not decreased over the past decades. New treatment modalities minimizing the risk of hypoglycemic episodes and attenuating hypoglycemic cognitive dysfunction are needed. We studied if treatment with the neuroprotective hormone erythropoietin (EPO) enhances cognitive function during hypoglycemia. Eleven patients with type 1 diabetes, hypoglycemia unawareness and recurrent severe hypoglycemia completed the study. In a double-blind, randomized, balanced, cross-over study using clamped hypoglycemia they were treated with 40,000 IU of EPO or placebo administered intravenously six days before the two experiments. Cognitive function (primary endpoint), hypoglycemic symptoms, and counter-regulatory hormonal response were recorded. Compared with placebo, EPO treatment was associated with a significant reduction in errors in the most complex reaction time task (-4.7 (-8.1 to -1.3), p = 0.01) and a less reaction time prolongation (-66 (-117 to -16) msec, p = 0.02). EPO treatment did not change performance in other measures of cognition. Hypoglycemic symptoms, EEG-changes, and counter-regulatory hormone concentrations did not differ between EPO and placebo treatment. In patients with type 1 diabetes and hypoglycemia unawareness, treatment with EPO is associated with a beneficial effect on cognitive function in a complex reaction time task assessing sustained attention/working memory. Hypoglycemic symptoms and hormonal responses were not changed by EPO treatment. ClinicalTrials.gov NCT00615368.

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

Gold(I)-assisted catalysis - a comprehensive view on the [3,3]-sigmatropic rearrangement of allyl acetate

NASA Astrophysics Data System (ADS)

Freindorf, Marek; Cremer, Dieter; Kraka, Elfi

2018-03-01

The unified reaction valley approach (URVA) combined with the local mode, ring puckering and electron density analysis is applied to elucidate the mechanistic differences of the non-catalysed and the Au[I]-N-heterocyclic carbene (NHC)-catalysed [3,3]-sigmatropic rearrangement of allyl acetate. Using a dual-level approach (DFT and DLPNO-CCSD(T)), the influence of solvation, counter-ions, bulky and electron withdrawing/donating substituents as well as the exchange of the Au[I]-NHC with a Au[I]-phosphine catalyst is investigated. The catalyst breaks up the rearrangement into two steps by switching between Au[I]-π and Au[I]-σ complexation, thus avoiding the energy-consuming CO cleavage in the first step. Based on local stretching force constants ka(C=C), we derive for the first time a quantitative measure of the π-acidity of the Au[I] catalyst; in all catalysed reactions, the bond order n(C=C) drops from 2 to 1.65. The ring puckering analysis clarifies that all reactions start and end via a six-membered ring with a boat form. All Au[I]-σ-complex intermediates show a considerable admixture of the chair form. The non-catalysed [3,3]-sigmatropic rearrangement goes through a maximum of charge separation between the allyl and acetate units at the transition state, while all catalysed reactions proceed via a minimum of charge separation reached in the region of the Au[I]-σ-complex.

Group 4 Metalloporphyrin diolato Complexes and Catalytic Application of Metalloporphyrins and Related Transition Metal Complexes

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

Du, Guodong

In this work, the first examples of group 4 metalloporphyrin 1,2-diolato complexes were synthesized through a number of strategies. In general, treatment of imido metalloporphyrin complexes, (TTP)M=NR, (M = Ti, Zr, Hf), with vicinal diols led to the formation of a series of diolato complexes. Alternatively, the chelating pinacolate complexes could be prepared by metathesis of (TTP)MCl 2 (M = Ti, Hf) with disodium pinacolate. These complexes were found to undergo C-C cleavage reactions to produce organic carbonyl compounds. For titanium porphyrins, treatment of a titanium(II) alkyne adduct, (TTP)Ti(η 2-PhC≡CPh), with aromatic aldehydes or aryl ketones resulted in reductive couplingmore » of the carbonyl groups to produce the corresponding diolato complexes. Aliphatic aldehydes or ketones were not reactive towards (TTP)Ti(η 2-PhC≡CPh). However, these carbonyl compounds could be incorporated into a diolato complex on reaction with a reactive precursor, (TTP)Ti[O(Ph) 2C(Ph) 2O] to provide unsymmetrical diolato complexes via cross coupling reactions. In addition, an enediolato complex (TTP)Ti(OCPhCPhO) was obtained from the reaction of (TTP)Ti(η 2-PhC≡CPh) with benzoin. Titanium porphyrin diolato complexes were found to be intermediates in the (TTP)Ti=O-catalyzed cleavage reactions of vicinal diols, in which atmospheric oxygen was the oxidant. Furthermore, (TTP)Ti=O was capable of catalyzing the oxidation of benzyl alcohol and α-hydroxy ketones to benzaldehyde and α-diketones, respectively. Other high valent metalloporphyrin complexes also can catalyze the oxidative diol cleavage and the benzyl alcohol oxidation reactions with dioxygen. A comparison of Ti(IV) and Sn(IV) porphyrin chemistry was undertaken. While chelated diolato complexes were invariably obtained for titanium porphyrins on treatment with 1,2-diols, the reaction of vicinal diols with tin porphyrins gave a number of products, including mono-, bis-alkoxo, and chelating diolato complexes, depending on the identity of diols and the stoichiometry employed. It was also found that tin porphyrin complexes promoted the oxidative cleavage of vicinal diols and the oxidation of α-ketols to α-diketones with dioxygen. In extending the chemistry of metalloporphyrins and analogous complexes, a series of chiral tetraaza macrocyclic ligands and metal complexes were designed and synthesized. Examination of iron(II) complexes showed that they were efficient catalysts for the cyclopropanation of styrene by diazo reagents. Good yields and high diastereoselectivity were obtained with modest enantioselectivity. A rationalization of the stereoselectivity was presented on the basis of structural factors in a carbene intermediate.« less

New insights into low-temperature oxidation of propane from synchrotron photoionization mass spectrometry and multi-scale informatics modeling

DOE PAGES

Welz, Oliver; Burke, Michael P.; Antonov, Ivan O.; ...

2015-04-10

We studied low-temperature propane oxidation at P = 4 Torr and T = 530, 600, and 670 K by time-resolved multiplexed photoionization mass spectrometry (MPIMS), which probes the reactants, intermediates, and products with isomeric selectivity using tunable synchrotron vacuum UV ionizing radiation. The oxidation is initiated by pulsed laser photolysis of oxalyl chloride, (COCl) 2, at 248 nm, which rapidly generates a ~1:1 mixture of 1-propyl (n-propyl) and 2-propyl (i-propyl) radicals via the fast Cl + propane reaction. At all three temperatures, the major stable product species is propene, formed in the propyl + O 2 reactions by direct HOmore » 2 elimination from both n- and i-propyl peroxy radicals. The experimentally derived propene yields relative to the initial concentration of Cl atoms are (20 ± 4)% at 530 K, (55 ± 11)% at 600 K, and (86 ± 17)% at 670 K at a reaction time of 20 ms. The lower yield of propene at low temperature reflects substantial formation of propyl peroxy radicals, which do not completely decompose on the experimental time scale. In addition, C 3H 6O isomers methyloxirane, oxetane, acetone, and propanal are detected as minor products. Our measured yields of oxetane and methyloxirane, which are coproducts of OH radicals, suggest a revision of the OH formation pathways in models of low-temperature propane oxidation. The experimental results are modeled and interpreted using a multiscale informatics approach, presented in detail in a separate publication (Burke, M. P.; Goldsmith, C. F.; Klippenstein, S. J.; Welz, O.; Huang H.; Antonov I. O.; Savee J. D.; Osborn D. L.; Zádor, J.; Taatjes, C. A.; Sheps, L. Multiscale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Reactions. J. Phys. Chem A. 2015, DOI: 10.1021/acs.jpca.5b01003). Additionally, we found that the model predicts the time profiles and yields of the experimentally observed primary products well, and shows satisfactory agreement for products formed mostly via secondary radical–radical reactions.« less

Phase locking route behind complex periodic windows in a forced oscillator

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Direct asymmetric aldol reaction of aryl ketones with aryl aldehydes catalyzed by chiral BINOL-derived zincate catalyst.

PubMed

Li, Hong; Da, Chao-Shan; Xiao, Yu-Hua; Li, Xiao; Su, Ya-Ning

2008-09-19

Direct asymmetric aldol reaction of aryl ketones with aryl aldehydes catalyzed by chiral metal complex is reported for the first time herein. Two novel semicrown chiral ligands 1a and 1b were synthesized from (S)- and (R)-BINOL, respectively, and then employed to catalyze the direct asymmetric aldol addition of aryl ketones to aryl aldehydes. Introduced with 2.0 equiv of diethylzinc, 1b had higher enantioselectivity than 1a. Up to 97% yield and up to 80% enantioselectivity were achieved.

Toward hypoxia-selective rhenium and technetium tricarbonyl complexes.

PubMed

North, Andrea J; Hayne, David J; Schieber, Christine; Price, Katherine; White, Anthony R; Crouch, Peter J; Rigopoulos, Angela; O'Keefe, Graeme J; Tochon-Danguy, Henri; Scott, Andrew M; White, Jonathan M; Ackermann, Uwe; Donnelly, Paul S

2015-10-05

With the aim of preparing hypoxia-selective imaging and therapeutic agents, technetium(I) and rhenium(I) tricarbonyl complexes with pyridylhydrazone, dipyridylamine, and pyridylaminocarboxylate ligands containing nitrobenzyl or nitroimidazole functional groups have been prepared. The rhenium tricarbonyl complexes were synthesized with short reaction times using microwave irradiation. Rhenium tricarbonyl complexes with deprotonated p-nitrophenyl pyridylhydrazone ligands are luminescent, and this has been used to track their uptake in HeLa cells using confocal fluorescent microscopy. Selected rhenium tricarbonyl complexes displayed higher uptake in hypoxic cells when compared to normoxic cells. A (99m)Tc tricarbonyl complex with a dipyridylamine ligand bearing a nitroimidazole functional group is stable in human serum and was shown to localize in a human renal cell carcinoma (RCC; SK-RC-52) tumor in a mouse.

Monte Carlo isotopic inventory analysis for complex nuclear systems

NASA Astrophysics Data System (ADS)

Phruksarojanakun, Phiphat

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

Delayed vaccine virus replication in chickens vaccinated subcutaneously with an immune complex infectious bursal disease vaccine: Quantification of vaccine virus by real-time polymerase chain reaction

PubMed Central

2005-01-01

Abstract The distribution of the immune complex vaccine virus for infectious bursal disease (IBD) in tissue was examined and the viral loads of the organs were quantitatively compared. One-day-old specific pathogen free (SPF) and maternally immune broiler chickens were injected subcutaneously with the vaccine. Lymphoid and non-lymphoid tissues were collected at various time intervals during the experiment to test for infectious bursal disease virus (IBDV)-RNA by using reverse transcriptase-polymerase chain reaction (RT-PCR). Only the bursa of Fabricius was found to be positive with unusually long viral persistence in the broiler group. The positive bursa samples were further investigated by using real-time PCR coupled with a TaqMan probe. The highest amounts of the virus were detected at its first appearance in the bursa: on day 14 post vaccination (PV) in the SPF chickens and on day 17 and day 21 PV in the maternally immune broiler group. The virus then gradually cleared, most likely due to the parallel appearance of the active immune response indicated by seroconversion. PMID:15971678

Quantum chemistry and TST study of the mechanism and kinetics of the butadiene and isoprene reactions with mercapto radicals

NASA Astrophysics Data System (ADS)

Francisco-Márquez, Misaela; Alvarez-Idaboy, J. Raul; Galano, Annia; Vivier-Bunge, Annik

2008-03-01

The reactions of isoprene and butadiene with SH rad radicals have been investigated by density functional theory and ab initio molecular orbital theories. We report the thermodynamics and kinetics of four different pathways, involving addition of SH rad radicals to all double-bonded carbon atoms. Calculations have been performed on all stationary points using BHandHLYP functional, Moller-Plesset perturbation theory to second-order (MP2) and the composite CBS-QB3 method at the MP2 optimized geometries and frequencies. Pre-reactive complexes have been identified. The apparent activation energies are negative for SH rad addition at the terminal carbon atoms and are slightly smaller than those for OH rad addition at the same positions. The calculated overall rate coefficient for butadiene + SH rad reaction at 298 K is in excellent agreement with the only available experimentally measured value. Activation energies and overall rate coefficients at different temperatures are predicted for the first time for butadiene + SH rad and isoprene + SH rad reactions. The reactions of butadiene and isoprene with SH rad radicals were found to be about four times faster than with OH rad radicals.

Reactivity of molecular dioxygen towards a series of isostructural dichloroiron(III) complexes with tripodal tetraamine ligands: general access to mu-oxodiiron(III) complexes and effect of alpha-fluorination on the reaction kinetics.

PubMed

Thallaj, Nasser K; Rotthaus, Olaf; Benhamou, Leila; Humbert, Nicolas; Elhabiri, Mourad; Lachkar, Mohammed; Welter, Richard; Albrecht-Gary, Anne-Marie; Mandon, Dominique

2008-01-01

We have synthesized the mono, di-, and tri-alpha-fluoro ligands in the tris(2-pyridylmethyl)amine (TPA) series, namely, FTPA, F(2)TPA and F(3)TPA, respectively. Fluorination at the alpha-position of these nitrogen-containing tripods shifts the oxidation potential of the ligand by 45-70 mV per added fluorine atom. The crystal structures of the dichloroiron(II) complexes with FTPA and F(2)TPA reveal that the iron center lies in a distorted octahedral geometry comparable to that already found in TPAFeCl(2). All spectroscopic data indicate that the geometry is retained in solution. These three isostructural complexes all react with molecular dioxygen to yield stable mu-oxodiiron(III) complexes. Crystal structure analyses are reported for each of these three mu-oxo compounds. With TPA, a symmetrical structure is obtained for a dicationic compound with the tripod coordinated in the kappa(4)N coordination mode. With FTPA, the compound is a neutral mu-oxodiiron(III) complex with a kappa(3)N coordination mode of the ligand. Oxygenation of the F(2)TPA complex gave a neutral unsymmetrical compound, the structure of which is reminiscent of that already found with the trifluorinated ligand. On reduction, all mu-oxodiiron(III) complexes revert to the starting iron(II) species. The oxygenation reaction parallels the well-known formation of mu-oxo derivatives from dioxygen in the chemistry of porphyrins reported almost three decades ago. The striking feature of the series of iron(II) precursors is the effect of the ligand on the kinetics of oxygenation of the complexes. Whereas the parent complex undergoes 90 % conversion over 40 h, the monofluorinated ligand provides a complex that has fully reacted after 30 h, whereas the reaction time for the complex with the difluorinated ligand is only 10 h. Analysis of the spectroscopic data reveals that formation of the mu-oxo complexes proceeds in two distinct reversible kinetic steps with k(1) approximately 10 k(2). For TPAFeCl(2) and FTPAFeCl(2) only small variations in the k(1) and k(2) values are observed. By contrast, F(2)TPAFeCl(2) exhibits k(1) and k(2) values that are ten times higher. These differences in kinetics are interpreted in the light of structural and electronic effects, especially the Lewis acidity at the metal center. Our results suggest coordination of dioxygen as an initial step in the process leading to formation of mu-oxodiiron(III) compounds, by contrast with an unlikely outer-sphere reduction of dioxygen, which generally occurs at negative potentials.

Biphasic catalysis in water/carbon dioxide micellar systems

DOEpatents

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

2002-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2007-01-01

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

The radiolysis of CMPO: effects of acid, metal complexation and alpha vs. gamma radiation

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

Bruce J. Mincher; Stephen P. Mezyk; Gary S. Groenewold

Abstract The group actinide/lanthanide complexing agent octylphenylcarbamoylmethyl phosphine oxide (CMPO) has been examined for its radiation stability by measuring the kinetics of its reactions with free radicals in both the aqueous and organic phases for the free and metal-complexed ligand, identifying its degradation products for both alpha and gamma irradiation, measuring the effects on solvent extraction performance, and measuring the G-values for its degradation under various conditions. This includes the G-values for CMPO in the absence of, and in contact with the acidic aqueous phase, where it is shown that the acidic aqueous phase provides radio-protection for this ligand. Itmore » was found that both solvent and metal complexation affect the kinetics of the reaction of the •NO3 radical, a product of HNO3 radiolysis, with CMPO. For example, CMPO complexed with lanthanides has a rate constant for this reaction an order of magnitude higher than for the free ligand, and the reaction for the free ligand in the organic phase is about three times faster than in the aqueous phase. In steady state radiolysis kinetics it was determined that HNO3, although not NO3- anion, provides radio-protection to CMPO, with the G-value for its degradation decreasing with increasing acidity, until it was almost completely suppressed by irradiation in contact with 5 M HNO3. The same degradation products were produced by irradiation with alpha and gamma-sources, except that the relative abundances of these products varied. For example, the product of C-C bond scission was produced only in low amounts for gamma-radiolysis, but it was an important product for samples irradiated with a He ion beam. These results are compared to the new data appearing in the literature on DGA radiolysis, since CMPO and the DGAs both contain the amide functional group.« less

Protein kinase A catalytic subunit primed for action: Time-lapse crystallography of Michaelis complex formation

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

Das, Amit; Gerlits, Oksana O.; Parks, Jerry M.

The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg 2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopeptide substrate and unreacted Mg 2ATP, including the Michaelis complex, that reveal important geometric rearrangements in and near the active site preceding the phosphoryl transfer reaction. Contrary to the prevailing view, Mg 2+ binds first to the M1 site as a complex with ATP and is followed by Mg 2+ binding to themore » M2 site. Furthermore, the target serine hydroxyl of the peptide substrate rotates away from the active site toward the bulk solvent, which breaks the hydrogen bond with D166. In conclusion, the serine hydroxyl of the substrate rotates back toward D166 to form the Michaelis complex with the active site primed for phosphoryl transfer.« less

Protein kinase A catalytic subunit primed for action: Time-lapse crystallography of Michaelis complex formation

DOE PAGES

Das, Amit; Gerlits, Oksana O.; Parks, Jerry M.; ...

2015-11-12

The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg 2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopeptide substrate and unreacted Mg 2ATP, including the Michaelis complex, that reveal important geometric rearrangements in and near the active site preceding the phosphoryl transfer reaction. Contrary to the prevailing view, Mg 2+ binds first to the M1 site as a complex with ATP and is followed by Mg 2+ binding to themore » M2 site. Furthermore, the target serine hydroxyl of the peptide substrate rotates away from the active site toward the bulk solvent, which breaks the hydrogen bond with D166. In conclusion, the serine hydroxyl of the substrate rotates back toward D166 to form the Michaelis complex with the active site primed for phosphoryl transfer.« less

Attainable region analysis for continuous production of second generation bioethanol

PubMed Central

2013-01-01

Background Despite its semi-commercial status, ethanol production from lignocellulosics presents many complexities not yet fully solved. Since the pretreatment stage has been recognized as a complex and yield-determining step, it has been extensively studied. However, economic success of the production process also requires optimization of the biochemical conversion stage. This work addresses the search of bioreactor configurations with improved residence times for continuous enzymatic saccharification and fermentation operations. Instead of analyzing each possible configuration through simulation, we apply graphical methods to optimize the residence time of reactor networks composed of steady-state reactors. Although this can be easily made for processes described by a single kinetic expression, reactions under analysis do not exhibit this feature. Hence, the attainable region method, able to handle multiple species and its reactions, was applied for continuous reactors. Additionally, the effects of the sugars contained in the pretreatment liquor over the enzymatic hydrolysis and simultaneous saccharification and fermentation (SSF) were assessed. Results We obtained candidate attainable regions for separate enzymatic hydrolysis and fermentation (SHF) and SSF operations, both fed with pretreated corn stover. Results show that, despite the complexity of the reaction networks and underlying kinetics, the reactor networks that minimize the residence time can be constructed by using plug flow reactors and continuous stirred tank reactors. Regarding the effect of soluble solids in the feed stream to the reactor network, for SHF higher glucose concentration and yield are achieved for enzymatic hydrolysis with washed solids. Similarly, for SSF, higher yields and bioethanol titers are obtained using this substrate. Conclusions In this work, we demonstrated the capabilities of the attainable region analysis as a tool to assess the optimal reactor network with minimum residence time applied to the SHF and SSF operations for lignocellulosic ethanol production. The methodology can be readily modified to evaluate other kinetic models of different substrates, enzymes and microorganisms when available. From the obtained results, the most suitable reactor configuration considering residence time and rheological aspects is a continuous stirred tank reactor followed by a plug flow reactor (both in SSF mode) using washed solids as substrate. PMID:24286451

Attainable region analysis for continuous production of second generation bioethanol.

PubMed

Scott, Felipe; Conejeros, Raúl; Aroca, Germán

2013-11-29

Despite its semi-commercial status, ethanol production from lignocellulosics presents many complexities not yet fully solved. Since the pretreatment stage has been recognized as a complex and yield-determining step, it has been extensively studied. However, economic success of the production process also requires optimization of the biochemical conversion stage. This work addresses the search of bioreactor configurations with improved residence times for continuous enzymatic saccharification and fermentation operations. Instead of analyzing each possible configuration through simulation, we apply graphical methods to optimize the residence time of reactor networks composed of steady-state reactors. Although this can be easily made for processes described by a single kinetic expression, reactions under analysis do not exhibit this feature. Hence, the attainable region method, able to handle multiple species and its reactions, was applied for continuous reactors. Additionally, the effects of the sugars contained in the pretreatment liquor over the enzymatic hydrolysis and simultaneous saccharification and fermentation (SSF) were assessed. We obtained candidate attainable regions for separate enzymatic hydrolysis and fermentation (SHF) and SSF operations, both fed with pretreated corn stover. Results show that, despite the complexity of the reaction networks and underlying kinetics, the reactor networks that minimize the residence time can be constructed by using plug flow reactors and continuous stirred tank reactors. Regarding the effect of soluble solids in the feed stream to the reactor network, for SHF higher glucose concentration and yield are achieved for enzymatic hydrolysis with washed solids. Similarly, for SSF, higher yields and bioethanol titers are obtained using this substrate. In this work, we demonstrated the capabilities of the attainable region analysis as a tool to assess the optimal reactor network with minimum residence time applied to the SHF and SSF operations for lignocellulosic ethanol production. The methodology can be readily modified to evaluate other kinetic models of different substrates, enzymes and microorganisms when available. From the obtained results, the most suitable reactor configuration considering residence time and rheological aspects is a continuous stirred tank reactor followed by a plug flow reactor (both in SSF mode) using washed solids as substrate.

Exercise and Cognitive Functioning in People With Chronic Whiplash-Associated Disorders: A Controlled Laboratory Study.

PubMed

Ickmans, Kelly; Meeus, Mira; De Kooning, Margot; De Backer, Annabelle; Kooremans, Daniëlle; Hubloue, Ives; Schmitz, Tom; Van Loo, Michel; Nijs, Jo

2016-02-01

Controlled laboratory study. In addition to persistent pain, people with chronic whiplash-associated disorders (WAD) commonly deal with cognitive dysfunctions. In healthy individuals, aerobic exercise has a positive effect on cognitive performance, and preliminary evidence in other chronic pain conditions reveals promising results as well. However, there is evidence that people with chronic WAD may show a worsening of the symptom complex following physical exertion. To examine postexercise cognitive performance in people with chronic WAD. People with chronic WAD (n = 27) and healthy, inactive, sex- and age-matched controls (n = 27) performed a single bout of an incremental submaximal cycling exercise. Before and after the exercise, participants completed 2 performance-based cognitive tests assessing selective and sustained attention, cognitive inhibition, and simple and choice reaction time. At baseline, people with chronic WAD displayed significantly lower scores on sustained attention and simple reaction time (P<.001), but not on selective attention, cognitive inhibition, and choice reaction time (P>.05), compared with healthy controls. Postexercise, both groups showed significantly improved selective attention and choice reaction time (chronic WAD, P = .001; control, P<.001), while simple reaction time significantly increased (P = .037) only in the control group. In both groups, no other significant changes in sustained attention, cognitive inhibition, pain, and fatigue were observed (P>.05). In the short term, postexercise cognitive functioning, pain, and fatigue were not aggravated in people with chronic WAD. However, randomized controlled trials are required to study the longer-term and isolated effects of exercise on cognitive functioning.

