Simulating metabolism with statistical thermodynamics.

PubMed

Cannon, William R

2014-01-01

New methods are needed for large scale modeling of metabolism that predict metabolite levels and characterize the thermodynamics of individual reactions and pathways. Current approaches use either kinetic simulations, which are difficult to extend to large networks of reactions because of the need for rate constants, or flux-based methods, which have a large number of feasible solutions because they are unconstrained by the law of mass action. This report presents an alternative modeling approach based on statistical thermodynamics. The principles of this approach are demonstrated using a simple set of coupled reactions, and then the system is characterized with respect to the changes in energy, entropy, free energy, and entropy production. Finally, the physical and biochemical insights that this approach can provide for metabolism are demonstrated by application to the tricarboxylic acid (TCA) cycle of Escherichia coli. The reaction and pathway thermodynamics are evaluated and predictions are made regarding changes in concentration of TCA cycle intermediates due to 10- and 100-fold changes in the ratio of NAD+:NADH concentrations. Finally, the assumptions and caveats regarding the use of statistical thermodynamics to model non-equilibrium reactions are discussed.

Multistage reaction pathways in detonating high explosives

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; CACS Collaboration; ALCF Team

2015-06-01

Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N2 and H2O within 10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct uni-molecular and intermolecular reaction pathways, respectively, for the rapid N2 and H2O productions. This work was supported by the Office of Naval Research Grant No. N000014-12-1-0555 and the Basic Research Program of Defense Threat Reduction Agency (DTRA) Grant No. HDTRA1-08-1-0036. All the simulations were performed at USC and Argonne LCF.

Weak Acid Ionization Constants and the Determination of Weak Acid-Weak Base Reaction Equilibrium Constants in the General Chemistry Laboratory

ERIC Educational Resources Information Center

Nyasulu, Frazier; McMills, Lauren; Barlag, Rebecca

2013-01-01

A laboratory to determine the equilibrium constants of weak acid negative weak base reactions is described. The equilibrium constants of component reactions when multiplied together equal the numerical value of the equilibrium constant of the summative reaction. The component reactions are weak acid ionization reactions, weak base hydrolysis…

Bridge-bonded formate: active intermediate or spectator species in formic acid oxidation on a Pt film electrode?

PubMed

Chen, Y-X; Heinen, M; Jusys, Z; Behm, R J

2006-12-05

We present and discuss the results of an in situ IR study on the mechanism and kinetics of formic acid oxidation on a Pt film/Si electrode, performed in an attenuated total reflection (ATR) flow cell configuration under controlled mass transport conditions, which specifically aimed at elucidating the role of the adsorbed bridge-bonded formates in this reaction. Potentiodynamic measurements show a complex interplay between formation and desorption/oxidation of COad and formate species and the total Faradaic current. The notably faster increase of the Faradaic current compared to the coverage of bridge-bonded formate in transient measurements at constant potential, but with different formic acid concentrations, reveals that adsorbed formate decomposition is not rate-limiting in the dominant reaction pathway. If being reactive intermediate at all, the contribution of formate adsorption/decomposition to the reaction current decreases with increasing formic acid concentration, accounting for at most 15% for 0.2 M DCOOH at 0.7 VRHE. The rapid build-up/removal of the formate adlayer and its similarity with acetate or (bi-)sulfate adsorption/desorption indicate that the formate adlayer coverage is dominated by a fast dynamic adsorption-desorption equilibrium with the electrolyte, and that formate desorption is much faster than its decomposition. The results corroborate the proposal of a triple pathway reaction mechanism including an indirect pathway, a formate pathway, and a dominant direct pathway, as presented previously (Chen, Y. X.; et al. Angew. Chem. Int. Ed. 2006, 45, 981), in which adsorbed formates act as a site-blocking spectator in the dominant pathway rather than as an active intermediate.

Are the Concepts of Dynamic Equilibrium and the Thermodynamic Criteria for Spontaneity, Nonspontaneity, and Equilibrium Compatible?

ERIC Educational Resources Information Center

Silverberg, Lee J.; Raff, Lionel M.

2015-01-01

Thermodynamic spontaneity-equilibrium criteria require that in a single-reaction system, reactions in either the forward or reverse direction at equilibrium be nonspontaneous. Conversely, the concept of dynamic equilibrium holds that forward and reverse reactions both occur at equal rates at equilibrium to the extent allowed by kinetic…

How reliable are thermodynamic feasibility statements of biochemical pathways?

PubMed

Maskow, Thomas; von Stockar, Urs

2005-10-20

The driving force for organo- or lithotrophic growth as well as for each step in the metabolic network is the Gibbs reaction energy. For each enzymatic step it must be negative. Thermodynamics contributes therefore to the in-silico description of living systems. It may be used for assessing the feasibility of a given pathway because it provides a further constraint for those pathways which are feasible from the point of view of mass balance calculations (metabolic flux analysis) and the genetic potential of an organism. However, when this constraint was applied to lactic acid fermentation according to a method proposed by Mavrovouniotis (1993a, ISMB 93:273-283) it turned out that an unrealistically wide metabolite concentration range had to be assumed to make this well-known glycolytic pathway thermodynamically feasible. During a search for the reasons of this surprising result the insufficient consideration of the activity coefficients was identified as main cause. However, it is shown in the present contribution that the influence of the activity coefficients on Gibbs reaction energy can be easily taken into account based on the intracellular ionic strength. The uncertainty of the tabulated equilibrium constants and of the apparent standard Gibbs energies derived from them was found to be the second most important reason for the erroneous result of the feasibility analysis. Deviations of intracellular pH from the standard value and bad estimations of currency metabolites, e.g., NAD(+) and NADH, were found to be of lesser importance but not negligible. The pH dependency of Gibbs reaction enthalpy was proved to be easily taken into account. Therefore, the application of thermodynamics for a better in-silico prediction of the behavior of living cell factories calls predominantly for better equilibrium data determined under well defined conditions and also for a more detailed knowledge about the intracellular ionic strength and pH value. Copyright 2005 Wiley Periodicals, Inc.

Perspective: Maximum caliber is a general variational principle for dynamical systems

NASA Astrophysics Data System (ADS)

Dixit, Purushottam D.; Wagoner, Jason; Weistuch, Corey; Pressé, Steve; Ghosh, Kingshuk; Dill, Ken A.

2018-01-01

We review here Maximum Caliber (Max Cal), a general variational principle for inferring distributions of paths in dynamical processes and networks. Max Cal is to dynamical trajectories what the principle of maximum entropy is to equilibrium states or stationary populations. In Max Cal, you maximize a path entropy over all possible pathways, subject to dynamical constraints, in order to predict relative path weights. Many well-known relationships of non-equilibrium statistical physics—such as the Green-Kubo fluctuation-dissipation relations, Onsager's reciprocal relations, and Prigogine's minimum entropy production—are limited to near-equilibrium processes. Max Cal is more general. While it can readily derive these results under those limits, Max Cal is also applicable far from equilibrium. We give examples of Max Cal as a method of inference about trajectory distributions from limited data, finding reaction coordinates in bio-molecular simulations, and modeling the complex dynamics of non-thermal systems such as gene regulatory networks or the collective firing of neurons. We also survey its basis in principle and some limitations.

Perspective: Maximum caliber is a general variational principle for dynamical systems.

PubMed

Dixit, Purushottam D; Wagoner, Jason; Weistuch, Corey; Pressé, Steve; Ghosh, Kingshuk; Dill, Ken A

2018-01-07

We review here Maximum Caliber (Max Cal), a general variational principle for inferring distributions of paths in dynamical processes and networks. Max Cal is to dynamical trajectories what the principle of maximum entropy is to equilibrium states or stationary populations. In Max Cal, you maximize a path entropy over all possible pathways, subject to dynamical constraints, in order to predict relative path weights. Many well-known relationships of non-equilibrium statistical physics-such as the Green-Kubo fluctuation-dissipation relations, Onsager's reciprocal relations, and Prigogine's minimum entropy production-are limited to near-equilibrium processes. Max Cal is more general. While it can readily derive these results under those limits, Max Cal is also applicable far from equilibrium. We give examples of Max Cal as a method of inference about trajectory distributions from limited data, finding reaction coordinates in bio-molecular simulations, and modeling the complex dynamics of non-thermal systems such as gene regulatory networks or the collective firing of neurons. We also survey its basis in principle and some limitations.

In situ {sup 13}C MAS NMR study of n-hexane conversion on Pt and Pd supported on basic materials

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

Ivanova, I.I.; Pasau-Claerbout, A.; Seivert, M.

n-Hexane conversion was studied in situ on Pt and Pd supported on aluminum-stabilized magnesium oxide and Pt on Zeolite KL catalysts (Pt/Mg(Al)O, Pd/Mg(Al)O and Pt/KL) by means of {sup 13}C MAS NMR spectroscopy. n-Hexane 1-{sup 13}C was used as a labelled reactant. Forty NMR lines corresponding to 14 different products were resolved and identified. The NMR line assignments were confirmed by adsorption of model compounds. The NMR results were further quantified and compared with continuous flow microreactor tests. Four parallel reaction pathways were identified under flow conditions: isomerization, cracking, dehydrocyclization, and dehydrogenation. Aromatization occurs via two reaction routes: (1) n-hexanemore » dehydrogenation towards hexadienes and hexatrienes, followed by dehydrogenation of a cyclic intermediate. The former reaction pathway is prevented under NMR batch conditions. High pressures induced in the NMR cells at high reaction temperatures (573, 653 K) shift the reaction equilibrium towards hydrogenation. NMR experiments showed that on Pt catalysts aromatization occurs via a cyclohexane intermediate, whereas on Pd it takes place via methylcyclopentane ring enlargement. 54 refs., 15 figs., 3 tabs.« less

Calculation of individual isotope equilibrium constants for implementation in geochemical models

USGS Publications Warehouse

Thorstenson, Donald C.; Parkhurst, David L.

2002-01-01

Theory is derived from the work of Urey to calculate equilibrium constants commonly used in geochemical equilibrium and reaction-transport models for reactions of individual isotopic species. Urey showed that equilibrium constants of isotope exchange reactions for molecules that contain two or more atoms of the same element in equivalent positions are related to isotope fractionation factors by , where is n the number of atoms exchanged. This relation is extended to include species containing multiple isotopes, for example and , and to include the effects of nonideality. The equilibrium constants of the isotope exchange reactions provide a basis for calculating the individual isotope equilibrium constants for the geochemical modeling reactions. The temperature dependence of the individual isotope equilibrium constants can be calculated from the temperature dependence of the fractionation factors. Equilibrium constants are calculated for all species that can be formed from and selected species containing , in the molecules and the ion pairs with where the subscripts g, aq, l, and s refer to gas, aqueous, liquid, and solid, respectively. These equilibrium constants are used in the geochemical model PHREEQC to produce an equilibrium and reaction-transport model that includes these isotopic species. Methods are presented for calculation of the individual isotope equilibrium constants for the asymmetric bicarbonate ion. An example calculates the equilibrium of multiple isotopes among multiple species and phases.

A mechanistical study on non-equilibrium reaction pathways in solid nitromethane (CH3NO2) and D3-nitromethane (CD3NO2) upon interaction with ionizing radiation

NASA Astrophysics Data System (ADS)

Kaiser, Ralf I.; Maksyutenko, Pavlo

2015-07-01

Thin films of homogeneously mixed nitromethane (CH3NO2) and D3-nitromethane (CD3NO2) ices were exposed to energetic electrons and Lyman α photons. The isotopically mixed reaction products were probed in situ via reflectron time-of-flight mass spectrometry coupled with pulsed photoionization during temperature programmed desorption. This study provides compelling evidence on three high energy pathways, which have not been observed under collisionless conditions in the gas phase. These are decomposition of nitromethane (CH3NO2) via atomic oxygen loss to nitrosomethane (CH3NO), fragmentation of nitromethane (CH3NO2) and/or methylnitrite (CH3ONO) via carbene (CH2) loss, and carbonsbnd hydrogen bond rupture processes in nitromethane (CH3NO2) and/or methylnitrite (CH3ONO).

Kinetic, Thermodynamic, and Structural Insight into the Mechanism of Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis

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

Wubben, Thomas J.; Mesecar, Andrew D.; UIC)

Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine (PhP) to form dephosphocoenzyme A. This reaction sits at the branch point between the de novo pathway and the salvage pathway, and has been shown to be a rate-limiting step in the biosynthesis of CoA. Importantly, bacterial and mammalian PPATs share little sequence homology, making the enzyme a potential target for antibiotic development. A series of steady-state kinetic, product inhibition, and direct binding studies with Mycobacterium tuberculosis PPAT (MtPPAT) was conducted and suggests that the enzyme utilizesmore » a nonrapid-equilibrium random bi-bi mechanism. The kinetic response of MtPPAT to the binding of ATP was observed to be sigmoidal under fixed PhP concentrations, but substrate inhibition was observed at high PhP concentrations under subsaturating ATP concentrations, suggesting a preferred pathway to ternary complex formation. Negative cooperativity in the kinetic response of MtPPAT to PhP binding was observed under certain conditions and confirmed thermodynamically by isothermal titration calorimetry, suggesting the formation of an asymmetric quaternary structure during sequential ligation of substrates. Asymmetry in binding was also observed in isothermal titration calorimetry experiments with dephosphocoenzyme A and CoA. X-ray structures of MtPPAT in complex with PhP and the nonhydrolyzable ATP analogue adenosine-5'-[({alpha},{beta})-methyleno]triphosphate were solved to 1.57 {angstrom} and 2.68 {angstrom}, respectively. These crystal structures reveal small conformational changes in enzyme structure upon ligand binding, which may play a role in the nonrapid-equilibrium mechanism. We suggest that the proposed kinetic mechanism and asymmetric character in MtPPAT ligand binding may provide a means of reaction and pathway regulation in addition to that of the previously determined CoA feedback.« less

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

USGS Publications Warehouse

Friedly, John C.; Rubin, Jacob

1992-01-01

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

A reaction-based paradigm to model reactive chemical transport in groundwater with general kinetic and equilibrium reactions.

PubMed

Zhang, Fan; Yeh, Gour-Tsyh; Parker, Jack C; Brooks, Scott C; Pace, Molly N; Kim, Young-Jin; Jardine, Philip M; Watson, David B

2007-06-16

This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing N(E) equilibrium reactions and a set of reactive transport equations of M-N(E) kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions.

Concordant Chemical Reaction Networks and the Species-Reaction Graph

PubMed Central

Shinar, Guy; Feinberg, Martin

2015-01-01

In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies within the very broad and natural weakly monotonic class. In particular, multiple equilibria are precluded, as are degenerate positive equilibria. Moreover, under certain circumstances, also related to concordance, all real eigenvalues associated with a positive equilibrium are negative. Although concordance of a reaction network can be decided by readily available computational means, we show here that, when a nondegenerate network’s Species-Reaction Graph satisfies certain mild conditions, concordance and its dynamical consequences are ensured. These conditions are weaker than earlier ones invoked to establish kinetic system injectivity, which, in turn, is just one ramification of network concordance. Because the Species-Reaction Graph resembles pathway depictions often drawn by biochemists, results here expand the possibility of inferring significant dynamical information directly from standard biochemical reaction diagrams. PMID:22940368

Stepwise formation of H3O(+)(H2O)n in an ion drift tube: Empirical effective temperature of association/dissociation reaction equilibrium in an electric field.

PubMed

Nakai, Yoichi; Hidaka, Hiroshi; Watanabe, Naoki; Kojima, Takao M

2016-06-14

We measured equilibrium constants for H3O(+)(H2O)n-1 + H2O↔H3O(+)(H2O)n (n = 4-9) reactions taking place in an ion drift tube with various applied electric fields at gas temperatures of 238-330 K. The zero-field reaction equilibrium constants were determined by extrapolation of those obtained at non-zero electric fields. From the zero-field reaction equilibrium constants, the standard enthalpy and entropy changes, ΔHn,n-1 (0) and ΔSn,n-1 (0), of stepwise association for n = 4-8 were derived and were in reasonable agreement with those measured in previous studies. We also examined the electric field dependence of the reaction equilibrium constants at non-zero electric fields for n = 4-8. An effective temperature for the reaction equilibrium constants at non-zero electric field was empirically obtained using a parameter describing the electric field dependence of the reaction equilibrium constants. Furthermore, the size dependence of the parameter was thought to reflect the evolution of the hydrogen-bond structure of H3O(+)(H2O)n with the cluster size. The reflection of structural information in the electric field dependence of the reaction equilibria is particularly noteworthy.

Calculation of individual isotope equilibrium constants for geochemical reactions

USGS Publications Warehouse

Thorstenson, D.C.; Parkhurst, D.L.

2004-01-01

Theory is derived from the work of Urey (Urey H. C. [1947] The thermodynamic properties of isotopic substances. J. Chem. Soc. 562-581) to calculate equilibrium constants commonly used in geochemical equilibrium and reaction-transport models for reactions of individual isotopic species. Urey showed that equilibrium constants of isotope exchange reactions for molecules that contain two or more atoms of the same element in equivalent positions are related to isotope fractionation factors by ?? = (Kex)1/n, where n is the number of atoms exchanged. This relation is extended to include species containing multiple isotopes, for example 13C16O18O and 1H2H18O. The equilibrium constants of the isotope exchange reactions can be expressed as ratios of individual isotope equilibrium constants for geochemical reactions. Knowledge of the equilibrium constant for the dominant isotopic species can then be used to calculate the individual isotope equilibrium constants. Individual isotope equilibrium constants are calculated for the reaction CO2g = CO2aq for all species that can be formed from 12C, 13C, 16O, and 18O; for the reaction between 12C18 O2aq and 1H218Ol; and among the various 1H, 2H, 16O, and 18O species of H2O. This is a subset of a larger number of equilibrium constants calculated elsewhere (Thorstenson D. C. and Parkhurst D. L. [2002] Calculation of individual isotope equilibrium constants for implementation in geochemical models. Water-Resources Investigation Report 02-4172. U.S. Geological Survey). Activity coefficients, activity-concentration conventions for the isotopic variants of H2O in the solvent 1H216Ol, and salt effects on isotope fractionation have been included in the derivations. The effects of nonideality are small because of the chemical similarity of different isotopic species of the same molecule or ion. The temperature dependence of the individual isotope equilibrium constants can be calculated from the temperature dependence of the fractionation factors. The derivations can be extended to calculation of individual isotope equilibrium constants for ion pairs and equilibrium constants for isotopic species of other chemical elements. The individual isotope approach calculates the same phase isotopic compositions as existing methods, but also provides concentrations of individual species, which are needed in calculations of mass-dependent effects in transport processes. The equilibrium constants derived in this paper are used to calculate the example of gas-water equilibrium for CO2 in an acidic aqueous solution. ?? 2004 Elsevier Ltd.

Hydroxyhydroperoxide (HHP) Formation From H2O2 Addition to Carbonyls in the Aqueous Phase and Its Environmental Implications

NASA Astrophysics Data System (ADS)

Zhao, R.; Soong, R.; Simpson, A. J.; Abbatt, J.

2012-12-01

Organic peroxides are major components of secondary organic aerosol (SOA), affecting the toxicity of SOA and its oxidative capacity. Hydroxyhydroperoxide (HHP) is a class of organic peroxide observed in ambient air, rain water, and cloud water. However, the formation pathway of HHPs remains under debate, with one potential path via reaction of water with Criegee Intermediates. The current study focuses on a formation mechanism involving reversible nucleophilic addition of H2O2 to aldehydes. This formation pathway of HHPs has been known for decades, but has long been considered as a minor reaction. This is because HHPs were observed to decompose rapidly into H2O2 and the corresponding aldehydes in dilute aqueous solutions. In the current study, proton transfer reaction mass spectrometry (PTR-MS) and proton nuclear magnetic resonance (1H NMR) spectrometry were employed to determine the equilibrium constants (Keq) of H2O2 addition to a variety of atmospherically relevant carbonyls in the aqueous phase. HHP formation was insignificant from ketones and methacrolein, but was significant from formaldehyde, acetaldehyde and propionaldehyde. The Keq values ranged from 80 to 150 M-1 at 25 °C. Based on these values, the environmental implications of HHP formation via this pathway suggest that HHP formation is unlikely to be significant in cloud water. However, in aerosol liquid water, where the concentrations of aldehydes and H2O2 can be at the mM level, this pathway may be significant.

Understanding Chemical Reaction Kinetics and Equilibrium with Interlocking Building Blocks

ERIC Educational Resources Information Center

Cloonan, Carrie A.; Nichol, Carolyn A.; Hutchinson, John S.

2011-01-01

Chemical reaction kinetics and equilibrium are essential core concepts of chemistry but are challenging topics for many students, both at the high school and undergraduate university level. Visualization at the molecular level is valuable to aid understanding of reaction kinetics and equilibrium. This activity provides a discovery-based method to…

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

PubMed

Lennox, J Christian; Dempsey, Jillian L

2017-11-22

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

Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition

NASA Technical Reports Server (NTRS)

Grodzka, P.; Facemire, B.

1977-01-01

Three investigations conducted aboard Skylab IV and Apollo-Soyuz involved phenomena that are of interest to the biochemistry community. The formaldehyde clock reaction and the equilibrium shift reaction experiments conducted aboard Apollo Soyuz demonstrate the effect of low-g foams or air/liquid dispersions on reaction rate and chemical equilibrium. The electrodeposition reaction experiment conducted aboard Skylab IV demonstrate the effect of a low-g environment on an electrochemical displacement reaction. The implications of the three space experiments for various applications are considered.

Evaluation of the pathways of tropospheric nitrophenol formation using a multiphase model

NASA Astrophysics Data System (ADS)

Harrison, M. A. J.; Heal, M. R.; Cape, J. N.

2005-03-01

Phenols are a major class of volatile organic compounds (VOC) whose reaction within, and partitioning between, the gas and liquid phases affects their lifetime within the atmosphere, the local oxidising capacity, and the extent of production of nitrophenols, which are toxic chemicals. In this work, a zero-dimension box model was constructed to quantify the relative nitration pathways, and partitioning into the liquid phase, of mono-aromatic compounds in order to help elucidate the formation pathways of 2- and 4-nitrophenol in the troposphere. The liquid phase contributed significantly to the production of nitrophenols for liquid water content (Lc) values exceeding 3×10-9, and for a range of assumed liquid droplet diameter, even though the resultant equilibrium partitioning to the liquid phase was much lower. For example, in a ''typical'' model scenario, with Lc=3×10-7, 58% of nitrophenol production occurred in the liquid phase but only 2% of nitrophenol remained there, i.e. a significant proportion of nitrophenol observed in the gas phase may actually be produced via the liquid phase. The importance of the liquid phase was enhanced at lower temperatures, by a factor ~1.5-2 at 278 K cf. 298 K. The model showed that nitrophenol production was particularly sensitive to the values of the rate coefficients for the liquid phase reactions between phenol and OH or NO3 reactions, but insensitive to the rate coefficient for the reaction between benzene and OH, thus identifying where further experimental data are required.

Thermodynamics and Kinetics of Chemical Equilibrium in Solution.

ERIC Educational Resources Information Center

Leenson, I. A.

1986-01-01

Discusses theory of thermodynamics of the equilibrium in solution and dissociation-dimerization kinetics. Describes experimental procedure including determination of molar absorptivity and equilibrium constant, reaction enthalpy, and kinetics of the dissociation-dimerization reaction. (JM)

Single molecule RNA folding studied with optical trapping

NASA Astrophysics Data System (ADS)

Vieregg, Jeffrey Robert

The RNA folding problem (predicting the equilibrium structure and folding pathway of an RNA molecule from its sequence) is one of the classic problems of biophysics. Recent discoveries of many new functions for RNA have increased its importance, and new instrumental techniques have provided new ways to characterize molecular behavior. In particular, optical trapping (optical tweezers) allows controlled mechanical force to be applied to single RNA molecules while their end-to-end extension is monitored in real time. This enables characterization of RNA folding dynamics at a level unreachable by traditional bulk methods. Furthermore, recent advances in statistical mechanics make it possible to recover equilibrium quantities such as free energy from reactions which occur away from equilibrium. This dissertation describes the application of optical trapping and non-equilibrium statistical mechanics to quantitatively characterize folding of RNA secondary structures. By measuring the folding free energy of several specially designed hairpins in solutions containing various amounts of sodium and potassium, we were able to determine that RNA secondary structure thermodynamics depends not only on monovalent cation concentration but also surprisingly, on species. We also investigated the temperature dependence of hairpin folding thermodynamics and kinetics, which provided a direct measurement of enthalpy and entropy for RNA folding at physiological temperatures. We found that the folding pathway was quite sensitive to both salt and temperature, as measured by the folding success rate of a biologically important hairpin from the HIV-1 viral genome. Finally, I discuss modeling of force-induced RNA folding and unfolding, as well as a series of efforts which have dramatically improved the performance of our optical trapping instrument.

Non-equilibrium supramolecular polymerization.

PubMed

Sorrenti, Alessandro; Leira-Iglesias, Jorge; Markvoort, Albert J; de Greef, Tom F A; Hermans, Thomas M

2017-09-18

Supramolecular polymerization has been traditionally focused on the thermodynamic equilibrium state, where one-dimensional assemblies reside at the global minimum of the Gibbs free energy. The pathway and rate to reach the equilibrium state are irrelevant, and the resulting assemblies remain unchanged over time. In the past decade, the focus has shifted to kinetically trapped (non-dissipative non-equilibrium) structures that heavily depend on the method of preparation (i.e., pathway complexity), and where the assembly rates are of key importance. Kinetic models have greatly improved our understanding of competing pathways, and shown how to steer supramolecular polymerization in the desired direction (i.e., pathway selection). The most recent innovation in the field relies on energy or mass input that is dissipated to keep the system away from the thermodynamic equilibrium (or from other non-dissipative states). This tutorial review aims to provide the reader with a set of tools to identify different types of self-assembled states that have been explored so far. In particular, we aim to clarify the often unclear use of the term "non-equilibrium self-assembly" by subdividing systems into dissipative, and non-dissipative non-equilibrium states. Examples are given for each of the states, with a focus on non-dissipative non-equilibrium states found in one-dimensional supramolecular polymerization.

Non-equilibrium supramolecular polymerization

PubMed Central

Sorrenti, Alessandro; Leira-Iglesias, Jorge; Markvoort, Albert J.

2017-01-01

Supramolecular polymerization has been traditionally focused on the thermodynamic equilibrium state, where one-dimensional assemblies reside at the global minimum of the Gibbs free energy. The pathway and rate to reach the equilibrium state are irrelevant, and the resulting assemblies remain unchanged over time. In the past decade, the focus has shifted to kinetically trapped (non-dissipative non-equilibrium) structures that heavily depend on the method of preparation (i.e., pathway complexity), and where the assembly rates are of key importance. Kinetic models have greatly improved our understanding of competing pathways, and shown how to steer supramolecular polymerization in the desired direction (i.e., pathway selection). The most recent innovation in the field relies on energy or mass input that is dissipated to keep the system away from the thermodynamic equilibrium (or from other non-dissipative states). This tutorial review aims to provide the reader with a set of tools to identify different types of self-assembled states that have been explored so far. In particular, we aim to clarify the often unclear use of the term “non-equilibrium self-assembly” by subdividing systems into dissipative, and non-dissipative non-equilibrium states. Examples are given for each of the states, with a focus on non-dissipative non-equilibrium states found in one-dimensional supramolecular polymerization. PMID:28349143

Model-based analysis of coupled equilibrium-kinetic processes: indirect kinetic studies of thermodynamic parameters using the dynamic data.

PubMed

Emami, Fereshteh; Maeder, Marcel; Abdollahi, Hamid

2015-05-07

Thermodynamic studies of equilibrium chemical reactions linked with kinetic procedures are mostly impossible by traditional approaches. In this work, the new concept of generalized kinetic study of thermodynamic parameters is introduced for dynamic data. The examples of equilibria intertwined with kinetic chemical mechanisms include molecular charge transfer complex formation reactions, pH-dependent degradation of chemical compounds and tautomerization kinetics in micellar solutions. Model-based global analysis with the possibility of calculating and embedding the equilibrium and kinetic parameters into the fitting algorithm has allowed the complete analysis of the complex reaction mechanisms. After the fitting process, the optimal equilibrium and kinetic parameters together with an estimate of their standard deviations have been obtained. This work opens up a promising new avenue for obtaining equilibrium constants through the kinetic data analysis for the kinetic reactions that involve equilibrium processes.

Rates of nickel(II) capture from complexes with NTA, EDDA, and related tetradentate chelating agents by the hexadentate chelating agents EDTA and CDTA: Evidence of a "semijunctive" ligand exchange pathway

NASA Astrophysics Data System (ADS)

Boland, Nathan E.; Stone, Alan T.

2017-09-01

Many siderophores and metallophores produced by soil organisms, as well as anthropogenic chelating agent soil amendments, rely upon amine and carboxylate Lewis base groups for metal ion binding. UV-visible spectra of metal ion-chelating agent complexes are often similar and, as a consequence, whole-sample absorbance measurements are an unreliable means of monitoring the progress of exchange reactions. In the present work, we employ capillary electrophoresis to physically separate Ni(II)-tetradentate chelating agent complexes (NiL) from Ni(II)-hexadentate chelating agent complexes (NiY) prior to UV detection, such that progress of the reaction NiL + Y → NiY + L can be conveniently monitored. Rates of ligand exchange for Ni(II) are lower than for other +II transition metal ions. Ni(II) speciation in environmental media is often under kinetic rather than equilibrium control. Nitrilotriacetic acid (NTA), with three carboxylate groups all tethered to a central amine Lewis base group, ethylenediamine-N,N‧-diacetic acid (EDDA), with carboxylate-amine-amine-carboxylate groups arranged linearly, plus four structurally related compounds, are used as tetradentate chelating agents. Ethylenediaminetetraacetic acid (EDTA) and the structurally more rigid analog trans-cyclohexaneethylenediaminetetraacetic acid (CDTA) are used as hexadentate chelating agents. Effects of pH and reactant concentration are explored. Ni(II) capture by EDTA was consistently more than an order of magnitude faster than capture by CDTA, and too fast to quantify using our capillary electrophoresis-based technique. Using NiNTA as a reactant, Ni(II) capture by CDTA is independent of CDTA concentration and greatly enhanced by a proton-catalyzed pathway at low pH. Using NiEDDA as reactant, Ni(II) capture by CDTA is first order with respect to CDTA concentration, and the contribution from the proton-catalyzed pathway diminished by CDTA protonation. While the convention is to assign either a disjunctive pathway or adjunctive pathway to multidentate ligand exchange reactions, our results indicate that a third "semijunctive" pathway is necessary to account for slow reactions progressing through Lsbnd Nisbnd Y ternary complexes. Ligand exchange pathways with NTA-type chelating agents are assigned a disjunctive pathway, while pathways with EDDA-type chelating agents are assigned a semijunctive pathway. Based upon operative mechanism(s), magnitudes of exchange rates and effects of ambient geochemical conditions can be predicted.

Is the Reaction Equilibrium Composition in Non-ideal Mixtures Uniquely Determined by the Initial Composition?

NASA Astrophysics Data System (ADS)

Sefcik, Jan

1998-05-01

Reaction equilibrium can be mathematically described by the equilibrium equation and the reaction equilibrium composition can be calculated by solving this equation. It can be proved by non-elementary thermodynamic arguments that for a generic system with given initial composition, temperature and pressure there is a unique stable equilibrium state corresponding to the global minimum of the Gibbs free energy function. However, when the concept of equilibrium is introduced in undergraduate chemistry and chemical engineering courses, such arguments are generally not accessible. When there is a single reaction equilibrium among mixture components and the components form an ideal mixture, it has been demonstrated by a simple, elegant mathematical argument that there is a unique composition satisfying the equilibrium equation. It has been also suggested that this particular argument extends to non-ideal mixtures by simply incorporating activity coefficients. We show that the argument extension to non-ideal systems is not generally valid. Increasing non-ideality can result in non-monotonicity of the function crucial for the simple uniqueness argument, and only later it leads to non-uniqueness and hence phase separation. The main feature responsible for this is a composition dependence of activity coefficients in non-ideal mixtures.

Non-equilibrium reactive flux: A unified framework for slow and fast reaction kinetics.

PubMed

Bose, Amartya; Makri, Nancy

2017-10-21

The flux formulation of reaction rate theory is recast in terms of the expectation value of the reactive flux with an initial condition that corresponds to a non-equilibrium, factorized reactant density. In the common case of slow reactive processes, the non-equilibrium expression reaches the plateau regime only slightly slower than the equilibrium flux form. When the reactants are described by a single quantum state, as in the case of electron transfer reactions, the factorized reactant density describes the true initial condition of the reactive process. In such cases, the time integral of the non-equilibrium flux expression yields the reactant population as a function of time, allowing characterization of the dynamics in cases where there is no clear separation of time scales and thus a plateau regime cannot be identified. The non-equilibrium flux offers a unified approach to the kinetics of slow and fast chemical reactions and is ideally suited to mixed quantum-classical methods.

Evaluation of the pathways of tropospheric nitrophenol formation from benzene and phenol using a multiphase model

NASA Astrophysics Data System (ADS)

Harrison, M. A. J.; Heal, M. R.; Cape, J. N.

2005-07-01

Phenols are a major class of volatile organic compounds (VOC) whose reaction within, and partitioning between, the gas and liquid phases affects their lifetime within the atmosphere, the local oxidising capacity, and the extent of production of nitrophenols, which are toxic chemicals. In this work, a zero-dimension box model was constructed to quantify the relative importance of different nitration pathways, and partitioning into the liquid phase, of mono-aromatic compounds in order to help elucidate the formation pathways of 2- and 4-nitrophenol in the troposphere. The liquid phase contributed significantly to the production of nitrophenols for liquid water content (Lc) values exceeding 3x10-9, and for a range of assumed liquid droplet diameter, even though the resultant equilibrium partitioning to the liquid phase was much lower. For example, in a "typical" model scenario, with Lc=3x10-7, 58% of nitrophenol production occurred in the liquid phase but only 2% of nitrophenol remained there, i.e. a significant proportion of nitrophenol observed in the gas phase may actually be produced via the liquid phase. The importance of the liquid phase was enhanced at lower temperatures, by a factor ~1.5-2 at 278K c.f. 298K. The model showed that nitrophenol production was particularly sensitive to the values of the rate coefficients for the liquid phase reactions between phenol and OH or NO3 reactions, but insensitive to the rate coefficient for the reaction between benzene and OH, thus identifying where further experimental data are required.

A kinetic study on the chemical cleavage of nucleoside diphosphate sugars.

PubMed

Huhta, Eija; Parjanen, Atte; Mikkola, Satu

2010-03-30

Nucleoside diphosphate sugars serve in essential roles in metabolic processes. They have, therefore, been used in mechanistic studies on glycosylation reactions, and their analogues have been synthesised as enzyme and receptor inhibitors. Despite extensive biochemical research, little is known about their chemical reactions. In the present work the chemical cleavage of two different types of nucleoside diphosphate sugars has been studied. UDP-Glc is phosphorylated at the anomeric carbon, whereas in ADP-Rib C-1 is unsubstituted, allowing hence the equilibrium between cyclic hemiacetal and acyclic carbonyl forms. Due to the structural difference, these substrates react via different pathways under slightly alkaline conditions: while UDP-Glc reacts exclusively by a nucleophilic attack of a glucose hydroxyl group on the diphosphate moiety, ADP-Rib undergoes a complex reaction sequence that involves isomerisation processes of the acyclic ribose sugar and results in a release of ADP. Copyright 2009 Elsevier Ltd. All rights reserved.

Chemical and electrochemical behavior of the Cr(3)/Cr(2) half cell in the NASA Redox Energy Storage System

NASA Technical Reports Server (NTRS)

Johnson, D. A.; Reid, M. A.

1982-01-01

The Cr(III) complexes in the NASA Redox Energy Storage System were isolated and identified as Cr(H2O)6(+3) and Cr(H2O)5Cl(+2) by ion exchange chromatography and visible spectrophotometry. The cell reactions during charge-discharge cycles were followed by means of visible spectrophotometry. The spectral bands were resolved into component peaks and concentrations calculated using Beer's Law. During the charge mode Cr(H2O)5Cl(+2) is reduced to Cr(H2O)5Cl(+) and during the discharge mode Cr(H2O)5Cl(+) is oxidized back to Cr(H2O)5Cl(+2). Both electrode reactions occur via a chloride-bridge inner-sphere reaction pathway. Hysteresis effects can be explained by the slow attainment of equilibrium between Cr(H2O)6(+3) and Cr(H2O)5Cl(+2).

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.

Modeling free energy availability from Hadean hydrothermal systems to the first metabolism.

PubMed

Simoncini, E; Russell, M J; Kleidon, A

2011-12-01

Off-axis Hydrothermal Systems (HSs) are seen as the possible setting for the emergence of life. As the availability of free energy is a general requirement to drive any form of metabolism, we ask here under which conditions free energy generation by geologic processes is greatest and relate these to the conditions found at off-axis HSs. To do so, we present a conceptual model in which we explicitly capture the energetics of fluid motion and its interaction with exothermic reactions to maintain a state of chemical disequilibrium. Central to the interaction is the temperature at which the exothermic reactions take place. This temperature not only sets the equilibrium constant of the chemical reactions and thereby the distance of the actual state to chemical equilibrium, but these reactions also shape the temperature gradient that drives convection and thereby the advection of reactants to the reaction sites and the removal of the products that relate to geochemical free energy generation. What this conceptual model shows is that the positive feedback between convection and the chemical kinetics that is found at HSs favors a greater rate of free energy generation than in the absence of convection. Because of the lower temperatures and because the temperature of reactions is determined more strongly by these dynamics rather than an external heat flux, the conditions found at off-axis HSs should result in the greatest rates of geochemical free energy generation. Hence, we hypothesize from these thermodynamic considerations that off-axis HSs seem most conducive for the emergence of protometabolic pathways as these provide the greatest, abiotic generation rates of chemical free energy.

Rapid-Equilibrium Enzyme Kinetics

ERIC Educational Resources Information Center

Alberty, Robert A.

2008-01-01

Rapid-equilibrium rate equations for enzyme-catalyzed reactions are especially useful because if experimental data can be fit by these simpler rate equations, the Michaelis constants can be interpreted as equilibrium constants. However, for some reactions it is necessary to use the more complicated steady-state rate equations. Thermodynamics is…

Quantum chemical study of the mechanism of reaction between NH (X 3sigma-) and H2, H2O, and CO2 under combustion conditions.

PubMed

Mackie, John C; Bacskay, George B

2005-12-29

Reactions of ground-state NH (3sigma-) radicals with H2, H2O, and CO2 have been investigated quantum chemically, whereby the stationary points of the appropriate reaction potential energy surfaces, that is, reactants, products, intermediates, and transition states, have been identified at the G3//B3LYP level of theory. Reaction between NH and H2 takes place via a simple abstraction transition state, and the rate coefficient for this reaction as derived from the quantum chemical calculations, k(NH + H2) = (1.1 x 10(14)) exp(-20.9 kcal mol(-1)/RT) cm3 mol(-1) s(-1) between 1000 and 2000 K, is found to be in good agreement with experiment. For reaction between triplet NH and H2O, no stable intermediates were located on the triplet reaction surface although several stable species were found on the singlet surface. No intersystem crossing seam between triplet NH + H2O and singlet HNO + H2 (the products of lowest energy) was found; hence there is no evidence to support the existence of a low-energy pathway to these products. A rate coefficient of k(NH + H2O) = (6.1 x 10(13)) exp(-32.8 kcal mol(-1)/RT) cm3 mol(-1) s(-1) between 1000 and 2000 K for the reaction NH (3sigma-) + H2O --> NH2 (2B) + OH (2pi) was derived from the quantum chemical results. The reverse rate coefficient, calculated via the equilibrium constant, is in agreement with values used in modeling the thermal de-NO(x) process. For the reaction between triplet NH and CO2, several stable intermediates on both triplet and singlet reaction surfaces were located. Although a pathway from triplet NH + CO2 to singlet HNO + CO involving intersystem crossing in an HN-CO2 adduct was discovered, no pathway of sufficiently low activation energy was discovered to compare with that found in an earlier experiment [Rohrig, M.; Wagner, H. G. Proc. Combust. Inst. 1994, 25, 993.].

Mechanochemical Association Reaction of Interfacial Molecules Driven by Shear.

PubMed

Khajeh, Arash; He, Xin; Yeon, Jejoon; Kim, Seong H; Martini, Ashlie

2018-05-29

Shear-driven chemical reaction mechanisms are poorly understood because the relevant reactions are often hidden between two solid surfaces moving in relative motion. Here, this phenomenon is explored by characterizing shear-induced polymerization reactions that occur during vapor phase lubrication of α-pinene between sliding hydroxylated and dehydroxylated silica surfaces, complemented by reactive molecular dynamics simulations. The results suggest that oxidative chemisorption of the α-pinene molecules at reactive surface sites, which transfers oxygen atoms from the surface to the adsorbate molecule, is the critical activation step. Such activation takes place more readily on the dehydroxylated surface. During this activation, the most strained part of the α-pinene molecules undergoes a partial distortion from its equilibrium geometry, which appears to be related to the critical activation volume for mechanical activation. Once α-pinene molecules are activated, association reactions occur between the newly attached oxygen and one of the carbon atoms in another molecule, forming ether bonds. These findings have general implications for mechanochemistry because they reveal that shear-driven reactions may occur through reaction pathways very different from their thermally induced counterparts and specifically the critical role of molecular distortion in such reactions.

[The accuracy of rapid equilibrium assumption in steady-state enzyme kinetics is the function of equilibrium segment structure and properties].

PubMed

Vrzheshch, P V

2015-01-01

Quantitative evaluation of the accuracy of the rapid equilibrium assumption in the steady-state enzyme kinetics was obtained for an arbitrary mechanism of an enzyme-catalyzed reaction. This evaluation depends only on the structure and properties of the equilibrium segment, but doesn't depend on the structure and properties of the rest (stationary part) of the kinetic scheme. The smaller the values of the edges leaving equilibrium segment in relation to values of the edges within the equilibrium segment, the higher the accuracy of determination of intermediate concentrations and reaction velocity in a case of the rapid equilibrium assumption.

Extension of a Kinetic-Theory Approach for Computing Chemical-Reaction Rates to Reactions with Charged Particles

NASA Technical Reports Server (NTRS)

Liechty, Derek S.; Lewis, Mark J.

2010-01-01

Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties (i.e., no macroscopic reaction rate information) are extended to include reactions involving charged particles and electronic energy levels. The proposed extensions include ionization reactions, exothermic associative ionization reactions, endothermic and exothermic charge exchange reactions, and other exchange reactions involving ionized species. The extensions are shown to agree favorably with the measured Arrhenius rates for near-equilibrium conditions.

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

NASA Astrophysics Data System (ADS)

Moradi, Mahmoud; Sagui, Celeste; Roland, Christopher

2014-01-01

We have developed a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. In this paper, we set the theoretical framework for employing nonequilibrium work relations to estimate the relative reaction rates associated with different classes of transition pathways. Particularly, we derive an extension of Crook's transient fluctuation theorem, which relates the relative transition rates of driven systems in the forward and reverse directions, and allows for the calculation of these relative rates using work measurements (e.g., in Steered Molecular Dynamics). The formalism presented here can be combined with Transition Path Theory to relate the equilibrium and driven transition rates. The usefulness of this framework is illustrated by means of a Gaussian model and a driven proline dimer.

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.

Infrared Stark and Zeeman spectroscopy of OH–CO: The entrance channel complex along the OH + CO → trans-HOCO reaction pathway

DOE PAGES

Brice, Joseph T.; Liang, Tao; Raston, Paul L.; ...

2016-09-27

Here, sequential capture of OH and CO by superfluid helium droplets leads exclusively to the formation of the linear, entrance-channel complex, OH-CO. This species is characterized by infrared laser Stark and Zeeman spectroscopy via measurements of the fundamental OH stretching vibration. Experimental dipole moments are in disagreement with ab initio calculations at the equilibrium geometry, indicating large-amplitude motion on the ground state potential energy surface. Vibrational averaging along the hydroxyl bending coordinate recovers 80% of the observed deviation from the equilibrium dipole moment. Inhomogeneous line broadening in the zero-field spectrum is modeled with an effective Hamiltonian approach that aims tomore » account for the anisotropic molecule-helium interaction potential that arises as the OH-CO complex is displaced from the center of the droplet.« less

Reactivity of Free Malondialdehyde during In Vitro Simulated Gastrointestinal Digestion.

PubMed

Vandemoortele, Angelique; Babat, Pinar; Yakubu, Mariam; De Meulenaer, Bruno

2017-03-15

An aqueous buffer, a saturated glycerol triheptanoate oil, and a Tween 20 stabilized fully hydrogenated coconut oil-in-water emulsion, all spiked with malondialdehyde, were subjected to in vitro digestion. A dynamic equilibrium between malondialdehyde, its aldol self-condensation products, and its hydrolytic cleavage products was observed. This equilibrium depended upon the kind of sample and the temperature at which these samples were preincubated during 24 h. The presence of oil during gastric digestion protected the aldol self-condensation and cleavage products from conversion to malondialdehyde, which occurred in the aqueous acidic gastric chyme. In parallel, the presence of oil enhanced the reactivity of malondialdehyde throughout the gastrointestinal digestion process. Malondialdehyde recoveries after digestion varied between 42 and 90%, depending upon the model system studied, with the aldol self-condensation as the main reaction pathway. In conclusion, this study revealed that malondialdehyde is a very reactive molecule whose reactivity does not stop at the point of ingestion.