Development of interactive graphic user interfaces for modeling reaction-based biogeochemical processes in batch systems with BIOGEOCHEM

NASA Astrophysics Data System (ADS)

Chang, C.; Li, M.; Yeh, G.

2010-12-01

The BIOGEOCHEM numerical model (Yeh and Fang, 2002; Fang et al., 2003) was developed with FORTRAN for simulating reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions in batch systems. A complete suite of reactions including aqueous complexation, adsorption/desorption, ion-exchange, redox, precipitation/dissolution, acid-base reactions, and microbial mediated reactions were embodied in this unique modeling tool. Any reaction can be treated as fast/equilibrium or slow/kinetic reaction. An equilibrium reaction is modeled with an implicit finite rate governed by a mass action equilibrium equation or by a user-specified algebraic equation. A kinetic reaction is modeled with an explicit finite rate with an elementary rate, microbial mediated enzymatic kinetics, or a user-specified rate equation. None of the existing models has encompassed this wide array of scopes. To ease the input/output learning curve using the unique feature of BIOGEOCHEM, an interactive graphic user interface was developed with the Microsoft Visual Studio and .Net tools. Several user-friendly features, such as pop-up help windows, typo warning messages, and on-screen input hints, were implemented, which are robust. All input data can be real-time viewed and automated to conform with the input file format of BIOGEOCHEM. A post-processor for graphic visualizations of simulated results was also embedded for immediate demonstrations. By following data input windows step by step, errorless BIOGEOCHEM input files can be created even if users have little prior experiences in FORTRAN. With this user-friendly interface, the time effort to conduct simulations with BIOGEOCHEM can be greatly reduced.

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

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

Maggi, F.M.; Riley, W.J.

2009-11-01

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

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

PubMed

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

2012-10-01

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

Emotions over time: synchronicity and development of subjective, physiological, and facial affective reactions to music.

PubMed

Grewe, Oliver; Nagel, Frederik; Kopiez, Reinhard; Altenmüller, Eckart

2007-11-01

Most people are able to identify basic emotions expressed in music and experience affective reactions to music. But does music generally induce emotion? Does it elicit subjective feelings, physiological arousal, and motor reactions reliably in different individuals? In this interdisciplinary study, measurement of skin conductance, facial muscle activity, and self-monitoring were synchronized with musical stimuli. A group of 38 participants listened to classical, rock, and pop music and reported their feelings in a two-dimensional emotion space during listening. The first entrance of a solo voice or choir and the beginning of new sections were found to elicit interindividual changes in subjective feelings and physiological arousal. Quincy Jones' "Bossa Nova" motivated movement and laughing in more than half of the participants. Bodily reactions such as "goose bumps" and "shivers" could be stimulated by the "Tuba Mirum" from Mozart's Requiem in 7 of 38 participants. In addition, the authors repeated the experiment seven times with one participant to examine intraindividual stability of effects. This exploratory combination of approaches throws a new light on the astonishing complexity of affective music listening.

Driving Ability of HMX based Aluminized Explosive Affected by the Reaction Degree of Aluminum Powder

NASA Astrophysics Data System (ADS)

Duan, Yingliang

2017-06-01

Due to the time scale of aluminum reaction, the detonation process of the aluminized explosive becomes very complex, and there is less agreement on the reaction mechanism of aluminum powder. If the reaction of aluminum occurs in the reaction zone, the energy released will further strengthen the work ability of detonation wave. So it is very important for characterizing the detonation parameters and detonation driving ability to accurately understand the role of aluminum powder in the reaction zone. In this paper, detonation driving process of HMX based aluminized explosive was studied by cylinder test, obtaining the expansion track of cylinder wall. In order to further research the reaction degree (λ) of aluminum in the reaction zone, the thermodynamic program VHL was used to calculate the detonation process at different reaction degrees, obtaining the parameters of detonation products thermodynamic state. Using the dynamic software LS-DYNA and the JWL equation of state by fitting the pressure and relative volume relationship, the cylinder test was simulated. Compared with the experimental results, when the reaction degree is 20%, the driving ability is found to be in agreement with measured ones. It is concluded that the driving ability of HMX based aluminized explosive can be more accurately characterized by considering the reaction degree of aluminum powder in the reaction zone.

C-Cl bond activation and catalytic hydrodechlorination of hexachlorobenzene by cobalt and nickel complexes with sodium formate as a reducing agent.

PubMed

Li, Junye; Li, Xiaoyan; Wang, Lin; Hu, Qingping; Sun, Hongjian

2014-05-14

A benzyne cobalt complex, Co(η(2)-C6Cl4)(PMe3)3 (2), was generated from the reaction of hexachlorobenzene with 2 equiv. of Co(PMe3)4 through selective activation of two C-Cl bonds of hexachlorobenzene. Meanwhile, the byproduct CoCl2(PMe3)3 was also confirmed by IR spectra. The cobalt(II) complex, CoCl(C6Cl5)(PMe3)3 (1), as an intermediate in the formation of aryne complex 2, was also isolated by the reaction of hexachlorobenzene with the stoichiometric amount of Co(PMe3)4. Complex 2 could be obtained by the reaction of 1 with Co(PMe3)4. Under similar reaction conditions, the reaction of Ni(PMe3)4 with hexachlorobenzene afforded only a mono-(C-Cl) bond activation nickel(II) complex, NiCl(C6H5)(PMe3)2 (5). The expected benzyne nickel complex was not formed. The structures of complexes 2 and 5 were determined by X-ray single crystal diffraction. Successful selective hydrodechlorinations of hexachlorobenzene were studied and in the presence of Co(PMe3)4 or Ni(PMe3)4 as catalysts and sodium formate as a reducing agent pentachlorobenzene and 1,2,4,5-tetrachlorobenzene were obtained. The catalytic hydrodechlorination mechanism is proposed and discussed.

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

NASA Technical Reports Server (NTRS)

Sarani, Siamak

2010-01-01

This paper describes a methodology for accurate and flight-calibrated determination of the on-times of the Cassini spacecraft Reaction Control System (RCS) thrusters, without any form of dynamic simulation, for the reaction wheel biases. The hydrazine usage and the delta V vector in body frame are also computed from the respective thruster on-times. The Cassini spacecraft, the largest and most complex interplanetary spacecraft ever built, continues to undertake ambitious and unique scientific observations of planet Saturn, Titan, Enceladus, and other moons of Saturn. In order to maintain a stable attitude during the course of its mission, this three-axis stabilized spacecraft uses two different control systems: the RCS and the reaction wheel assembly control system. The RCS is used to execute a commanded spacecraft slew, to maintain three-axis attitude control, control spacecraft's attitude while performing science observations with coarse pointing requirements, e.g. during targeted low-altitude Titan and Enceladus flybys, bias the momentum of reaction wheels, and to perform RCS-based orbit trim maneuvers. The use of RCS often imparts undesired delta V on the spacecraft. The Cassini navigation team requires accurate predictions of the delta V in spacecraft coordinates and inertial frame resulting from slews using RCS thrusters and more importantly from reaction wheel bias events. It is crucial for the Cassini spacecraft attitude control and navigation teams to be able to, quickly but accurately, predict the hydrazine usage and delta V for various reaction wheel bias events without actually having to spend time and resources simulating the event in flight software-based dynamic simulation or hardware-in-the-loop simulation environments. The methodology described in this paper, and the ground software developed thereof, are designed to provide just that. This methodology assumes a priori knowledge of thrust magnitudes and thruster pulse rise and tail-off time constants for eight individual attitude control thrusters, the spacecraft's wet mass and its center of mass location, and a few other key parameters.

David Brandner | NREL

Science.gov Websites

chemical reaction engineering and transport phenomena Analytical analysis of complex bio-derived samples and Lignin Areas of Expertise Analytical analysis of complex samples Chemical reaction engineering and

Synthesis and catalytic activity of N-heterocyclic silylene (NHSi) cobalt hydride for Kumada coupling reactions.

PubMed

Qi, Xinghao; Sun, Hongjian; Li, Xiaoyan; Fuhr, Olaf; Fenske, Dieter

2018-02-20

The electron-rich silylene Co(i) chloride 5 was obtained through the reaction of CoCl(PMe 3 ) 3 with chlorosilylene. Complex 5 reacted with 1,3-siladiazole HSiMe(NCH 2 PPh 2 ) 2 C 6 H 4 to give the silylene Co(iii) hydride 6 through chelate-assisted Si-H activation. To the best of our knowledge, complex 6 is the first example of Co(iii) hydride supported by N-heterocyclic silylene. Complexes 5 and 6 were fully characterized by spectroscopic methods and X-ray diffraction analysis. Complex 6 was used as an efficient precatalyst for Kumada cross-coupling reactions. Compared with the related complex 3 supported by only trimethylphosphine, complex 6 as a catalyst supported by both chlorosilylene and trimethylphosphine exhibits a more efficient performance for the Kumada cross-coupling reactions. A novel catalytic radical mechanism was suggested and experimentally verified. As an intermediate silylene cobalt(ii) chloride 6d was isolated and structurally characterized.

Controlling Complex Systems and Developing Dynamic Technology

NASA Astrophysics Data System (ADS)

Avizienis, Audrius Victor

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

Monolithic Microfluidic Mixing-Spraying Devices for Time-Resolved Cryo-Electron Microscopy

PubMed Central

Lu, Zonghuan; Shaikh, Tanvir R.; Barnard, David; Meng, Xing; Mohamed, Hisham; Yassin, Aymen; Mannella, Carmen A.; Agrawal, Rajendra K.; Lu, Toh-Ming

2009-01-01

The goal of time-resolved cryo-electron microscopy is to determine structural models for transient functional states of large macromolecular complexes such as ribosomes and viruses. The challenge of time-resolved cryo-electron microscopy is to rapidly mix reactants, and then, following a defined time interval, to rapidly deposit them as a thin film and freeze the sample to the vitreous state. Here we describe a methodology in which reaction components are mixed and allowed to react, and are then sprayed onto an EM grid as it is being plunged into cryogen. All steps are accomplished by a monolithic, microfabricated silicon device that incorporates a mixer, reaction channel, and pneumatic sprayer in a single chip. We have found that microdroplets produced by air atomization spread to sufficiently thin films on a millisecond time scale provided that the carbon supporting film is made suitably hydrophilic. The device incorporates two T-mixers flowing into a single channel of four butterfly-shaped mixing elements that ensure effective mixing, followed by a microfluidic reaction channel whose length can be varied to achieve the desired reaction time. The reaction channel is flanked by two ports connected to compressed humidified nitrogen gas (at 50 psi) to generate the spray. The monolithic mixer-sprayer is incorporated into a computer-controlled plunging apparatus. To test the mixing performance and the suitability of the device for preparation of biological macromolecules for cryo-EM, ribosomes and ferritin were mixed in the device and sprayed onto grids. Three-dimensional reconstructions of the ribosomes demonstrated retention of native structure, and 30S and 50S subunits were shown to be capable of reassociation into ribosomes after passage through the device. PMID:19683579

Enzymatic synthesis of chiral amino‐alcohols by coupling transketolase and transaminase‐catalyzed reactions in a cascading continuous‐flow microreactor system

PubMed Central

Gruber, Pia; Carvalho, Filipe; Marques, Marco P. C.; O'Sullivan, Brian; Subrizi, Fabiana; Dobrijevic, Dragana; Ward, John; Hailes, Helen C.; Fernandes, Pedro; Wohlgemuth, Roland; Baganz, Frank

2017-01-01

Abstract Rapid biocatalytic process development and intensification continues to be challenging with currently available methods. Chiral amino‐alcohols are of particular interest as they represent key industrial synthons for the production of complex molecules and optically pure pharmaceuticals. (2S,3R)‐2‐amino‐1,3,4‐butanetriol (ABT), a building block for the synthesis of protease inhibitors and detoxifying agents, can be synthesized from simple, non‐chiral starting materials, by coupling a transketolase‐ and a transaminase‐catalyzed reaction. However, until today, full conversion has not been shown and, typically, long reaction times are reported, making process modifications and improvement challenging. In this contribution, we present a novel microreactor‐based approach based on free enzymes, and we report for the first time full conversion of ABT in a coupled enzyme cascade for both batch and continuous‐flow systems. Using the compartmentalization of the reactions afforded by the microreactor cascade, we overcame inhibitory effects, increased the activity per unit volume, and optimized individual reaction conditions. The transketolase‐catalyzed reaction was completed in under 10 min with a volumetric activity of 3.25 U ml−1. Following optimization of the transaminase‐catalyzed reaction, a volumetric activity of 10.8 U ml−1 was attained which led to full conversion of the coupled reaction in 2 hr. The presented approach illustrates how continuous‐flow microreactors can be applied for the design and optimization of biocatalytic processes. PMID:28986983

Synthesis and characterization of novel Cu(II) complex coated Fe3O4@SiO2 nanoparticles for catalytic performance

NASA Astrophysics Data System (ADS)

Nasrollahzadeh, Mahmoud; Sajjadi, Mohaddeseh; Khonakdar, Hossein Ali

2018-06-01

In this study, a convenient method for the synthesis of arylaminotetrazoles has been developed using a copper (II)-aminotetrazole complex immobilized on silica-coated Fe3O4 (Fe3O4@SiO2) nanoparticles (Fe3O4@SiO2-aminotet-Cu(II)) as a novel and efficient magnetically catalyst. The constructed superparamagnetic core-shell nanoparticles were successfully prepared, as proven using different spectroscopic techniques such as fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), transmission electron microscope (TEM), field emission scanning electron microscopy (FESEM), energy dispersive X-ray spectroscopy (EDS), thermogravimetry and differential thermogravimetry (TG-DTG) and vibrating sample magnetometer (VSM) analysis. The applicability of Fe3O4@SiO2-aminotet-Cu(II) magnetic catalyst allows the efficient synthesis of a variety of arylaminotetrazoles from the reaction between various arylcyanamides with sodium azide in high yields. The effect of catalyst loading was investigated. In addition, the reaction mechanism for the synthesis of arylaminotetrazoles was reasonably proposed. Results show that the 1-aryl-5-amino-1H-tetrazole (B isomer) and 5-arylamino-1H-tetrazole (A isomer) can be obtained from the arylcyanamides carrying electron-donating and electron-withdrawing substituents, respectively. This procedure offers a simple methodology, relatively short reaction times, easy work-up, high yields of the products and a cleaner reaction with elimination of hydrazoic acid (HN3). Moreover, catalyst can be conveniently recovered through the use of external magnet and reused for at least 6 times without any significant loss of its activity.

Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noise

NASA Astrophysics Data System (ADS)

Leier, André; Marquez-Lago, Tatiana T.; Burrage, Kevin

2008-05-01

The delay stochastic simulation algorithm (DSSA) by Barrio et al. [Plos Comput. Biol. 2, 117(E) (2006)] was developed to simulate delayed processes in cell biology in the presence of intrinsic noise, that is, when there are small-to-moderate numbers of certain key molecules present in a chemical reaction system. These delayed processes can faithfully represent complex interactions and mechanisms that imply a number of spatiotemporal processes often not explicitly modeled such as transcription and translation, basic in the modeling of cell signaling pathways. However, for systems with widely varying reaction rate constants or large numbers of molecules, the simulation time steps of both the stochastic simulation algorithm (SSA) and the DSSA can become very small causing considerable computational overheads. In order to overcome the limit of small step sizes, various τ-leap strategies have been suggested for improving computational performance of the SSA. In this paper, we present a binomial τ-DSSA method that extends the τ-leap idea to the delay setting and avoids drawing insufficient numbers of reactions, a common shortcoming of existing binomial τ-leap methods that becomes evident when dealing with complex chemical interactions. The resulting inaccuracies are most evident in the delayed case, even when considering reaction products as potential reactants within the same time step in which they are produced. Moreover, we extend the framework to account for multicellular systems with different degrees of intercellular communication. We apply these ideas to two important genetic regulatory models, namely, the hes1 gene, implicated as a molecular clock, and a Her1/Her 7 model for coupled oscillating cells.

Solving of the coefficient inverse problems for a nonlinear singularly perturbed reaction-diffusion-advection equation with the final time data

NASA Astrophysics Data System (ADS)

Lukyanenko, D. V.; Shishlenin, M. A.; Volkov, V. T.

2018-01-01

We propose the numerical method for solving coefficient inverse problem for a nonlinear singularly perturbed reaction-diffusion-advection equation with the final time observation data based on the asymptotic analysis and the gradient method. Asymptotic analysis allows us to extract a priory information about interior layer (moving front), which appears in the direct problem, and boundary layers, which appear in the conjugate problem. We describe and implement the method of constructing a dynamically adapted mesh based on this a priory information. The dynamically adapted mesh significantly reduces the complexity of the numerical calculations and improve the numerical stability in comparison with the usual approaches. Numerical example shows the effectiveness of the proposed method.

DNA curtains for high-throughput single-molecule optical imaging.

PubMed

Greene, Eric C; Wind, Shalom; Fazio, Teresa; Gorman, Jason; Visnapuu, Mari-Liis

2010-01-01

Single-molecule approaches provide a valuable tool in the arsenal of the modern biologist, and new discoveries continue to be made possible through the use of these state-of-the-art technologies. However, it can be inherently difficult to obtain statistically relevant data from experimental approaches specifically designed to probe individual reactions. This problem is compounded with more complex biochemical reactions, heterogeneous systems, and/or reactions requiring the use of long DNA substrates. Here we give an overview of a technology developed in our laboratory, which relies upon simple micro- or nanofabricated structures in combination with "bio-friendly" lipid bilayers, to align thousands of long DNA molecules into defined patterns on the surface of a microfluidic sample chamber. We call these "DNA curtains," and we have developed several different versions varying in complexity and DNA substrate configuration, which are designed to meet different experimental needs. This novel approach to single-molecule imaging provides a powerful experimental platform that offers the potential for concurrent observation of hundreds or even thousands of protein-DNA interactions in real time. Copyright 2010 Elsevier Inc. All rights reserved.

[Parametabolism as Non-Specific Modifier of Supramolecular Interactions in Living Systems].

PubMed

Kozlov, V A; Sapozhnikov, S P; Sheptuhina, A I; Golenkov, A V

2015-01-01

As it became known recently, in addition to the enzyme (enzymes and/or ribozymes) in living organisms occur a large number of ordinary chemical reactions without the participation of biological catalysts. These reactions are distinguished by low speed and, as a rule, the irreversibility. For example, along with diabetes mellitus, glycation and fructosilation of proteins are observed resulted in posttranslational modification with the low- or nonfunctioning protein formation which is poorly exposed to enzymatic proteolysis and therefore accumulates in the body. In addition, the known processes such as the nonenzymatic carbomoylation, pyridoxylation and thiamiation proteins. There is a reasonable basis to believe that alcoholic injury also realized through parametabolic secondary metabolites synthesis such as acetaldehyde. At the same time, the progress in supramolecular chemistry proves that in biological objects there is another large group ofparametabolic reactions caused by the formation of supramolecular complexes. Obviously, known parameterizes interactions can modify the formation of supramolecular complexes in living objects. These processes are of considerable interest for fundamental biology and fundamental and practical medicine, but they remain unexplored due to a lack of awareness of a wide range of researchers.

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

PubMed

Ifeduba, Ebenezer A; Akoh, Casimir C

2016-05-15

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

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

NASA Astrophysics Data System (ADS)

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

2010-03-01

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

Microwave Synthesis of a Long-Lasting Phosphor

ERIC Educational Resources Information Center

Filhol, Jean-Sebastien; Zitoun, David; Bernaud, Laurent; Manteghetti, Alain

2009-01-01

Efficient glow-in-the-dark materials are usually difficult to synthesize and need complex experiments with long reaction times that are not appropriate for conventional lab teaching. Therefore, we describe a new experimental procedure that allows the production of one of the most efficient "glow-in-the-dark" materials (SrAl[subscript 2]O[subscript…

Physical understanding of complex multiscale biochemical models via algorithmic simplification: Glycolysis in Saccharomyces cerevisiae

NASA Astrophysics Data System (ADS)

Kourdis, Panayotis D.; Steuer, Ralf; Goussis, Dimitris A.

2010-09-01

Large-scale models of cellular reaction networks are usually highly complex and characterized by a wide spectrum of time scales, making a direct interpretation and understanding of the relevant mechanisms almost impossible. We address this issue by demonstrating the benefits provided by model reduction techniques. We employ the Computational Singular Perturbation (CSP) algorithm to analyze the glycolytic pathway of intact yeast cells in the oscillatory regime. As a primary object of research for many decades, glycolytic oscillations represent a paradigmatic candidate for studying biochemical function and mechanisms. Using a previously published full-scale model of glycolysis, we show that, due to fast dissipative time scales, the solution is asymptotically attracted on a low dimensional manifold. Without any further input from the investigator, CSP clarifies several long-standing questions in the analysis of glycolytic oscillations, such as the origin of the oscillations in the upper part of glycolysis, the importance of energy and redox status, as well as the fact that neither the oscillations nor cell-cell synchronization can be understood in terms of glycolysis as a simple linear chain of sequentially coupled reactions.

Extractive Atmospheric Pressure Photoionization (EAPPI) Mass Spectrometry: Rapid Analysis of Chemicals in Complex Matrices.

PubMed

Liu, Chengyuan; Yang, Jiuzhong; Wang, Jian; Hu, Yonghua; Zhao, Wan; Zhou, Zhongyue; Qi, Fei; Pan, Yang

2016-10-01

Extractive atmospheric pressure photoionization (EAPPI) mass spectrometry was designed for rapid qualitative and quantitative analysis of chemicals in complex matrices. In this method, an ultrasonic nebulization system was applied to sample extraction, nebulization, and vaporization. Mixed with a gaseous dopant, vaporized analytes were ionized through ambient photon-induced ion-molecule reactions, and were mass-analyzed by a high resolution time-of-flight mass spectrometer (TOF-MS). After careful optimization and testing with pure sample solution, EAPPI was successfully applied to the fast screening of capsules, soil, natural products, and viscous compounds. Analysis was completed within a few seconds without the need for preseparation. Moreover, the quantification capability of EAPPI for matrices was evaluated by analyzing six polycyclic aromatic hydrocarbons (PAHs) in soil. The correlation coefficients (R (2) ) for standard curves of all six PAHs were above 0.99, and the detection limits were in the range of 0.16-0.34 ng/mg. In addition, EAPPI could also be used to monitor organic chemical reactions in real time. Graphical Abstract ᅟ.

Remote Monitoring for Follow-up of Patients with Cardiac Implantable Electronic Devices

PubMed Central

Morichelli, Loredana; Varma, Niraj

2014-01-01

Follow-up of patients with cardiac implantable electronic devices is challenging due to the increasing number and technical complexity of devices coupled to increasing clinical complexity of patients. Remote monitoring (RM) offers the opportunity to optimise clinic workflow and to improve device monitoring and patient management. Several randomised clinical trials and registries have demonstrated that RM may reduce number of hospital visits, time required for patient follow-up, physician and nurse time, hospital and social costs. Furthermore, patient retention and adherence to follow-up schedule are significantly improved by RM. Continuous wireless monitoring of data stored in the device memory with automatic alerts allows early detection of device malfunctions and of events requiring clinical reaction, such as atrial fibrillation, ventricular arrhythmias and heart failure. Early reaction may improve patient outcome. RM is easy to use and patients showed a high level of acceptance and satisfaction. Implementing RM in daily practice may require changes in clinic workflow. To this purpose, new organisational models have been introduced. In spite of a favourable cost:benefit ratio, RM reimbursement still represents an issue in several European countries. PMID:26835079

Reaction Dynamics Following Ionization of Ammonia Dimer Adsorbed on Ice Surface.

PubMed

Tachikawa, Hiroto

2016-09-22

The ice surface provides an effective two-dimensional reaction field in interstellar space. However, how the ice surface affects the reaction mechanism is still unknown. In the present study, the reaction of an ammonia dimer cation adsorbed both on water ice and cluster surface was theoretically investigated using direct ab initio molecular dynamics (AIMD) combined with our own n-layered integrated molecular orbital and molecular mechanics (ONIOM) method, and the results were compared with reactions in the gas phase and on water clusters. A rapid proton transfer (PT) from NH3(+) to NH3 takes place after the ionization and the formation of intermediate complex NH2(NH4(+)) is found. The reaction rate of PT was significantly affected by the media connecting to the ammonia dimer. The time of PT was calculated to be 50 fs (in the gas phase), 38 fs (on ice), and 28-33 fs (on water clusters). The dissociation of NH2(NH4(+)) occurred on an ice surface. The reason behind the reaction acceleration on an ice surface is discussed.