Porosity developed during mineral replacement reactions: implications for fluid flux in the Earth

NASA Astrophysics Data System (ADS)

Putnis, Christine V.; Trindade Pedrosa, Elisabete; Hövelmann, Jörn; Renard, François; Ruiz-Agudo, Encarnacion

2017-04-01

Aqueous fluids, that are ubiquitous in the crust of the Earth, will move through possible pathways in rocks. Rocks characteristically have low permeability but fractures can provide fast fluid channels. Mineral grain boundaries also present easy fluid pathways. However, porosity within minerals forms when a mineral is out of equilibrium with an aqueous fluid and reactions take place in an attempt to reach a new equilibrium. Commonly, dissolution at a mineral-fluid interface initiates one or several coupled reactions involving dissolution and precipitation (Putnis C.V. and Ruiz-Agudo E., 2013; Ruiz-Agudo et al., 2014). In pseudomorphic volume-deficit reactions, a new phase forms while porosity is created, and thereby reactive fluid flow through the originally solid mineral is enhanced. These coupled dissolution-replacement reactions therefore will constrain the flux of material carried by the fluid. These reactions are common during such processes as metamorphism, metasomatism, and weathering. When rock-forming minerals such as feldspars, olivine, pyroxenes and carbonates are in contact with aqueous fluids (typically NaCl-rich) porosity is formed during the interfacial replacement reactions. Elements present in the parent mineral are released to the fluid and therefore mobilized for transport elsewhere. Porosity formation has been shown in a number of systems, such as during the albitisation of feldspars (Hövelmann et al., 2009) and the replacement of carbonates by apatite phases (Pedrosa et al., 2016). Some of these examples will be presented as well as examples from atomic force microscopy (AFM) experiments used to image these reactions at a nanoscale, especially at the calcite-fluid interface, when new phases can be directly observed forming. This mechanism has also been shown as a means of carbon and phosphorus sequestration and for the removal of toxic elements from superficial waters, such as Se and As. References Ruiz-Agudo E., Putnis C.V., Putnis A. (2014) Coupled dissolution and precipitation at mineral-fluid interfaces. Chem. Geol., 383, 132-146. Putnis C.V. and Ruiz-Agudo E. (2013) The mineral-water interface: where minerals react with the environment. Elements, 9, 177-182. Hövelmann J., Putnis A., Geisler T., Schmidt B.C., Golla-Schindler U. (2009) The replacement of plagioclase feldspars by albite: observations from hydrothermal experiments. Contrib. Min. and Pet. 159, 43-59. Pedrosa E.T., Putnis C.V., Putnis A. (2016) The pseudomorphic replacement of marble by apatite: the role of fluid composition. Chem. Geol., 425, 1-11.

Uptake of Small Organic Compounds by Sulfuric Acid Aerosols: Dissolution and Reaction

NASA Technical Reports Server (NTRS)

Iraci, L. T.; Michelsen, R. R.; Ashbourn, S. F. M.; Staton, S. J. R.

2003-01-01

To assess the role of oxygenated volatile organic compounds in the upper troposphere and lower stratosphere, the interactions of a series of small organic compounds with low-temperature aqueous sulfuric acid will be evaluated. The total amount of organic material which may be taken up from the gas phase by dissolution, surface layer formation, and reaction during the particle lifetime will be quantified. Our current results for acetaldehyde uptake on 40 - 80 wt% sulfuric acid solutions will be compared to those of methanol, formaldehyde, and acetone to investigate the relationships between chemical functionality and heterogeneous activity. Where possible, equilibrium uptake will be ascribed to component pathways (hydration, protonation, etc.) to facilitate evaluation of other species not yet studied in low temperature aqueous sulfuric acid.

Non-equilibrium reaction rates in chemical kinetic equations

NASA Astrophysics Data System (ADS)

Gorbachev, Yuriy

2018-05-01

Within the recently proposed asymptotic method for solving the Boltzmann equation for chemically reacting gas mixture, the chemical kinetic equations has been derived. Corresponding one-temperature non-equilibrium reaction rates are expressed in terms of specific heat capacities of the species participate in the chemical reactions, bracket integrals connected with the internal energy transfer in inelastic non-reactive collisions and energy transfer coefficients. Reactions of dissociation/recombination of homonuclear and heteronuclear diatomic molecules are considered. It is shown that all reaction rates are the complex functions of the species densities, similarly to the unimolecular reaction rates. For determining the rate coefficients it is recommended to tabulate corresponding bracket integrals, additionally to the equilibrium rate constants. Correlation of the obtained results with the irreversible thermodynamics is established.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-01-20

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

Standard Gibbs energy of metabolic reactions: II. Glucose-6-phosphatase reaction and ATP hydrolysis.

PubMed

Meurer, Florian; Do, Hoang Tam; Sadowski, Gabriele; Held, Christoph

2017-04-01

ATP (adenosine triphosphate) is a key reaction for metabolism. Tools from systems biology require standard reaction data in order to predict metabolic pathways accurately. However, literature values for standard Gibbs energy of ATP hydrolysis are highly uncertain and differ strongly from each other. Further, such data usually neglect the activity coefficients of reacting agents, and published data like this is apparent (condition-dependent) data instead of activity-based standard data. In this work a consistent value for the standard Gibbs energy of ATP hydrolysis was determined. The activity coefficients of reacting agents were modeled with electrolyte Perturbed-Chain Statistical Associating Fluid Theory (ePC-SAFT). The Gibbs energy of ATP hydrolysis was calculated by combining the standard Gibbs energies of hexokinase reaction and of glucose-6-phosphate hydrolysis. While the standard Gibbs energy of hexokinase reaction was taken from previous work, standard Gibbs energy of glucose-6-phosphate hydrolysis reaction was determined in this work. For this purpose, reaction equilibrium molalities of reacting agents were measured at pH7 and pH8 at 298.15K at varying initial reacting agent molalities. The corresponding activity coefficients at experimental equilibrium molalities were predicted with ePC-SAFT yielding the Gibbs energy of glucose-6-phosphate hydrolysis of -13.72±0.75kJ·mol -1 . Combined with the value for hexokinase, the standard Gibbs energy of ATP hydrolysis was finally found to be -31.55±1.27kJ·mol -1 . For both, ATP hydrolysis and glucose-6-phosphate hydrolysis, a good agreement with own and literature values were obtained when influences of pH, temperature, and activity coefficients were explicitly taken into account in order to calculate standard Gibbs energy at pH7, 298.15K and standard state. Copyright © 2017 Elsevier B.V. All rights reserved.

Serpentinization as a reactive transport process: The brucite silicification reaction

NASA Astrophysics Data System (ADS)

Tutolo, B. M.; Luhmann, A. J.; Tosca, N. J.; Seyfried, W. E., Jr.

2017-12-01

Serpentinization plays a fundamental role in the biogeochemical and tectonic evolution of the Earth and perhaps many other rocky planetary bodies. Yet, geochemical models still fail to produce accurate predictions of the various modes of serpentinization, which limits our ability to predict a variety of related geological phenomena over many spatial and temporal scales. Here, we utilize kinetic and reactive transport experiments to parameterize the brucite silicification reaction and provide fundamental constraints on SiO2 transport during serpentinization. We show that, at temperatures characteristic of the sub-seafloor at the serpentinite-hosted Lost City Hydrothermal Field, the assembly of Si tetrahedra onto MgOH2 (i.e., brucite) surfaces is a rate-limiting elementary reaction in the production of serpentine and/or talc from olivine. Moreover, a kinetic rate law extracted from our laboratory experiments shows that this reaction is exponentially dependent on the activity of aqueous silica (aSiO2(aq)), such that its rate is orders of magnitude slower near-equilibrium than it is far-from-equilibrium. Calculations performed with this rate law demonstrate that both brucite and Si are surprisingly persistent in serpentinizing environments, leading to elevated Si concentrations in fluids that can be transported over comparatively large distances without equilibrating with brucite. Moreover, applying this rate law to an open-system reactive transport experiment indicates that advection, preferential flow pathways, and reactive surface area armoring can diminish the net rate of Si uptake resulting from this reaction even further. Because brucite silicification is a fundamentally rate-limiting elementary reaction for the production of both serpentine and talc from forsterite, our new constraints are applicable across the many environments where serpentinization occurs. The unexpected but highly consequential behavior of this simple reaction emphasizes the need for considering serpentinization and many other hydrothermal processes in a reactive transport framework whereby fluid, solute, and heat transport are intimately coupled to kinetically-controlled reactions.

Self-assembled materials and supramolecular chemistry within microfluidic environments: from common thermodynamic states to non-equilibrium structures.

PubMed

Sevim, S; Sorrenti, A; Franco, C; Furukawa, S; Pané, S; deMello, A J; Puigmartí-Luis, J

2018-05-01

Self-assembly is a crucial component in the bottom-up fabrication of hierarchical supramolecular structures and advanced functional materials. Control has traditionally relied on the use of encoded building blocks bearing suitable moieties for recognition and interaction, with targeting of the thermodynamic equilibrium state. On the other hand, nature leverages the control of reaction-diffusion processes to create hierarchically organized materials with surprisingly complex biological functions. Indeed, under non-equilibrium conditions (kinetic control), the spatio-temporal command of chemical gradients and reactant mixing during self-assembly (the creation of non-uniform chemical environments for example) can strongly affect the outcome of the self-assembly process. This directly enables a precise control over material properties and functions. In this tutorial review, we show how the unique physical conditions offered by microfluidic technologies can be advantageously used to control the self-assembly of materials and of supramolecular aggregates in solution, making possible the isolation of intermediate states and unprecedented non-equilibrium structures, as well as the emergence of novel functions. Selected examples from the literature will be used to confirm that microfluidic devices are an invaluable toolbox technology for unveiling, understanding and steering self-assembly pathways to desired structures, properties and functions, as well as advanced processing tools for device fabrication and integration.

The Conceptual Change Approach to Teaching Chemical Equilibrium

ERIC Educational Resources Information Center

Canpolat, Nurtac; Pinarbasi, Tacettin; Bayrakceken, Samih; Geban, Omer

2006-01-01

This study investigates the effect of a conceptual change approach over traditional instruction on students' understanding of chemical equilibrium concepts (e.g. dynamic nature of equilibrium, definition of equilibrium constant, heterogeneous equilibrium, qualitative interpreting of equilibrium constant, changing the reaction conditions). This…

Approaches to the Treatment of Equilibrium Perturbations

NASA Astrophysics Data System (ADS)

Canagaratna, Sebastian G.

2003-10-01

Perturbations from equilibrium are treated in the textbooks by a combination of Le Châtelier's principle, the comparison of the equilibrium constant K with the reaction quotient Q,and the kinetic approach. Each of these methods is briefly reviewed. This is followed by derivations of the variation of the equilibrium value of the extent of reaction, ξeq, with various parameters on which it depends. Near equilibrium this relationship can be represented by a straight line. The equilibrium system can be regarded as moving on this line as the parameter is varied. The slope of the line depends on quantities like enthalpy of reaction, volume of reaction and so forth. The derivation shows that these quantities pertain to the equilibrium system, not the standard state. Also, the derivation makes clear what kind of assumptions underlie our conclusions. The derivation of these relations involves knowledge of thermodynamics that is well within the grasp of junior level physical chemistry students. The conclusions that follow from the derived relations are given as subsidiary rules in the form of the slope of ξeq, with T, p, et cetera. The rules are used to develop a visual way of predicting the direction of shift of a perturbed system. This method can be used to supplement one of the other methods even at the introductory level.

Chemical Principles Revisited: Chemical Equilibrium.

ERIC Educational Resources Information Center

Mickey, Charles D.

1980-01-01

Describes: (1) Law of Mass Action; (2) equilibrium constant and ideal behavior; (3) general form of the equilibrium constant; (4) forward and reverse reactions; (5) factors influencing equilibrium; (6) Le Chatelier's principle; (7) effects of temperature, changing concentration, and pressure on equilibrium; and (8) catalysts and equilibrium. (JN)

Investigation of the hydrochlorination of SiCl4

NASA Technical Reports Server (NTRS)

Mui, J. Y. P.

1983-01-01

A basic, experimental study on the hydrochlorination of silicon tetrachloride and metallurgical grade silicon with hydrogen gas to form trichlorosilane was carried out to greatly expand the range of reaction conditions. The equilibrium constant, K sub p, for the hydrochlorination reaction was measured as a function of temperature, pressure and concentration. The variation of the equilibrium constant as a function of temperature provided the measurement on the heat of reaction, delta H, by the Second Law Method. The value of delta H was measured to give 10.6 Kcal/mole. The equilibrium constant was also studied as a function of concentration. In agreement with the theory, the equilibrium constant remained constant with respect to the varying H2/SiCl4 feed ratios. On the other hand, the effect of pressure on the equilibrium constant was found to be more complex.

Studying Equilibrium in the Chemical Reaction between Ferric and Iodide Ions in Solution Using a Simple and Inexpensive Approach

ERIC Educational Resources Information Center

Nikolaychuk, Pavel Anatolyevich; Kuvaeva, Alyona Olegovna

2016-01-01

A laboratory experiment on the study of the chemical equilibrium based on the reaction between ferric and iodide ions in solution with the formation of ferrous ions, free iodine, and triiodide ions is developed. The total concentration of iodide and triiodide ions in the reaction mixture during the reaction is determined by the argentometric…

Modulating the DNA polymerase β reaction equilibrium to dissect the reverse reaction

PubMed Central

Shock, David D.; Freudenthal, Bret D.; Beard, William A.; Wilson, Samuel H.

2017-01-01

DNA polymerases catalyze efficient and high fidelity DNA synthesis. While this reaction favors nucleotide incorporation, polymerases also catalyze a reverse reaction, pyrophosphorolysis, removing the DNA primer terminus and generating deoxynucleoside triphosphates. Since pyrophosphorolysis can influence polymerase fidelity and sensitivity to chain-terminating nucleosides, we analyzed pyrophosphorolysis with human DNA polymerase β and found the reaction to be inefficient. The lack of a thio-elemental effect indicated that it was limited by a non-chemical step. Utilizing a pyrophosphate analog, where the bridging oxygen is replaced with an imido-group (PNP), increased the rate of the reverse reaction and displayed a large thio-elemental effect indicating that chemistry was now rate determining. Time-lapse crystallography with PNP captured structures consistent with a chemical equilibrium that favored the reverse reaction. These results highlight the importance of the bridging atom between the β- and γ-phosphates of the incoming nucleotide in reaction chemistry, enzyme conformational changes, and overall reaction equilibrium. PMID:28759020

The equilibrium assumption is valid for the kinetic treatment of most time-dependent protein-modification reactions.

PubMed Central

Brocklehurst, K

1979-01-01

To facilitate mechanistic interpretation of the kinetics of time-dependent inhibition of enzymes and of similar protein modification reactions, it is important to know when the equilibrium assumption may be applied to the model: formula: (see text). The conventional criterion of quasi-equilibrium, k + 2 less than k-1, is not always easy to assess, particularly when k + 2 cannot be separately determined. It is demonstrated that the condition k + 2 less than k-1 is necessarily true, however, when the value of the apparent second-order rate constant for the modification reaction is much smaller than the value of k + 1. Since k + 1 is commonly at least 10(7)M-1.S-1 for substrates, it is probable that the equilibrium assumption may be properly applied to most irreversible inhibitions and modification reactions. PMID:518556

Real-Time NMR Studies of Oxyamine Ligations of Reducing Carbohydrates under Equilibrium Conditions.

PubMed

Baudendistel, Oliver R; Wieland, Daniel E; Schmidt, Magnus S; Wittmann, Valentin

2016-11-21

Ligation reactions at the anomeric center of carbohydrates have gained increasing importance in the field of glycobiology. Oxyamines are frequently used in labeling, immobilization, and bioconjugation of reducing carbohydrates. Herein, we present a systematic investigation of these ligation reactions under aqueous conditions. A series of four unprotected monosaccharides (glucose, N-acetylglucosamine, mannose, and 2-deoxyglucose) and one disaccharide (N,N'-diacetylchitobiose) was reacted with three primary and one secondary oxyamine. We monitored the concentrations of the starting materials and products by 1 H NMR spectroscopy and determined reaction times and equilibrium yields. Our experiments show that the outcome of the ligation reaction is not only dependent on the sugar and oxyamine used but also strongly on the reaction conditions. In the case of glucose, lowering the pH from 6 to 3 led to steadily increasing reaction rates, whereas the yields were decreasing at the same time. Variation of the temperature did not only influence the product ratio in equilibrium but can also have a strong impact on the equilibrium yield. In the case of reactions of a primary oxyamine, increased temperatures led to a higher proportion of acyclic products. Reaction of the secondary oxyamine with glucose unexpectedly led to lower yields at higher temperatures. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding Chemical Equilibrium Using Entropy Analysis: The Relationship between [delta]S[subscript tot](sys[superscript o]) and the Equilibrium Constant

ERIC Educational Resources Information Center

Bindel, Thomas H.

2010-01-01

Entropy analyses as a function of the extent of reaction are presented for a number of physicochemical processes, including vaporization of a liquid, dimerization of nitrogen dioxide, and the autoionization of water. Graphs of the total entropy change versus the extent of reaction give a visual representation of chemical equilibrium and the second…

Navier-Stokes simulation of real gas flows in nozzles

NASA Technical Reports Server (NTRS)

Nagaraj, N.; Lombard, C. K.

1987-01-01

Air flow in a hypersonic nozzle causes real gas effects due to reaction among the species constituting air. Such reactions may be in chemical equilibrium or in chemical nonequilibrium. Here using the CSCM upwind scheme for the compressible Navier-Stokes equations, the real gas flowfield in an arcjet nozzle is computed for both the equilibrium case and the nonequilibrium case. A hypersonic nozzle flow arising from a pebble bed heated plenum is also computed for the equilibrium situation. Between the equilibrium cases, the chemistry is treated by two different schemes and comments are made as to computational complexity. For the nonequilibrium case, a full set of seventeen reactions and full implicit coupling of five species with gasdynamics is employed to compute the flowfield. For all cases considered here the gas is assumed to be a calorically imperfect mixture of ideal gases in thermal equilibrium.

Non-equilibrium Quasi-Chemical Nucleation Model

NASA Astrophysics Data System (ADS)

Gorbachev, Yuriy E.

2018-04-01

Quasi-chemical model, which is widely used for nucleation description, is revised on the basis of recent results in studying of non-equilibrium effects in reacting gas mixtures (Kolesnichenko and Gorbachev in Appl Math Model 34:3778-3790, 2010; Shock Waves 23:635-648, 2013; Shock Waves 27:333-374, 2017). Non-equilibrium effects in chemical reactions are caused by the chemical reactions themselves and therefore these contributions should be taken into account in the corresponding expressions for reaction rates. Corrections to quasi-equilibrium reaction rates are of two types: (a) spatially homogeneous (caused by physical-chemical processes) and (b) spatially inhomogeneous (caused by gas expansion/compression processes and proportional to the velocity divergency). Both of these processes play an important role during the nucleation and are included into the proposed model. The method developed for solving the generalized Boltzmann equation for chemically reactive gases is applied for solving the set of equations of the revised quasi-chemical model. It is shown that non-equilibrium processes lead to essential deviation of the quasi-stationary distribution and therefore the nucleation rate from its traditional form.

Achieving Chemical Equilibrium: The Role of Imposed Conditions in the Ammonia Formation Reaction

ERIC Educational Resources Information Center

Tellinghuisen, Joel

2006-01-01

Under conditions of constant temperature T and pressure P, chemical equilibrium occurs in a closed system (fixed mass) when the Gibbs free energy G of the reaction mixture is minimized. However, when chemical reactions occur under other conditions, other thermodynamic functions are minimized or maximized. For processes at constant T and volume V,…

Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces.

PubMed

Spezia, Riccardo; Martínez-Nuñez, Emilio; Vazquez, Saulo; Hase, William L

2017-04-28

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'. © 2017 The Author(s).

Self-Consistency of the Theory of Elementary Stage Rates of Reversible Processes and the Equilibrium Distribution of Reaction Mixture Components

NASA Astrophysics Data System (ADS)

Tovbin, Yu. K.

2018-06-01

An analysis is presented of one of the key concepts of physical chemistry of condensed phases: the theory self-consistency in describing the rates of elementary stages of reversible processes and the equilibrium distribution of components in a reaction mixture. It posits that by equating the rates of forward and backward reactions, we must obtain the same equation for the equilibrium distribution of reaction mixture components, which follows directly from deducing the equation in equilibrium theory. Ideal reaction systems always have this property, since the theory is of a one-particle character. Problems arise in considering interparticle interactions responsible for the nonideal behavior of real systems. The Eyring and Temkin approaches to describing nonideal reaction systems are compared. Conditions for the self-consistency of the theory for mono- and bimolecular processes in different types of interparticle potentials, the degree of deviation from the equilibrium state, allowing for the internal motions of molecules in condensed phases, and the electronic polarization of the reagent environment are considered within the lattice gas model. The inapplicability of the concept of an activated complex coefficient for reaching self-consistency is demonstrated. It is also shown that one-particle approximations for considering intermolecular interactions do not provide a theory of self-consistency for condensed phases. We must at a minimum consider short-range order correlations.

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

PubMed

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

2016-07-27

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

Process for operating equilibrium controlled reactions

DOEpatents

Nataraj, Shankar; Carvill, Brian Thomas; Hufton, Jeffrey Raymond; Mayorga, Steven Gerard; Gaffney, Thomas Richard; Brzozowski, Jeffrey Richard

2001-01-01

A cyclic process for operating an equilibrium controlled reaction in a plurality of reactors containing an admixture of an adsorbent and a reaction catalyst suitable for performing the desired reaction which is operated in a predetermined timed sequence wherein the heating and cooling requirements in a moving reaction mass transfer zone within each reactor are provided by indirect heat exchange with a fluid capable of phase change at temperatures maintained in each reactor during sorpreaction, depressurization, purging and pressurization steps during each process cycle.

Rate and Equilibrium Constants for the Addition of N-Heterocyclic Carbenes into Benzaldehydes: A Remarkable 2-Substituent Effect**

PubMed Central

Collett, Christopher J; Massey, Richard S; Taylor, James E; Maguire, Oliver R; O'Donoghue, AnnMarie C; Smith, Andrew D

2015-01-01

Rate and equilibrium constants for the reaction between N-aryl triazolium N-heterocyclic carbene (NHC) precatalysts and substituted benzaldehyde derivatives to form 3-(hydroxybenzyl)azolium adducts under both catalytic and stoichiometric conditions have been measured. Kinetic analysis and reaction profile fitting of both the forward and reverse reactions, plus onwards reaction to the Breslow intermediate, demonstrate the remarkable effect of the benzaldehyde 2-substituent in these reactions and provide insight into the chemoselectivity of cross-benzoin reactions. PMID:25908493

Rate and Equilibrium Constants for the Addition of N‐Heterocyclic Carbenes into Benzaldehydes: A Remarkable 2‐Substituent Effect†

PubMed Central

Collett, Christopher J.; Massey, Richard S.; Taylor, James E.; Maguire, Oliver R.

2015-01-01

Abstract Rate and equilibrium constants for the reaction between N‐aryl triazolium N‐heterocyclic carbene (NHC) precatalysts and substituted benzaldehyde derivatives to form 3‐(hydroxybenzyl)azolium adducts under both catalytic and stoichiometric conditions have been measured. Kinetic analysis and reaction profile fitting of both the forward and reverse reactions, plus onwards reaction to the Breslow intermediate, demonstrate the remarkable effect of the benzaldehyde 2‐substituent in these reactions and provide insight into the chemoselectivity of cross‐benzoin reactions. PMID:27478264

Evidence for Alkene cis-Aminocupration, an Aminooxygenation Case Study: Kinetics, EPR Spectroscopy, and DFT Calculations

PubMed Central

Paderes, Monissa C.; Belding, Lee; Fanovic, Branden; Dudding, Travis; Keister, Jerome B.

2012-01-01

Alkene difunctionalization reactions are important in organic synthesis. We have recently shown that copper(II) complexes can promote and catalyze intramolecular alkene aminooxygenation, carboamination, and diamination reactions. In this contribution, we report a combined experimental and theoretical examination of the mechanism of the copper(II)-promoted olefin aminooxygenation reaction. Kinetics experiments revealed a mechanistic pathway involving an equilibrium reaction between a copper(II) carboxylate complex and the γ-alkenyl sulfonamide substrate and a rate-limiting intramolecular cis-addition of N–Cu across the olefin. Kinetic isotope effect studies support that the cis-aminocupration is the rate-determining step. UV/Vis spectra support a role for the base in the break-up of copper(II) carboxylate dimer to monomeric species. Electron paramagnetic resonance (EPR) spectra provide evidence for a kinetically competent N–Cu intermediate with a CuII oxidation state. Due to the highly similar stereochemical and reactivity trends among the CuII-promoted and catalyzed alkene difunctionalization reactions we have developed, the cis-aminocupration mechanism can reasonably be generalized across the reaction class. The methods and findings disclosed in this report should also prove valuable to the mechanism analysis and optimization of other copper(-II) carboxylate promoted reactions, especially those that take place in aprotic organic solvents. PMID:22237868

Chemical reactions simulated by ground-water-quality models

USGS Publications Warehouse

Grove, David B.; Stollenwerk, Kenneth G.

1987-01-01

Recent literature concerning the modeling of chemical reactions during transport in ground water is examined with emphasis on sorption reactions. The theory of transport and reactions in porous media has been well documented. Numerous equations have been developed from this theory, to provide both continuous and sequential or multistep models, with the water phase considered for both mobile and immobile phases. Chemical reactions can be either equilibrium or non-equilibrium, and can be quantified in linear or non-linear mathematical forms. Non-equilibrium reactions can be separated into kinetic and diffusional rate-limiting mechanisms. Solutions to the equations are available by either analytical expressions or numerical techniques. Saturated and unsaturated batch, column, and field studies are discussed with one-dimensional, laboratory-column experiments predominating. A summary table is presented that references the various kinds of models studied and their applications in predicting chemical concentrations in ground waters.

Exploring Chemical Equilibrium with Poker Chips: A General Chemistry Laboratory Exercise

ERIC Educational Resources Information Center

Bindel, Thomas H.

2012-01-01

A hands-on laboratory exercise at the general chemistry level introduces students to chemical equilibrium through a simulation that uses poker chips and rate equations. More specifically, the exercise allows students to explore reaction tables, dynamic chemical equilibrium, equilibrium constant expressions, and the equilibrium constant based on…

Multi-Step Lithiation of Tin Sulfide: An Investigation Using In Situ Electron Microscopy

DOE PAGES

Hwang, Sooyeon; Yao, Zhenpeng; Zhang, Lei; ...

2018-04-03

Two-dimensional metal sulfides have been widely explored as promising electrodes for lithium ion batteries since their two-dimensional layered structure allows lithium ions to intercalate between layers. For tin disulfide, the lithiation process proceeds via a sequence of three different types of reactions: intercalation, conversion, and alloying but the full scenario of reaction dynamics remains nebulous. In this paper, we investigate the dynamical process of the multi-step reactions using in situ electron microscopy and discover an intermediate rock-salt phase with the disordering of Li and Sn cations, after the initial 2-dimensional intercalation. The disordered cations occupy all the octahedral sites andmore » block the channels for intercalation, which alter the reaction pathways during further lithiation. Our first principles calculations of the non-equilibrium lithiation of SnS2 corroborate the energetic preference of the disordered rock-salt structure over known layered polymorphs. The in situ observations and calculations suggest a two-phase reaction nature for intercalation, disordering, and following conversion reactions. In addition, in situ de-lithiation observation confirms that the alloying reaction is reversible while the conversion reaction is not, which is consistent to the ex situ analysis. This work reveals the full lithiation characteristic of SnS2 and sheds light on the understanding of complex multistep reactions in two-dimensional materials.« less

Multi-Step Lithiation of Tin Sulfide: An Investigation Using In Situ Electron Microscopy

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

Hwang, Sooyeon; Yao, Zhenpeng; Zhang, Lei

Two-dimensional metal sulfides have been widely explored as promising electrodes for lithium ion batteries since their two-dimensional layered structure allows lithium ions to intercalate between layers. For tin disulfide, the lithiation process proceeds via a sequence of three different types of reactions: intercalation, conversion, and alloying but the full scenario of reaction dynamics remains nebulous. In this paper, we investigate the dynamical process of the multi-step reactions using in situ electron microscopy and discover an intermediate rock-salt phase with the disordering of Li and Sn cations, after the initial 2-dimensional intercalation. The disordered cations occupy all the octahedral sites andmore » block the channels for intercalation, which alter the reaction pathways during further lithiation. Our first principles calculations of the non-equilibrium lithiation of SnS2 corroborate the energetic preference of the disordered rock-salt structure over known layered polymorphs. The in situ observations and calculations suggest a two-phase reaction nature for intercalation, disordering, and following conversion reactions. In addition, in situ de-lithiation observation confirms that the alloying reaction is reversible while the conversion reaction is not, which is consistent to the ex situ analysis. This work reveals the full lithiation characteristic of SnS2 and sheds light on the understanding of complex multistep reactions in two-dimensional materials.« less

Numerical simulation of hypersonic inlet flows with equilibrium or finite rate chemistry

NASA Technical Reports Server (NTRS)

Yu, Sheng-Tao; Hsieh, Kwang-Chung; Shuen, Jian-Shun; Mcbride, Bonnie J.

1988-01-01

An efficient numerical program incorporated with comprehensive high temperature gas property models has been developed to simulate hypersonic inlet flows. The computer program employs an implicit lower-upper time marching scheme to solve the two-dimensional Navier-Stokes equations with variable thermodynamic and transport properties. Both finite-rate and local-equilibrium approaches are adopted in the chemical reaction model for dissociation and ionization of the inlet air. In the finite rate approach, eleven species equations coupled with fluid dynamic equations are solved simultaneously. In the local-equilibrium approach, instead of solving species equations, an efficient chemical equilibrium package has been developed and incorporated into the flow code to obtain chemical compositions directly. Gas properties for the reaction products species are calculated by methods of statistical mechanics and fit to a polynomial form for C(p). In the present study, since the chemical reaction time is comparable to the flow residence time, the local-equilibrium model underpredicts the temperature in the shock layer. Significant differences of predicted chemical compositions in shock layer between finite rate and local-equilibrium approaches have been observed.

Chemistry Research

NASA Technical Reports Server (NTRS)

1987-01-01

Philip Morris research center scientists use a computer program called CECTRP, for Chemical Equilibrium Composition and Transport Properties, to gain insight into the behavior of atoms as they progress along the reaction pathway. Use of the program lets the scientist accurately predict the behavior of a given molecule or group of molecules. Computer generated data must be checked by laboratory experiment, but the use of CECTRP saves the researchers hundreds of hours of laboratory time since experiments must run only to validate the computer's prediction. Philip Morris estimates that had CECTRP not been available, at least two man years would have been required to develop a program to perform similar free energy calculations.

A Springloaded Metal-Ligand Mesocate Allows Access to Trapped Intermediates of Self-Assembly.

PubMed

Bogie, Paul M; Holloway, Lauren R; Lyon, Yana; Onishi, Nicole C; Beran, Gregory J O; Julian, Ryan R; Hooley, Richard J

2018-04-02

A strained, "springloaded" Fe 2 L 3 iminopyridine mesocate shows highly variable reactivity upon postassembly reaction with competitive diamines. The strained assembly is reactive toward transimination in minutes at ambient temperature and allows observation of kinetically trapped intermediates in the self-assembly pathway. When diamines are used that can only form less favored cage products upon full equilibration, trapped ML 3 fragments with pendant, "hanging" NH 2 groups are selectively formed instead. Slight variations in diamine structure have large effects on the product outcome: less rigid diamines convert the mesocate to more favored self-assembled cage complexes under mild conditions and allow observation of heterocomplex intermediates in the displacement pathway. The mesocate allows control of equilibrium processes and direction of product outcomes via small, iterative changes in added subcomponent structure and provides a method of accessing metal-ligand cage structures not normally observed in multicomponent Fe-iminopyridine self-assembly.

Microimaging of transient guest profiles to monitor mass transfer in nanoporous materials

NASA Astrophysics Data System (ADS)

Kärger, Jörg; Binder, Tomas; Chmelik, Christian; Hibbe, Florian; Krautscheid, Harald; Krishna, Rajamani; Weitkamp, Jens

2014-04-01

The intense interactions of guest molecules with the pore walls of nanoporous materials is the subject of continued fundamental research. Stimulated by their thermal energy, the guest molecules in these materials are subject to a continuous, irregular motion, referred to as diffusion. Diffusion, which is omnipresent in nature, influences the efficacy of nanoporous materials in reaction and separation processes. The recently introduced techniques of microimaging by interference and infrared microscopy provide us with a wealth of information on diffusion, hitherto inaccessible from commonly used techniques. Examples include the determination of surface barriers and the sticking coefficient's analogue, namely the probability that, on colliding with the particle surface, a molecule may continue its diffusion path into the interior. Microimaging is further seen to open new vistas in multicomponent guest diffusion (including the detection of a reversal in the preferred diffusion pathways), in guest-induced phase transitions in nanoporous materials and in matching the results of diffusion studies under equilibrium and non-equilibrium conditions.

Communication: Probing non-equilibrium vibrational relaxation pathways of highly excited C≡N stretching modes following ultrafast back-electron transfer.

PubMed

Lynch, Michael S; Slenkamp, Karla M; Khalil, Munira

2012-06-28

Fifth-order nonlinear visible-infrared spectroscopy is used to probe coherent and incoherent vibrational energy relaxation dynamics of highly excited vibrational modes indirectly populated via ultrafast photoinduced back-electron transfer in a trinuclear cyano-bridged mixed-valence complex. The flow of excess energy deposited into four C≡N stretching (ν(CN)) modes of the molecule is monitored by performing an IR pump-probe experiment as a function of the photochemical reaction (τ(vis)). Our results provide experimental evidence that the nuclear motions of the molecule are both coherently and incoherently coupled to the electronic charge transfer process. We observe that intramolecular vibrational relaxation dynamics among the highly excited ν(CN) modes change significantly en route to equilibrium. The experiment also measures a 7 cm(-1) shift in the frequency of a ∼57 cm(-1) oscillation reflecting a modulation of the coupling between the probed high-frequency ν(CN) modes for τ(vis) < 500 fs.

Chemical partitioning for the Co--Pr system: First-principles, experiments and energetic calculations to investigate the hard magnetic phase

DOE PAGES

Zhou, S. H.; Kramer, M. J.; Meng, F. Q.; ...

2015-11-14

Co 5Pr-D2 d is promising permanent magnet. Due to its peritectic formation feature, there is a synthetic challenge to produce single Co 5Pr-D2 d phase. The object of our study is to assess thermodynamic pathways for crystalline phases under far-from-equilibrium conditions by combining first-principles calculations and experimental measurements into a robust description of the thermodynamic behavior. The energetic calculations, temperature and time dependent phase selections are predicted under varying degrees of chemical partitioning. Our calculation to assess the chemical partitioning-temperatures indicates that the major magnetic compounds: Co 17Pr 2-α, Co 5Pr-D2 d, Co 19Pr 5-β, and Co 7Pr 2-χ formmore » from a congruent manner to eutectic reactions with decreasing cooling rate. The compositions of the compounds from these highly driven liquids can be far from equilibrium.« less

Proton bombarded reactions of Calcium target nuclei

NASA Astrophysics Data System (ADS)

Tel, Eyyup; Sahan, Muhittin; Sarpün, Ismail Hakki; Kavun, Yusuf; Gök, Ali Armagan; Depedelen, Mesut

2017-09-01

In this study, proton bombarded nuclear reactions calculations of Calcium target nuclei have been investigated in the incident proton energy range of 1-50 MeV. The excitation functions for 40Ca target nuclei reactions have been calculated by using PCROSS nuclear reaction calculation code. Weisskopf-Ewing and the full exciton models were used for equilibrium and for pre-equilibrium calculations, respectively. The excitation functions for 40Ca target nuclei reactions (p,α), (p,n), (p,p) have been calculated using the semi-empirical formula Tel et al. [5].

Equilibrium chemical reaction of supersonic hydrogen-air jets (the ALMA computer program)

NASA Technical Reports Server (NTRS)

Elghobashi, S.

1977-01-01

The ALMA (axi-symmetrical lateral momentum analyzer) program is concerned with the computation of two dimensional coaxial jets with large lateral pressure gradients. The jets may be free or confined, laminar or turbulent, reacting or non-reacting. Reaction chemistry is equilibrium.

Chemical equilibrium. [maximizing entropy of gas system to derive relations between thermodynamic variables

NASA Technical Reports Server (NTRS)

1976-01-01

The entropy of a gas system with the number of particles subject to external control is maximized to derive relations between the thermodynamic variables that obtain at equilibrium. These relations are described in terms of the chemical potential, defined as equivalent partial derivatives of entropy, energy, enthalpy, free energy, or free enthalpy. At equilibrium, the change in total chemical potential must vanish. This fact is used to derive the equilibrium constants for chemical reactions in terms of the partition functions of the species involved in the reaction. Thus the equilibrium constants can be determined accurately, just as other thermodynamic properties, from a knowledge of the energy levels and degeneracies for the gas species involved. These equilibrium constants permit one to calculate the equilibrium concentrations or partial pressures of chemically reacting species that occur in gas mixtures at any given condition of pressure and temperature or volume and temperature.

The Equilibrium and Pre-equilibrium Triton Emission Spectra of Some Target Nuclei for ( n, xt) Reactions up to 45 MeV Energy

NASA Astrophysics Data System (ADS)

Tel, E.; Kaplan, A.; Aydın, A.; Özkorucuklu, S.; Büyükuslu, H.; Yıldırım, G.

2010-08-01

Although there have been significant research and development studies on the inertial and magnetic fusion reactor technology, there is still a long way to go to penetrate commercial fusion reactors to the energy market. Tritium self-sufficiency must be maintained for a commercial power plant. For self-sustaining (D-T) fusion driver tritium breeding ratio should be greater than 1.05. So, working out the systematics of ( n,t) reaction cross sections and triton emission differential data are important for the given reaction taking place on various nuclei at different energies. In this study, ( n,xt) reactions for some target nuclei as 16O, 27Al, 59Co and 209Bi have been investigated up to 45 MeV incident neutron energy. In the calculations of the triton emission spectra, the pre-equilibrium and equilibrium effects have been used. The calculated results have been compared with the experimental data taken from the literature.

A Compartmentalized Out-of-Equilibrium Enzymatic Reaction Network for Sustained Autonomous Movement

PubMed Central

2016-01-01

Every living cell is a compartmentalized out-of-equilibrium system exquisitely able to convert chemical energy into function. In order to maintain homeostasis, the flux of metabolites is tightly controlled by regulatory enzymatic networks. A crucial prerequisite for the development of lifelike materials is the construction of synthetic systems with compartmentalized reaction networks that maintain out-of-equilibrium function. Here, we aim for autonomous movement as an example of the conversion of feedstock molecules into function. The flux of the conversion is regulated by a rationally designed enzymatic reaction network with multiple feedforward loops. By compartmentalizing the network into bowl-shaped nanocapsules the output of the network is harvested as kinetic energy. The entire system shows sustained and tunable microscopic motion resulting from the conversion of multiple external substrates. The successful compartmentalization of an out-of-equilibrium reaction network is a major first step in harnessing the design principles of life for construction of adaptive and internally regulated lifelike systems. PMID:27924313

On the thermalization achieved in the reactions involving superheavy nuclei

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

Bansal, Rajni

In the present study, we aim to explore the role of Coulomb potential on the thermalization achieved in the reactions involving superheavy nuclei. Particularly, we shall study the degree of the equilibrium attained in a reaction by the 3D density plots, anisotropy ratio as well as by the rapidity distribution of the nucleons. Our study reveals that the degree of the equilibrium attained in the central reactions of the superheavy nuclei remains unaffected by the Coulomb potential.

Local thermodynamic equilibrium for globally disequilibrium open systems under stress

NASA Astrophysics Data System (ADS)

Podladchikov, Yury

2016-04-01

Predictive modeling of far and near equilibrium processes is essential for understanding of patterns formation and for quantifying of natural processes that are never in global equilibrium. Methods of both equilibrium and non-equilibrium thermodynamics are needed and have to be combined. For example, predicting temperature evolution due to heat conduction requires simultaneous use of equilibrium relationship between internal energy and temperature via heat capacity (the caloric equation of state) and disequilibrium relationship between heat flux and temperature gradient. Similarly, modeling of rocks deforming under stress, reactions in system open for the porous fluid flow, or kinetic overstepping of the equilibrium reaction boundary necessarily needs both equilibrium and disequilibrium material properties measured under fundamentally different laboratory conditions. Classical irreversible thermodynamics (CIT) is the well-developed discipline providing the working recipes for the combined application of mutually exclusive experimental data such as density and chemical potential at rest under constant pressure and temperature and viscosity of the flow under stress. Several examples will be presented.

Communication: Equilibrium rate coefficients from atomistic simulations: The O((3)P) + NO((2)Π) → O2(X(3)Σg(-)) + N((4)S) reaction at temperatures relevant to the hypersonic flight regime.

PubMed

Castro-Palacio, Juan Carlos; Bemish, Raymond J; Meuwly, Markus

2015-03-07

The O((3)P) + NO((2)Π) → O2(X(3)Σg(-)) + N((4)S) reaction is among the N- and O- involving reactions that dominate the energetics of the reactive air flow around spacecraft during hypersonic atmospheric re-entry. In this regime, the temperature in the bow shock typically ranges from 1000 to 20,000 K. The forward and reverse rate coefficients for this reaction derived directly from trajectory calculations over this range of temperature are reported in this letter. Results compare well with the established equilibrium constants for the same reaction from thermodynamic quantities derived from spectroscopy in the gas phase which paves the way for large-scale in silico investigations of equilibrium rates under extreme conditions.

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.

Differential Selectivity of the Escherichia coli Cell Membrane Shifts the Equilibrium for the Enzyme-Catalyzed Isomerization of Galactose to Tagatose▿

PubMed Central

Kim, Jin-Ha; Lim, Byung-Chul; Yeom, Soo-Jin; Kim, Yeong-Su; Kim, Hye-Jung; Lee, Jung-Kul; Lee, Sook-Hee; Kim, Seon-Won; Oh, Deok-Kun

2008-01-01

An Escherichia coli galactose kinase gene knockout (ΔgalK) strain, which contains the l-arabinose isomerase gene (araA) to isomerize d-galactose to d-tagatose, showed a high conversion yield of tagatose compared with the original galK strain because galactose was not metabolized by endogenous galactose kinase. In whole cells of the ΔgalK strain, the isomerase-catalyzed reaction exhibited an equilibrium shift toward tagatose, producing a tagatose fraction of 68% at 37°C, whereas the purified l-arabinose isomerase gave a tagatose equilibrium fraction of 36%. These equilibrium fractions are close to those predicted from the measured equilibrium constants of the isomerization reaction catalyzed in whole cells and by the purified enzyme. The equilibrium shift in these cells resulted from the higher uptake and lower release rates for galactose, which is a common sugar substrate, than for tagatose, which is a rare sugar product. A ΔmglB mutant had decreased uptake rates for galactose and tagatose, indicating that a methylgalactoside transport system, MglABC, is the primary contributing transporter for the sugars. In the present study, whole-cell conversion using differential selectivity of the cell membrane was proposed as a method for shifting the equilibrium in sugar isomerization reactions. PMID:18263746

Differential selectivity of the Escherichia coli cell membrane shifts the equilibrium for the enzyme-catalyzed isomerization of galactose to tagatose.

PubMed

Kim, Jin-Ha; Lim, Byung-Chul; Yeom, Soo-Jin; Kim, Yeong-Su; Kim, Hye-Jung; Lee, Jung-Kul; Lee, Sook-Hee; Kim, Seon-Won; Oh, Deok-Kun

2008-04-01

An Escherichia coli galactose kinase gene knockout (DeltagalK) strain, which contains the l-arabinose isomerase gene (araA) to isomerize d-galactose to d-tagatose, showed a high conversion yield of tagatose compared with the original galK strain because galactose was not metabolized by endogenous galactose kinase. In whole cells of the DeltagalK strain, the isomerase-catalyzed reaction exhibited an equilibrium shift toward tagatose, producing a tagatose fraction of 68% at 37 degrees C, whereas the purified l-arabinose isomerase gave a tagatose equilibrium fraction of 36%. These equilibrium fractions are close to those predicted from the measured equilibrium constants of the isomerization reaction catalyzed in whole cells and by the purified enzyme. The equilibrium shift in these cells resulted from the higher uptake and lower release rates for galactose, which is a common sugar substrate, than for tagatose, which is a rare sugar product. A DeltamglB mutant had decreased uptake rates for galactose and tagatose, indicating that a methylgalactoside transport system, MglABC, is the primary contributing transporter for the sugars. In the present study, whole-cell conversion using differential selectivity of the cell membrane was proposed as a method for shifting the equilibrium in sugar isomerization reactions.