A New Look on Protein-Polyphenol Complexation during Honey Storage: Is This a Random or Organized Event with the Help of Dirigent-Like Proteins?

PubMed Central

Brudzynski, Katrina; Sjaarda, Calvin; Maldonado-Alvarez, Liset

2013-01-01

Honey storage initiates melanoidin formation that involves a cascade of seemingly unguided redox reactions between amino acids/proteins, reducing sugars and polyphenols. In the process, high molecular weight protein-polyphenol complexes are formed, but the mechanism involved remains unknown. The objective of this study was twofold: to determine quantitative and qualitative changes in proteins in honeys stored for prolonged times and in different temperatures and to relate these changes to the formation of protein-polyphenol complexes. Six -month storage decreased the protein content by 46.7% in all tested honeys (t-test, p<0.002) with the rapid reduction occurring during the first three month. The changes in protein levels coincided with alterations in molecular size and net charge of proteins on SDS –PAGE. Electro-blotted proteins reacted with a quinone-specific nitro blue tetrazolium (NBT) on nitrocellulose membranes indicating that quinones derived from oxidized polyphenols formed covalent bonds with proteins. Protein-polyphenol complexes isolated by size-exclusion chromatography differed in size and stoichiometry and fall into two categories: (a) high molecular weight complexes (230–180 kDa) enriched in proteins but possessing a limited reducing activity toward the NBT and (b) lower molecular size complexes (110–85 kDa) enriched in polyphenols but strongly reducing the dye. The variable stoichiometry suggest that the large, “protein-type” complexes were formed by protein cross-linking, while in the smaller, “polyphenol-type” complexes polyphenols were first polymerized prior to protein binding. Quinones preferentially bound a 31 kDa protein which, by the electrospray quadrupole time of flight mass spectrometry (ESI-Qtof-MS) analysis, showed homology to dirigent-like proteins known for assisting in radical coupling and polymerization of phenolic compounds. These findings provide a new look on protein-polyphenol interaction in honey where the reaction of quinones with proteins and polyphenols could possibly be under assumed guidance of dirigent proteins. PMID:24023654

Ultrafast Primary Reactions in the Photosystems of Oxygen-Evolving Organisms

NASA Astrophysics Data System (ADS)

Holzwarth, A. R.

In oxygen-evolving photosynthetic organisms (plants, green algae, cyanobacteria), the primary steps of photosynthesis occur in two membrane-bound protein supercomplexes, Photosystem I (PS I) and Photosystem II (PS II), located in the thylakoid membrane (c.f. Fig. 7.1) along with two other important protein complexes, the cytochrome b6/f complex and the ATP-synthase [1]. Each of the photosystems consists of a reaction center (RC) where the photoinduced early electron transfer processes occur, of a so-called core antenna consisting of chlorophyll (Chl) protein complexes responsible for light absorption and ultrafast energy transfer to the RC pigments, and additional peripheral antenna complexes of various kinds that increase the absorption cross-section. The peripheral complexes are Chl a/b-protein complexes in higher plants and green algae (LHC I or LHC II for PS I or PS II, respectively) and so-called phycobilisomes in cyanobacteria and red algae [2-4]. The structures and light-harvesting functions of these antenna systems have been extensively reviewed [2, 5-9]. Recently, X-ray structures of both PS I and PS II antenna/RC complexes have been determined, some to atomic resolution. Although many details of the pigment content and organization of the RCs and antenna systems of PS I and PS II have been known before, the high resolution structures of the integral complexes allow us for the first time to try to understand structure/function relationships in detail. This article covers our present understanding of the ultrafast energy transfer and early electron transfer processes occurring in the photosystems of oxygen-evolving organisms. The main emphasis will be on the electron transfer processes. However, in both photosystems the kinetics of the energy transfer processes in the core antennae is intimately interwoven with the kinetics of the electron transfer steps. Since both types of processes occur on a similar time scale, their kinetics cannot be considered separately in any experiment and consequently they have to be discussed together.

A new look on protein-polyphenol complexation during honey storage: is this a random or organized event with the help of dirigent-like proteins?

PubMed

Brudzynski, Katrina; Sjaarda, Calvin; Maldonado-Alvarez, Liset

2013-01-01

Honey storage initiates melanoidin formation that involves a cascade of seemingly unguided redox reactions between amino acids/proteins, reducing sugars and polyphenols. In the process, high molecular weight protein-polyphenol complexes are formed, but the mechanism involved remains unknown. The objective of this study was twofold: to determine quantitative and qualitative changes in proteins in honeys stored for prolonged times and in different temperatures and to relate these changes to the formation of protein-polyphenol complexes. Six -month storage decreased the protein content by 46.7% in all tested honeys (t-test, p<0.002) with the rapid reduction occurring during the first three month. The changes in protein levels coincided with alterations in molecular size and net charge of proteins on SDS -PAGE. Electro-blotted proteins reacted with a quinone-specific nitro blue tetrazolium (NBT) on nitrocellulose membranes indicating that quinones derived from oxidized polyphenols formed covalent bonds with proteins. Protein-polyphenol complexes isolated by size-exclusion chromatography differed in size and stoichiometry and fall into two categories: (a) high molecular weight complexes (230-180 kDa) enriched in proteins but possessing a limited reducing activity toward the NBT and (b) lower molecular size complexes (110-85 kDa) enriched in polyphenols but strongly reducing the dye. The variable stoichiometry suggest that the large, "protein-type" complexes were formed by protein cross-linking, while in the smaller, "polyphenol-type" complexes polyphenols were first polymerized prior to protein binding. Quinones preferentially bound a 31 kDa protein which, by the electrospray quadrupole time of flight mass spectrometry (ESI-Qtof-MS) analysis, showed homology to dirigent-like proteins known for assisting in radical coupling and polymerization of phenolic compounds. These findings provide a new look on protein-polyphenol interaction in honey where the reaction of quinones with proteins and polyphenols could possibly be under assumed guidance of dirigent proteins.

Platinum Eta 2 -Disilene Complexes: Syntheses, Reactivity, and Structures

DTIC Science & Technology

1990-01-01

CP ýsq:.Prl 25 C. 7 x, ’ .P’ NSi-...H Reaction of R 2Si(H)Si(H)R.2 with Pt Complexes. PI Ih t~ Oxidative additions of monomeric silanes to platinumPhh2...thermally to product I1 2-complexes 2a,b. The reaction of tetrasubstituted 1,2-dihydridodisi- lanes (R2SiH)2 with bis(phosphine);laitinum equivalents...e.g. (diphos)PtCl2 /Li or (diphos)-. Pt(CH2 -CH2) also yielded platinum ’? 2=disilene complexes f6a (R -i-Pr), Qb (R-He), and kc (R- Ph). Reaction of

Diffusion-controlled reactions modeling in Geant4-DNA

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

Karamitros, M., E-mail: matkara@gmail.com; CNRS, INCIA, UMR 5287, F-33400 Talence; Luan, S.

2014-10-01

Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing allmore » the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k–d tree data structure for quickly locating, for a given molecule, its closest reactants. The performance advantage is presented in terms of complexity, and the accuracy of the new algorithm is demonstrated by simulating radiation chemistry in the context of the Geant4-DNA project. Application The time-dependent radiolytic yields of the main chemical species formed after irradiation are computed for incident protons at different energies (from 50 MeV to 500 keV). Both the time-evolution and energy dependency of the yields are discussed. The evolution, at one microsecond, of the yields of hydroxyls and solvated electrons with respect to the linear energy transfer is compared to theoretical and experimental data. According to our results, at high linear energy transfer, modeling radiation chemistry in the trading compartment representation might be adopted.« less

Protoenzymes: the case of hyperbranched polyesters

NASA Astrophysics Data System (ADS)

Mamajanov, Irena; Cody, George D.

2017-11-01

Enzymes are biopolymeric complexes that catalyse biochemical reactions and shape metabolic pathways. Enzymes usually work with small molecule cofactors that actively participate in reaction mechanisms and complex, usually globular, polymeric structures capable of specific substrate binding, encapsulation and orientation. Moreover, the globular structures of enzymes possess cavities with modulated microenvironments, facilitating the progression of reaction(s). The globular structure is ensured by long folded protein or RNA strands. Synthesis of such elaborate complexes has proven difficult under prebiotically plausible conditions. We explore here that catalysis may have been performed by alternative polymeric structures, namely hyperbranched polymers. Hyperbranched polymers are relatively complex structures that can be synthesized under prebiotically plausible conditions; their globular structure is ensured by virtue of their architecture rather than folding. In this study, we probe the ability of tertiary amine-bearing hyperbranched polyesters to form hydrophobic pockets as a reaction-promoting medium for the Kemp elimination reaction. Our results show that polyesters formed upon reaction between glycerol, triethanolamine and organic acid containing hydrophobic groups, i.e. adipic and methylsuccinic acid, are capable of increasing the rate of Kemp elimination by a factor of up to 3 over monomeric triethanolamine. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Optimizing the Readout of Lanthanide-DOTA Complexes for the Detection of Ligand-Bound Copper(I).

PubMed

Hanna, Jill R; Allan, Christopher; Lawrence, Charlotte; Meyer, Odile; Wilson, Neil D; Hulme, Alison N

2017-05-14

The CuAAC 'click' reaction was used to couple alkyne-functionalized lanthanide-DOTA complexes to a range of fluorescent antennae. Screening of the antenna components was aided by comparison of the luminescent output of the resultant sensors using data normalized to account for reaction conversion as assessed by IR. A maximum 82-fold enhanced signal:background luminescence output was achieved using a Eu(III)-DOTA complex coupled to a coumarin-azide, in a reaction which is specific to the presence of copper(I). This optimized complex provides a new lead design for lanthanide-DOTA complexes which can act as irreversible 'turn-on' catalytic sensors for the detection of ligand-bound copper(I).

Resting State and Elementary Steps of the Coupling of Aryl Halides with Thiols Catalyzed by Alkylbisphosphine Complexes of Palladium

PubMed Central

Alvaro, Elsa

2010-01-01

Detailed mechanistic studies on the coupling of aryl halides with thiols catalyzed by palladium complexes of the alkylbisphosphine ligand CyPF-tBu (1-dicyclohexylphosphino-2-di-tert-butylphosphinoethylferrocene) are reported. The elementary steps that constitute the catalytic cycle, i.e. oxidative addition, transmetalation and reductive elimination, have been studied, and their relative rates are reported. Each of the steps of the catalytic process occurs at temperatures that are much lower than those required for the reactions catalyzed by a combination of palladium precursors and CyPF-tBu. To explain these differences in rates between the catalytic and stoichiometric reactions, studies were conducted to identify the resting state of the catalyst of the reactions catalyzed by a combination of Pd(OAc)2 and CyPF-tBu, a combination of Pd(dba)2 and CyPF-tBu, or the likely intermediate Pd(CyPF-tBu)(Ar)(Br). These show that the major palladium complex in each case lies off of the catalytic cycle. The resting state of the reactions catalyzed by Pd(OAc)2 and CyPF-tBu was the palladium bis-thiolate complex [Pd(CyPF-tBu)(SR)2] (R = alkyl or aryl). The resting state in reactions catalyzed by Pd2(dba)3 and CyPF-tBu was the binuclear complex [Pd(CyPF-tBu)]2(μ2, η2-dba) (9). The resting state of reactions of both aromatic and aliphatic thiols catalyzed by [Pd(CyPF-tBu)(p-tolyl)(Br)] (3a) was the hydridopalladium thiolate complex [Pd(CyPF-tBu)(H)(SR)] (R= alkyl and aryl). All these palladium species have been prepared independently, and the mechanisms by which they enter the catalytic cycle have been examined in detail. These features of the reaction catalyzed by palladium and CyPF-tBu have been compared with those of reactions catalyzed by the alkylbisphosphine DiPPF and Pd(OAc)2 or Pd(dba)2. Our data indicate that the resting states of these reactions are similar to each other and that our mechanistic conclusions about reactions catalyzed by palladium and CyPF-tBu can be extrapolated to reactions catalyzed by complexes of other electron-rich bisphosphines. PMID:19453106

Effect of β-Cyclodextrin Complexation on Solubility and Enzymatic Conversion of Naringin

PubMed Central

Cui, Li; Zhang, Zhen-Hai; Sun, E; Jia, Xiao-Bin

2012-01-01

In the present paper, the effect of β-cyclodextrin (β-CD) inclusion complexation on the solubility and enzymatic hydrolysis of naringin was investigated. The inclusion complex of naringin/β-CD at the molar ratio of 1:1 was obtained by the dropping method and was characterized by differential scanning calorimetry. The solubility of naringin complexes in water at 37 ± 0.1 °C was 15 times greater than that of free naringin. Snailase-involved hydrolysis conditions were tested for the bioconversion of naringin into naringenin using the univariate experimental design. Naringin can be transformed into naringenin by snailase-involved hydrolysis. The optimum conditions for enzymatic hydrolysis were determined as follows: pH 5.0, temperature 37 °C, ratio of snailase/substrate 0.8, substrate concentration 20 mg·mL−1, and reaction time 12 h. Under the optimum conditions, the transforming rate of naringenin from naringin for inclusion complexes and free naringin was 98.7% and 56.2% respectively, suggesting that β-CD complexation can improve the aqueous solubility and consequently the enzymatic hydrolysis rate of naringin. PMID:23203062

Spectral and kinetic effects accompanying the assembly of core complexes of Rhodobacter sphaeroides.

PubMed

Freiberg, Arvi; Chenchiliyan, Manoop; Rätsep, Margus; Timpmann, Kõu

2016-11-01

In the present work, spectral and kinetic changes accompanying the assembly of the light-harvesting 1 (LH1) complex with the reaction center (RC) complex into monomeric RC-LH1 and dimeric RC-LH1-PufX core complexes of the photosynthetic purple bacterium Rhodobacter sphaeroides are systematically studied over the temperature range of 4.5-300K. The samples were interrogated with a combination of optical absorption, hole burning, fluorescence excitation, steady state and picosecond time resolved fluorescence spectroscopy. Fair additivity of the LH1 and RC absorption spectra suggests rather weak electronic coupling between them. A low-energy tail revealed at cryogenic temperatures in the absorption spectra of both monomeric and dimeric core complexes is proved to be due to the special pair of the RC. At selected excitation intensity and temperature, the fluorescence decay time of core complexes is shown to be a function of multiple factors, most importantly of the presence/absence of RCs, the supramolecular architecture (monomeric or dimeric) of the complexes, and whether the complexes were studied in a native membrane environment or in a detergent - purified state. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular-level spectroscopic investigations of the complexation and photodegradation of catechol to/by iron(III)

NASA Astrophysics Data System (ADS)

Al-Abadleh, Hind; Tofan-Lazar, Julia; Situm, Arthur; Slikboer, Samantha

2014-05-01

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

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

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

PubMed

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

2016-02-01

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

Insights into the Binding Sites of Organometallic Ruthenium Anticancer Compounds on Peptides Using Ultra-High Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Wills, Rebecca H.; Habtemariam, Abraha; Lopez-Clavijo, Andrea F.; Barrow, Mark P.; Sadler, Peter J.; O'Connor, Peter B.

2014-04-01

The binding sites of two ruthenium(II) organometallic complexes of the form [(η6-arene)Ru( N, N)Cl]+, where arene/ N, N = biphenyl (bip)/bipyridine (bipy) for complex AH076, and biphenyl (bip)/ o-phenylenediamine ( o-pda) for complex AH078, on the peptides angiotensin and bombesin have been investigated using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. Fragmentation was performed using collisionally activated dissociation (CAD), with, in some cases, additional data being provided by electron capture dissociation (ECD). The primary binding sites were identified as methionine and histidine, with further coordination to phenylalanine, potentially through a π-stacking interaction, which has been observed here for the first time. This initial peptide study was expanded to investigate protein binding through reaction with insulin, on which the binding sites proposed are histidine, glutamic acid, and tyrosine. Further reaction of the ruthenium complexes with the oxidized B chain of insulin, in which two cysteine residues are oxidized to cysteine sulfonic acid (Cys-SO3H), and glutathione, which had been oxidized with hydrogen peroxide to convert the cysteine to cysteine sulfonic acid, provided further support for histidine and glutamic acid binding, respectively.

Didactic Time, Epistemic Gain and Consistent Tool: Taking Care of Teachers' Needs for Classroom Use of CAS--A Reaction to Barzel's "New Technology? New Ways of Teaching--No Time Left for That!"

ERIC Educational Resources Information Center

Lagrange, Jean-Baptiste

2007-01-01

The relationship between teachers and Computer Algebra Systems is generally problematic. The extensive capabilities of CAS provide opportunities for learning but also bring a new complexity that makes it difficult for teachers to take advantage of these opportunities. Barzel's paper contrasts with this observation: in a "Lernwerkstatt"…

An entropic barriers diffusion theory of decision-making in multiple alternative tasks

PubMed Central

Sigman, Mariano; Cecchi, Guillermo A.

2018-01-01

We present a theory of decision-making in the presence of multiple choices that departs from traditional approaches by explicitly incorporating entropic barriers in a stochastic search process. We analyze response time data from an on-line repository of 15 million blitz chess games, and show that our model fits not just the mean and variance, but the entire response time distribution (over several response-time orders of magnitude) at every stage of the game. We apply the model to show that (a) higher cognitive expertise corresponds to the exploration of more complex solution spaces, and (b) reaction times of users at an on-line buying website can be similarly explained. Our model can be seen as a synergy between diffusion models used to model simple two-choice decision-making and planning agents in complex problem solving. PMID:29499036

Multifaceted regulation of V(D)J recombination

NASA Astrophysics Data System (ADS)

Wang, Guannan

V(D)J recombination is responsible for generating an enormous repertoire of immunoglobulins and T cell receptors, therefore it is a centerpiece to the formation of the adaptive immune system. The V(D)J recombination process proceeds through two steps, site-specific cleavage at RSS (Recombination Signal Sequence) site mediated by the RAG recombinase (RAG1/2) and the subsequent imprecise resolution of the DNA ends, which is carried out by the ubiquitous non-homologous end joining pathway (NHEJ). The V(D)J recombination reaction is obliged to be tightly controlled under all circumstances, as it involves generations of DNA double strand breaks, which are considered the most dangerous lesion to a cell. Multifaceted regulatory mechanisms have been evolved to create great diversity of the antigen receptor repertoire while ensuring genome stability. The RAG-mediated cleavage reaction is stringently regulated at both the pre-cleavage stage and the post-cleavage stage. Specifically, RAG1/2 first forms a pre-cleavage complex assembled at the boarder of RSS and coding flank, which ensures the appropriate DNA targeting. Subsequently, this complex initiates site-specific cleavage, generating two types of double stranded DNA breaks, hairpin-ended coding ends (HP-CEs) and blunt signal ends (SEs). After the cleavage, RAG1/2 proteins bind and retain the recombination ends to form post-cleavage complexes (PCC), which collaborates with the NHEJ machinery for appropriate transfer of recombination ends to NHEJ for proper end resolution. However, little is known about the molecular basis of this collaboration, partly attributed to the lack of sensitive assays to reveal the interaction of PCC with HP-CEs. Here, for the first time, by using two complementary fluorescence-based techniques, fluorescence anisotropy and fluorescence resonance energy transfer (FRET), I managed to monitor the RAG1/2-catalyzed cleavage reaction in real time, from the pre-cleavage to the post-cleavage stages. By examining the dynamic fluorescence changes during the RAG-mediated cleavage reactions, and by manipulating the reaction conditions, I was able to characterize some fundamental properties of RAG-DNA interactions before and after cleavage. Firstly, Mg 2+, known as a physiological cofactor at the excision step, also promotes the HP-CEs retention in the RAG complex after cleavage. Secondly, the structure of pre-cleavage complex may affect the subsequent collaborations with NHEJ for end resolution. Thirdly, the non-core region of RAG2 may have differential influences on the PCC retention of HP-CEs and SEs. Furthermore, I also provide the first evidence of RAG1-mediated regulation of RAG2. Our study provides important insights into the multilayered regulatory mechanisms, in modulating recombination events in developing lymphocytes and paves the way for possible development of detection and diagnotic markers for defective recombination events that are often associated immunodeficiency and/or lymphoid malignancy.

Solute transport with equilibrium aqueous complexation and either sorption or ion exchange: Simulation methodology and applications

USGS Publications Warehouse

Lewis, F.M.; Voss, C.I.; Rubin, J.

1987-01-01

Methodologies that account for specific types of chemical reactions in the simulation of solute transport can be developed so they are compatible with solution algorithms employed in existing transport codes. This enables the simulation of reactive transport in complex multidimensional flow regimes, and provides a means for existing codes to account for some of the fundamental chemical processes that occur among transported solutes. Two equilibrium-controlled reaction systems demonstrate a methodology for accommodating chemical interaction into models of solute transport. One system involves the sorption of a given chemical species, as well as two aqueous complexations in which the sorbing species is a participant. The other reaction set involves binary ion exchange coupled with aqueous complexation involving one of the exchanging species. The methodology accommodates these reaction systems through the addition of nonlinear terms to the transport equations for the sorbing species. Example simulation results show (1) the effect equilibrium chemical parameters have on the spatial distributions of concentration for complexing solutes; (2) that an interrelationship exists between mechanical dispersion and the various reaction processes; (3) that dispersive parameters of the porous media cannot be determined from reactive concentration distributions unless the reaction is accounted for or the influence of the reaction is negligible; (4) how the concentration of a chemical species may be significantly affected by its participation in an aqueous complex with a second species which also sorbs; and (5) that these coupled chemical processes influencing reactive transport can be demonstrated in two-dimensional flow regimes. ?? 1987.

Dynamic study of excited state hydrogen-bonded complexes of harmane in cyclohexane-toluene mixtures.

PubMed

Carmona, Carmen; Balón, Manuel; Galán, Manuel; Guardado, Pilar; Muñoz, María A

2002-09-01

Photoinduced proton transfer reactions of harmane or 1-methyl-9H-pyrido[3,4-b]indole (HN) in the presence of the proton donor hexafluoroisopropanol (HFIP) in cyclohexane-toluene mixtures (CY-TL; 10% vol/vol of TL) have been studied. Three excited state species have been identified: a 1:2 hydrogen-bonded proton transfer complex (PTC), between the pyridinic nitrogen of the substrate and the proton donor, a hydrogen-bonded cation-like exciplex (CL*) with a stoichiometry of at least 1:3 and a zwitterionic exciplex (Z*). Time-resolved fluorescence measurements evidence that upon excitation of ground state PTC, an excited state equilibrium is established between PTC* and the cationlike exciplex, CL*, lambdaem approximately/= 390 nm. This excited state reaction is assisted by another proton donor molecule. Further reaction of CL* with an additional HFIP molecule produces the zwitterionic species, Z*, lambda(em) approximately/= 500 nm. From the analysis of the multiexponential decays, measured at different emission wavelengths and as a function of HFIP concentration, the mechanism of these excited state reactions has been established. Thus, three rate constants and three reciprocal lifetimes have been determined. The simultaneous study of 1,9-dimethyl-9H-pyrido[3,4-b]indole (MHN) under the same experimental conditions has helped to understand the excited state kinetics of these processes.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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

PubMed

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

2013-09-01

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

Lead(II) coordination polymers based on rigid-flexible 3,5-bis-oxyacetate-benzoic acid: Structural transition driven by temperature control

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

Chen, Yong-Qiang, E-mail: chenjzxy@126.com; Tian, Yuan

2017-03-15

Three Pb(II) complexes ([Pb{sub 3}(BOABA){sub 2}(H{sub 2}O)]·H{sub 2}O){sub n} (1), ([Pb{sub 4}(BOABA){sub 2}(µ{sub 4}-O)(H{sub 2}O){sub 2}]·H{sub 2}O){sub n} (2), and [Pb{sub 3}(BOABA){sub 2}(H{sub 2}O)]{sub n} (3) (H{sub 3}BOABA=3,5-bis-oxyacetate-benzoic acid) were obtained under the same reaction systems with different temperatures. Complexes 1 and 2 are two dimensional (2D) networks based on Pb-BOABA chains and Pb{sub 4}(µ{sub 4}-O)(COO){sub 6} SBUs, respectively. Complex 3 presents an interesting three dimensional (3D) framework, was obtained by increasing the reaction temperature. Structural transition of the crystallization products is largely dependent on the reaction temperature. Moreover, the fluorescence properties of complexes 1–3 have been investigated. - Graphicalmore » abstract: Three Pb(II) coordination polymers were obtained under the same reaction systems with different temperatures. Both of complexes 1 and 2 are 2D network. 3 presents a 3D framework based on Pb–O–C rods SBUs. The 2D to 3D structures transition between three complexes was achieved successfully by temperature control. - Highlights: • Three Pb(II) complexes were obtained under the same reaction systems with different temperatures. • Structural transition of the crystallization products is largely dependent on the reaction temperature. • The luminescence properties studies reveal that three complexes exhibit yellow fluorescence emission behavior, which might be good candidates for obtaining photoluminescent materials.« less

Time-resolved luminescence measurements of the magnetic field effect on paramagnetic photosensitizers in photodynamic reactions

NASA Astrophysics Data System (ADS)

Mermut, O.; Bouchard, J.-P.; Cormier, J.-F.; Desroches, P.; Diamond, K. R.; Fortin, M.; Gallant, P.; Leclair, S.; Marois, J.-S.; Noiseux, I.; Morin, J.-F.; Patterson, M. S.; Vernon, M.