Pathways through equilibrated states with coexisting phases for gas hydrate formation

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

Malolepsza, Edyta; Keyes, Tom

Under ambient conditions, water freezes to either hexagonal ice or a hexagonal/cubic composite ice. The presence of hydrophobic guest molecules introduces a competing pathway: gas hydrate formation, with the guests in clathrate cages. Here, the pathways of the phase transitions are sought as sequences of states with coexisting phases, using a generalized replica exchange algorithm designed to sample them in equilibrium, avoiding nonequilibrium processes. For a dilute solution of methane in water under 200 atm, initializing the simulation with the full set of replicas leads to methane trapped in hexagonal/cubic ice, while gradually adding replicas with decreasing enthalpy produces themore » initial steps of hydrate growth. Once a small amount of hydrate is formed, water rearranges to form empty cages, eventually transforming the remainder of the system to metastable β ice, a scaffolding for hydrates. It is suggested that configurations with empty cages are reaction intermediates in hydrate formation when more guest molecules are available. Furthermore, free energy profiles show that methane acts as a catalyst reducing the barrier for β ice versus hexagonal/cubic ice formation.« less

Pathways through equilibrated states with coexisting phases for gas hydrate formation

DOE PAGES

Malolepsza, Edyta; Keyes, Tom

2015-12-01

Under ambient conditions, water freezes to either hexagonal ice or a hexagonal/cubic composite ice. The presence of hydrophobic guest molecules introduces a competing pathway: gas hydrate formation, with the guests in clathrate cages. Here, the pathways of the phase transitions are sought as sequences of states with coexisting phases, using a generalized replica exchange algorithm designed to sample them in equilibrium, avoiding nonequilibrium processes. For a dilute solution of methane in water under 200 atm, initializing the simulation with the full set of replicas leads to methane trapped in hexagonal/cubic ice, while gradually adding replicas with decreasing enthalpy produces themore » initial steps of hydrate growth. Once a small amount of hydrate is formed, water rearranges to form empty cages, eventually transforming the remainder of the system to metastable β ice, a scaffolding for hydrates. It is suggested that configurations with empty cages are reaction intermediates in hydrate formation when more guest molecules are available. Furthermore, free energy profiles show that methane acts as a catalyst reducing the barrier for β ice versus hexagonal/cubic ice formation.« less

Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

PubMed

Qian, Hong; Beard, Daniel A

2005-04-22

The principles of thermodynamics apply to both equilibrium and nonequilibrium biochemical systems. The mathematical machinery of the classic thermodynamics, however, mainly applies to systems in equilibrium. We introduce a thermodynamic formalism for the study of metabolic biochemical reaction (open, nonlinear) networks in both time-dependent and time-independent nonequilibrium states. Classical concepts in equilibrium thermodynamics-enthalpy, entropy, and Gibbs free energy of biochemical reaction systems-are generalized to nonequilibrium settings. Chemical motive force, heat dissipation rate, and entropy production (creation) rate, key concepts in nonequilibrium systems, are introduced. Dynamic equations for the thermodynamic quantities are presented in terms of the key observables of a biochemical network: stoichiometric matrix Q, reaction fluxes J, and chemical potentials of species mu without evoking empirical rate laws. Energy conservation and the Second Law are established for steady-state and dynamic biochemical networks. The theory provides the physiochemical basis for analyzing large-scale metabolic networks in living organisms.

Experimental determination of thermodynamic equilibrium in biocatalytic transamination.

PubMed

Tufvesson, Pär; Jensen, Jacob S; Kroutil, Wolfgang; Woodley, John M

2012-08-01

The equilibrium constant is a critical parameter for making rational design choices in biocatalytic transamination for the synthesis of chiral amines. However, very few reports are available in the scientific literature determining the equilibrium constant (K) for the transamination of ketones. Various methods for determining (or estimating) equilibrium have previously been suggested, both experimental as well as computational (based on group contribution methods). However, none of these were found suitable for determining the equilibrium constant for the transamination of ketones. Therefore, in this communication we suggest a simple experimental methodology which we hope will stimulate more accurate determination of thermodynamic equilibria when reporting the results of transaminase-catalyzed reactions in order to increase understanding of the relationship between substrate and product molecular structure on reaction thermodynamics. Copyright © 2012 Wiley Periodicals, Inc.

Evidence-Based Approaches to Improving Chemical Equilibrium Instruction

ERIC Educational Resources Information Center

Davenport, Jodi L.; Leinhardt, Gaea; Greeno, James; Koedinger, Kenneth; Klahr, David; Karabinos, Michael; Yaron, David J.

2014-01-01

Two suggestions for instruction in chemical equilibrium are presented, along with the evidence that supports these suggestions. The first is to use diagrams to connect chemical reactions to the effects of reactions on concentrations. The second is the use of the majority and minority species (M&M) strategy to analyze chemical equilibrium…

Metastable equilibria among dicarboxylic acids and the oxidation state during aqueous alteration on the CM2 chondrite parent body

NASA Astrophysics Data System (ADS)

McAlister, Jason A.; Kettler, Richard M.

2008-01-01

Linear saturated dicarboxylic acids are present in carbonaceous chondrite samples at concentrations that suggest aqueous alteration under conditions of metastable equilibrium. In this study, previously published values of dicarboxylic acid concentrations measured in Murchison, Yamato-791198, and Tagish Lake carbonaceous chondrites are converted to aqueous activities during aqueous alteration assuming water:rock ratios that range from 1:10 to 10:1. Logarithmic plots of the aqueous activities of any two dicarboxylic acids are proximal to lines whose slope is fixed by the stoichiometry of reactions describing the oxidation-reduction equilibrium between the two species. The precise position of any line is controlled by the equilibrium constant of the reaction relating the species and the hydrogen fugacity for the reaction of interest. Reactions among succinic (C4), glutaric (C5), and adipic (C6) acids obtained from CM2 chondrites show evidence of metastable equilibrium and yield logf values that agree to within 0.3 log units at 298.15 K and 0.6 log units at 473.15 K. At a water:rock ratio of 1:1, metastable equilibrium among succinic, glutaric, and adipic acids results in calculated logf values during aqueous alteration that range from -6.2 at 298.15 K to -3.3 at 373.15 K. These values are consistent with those obtained in previous work on carbonaceous chondrites and with metastable equilibrium at temperatures ranging from 300 to 355 K in contact with cronstedtite + magnetite.

A Combined Experimental and Theoretical Study on the Formation of Interstellar Propylene Oxide (CH3CHCH2O)—A Chiral Molecule

NASA Astrophysics Data System (ADS)

Bergantini, Alexandre; Abplanalp, Matthew J.; Pokhilko, Pavel; Krylov, Anna I.; Shingledecker, Christopher N.; Herbst, Eric; Kaiser, Ralf I.

2018-06-01

This work reveals via a combined experimental, computational, and astrochemical modeling study that racemic propylene oxide (c-C3H6O)—the first chiral molecule detected outside Earth toward the high-mass star-forming region Sagittarius B2(N)—can be synthesized by non-equilibrium reactions initiated by the effects of secondary electrons generated in the track of cosmic rays interacting with ice-coated interstellar grains through excited-state and spin-forbidden reaction pathways operating within low-temperature interstellar ices at 10 K. Our findings confront traditional hypotheses that thermal chemistries followed by processing of interstellar grains dictate the formation of complex organic molecules (COMs) in molecular clouds. Instead, we reveal a hitherto poorly quantified reaction class involving excited-state and spin-forbidden chemistry leading to racemic mixtures of COMs inside interstellar ices prior to their sublimation in star-forming regions. This fundamental production mechanism is of essential consequence in aiding our understanding of the origin and evolution of chiral molecules in the universe.

Kinetic Folding Mechanism of Erythropoietin

PubMed Central

Banks, Douglas D.; Scavezze, Joanna L.; Siska, Christine C.

2009-01-01

This report describes what to our knowledge is the first kinetic folding studies of erythropoietin, a glycosylated four-helical bundle cytokine responsible for the regulation of red blood cell production. Kinetic responses for folding and unfolding reactions initiated by manual mixing were monitored by far-ultraviolet circular dichroism and fluorescence spectroscopy, and folding reactions initiated by stopped-flow mixing were monitored by fluorescence. The urea concentration dependence of the observed kinetics were best described by a three-state model with a transiently populated intermediate species that is on-pathway and obligatory. This folding scheme was further supported by the excellent agreement between the free energy of unfolding and m-value calculated from the microscopic rate constants derived from this model and these parameters determined from separate equilibrium unfolding experiments. Compared to the kinetics of other members of the four-helical bundle cytokine family, erythropoietin folding and unfolding reactions were slower and less susceptible to aggregation. We tentatively attribute these slower rates and protection from association events to the large amount of carbohydrate attached to erythropoietin at four sites. PMID:19450492

Conjugate Acid-Base Pairs, Free Energy, and the Equilibrium Constant

ERIC Educational Resources Information Center

Beach, Darrell H.

1969-01-01

Describes a method of calculating the equilibrium constant from free energy data. Values of the equilibrium constants of six Bronsted-Lowry reactions calculated by the author's method and by a conventional textbook method are compared. (LC)

REACTION OF AMINO-ACIDS AND PEPTIDE BONDS WITH FORMALDEHYDE AS MEASURED BY CHANGES IN THE ULTRA-VIOLET SPECTRA,

DTIC Science & Technology

AMINO ACIDS , CHEMICAL REACTIONS), (*PEPTIDES, CHEMICAL REACTIONS), (*FORMALDEHYDE, CHEMICAL REACTIONS), (*ULTRAVIOLET SPECTROSCOPY, PROTEINS), ABSORPTION SPECTRA, CHEMICAL BONDS, AMIDES, CHEMICAL EQUILIBRIUM, REACTION KINETICS

Investigation of the hydrochlorination of SiCL4

NASA Technical Reports Server (NTRS)

Mui, J. Y. P.

1982-01-01

Reaction kinetic measurements on the hydrochlorination of SiCl4 and metallurgical grade (m.g.) silicon metal were made at a wide range of experimental variables. The effect of pressure on the reaction rate was studied at 25 psig, 100 psig, 150 psig and 200 psig, respectively. Results of these experiments show a large pressure effect on the hydrochlorination reaction. As expected, higher pressures produce a higher equilibrium SiHC13 conversion, since the hydrochlorination reaction results in a net volume contraction as product SiHC1 is formed. However, the reaction rate, namely, the rate at which the hydrochlorination reaction reaches its equilibrium SiHC13 conversion, was found to be much faster at low pressures.

Thermodynamics of enzyme-catalyzed esterifications: II. Levulinic acid esterification with short-chain alcohols.

PubMed

Altuntepe, Emrah; Emel'yanenko, Vladimir N; Forster-Rotgers, Maximilian; Sadowski, Gabriele; Verevkin, Sergey P; Held, Christoph

2017-10-01

Levulinic acid was esterified with methanol, ethanol, and 1-butanol with the final goal to predict the maximum yield of these equilibrium-limited reactions as function of medium composition. In a first step, standard reaction data (standard Gibbs energy of reaction Δ R g 0 ) were determined from experimental formation properties. Unexpectedly, these Δ R g 0 values strongly deviated from data obtained with classical group contribution methods that are typically used if experimental standard data is not available. In a second step, reaction equilibrium concentrations obtained from esterification catalyzed by Novozym 435 at 323.15 K were measured, and the corresponding activity coefficients of the reacting agents were predicted with perturbed-chain statistical associating fluid theory (PC-SAFT). The so-obtained thermodynamic activities were used to determine Δ R g 0 at 323.15 K. These results could be used to cross-validate Δ R g 0 from experimental formation data. In a third step, reaction-equilibrium experiments showed that equilibrium position of the reactions under consideration depends strongly on the concentration of water and on the ratio of levulinic acid: alcohol in the initial reaction mixtures. The maximum yield of the esters was calculated using Δ R g 0 data from this work and activity coefficients of the reacting agents predicted with PC-SAFT for varying feed composition of the reaction mixtures. The use of the new Δ R g 0 data combined with PC-SAFT allowed good agreement to the measured yields, while predictions based on Δ R g 0 values obtained with group contribution methods showed high deviations to experimental yields.

Non-equilibrium effects in high temperature chemical reactions

NASA Technical Reports Server (NTRS)

Johnson, Richard E.

1987-01-01

Reaction rate data were collected for chemical reactions occurring at high temperatures during reentry of space vehicles. The principle of detailed balancing is used in modeling kinetics of chemical reactions at high temperatures. Although this principle does not hold for certain transient or incubation times in the initial phase of the reaction, it does seem to be valid for the rates of internal energy transitions that occur within molecules and atoms. That is, for every rate of transition within the internal energy states of atoms or molecules, there is an inverse rate that is related through an equilibrium expression involving the energy difference of the transition.

Pressure-induced silica quartz amorphization studied by iterative stochastic surface walking reaction sampling.

PubMed

Zhang, Xiao-Jie; Shang, Cheng; Liu, Zhi-Pan

2017-02-08

The crystal to amorphous transformation is a common phenomenon in Nature and has important impacts on material properties. Our current knowledge on such complex solid transformation processes is, however, limited because of their slow kinetics and the lack of long-range ordering in amorphous structures. To reveal the kinetics in the amorphization of solids, this work, by developing iterative reaction sampling based on the stochastic surface walking global optimization method, investigates the well-known crystal to amorphous transformation of silica (SiO 2 ) under external pressures, the mechanism of which has long been debated for its non-equilibrium, pressure-sensitive kinetics and complex product components. Here we report for the first time the global potential energy surface (PES) and the lowest energy pathways for α-quartz amorphization from first principles. We show that the pressurization at 15 GPa, the reaction condition, can lift the quartz phase energetically close to the amorphous zone, which thermodynamically initializes the amorphization. More importantly, the large flexibility of Si cation coordination (including four, five and six coordination) results in many kinetically competing routes to more stable dense forms, including the known MI, stishovite, newly-identified MII and TI phases. All these pathways have high barriers due to the local Si-O bond breaking and are mediated by amorphous structures with five-fold Si. This causes simultaneous crystal-to-crystal and crystal-to-amorphous transitions. The high barrier and the reconstructive nature of the phase transition are the key kinetics origin for silica amorphization under pressures.

Communication: Equilibrium rate coefficients from atomistic simulations: The O({sup 3}P) + NO({sup 2}Π) → O{sub 2}(X{sup 3}Σ{sub g}{sup −}) + N({sup 4}S) reaction at temperatures relevant to the hypersonic flight regime

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

Castro-Palacio, Juan Carlos; Bemish, Raymond J.; Meuwly, Markus, E-mail: m.meuwly@unibas.ch

2015-03-07

The O({sup 3}P) + NO({sup 2}Π) → O{sub 2}(X{sup 3}Σ{sub g}{sup −}) + N({sup 4}S) reaction is among the N- and O- involving reactions that dominate the energetics of the reactive air flow around spacecraft during hypersonic atmospheric re-entry. In this regime, the temperature in the bow shock typically ranges from 1000 to 20 000 K. The forward and reverse rate coefficients for this reaction derived directly from trajectory calculations over this range of temperature are reported in this letter. Results compare well with the established equilibrium constants for the same reaction from thermodynamic quantities derived from spectroscopy in the gasmore » phase which paves the way for large-scale in silico investigations of equilibrium rates under extreme conditions.« less

Derivation of the chemical-equilibrium rate coefficient using scattering theory

NASA Technical Reports Server (NTRS)

Mickens, R. E.

1977-01-01

Scattering theory is applied to derive the equilibrium rate coefficient for a general homogeneous chemical reaction involving ideal gases. The reaction rate is expressed in terms of the product of a number of normalized momentum distribution functions, the product of the number of molecules with a given internal energy state, and the spin-averaged T-matrix elements. An expression for momentum distribution at equilibrium for an arbitrary molecule is presented, and the number of molecules with a given internal-energy state is represented by an expression which includes the partition function.

Na(+) transport, and the E(1)P-E(2)P conformational transition of the Na(+)/K(+)-ATPase.

PubMed Central

Babes, A; Fendler, K

2000-01-01

We have used admittance analysis together with the black lipid membrane technique to analyze electrogenic reactions within the Na(+) branch of the reaction cycle of the Na(+)/K(+)-ATPase. ATP release by flash photolysis of caged ATP induced changes in the admittance of the compound membrane system that are associated with partial reactions of the Na(+)/K(+)-ATPase. Frequency spectra and the Na(+) dependence of the capacitive signal are consistent with an electrogenic or electroneutral E(1)P <--> E(2)P conformational transition which is rate limiting for a faster electrogenic Na(+) dissociation reaction. We determine the relaxation rate of the rate-limiting reaction and the equilibrium constants for both reactions at pH 6.2-8.5. The relaxation rate has a maximum value at pH 7.4 (approximately 320 s(-1)), which drops to acidic (approximately 190 s(-1)) and basic (approximately 110 s(-1)) pH. The E(1)P <--> E(2)P equilibrium is approximately at a midpoint position at pH 6.2 (equilibrium constant approximately 0.8) but moves more to the E(1)P side at basic pH 8.5 (equilibrium constant approximately 0.4). The Na(+) affinity at the extracellular binding site decreases from approximately 900 mM at pH 6.2 to approximately 200 mM at pH 8.5. The results suggest that during Na(+) transport the free energy supplied by the hydrolysis of ATP is mainly used for the generation of a low-affinity extracellular Na(+) discharge site. Ionic strength and lyotropic anions both decrease the relaxation rate. However, while ionic strength does not change the position of the conformational equilibrium E(1)P <--> E(2)P, lyotropic anions shift it to E(1)P. PMID:11053130

Spontaneity and Equilibrium II: Multireaction Systems

ERIC Educational Resources Information Center

Raff, Lionel M.

2014-01-01

The thermodynamic criteria for spontaneity and equilibrium in multireaction systems are developed and discussed. When N reactions are occurring simultaneously, it is shown that G and A will depend upon N independent reaction coordinates, ?a (a = 1,2, ..., N), in addition to T and p for G or T and V for A. The general criteria for spontaneity and…

Rational design of functional and tunable oscillating enzymatic networks

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

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.

Computer model of one-dimensional equilibrium controlled sorption processes

USGS Publications Warehouse

Grove, D.B.; Stollenwerk, K.G.

1984-01-01

A numerical solution to the one-dimensional solute-transport equation with equilibrium-controlled sorption and a first-order irreversible-rate reaction is presented. The computer code is written in FORTRAN language, with a variety of options for input and output for user ease. Sorption reactions include Langmuir, Freundlich, and ion-exchange, with or without equal valance. General equations describing transport and reaction processes are solved by finite-difference methods, with nonlinearities accounted for by iteration. Complete documentation of the code, with examples, is included. (USGS)

Investigation of the Hydrochlorination of SiCl4

NASA Technical Reports Server (NTRS)

Mui, J. Y. P.

1983-01-01

The hydrochlorination of silicon tetrachloride with hydrogen and metallurgical grade (m.g.) silicon metal, 3 SiCl4 + 2 H2 + Si yields 4 SiHCl3 was shown to be an efficient process to produce trichlorosilane. A research and development program was carried out to study the hydrochlorination reaction over a wide range of reaction conditions. Equilibrium constant and reaction kinetics measurements were made to provide the basis for a theoretical study on the hydrochlorination process. Thermodynamic properties of the hydrochlorination reaction were also measured. The effects of temperature, pressure, and concentration on the equilibrium constant, K sub p, were studied.

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

PubMed

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

2012-05-01

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

Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model.

PubMed

Wang, Wei Bu; Liang, Yu; Zhang, Jing; Wu, Yi Dong; Du, Jian Jun; Li, Qi Ming; Zhu, Jian Zhuo; Su, Ji Guo

2018-06-22

Intra-molecular energy transport between distant functional sites plays important roles in allosterically regulating the biochemical activity of proteins. How to identify the specific intra-molecular signaling pathway from protein tertiary structure remains a challenging problem. In the present work, a non-equilibrium dynamics method based on the elastic network model (ENM) was proposed to simulate the energy propagation process and identify the specific signaling pathways within proteins. In this method, a given residue was perturbed and the propagation of energy was simulated by non-equilibrium dynamics in the normal modes space of ENM. After that, the simulation results were transformed from the normal modes space to the Cartesian coordinate space to identify the intra-protein energy transduction pathways. The proposed method was applied to myosin and the third PDZ domain (PDZ3) of PSD-95 as case studies. For myosin, two signaling pathways were identified, which mediate the energy transductions form the nucleotide binding site to the 50 kDa cleft and the converter subdomain, respectively. For PDZ3, one specific signaling pathway was identified, through which the intra-protein energy was transduced from ligand binding site to the distant opposite side of the protein. It is also found that comparing with the commonly used cross-correlation analysis method, the proposed method can identify the anisotropic energy transduction pathways more effectively.

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

NASA Astrophysics Data System (ADS)

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

2012-06-01

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

An equilibrium ab initio atomistic thermodynamics study of chlorine adsorption on the Cu(001) surface.

PubMed

Suleiman, Ibrahim A; Radny, Marian W; Gladys, Michael J; Smith, Phillip V; Mackie, John C; Kennedy, Eric M; Dlugogorski, Bogdan Z

2011-06-07

The effect of chlorine (Cl) chemisorption on the energetics and atomic structure of the Cu(001) surface over a wide range of chlorine pressures and temperatures has been studied using equilibrium ab initio atomistic thermodynamics to elucidate the formation of cuprous chloride (CuCl) as part of the Deacon reaction on copper metal. The calculated surface free energies show that the 1/2 monolayer (ML) c(2 × 2)-Cl phase with chlorine atoms adsorbed at the hollow sites is the most stable structure for a wide range of Cl chemical potential, in agreement with experimental observations. It is also found that at very low pressure and exposure, but elevated temperature, the 1/9 ML and 1/4 ML phases become the most stable. By contrast, a high coverage of Cl does not lead to thermodynamically stable geometries. The subsurface adsorption of Cl atoms, however, dramatically increases the stability of the 1 ML and 2 ML adsorption configurations providing a possible pathway for the formation of the bulk-chloride surface phases in the kinetic regime.

Conversion of Chemical Reaction Energy into Useful Work in the Van't Hoff Equilibrium Box

ERIC Educational Resources Information Center

Bazhin, N. M.; Parmon, V. N.

2007-01-01

The ideal van't Hoff equilibrium box is described in detail. It shows that van't Hoff equilibrium box divided in two parts can simultaneously produce heat and useful work without violation of the first law of thermodynamics.