2008-02-01

The development of multimodal molecular probes and photosensitizing agents for use in photodynamic therapy (PDT) is vital for optimizing and monitoring cytotoxic responses. We propose a combinatorial approach utilizing photosensitizing molecules that are both paramagnetic and luminescent with multimodal functionality to perturb, control, and monitor molecular-scale reaction pathways in PDT. To this end, a time-domain single photon counting lifetime apparatus with a 400 nm excitation source has been developed and integrated with a variable low field magnet (0- 350mT). The luminescence lifetime decay function was measured in the presence of a sweeping magnetic field for a custom designed photosensitizing molecule in which photoinduced electron transfer was studied The photosensitizer studied was a donor-acceptor complex synthesized using a porphyrin linked to a fullerene molecule. The magneto-optic properties were investigated for the free-base photosensitizer complex as well as those containing either diamagnetic (paired electron) or paramagnetic (unpaired electron) metal centers, Zn(II) and Cu(II). The magnetic field was employed to affect and modify the spin states of radical pairs of the photosensitizing agents via magnetically induced hyperfine and Zeeman effects. Since the Type 1 reaction pathway of an excited triplet state photosensitizer involves the production of radical species, lifetime measurements were conducted at low dissolved oxygen concentration (0.01ppm) to elucidate the dependence of the magnetic perturbation on the photosensitization mechanistic pathway. To optimize the magnetic response, a solvent study was performed examining the dependence of the emission properties on the magnetic field in solutions of varying dielectric constants. Lastly, the cytotoxicity in murine tumor cell suspensions was investigated for the novel porphyrin-fullerene complex by inducing photodynamic treatments and determining the associated cell survival.

Molybdenum complexes of 1,2-bis(diphenylphosphino)benzene. Mononuclear molybdenum(II) species formed by facile metal-metal bond cleavage of the (Mo-/sup 4/Mo)/sup 4+/ core

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

Bakir, M.; Cotton, F.A.; Cudahy, M.M.

1988-07-27

The quadruply bonded dimolybdenum(II) complexes K/sub 4/Mo/sub 2/Cl/sub 8/, (NH/sub 4/)/sub 5/MoCl/sub 9/ /times/ H/sub 2/O, and (NH/sub 4/)/sub 4/Mo/sub 2/Br/sub 8/ react with 1,2-C/sub 6/H/sub 4/(PPh/sub 2/)/sub 2/(dppbe) in methanol at room temperature to afford /alpha/-Mo/sub 2/X/sub 4/(dppbe)/sub 2/ complexes (X = Cl, Br), which do not isomerize to the /beta/ isomers. Under more forcing reactions conditions (refluxing 1-propanol), these same reactions give mononuclear trans-MoX/sub 2/(dppbe)/sub 2/ in good yield (ca. 50%) together with some (MoOX(dppbe)/sub 2/)X /times/ nH/sub 2/O. An alternative synthetic strategy for the preparation of /alpha/-Mo/sub 2/X/sub 4/(dppbe)/sub 2/ involves the reaction of Mo/sub 2/(O/sub 2/CCH/submore » 3/)/sub 4/ with dppbe and Me/sub 3/SiX in THF. The compound MoCl/sub 2/(dppbe)/sub 2/ forms crystals in space group P2/sub 1//n, with the following unit cell parameters: a = 10.884 (2) /angstrom/, b = 12.753 (2) /angstrom/, c = 18.141 (4) /angstrom/, /beta/ = 91.43 (2)/degree/, V = 2517 (2) /angstrom//sup 3/, and Z = 2. The centrosymmetric trans molecule has Mo-Cl = 2.410 (1) /angstrom/, Mo-P = 2.481 (1), 2.511 (1) /angstrom/, and P-Mo-P(intra-ring) = 78.68 (4)/degree/. 25 refs., 1 fig., 4 tabs.« less

Pathways for the OH + Br2 → HOBr + Br and HOBr + Br → HBr + BrO Reactions.

PubMed

Wang, Hongyan; Qiu, Yudong; Schaefer, Henry F

2016-02-11

The OH radical reaction with Br2 and the subsequent reaction HOBr + Br are of exceptional importance to atmospheric chemistry and environmental chemistry. The entrance complex, transition state, and exit complex for both reactions have been determined using the coupled-cluster method with single, double, and perturbative triple excitations CCSD(T) with correlation consistent basis sets up to size cc-pV5Z and cc-pV5Z-PP. Coupled cluster effects with full triples (CCSDT) and full quadruples (CCSDTQ) are explicitly investigated. Scalar relativistic effects, spin-orbit coupling, and zero-point vibrational energy corrections are evaluated. The results from the all-electron basis sets are compared with those from the effective core potential (ECP) pseudopotential (PP) basis sets. The results are consistent. The OH + Br2 reaction is predicted to be exothermic 4.1 ± 0.5 kcal/mol, compared to experiment, 3.9 ± 0.2 kcal/mol. The entrance complex HO···BrBr is bound by 2.2 ± 0.2 kcal/mol. The transition state lies similarly well below the reactants OH + Br2. The exit complex HOBr···Br is bound by 2.7 ± 0.6 kcal/mol relative to separated HOBr + Br. The endothermicity of the reaction HOBr + Br → HBr + BrO is 9.6 ± 0.7 kcal/mol, compared with experiment 8.7 ± 0.3 kcal/mol. For the more important reverse (exothermic) HBr + BrO reaction, the entrance complex BrO···HBr is bound by 1.8 ± 0.6 kcal/mol. The barrier for the HBr + BrO reaction is 6.8 ± 0.9 kcal/mol. The exit complex (Br···HOBr) for the HBr + BrO reaction is bound by 1.9 ± 0.2 kcal/mol with respect to the products HOBr + Br.

A network dynamics approach to chemical reaction networks

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Mittag-Leffler synchronization of fractional neural networks with time-varying delays and reaction-diffusion terms using impulsive and linear controllers.

PubMed

Stamova, Ivanka; Stamov, Gani

2017-12-01

In this paper, we propose a fractional-order neural network system with time-varying delays and reaction-diffusion terms. We first develop a new Mittag-Leffler synchronization strategy for the controlled nodes via impulsive controllers. Using the fractional Lyapunov method sufficient conditions are given. We also study the global Mittag-Leffler synchronization of two identical fractional impulsive reaction-diffusion neural networks using linear controllers, which was an open problem even for integer-order models. Since the Mittag-Leffler stability notion is a generalization of the exponential stability concept for fractional-order systems, our results extend and improve the exponential impulsive control theory of neural network system with time-varying delays and reaction-diffusion terms to the fractional-order case. The fractional-order derivatives allow us to model the long-term memory in the neural networks, and thus the present research provides with a conceptually straightforward mathematical representation of rather complex processes. Illustrative examples are presented to show the validity of the obtained results. We show that by means of appropriate impulsive controllers we can realize the stability goal and to control the qualitative behavior of the states. An image encryption scheme is extended using fractional derivatives. Copyright © 2017 Elsevier Ltd. All rights reserved.

Study of the techniques feasible for food synthesis aboard a spacecraft

NASA Technical Reports Server (NTRS)

Weiss, A. H.

1972-01-01

Synthesis of sugars by Ca(OH)2 catalyzed formaldehyde condensation (the formose reaction) has produced branched carbohydrates that do not occur in nature. The kinetics and mechanisms of the homogeneously catalyzed autocatalytic condensation were studied and analogies between homogeneous and heterogeneous rate laws have been found. Aldol condensations proceed simultaneously with Cannizzaro and crossed-Cannizzaro reactions and Lobry de Bruyn-Van Eckenstein rearrangements. The separate steps as well as the interactions of this highly complex reaction system were elucidated. The system exhibits instabilities, competitive catalytic, mass action, and equilibrium phenomena, complexing, and parallel and consecutive reactions. Specific finding that have been made on the problem will be of interest for synthesizing sugars, both for sustained space flight and for large scale food manufacture. A contribution to methodology for studying complex catalyzed reactions and to understanding control of reaction selectivity was a broad goal of the project.

Enthalpy Changes during Photosynthetic Water Oxidation Tracked by Time-Resolved Calorimetry Using a Photothermal Beam Deflection Technique☆☆☆

PubMed Central

Krivanek, Roland; Dau, Holger; Haumann, Michael

2008-01-01

The energetics of the individual reaction steps in the catalytic cycle of photosynthetic water oxidation at the Mn4Ca complex of photosystem II (PSII) are of prime interest. We studied the electron transfer reactions in oxygen-evolving PSII membrane particles from spinach by a photothermal beam deflection technique, allowing for time-resolved calorimetry in the micro- to millisecond domain. For an ideal quantum yield of 100%, the enthalpy change, ΔH, coupled to the formation of the radical pair YZ⋅+QA− (where YZ is Tyr-161 of the D1 subunit of PSII) is estimated as −820 ± 250 meV. For a lower quantum yield of 70%, the enthalpy change is estimated to be −400 ± 250 meV. The observed nonthermal signal possibly is due to a contraction of the PSII protein volume (apparent ΔV of about −13 Å3). For the first time, the enthalpy change of the O2-evolving transition of the S-state cycle was monitored directly. Surprisingly, the reaction is only slightly exergonic. A value of ΔH(S3 ⇒ S0) of −210 meV is estimated, but also an enthalpy change of zero is within the error range. A prominent nonthermal photothermal beam deflection signal (apparent ΔV of about +42 Å3) may reflect O2 and proton release from the manganese complex, but also reorganization of the protein matrix. PMID:17993488

Ab initio study on the 1:2 reaction of CO 2 with dimethylamine

NASA Astrophysics Data System (ADS)

Jamróz, MichałH.; Dobrowolski, Jan Cz.; Borowiak, Marek A.

1997-02-01

The reaction between CO 2 and the dimethylamine molecule in the presence of a second dimethylamine molecule is modeled by the ab initio RHF/3-21G method. Starting from the most stable 1:2 complex, the most effective reaction pathway turned out to be proton transfer between amine molecules followed by immediate proton transfer from one of the amine molecules to the CO 2 moiety. The activation barrier for this pathway (9.54 kcal mol -1 with respect to the 1:2 complex) is within the range of activation energy values found in kinetic studies for similar reactions with different hydroxylamines (from 9.2 to 13.0 kcal mol -1). The reaction product is the cyclic hydrogen bonded complex of dimethylcarbamic acid with dimethylamine.

Process for making surfactant capped metal oxide nanocrystals, and products produced by the process

DOEpatents

Alivisatos, A. Paul; Rockenberger, Joerg

2006-01-10

Disclosed is a process for making surfactant capped nanocrystals of metal oxides which are dispersable in organic solvents. The process comprises decomposing a metal cupferron complex of the formula M^XCup_X, wherein M is a metal, and Cup is a N-substituted N-Nitroso hydroxylamine, in the presence of a coordinating surfactant, the reaction being conducted at a temperature ranging from about 150 to about 400.degree. C., for a period of time sufficient to complete the reaction. Also disclosed are compounds made by the process.

Novel approach to investigation of semiconductor MOCVD by microreactor technology

NASA Astrophysics Data System (ADS)

Konakov, S. A.; Krzhizhanovskaya, V. V.

2017-11-01

Metal-Organic Chemical Vapour Deposition is a very complex technology that requires further investigation and optimization. We propose to apply microreactors to (1) replace multiple expensive time-consuming macroscale experiments by just one microreactor deposition with many points on one substrate; (2) to derive chemical reaction rates from individual deposition profiles using theoretical analytical solution. In this paper we also present the analytical solution of a simplified equation describing the deposition rate dependency on temperature. It allows to solve an inverse problem and to obtain detailed information about chemical reaction mechanism of MOCVD process.

Formation of multi-stereogenic centers using a catalytic diastereoselective Henry reaction.

PubMed

Arai, Takayoshi; Taneda, Yoshinori; Endo, Yoko

2010-11-14

A diastereoselective Henry reaction of chiral aldehydes with nitroalkanes was developed using a chiral sulfonyldiamine (L1)-CuCl complex. The reaction of (R)-2-phenylpropanal and nitromethane was smoothly catalyzed by the (S,S,S)-L1-CuCl complex to give the adduct with 99/1 syn/anti selectivity in 99% ee. In the reaction of (S)-2-phenylpropanal and nitroethane, the (R,R,R)-L1-CuCl catalyst yielded the expected three contiguous stereogenic centers in a highly syn-selective Henry reaction.

Preprogramming Complex Hydrogel Responses using Enzymatic Reaction Networks.

PubMed

Postma, Sjoerd G J; Vialshin, Ilia N; Gerritsen, Casper Y; Bao, Min; Huck, Wilhelm T S

2017-02-06

The creation of adaptive matter is heavily inspired by biological systems. However, it remains challenging to design complex material responses that are governed by reaction networks, which lie at the heart of cellular complexity. The main reason for this slow progress is the lack of a general strategy to integrate reaction networks with materials. Herein we use a systematic approach to preprogram the response of a hydrogel to a trigger, in this case the enzyme trypsin, which activates a reaction network embedded within the hydrogel. A full characterization of all the kinetic rate constants in the system enabled the construction of a computational model, which predicted different hydrogel responses depending on the input concentration of the trigger. The results of the simulation are in good agreement with experimental findings. Our methodology can be used to design new, adaptive materials of which the properties are governed by reaction networks of arbitrary complexity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The evolutionary pathway from anoxygenic to oxygenic photosynthesis examined by comparison of the properties of photosystem II and bacterial reaction centers.

PubMed

Allen, J P; Williams, J C

2011-01-01

In photosynthetic organisms, such as purple bacteria, cyanobacteria, and plants, light is captured and converted into energy to create energy-rich compounds. The primary process of energy conversion involves the transfer of electrons from an excited donor molecule to a series of electron acceptors in pigment-protein complexes. Two of these complexes, the bacterial reaction center and photosystem II, are evolutionarily related and structurally similar. However, only photosystem II is capable of performing the unique reaction of water oxidation. An understanding of the evolutionary process that lead to the development of oxygenic photosynthesis can be found by comparison of these two complexes. In this review, we summarize how insight is being gained by examination of the differences in critical functional properties of these complexes and by experimental efforts to alter pigment-protein interactions of the bacterial reaction center in order to enable it to perform reactions, such as amino acid and metal oxidation, observable in photosystem II.

Wave packet and statistical quantum calculations for the He + NeH⁺ → HeH⁺ + Ne reaction on the ground electronic state.

PubMed

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N

2014-09-21

A real wave packet based time-dependent method and a statistical quantum method have been used to study the He + NeH(+) (v, j) reaction with the reactant in various ro-vibrational states, on a recently calculated ab initio ground state potential energy surface. Both the wave packet and statistical quantum calculations were carried out within the centrifugal sudden approximation as well as using the exact Hamiltonian. Quantum reaction probabilities exhibit dense oscillatory pattern for smaller total angular momentum values, which is a signature of resonances in a complex forming mechanism for the title reaction. Significant differences, found between exact and approximate quantum reaction cross sections, highlight the importance of inclusion of Coriolis coupling in the calculations. Statistical results are in fairly good agreement with the exact quantum results, for ground ro-vibrational states of the reactant. Vibrational excitation greatly enhances the reaction cross sections, whereas rotational excitation has relatively small effect on the reaction. The nature of the reaction cross section curves is dependent on the initial vibrational state of the reactant and is typical of a late barrier type potential energy profile.

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

PubMed

Duong, Minh V; Nguyen, Hieu T; Mai, Tam V-T; Huynh, Lam K

2018-01-03

Master equation/Rice-Ramsperger-Kassel-Marcus (ME/RRKM) has shown to be a powerful framework for modeling kinetic and dynamic behaviors of a complex gas-phase chemical system on a complicated multiple-species and multiple-channel potential energy surface (PES) for a wide range of temperatures and pressures. Derived from the ME time-resolved species profiles, the macroscopic or phenomenological rate coefficients are essential for many reaction engineering applications including those in combustion and atmospheric chemistry. Therefore, in this study, a least-squares-based approach named Global Minimum Profile Error (GMPE) was proposed and implemented in the MultiSpecies-MultiChannel (MSMC) code (Int. J. Chem. Kinet., 2015, 47, 564) to extract macroscopic rate coefficients for such a complicated system. The capability and limitations of the new approach were discussed in several well-defined test cases.

Observation of crystalline changes of titanium dioxide during lithium insertion by visible spectrum analysis.

PubMed

Nam, Inho; Park, Jongseok; Park, Soomin; Bae, Seongjun; Yoo, Young Geun; Han, Jeong Woo; Yi, Jongheop

2017-05-24

Real-time analysis of changes in the atomic environment of materials is a cutting edge technology that is being used to explain reaction dynamics in many fields of science. Previously, this kind of analysis was only possible using heavy nucleonic equipment such as XANES and EXAFS, or Raman spectroscopy on a moderate scale. Here, a new methodology is described that can be used to track changes in crystalline developments during complex Li insertion reactions via the observation of structural color. To be specific, the changes in atomic crystalline and nanostructure are shown during Li insertion in a complex TiO 2 polymorph. Structural color corresponds to the refractive indices of materials originating from their atomic bonding nature and precise wave interferences in accordance with their nanostructure. Therefore, this new analysis simultaneously reveals changes in the nanostructure as well as changes in the atomic bonding nature of materials.

Robust, Chiral, and Porous BINAP-Based Metal–Organic Frameworks for Highly Enantioselective Cyclization Reactions

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

Sawano, Takahiro; Thacker, Nathan C.; Lin, Zekai

2016-05-06

We report here the design of BINAP-based metal–organic frameworks and their postsynthetic metalation with Rh complexes to afford highly active and enantioselective single-site solid catalysts for the asymmetric cyclization reactions of 1,6-enynes. Robust, chiral, and porous Zr-MOFs of UiO topology, BINAP-MOF (I) or BINAP-dMOF (II), were prepared using purely BINAP-derived dicarboxylate linkers or by mixing BINAP-derived linkers with unfunctionalized dicarboxylate linkers, respectively. Upon metalation with Rh(nbd)2BF4 and [Rh(nbd)Cl]2/AgSbF6, the MOF precatalysts I·Rh(BF4) and I·Rh(SbF6) efficiently catalyzed highly enantioselective (up to 99% ee) reductive cyclization and Alder-ene cycloisomerization of 1,6-enynes, respectively. I·Rh catalysts afforded cyclization products at comparable enantiomeric excesses (ee’s)more » and 4–7 times higher catalytic activity than the homogeneous controls, likely a result of catalytic site isolation in the MOF which prevents bimolecular catalyst deactivation pathways. However, I·Rh is inactive in the more sterically encumbered Pauson–Khand reactions between 1,6-enynes and carbon monoxide. In contrast, with a more open structure, Rh-functionalized BINAP-dMOF, II·Rh, effectively catalyzed Pauson–Khand cyclization reactions between 1,6-enynes and carbon monoxide at 10 times higher activity than the homogeneous control. II·Rh was readily recovered and used three times in Pauson–Khand cyclization reactions without deterioration of yields or ee’s. Our work has expanded the scope of MOF-catalyzed asymmetric reactions and showed that the mixed linker strategy can effectively enlarge the open space around the catalytic active site to accommodate highly sterically demanding polycyclic metallocycle transition states/intermediates in asymmetric intramolecular cyclization reactions.« less

A Graphical User Interface for a Method to Infer Kinetics and Network Architecture (MIKANA)

PubMed Central

Mourão, Márcio A.; Srividhya, Jeyaraman; McSharry, Patrick E.; Crampin, Edmund J.; Schnell, Santiago

2011-01-01

One of the main challenges in the biomedical sciences is the determination of reaction mechanisms that constitute a biochemical pathway. During the last decades, advances have been made in building complex diagrams showing the static interactions of proteins. The challenge for systems biologists is to build realistic models of the dynamical behavior of reactants, intermediates and products. For this purpose, several methods have been recently proposed to deduce the reaction mechanisms or to estimate the kinetic parameters of the elementary reactions that constitute the pathway. One such method is MIKANA: Method to Infer Kinetics And Network Architecture. MIKANA is a computational method to infer both reaction mechanisms and estimate the kinetic parameters of biochemical pathways from time course data. To make it available to the scientific community, we developed a Graphical User Interface (GUI) for MIKANA. Among other features, the GUI validates and processes an input time course data, displays the inferred reactions, generates the differential equations for the chemical species in the pathway and plots the prediction curves on top of the input time course data. We also added a new feature to MIKANA that allows the user to exclude a priori known reactions from the inferred mechanism. This addition improves the performance of the method. In this article, we illustrate the GUI for MIKANA with three examples: an irreversible Michaelis–Menten reaction mechanism; the interaction map of chemical species of the muscle glycolytic pathway; and the glycolytic pathway of Lactococcus lactis. We also describe the code and methods in sufficient detail to allow researchers to further develop the code or reproduce the experiments described. The code for MIKANA is open source, free for academic and non-academic use and is available for download (Information S1). PMID:22096591

A graphical user interface for a method to infer kinetics and network architecture (MIKANA).

PubMed

Mourão, Márcio A; Srividhya, Jeyaraman; McSharry, Patrick E; Crampin, Edmund J; Schnell, Santiago

2011-01-01

One of the main challenges in the biomedical sciences is the determination of reaction mechanisms that constitute a biochemical pathway. During the last decades, advances have been made in building complex diagrams showing the static interactions of proteins. The challenge for systems biologists is to build realistic models of the dynamical behavior of reactants, intermediates and products. For this purpose, several methods have been recently proposed to deduce the reaction mechanisms or to estimate the kinetic parameters of the elementary reactions that constitute the pathway. One such method is MIKANA: Method to Infer Kinetics And Network Architecture. MIKANA is a computational method to infer both reaction mechanisms and estimate the kinetic parameters of biochemical pathways from time course data. To make it available to the scientific community, we developed a Graphical User Interface (GUI) for MIKANA. Among other features, the GUI validates and processes an input time course data, displays the inferred reactions, generates the differential equations for the chemical species in the pathway and plots the prediction curves on top of the input time course data. We also added a new feature to MIKANA that allows the user to exclude a priori known reactions from the inferred mechanism. This addition improves the performance of the method. In this article, we illustrate the GUI for MIKANA with three examples: an irreversible Michaelis-Menten reaction mechanism; the interaction map of chemical species of the muscle glycolytic pathway; and the glycolytic pathway of Lactococcus lactis. We also describe the code and methods in sufficient detail to allow researchers to further develop the code or reproduce the experiments described. The code for MIKANA is open source, free for academic and non-academic use and is available for download (Information S1).

Dramatic influence of an anionic donor on the oxygen-atom transfer reactivity of a Mn(V) -oxo complex.

PubMed

Neu, Heather M; Quesne, Matthew G; Yang, Tzuhsiung; Prokop-Prigge, Katharine A; Lancaster, Kyle M; Donohoe, James; DeBeer, Serena; de Visser, Sam P; Goldberg, David P

2014-11-03

Addition of an anionic donor to an Mn(V) (O) porphyrinoid complex causes a dramatic increase in 2-electron oxygen-atom-transfer (OAT) chemistry. The 6-coordinate [Mn(V) (O)(TBP8 Cz)(CN)](-) was generated from addition of Bu4 N(+) CN(-) to the 5-coordinate Mn(V) (O) precursor. The cyanide-ligated complex was characterized for the first time by Mn K-edge X-ray absorption spectroscopy (XAS) and gives MnO=1.53 Å, MnCN=2.21 Å. In combination with computational studies these distances were shown to correlate with a singlet ground state. Reaction of the CN(-) complex with thioethers results in OAT to give the corresponding sulfoxide and a 2e(-) -reduced Mn(III) (CN)(-) complex. Kinetic measurements reveal a dramatic rate enhancement for OAT of approximately 24 000-fold versus the same reaction for the parent 5-coordinate complex. An Eyring analysis gives ΔH(≠) =14 kcal mol(-1) , ΔS(≠) =-10 cal mol(-1)  K(-1) . Computational studies fully support the structures, spin states, and relative reactivity of the 5- and 6-coordinate Mn(V) (O) complexes. © 2014 The Authors. Published by Wiley-VCHVerlag GmbH & Co. KGaA. This is an open access article under the terms ofthe Creative Commons Attribution License, which permits use, distribution andreproduction in any medium, provided the original work is properly cited.

Rapid time-resolved diffraction studies of protein structures using synchrotron radiation

NASA Astrophysics Data System (ADS)

Bartunik, Hans D.; Bartunik, Lesley J.

1992-07-01

The crystal structure of intermediate states in biological reactions of proteins of multi-protein complexes may be studied by time-resolved X-ray diffraction techniques which make use of the high spectral brilliance, continuous wavelength distribution and pulsed time structure of synchrotron radiation. Laue diffraction methods provide a means of investigating intermediate structures with lifetimes in the millisecond time range at presently operational facilities. Third-generation storage rings which are under construction may permit one to reach a time resolution of one microsecond for non-cyclic and one nanosecond for cyclic reactions. The number of individual exposures required for exploring reciprocal space and hence the total time scale strongly depend on the lattice order that may be affected, e.g., by conformational changes. Time-resolved experiments require high population of a specific intermediate which has to be homogeneous over the crystal volume. A number of external excitation techniques have been developed including in situ liberation of active metabolites by laser pulse photolysis of photolabile inactive precursors. First applications to crystal structure analysis of catalytic intermediates of enzymes demonstrate the potential of time-resolved protein crystallography.

Mixing effects on apparent reaction rates and isotope fractionation during denitrification in a heterogeneous aquifer

USGS Publications Warehouse

Green, Christopher T.; Böhlke, John Karl; Bekins, Barbara A.; Phillips, Steven P.

2010-01-01

Gradients in contaminant concentrations and isotopic compositions commonly are used to derive reaction parameters for natural attenuation in aquifers. Differences between field‐scale (apparent) estimated reaction rates and isotopic fractionations and local‐scale (intrinsic) effects are poorly understood for complex natural systems. For a heterogeneous alluvial fan aquifer, numerical models and field observations were used to study the effects of physical heterogeneity on reaction parameter estimates. Field measurements included major ions, age tracers, stable isotopes, and dissolved gases. Parameters were estimated for the O2 reduction rate, denitrification rate, O2 threshold for denitrification, and stable N isotope fractionation during denitrification. For multiple geostatistical realizations of the aquifer, inverse modeling was used to establish reactive transport simulations that were consistent with field observations and served as a basis for numerical experiments to compare sample‐based estimates of “apparent” parameters with “true“ (intrinsic) values. For this aquifer, non‐Gaussian dispersion reduced the magnitudes of apparent reaction rates and isotope fractionations to a greater extent than Gaussian mixing alone. Apparent and true rate constants and fractionation parameters can differ by an order of magnitude or more, especially for samples subject to slow transport, long travel times, or rapid reactions. The effect of mixing on apparent N isotope fractionation potentially explains differences between previous laboratory and field estimates. Similarly, predicted effects on apparent O2threshold values for denitrification are consistent with previous reports of higher values in aquifers than in the laboratory. These results show that hydrogeological complexity substantially influences the interpretation and prediction of reactive transport.

Preparation, characterization, non-isothermal reaction kinetics, thermodynamic properties, and safety performances of high nitrogen compound: hydrazine 3-nitro-1,2,4-triazol-5-one complex.

PubMed

Yi, Jian-Hua; Zhao, Feng-Qi; Gao, Hong-Xu; Xu, Si-Yu; Wang, Min-Chang; Hu, Rong-Zu

2008-05-01

A new high nitrogen compound hydrazine 3-nitro-1,2,4-triazol-5-one complex (HNTO) was prepared by the reaction of 3-nitro-1,2,4-triazol-5-one with hydrazine hydrate, and its structure was characterized by means of organic elemental analyzer, FT-IR, XRD, (13)C NMR and (15)N NMR. The non-isothermal reaction kinetics of the main exothermic decomposition reaction of HNTO was investigated by means of DSC. The thermodynamic properties of HNTO were calculated. The results showed that the formation of HNTO is achieved by proton transfer of N(4) atom, and it makes a higher nitrogen content and lower acidity. The reaction mechanism of HNTO is classified as nucleation and growth, and the mechanism function is Avramo-Erofeev equation with n=2/5. The kinetic parameters of the reaction are E(a)=195.29 kJ mol(-1), lg(A (s(-1)))=19.37, respectively. The kinetic equation can be expressed as: d(alpha)/d(t) = 10(18.97)(1 - alpha)[-ln(1 - alpha)](3/5) e(-2.35 x 10(4)/T). The safety performances of HNTO were carried out. The critical temperature of thermal explosion are 464.26 and 474.37 K, the adiabatic time-to-explosion is 262s, the impact sensitivity H(50)=45.7 cm, the friction sensitivity P=20% and the electrostatic spark sensitivity E(50)>5.4J (no ignition). It shows that HNTO has an insensitive nature as RDX and NTO, etc.

Development of a novel europium complex-based luminescent probe for time-gated luminescence imaging of hypochlorous acid in living samples

NASA Astrophysics Data System (ADS)

Liu, Xiangli; Guo, Lianying; Song, Bo; Tang, Zhixin; Yuan, Jingli

2017-03-01

Luminescent lanthanide complexes are key reagents used in the time-gated luminescence bioassay technique, but functional lanthanide complexes that can act as luminescent probes for specifically responding to analytes are very limited. In this work, we designed and synthesized a novel Eu3+ complex-based luminescence probe for hypochlorous acid (HOCl), NPPTTA-Eu3+, by using terpyridine polyacid-Eu3+, dinitrophenyl, and hydrazine as luminophore, quencher and HOCl-recognizer moieties, respectively. In the absence of HOCl, the probe is non-luminescent due to the strong luminescence quenching of the dinitrophenyl group in the complex. However, upon reaction with HOCl, the dinitrophenyl moiety is rapidly cleaved from the probe, which affords a strongly luminescent Eu3+ complex CPTTA-Eu3+, accompanied by a ˜900-fold luminescence enhancement with a long luminescence lifetime of 1.41 ms. This unique luminescence response of NPPTTA-Eu3+ to HOCl allowed NPPTTA-Eu3+ to be conveniently used as a probe for highly selective and sensitive detection of HOCl under the time-gated luminescence mode. In addition, by loading NPPTTA-Eu3+ into RAW 264.7 macrophage cells and Daphnia magna, the generation of endogenous HOCl in RAW 264.7 cells and the uptake of exogenous HOCl by Daphnia magna were successfully imaged on a true-color time-gated luminescence microscope. The results demonstrated the practical applicability of NPPTTA-Eu3+ as an efficient probe for time-gated luminescence imaging of HOCl in living cells and organisms.

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.

Antibody-mediated cofactor-driven reactions

DOEpatents

Schultz, Peter G.

1993-01-01

Chemical reactions capable of being rate-enhanced by auxiliary species which interact with the reactants but do not become chemically bound to them in the formation of the final product are performed in the presence of antibodies which promote the reactions. The antibodies contain regions within their antigen binding sites which recognize the auxiliary species in a conformation which promotes the reaction. The antigen binding site frequently recognizes a particular transition state complex or other high energy complex along the reaction coordinate, thereby promoting the progress of the reaction along the desired route as opposed to other less favorable routes. Various classes of reaction together with appropriate antigen binding site specificities tailored for each are disclosed.

Theory and Modeling of Liquid Explosive Detonation

NASA Astrophysics Data System (ADS)

Tarver, Craig M.; Urtiew, Paul A.

2010-10-01

The current understanding of the detonation reaction zones of liquid explosives is discussed in this article. The physical and chemical processes that precede and follow exothermic chemical reaction within the detonation reaction zone are discussed within the framework of the nonequilibrium Zeldovich-von Neumann-Doring (NEZND) theory of self-sustaining detonation. Nonequilibrium chemical and physical processes cause finite time duration induction zones before exothermic chemical energy release occurs. This separation between the leading shock wave front and the chemical energy release needed to sustain it results in shock wave amplification and the subsequent formation of complex three-dimensional cellular structures in all liquid detonation waves. To develop a practical Zeldovich-von Neumann-Doring (ZND) reactive flow model for liquid detonation, experimental data on reaction zone structure, confined failure diameter, unconfined failure diameter, and failure wave velocity in the Dremin-Trofimov test for detonating nitromethane are calculated using the ignition and growth reactive flow model.

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Quantifying atom addition reactions on amorphous solid water: a review of recent laboratory advances

NASA Astrophysics Data System (ADS)

He, Jiao; Vidali, Gianfranco

2018-06-01

Complex organic molecules found in space are mostly formed on and in the ice mantle covering interstellar dust grains. In clouds where ionizing irradiation is insignificant, chemical reactions on the ice mantle are dominated by thermal processes. Modeling of grain surface chemistry requires detailed information from the laboratory, including sticking coefficients, binding energies, diffusion energy barriers, mechanism of reaction, and chemical desorption rates. In this talk, recent laboratory advances in obtaining these information would be reviewed. Specifically, this talk will focus on the efforts in our group in: 1) Determining the mechanism of atomic hydrogen addition reactions on amorphous solid water (ASW); 2) Measuring the chemical desorption coefficient of H+O3-->O2+OH using the time-resolved scattering technique; and 3) Measuring the diffusion energy barrier of volatile molecules on ASW. Further laboratory studies will be suggested.This research was supported by NSF Astronomy & Astrophysics Research Grant #1615897.

Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers.

PubMed

Jämbeck, Joakim P M; Lyubartsev, Alexander P

2013-06-06

Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in some cases, degrees of freedom (DOFs) orthogonal to the reaction coordinate have high energy barriers and/or long equilibration times, which prohibit proper sampling. Here we identify these orthogonal DOFs when studying the transfer of a solute from water to a model membrane. Important DOFs are identified in bulk liquids of different dielectric nature with metadynamics simulations and are used as reaction coordinates for the translocation process, resulting in two- and three-dimensional space of reaction coordinates. The results are in good agreement with experiments and elucidate the pitfalls of using one-dimensional reaction coordinates. The calculations performed here offer the most detailed free energy landscape of solutes embedded in lipid bilayers to date and show that free energy calculations can be used to study complex membrane translocation phenomena.

Mechanism-Based Condition Screening for Sustainable Catalysis in Single-Electron Steps by Cyclic Voltammetry.

PubMed

Liedtke, Theresa; Spannring, Peter; Riccardi, Ludovico; Gansäuer, Andreas

2018-04-23

A cyclic-voltammetry-based screening method for Cp 2 TiX-catalyzed reactions is introduced. Our mechanism-based approach enables the study of the influence of various additives on the electrochemically generated active catalyst Cp 2 TiX, which is in equilibrium with catalytically inactive [Cp 2 TiX 2 ] - . Thioureas and ureas are most efficient in the generation of Cp 2 TiX in THF. Knowing the precise position of the equilibrium between Cp 2 TiX and [Cp 2 TiX 2 ] - allowed us to identify reaction conditions for the bulk electrolysis of Cp 2 TiX 2 complexes and for Cp 2 TiX-catayzed radical arylations without having to carry out the reactions. Our time- and resource-efficient approach is of general interest for the design of catalytic reactions that proceed in single-electron steps. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of Boron Clusters on the Ignition Reaction of HNO3 and Dicynanamide-Based Ionic Liquids.

PubMed

Schmidt, Michael W; Gordon, Mark S

2017-10-19

Many ionic liquids containing the dicynamide anion (DCA - , formula N(CN) 2 - ) exhibit hypergolic ignition when exposed to the common oxidizer nitric acid. However, the ignition delay is often about 10 times longer than the desired 5 ms for rocket applications, so that improvements are desired. Experiments in the past decade have suggested both a mechanism for the early reaction steps and also that additives such as decaborane can reduce the ignition delay. The mechanisms for reactions of nitric acid with both DCA - and protonated DCAH are considered here, using accurate wave function methods. Complexation of DCA - or DCAH with borane clusters B 10 H 14 or B 9 H 14 - is found to modify these mechanisms slightly by changing the nature of some of the intermediate saddle points and by small reductions in the reaction barriers.

New Chemical and Stereochemical Applications of Organoiron Complexes

PubMed Central

Fatiadi, Alexander J.

1991-01-01

The objective of this review is to provide a current overview of the rapidly developing chemistry of organometallic complexes and particularly organoiron complexes useful in asymmetric and stereoselective reactions. Also covered are stereoselective reactions of α, β-unsaturated acyl ligands bound to the chiral auxiliary [(η5-C5H5) Fe(CO)(PPh3)] and new applications of organoiron complexes in the synthesis of natural products. The mechanistic aspects and stabilizing effects of the Fe(CO)3 group for alkenes or conjugated dienes are discussed. A brief summary of recent work on the special role of iron in biological reactions is also included. PMID:28184103

Silica functionalized Cu(II) acetylacetonate Schiff base complex: An efficient catalyst for the oxidative condensation reaction of benzyl alcohol with amines

NASA Astrophysics Data System (ADS)

Anbarasu, G.; Malathy, M.; Karthikeyan, P.; Rajavel, R.

2017-09-01

Silica functionalized Cu(II) acetylacetonate Schiff base complex via the one pot reaction of silica functionalized 3-aminopropyltriethoxysilane with acetyl acetone and copper acetate has been reported. The synthesized material was well characterized by analytical techniques such as FT-IR, UV-DRS, XRD, SEM-EDX, HR-TEM, EPR, ICP-AES and BET analysis. The characterization results confirmed the grafting of Cu(II) Schiff base complex on the silica surface. The catalytic activity of synthesized silica functionalized Cu(II) acetylacetonate Schiff base complex was evaluated through the oxidative condensation reaction of benzyl alcohol to imine.

Synthesis, spectral and thermal studies of the newly hydrogen bonded charge transfer complex of o-phenylenediamine with π acceptor picric acid

NASA Astrophysics Data System (ADS)

Khan, Ishaat M.; Ahmad, Afaq

2010-10-01

Newly proton or charge transfer complex [(OPDH) +(PA) -] was synthesized by the reaction of the donor, o-phenylenediamine (OPD) with acceptor, 2,4,6-trinitrophenol (PAH). The chemical reaction has occurred via strong hydrogen bonding followed by migration of proton from acceptor to donor. UV-vis, 1H NMR and FTIR spectra, in addition to the thermal and elemental analysis were used to confirm the proposed occurrence of the chemical reaction and to investigate the newly synthesized solid CT complex. The stoichiometry of the CT complex was found to be 1:1. The formation constant and molar extinction coefficient of the CT complex were evaluated by the Benesi-Hildebrand equation.

Interactions between iron and organic matter may influence the fate of permafrost carbon in the Arctic

NASA Astrophysics Data System (ADS)

Cory, R. M.; Trusiak, A.; Ward, C.; Kling, G. W.; Tfaily, M.; Paša-Tolić, L.; Noel, V.; Bargar, J.

2017-12-01

The ongoing thawing of permafrost soils is the only environmental change that allows tremendous stores of organic carbon (C) to be converted into carbon dioxide (CO2) on decadal time scales, thus providing a positive and accelerating feedback to global warming. Evidence suggests that iron enhances abiotic reactions that convert dissolved organic matter (DOM) to CO2 in dark soils and in sunlit surface waters depending on its redox state and association with DOM (i.e., iron-DOM complexation). However, the complexation of iron in surface waters and soils remains too poorly understood to predict how iron influences the rates of oxidation of DOM to CO2. To address this knowledge gap, we characterized iron-DOM complexation in iron-rich soil and surface waters of the Arctic, in combination with measurements of DOM oxidation to CO2. These waters contain high concentrations of dissolved iron and DOM (up to 1 and 2 mM, respectively), and low concentrations of other potential ligands for iron such as sulfide, carbonate, chloride, or bromide. Ultra-high resolution mass spectrometry (FT-ICR MS) was used to identify ligands for iron within the DOM pool, and synchrotron based X-ray analysis (XAS and EXAFS) was used to assess iron's oxidation state, to detect iron complexation, and to constrain the chemical composition of the complexes. Across a natural gradient of dissolved iron and DOM concentrations, many potential ligands were identified within DOM that are expected to complex with iron (e.g., aromatic acids). EXAFS showed substantial complexation of reduced ferrous iron (Fe(II)) to DOM in arctic soil waters, on the basis of comparison to Fe(II)-DOM reference spectra. Identification of iron complexed to DOM in soil waters is consistent with strongly co-varying iron and DOM concentrations in arctic soil and surface waters, and supports our hypothesis that complexation of iron by DOM influences dark and light redox reactions that oxidize DOM to CO2. Understanding the molecular controls on the biogeochemical reactions that convert permafrost carbon to CO2 is critical for understanding the role of the Arctic in current and future climate change.

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.

Massive Thermal Acceleration of the Emergence of Primordial Chemistry, the Incidence of Spontaneous Mutation, and the Evolution of Enzymes*

PubMed Central

Wolfenden, Richard

2014-01-01

Kelvin considered it unlikely that sufficient time had elapsed on the earth for life to have reached its present level of complexity. In the warm surroundings in which life first appeared, however, elevated temperatures would have reduced the kinetic barriers to reaction. Recent experiments disclose the profound extent to which very slow reactions are accelerated by elevated temperatures, collapsing the time that would have been required for early events in primordial chemistry before the advent of enzymes. If a primitive enzyme, like model catalysts and most modern enzymes, accelerated a reaction by lowering its enthalpy of activation, then the rate enhancement that it produced would have increased automatically as the environment cooled, quite apart from any improvements in catalytic activity that arose from mutation and natural selection. The chemical events responsible for spontaneous mutation are also highly sensitive to temperature, furnishing an independent mechanism for accelerating evolution. PMID:25210030

Degradation pathway of the naphthalene azo dye intermediate 1-diazo-2- naphthol-4-sulfonic acid using Fenton's reagent.

PubMed

Zhu, Nanwen; Gu, Lin; Yuan, Haiping; Lou, Ziyang; Wang, Liang; Zhang, Xin

2012-08-01

Degradation of naphthalene dye intermediate 1-diazo-2- naphthol-4-sulfonic acid (1,2,4-Acid) by Fenton process has been studied in depth for the purpose of learning more about the reactions involved in the oxidation of 1,2,4-Acid. During 1,2,4-Acid oxidation, the solution color initially takes on a dark red, then to dark black associated with the formation of quinodial-type structures, and then goes to dark brown and gradually disappears, indicating a fast degradation of azo group. The observed color changes of the solution are a result of main reaction intermediates, which can be an indicator of the level of oxidization reached. Nevertheless, complete TOC removal is not accomplished, in accordance with the presence of resistant carboxylic acids at the end of the reaction. The intermediates generated along the reaction time have been identified and quantified. UPLC-(ESI)-TOF-HRMS analysis allows the detection of 19 aromatic compounds of different size and complexity. Some of them share the same accurate mass but appear at different retention time, evidencing their different molecular structures. Heteroatom oxidation products like SO(4)(2-) have also been quantified and explanations of their release are proposed. Short-chain carboxylic acids are detected at long reaction time, as a previous step to complete the process of dye mineralization. Finally, considering all the findings of the present study and previous related works, the evolution from the original 1,2,4-Acid to the final products is proposed in a general reaction scheme. Copyright © 2012 Elsevier Ltd. All rights reserved.

Neural network modeling of the kinetics of SO2 removal by fly ash-based sorbent.

PubMed

Raymond-Ooi, E H; Lee, K T; Mohamed, A R; Chu, K H

2006-01-01

The mechanistic modeling of the sulfation reaction between fly ash-based sorbent and SO2 is a challenging task due to a variety reasons including the complexity of the reaction itself and the inability to measure some of the key parameters of the reaction. In this work, the possibility of modeling the sulfation reaction kinetics using a purely data-driven neural network was investigated. Experiments on SO2 removal by a sorbent prepared from coal fly ash/CaO/CaSO4 were conducted using a fixed bed reactor to generate a database to train and validate the neural network model. Extensive SO2 removal data points were obtained by varying three process variables, namely, SO2 inlet concentration (500-2000 mg/L), reaction temperature (60-80 degreesC), and relative humidity (50-70%), as a function of reaction time (0-60 min). Modeling results show that the neural network can provide excellent fits to the SO2 removal data after considerable training and can be successfully used to predict the extent of SO2 removal as a function of time even when the process variables are outside the training domain. From a modeling standpoint, the suitably trained and validated neural network with excellent interpolation and extrapolation properties could have immediate practical benefits in the absence of a theoretical model.

Exploring between the extremes: conversion-dependent kinetics of phosphite-modified hydroformylation catalysis.

PubMed

Kubis, Christoph; Selent, Detlef; Sawall, Mathias; Ludwig, Ralf; Neymeyr, Klaus; Baumann, Wolfgang; Franke, Robert; Börner, Armin

2012-07-09

The kinetics of the hydroformylation of 3,3-dimethyl-1-butene with a rhodium monophosphite catalyst has been studied in detail. Time-dependent concentration profiles covering the entire olefin conversion range were derived from in situ high-pressure FTIR spectroscopic data for both, pure organic components and catalytic intermediates. These profiles fit to Michaelis-Menten-type kinetics with competitive and uncompetitive side reactions involved. The characteristics found for the influence of the hydrogen concentration verify that the pre-equilibrium towards the catalyst substrate complex is not established. It has been proven experimentally that the hydrogenolysis of the intermediate acyl complex remains rate limiting even at high conversions when the rhodium hydride is the predominant resting state and the reaction is nearly of first order with respect to the olefin. Results from in situ FTIR and high-pressure (HP) NMR spectroscopy and from DFT calculations support the coordination of only one phosphite ligand in the dominating intermediates and a preferred axial position of the phosphite in the electronically saturated, trigonal bipyramidal (tbp)-structured acyl rhodium complex. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectrophotometric study of the thorium-morin mixed-color system

USGS Publications Warehouse

Fletcher, M.H.; Milkey, R.G.

1956-01-01

A spectrophotometric study was made of the thoriummorin reaction to evaluate the suitability of morin as a reagent for the determination of trace amounts of thorium. At pH 2, the equilibrium constant for the reaction is 1 ?? 106, and a single complex having a thorium-morin ratio of 1 to 2 is formed. The complex shows maximum absorbance at a wave length of 410 m??, and its absorbance obeys Beer's law. The absorbance readings are highly reproducible, and the sensitivity is relatively high, an absorbance difference of 0.001 being equivalent to 0.007 ?? of ThO2 per sq. cm. The effects of acid, alcohol, and morin concentration, time, temperature, and age of the morin reagent as well as the behavior of morin with zirconium(IV), iron(III), aluminum(III), ytterbium(III), yttrium(III), uranium(VI), praseodymium(III), lead(II), lanthanum(III), and calcium(II) ions are discussed. A method is presented for the determination of thorium in pure solutions. Appropriate separations for the isolation of thorium may extend the usefulness of the method and permit the determination of trace amounts of thorium in complex materials.

Oxidation of ZrB2 SiC TaSi2 Materials at Ultra High Temperatures

NASA Technical Reports Server (NTRS)

Opila, E.; Smith, J.; Levine, S.; Lorincz, J.; Reigel, M.