The Painting-Sponging Analogy for Chemical Equilibrium

NASA Astrophysics Data System (ADS)

Gamitz, Adoni

1997-05-01

An analogy for chemical equilibrium is presented, in which high school or younger students can follow the advance towards equilibrium and its final dynamic nature. The relative opposition between forward and backward processes in a real chemical reaction is exemplified by the distance of a road line that is painted by one person and erased by another, both with different skills and working speeds. The graphical results of the progress of the line distance is entirely similar to the increasing of products concentration in a chemical reaction starting from the reactants. In the analogy, the final equilibrium position is independent of the starting point, as well as in a real chemical process. A simple basic program is included for interactive learning purposes.

Improved Simulation of the Pre-equilibrium Triton Emission in Nuclear Reactions Induced by Nucleons

NASA Astrophysics Data System (ADS)

Konobeyev, A. Yu.; Fischer, U.; Pereslavtsev, P. E.; Blann, M.

2014-04-01

A new approach is proposed for the calculation of non-equilibrium triton energy distributions in nuclear reactions induced by nucleons of intermediate energies. It combines models describing the nucleon pick-up, the coalescence and the triton knock-out processes. Emission and absorption rates for excited particles are represented by the pre-equilibrium hybrid model. The model of Sato, Iwamoto, Harada is used to describe the nucleon pick-up and the coalescence of nucleons from exciton configurations starting from (2p,1h) states. The contribution of the direct nucleon pick-up is described phenomenologically. Multiple pre-equilibrium emission of tritons is accounted for. The calculated triton energy distributions are compared with available experimental data.

Quantifying the Pathway and Predicting Spontaneous Emulsification during Material Exchange in a Two Phase Liquid System.

PubMed

Spooner, Stephen; Rahnama, Alireza; Warnett, Jason M; Williams, Mark A; Li, Zushu; Sridhar, Seetharaman

2017-10-30

Kinetic restriction of a thermodynamically favourable equilibrium is a common theme in materials processing. The interfacial instability in systems where rate of material exchange is far greater than the mass transfer through respective bulk phases is of specific interest when tracking the transient interfacial area, a parameter integral to short processing times for productivity streamlining in all manufacturing where interfacial reaction occurs. This is even more pertinent in high-temperature systems for energy and cost savings. Here the quantified physical pathway of interfacial area change due to material exchange in liquid metal-molten oxide systems is presented. In addition the predicted growth regime and emulsification behaviour in relation to interfacial tension as modelled using phase-field methodology is shown. The observed in-situ emulsification behaviour links quantitatively the geometry of perturbations as a validation method for the development of simulating the phenomena. Thus a method is presented to both predict and engineer the formation of micro emulsions to a desired specification.

Laser Raman Diagnostics in Subsonic and Supersonic Turbulent Jet Diffusion Flames.

NASA Astrophysics Data System (ADS)

Cheng, Tsarng-Sheng

1991-02-01

UV spontaneous vibrational Raman scattering combined with laser-induced predissociative fluorescence (LIPF) is developed for temperature and multi-species concentration measurements. For the first time, simultaneous measurements of temperature, major species (H_2, O_2, N_2, H_2O), and minor species (OH) concentrations are made with a "single" narrowband KrF excimer laser in subsonic and supersonic lifted turbulent hydrogen-air diffusion flames. The UV Raman system is calibrated with a flat -flame diffusion burner operated at several known equivalence ratios from fuel-lean to fuel-rich. Temperature measurements made by the ratio of Stokes/anti-Stokes signal and by the ideal gas law are compared. Single-shot uncertainties for temperature and concentration measurements are analyzed with photon statistics. Calibration constants and bandwidth factors are used in the data reduction program to arrive at temperature and species concentration measurements. UV Raman measurements in the subsonic lifted turbulent diffusion flame indicate that fuel and oxidizer are in rich, premixed, and unignited conditions in the center core of the lifted flame base. The unignited mixtures are due to rapid turbulent mixing that affects chemical reaction. Combustion occurs in an intermittent annular turbulent flame brush with strong finite-rate chemistry effects. The OH radical exists in sub-equilibrium and super-equilibrium concentrations. Major species and temperature are found with non-equilibrium values. Further downstream the super-equilibrium OH radicals decay toward equilibrium through slow three-body recombination reactions. In the supersonic lifted flame, a little reaction occurs upstream of the flame base, due to shock wave interactions and mixing with hot vitiated air. The strong turbulent mixing and total enthalpy fluctuations lead to temperature, major, and minor species concentrations with non-equilibrium values. Combustion occurs farther downstream of the lifted region. Slow three-body recombination reactions result in super-equilibrium OH concentrations that depress temperature below the equilibrium values. Near the equilibrium region, ambient air entrainment contaminates flame properties. These simultaneous measurements of temperature and multi-species concentrations allow a better understanding of the complex turbulence-chemistry interactions and provide information for the input and validation of CFD models.

Direct Measurement of Equilibrium Constants for High-Affinity Hemoglobins

PubMed Central

Kundu, Suman; Premer, Scott A.; Hoy, Julie A.; Trent, James T.; Hargrove, Mark S.

2003-01-01

The biological functions of heme proteins are linked to their rate and affinity constants for ligand binding. Kinetic experiments are commonly used to measure equilibrium constants for traditional hemoglobins comprised of pentacoordinate ligand binding sites and simple bimolecular reaction schemes. However, kinetic methods do not always yield reliable equilibrium constants with more complex hemoglobins for which reaction mechanisms are not clearly understood. Furthermore, even where reaction mechanisms are clearly understood, it is very difficult to directly measure equilibrium constants for oxygen and carbon monoxide binding to high-affinity (KD ≪ 1 μM) hemoglobins. This work presents a method for direct measurement of equilibrium constants for high-affinity hemoglobins that utilizes a competition for ligands between the "target" protein and an array of "scavenger" hemoglobins with known affinities. This method is described for oxygen and carbon monoxide binding to two hexacoordinate hemoglobins: rice nonsymbiotic hemoglobin and Synechocystis hemoglobin. Our results demonstrate that although these proteins have different mechanisms for ligand binding, their affinities for oxygen and carbon monoxide are similar. Their large affinity constants for oxygen, 285 and ∼100 μM−1 respectively, indicate that they are not capable of facilitating oxygen transport. PMID:12770899

Microscopic modeling of direct pre-equilibrium emission from neutron induced reactions on even and odd actinides

NASA Astrophysics Data System (ADS)

Dupuis, M.; Hilaire, S.; Péru, S.; Bauge, E.; Kerveno, M.; Dessagne, P.; Henning, G.

2017-09-01

Direct inelastic scattering to discrete excitations and pre-equilibrium emission are described within a microscopic model. Nuclear structure information are obtained in the (Quasi) Random Phase Approximation ((Q)RPA) framework implemented with the Gogny force. The relevant optical and transition potentials are build considering the JLM folding model. Various successful applications are shown for (n,n), (n,n'), (n,xn) and (n,xnγ) reactions for spherical and axially deformed even-even or odd targets. The rearrangement corrections to transition potentials and the contribution of unnatural parity excitations to pre-equilibrium emission are discussed. Our model predictions for (n,n'γ) reactions, for intra- and inter-band transitions in 238U, and for the 239Pu(n,2n) cross section are analyzed.

Modeling Complex Chemical Systems: Problems and Solutions

NASA Astrophysics Data System (ADS)

van Dijk, Jan

2016-09-01

Non-equilibrium plasmas in complex gas mixtures are at the heart of numerous contemporary technologies. They typically contain dozens to hundreds of species, involved in hundreds to thousands of reactions. Chemists and physicists have always been interested in what are now called chemical reduction techniques (CRT's). The idea of such CRT's is that they reduce the number of species that need to be considered explicitly without compromising the validity of the model. This is usually achieved on the basis of an analysis of the reaction time scales of the system under study, which identifies species that are in partial equilibrium after a given time span. The first such CRT that has been widely used in plasma physics was developed in the 1960's and resulted in the concept of effective ionization and recombination rates. It was later generalized to systems in which multiple levels are effected by transport. In recent years there has been a renewed interest in tools for chemical reduction and reaction pathway analysis. An example of the latter is the PumpKin tool. Another trend is that techniques that have previously been developed in other fields of science are adapted as to be able to handle the plasma state of matter. Examples are the Intrinsic Low Dimension Manifold (ILDM) method and its derivatives, which originate from combustion engineering, and the general-purpose Principle Component Analysis (PCA) technique. In this contribution we will provide an overview of the most common reduction techniques, then critically assess the pros and cons of the methods that have gained most popularity in recent years. Examples will be provided for plasmas in argon and carbon dioxide.

Insight into the SEA amide thioester equilibrium. Application to the synthesis of thioesters at neutral pH.

PubMed

Pira, S L; El Mahdi, O; Raibaut, L; Drobecq, H; Dheur, J; Boll, E; Melnyk, O

2016-07-26

The bis(2-sulfanylethyl)amide (SEA) N,S-acyl shift thioester surrogate has found a variety of useful applications in the field of protein total synthesis. Here we present novel insights into the SEA amide/thioester equilibrium in water which is an essential step in any reaction involving the thioester surrogate properties of the SEA group. We also show that the SEA amide thioester equilibrium can be efficiently displaced at neutral pH for accessing peptide alkylthioesters, i.e. the key components of the native chemical ligation (NCL) reaction.

Experimental Insights into Multiphase (H2O-CO2) Fluid-Rock Interactions in Geothermal Systems

NASA Astrophysics Data System (ADS)

Kaszuba, J. P.; Lo Re, C.; Martin, J.; McPherson, B. J.; Moore, J. N.

2012-12-01

Integrated hydrothermal experiments and geochemical modeling elucidate fluid-rock interactions and reaction pathways in both natural and anthropogenic systems, including enhanced geothermal systems (EGS) in which CO2 is introduced as a working fluid. Experiments are conducted in rocker bombs and flexible Au-Ti reaction cells. Individual experiments require one to three months to complete; intensive in-situ fluid/gas sampling gauges reaction progress. Investigation of granitic reservoirs and associated vein minerals are broadly based on the Roosevelt Hot Springs thermal area, Utah, USA. The granite consists of subequal amounts of quartz, perthitic K-feldspar (~25% wt% albite and 75% wt% K-feldspar), and oligoclase (An23), and 4 wt% Fe-rich biotite. Vein minerals include epidote and chlorite (clinochlore). Experiments are conducted at 250°C and 25 to 45 MPa. Each experiment uses mineral powders (75 wt% of rock mass, ground to <45 um) to increase reactivity and also mineral pieces (0.1-0.7 cm in size) to promote petrologic evaluation of mineral reactions. The water (I ≈ 0.1 molal) initially contains millimolal quantities of SiO2, Al, Ca, Mg, K, SO4, and HCO3 and is designed to be saturated with all of the minerals present at the start of each experiment. Excess CO2 is injected to saturate the water and maintain an immiscible supercritical fluid phase. The entire evolutionary path of the natural system is not replicated at laboratory scales. Instead, experiments define a segment of the reaction path and, in combination with geochemical modeling, provide clear trajectories towards equilibrium. Reaction of granite+water yields illite+zeolite; smectite subsequently precipitates in response to CO2 injection. Reaction of granite+epidote+water yields illite+zeolite+smectite; zeolite does not precipitate after CO2 is injected. Water in all experiments become saturated with chalcedony. Carbonate minerals do not precipitate but are predicted as final equilbrium products. Enhanced Geothermal Systems are expected to follow similar reaction pathways and produce metastable minerals during initial development.

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

DOE PAGES

Park, Junyoung O.; Rubin, Sara A.; Xu, Yi -Fan; ...

2016-05-02

In metabolism, available free energy is limited and must be divided across pathway steps to maintain a negative Δ G throughout. For each reaction, Δ G is log proportional both to a concentration ratio (reaction quotient to equilibrium constant) and to a flux ratio (backward to forward flux). In this paper, we use isotope labeling to measure absolute metabolite concentrations and fluxes in Escherichia coli, yeast and a mammalian cell line. We then integrate this information to obtain a unified set of concentrations and Δ G for each organism. In glycolysis, we find that free energy is partitioned so asmore » to mitigate unproductive backward fluxes associated with Δ G near zero. Across metabolism, we observe that absolute metabolite concentrations and Δ G are substantially conserved and that most substrate (but not inhibitor) concentrations exceed the associated enzyme binding site dissociation constant ( K m or K i). Finally, the observed conservation of metabolite concentrations is consistent with an evolutionary drive to utilize enzymes efficiently given thermodynamic and osmotic constraints.« less

Timescale analysis of rule-based biochemical reaction networks

PubMed Central

Klinke, David J.; Finley, Stacey D.

2012-01-01

The flow of information within a cell is governed by a series of protein-protein interactions that can be described as a reaction network. Mathematical models of biochemical reaction networks can be constructed by repetitively applying specific rules that define how reactants interact and what new species are formed upon reaction. To aid in understanding the underlying biochemistry, timescale analysis is one method developed to prune the size of the reaction network. In this work, we extend the methods associated with timescale analysis to reaction rules instead of the species contained within the network. To illustrate this approach, we applied timescale analysis to a simple receptor-ligand binding model and a rule-based model of Interleukin-12 (IL-12) signaling in näive CD4+ T cells. The IL-12 signaling pathway includes multiple protein-protein interactions that collectively transmit information; however, the level of mechanistic detail sufficient to capture the observed dynamics has not been justified based upon the available data. The analysis correctly predicted that reactions associated with JAK2 and TYK2 binding to their corresponding receptor exist at a pseudo-equilibrium. In contrast, reactions associated with ligand binding and receptor turnover regulate cellular response to IL-12. An empirical Bayesian approach was used to estimate the uncertainty in the timescales. This approach complements existing rank- and flux-based methods that can be used to interrogate complex reaction networks. Ultimately, timescale analysis of rule-based models is a computational tool that can be used to reveal the biochemical steps that regulate signaling dynamics. PMID:21954150

LSENS, The NASA Lewis Kinetics and Sensitivity Analysis Code

NASA Technical Reports Server (NTRS)

Radhakrishnan, K.

2000-01-01

A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS (the NASA Lewis kinetics and sensitivity analysis code), are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include: static system; steady, one-dimensional, inviscid flow; incident-shock initiated reaction in a shock tube; and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method (LSODE, the Livermore Solver for Ordinary Differential Equations), which works efficiently for the extremes of very fast and very slow reactions, is used to solve the "stiff" ordinary differential equation systems that arise in chemical kinetics. For static reactions, the code uses the decoupled direct method to calculate sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters. Solution methods for the equilibrium and post-shock conditions and for perfectly stirred reactor problems are either adapted from or based on the procedures built into the NASA code CEA (Chemical Equilibrium and Applications).

Extension of the quantum-kinetic model to lunar and Mars return physics

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

Liechty, D. S.; Lewis, M. J.

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high-mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. A recently introduced molecular-level chemistry model, the quantum-kinetic, or Q-K, model that predicts reaction rates for gases in thermal equilibrium and non-equilibrium using only kinetic theory and fundamental molecular properties, is extended in the current work to include electronic energy level transitions and reactions involving charged particles. Like the Q-K procedures for neutral species chemical reactions, these new models are phenomenological procedures that aimmore » to reproduce the reaction/transition rates but do not necessarily capture the exact physics. These engineering models are necessarily efficient due to the requirement to compute billions of simulated collisions in direct simulation Monte Carlo (DSMC) simulations. The new models are shown to generally agree within the spread of reported transition and reaction rates from the literature for near equilibrium conditions.« less

The Nature of the Interplay among Components of Pedagogical Content Knowledge in Reaction Rate and Chemical Equilibrium Topics of Novice and Experienced Chemistry Teachers

ERIC Educational Resources Information Center

Akin, Fatma Nur; Uzuntiryaki-Kondakci, Esen

2018-01-01

We examined the interactions among pedagogical content knowledge (PCK) components of novice and experienced chemistry teachers in teaching reaction rate and chemical equilibrium topics in this qualitative multiple-case design study. For this aim, three chemistry teachers who had different levels of teaching experience in chemistry teaching were…

A density functional theory study on the adsorption and decomposition of methanol on B12N12 fullerene-like nanocage

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Nurazar, Roghaye

2014-03-01

The adsorption and dissociative reaction of methanol on B12N12 fullerene-like nanocage is investigated by using density functional calculations. Equilibrium geometries, adsorption energies, and electronic properties of CH3OH adsorption on the surface of the B12N12 were identified. The calculated adsorption energies range from -1.3 to -34.9 kcal/mol. It is found that the electrical conductivity of the nanocage can be modified upon the adsorption of CH3OH. The mechanism of methanol decomposition via CO and OH bond scissions is also studied. The results indicate that OH bond scission is the most favorable pathway on the B12N12 surface.

A generalized chemistry version of SPARK

NASA Technical Reports Server (NTRS)

Carpenter, Mark H.

1988-01-01

An extension of the reacting H2-air computer code SPARK is presented, which enables the code to be used on any reacting flow problem. Routines are developed calculating in a general fashion, the reaction rates, and chemical Jacobians of any reacting system. In addition, an equilibrium routine is added so that the code will have frozen, finite rate, and equilibrium capabilities. The reaction rate for the species is determined from the law of mass action using Arrhenius expressions for the rate constants. The Jacobian routines are determined by numerically or analytically differentiating the law of mass action for each species. The equilibrium routine is based on a Gibbs free energy minimization routine. The routines are written in FORTRAN 77, with special consideration given to vectorization. Run times for the generalized routines are generally 20 percent slower than reaction specific routines. The numerical efficiency of the generalized analytical Jacobian, however, is nearly 300 percent better than the reaction specific numerical Jacobian used in SPARK.

Modification of a method-of-characteristics solute-transport model to incorporate decay and equilibrium-controlled sorption or ion exchange

USGS Publications Warehouse

Goode, D.J.; Konikow, Leonard F.

1989-01-01

The U.S. Geological Survey computer model of two-dimensional solute transport and dispersion in ground water (Konikow and Bredehoeft, 1978) has been modified to incorporate the following types of chemical reactions: (1) first-order irreversible rate-reaction, such as radioactive decay; (2) reversible equilibrium-controlled sorption with linear, Freundlich, or Langmuir isotherms; and (3) reversible equilibrium-controlled ion exchange for monovalent or divalent ions. Numerical procedures are developed to incorporate these processes in the general solution scheme that uses method-of- characteristics with particle tracking for advection and finite-difference methods for dispersion. The first type of reaction is accounted for by an exponential decay term applied directly to the particle concentration. The second and third types of reactions are incorporated through a retardation factor, which is a function of concentration for nonlinear cases. The model is evaluated and verified by comparison with analytical solutions for linear sorption and decay, and by comparison with other numerical solutions for nonlinear sorption and ion exchange.

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.

Review and analysis of high temperature chemical reactions and the effect of non-equilibrium conditions

NASA Technical Reports Server (NTRS)

Johnson, R. E.

1986-01-01

Chemical reactions at high temperatures have been considered extensively because of their importance to the heating effects on re-entry of space vehicles. Data on these reactions however, are not abundant and even when found there are discrepancies in data collected by various investigators. In particular, data for recombination reactions are calculated from the dissociation reactions or vice versa through the equilibrium constant. This involves the use of the principle of detailed balancing. This principle is discussed in reference to conditions where it is valid as well as to those where it is not valid. Related topics that merit further study or for which applicable information was available are briefly mentioned in an appendix to this report.

Recommendations for terminology and databases for biochemical thermodynamics.

PubMed

Alberty, Robert A; Cornish-Bowden, Athel; Goldberg, Robert N; Hammes, Gordon G; Tipton, Keith; Westerhoff, Hans V

2011-05-01

Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K' for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction Δ(r)G'°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation Δ(f)G(i)'° of reactants, which can be calculated from the standard Gibbs energies of formation of species Δ(f)G(j)° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of Δ(r)G'° of reactions and Δ(f)G(i)'° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K' can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature. Copyright © 2011 Elsevier B.V. All rights reserved.

Distance-dependent diffusion-controlled reaction of •NO and O2•- at chemical equilibrium with ONOO-.

PubMed

Botti, Horacio; Möller, Matías N; Steinmann, Daniel; Nauser, Thomas; Koppenol, Willem H; Denicola, Ana; Radi, Rafael

2010-12-16

The fast reaction of (•)NO and O(2)(•-) to give ONOO(-) has been extensively studied at irreversible conditions, but the reasons for the wide variations in observed forward rate constants (3.8 ≤ k(f) ≤ 20 × 10(9) M(-1) s(-1)) remain unexplained. We characterized the diffusion-dependent aqueous (pH > 12) chemical equilibrium of the form (•)NO + O(2)(•-) = ONOO(-) with respect to its dependence on temperature, viscosity, and [ONOO(-)](eq) by determining [ONOO(-)](eq) and [(•)NO](eq). The equilibrium forward reaction rate constant (k(f)(eq)) has negative activation energy, in contrast to that found under irreversible conditions. In contradiction to the law of mass action, we demonstrate that the equilibrium constant depends on ONOO(-) concentration. Therefore, a wide range of k(f)(eq) values could be derived (7.5-21 × 10(9) M(-1) s(-1)). Of general interest, the variations in k(f) can thus be explained by its dependence on the distance between ONOO(-) particles (sites of generation of (•)NO and O(2)(•-)).

A Colorful Demonstration to Visualize and Inquire into Essential Elements of Chemical Equilibrium

ERIC Educational Resources Information Center

Eilks, Ingo; Gulacar, Ozcan

2016-01-01

One of the topics that chemistry teachers have a great challenge introducing is chemical equilibrium. When being introduced to chemical equilibrium, many students have difficulties in understanding that some reactions do not go to completion, as this contrasts most of their supposed prior experiences in chemistry lessons. Students may also…

Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of “hunger hormone” ghrelin

NASA Astrophysics Data System (ADS)

Yao, Jianzhuang; Yuan, Yaxia; Zheng, Fang; Zhan, Chang-Guo

2016-02-01

Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.4 kcal/mol), suggesting that the obtained mechanistic insights are reasonable. The single-step reaction pathway for the acylation is remarkably different from the well-known two-step acylation reaction pathway for numerous ester hydrolysis reactions catalyzed by a serine esterase. This is the first time demonstrating that a single-step reaction pathway is possible for an ester hydrolysis reaction catalyzed by a serine esterase and, therefore, one no longer can simply assume that the acylation process must follow the well-known two-step reaction pathway.

Modeling multicomponent ion exchange equilibrium utilizing hydrous crystalline silicotitanates by a multiple interactive ion exchange site model

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

Zheng, Z.; Anthony, R.G.; Miller, J.E.