2008-01-01

ZrB2 - 20v% SiC - 20v% TaSi2 was oxidized in stagnant air for ten minute cycles for times up to 100 minutes at 1627 C and 1927 C. The sample oxidized at 1627 C showed oxidation resistance better than that of the standard ZrB2 - 20v% SiC. The sample oxidized at 1927 C, however, showed evidence of liquid phase formation and complex oxidation products. The sample exposed at 1927 C was analyzed in detail by scanning electron microprobe and wavelength dispersive spectroscopy to understand the complex oxidation and melting reactions occurring during exposure. The as hot-pressed material shows the formation of a Zr(Ta)B2 phase in addition to the three phases in the nominal composition already noted. After oxidation, the TaSi2 in the matrix was completely reacted to form Ta(Zr)C. The layered oxidation products included SiO2, ZrO2, Ta2O5, and a complex oxide containing both Zr and Ta. Likely reactions are proposed based on thermodynamic phase stability and phase morphology.

Reversibility of electrochemical reactions of sulfur supported on inverse opal carbon in glyme-Li salt molten complex electrolytes.

PubMed

Tachikawa, Naoki; Yamauchi, Kento; Takashima, Eriko; Park, Jun-Woo; Dokko, Kaoru; Watanabe, Masayoshi

2011-07-28

Electrochemical reactions of sulfur supported on three-dimensionally ordered macroporous carbon in glyme-Li salt molten complex electrolytes exhibit good reversibility and large capacity based on the mass of sulfur, which suggests that glyme-Li salt molten complexes are suitable electrolytes for Li-S batteries.

From Complex Data to Actionable Information: Institutional Research Supporting Enrollment Management

ERIC Educational Resources Information Center

Anderson, Douglas K.; Milner, Bridgett J.; Foley, Chris J.

2008-01-01

Producing analyses that are accurate, timely, and simple is a constant challenge for institutional researchers. The stakes are high: when the analysis is incomplete, arrives too late, does not adequately address the question, or is simply too much to comprehend, decision makers fall back on anecdotal thinking or gut-level reactions that can lead…

Implicit Sequence Learning in Dyslexia: A Within-Sequence Comparison of First- and Higher-Order Information

ERIC Educational Resources Information Center

Du, Wenchong; Kelly, Steve W.

2013-01-01

The present study examines implicit sequence learning in adult dyslexics with a focus on comparing sequence transitions with different statistical complexities. Learning of a 12-item deterministic sequence was assessed in 12 dyslexic and 12 non-dyslexic university students. Both groups showed equivalent standard reaction time increments when the…

The Development of Visual Expectations in the First Year.

ERIC Educational Resources Information Center

Reznick, J. Steven; Chawarska, Katarzyna; Betts, Stephanie

2000-01-01

Two experiments used Visual Expectations Procedure to investigate development of expectations in infants up to 12 months old. Reaction time improved and the percentage of anticipations increased between 6 and 9 months using an alternation pattern or a complex pivot pattern, and between 4 and 8 months when using a left-right alternation or a…

The Evolution of Children's Mental Addition.

ERIC Educational Resources Information Center

Ashcraft, Mark H.; Hamann, Mary Sue

Students in grades 1, 4, 7, and 10 were tested in a two-part investigation of simple and complex mental addition (with college students as a reference point). One session involved a normal reaction time task in which children made true/false judgments about a series of addition examples. The other session involved a verbal protocol interview, the…

Working Memory Deficits in Children with Reading Difficulties: Memory Span and Dual Task Coordination

ERIC Educational Resources Information Center

Wang, Shinmin; Gathercole, Susan E.

2013-01-01

The current study investigated the cause of the reported problems in working memory in children with reading difficulties. Verbal and visuospatial simple and complex span tasks, and digit span and reaction times tasks performed singly and in combination, were administered to 46 children with single word reading difficulties and 45 typically…

Gold (I)-Catalyzed Diastereo- and Enantioselective 1,3-Dipolar Cycloaddition and Mannich Reactions of Azlactones

PubMed Central

Melhado, Asa D.; Amarante, Giovanni W.; Wang, Z. Jane; Luparia, Marco; Toste, F. Dean

2011-01-01

Azlactones participate in stereoselective reactions with electron-deficient alkenes and N-sulfonyl aldimines to give products of 1,3-dipolar cycloaddition and Mannich addition reactions respectively. Both of these reactions proceed with good to excellent diastereo- and enantioselectivity using a single class of gold-catalysts, namely C2-symmetric bis(phosphinegold(I) carboxylate)complexes. The development of the azlactone Mannich reaction to provide fully protected anti-α,β-diamino acid derivatives is described. 1,3-Dipolar cycloaddition reactions of several acyclic 1,2-disubstituted alkenes, and the chemistry of the resultant cycloadducts, are examined to probe the stereochemical course of this reaction. Reaction kinetics and tandem MS studies of both the cycloaddition and Mannich reactions are reported. These studies support a mechanism in which the gold complexes catalyze addition reactions through nucleophile activation rather than the more typical activation of the electrophilic reaction component. PMID:21341677

A new preparation of a bifunctional crystalline heterogeneous copper electrocatalyst by electrodeposition using a Robson-type macrocyclic dinuclear copper complex for efficient hydrogen and oxygen evolution from water.

PubMed

Majumder, Samit; Abdel Haleem, Ashraf; Nagaraju, Perumandla; Naruta, Yoshinori

2017-07-18

The development of low-cost, stable bifunctional electrocatalysts, which operate in the same electrolyte with a low overpotential for water splitting, including the oxygen evolution reaction and the hydrogen evolution reaction, remains an attractive prospect and a great challenge. In this study, a water soluble Robson-type macrocyclic dicopper(ii) complex has been used for the first time as a catalyst precursor for the generation of a copper-based bifunctional heterogeneous catalyst film, which can be used for both HER and OER at a near neutral pH. In sodium borate buffer at pH 9.20, this complex decomposed to give a Cu(OH) 2 /Cu 2 O-based thin film on FTO that catalyzes both hydrogen production and water oxidation. The morphology, nature and composition of the thin film were fully characterized by scanning electron microscopy, powder X-ray diffraction, X-ray photoelectron, and energy dispersive X-ray spectroscopies. The catalyst film showed high stability during the course of electrolysis in either the cathodic or the anodic direction for more than 4 h. Faradaic efficiencies of ∼92% for HER and ∼96% for OER were achieved. The switch between the two half-reactions of catalytic water splitting was fully reversible in nature.

Catalytic Synthesis of n-Butyl Oleate by Cerium Complex Doped Y/SBA-15 Composite Molecular Sieve

NASA Astrophysics Data System (ADS)

Shi, Chunwei; Bian, Xue; Wu, Yongfu; Cong, Yufeng; Pei, Mingyuan

2018-01-01

Cerium ion was successfully incorporated into Y/SBA-15 micro-mesoporous molecular sieves via the hydrothermal synthesis method to give a series of composite materials. The prepared materials were thoroughly characterized using Fourier transform infrared spectroscopy (FT-IR), X-ray fluorescence spectroscopy (XRF), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) and differential thermo gravimetric analysis (TG-DTG). The results showed that the prepared composite materials retained the highly ordered mesoporous two-dimensional hexagonal structure of SBA-15 and the octagonal structure of Y. The catalyst Ce-Y/SBA-15 was prepared and characterized, then the esterification of n-butanol and oleic acid was studied with bismuth phosphotungstate as a catalyst. Using this model reaction, the effects of Ce-HY/SBA-15, molar ratio of alcohol to oleic acid, amount of catalysts, reaction time and reaction temperature were investigated. The experimental results show that the optimal reaction conditions were: 1.8:1 molar ratio of alcohol to acid, 5 % catalyst amount (based on weight of oleic acid), 4 h reaction time and reflux conditions. Under these conditions, the yield of esterification was 90.6 %. The results suggest that the addition of Ce can effectively improve the catalytic properties of composite molecular sieves.

Reaction-diffusion controlled growth of complex structures

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

Genome Analysis of Structure–Function Relationships in Respiratory Complex I, an Ancient Bioenergetic Enzyme

PubMed Central

Degli Esposti, Mauro

2016-01-01

Respiratory complex I (NADH:ubiquinone oxidoreductase) is a ubiquitous bioenergetic enzyme formed by over 40 subunits in eukaryotes and a minimum of 11 subunits in bacteria. Recently, crystal structures have greatly advanced our knowledge of complex I but have not clarified the details of its reaction with ubiquinone (Q). This reaction is essential for bioenergy production and takes place in a large cavity embedded within a conserved module that is homologous to the catalytic core of Ni–Fe hydrogenases. However, how a hydrogenase core has evolved into the protonmotive Q reductase module of complex I has remained unclear. This work has exploited the abundant genomic information that is currently available to deduce structure–function relationships in complex I that indicate the evolutionary steps of Q reactivity and its adaptation to natural Q substrates. The results provide answers to fundamental questions regarding various aspects of complex I reaction with Q and help re-defining the old concept that this reaction may involve two Q or inhibitor sites. The re-definition leads to a simplified classification of the plethora of complex I inhibitors while throwing a new light on the evolution of the enzyme function. PMID:26615219

Preparation of microcapsules by complex coacervation of gum Arabic and chitosan.

PubMed

Butstraen, Chloé; Salaün, Fabien

2014-01-01

Gum Arabic-chitosan microcapsules containing a commercially available blend of triglycerides (Miglyol 812 N) as core phase were synthesized by complex coacervation. This study was conducted to clarify the influence of different parameters on the encapsulation process, i.e. during the emulsion formation steps and during the shell formation, using conductometry, zeta potential, surface and interface tension measurement and Fourier-transform infrared spectroscopy. By carefully analyzing the influencing factors including phase volume ratio, stirring rate and time, pH, reaction time, biopolymer ratio and crosslinking effect, the optimum synthetic conditions were found out. For the emulsion step, the optimum phase volume ratio chosen was 0.10 and an emulsion time of 15 min at 11,000 rpm was selected. The results also indicated that the optimum formation of these complexes appears at a pH value of 3.6 and a weight ratio of chitosan to gum Arabic mixtures of 0.25. Copyright © 2013 Elsevier Ltd. All rights reserved.

Selective Conversion of CO2 into Isocyanate by Low-Coordinate Iron Complexes.

PubMed

Broere, Daniël L J; Mercado, Brandon Q; Holland, Patrick L

2018-04-06

Discovery of the mechanisms for selective transformations of CO 2 into organic compounds is a challenge. Herein, we describe the reaction of low-coordinate Fe silylamide complexes with CO 2 to give trimethylsilyl isocyanate and the corresponding Fe siloxide complex. Kinetic studies show that this is a two-stage reaction, and the presence of a single equivalent of THF influences the rates of both steps. Isolation of a thermally unstable intermediate provides mechanistic insight that explains both the effect of THF in this reaction, and the way in which the reaction achieves high selectivity for isocyanate formation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exposure-time based modeling of nonlinear reactive transport in porous media subject to physical and geochemical heterogeneity.

PubMed

Sanz-Prat, Alicia; Lu, Chuanhe; Amos, Richard T; Finkel, Michael; Blowes, David W; Cirpka, Olaf A

2016-09-01

Transport of reactive solutes in groundwater is affected by physical and chemical heterogeneity of the porous medium, leading to complex spatio-temporal patterns of concentrations and reaction rates. For certain cases of bioreactive transport, it could be shown that the concentrations of reactive constituents in multi-dimensional domains are approximately aligned with isochrones, that is, lines of identical travel time, provided that the chemical properties of the matrix are uniform. We extend this concept to combined physical and chemical heterogeneity by additionally considering the time that a water parcel has been exposed to reactive materials, the so-called exposure time. We simulate bioreactive transport in a one-dimensional domain as function of time and exposure time, rather than space. Subsequently, we map the concentrations to multi-dimensional heterogeneous domains by means of the mean exposure time at each location in the multi-dimensional domain. Differences in travel and exposure time at a given location are accounted for as time difference. This approximation simplifies reactive-transport simulations significantly under conditions of steady-state flow when reactions are restricted to specific locations. It is not expected to be exact in realistic applications because the underlying assumption, such as neglecting transverse mixing altogether, may not hold. We quantify the error introduced by the approximation for the hypothetical case of a two-dimensional, binary aquifer made of highly-permeable, non-reactive and low-permeable, reactive materials releasing dissolved organic matter acting as electron donor for aerobic respiration and denitrification. The kinetically controlled reactions are catalyzed by two non-competitive bacteria populations, enabling microbial growth. Even though the initial biomass concentrations were uniform, the interplay between transport, non-uniform electron-donor supply, and bio-reactions led to distinct spatial patterns of the two types of biomass at late times. Results obtained by mapping the exposure-time based results to the two-dimensional domain are compared with simulations based on the two-dimensional, spatially explicit advection-dispersion-reaction equation. Once quasi-steady state has been reached, we find a good agreement in terms of the chemical-compound concentrations between the two approaches inside the reactive zones, whereas the exposure-time based model is not able to capture reactions occurring in the zones with zero electron-donor release. We conclude that exposure-time models provide good approximations of nonlinear bio-reactive transport when transverse mixing is not the overall controlling process and all reactions are essentially restricted to distinct reactive zones. Copyright © 2016 Elsevier B.V. All rights reserved.

Features of proteolytic properties of tetraphenylporphyrin complex with lanthanide group metals

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Synthesis of Some "Cobaloxime" Derivatives: A Demonstration of "Umpolung" in the Reactivity of an Organometallic Complex

NASA Astrophysics Data System (ADS)

Jameson, Donald L.; Grzybowski, Joseph J.; Hammels, Deb E.; Castellano, Ronald K.; Hoke, Molly E.; Freed, Kimberly; Basquill, Sean; Mendel, Angela; Shoemaker, William J.

1998-04-01

This article describes a four-reaction sequence for the synthesis of two organometallic "cobaloxime" derivatives. The concept of "Umpolung" or reversal of reactivity is demonstrated in the preparation of complexes. The complex Co(dmgH)2(4-t-BuPy)Et is formed by the reaction of a cobalt (I) intermediate (cobalt in the role of nucleophile) with ethyl iodide. The complex Co(dmgH)2(4-t-BuPy)Ph is formed by the reaction of PhMgBr with a cobalt (III) intermediate (cobalt in the role of electrophile). All the products contain cobalt in the diamagnetic +3 oxidation state and are readily characterized by proton and carbon NMR. The four reaction sequence may be completed in two 4-hour lab periods. Cobaloximes are well known as model complexes for Vitamin B-12 and the experiment exposes students to aspects of classical coordination chemistry, organometallic chemistry and bioinorganic chemistry. The experiment also illustrates an important reactivity parallel between organic and organometallic chemistry.

Spectro- and electrochemical studies of some ruthenium and osmium complexes of 2-(2'-pyridyl)benzimidazole; complexes with intra-molecular charge transfer.

PubMed

Khalil, M M; Ali, S A; Ramadan, R M

2001-04-01

Reaction of Ru3(CO)12, with 2-(2'-pyridyl)benzimidazole (HPBI) resulted in the formation of Ru(CO)3(HPBI) (I) complex. In presence of pyridine or dipyridine, the two derivatives [Ru(CO)3(HPBI)].Py (II) and [Ru(CO)3(HPBI)].dpy (III) were isolated. The corresponding reactions of Os3(CO)12 yielded only one single product; Os(CO)2(HPBI)2 (IV). Spectroscopic studies of these complexes revealed intramolecular metal to ligand CT interactions. Reactions of RuCl3 with HPBI gave three distinct products; [Ru(HPBI)2Cl2]Cl (V), [Ru(HPBI)(dipy)Cl2]C1 (VI) and [Ru(PBI)2(py)2]Cl (VII). The UV-vis studies indicated the presence of intramolecular ligand to metal CT interactions. Electrochemical investigation of the complexes showed some irreversible, reversible and quasi-reversible redox reactions due to tautomeric interconversions through electron transfer.

Transient isomers in the photodissociation of bromoiodomethane

NASA Astrophysics Data System (ADS)

Marcellini, Moreno; Nasedkin, Alexandr; Zietz, Burkhard; Petersson, Jonas; Vincent, Jonathan; Palazzetti, Federico; Malmerberg, Erik; Kong, Qingyu; Wulff, Michael; van der Spoel, David; Neutze, Richard; Davidsson, Jan

2018-04-01

The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH2IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH2I-Br and CH2Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule. We observe the internal rearrangement of CH2Br-I to CH2I-Br in cyclohexane by extending the time window up to 3 μs. We track the photoproduct kinetics of CH2Br-I in methanol solution where only one isomer is observed. The effect of the polarity of solvent on the geminate recombination pathways is discussed.

A Neuroergonomic Quasi-Experiment: Predictors of Situation Awareness and Display Usability with USAF Pilots while Performing Complex Tasks

DTIC Science & Technology

2015-02-01

adverse reactions possibly associated with electrode placement, such as urticarial (hives) or contact dermatitis . In such an event, the medical... contact (airplane’s wheels time of impact with the runway). The human brain uses internal trigonometry and calculus to solve the Time of arrival...and regulations, and that if you desire further information you may contact the base legal office (ASC/JA, 257-6143 for Wright-Patterson AFB). In

Bat white-nose syndrome: A real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructans

Treesearch

Laura K Muller; Jeffrey M. Lorch; Daniel L. Lindner; Michael O' Connor; Andrea Gargas; David S. Blehert

2013-01-01

The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The...

We should be using nonlinear indices when relating heart-rate dynamics to cognition and mood

PubMed Central

Young, Hayley; Benton, David

2015-01-01

Both heart rate (HR) and brain functioning involve the integrated output of a multitude of regulatory mechanisms, that are not quantified adequately by linear approximations such as means and standard deviations. It was therefore considered whether non-linear measures of HR complexity are more strongly associated with cognition and mood. Whilst resting, the inter-beat (R-R) time series of twenty-one males and twenty-four females were measured for five minutes. The data were summarised using time, frequency and nonlinear complexity measures. Attention, memory, reaction times, mood and cortisol levels were assessed. Nonlinear HR indices captured additional information, enabling a greater percentage of the variance in behaviour to be explained. On occasions non-linear indices were related to aspects for behaviour, for example focused attention and cortisol production, when time or frequency indices were not. These effects were sexually dimorphic with HR complexity being more strongly associated with the behaviour of females. It was concluded that nonlinear rather than linear methods of summarizing the HR times series offers a novel way of relating brain functioning and behaviour. It should be considered whether non-linear measures of HR complexity can be used as a biomarker of the integrated functioning of the brain. PMID:26565560

Development of sandwich-form biosensor to detect Mycobacterium tuberculosis complex in clinical sputum specimens.

PubMed

Shojaei, Taha Roodbar; Mohd Salleh, Mohamad Amran; Tabatabaei, Meisam; Ekrami, Alireza; Motallebi, Roya; Rahmani-Cherati, Tavoos; Hajalilou, Abdollah; Jorfi, Raheleh

2014-01-01

Mycobacterium tuberculosis, the causing agent of tuberculosis, comes second only after HIV on the list of infectious agents slaughtering many worldwide. Due to the limitations behind the conventional detection methods, it is therefore critical to develop new sensitive sensing systems capable of quick detection of the infectious agent. In the present study, the surface modified cadmium-telluride quantum dots and gold nanoparticles conjunct with two specific oligonucleotides against early secretory antigenic target 6 were used to develop a sandwich-form fluorescence resonance energy transfer-based biosensor to detect M. tuberculosis complex and differentiate M. tuberculosis and M. bovis Bacille Calmette-Guerin simultaneously. The sensitivity and specificity of the newly developed biosensor were 94.2% and 86.6%, respectively, while the sensitivity and specificity of polymerase chain reaction and nested polymerase chain reaction were considerably lower, 74.2%, 73.3% and 82.8%, 80%, respectively. The detection limits of the sandwich-form fluorescence resonance energy transfer-based biosensor were far lower (10 fg) than those of the polymerase chain reaction and nested polymerase chain reaction (100 fg). Although the cost of the developed nanobiosensor was slightly higher than those of the polymerase chain reaction-based techniques, its unique advantages in terms of turnaround time, higher sensitivity and specificity, as well as a 10-fold lower detection limit would clearly recommend this test as a more appropriate and cost-effective tool for large scale operations. Copyright © 2014 Elsevier Editora Ltda. All rights reserved.

The Differential Gibbs Free Energy of Activation and its Implications in the Transition-State of Enzymatic Reactions

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2016-12-01

We propose a mathematical framework to introduce the concept of differential free energy of activation in enzymatically catalyzed reactions, and apply it to N uptake by microalgae and bacteria. This framework extends the thermodynamic capabilities of the classical transition-state theory in and harmonizes the consolidated definitions of kinetic parameters with their thermodynamic and physical meaning. Here, the activation energy is assumed to be a necessary energetic level for equilibrium complexation between reactants and activated complex; however, an additional energy contribution is required for the equilibrium activated complex to release reaction products. We call this "differential free energy of activation"; it can be described by a Boltzmann distribution, and corresponds to a free energy level different from that of complexation. Whether this level is above or below the free energy of activation depends on the reaction, and defines energy domains that correspond to "superactivated", "activated", and "subactivated" complexes. The activated complex reaching one of those states will eventually release the products from an energy level different than that of activation. The concept of differential free energy of activation was tested on 57 independent experiments of NH­4+ and NO3- uptake by various microalgae and bacteria at temperatures ranging between 1 and 45oC. Results showed that the complexation equilibrium always favored the activated complex, but the differential energy of activation led to an apparent energy barrier consistent with observations. Temperature affected all energy levels within this framework but did not alter substantially these thermodynamic features. Overall the approach: (1) provides a thermodynamic and mathematical link between Michaelis-Menten and rate constants; (2) shows that both kinetic parameters can be described or approximated by Arrhenius' like equations; (3) describes the likelihood of formation of sub-, super-, and activated complexes; and (4) shows direction and thermodynamic likelihood of each reaction branch within the transition state. The approach suites particularly well for calibration of kinetic parameters against experimentally acquired reaction dynamics measurements of nutrient biogeochemical cycles.

Facile synthesis and shape evolution of oleic acid decorated Cu2O microcrystals

NASA Astrophysics Data System (ADS)

Xu, Bin; Cao, Xiaohai; Zhu, Bingchun; Lou, Baiyang; Ma, Xiaocun; Li, Xiao; Wang, Yuguang

2015-11-01

A facile synthetic method of oleic acid decorated Cu2O microcrystals has been developed by thermal decomposition of copper formate-octylamine complexes in paraffin using oleic acid as dispersing agent. This new method showed many advantages, which include free-reducing agent, enhancing antioxidant properties of Cu2O and good dispersity in paraffin, etc. The phase structure and morphology were investigated by means of XRD, SEM and TEM. It is found that the reaction time and temperature play the important roles in the crystallite morphology. With the increase of the reaction time, the Cu2O rhombic dodecahedron is gradually transformed into the spherical particle by intraparticle ripening. The shape evolution of Cu2O microcrystals can be accelerated with the increase of temperature.

Spectrophotometric determination of fenoprofen calcium drug in pure and pharmaceutical preparations. Spectroscopic characterization of the charge transfer solid complexes

NASA Astrophysics Data System (ADS)

Mohamed, Marwa E.; Frag, Eman Y. Z.; Hathoot, Abla A.; Shalaby, Essam A.

2018-01-01

Simple, accurate and robust spectrophotometric method was developed for determination of fenoprofen calcium drug (FPC). The proposed method was based on the charge transfer (CT) reaction of FPC drug (as n-electron donor) with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), 2,4,6-trinitrophenol (picric acid, PA) or 1,2,5,8-tetrahydroxyanthraquinone (Quinalizarin, QZ) (as π-acceptors) to give highly colored charge transfer complexes. Different variables affecting the reaction such as reagent concentration, temperature and time have been carefully optimized to achieve the highest sensitivity. Beer's law was obeyed over the concentration ranges of 2-60, 0.6-90 and 4-30 μg mL- 1 using DDQ, PA and QZ CT reagents, respectively, with correlation coefficients of 0.9986, 0.9989 and 0.997 and detection limits of 1.78, 0.48 and 2.6 μg mL- 1 for the CT reagents in the same order. Elucidation of the chemical structure of the solid CT complexes formed via reaction between the drug under study and π-acceptors was done using elemental, thermal analyses, IR, 1H NMR and mass spectrometry. X-ray diffraction was used to estimate the crystallinity of the CT complexes. Their biological activities were screened against different bacterial and fungal organisms. The method was applied successfully with satisfactory results for the determination of FPC drug in fenoprofen capsules. The method was validated with respect to linearity, limit of detection and quantification, inter- and intra-days precision and accuracy. The proposed method gave comparable results with the official method.

Two-dimensional pH distributions and dynamics in bioturbated marine sediments

NASA Astrophysics Data System (ADS)

Zhu, Qingzhi; Aller, Robert C.; Fan, Yanzhen

2006-10-01

The seafloor is the site of intense biogeochemical and mineral dissolution-precipitation reactions which generate strong gradients in pH near the sediment-overlying water interface. These gradients are usually measured in one-dimension vertically with depth. Two-dimensional pH distributions in marine sediments were examined at high resolution (65 × 65 μm pixel) and analytical precision over areas of ˜150 to 225 cm 2 using a newly developed pH planar fluorosensor. Dramatic three-dimensional gradients, complex heterogeneity, and dynamic changes of pH occur in the surficial zone of deposits inhabited by macrofauna. pH can vary by ±2 units horizontally as well as vertically over millimeter scales. pH minima zones often form in association with redoxclines within a few millimeters of inner burrow walls, and become more pronounced with time if burrows remain stable and irrigated for extended periods. Microenvironmental pH minima also form locally around decaying biomass and relict burrow tracks, and dissipate with time (˜5 d). H + concentrations and fluxes in sandy mud show complex acid-base reaction distributions with net H + fluxes around burrows up to ˜12 nmol cm -2 d -1 and maximum net reaction rates varying between -90 (consumption) to 120 (production) μM d -1 (˜90 nmol cm -1 d -1 burrow length). Acid producing zones that surround irrigated burrows are largely balanced by acid titration zones along inner burrow walls and outer radial boundaries. The geometry and scaling of pH microenvironments are functions of diagenetic reaction rates and three-dimensional transport patterns determined by sediment properties, such as diffusive tortuosity, and by benthic community characteristics such as the abundance, mobility, and size of infauna. Previously, undocumented biogeochemical phenomena such as low pH regions associated with in-filled relict biogenic structures and burrowing tracks are readily demonstrated by two-dimensional and time-dependent images of pH and sedimentary structure.

Enzymatic synthesis of chiral amino-alcohols by coupling transketolase and transaminase-catalyzed reactions in a cascading continuous-flow microreactor system.

PubMed

Gruber, Pia; Carvalho, Filipe; Marques, Marco P C; O'Sullivan, Brian; Subrizi, Fabiana; Dobrijevic, Dragana; Ward, John; Hailes, Helen C; Fernandes, Pedro; Wohlgemuth, Roland; Baganz, Frank; Szita, Nicolas

2018-03-01

Rapid biocatalytic process development and intensification continues to be challenging with currently available methods. Chiral amino-alcohols are of particular interest as they represent key industrial synthons for the production of complex molecules and optically pure pharmaceuticals. (2S,3R)-2-amino-1,3,4-butanetriol (ABT), a building block for the synthesis of protease inhibitors and detoxifying agents, can be synthesized from simple, non-chiral starting materials, by coupling a transketolase- and a transaminase-catalyzed reaction. However, until today, full conversion has not been shown and, typically, long reaction times are reported, making process modifications and improvement challenging. In this contribution, we present a novel microreactor-based approach based on free enzymes, and we report for the first time full conversion of ABT in a coupled enzyme cascade for both batch and continuous-flow systems. Using the compartmentalization of the reactions afforded by the microreactor cascade, we overcame inhibitory effects, increased the activity per unit volume, and optimized individual reaction conditions. The transketolase-catalyzed reaction was completed in under 10 min with a volumetric activity of 3.25 U ml -1 . Following optimization of the transaminase-catalyzed reaction, a volumetric activity of 10.8 U ml -1 was attained which led to full conversion of the coupled reaction in 2 hr. The presented approach illustrates how continuous-flow microreactors can be applied for the design and optimization of biocatalytic processes. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

Time-resolved gas-phase kinetic, quantum chemical, and RRKM studies of reactions of silylene with alcohols.

PubMed

Becerra, Rosa; Cannady, J Pat; Walsh, Robin

2011-05-05

Time-resolved kinetic studies of silylene, SiH(2), generated by laser flash photolysis of 1-silacyclopent-3-ene and phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with methanol, ethanol, 1-propanol, 1-butanol, and 2-methyl-1-butanol. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF(6) bath gas, at room temperature. In the study with methanol several buffer gases were used. All five reactions showed pressure dependences characteristic of third body assisted association reactions. The rate constant pressure dependences were modeled using RRKM theory, based on E(0) values of the association complexes obtained by ab initio calculation (G3 level). Transition state models were adjusted to fit experimental fall-off curves and extrapolated to obtain k(∞) values in the range (1.9-4.5) × 10(-10) cm(3) molecule(-1) s(-1). These numbers, corresponding to the true bimolecular rate constants, indicate efficiencies of between 16% and 67% of the collision rates for these reactions. In the reaction of SiH(2) + MeOH there is a small kinetic component to the rate which is second order in MeOH (at low total pressures). This suggests an additional catalyzed reaction pathway, which is supported by the ab initio calculations. These calculations have been used to define specific MeOH-for-H(2)O substitution effects on this catalytic pathway. Where possible our experimental and theoretical results are compared with those of previous studies.

Complexation between carrageenan and methylene blue for sensor design

NASA Astrophysics Data System (ADS)

Ling, Yew Pei; Heng, Lee Yook

2013-11-01

Theoretical studies on the methylene blue (MB)-carrageenans complexation at solution and solid states have been carried out via ultraviolet spectrophotoscopy and reflectometry methods. The equilibrium constant (Ka) of the MBcarrageenans complexation follows the order of Iota > Lambda > Kappa carrageenans, which indicated Iota-carrageenan forms a stable complex. MB-carrageenan complexation reaction showed decrease in Ka value from 210.71 ppm-1 to 114.57 ppm-1 when the reaction temperature increased from 298 K to 323 K. Le Chatelier's principle and mass action law explained that the MB-carrageenan complexation was an exothermic reaction (ΔH=-18.54 kJmol-1) that release heat. Thus MB-carrageenan complex was less stable at high temperature and tend to dissociate into free MB and carrageenan molecules. It was also supported by the van't Hoff equation. The reaction is a spontaneous process (ΔG=-13.23 kJmol-1) where the randomness of the molecules reduced (ΔS=-17.83 Jmol-1K-1) due to complexation. Besides, linear regression of the concentration and absorption of the MB-carrageenan reaction obeys the Beer Lambert law, which elucidated that the complexation process was not affected by any concentration dependent factors such as aggregation and self-quenching. Moreover, linear Benesi Hilderbrend plot revealed that the interaction between MB and carrageenan was a reversible and stoichiometric reaction with 1:1 ratio. However, the molar extinction coefficient (ɛ) and molar adsorption coefficient (μa) of the MB-carrageenan complex were lower compared to free MB, described that the complex was less adsorptive. The sensor constructed based on these theoretical investigations showed response behavior that was similar with solution test as both have attraction for carrageenans in the sequence of Iota-, Lambda-, Kappa- carrageenans. Likewise, carrageenan sensor was more selective towards Iota-carrageenan than to Lambda- and Kappa-carrageenans, and no response observed when tested with agar, alginate and glucose. Therefore the sensor is able to detect carrageenans specifically and offers rapid detection without the need of sample pretreatment when compared to conventional methods.

Effects of CPAP therapy on cognitive and psychomotor performances in patients with severe obstructive sleep apnea: a prospective 1-year study.

PubMed

Pecotic, Renata; Dodig, Ivana Pavlinac; Valic, Maja; Galic, Tea; Kalcina, Linda Lusic; Ivkovic, Natalija; Dogas, Zoran

2018-02-16

We prospectively investigated the effects of continuous positive airway pressure (CPAP) on long-term cognitive and psychomotor performances, and excessive daytime sleepiness in severe obstructive sleep apnea (OSA) patients. A total of 40 patients were recruited and 23 patients with severe OSA fully completed the study protocol to investigate the effects of CPAP therapy on psychomotor performance at 1, 3, and 6 months and 1 year following initiation of the therapy. Psychomotor CRD-series tests measuring reaction times of light stimulus perception, solving simple arithmetic operations, and complex psychomotor limb coordination, were used in this study. The data collected following CPAP therapy were compared to baseline values prior to the CPAP treatment for each patient. All of the measured variables improved following CPAP treatment. However, the most pronounced effect was observed in improvement of reaction times to complex psychomotor limb coordination test (p < 0.05). Self-reported evaluation of excessive daytime sleepiness measured by Epworth Sleepiness Scale (ESS) showed significant decrease from 10.0 ± 1.1 before to 3.5 ± 0.5 (p < 0.001), after 1 year on CPAP therapy. The CPAP therapy improved cognitive and psychomotor performance on CRD-series tests with the most significant improvement observed in complex psychomotor limb coordination of severe OSA patients.

Anticancer efficacy of a supramolecular complex of a 2-diethylaminoethyl-dextran-MMA graft copolymer and paclitaxel used as an artificial enzyme.

PubMed

Onishi, Yasuhiko; Eshita, Yuki; Ji, Rui-Cheng; Onishi, Masayasu; Kobayashi, Takashi; Mizuno, Masaaki; Yoshida, Jun; Kubota, Naoji

2014-01-01

The anticancer efficacy of a supramolecular complex that was used as an artificial enzyme against multi-drug-resistant cancer cells was confirmed. A complex of diethylaminoethyl-dextran-methacrylic acid methylester copolymer (DDMC)/paclitaxel (PTX), obtained with PTX as the guest and DDMC as the host, formed a nanoparticle 50-300 nm in size. This complex is considered to be useful as a drug delivery system (DDS) for anticancer compounds since it formed a stable polymeric micelle in water. The resistance of B16F10 melanoma cells to PTX was shown clearly through a maximum survival curve. Conversely, the DDMC/PTX complex showed a superior anticancer efficacy and cell killing rate, as determined through a Michaelis-Menten-type equation, which may promote an allosteric supramolecular reaction to tubulin, in the same manner as an enzymatic reaction. The DDMC/PTX complex showed significantly higher anticancer activity compared to PTX alone in mouse skin in vivo. The median survival times of the saline, PTX, DDMC/PTX4 (particle size 50 nm), and DDMC/PTX5 (particle size 290 nm) groups were 120 h (treatment (T)/control (C), 1.0), 176 h (T/C, 1.46), 328 h (T/C, 2.73), and 280 h (T/C, 2.33), respectively. The supramolecular DDMC/PTX complex showed twice the effectiveness of PTX alone (p < 0.036). Above all, the DDMC/PTX complex is not degraded in cells and acts as an intact supramolecular assembly, which adds a new species to the range of DDS.

Student Misinterpretations and Misconceptions Based on Their Explanations of Two Computer Animations of Varying Complexity Depicting the Same Oxidation-Reduction Reaction

ERIC Educational Resources Information Center

Rosenthal, Deborah P.; Sanger, Michael J.

2012-01-01

A group of 55 students were shown unnarrated versions of two different particulate-level computer animations of varying complexity depicting the oxidation-reduction reaction of aqueous silver nitrate and solid copper metal. These students were asked to explain their understanding of the chemical reaction based on their interpretations of these…

Hydrosilylation of aldehydes and ketones catalyzed by hydrido iron complexes bearing imine ligands.

PubMed

Zuo, Zhenyu; Sun, Hongjian; Wang, Lin; Li, Xiaoyan

2014-08-14

Two new hydrido iron complexes (2 and 4) were synthesized by the reactions of (4-methoxyphenyl)phenylketimine ((4-MeOPh)PhC=NH) with Fe(PMe3)4 or FeMe2(PMe3)4. The molecular structures of complexes 2 and 4 were confirmed by X-ray single crystal diffraction. Using hydrido iron complexes (1-4) as catalysts, the hydrosilylations of aldehydes and ketones were investigated. The four complexes were effective catalysts for this reduction reaction. Complex 1 among them is the best catalyst.

A Networks Approach to Modeling Enzymatic Reactions.

PubMed

Imhof, P

2016-01-01

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

The evolution of the temperature field during cavity collapse in liquid nitromethane. Part II: reactive case

NASA Astrophysics Data System (ADS)

Michael, L.; Nikiforakis, N.

2018-02-01

This work is concerned with the effect of cavity collapse in non-ideal explosives as a means of controlling their sensitivity. The main objective is to understand the origin of localised temperature peaks (hot spots) which play a leading order role at the early stages of ignition. To this end, we perform two- and three-dimensional numerical simulations of shock-induced single gas-cavity collapse in liquid nitromethane. Ignition is the result of a complex interplay between fluid dynamics and exothermic chemical reaction. In the first part of this work, we focused on the hydrodynamic effects in the collapse process by switching off the reaction terms in the mathematical formulation. In this part, we reinstate the reactive terms and study the collapse of the cavity in the presence of chemical reactions. By using a multi-phase formulation which overcomes current challenges of cavity collapse modelling in reactive media, we account for the large density difference across the material interface without generating spurious temperature peaks, thus allowing the use of a temperature-based reaction rate law. The mathematical and physical models are validated against experimental and analytic data. In Part I, we demonstrated that, compared to experiments, the generated hot spots have a more complex topological structure and that additional hot spots arise in regions away from the cavity centreline. Here, we extend this by identifying which of the previously determined high-temperature regions in fact lead to ignition and comment on the reactive strength and reaction growth rate in the distinct hot spots. We demonstrate and quantify the sensitisation of nitromethane by the collapse of the isolated cavity by comparing the ignition times of nitromethane due to cavity collapse and the ignition time of the neat material. The ignition in both the centreline hot spots and the hot spots generated by Mach stems occurs in less than half the ignition time of the neat material. We compare two- and three-dimensional simulations to examine the change in topology, temperatures, and reactive strength of the hot spots by the third dimension. It is apparent that belated ignition times can be avoided by the use of three-dimensional simulations. The effect of the chemical reactions on the topology and strength of the hot spots in the timescales considered is also studied, in a comparison between inert and reactive simulations where maximum temperature fields and their growth rates are examined.

Diastereoselective chain-elongation reactions using microreactors for applications in complex molecule assembly.

PubMed

Carter, Catherine F; Lange, Heiko; Sakai, Daiki; Baxendale, Ian R; Ley, Steven V

2011-03-14

Diastereoselective chain-elongation reactions are important transformations for the assembly of complex molecular structures, such as those present in polyketide natural products. Here we report new methods for performing crotylation reactions and homopropargylation reactions by using newly developed low-temperature flow-chemistry technology. In-line purification protocols are described, as well as the application of the crotylation protocol in an automated multi-step sequence. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient Destruction of Pollutants in Water by a Dual-Reaction-Center Fenton-like Process over Carbon Nitride Compounds-Complexed Cu(II)-CuAlO2.

PubMed

Lyu, Lai; Yan, Dengbiao; Yu, Guangfei; Cao, Wenrui; Hu, Chun

2018-04-03

Carbon nitride compounds (CN) complexed with the in-situ-produced Cu(II) on the surface of CuAlO 2 substrate (CN-Cu(II)-CuAlO 2 ) is prepared via a surface growth process for the first time and exhibits exceptionally high activity and efficiency for the degradation of the refractory pollutants in water through a Fenton-like process in a wide pH range. The reaction rate for bisphenol A removal is ∼25 times higher than that of the CuAlO 2 . According to the characterization, Cu(II) generation on the surface of CuAlO 2 during the surface growth process results in the marked decrease of the surface oxygen vacancies and the formation of the C-O-Cu bridges between CN and Cu(II)-CuAlO 2 in the catalyst. The electron paramagnetic resonance (EPR) analysis and density functional theory (DFT) calculations demonstrate that the dual reaction centers are produced around the Cu and C sites due to the cation-π interactions through the C-O-Cu bridges in CN-Cu(II)-CuAlO 2 . During the Fenton-like reactions, the electron-rich center around Cu is responsible for the efficient reduction of H 2 O 2 to • OH, and the electron-poor center around C captures electrons from H 2 O 2 or pollutants and diverts them to the electron-rich area via the C-O-Cu bridge. Thus, the catalyst exhibits excellent catalytic performance for the refractory pollutant degradation. This study can deepen our understanding on the enhanced Fenton reactivity for water purification through functionalizing with organic solid-phase ligands on the catalyst surface.

Metabolites involved in cellular communication among human cumulus-oocyte-complex and sperm during in vitro fertilization.

PubMed

Gómez-Torres, María José; García, Eva María; Guerrero, Jaime; Medina, Sonia; Izquierdo-Rico, María José; Gil-Izquierdo, Ángel; Orduna, Jesús; Savirón, María; González-Brusi, Leopoldo; Ten, Jorge; Bernabeu, Rafael; Avilés, Manuel

2015-11-09

Fertilization is a key physiological process for the preservation of the species. Consequently, different mechanisms affecting the sperm and the oocyte have been developed to ensure a successful fertilization. Thus, sperm acrosome reaction is necessary for the egg coat penetration and sperm-oolema fusion. Several molecules are able to induce the sperm acrosome reaction; however, this process should be produced coordinately in time and in the space to allow the success of fertilization between gametes. The goal of this study was to analyze the metabolites secreted by cumulus-oocyte-complex (COC) to find out new components that could contribute to the induction of the human sperm acrosome reaction and other physiological processes at the time of gamete interaction and fertilization. For the metabolomic analysis, eighteen aliquots of medium were used in each group, containing: a) only COC before insemination and after 3 h of incubation; b) COC and capacitated spermatozoa after insemination and incubated for 16-20 hours; c) only capacitated sperm after 16-20 h in culture and d) only fertilization medium as control. Six patients undergoing assisted reproduction whose male partners provided normozoospermic samples were included in the study. Seventy-two COC were inseminated. The metabolites identified were monoacylglycerol (MAG), lysophosphatidylcholine (LPC) and phytosphingosine (PHS). Analysis by PCR and in silico of the gene expression strongly suggests that the cumulus cells contribute to the formation of the PHS and LPC. LPC and PHS are secreted by cumulus cells during in vitro fertilization and they could be involved in the induction of human acrosome reaction (AR). The identification of new molecules with a paracrine effect on oocytes, cumulus cells and spermatozoa will provide a better understanding of gamete interaction.

THE BIOLOGICAL ACTIVITY OF SOLUBLE ANTIGEN-ANTIBODY COMPLEXES

PubMed Central

Ishizaka, Kimishige; Ishizaka, Teruko; Campbell, Dan H.

1959-01-01

Soluble BSA-anti-BSA complexes, formed in antigen excess, give immediate skin reactions in normal guinea pigs. The mechanism of the reaction is not that of passive or reversed passive anaphylaxis. The complex itself is toxic. Skin activity of the complex depends on its composition. It has become obvious that the complex composed of two antigen molecules and one antibody molecule, (Ag2Ab), does not have the activity, whereas, Ag3Ab2 and more complicated complexes do. The role of complement as well as speculation on the structural changes of antibody-antigen complexes is presented. PMID:13620844

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

PubMed

Zimmermann, Tomás; Burda, Jaroslav V

2010-02-07

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

KO(t)Bu-Mediated Coupling of Indoles and [60]Fullerene: Transition-Metal-Free and General Synthesis of 1,2-(3-Indole)(hydro)[60]fullerenes.

PubMed

Li, Fei; Haj Elhussin, Imad Elddin; Li, Shengli; Zhou, Hongping; Wu, Jieying; Tian, Yupeng

2015-11-06

Direct coupling of indoles with C60 has been achieved for the first time. Transition-metal-free KO(t)Bu-mediated reaction of indoles to [60]fullerene has been developed as a practical and efficient method for the synthesis of various 1,2-(3-indole)(hydro)[60]fullerenes that are otherwise difficult to direct synthesize in an efficient and selective manner. This methodology tolerates sensitive functionalities such as chloro, ester, and nitro on indole and builds molecular complexity rapidly, with most reactions reaching completion in <1 h. A plausible reaction mechanism is proposed to explain the high regioselectivity at the 3-position of the indoles and the formation of 1,2-(3-indole)(hydro)[60]fullerenes.

Surface complexation modeling

USDA-ARS?s Scientific Manuscript database

Adsorption-desorption reactions are important processes that affect the transport of contaminants in the environment. Surface complexation models are chemical models that can account for the effects of variable chemical conditions, such as pH, on adsorption reactions. These models define specific ...

Calibration of Complex Subsurface Reaction Models Using a Surrogate-Model Approach

EPA Science Inventory

Application of model assessment techniques to complex subsurface reaction models involves numerous difficulties, including non-trivial model selection, parameter non-uniqueness, and excessive computational burden. To overcome these difficulties, this study introduces SAMM (Simult...

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

PubMed

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

2016-09-19

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

Synthesis, spectral and thermal studies of the newly hydrogen bonded charge transfer complex of o-phenylenediamine with pi acceptor picric acid.

PubMed

Khan, Ishaat M; Ahmad, Afaq

2010-10-01

Newly proton or charge transfer complex [(OPDH)(+)(PA)(-)] was synthesized by the reaction of the donor, o-phenylenediamine (OPD) with acceptor, 2,4,6-trinitrophenol (PAH). The chemical reaction has occurred via strong hydrogen bonding followed by migration of proton from acceptor to donor. UV-vis, (1)H NMR and FTIR spectra, in addition to the thermal and elemental analysis were used to confirm the proposed occurrence of the chemical reaction and to investigate the newly synthesized solid CT complex. The stoichiometry of the CT complex was found to be 1:1. The formation constant and molar extinction coefficient of the CT complex were evaluated by the Benesi-Hildebrand equation. Copyright 2010 Elsevier B.V. All rights reserved.

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

PubMed Central

Kaltenbacher, Barbara; Hasenauer, Jan

2017-01-01

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

A hybrid continuous-discrete method for stochastic reaction-diffusion processes.

PubMed

Lo, Wing-Cheong; Zheng, Likun; Nie, Qing

2016-09-01

Stochastic fluctuations in reaction-diffusion processes often have substantial effect on spatial and temporal dynamics of signal transductions in complex biological systems. One popular approach for simulating these processes is to divide the system into small spatial compartments assuming that molecules react only within the same compartment and jump between adjacent compartments driven by the diffusion. While the approach is convenient in terms of its implementation, its computational cost may become prohibitive when diffusive jumps occur significantly more frequently than reactions, as in the case of rapid diffusion. Here, we present a hybrid continuous-discrete method in which diffusion is simulated using continuous approximation while reactions are based on the Gillespie algorithm. Specifically, the diffusive jumps are approximated as continuous Gaussian random vectors with time-dependent means and covariances, allowing use of a large time step, even for rapid diffusion. By considering the correlation among diffusive jumps, the approximation is accurate for the second moment of the diffusion process. In addition, a criterion is obtained for identifying the region in which such diffusion approximation is required to enable adaptive calculations for better accuracy. Applications to a linear diffusion system and two nonlinear systems of morphogens demonstrate the effectiveness and benefits of the new hybrid method.

Signals of monocyte activation in patients with SLE.

PubMed Central

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

1983-01-01

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

A polysaccharide-peptide complex from abalone mushroom (Pleurotus abalonus) fruiting bodies increases activities and gene expression of antioxidant enzymes and reduces lipid peroxidation in senescence-accelerated mice.

PubMed

Li, L; Ng, T B; Song, M; Yuan, F; Liu, Z K; Wang, C L; Jiang, Y; Fu, M; Liu, F

2007-06-01

The antioxidant effects of a polysaccharide-peptide complex (F22) from mushroom (Pleurotus abalonus)-fruiting bodies were studied. The activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) in the liver, kidney, and brain of senescence-accelerated mice showed a marked increase after treatment with the polysaccharide-peptide complex. Concurrently, the gene expression levels of SOD, CAT, and GPx, as determined with real-time polymerase chain reaction, were up-regulated in the liver, kidney, and brain, whereas the MDA content in these organs declined. The maximal lifespan of the mice was prolonged.

Photochemical syntheses, transformations, and bioorthogonal chemistry of trans-cycloheptene and sila trans-cycloheptene Ag(i) complexes† †Electronic supplementary information (ESI) available: Full procedures, computational details and characterization data. CCDC 1583975 and 1583976. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04773h

PubMed Central

Fang, Yinzhi; Zhang, Han; Huang, Zhen; Scinto, Samuel L.; Yang, Jeffrey C.; am Ende, Christopher W.; Dmitrenko, Olga; Johnson, Douglas S.