1997-06-01

An equilibrium multicomponent ion exchange model is presented for the ion exchange of group I metals by TAM-5, a hydrous crystalline silicotitanate. On the basis of the data from ion exchange and structure studies, the solid phase is represented as Na{sub 3}X instead of the usual form of NaX. By using this solid phase representation, the solid can be considered as an ideal phase. A set of model ion exchange reactions is proposed for ion exchange between H{sup +}, Na{sup +}, K{sup +}, Rb{sup +}, and Cs{sup +}. The equilibrium constants for these reactions were estimated from experiments with simplemore » ion exchange systems. Bromley`s model for activity coefficients of electrolytic solutions was used to account for liquid phase nonideality. Bromley`s model parameters for CsOH at high ionic strength and for NO{sub 2}{sup {minus}} and Al(OH){sub 4}{sup {minus}} were estimated in order to apply the model for complex waste simulants. The equilibrium compositions and distribution coefficients of counterions were calculated for complex simulants typical of DOE wastes by solving the equilibrium equations for the model reactions and material balance equations. The predictions match the experimental results within 10% for all of these solutions.« less

Mesoscale simulations of shockwave energy dissipation via chemical reactions.

PubMed

Antillon, Edwin; Strachan, Alejandro

2015-02-28

We use a particle-based mesoscale model that incorporates chemical reactions at a coarse-grained level to study the response of materials that undergo volume-reducing chemical reactions under shockwave-loading conditions. We find that such chemical reactions can attenuate the shockwave and characterize how the parameters of the chemical model affect this behavior. The simulations show that the magnitude of the volume collapse and velocity at which the chemistry propagates are critical to weaken the shock, whereas the energetics in the reactions play only a minor role. Shock loading results in transient states where the material is away from local equilibrium and, interestingly, chemical reactions can nucleate under such non-equilibrium states. Thus, the timescales for equilibration between the various degrees of freedom in the material affect the shock-induced chemistry and its ability to attenuate the propagating shock.

Morphological Transformation between Nanocoils and Nanoribbons via Defragmentation Structural Rearrangement or Fragmentation-recombination Mechanism

NASA Astrophysics Data System (ADS)

Zhang, Yibin; Zheng, Yingxuan; Xiong, Wei; Peng, Cheng; Zhang, Yifan; Duan, Ran; Che, Yanke; Zhao, Jincai

2016-06-01

Kinetic control over the assembly pathways towards novel metastable functional materials or far-from-equilibrium systems has been much less studied compared to the thermodynamic equilibrium self-assembly. Herein, we report the distinct morphological transformation between nanocoils and nanoribbons in the self-assembly of unsymmetric perylene diimide (PDI) molecules. We demonstrate that the morphological transformation of the kinetically trapped assemblies into the thermodynamically stable forms proceeds via two distinct mechanisms, i.e., a direct structural rearrangement (molecule 1 or 2) and a fragmentation-recombination mechanism (molecule 4), respectively. The subtle interplay of the steric hindrance of the bulky substituents and the flexibility of the linker structure between the bulky moiety and the perylene core was demonstrated to enable the effective modulation of the energetic landscape of the assemblies and thus modulation of the assembly pathways. Herein, our work presents a new approach to control the self-assembly pathways and thereby can be used to achieve novel far-from-equilibrium systems.

Enhanced chlorine dioxide decay in the presence of metal oxides: relevance to drinking water distribution systems.

PubMed

Liu, Chao; von Gunten, Urs; Croué, Jean-Philippe

2013-08-06

Chlorine dioxide (ClO2) decay in the presence of typical metal oxides occurring in distribution systems was investigated. Metal oxides generally enhanced ClO2 decay in a second-order process via three pathways: (1) catalytic disproportionation with equimolar formation of chlorite and chlorate, (2) reaction to chlorite and oxygen, and (3) oxidation of a metal in a reduced form (e.g., cuprous oxide) to a higher oxidation state. Cupric oxide (CuO) and nickel oxide (NiO) showed significantly stronger abilities than goethite (α-FeOOH) to catalyze the ClO2 disproportionation (pathway 1), which predominated at higher initial ClO2 concentrations (56-81 μM). At lower initial ClO2 concentrations (13-31 μM), pathway 2 also contributed. The CuO-enhanced ClO2 decay is a base-assisted reaction with a third-order rate constant of 1.5 × 10(6) M(-2) s(-1) in the presence of 0.1 g L(-1) CuO at 21 ± 1 °C, which is 4-5 orders of magnitude higher than in the absence of CuO. The presence of natural organic matter (NOM) significantly enhanced the formation of chlorite and decreased the ClO2 disproportionation in the CuO-ClO2 system, probably because of a higher reactivity of CuO-activated ClO2 with NOM. Furthermore, a kinetic model was developed to simulate CuO-enhanced ClO2 decay at various pH values. Model simulations that agree well with the experimental data include a pre-equilibrium step with the rapid formation of a complex, namely, CuO-activated Cl2O4. The reaction of this complex with OH(-) is the rate-limiting and pH-dependent step for the overall reaction, producing chlorite and an intermediate that further forms chlorate and oxygen in parallel. These novel findings suggest that the possible ClO2 loss and the formation of chlorite/chlorate should be carefully considered in drinking water distribution systems containing copper pipes.

Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Gō-model simulation

PubMed Central

Gu, Zhenyu; Rao, Maithreyi K.; Forsyth, William R.

2009-01-01

The structures of partially-folded states appearing during the folding of a (βα)8 TIM barrel protein, the indole-3-glycerol phosphate synthase from S. solfataricus (sIGPS), was assessed by hydrogen exchange mass spectrometry (HX-MS) and Gō-model simulations. HX-MS analysis of the peptic peptides derived from the pulse-labeled product of the sub-millisecond folding reaction from the urea-denatured state revealed strong protection in the (βα)4 region, modest protection in the neighboring (βα)1–3 and (βα)5β6 segments and no significant protection in the remaining N- and C-terminal segments. These results demonstrate that this species is not a collapsed form of the unfolded state under native-favoring conditions nor is it the native state formed via fast-track folding. However, the striking contrast of these results with the strong protection observed in the (βα)2–5β6 region after 5 s of folding demonstrates that these species represent kinetically-distinct folding intermediates that are not identical as previously thought. A re-examination of the kinetic folding mechanism by chevron analysis of fluorescence data confirmed distinct roles for these two species: the burst-phase intermediate is predicted to be a misfolded, off-pathway intermediate while the subsequent 5 s intermediate corresponds to an on-pathway equilibrium intermediate. Comparison with the predictions using a Cα Gō-model simulation of the kinetic folding reaction for sIGPS shows good agreement with the core of structure offering protection against exchange in the on-pathway intermediate(s). Because the native-centric Gō-model simulations do not explicitly include sequence-specific information, the simulation results support the hypothesis that the topology of TIM barrel proteins is a primary determinant of the folding free energy surface for the productive folding reaction. The early misfolding reaction must involve aspects of non-native structure not detected by the Gō-model simulation. PMID:17942114

Heat capacity and entropy of fayalite (Fe2SiO4) between 5.1 and 383 K: comparison of calorimetric and equilibrium valus for the QFM buffer reaction.

USGS Publications Warehouse

Robie, R.A.; Finch, C.B.; Hemingway, B.S.

1982-01-01

At 298.15 K, 017Cop and So are 131.9 and 151.0 J/(mole.K). Also 045DELTA Hof,298 = -1478.17 and 045DELTA Gof,298 = -1378.98 kJ/mole. The temperature dependence of the equilibrium constant for the quartz - fayalite - magnetite buffer reaction is thus calculated.-K.A.R.

Dynamic Disorder in Quasi-Equilibrium Enzymatic Systems

PubMed Central

Chaudhury, Srabanti; Igoshin, Oleg A.

2010-01-01

Conformations and catalytic rates of enzymes fluctuate over a wide range of timescales. Despite these fluctuations, there exist some limiting cases in which the enzymatic catalytic rate follows the macroscopic rate equation such as the Michaelis-Menten law. In this paper we investigate the applicability of macroscopic rate laws for fluctuating enzyme systems in which catalytic transitions are slower than ligand binding-dissociation reactions. In this quasi-equilibrium limit, for an arbitrary reaction scheme we show that the catalytic rate has the same dependence on ligand concentrations as obtained from mass-action kinetics even in the presence of slow conformational fluctuations. These results indicate that the timescale of conformational dynamics – no matter how slow – will not affect the enzymatic rate in quasi-equilibrium limit. Our numerical results for two enzyme-catalyzed reaction schemes involving multiple substrates and inhibitors further support our general theory. PMID:20808776

State-to-State Internal Energy Relaxation Following the Quantum-Kinetic Model in DSMC

NASA Technical Reports Server (NTRS)

Liechty, Derek S.

2014-01-01

A new model for chemical reactions, the Quantum-Kinetic (Q-K) model of Bird, has recently been introduced that does not depend on macroscopic rate equations or values of local flow field data. Subsequently, the Q-K model has been extended to include reactions involving charged species and electronic energy level transitions. Although this is a phenomenological model, it has been shown to accurately reproduce both equilibrium and non-equilibrium reaction rates. The usefulness of this model becomes clear as local flow conditions either exceed the conditions used to build previous models or when they depart from an equilibrium distribution. Presently, the applicability of the relaxation technique is investigated for the vibrational internal energy mode. The Forced Harmonic Oscillator (FHO) theory for vibrational energy level transitions is combined with the Q-K energy level transition model to accurately reproduce energy level transitions at a reduced computational cost compared to the older FHO models.

The intrinsic role of nanoconfinement in chemical equilibrium: evidence from DNA hybridization.

PubMed

Rubinovich, Leonid; Polak, Micha

2013-05-08

Recently we predicted that when a reaction involving a small number of molecules occurs in a nanometric-scale domain entirely segregated from the surrounding media, the nanoconfinement can shift the position of equilibrium toward products via reactant-product reduced mixing. In this Letter, we demonstrate how most-recently reported single-molecule fluorescence measurements of partial hybridization of ssDNA confined within nanofabricated chambers provide the first experimental confirmation of this entropic nanoconfinement effect. Thus, focusing separately on each occupancy-specific equilibrium constant, quantitatively reveals extra stabilization of the product upon decreasing the chamber occupancy or size. Namely, the DNA hybridization under nanoconfined conditions is significantly favored over the identical reaction occurring in bulk media with the same reactant concentrations. This effect, now directly verified for DNA, can be relevant to actual biological processes, as well as to diverse reactions occurring within molecular capsules, nanotubes, and other functional nanospaces.

Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

PubMed

Huang, Yiran; Zhong, Cheng; Lin, Hai Xiang; Huang, Jing

2016-01-01

Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions) by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.

Role of (n,2n) reactions in transmutation of long-lived fission products

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

Apse, V. A.; Kulikov, G. G., E-mail: ggkulikov@mephi.ru; Kulikov, E. G.

2016-12-15

The conditions under which (n,γ) and (n,2n) reactions can help or hinder each other in neutron transmutation of long-lived fission products (LLFPs) are considered. Isotopic and elemental transmutation for the main long-lived fission products, {sup 79}Se, {sup 93}Zr, {sup 99}Tc, {sup 107}Pd, {sup 126}Sn, {sup 129}I, and {sup 135}Cs, are considered. The effect of (n,2n) reactions on the equilibrium amount of nuclei of the transmuted isotope and the neutron consumption required for the isotope processing is estimated. The aim of the study is to estimate the influence of (n,2n) reactions on efficiency of neutron LLFP transmutation. The code TIME26 andmore » the libraries of evaluated nuclear data ABBN-93, JEF-PC, and JANIS system are applied. The following results are obtained: (1) The effect of (n,2n) reactions on the minimum number of neutrons required for transmutation and the equilibrium amount of LLFP nuclei is estimated. (2) It is demonstrated that, for three LLFP isotopes ({sup 126}Sn, {sup 129}I, and {sup 135}Cs), (n,γ) and (n,2n) reactions are partners facilitating neutron transmutation. The strongest effect of (n,2n) reaction is found for {sup 126}Sn transmutation (reduction of the neutron consumption by 49% and the equilibrium amount of nuclei by 19%).« less

Response to Contradiction: Conflict Resolution Strategies Used by Students in Solving Problems of Chemical Equilibrium.

ERIC Educational Resources Information Center

Niaz, Mansoor

2001-01-01

Illustrates how a novel problem of chemical equilibrium based on a closely related sequence of items can facilitate students' conceptual understanding. Students were presented with a chemical reaction in equilibrium to which a reactant was added as an external effect. Three studies were conducted to assess alternative conceptions. (Author/SAH)

Calculation of biochemical net reactions and pathways by using matrix operations.

PubMed Central

Alberty, R A

1996-01-01

Pathways for net biochemical reactions can be calculated by using a computer program that solves systems of linear equations. The coefficients in the linear equations are the stoichiometric numbers in the biochemical equations for the system. The solution of the system of linear equations is a vector of the stoichiometric numbers of the reactions in the pathway for the net reaction; this is referred to as the pathway vector. The pathway vector gives the number of times the various reactions have to occur to produce the desired net reaction. Net reactions may involve unknown numbers of ATP, ADP, and Pi molecules. The numbers of ATP, ADP, and Pi in a desired net reaction can be calculated in a two-step process. In the first step, the pathway is calculated by solving the system of linear equations for an abbreviated stoichiometric number matrix without ATP, ADP, Pi, NADred, and NADox. In the second step, the stoichiometric numbers in the desired net reaction, which includes ATP, ADP, Pi, NADred, and NADox, are obtained by multiplying the full stoichiometric number matrix by the calculated pathway vector. PMID:8804633

Calculations of Excitation Functions of Some Structural Fusion Materials for ( n, t) Reactions up to 50 MeV Energy

NASA Astrophysics Data System (ADS)

Tel, E.; Durgu, C.; Aktı, N. N.; Okuducu, Ş.

2010-06-01

Fusion serves an inexhaustible energy for humankind. Although there have been significant research and development studies on the inertial and magnetic fusion reactor technology, there is still a long way to go to penetrate commercial fusion reactors to the energy market. Tritium self-sufficiency must be maintained for a commercial power plant. For self-sustaining (D-T) fusion driver tritium breeding ratio should be greater than 1.05. So, the working out the systematics of ( n, t) reaction cross sections is of great importance for the definition of the excitation function character for the given reaction taking place on various nuclei at different energies. In this study, ( n, t) reactions for some structural fusion materials such as 27Al, 51V, 52Cr, 55Mn, and 56Fe have been investigated. The new calculations on the excitation functions of 27Al( n, t)25Mg, 51V( n, t)49Ti, 52Cr( n, t)50V, 55Mn( n, t)53Cr and 56Fe( n, t)54Mn reactions have been carried out up to 50 MeV incident neutron energy. In these calculations, the pre-equilibrium and equilibrium effects have been investigated. The pre-equilibrium calculations involve the new evaluated the geometry dependent hybrid model, hybrid model and the cascade exciton model. Equilibrium effects are calculated according to the Weisskopf-Ewing model. Also in the present work, we have calculated ( n, t) reaction cross-sections by using new evaluated semi-empirical formulas developed by Tel et al. at 14-15 MeV energy. The calculated results are discussed and compared with the experimental data taken from the literature.

Out-of-equilibrium catalysis of chemical reactions by electronic tunnel currents.

PubMed

Dzhioev, Alan A; Kosov, Daniel S; von Oppen, Felix

2013-04-07

We present an escape rate theory for current-induced chemical reactions. We use Keldysh nonequilibrium Green's functions to derive a Langevin equation for the reaction coordinate. Due to the out of equilibrium electronic degrees of freedom, the friction, noise, and effective temperature in the Langevin equation depend locally on the reaction coordinate. As an example, we consider the dissociation of diatomic molecules induced by the electronic current from a scanning tunnelling microscope tip. In the resonant tunnelling regime, the molecular dissociation involves two processes which are intricately interconnected: a modification of the potential energy barrier and heating of the molecule. The decrease of the molecular barrier (i.e., the current induced catalytic reduction of the barrier) accompanied by the appearance of the effective, reaction-coordinate-dependent temperature is an alternative mechanism for current-induced chemical reactions, which is distinctly different from the usual paradigm of pumping vibrational degrees of freedom.

Chemical bonding and the equilibrium composition of Grignard reagents in ethereal solutions.

PubMed

Henriques, André M; Barbosa, André G H

2011-11-10

A thorough analysis of the electronic structure and thermodynamic aspects of Grignard reagents and its associated equilibrium composition in ethereal solutions is performed. Considering methylmagnesium halides containing fluorine, chlorine, and bromine, we studied the neutral, charged, and radical species associated with their chemical equilibrium in solution. The ethereal solvents considered, tetrahydrofuran (THF) and ethyl ether (Et(2)O), were modeled using the polarizable continuum model (PCM) and also by explicit coordination to the Mg atoms in a cluster. The chemical bonding of the species that constitute the Grignard reagent is analyzed in detail with generalized valence bond (GVB) wave functions. Equilibrium constants were calculated with the DFT/M06 functional and GVB wave functions, yielding similar results. According to our calculations and existing kinetic and electrochemical evidence, the species R(•), R(-), (•)MgX, and RMgX(2)(-) must be present in low concentration in the equilibrium. We conclude that depending on the halogen, a different route must be followed to produce the relevant equilibrium species in each case. Chloride and bromide must preferably follow a "radical-based" pathway, and fluoride must follow a "carbanionic-based" pathway. These different mechanisms are contrasted against the available experimental results and are proven to be consistent with the existing thermodynamic data on the Grignard reagent equilibria.

Vibrational non-equilibrium in the hydrogen-oxygen reaction. Comparison with experiment

NASA Astrophysics Data System (ADS)

Skrebkov, Oleg V.

2015-03-01

A theoretical model is proposed for the chemical and vibrational kinetics of hydrogen oxidation based on consistent accounting of the vibrational non-equilibrium of the HO2 radical that forms as a result of the bimolecular recombination H+O2 → HO2. In the proposed model, the chain branching H+O2 = O+OH and inhibiting H+O2+M = HO2+M formal reactions are treated (in the terms of elementary processes) as a single multi-channel process of forming, intramolecular energy redistribution between modes, relaxation, and unimolecular decay of the comparatively long-lived vibrationally excited HO2 radical, which is able to react and exchange energy with the other components of the mixture. The model takes into account the vibrational non-equilibrium of the starting (primary) H2 and O2 molecules, as well as the most important molecular intermediates HO2, OH, O2(1Δ), and the main reaction product H2O. It is shown that the hydrogen-oxygen reaction proceeds in the absence of vibrational equilibrium, and the vibrationally excited HO2(v) radical acts as a key intermediate in a fundamentally important chain branching process and in the generation of electronically excited species O2(1Δ), O(1D), and OH(2Σ+). The calculated results are compared with the shock tube experimental data for strongly diluted H2-O2 mixtures at 1000 < T < 2500 K, 0.5 < p < 4 atm. It is demonstrated that this approach is promising from the standpoint of reconciling the predictions of the theoretical model with experimental data obtained by different authors for various compositions and conditions using different methods. For T < 1500 K, the nature of the hydrogen-oxygen reaction is especially non-equilibrium, and the vibrational non-equilibrium of the HO2 radical is the essence of this process. The quantitative estimation of the vibrational relaxation characteristic time of the HO2 radical in its collisions with H2 molecules has been obtained as a result of the comparison of different experimental data on induction time measurements with the relevant calculations.

Multivariate curve resolution of incomplete fused multiset data from chromatographic and spectrophotometric analyses for drug photostability studies.

PubMed

De Luca, Michele; Ragno, Gaetano; Ioele, Giuseppina; Tauler, Romà

2014-07-21

An advanced and powerful chemometric approach is proposed for the analysis of incomplete multiset data obtained by fusion of hyphenated liquid chromatographic DAD/MS data with UV spectrophotometric data from acid-base titration and kinetic degradation experiments. Column- and row-wise augmented data blocks were combined and simultaneously processed by means of a new version of the multivariate curve resolution-alternating least squares (MCR-ALS) technique, including the simultaneous analysis of incomplete multiset data from different instrumental techniques. The proposed procedure was applied to the detailed study of the kinetic photodegradation process of the amiloride (AML) drug. All chemical species involved in the degradation and equilibrium reactions were resolved and the pH dependent kinetic pathway described. Copyright © 2014 Elsevier B.V. All rights reserved.

A Mechanical Analogue for Chemical Potential, Extent of Reaction, and the Gibbs Energy.

ERIC Educational Resources Information Center

Glass, Samuel V.; DeKock, Roger L.

1998-01-01

Presents an analogy that relates the one-dimensional mechanical equilibrium of a rigid block between two Hooke's law springs and the chemical equilibrium of two perfect gases using ordinary materials. (PVD)

Direct structural evidence of protein redox regulation obtained by in-cell NMR.

PubMed

Mercatelli, Eleonora; Barbieri, Letizia; Luchinat, Enrico; Banci, Lucia

2016-02-01

The redox properties of cellular environments are critical to many functional processes, and are strictly controlled in all living organisms. The glutathione-glutathione disulfide (GSH-GSSG) couple is the most abundant intracellular redox couple. A GSH redox potential can be calculated for each cellular compartment, which reflects the redox properties of that environment. This redox potential is often used to predict the redox state of a disulfide-containing protein, based on thermodynamic considerations. However, thiol-disulfide exchange reactions are often catalyzed by specific partners, and the distribution of the redox states of a protein may not correspond to the thermodynamic equilibrium with the GSH pool. Ideally, the protein redox state should be measured directly, bypassing the need to extrapolate from the GSH. Here, by in-cell NMR, we directly observe the redox state of three human proteins, Cox17, Mia40 and SOD1, in the cytoplasm of human and bacterial cells. We compare the observed distributions of redox states with those predicted by the GSH redox potential, and our results partially agree with the predictions. Discrepancies likely arise from the fact that the redox state of SOD1 is controlled by a specific partner, its copper chaperone (CCS), in a pathway which is not linked to the GSH redox potential. In principle, in-cell NMR allows determining whether redox proteins are at the equilibrium with GSH, or they are kinetically regulated. Such approach does not need assumptions on the redox potential of the environment, and provides a way to characterize each redox-regulating pathway separately. Copyright © 2015 Elsevier B.V. All rights reserved.

Direct vs. indirect pathway for nitrobenzene reduction reaction on a Ni catalyst surface: a density functional study.

PubMed

Mahata, Arup; Rai, Rohit K; Choudhuri, Indrani; Singh, Sanjay K; Pathak, Biswarup

2014-12-21

Density functional theory (DFT) calculations are performed to understand and address the previous experimental results that showed the reduction of nitrobenzene to aniline prefers direct over indirect reaction pathways irrespective of the catalyst surface. Nitrobenzene to aniline conversion occurs via the hydroxyl amine intermediate (direct pathway) or via the azoxybenzene intermediate (indirect pathway). Through our computational study we calculated the spin polarized and dispersion corrected reaction energies and activation barriers corresponding to various reaction pathways for the reduction of nitrobenzene to aniline over a Ni catalyst surface. The adsorption behaviour of the substrate, nitrobenzene, on the catalyst surface was also considered and the energetically most preferable structural orientation was elucidated. Our study indicates that the parallel adsorption behaviour of the molecules over a catalyst surface is preferable over vertical adsorption behaviour. Based on the reaction energies and activation barrier of the various elementary steps involved in direct or indirect reaction pathways, we find that the direct reduction pathway of nitrobenzene over the Ni(111) catalyst surface is more favourable than the indirect reaction pathway.