2018-01-01

A photochemical synthesis of AgNO3 complexes of trans-cycloheptene (TCH) and trans-1-sila-4-cycloheptene (Si-TCH) derivatives is described. A low temperature flow photoreactor was designed to enable the synthesis of carbocyclic TCH derivatives due to their thermal sensitivity in the absence of metal coordination. Unlike the free carbocycles, TCH·AgNO3 complexes can be handled at rt and stored for weeks in the freezer (–18 °C). Si-TCH·AgNO3 complexes are especially robust, and are bench stable for days at rt, and for months in the freezer. X-ray crystallography was used to characterize a Si-TCH·AgNO3 complex for the first time. With decomplexation of AgNO3in situ, metal-free TCO and Si-TCH derivatives can engage in a range of cycloaddition reactions as well as dihydroxylation reactions. Computation was used to predict that Si-TCH would engage in bioorthogonal reactions that are more rapid than the most reactive trans-cyclooctenes. Metal-free Si-TCH derivatives were shown to display good stability in solution, and to engage in the fastest bioorthogonal reaction reported to date (k2 1.14 × 107 M–1 s–1 in 9 : 1 H2O : MeOH). Utility in bioorthogonal protein labeling in live cells is described, including labeling of GFP with an unnatural tetrazine-containing amino acid. The reactivity and specificity of the Si-TCH reagents with tetrazines in live mammalian cells was also evaluated using the HaloTag platform. The cell labeling experiments show that Si-TCH derivatives are best suited as probe molecules in the cellular environment. PMID:29675242

Formation of metal-nicotianamine complexes as affected by pH, ligand exchange with citrate and metal exchange. A study by electrospray ionization time-of-flight mass spectrometry.

PubMed

Rellán-Alvarez, Rubén; Abadía, Javier; Alvarez-Fernández, Ana

2008-05-01

Nicotianamine (NA) is considered as a key element in plant metal homeostasis. This non-proteinogenic amino acid has an optimal structure for chelation of metal ions, with six functional groups that allow octahedral coordination. The ability to chelate metals by NA is largely dependent on the pK of the resulting complex and the pH of the solution, with most metals being chelated at neutral or basic pH values. In silico calculations using pKa and pK values have predicted the occurrence of metal-NA complexes in plant fluids, but the use of soft ionization techniques (e.g. electrospray), together with high-resolution mass spectrometers (e.g. time-of-flight mass detector), can offer direct and metal-specific information on the speciation of NA in solution. We have used direct infusion electrospray ionization mass spectrometry (time-of-flight) ESI-MS(TOF) to study the complexation of Mn, Fe(II), Fe(III), Ni, Cu by NA. The pH dependence of the metal-NA complexes in ESI-MS was compared to that predicted in silico. Possible exchange reactions that may occur between Fe-NA and other metal micronutrients as Zn and Cu, as well as between Fe-NA and citrate, another possible Fe ligand candidate in plants, were studied at pH 5.5 and 7.5, values typical of the plant xylem and phloem saps. Metal-NA complexes were generally observed in the ESI-MS experiments at a pH value approximately 1-2 units lower than that predicted in silico, and this difference could be only partially explained by the estimated error, approximately 0.3 pH units, associated with measuring pH in organic solvent-containing solutions. Iron-NA complexes are less likely to participate in ligand- and metal-exchange reactions at pH 7.5 than at pH 5.5. Results support that NA may be the ligand chelating Fe at pH values usually found in phloem sap, whereas in the xylem sap NA is not likely to be involved in Fe transport, conversely to what occurs with other metals such as Cu and Ni. Some considerations that need to be addressed when studying metal complexes in plant compartments by ESI-MS are also discussed.

Modification of heterogeneous chemistry by complex substrate morphology

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

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

1998-12-31

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

Charge-transfer-to-solvent reactions from I{sup −} to water, methanol, and ethanol studied by time-resolved photoelectron spectroscopy of liquids

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

Okuyama, Haruki; Karashima, Shutaro; Suzuki, Toshinori, E-mail: suzuki@kuchem.kyoto-u.ac.jp

The charge-transfer-to-solvent (CTTS) reactions from iodide (I{sup −}) to H{sub 2}O, D{sub 2}O, methanol, and ethanol were studied by time-resolved photoelectron spectroscopy of liquid microjets using a magnetic bottle time-of-flight spectrometer with variable pass energy. Photoexcited iodide dissociates into a weak complex (a contact pair) of a solvated electron and an iodine atom in similar reaction times, 0.3 ps in H{sub 2}O and D{sub 2}O and 0.5 ps in methanol and ethanol, which are much shorter than their dielectric relaxation times. The results indicate that solvated electrons are formed with minimal solvent reorganization in the long-range solvent polarization field createdmore » for I{sup −}. The photoelectron spectra for CTTS in H{sub 2}O and D{sub 2}O—measured with higher accuracy than in our previous study [Y. I. Suzuki et al., Chem. Sci. 2, 1094 (2011)]—indicate that internal conversion yields from the photoexcited I{sup −*} (CTTS) state are less than 10%, while alcohols provide 2–3 times greater yields of internal conversion from I{sup −*}. The overall geminate recombination yields are found to be in the order of H{sub 2}O > D{sub 2}O > methanol > ethanol, which is opposite to the order of the mutual diffusion rates of an iodine atom and a solvated electron. This result is consistent with the transition state theory for an adiabatic outer-sphere electron transfer process, which predicts that the recombination reaction rate has a pre-exponential factor inversely proportional to a longitudinal solvent relaxation time.« less

Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

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

Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon, E-mail: shs3@illinois.edu

2014-01-21

The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents formore » a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible systems.« less

anti-Selective Asymmetric Henry Reaction Catalyzed by a Heterobimetallic Cu-Sm-Aminophenol Sulfonamide Complex.

PubMed

Li, Yang; Deng, Ping; Zeng, Youmao; Xiong, Yan; Zhou, Hui

2016-04-01

A novel heterobimetallic Cu/Sm/aminophenol sulfonamide complex has been developed by a convenient one-pot method for the anti-selective asymmetric Henry reaction. The corresponding anti-β-nitro alcohols are obtained in up to 99% yield, >30:1 dr, and 98% ee. The results of control experiments and ESI-MS analysis of the complex indicate that the monomeric bimetallic Cu/Sm/1 complex would be the active species.

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

PubMed

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

2014-02-18

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

Signal transduction in a covalent post-assembly modification cascade

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Deciphering Front-Side Complex Formation in SN2 Reactions via Dynamics Mapping.

PubMed

Szabó, István; Olasz, Balázs; Czakó, Gábor

2017-07-06

Due to their importance in organic chemistry, the atomistic understanding of bimolecular nucleophilic substitution (S N 2) reactions shows exponentially growing interest. In this publication, the effect of front-side complex (FSC) formation is uncovered via quasi-classical trajectory computations combined with a novel analysis method called trajectory orthogonal projection (TOP). For both F - + CH 3 Y [Y = Cl,I] reactions, the lifetime distributions of the F - ···YCH 3 front-side complex revealed weakly trapped nucleophiles (F - ). However, only the F - + CH 3 I reaction features strongly trapped nucleophiles in the front-side region of the prereaction well. Interestingly, both back-side and front-side attack show propensity to long-lived FSC formation. Spatial distributions of the nucleophile demonstrate more prominent FSC formation in case of the F - + CH 3 I reaction compared to F - + CH 3 Cl. The presence of front-side intermediates and the broad spatial distribution in the back-side region may explain the indirect nature of the F - + CH 3 I reaction.

Functionalisation of lanthanide complexes via microwave-enhanced Cu(I)-catalysed azide-alkyne cycloaddition.

PubMed

Szíjjártó, Csongor; Pershagen, Elias; Borbas, K Eszter

2012-07-07

Cu(I)-catalysed azide-alkyne cycloaddition reactions were used to functionalise lanthanide(III)-complexes (Ln; La, Eu and Tb) incorporating alkyne or azide reactive groups. Microwave irradiation significantly accelerated the reactions, enabling full conversion to the triazole products in some cases in 5 min. Alkyl and aryl azides and alkyl and aryl alkynes could all serve as coupling partners. These reaction conditions proved efficient for cyclen-tricarboxylates and previously unreactive cyclen-tris-primary amide chelates. The synthesis of heterobimetallic (Eu/Tb, EuTb17 and Eu/La, EuLa17) and heterotrimetallic (Eu/La/Eu) complexes was achieved in up to 60% isolated yield starting from coumarin 2-appended alkynyl complexes Tb16 or La16 and an azido-Eu complex Eu4, and bis-alkynyl La-complex La5 and Eu4, respectively. EuTb17 displayed dual Eu(III) and Tb(III)-emission upon antenna-centred excitation.

Focal adhesion kinase is required for actin polymerization and remodeling of the cytoskeleton during sperm capacitation

PubMed Central

Roa-Espitia, Ana L.; Hernández-Rendón, Eva R.; Baltiérrez-Hoyos, Rafael; Muñoz-Gotera, Rafaela J.; Cote-Vélez, Antonieta; Jiménez, Irma; González-Márquez, Humberto

2016-01-01

ABSTRACT Several focal adhesion proteins are known to cooperate with integrins to link the extracellular matrix to the actin cytoskeleton; as a result, many intracellular signaling pathways are activated and several focal adhesion complexes are formed. However, how these proteins function in mammalian spermatozoa remains unknown. We confirm the presence of focal adhesion proteins in guinea pig spermatozoa, and we explore their role during capacitation and the acrosome reaction, and their relationship with the actin cytoskeleton. Our results suggest the presence of a focal adhesion complex formed by β1-integrin, focal adhesion kinase (FAK), paxillin, vinculin, talin, and α-actinin in the acrosomal region. Inhibition of FAK during capacitation affected the protein tyrosine phosphorylation associated with capacitation that occurs within the first few minutes of capacitation, which caused the acrosome reaction to become increasingly Ca2+ dependent and inhibited the polymerization of actin. The integration of vinculin and talin into the complex, and the activation of FAK and paxillin during capacitation, suggests that the complex assembles at this time. We identify that vinculin and α-actinin increase their interaction with F-actin while it remodels during capacitation, and that during capacitation focal adhesion complexes are structured. FAK contributes to acrosome integrity, likely by regulating the polymerization and the remodeling of the actin cytoskeleton. PMID:27402964

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

NASA Astrophysics Data System (ADS)

Ioannou, Aristos; Daskalakis, Vangelis; Varotsis, Constantinos

2017-08-01

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

Efficient estimators for likelihood ratio sensitivity indices of complex stochastic dynamics.

PubMed

Arampatzis, Georgios; Katsoulakis, Markos A; Rey-Bellet, Luc

2016-03-14

We demonstrate that centered likelihood ratio estimators for the sensitivity indices of complex stochastic dynamics are highly efficient with low, constant in time variance and consequently they are suitable for sensitivity analysis in long-time and steady-state regimes. These estimators rely on a new covariance formulation of the likelihood ratio that includes as a submatrix a Fisher information matrix for stochastic dynamics and can also be used for fast screening of insensitive parameters and parameter combinations. The proposed methods are applicable to broad classes of stochastic dynamics such as chemical reaction networks, Langevin-type equations and stochastic models in finance, including systems with a high dimensional parameter space and/or disparate decorrelation times between different observables. Furthermore, they are simple to implement as a standard observable in any existing simulation algorithm without additional modifications.

Efficient estimators for likelihood ratio sensitivity indices of complex stochastic dynamics

NASA Astrophysics Data System (ADS)

Arampatzis, Georgios; Katsoulakis, Markos A.; Rey-Bellet, Luc

2016-03-01

We demonstrate that centered likelihood ratio estimators for the sensitivity indices of complex stochastic dynamics are highly efficient with low, constant in time variance and consequently they are suitable for sensitivity analysis in long-time and steady-state regimes. These estimators rely on a new covariance formulation of the likelihood ratio that includes as a submatrix a Fisher information matrix for stochastic dynamics and can also be used for fast screening of insensitive parameters and parameter combinations. The proposed methods are applicable to broad classes of stochastic dynamics such as chemical reaction networks, Langevin-type equations and stochastic models in finance, including systems with a high dimensional parameter space and/or disparate decorrelation times between different observables. Furthermore, they are simple to implement as a standard observable in any existing simulation algorithm without additional modifications.

Efficient estimators for likelihood ratio sensitivity indices of complex stochastic dynamics

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

Arampatzis, Georgios; Katsoulakis, Markos A.; Rey-Bellet, Luc

2016-03-14

We demonstrate that centered likelihood ratio estimators for the sensitivity indices of complex stochastic dynamics are highly efficient with low, constant in time variance and consequently they are suitable for sensitivity analysis in long-time and steady-state regimes. These estimators rely on a new covariance formulation of the likelihood ratio that includes as a submatrix a Fisher information matrix for stochastic dynamics and can also be used for fast screening of insensitive parameters and parameter combinations. The proposed methods are applicable to broad classes of stochastic dynamics such as chemical reaction networks, Langevin-type equations and stochastic models in finance, including systemsmore » with a high dimensional parameter space and/or disparate decorrelation times between different observables. Furthermore, they are simple to implement as a standard observable in any existing simulation algorithm without additional modifications.« less

Reaction of an Iron(IV) Nitrido Complex with Cyclohexadienes: Cycloaddition and Hydrogen-Atom Abstraction

PubMed Central

2015-01-01

The iron(IV) nitrido complex PhB(MesIm)3Fe≡N reacts with 1,3-cyclohexadiene to yield the iron(II) pyrrolide complex PhB(MesIm)3Fe(η5-C4H4N) in high yield. The mechanism of product formation is proposed to involve sequential [4 + 1] cycloaddition and retro Diels–Alder reactions. Surprisingly, reaction with 1,4-cyclohexadiene yields the same iron-containing product, albeit in substantially lower yield. The proposed reaction mechanism, supported by electronic structure calculations, involves hydrogen-atom abstraction from 1,4-cyclohexadiene to provide the cyclohexadienyl radical. This radical is an intermediate in substrate isomerization to 1,3-cyclohexadiene, leading to formation of the pyrrolide product. PMID:25068927

Hydride-Meisenheimer Complex Formation and Protonation as Key Reactions of 2,4,6-Trinitrophenol Biodegradation by Rhodococcus erythropolis

PubMed Central

Rieger, Paul-Gerhard; Sinnwell, Volker; Preuß, Andrea; Francke, Wittko; Knackmuss, Hans-Joachim

1999-01-01

Biodegradation of 2,4,6-trinitrophenol (picric acid) by Rhodococcus erythropolis HLPM-1 proceeds via initial hydrogenation of the aromatic ring system. Here we present evidence for the formation of a hydride-Meisenheimer complex (anionic ς-complex) of picric acid and its protonated form under physiological conditions. These complexes are key intermediates of denitration and productive microbial degradation of picric acid. For comparative spectroscopic identification of the hydride complex, it was necessary to synthesize this complex for the first time. Spectroscopic data revealed the initial addition of a hydride ion at position 3 of picric acid. This hydride complex readily picks up a proton at position 2, thus forming a reactive species for the elimination of nitrite. Cell extracts of R. erythropolis HLPM-1 transform the chemically synthesized hydride complex into 2,4-dinitrophenol. Picric acid is used as the sole carbon, nitrogen, and energy source by R. erythropolis HLPM-1. PMID:9973345

Sir John Pople, Gaussian Code, and Complex Chemical Reactions

Science.gov Websites

tool that describes the dance of molecules in chemical reactions ... . Dr. Pople was among the first to colors of light they will absorb or emit, and the pace of chemical reactions. The work culminated in a dropdown arrow Site Map A-Z Index Menu Synopsis Sir John Pople, Gaussian Code, and Complex Chemical

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

PubMed

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

2014-05-21

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

New Insights into Low-Temperature Oxidation of Propane from Synchrotron Photoionization Mass Spectrometry and Multiscale Informatics Modeling

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

Welz, Oliver; Burke, Michael P.; Antonov, Ivan O.

2015-07-16

We investigated the low-temperature oxidation of propane at 4 Torr and temperatures of 530, 600, and 670 K. The oxidation is initiated by pulsed laser photolysis of oxalyl chloride, (COCl)2, at 248 nm, which rapidly generates a ~1:1 mixture of 1-propyl (n-propyl) and 2-propyl (i-propyl) radicals via the fast Cl + propane reaction. Reactants, intermediates and products are probed with isomeric selectivity by time-resolved multiplexed photoionization mass spectrometry (MPIMS) with tunable synchrotron vacuum UV radiation as the ionization source. At all three temperatures, the major stable product species is propene, formed in the C3H7 + O2 reactions by direct HO2-eliminationmore » from both n- and i-propyl peroxy radicals. The experimentally derived propene yields relative to the initial concentration of Cl atoms are (20 ± 4)% at 530 K, (55 ± 11)% at 600 K, and (86 ± 17)% at 670 K at a reaction time of 20 ms. The lower yield of propene at low temperature reflects substantial formation of propyl peroxy radicals, which do not completely decompose on the experimental time scale. In addition, we detect the C3H6O isomers methyloxirane, oxetane, acetone and propanal as minor products. Our measured yields of oxetane and methyloxirane, which are co-products of OH radicals, suggest a revision of the OH formation pathways in models of low-temperature propane oxidation. The experimental results are modeled and interpreted using a multi-scale informatics approach that is presented in detail in a separate publication (Burke, M. P.; Goldsmith, C. F.; Klippenstein, S. J.; Welz, O.; Huang H.; Antonov I. O.; Savee J. D.; Osborn D. L.; Zádor, J.; Taatjes, C. A.; Sheps, L., Multi-Scale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Rections, submitted, 2015). The model predicts the time profiles and yields of the experimentally observed primary products well, and shows satisfactory agreement for products formed mostly via secondary radical-radical reactions.« less

Peptide Reactivity of Isothiocyanates - Implications for Skin Allergy

NASA Astrophysics Data System (ADS)

Karlsson, Isabella; Samuelsson, Kristin; Ponting, David J.; Törnqvist, Margareta; Ilag, Leopold L.; Nilsson, Ulrika

2016-02-01

Skin allergy is a chronic condition that affects about 20% of the population of the western world. This disease is caused by small reactive compounds, haptens, able to penetrate into the epidermis and modify endogenous proteins, thereby triggering an immunogenic reaction. Phenyl isothiocyanate (PITC) and ethyl isothiocyanate (EITC) have been suggested to be responsible for allergic skin reactions to chloroprene rubber, the main constituent of wetsuits, orthopedic braces, and many types of sports gear. In the present work we have studied the reactivity of the isothiocyanates PITC, EITC, and tetramethylrhodamine-6-isothiocyanate (6-TRITC) toward peptides under aqueous conditions at physiological pH to gain information about the types of immunogenic complexes these compounds may form in the skin. We found that all three compounds reacted quickly with cysteine moieties. For PITC and 6-TRITC the cysteine adducts decomposed over time, while stable adducts with lysine were formed. These experimental findings were verified by DFT calculations. Our results may suggest that the latter are responsible for allergic reactions to isothiocyanates. The initial adduct formation with cysteine residues may still be of great importance as it prevents hydrolysis and facilitates the transport of isothiocyanates into epidermis where they can form stable immunogenic complexes with lysine-containing proteins.

Production of o-diphenols by immobilized mushroom tyrosinase.

PubMed

Marín-Zamora, María Elisa; Rojas-Melgarejo, Francisco; García-Cánovas, Francisco; García-Ruiz, Pedro Antonio

2009-01-15

The o-diphenols 4-tert-butyl-catechol, 4-methyl-catechol, 4-methoxy-catechol, 3,4-dihydroxyphenylpropionic acid and 3,4-dihydroxyphenylacetic acid were produced from the corresponding monophenols (4-tert-butyl-phenol, 4-methyl-phenol, 4-methoxy-phenol, p-hydroxyphenylpropionic acid and p-hydroxyphenylacetic acid) using immobilized mushroom tyrosinase from Agaricus bisporus. In all cases the yield was R(diphenol)> or =88-96%, which, according to the literature, is the highest yield so far, obtained using tyrosinase. The reaction was carried out in 0.5M borate buffer pH 9.0 which was used to minimize the diphenolase activity of tyrosinase by complexing the o-diphenols generated. Hydroxylamine and ascorbic acid were also present in the reaction medium, the former being used to reduce mettyrosinase to deoxytyrosinase, closing the catalytic cycle, and the latter to reduce the o-quinone produced to o-diphenol. Inactivation of the tyrosinase by ascorbic acid was also minimized due to the formation of an ascorbic acid-borate complex. Concentrations of the o-diphenolic compounds obtained at several reaction times were determined by gas chromatography-mass spectrometry (GC-MS) and UV-vis spectroscopy. The experimental results are discussed.

Perspective: Two-dimensional resonance Raman spectroscopy

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Pore-scale study of effects of macroscopic pores and their distributions on reactive transport in hierarchical porous media

DOE PAGES

Chen, Li; Zhang, Ruiyuan; Min, Ting; ...

2018-05-19

For applications of reactive transport in porous media, optimal porous structures should possess both high surface area for reactive sites loading and low mass transport resistance. Hierarchical porous media with a combination of pores at different scales are designed for this purpose. In this paper, using the lattice Boltzmann method, pore-scale numerical studies are conducted to investigate diffusion-reaction processes in 2D hierarchical porous media generated by self-developed reconstruction scheme. Complex interactions between porous structures and reactive transport are revealed under different conditions. Simulation results show that adding macropores can greatly enhance the mass transport, but at the same time reducemore » the reactive surface, leading to complex change trend of the total reaction rate. Effects of gradient distribution of macropores within the porous medium are also investigated. It is found that a front-loose, back-tight (FLBT) hierarchical structure is desirable for enhancing mass transport, increasing total reaction rate, and improving catalyst utilization. Finally, on the whole, from the viewpoint of reducing cost and improving material performance, hierarchical porous structures, especially gradient structures with the size of macropores gradually decreasing along the transport direction, are desirable for catalyst application.« less

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

PubMed

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

2014-01-01

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

Pore-scale study of effects of macroscopic pores and their distributions on reactive transport in hierarchical porous media

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

Chen, Li; Zhang, Ruiyuan; Min, Ting

For applications of reactive transport in porous media, optimal porous structures should possess both high surface area for reactive sites loading and low mass transport resistance. Hierarchical porous media with a combination of pores at different scales are designed for this purpose. In this paper, using the lattice Boltzmann method, pore-scale numerical studies are conducted to investigate diffusion-reaction processes in 2D hierarchical porous media generated by self-developed reconstruction scheme. Complex interactions between porous structures and reactive transport are revealed under different conditions. Simulation results show that adding macropores can greatly enhance the mass transport, but at the same time reducemore » the reactive surface, leading to complex change trend of the total reaction rate. Effects of gradient distribution of macropores within the porous medium are also investigated. It is found that a front-loose, back-tight (FLBT) hierarchical structure is desirable for enhancing mass transport, increasing total reaction rate, and improving catalyst utilization. Finally, on the whole, from the viewpoint of reducing cost and improving material performance, hierarchical porous structures, especially gradient structures with the size of macropores gradually decreasing along the transport direction, are desirable for catalyst application.« less

Turbulence interacting with chemical kinetics in airbreathing combustion of ducted rockets

NASA Astrophysics Data System (ADS)

Chung, T. J.; Yoon, W. S.

1992-10-01

Physical interactions between turbulence and shock waves are very complex phenomena. If these interactions take place in chemically reacting flows the degree of complexity increases dramatically. Examples of applications may be cited in the area of supersonic combustion, in which the controlled generation of turbulence and/or large scale vortices in the mixing and flame holding zones is crucial for efficient combustion. Equally important, shock waves interacting with turbulence and chemical reactions affect the combustor flowfield resulting in enhanced relaxation and chemical reaction rates. Chemical reactions in turn contribute to dispersion of shock waves and reduction of turbulent kinetic energies. Computational schemes to address these physical phenomena must be capable of resolving various length and time scales. These scales are widely disparate and the most optimum approach is found in explicit/ implicit adjustable schemes for the Navier-Stokes solver. This is accomplished by means of the generalized Taylor-Galerkin (GTG) finite element formulations. Adaptive meshes are used in order to assure efficiency and accuracy of solutions. Various benchmark problems are presented for illustration of the theory and applications. Geometries of ducted rockets, supersonic diffusers, flame holders, and hypersonic inlets are included. Merits of proposed schemes are demonstrated through these example problems.

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

PubMed Central

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

2014-01-01

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