Equilibrium I: Principles. Independent Learning Project for Advanced Chemistry (ILPAC). Unit P2.

ERIC Educational Resources Information Center

Inner London Education Authority (England).

This unit on the principles of equilibrium is one of 10 first year units produced by the Independent Learning Project for Advanced Chemistry (ILPAC). The unit consists of two levels. After a treatment of non-mathematical aspects in level one (the idea of a reversible reaction, characteristics of an equilibrium state, the Le Chatelier's principle),…

Fusion reactions initiated by laser-accelerated particle beams in a laser-produced plasma.

PubMed

Labaune, C; Baccou, C; Depierreux, S; Goyon, C; Loisel, G; Yahia, V; Rafelski, J

2013-01-01

The advent of high-intensity-pulsed laser technology enables the generation of extreme states of matter under conditions that are far from thermal equilibrium. This in turn could enable different approaches to generating energy from nuclear fusion. Relaxing the equilibrium requirement could widen the range of isotopes used in fusion fuels permitting cleaner and less hazardous reactions that do not produce high-energy neutrons. Here we propose and implement a means to drive fusion reactions between protons and boron-11 nuclei by colliding a laser-accelerated proton beam with a laser-generated boron plasma. We report proton-boron reaction rates that are orders of magnitude higher than those reported previously. Beyond fusion, our approach demonstrates a new means for exploring low-energy nuclear reactions such as those that occur in astrophysical plasmas and related environments.

Lateral interactions and non-equilibrium in surface kinetics

NASA Astrophysics Data System (ADS)

Menzel, Dietrich

2016-08-01

Work modelling reactions between surface species frequently use Langmuir kinetics, assuming that the layer is in internal equilibrium, and that the chemical potential of adsorbates corresponds to that of an ideal gas. Coverage dependences of reacting species and of site blocking are usually treated with simple power law coverage dependences (linear in the simplest case), neglecting that lateral interactions are strong in adsorbate and co-adsorbate layers which may influence kinetics considerably. My research group has in the past investigated many co-adsorbate systems and simple reactions in them. We have collected a number of examples where strong deviations from simple coverage dependences exist, in blocking, promoting, and selecting reactions. Interactions can range from those between next neighbors to larger distances, and can be quite complex. In addition, internal equilibrium in the layer as well as equilibrium distributions over product degrees of freedom can be violated. The latter effect leads to non-equipartition of energy over molecular degrees of freedom (for products) or non-equal response to those of reactants. While such behavior can usually be described by dynamic or kinetic models, the deeper reasons require detailed theoretical analysis. Here, a selection of such cases is reviewed to exemplify these points.

Oxygen isotope effects of enzyme-catalyzed organophosphorus hydrolysis reactions: implications for interpretation of dissolved PO4 δ18O values in natural waters

NASA Astrophysics Data System (ADS)

Liang, Y.; Blake, R. E.

2002-12-01

The geochemical cycling of P in Earth surface environments is controlled largely by biota. It has been recently demonstrated that intracellular cycling of P in microbial cultures and biological turnover of P in natural waters leads to temperature-dependent O isotope equilibrium between dissolved inorganic PO4 (Pi) and ambient water, and that the δ18O of Pi can be a useful tracer of biological reactions and P cycling in aquatic systems/sediments. Oxygen isotope exchange between Pi and water during biological turnover of P is catalyzed by enzymes at low-temperature. Phosphoenzymes play a crucial role in the intracellular functions of all living organisms and also have important extracellular functions in aquatic ecosystems such as regeneration of Pi from organophosphorus compounds (e.g., phosphoesters). Laboratory experiments indicate that extracellular enzyme reactions may result in incomplete Pi turnover and non-equilibrium Pi-water O isotope exchange. Determination of the O isotope effects of phosphoenzyme-catalyzed reactions is fundamental to the understanding of mechanisms of PO4-water O isotope exchange, pathways of biogeochemical P cycling, and interpretation of PO4 δ18O values from natural systems. Here we report on the O isotope fractionation between enzymatically-released Pi and water, in cell-free abiotic systems. Alkaline phosphatase (Apase) is a non-specific phosphohydrolase commonly found in fresh and marine coastal waters that catalyzes the hydrolysis of Pi from phosphomonoesters. We examined the O isotope effects of Apase derived from both microbial and eukaryotic sources and acting on different phosphomonoester substrates (e.g., α-D-Glucose 1-Phosphate, β-Glycerophosphate, AMP) in 18O-labeled waters. Oxygen isotope ratios of Pi released by Apase indicate that only 1 of the 4 O atoms in PO4 is incorporated from water with little or no apparent O isotopic fractionation at the site of incorporation. This observation is consistent with phosphomonoester structure and the Apase active site configuration and reaction mechanism. 5'-nucleotidase is another important phosphoenzyme identified in marine ecosystems. The O isotope effects of 5'-nucleotidase- catalyzed reactions will also be presented and implications of these results for interpretation of PO4 δ18O values in natural systems will be discussed.

Alternative ground states enable pathway switching in biological electron transfer

DOE PAGES

Abriata, Luciano A.; Alvarez-Paggi, Damian; Ledesma, Gabirela N.; ...

2012-10-10

Electron transfer is the simplest chemical reaction and constitutes the basis of a large variety of biological processes, such as photosynthesis and cellular respiration. Nature has evolved specific proteins and cofactors for these functions. The mechanisms optimizing biological electron transfer have been matter of intense debate, such as the role of the protein milieu between donor and acceptor sites. Here we propose a mechanism regulating long-range electron transfer in proteins. Specifically, we report a spectroscopic, electrochemical, and theoretical study on WT and single-mutant CuA redox centers from Thermus thermophilus, which shows that thermal fluctuations may populate two alternative ground-state electronicmore » wave functions optimized for electron entry and exit, respectively, through two different and nearly perpendicular pathways. In conclusion, these findings suggest a unique role for alternative or “invisible” electronic ground states in directional electron transfer. Moreover, it is shown that this energy gap and, therefore, the equilibrium between ground states can be fine-tuned by minor perturbations, suggesting alternative ways through which protein–protein interactions and membrane potential may optimize and regulate electron–proton energy transduction.« less

Implementation of a vibrationally linked chemical reaction model for DSMC

NASA Technical Reports Server (NTRS)

Carlson, A. B.; Bird, Graeme A.

1994-01-01

A new procedure closely linking dissociation and exchange reactions in air to the vibrational levels of the diatomic molecules has been implemented in both one- and two-dimensional versions of Direct Simulation Monte Carlo (DSMC) programs. The previous modeling of chemical reactions with DSMC was based on the continuum reaction rates for the various possible reactions. The new method is more closely related to the actual physics of dissociation and is more appropriate to the particle nature of DSMC. Two cases are presented: the relaxation to equilibrium of undissociated air initially at 10,000 K, and the axisymmetric calculation of shuttle forebody heating during reentry at 92.35 km and 7500 m/s. Although reaction rates are not used in determining the dissociations or exchange reactions, the new method produces rates which agree astonishingly well with the published rates derived from experiment. The results for gas properties and surface properties also agree well with the results produced by earlier DSMC models, equilibrium air calculations, and experiment.

Wave propagation in a quasi-chemical equilibrium plasma

NASA Technical Reports Server (NTRS)

Fang, T.-M.; Baum, H. R.

1975-01-01

Wave propagation in a quasi-chemical equilibrium plasma is studied. The plasma is infinite and without external fields. The chemical reactions are assumed to result from the ionization and recombination processes. When the gas is near equilibrium, the dominant role describing the evolution of a reacting plasma is played by the global conservation equations. These equations are first derived and then used to study the small amplitude wave motion for a near-equilibrium situation. Nontrivial damping effects have been obtained by including the conduction current terms.

Colorimetric Determination of the Iron(III)-Thiocyanate Reaction Equilibrium Constant with Calibration and Equilibrium Solutions Prepared in a Cuvette by Sequential Additions of One Reagent to the Other

ERIC Educational Resources Information Center

Nyasulu, Frazier; Barlag, Rebecca

2011-01-01

The well-known colorimetric determination of the equilibrium constant of the iron(III-thiocyanate complex is simplified by preparing solutions in a cuvette. For the calibration plot, 0.10 mL increments of 0.00100 M KSCN are added to 4.00 mL of 0.200 M Fe(NO[subscript 3])[subscript 3], and for the equilibrium solutions, 0.50 mL increments of…

Retinol esterification in bovine retinal pigment epithelium: reversibility of lecithin:retinol acyltransferase.

PubMed Central

Saari, J C; Bredberg, D L; Farrell, D F

1993-01-01

Esterification of all-trans-retinol is a key reaction of the vertebrate visual cycle, since it produces an insoluble, relatively non-toxic, form of the vitamin for storage and supplies substrate for the isomerization reaction. CoA-dependent and -independent pathways have been described for retinol esterification in retinal pigment epithelium (RPE). The CoA-independent reaction, catalysed by lecithin:retinol acyltransferase (LRAT) was examined in more detail in this study. Addition of retinol to RPE microsomes results in a burst of retinyl ester synthesis, followed by a rapid apparent cessation of the reaction. However, [3H]retinol, added when retinyl ester synthesis has apparently ceased, is rapidly incorporated into retinyl ester without a net increase in the amount of ester. The specific radioactivities of [3H]retinol and [3H]retinyl ester reach the same value. [14C]Palmitate from palmitoyl-CoA is incorporated into preexisting retinyl ester in the absence of net ester synthesis, too. These exchange reactions suggest that the reaction has reached equilibrium at the plateau of the progress curve and that only the accumulation of retinyl ester, and not its synthesis, has stopped during this phase of the reaction. Studies with geometrical isomers of retinol revealed that the rate of exchange of all-trans-retinol with all-trans-retinyl esters was about 6 times more rapid than exchange of 11-cis-retinol with 11-cis-retinyl ester. This is the first demonstration of the reversibility of LRAT and the first example of stereospecificity of retinyl ester synthesis in the visual system. Reversal of the LRAT reaction could contribute to the mobilization of 11-cis-retinol from 11-cis-retinyl ester pools. Images Figure 3 PMID:8489497

Statistical effects related to low numbers of reacting molecules analyzed for a reversible association reaction A + B = C in ideally dispersed systems: An apparent violation of the law of mass action

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

Szymanski, R., E-mail: rszymans@cbmm.lodz.pl; Sosnowski, S.; Maślanka, Ł.

2016-03-28

Theoretical analysis and computer simulations (Monte Carlo and numerical integration of differential equations) show that the statistical effect of a small number of reacting molecules depends on a way the molecules are distributed among the small volume nano-reactors (droplets in this study). A simple reversible association A + B = C was chosen as a model reaction, enabling to observe both thermodynamic (apparent equilibrium constant) and kinetic effects of a small number of reactant molecules. When substrates are distributed uniformly among droplets, all containing the same equal number of substrate molecules, the apparent equilibrium constant of the association is highermore » than the chemical one (observed in a macroscopic—large volume system). The average rate of the association, being initially independent of the numbers of molecules, becomes (at higher conversions) higher than that in a macroscopic system: the lower the number of substrate molecules in a droplet, the higher is the rate. This results in the correspondingly higher apparent equilibrium constant. A quite opposite behavior is observed when reactant molecules are distributed randomly among droplets: the apparent association rate and equilibrium constants are lower than those observed in large volume systems, being the lower, the lower is the average number of reacting molecules in a droplet. The random distribution of reactant molecules corresponds to ideal (equal sizes of droplets) dispersing of a reaction mixture. Our simulations have shown that when the equilibrated large volume system is dispersed, the resulting droplet system is already at equilibrium and no changes of proportions of droplets differing in reactant compositions can be observed upon prolongation of the reaction time.« less

In Situ Tracking Kinetic Pathways of Li+/Na+ Substitution during Ion-Exchange Synthesis of LixNa1.5-xVOPO4F0.5.

PubMed

Park, Young-Uk; Bai, Jianming; Wang, Liping; Yoon, Gabin; Zhang, Wei; Kim, Hyungsub; Lee, Seongsu; Kim, Sung-Wook; Looney, J Patrick; Kang, Kisuk; Wang, Feng

2017-09-13

Ion exchange is a ubiquitous phenomenon central to wide industrial applications, ranging from traditional (bio)chemical separation to the emerging chimie douce synthesis of materials with metastable structure for batteries and other energy applications. The exchange process is complex, involving substitution and transport of different ions under non-equilibrium conditions, and thus difficult to probe, leaving a gap in mechanistic understanding of kinetic exchange pathways toward final products. Herein, we report in situ tracking kinetic pathways of Li + /Na + substitution during solvothermal ion-exchange synthesis of Li x Na 1.5-x VOPO 4 F 0.5 (0 ≤ x ≤ 1.5), a promising multi-Li polyanionic cathode for batteries. The real-time observation, corroborated by first-principles calculations, reveals a selective replacement of Na + by Li + , leading to peculiar Na + /Li + /vacancy orderings in the intermediates. Contradicting the traditional belief of facile topotactic substitution via solid solution reaction, an abrupt two-phase transformation occurs and predominantly governs the kinetics of ion exchange and transport in the 1D polyanionic framework, consequently leading to significant difference of Li stoichiometry and electrochemical properties in the exchanged products. The findings may help to pave the way for rational design of ion exchange synthesis for making new materials.

Remarkable nanoconfinement effects on chemical equilibrium manifested in nucleotide dimerization and H-D exchange reactions.

PubMed

Polak, Micha; Rubinovich, Leonid

2011-10-06

Nanoconfinement entropic effects on chemical equilibrium involving a small number of molecules, which we term NCECE, are revealed by two widely diverse types of reactions. Employing statistical-mechanical principles, we show how the NCECE effect stabilizes nucleotide dimerization observed within self-assembled molecular cages. Furthermore, the effect provides the basis for dimerization even under an aqueous environment inside the nanocage. Likewise, the NCECE effect is pertinent to a longstanding issue in astrochemistry, namely the extra deuteration commonly observed for molecules reacting on interstellar dust grain surfaces. The origin of the NCECE effect is elucidated by means of the probability distributions of the reaction extent and related variations in the reactant-product mixing entropy. Theoretical modelling beyond our previous preliminary work highlights the role of the nanospace size in addition to that of the nanosystem size, namely the limited amount of molecules in the reaction mixture. Furthermore, the NCECE effect can depend also on the reaction mechanism, and on deviations from stoichiometry. The NCECE effect, leading to enhanced, greatly variable equilibrium "constants", constitutes a unique physical-chemical phenomenon, distinguished from the usual thermodynamical properties of macroscopically large systems. Being significant particularly for weakly exothermic reactions, the effects should stabilize products in other closed nanoscale structures, and thus can have notable implications for the growing nanotechnological utilization of chemical syntheses conducted within confined nanoreactors.

Co-solvent effects on reaction rate and reaction equilibrium of an enzymatic peptide hydrolysis.

PubMed

Wangler, A; Canales, R; Held, C; Luong, T Q; Winter, R; Zaitsau, D H; Verevkin, S P; Sadowski, G

2018-04-25

This work presents an approach that expresses the Michaelis constant KaM and the equilibrium constant Kth of an enzymatic peptide hydrolysis based on thermodynamic activities instead of concentrations. This provides KaM and Kth values that are independent of any co-solvent. To this end, the hydrolysis reaction of N-succinyl-l-phenylalanine-p-nitroanilide catalysed by the enzyme α-chymotrypsin was studied in pure buffer and in the presence of the co-solvents dimethyl sulfoxide, trimethylamine-N-oxide, urea, and two salts. A strong influence of the co-solvents on the measured Michaelis constant (KM) and equilibrium constant (Kx) was observed, which was found to be caused by molecular interactions expressed as activity coefficients. Substrate and product activity coefficients were used to calculate the activity-based values KaM and Kth for the co-solvent free reaction. Based on these constants, the co-solvent effect on KM and Kx was predicted in almost quantitative agreement with the experimental data. The approach presented here does not only reveal the importance of understanding the thermodynamic non-ideality of reactions taking place in biological solutions and in many technological applications, it also provides a framework for interpreting and quantifying the multifaceted co-solvent effects on enzyme-catalysed reactions that are known and have been observed experimentally for a long time.

A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo.

PubMed

Ruminski, Dana J; Watson, Peter Y; Mahen, Elisabeth M; Fedor, Martha J

2016-03-01

RNAs must assemble into specific structures in order to carry out their biological functions, but in vitro RNA folding reactions produce multiple misfolded structures that fail to exchange with functional structures on biological time scales. We used carefully designed self-cleaving mRNAs that assemble through well-defined folding pathways to identify factors that differentiate intracellular and in vitro folding reactions. Our previous work showed that simple base-paired RNA helices form and dissociate with the same rate and equilibrium constants in vivo and in vitro. However, exchange between adjacent secondary structures occurs much faster in vivo, enabling RNAs to quickly adopt structures with the lowest free energy. We have now used this approach to probe the effects of an extensively characterized DEAD-box RNA helicase, Mss116p, on a series of well-defined RNA folding steps in yeast. Mss116p overexpression had no detectable effect on helix formation or dissociation kinetics or on the stability of interdomain tertiary interactions, consistent with previous evidence that intracellular factors do not affect these folding parameters. However, Mss116p overexpression did accelerate exchange between adjacent helices. The nonprocessive nature of RNA duplex unwinding by DEAD-box RNA helicases is consistent with a branch migration mechanism in which Mss116p lowers barriers to exchange between otherwise stable helices by the melting and annealing of one or two base pairs at interhelical junctions. These results suggest that the helicase activity of DEAD-box proteins like Mss116p distinguish intracellular RNA folding pathways from nonproductive RNA folding reactions in vitro and allow RNA structures to overcome kinetic barriers to thermodynamic equilibration in vivo. © 2016 Ruminski et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

THE KINETICS AND THERMODYNAMICS OF REVERSIBLE DENATURATION OF CRYSTALLINE SOYBEAN TRYPSIN INHIBITOR

PubMed Central

Kunitz, M.

1948-01-01

Crystalline soybean trypsin inhibitor protein undergoes denaturation on heating which is reversed on cooling. In the range of temperature of 35 to 50°C. a solution of the protein consists of a mixture of native and denatured forms in equilibrium with each other. The equilibrium is only slowly established and its final value at any temperature is the same whether a heated, denatured solution of the protein is cooled to the given temperature or whether a fresh solution is raised to that temperature. The kinetics of reversible denaturation of the soybean protein as well as the reversal of denaturation is that of a reversible unimolecular reaction, each process consisting at a given temperature of the same two simultaneous reactions acting in opposite directions. The experimental data on the effect of temperature on the velocity and the equilibrium constants of the opposing reaction were utilized in evaluating the reaction energies and activation energies. The reaction energies for denaturation were found to be as follows:— Change in total heat of reaction ΔH = 57,000 calories per mole Change in entropy of reaction ΔS = 180 calories per degree per mole The heat of activation ΔH 1 ‡ for denaturation = 55,000 The heat of activation ΔH 2 ‡ for the reversal of denaturation = –1900 The entropy ΔS 1 ‡ for denaturation = 95 The entropy ΔS 2 ‡ for reversal of denaturation = –84 PMID:18891149

Molecular Mechanisms of Stress-Responsive Changes in Collagen and Elastin Networks in Skin.

PubMed

Aziz, Jazli; Shezali, Hafiz; Radzi, Zamri; Yahya, Noor Azlin; Abu Kassim, Noor Hayaty; Czernuszka, Jan; Rahman, Mohammad Tariqur

2016-01-01

Collagen and elastin networks make up the majority of the extracellular matrix in many organs, such as the skin. The mechanisms which are involved in the maintenance of homeostatic equilibrium of these networks are numerous, involving the regulation of genetic expression, growth factor secretion, signalling pathways, secondary messaging systems, and ion channel activity. However, many factors are capable of disrupting these pathways, which leads to an imbalance of homeostatic equilibrium. Ultimately, this leads to changes in the physical nature of skin, both functionally and cosmetically. Although various factors have been identified, including carcinogenesis, ultraviolet exposure, and mechanical stretching of skin, it was discovered that many of them affect similar components of regulatory pathways, such as fibroblasts, lysyl oxidase, and fibronectin. Additionally, it was discovered that the various regulatory pathways intersect with each other at various stages instead of working independently of each other. This review paper proposes a model which elucidates how these molecular pathways intersect with one another, and how various internal and external factors can disrupt these pathways, ultimately leading to a disruption in collagen and elastin networks. © 2016 S. Karger AG, Basel.

Reaction rates of oxygen with hemoglobin measured by non-equilibrium facilitated oxygen diffusion through hemoglobin solutions.

PubMed

Bouwer, S T; Hoofd, L; Kreuzer, F

2001-02-16

The purpose of this study was to verify the concept of non-equilibrium facilitated oxygen diffusion. This work succeeds our previous study, where facilitated oxygen diffusion by hemoglobin was measured at conditions of chemical equilibrium, and which yielded diffusion coefficients of hemoglobin and of oxygen. In the present work chemical non-equilibrium was induced using very thin diffusion layers. As a result, facilitation was decreased as predicted by theory. Thus, this work presents the first experimental demonstration of non-equilibrium facilitated oxygen diffusion. In addition, association and dissociation rate parameters of the reaction between oxygen and bovine and human hemoglobin were calculated and the effect of the homotropic and heterotropic interactions on each rate parameter was demonstrated. The results indicate that the homotropic interaction--which leads to increasing oxygen affinity with increasing oxygenation--is predominantly due to an increase in the association rate. The heterotropic interaction--which leads to decreasing oxygen affinity by anionic ligands--appears to be effected in two ways. Cl- increases the dissociation rate. In contrast, 2,3-diphosphoglycerate decreases the association rate.

Electrochemical Transfer of S Between Molten Steel and Molten Slag

NASA Astrophysics Data System (ADS)

Kim, Dong-Hyun; Kim, Wook; Kang, Youn-Bae

2018-06-01

S transfer between molten steel and molten slag was investigated in view of the electrochemical character of S transfer. C-saturated molten steel containing S was allowed to react with CaO-SiO2-Al2O3-MgO slag at 1673 K (1400 °C) until the two phases arrive at a chemical equilibrium. The application of an electric field of constant current through graphite electrodes lowered the S content in the molten steel below its chemical equilibrium level, and the system arrived at a new equilibrium level (electrochemical equilibrium). However, subsequent shutting off of the electric field did not lead to the system reverting to the original chemical equilibrium: reversion of S was observed but to a limited extent. The application of an electric field of opposite direction or flowing of CO gas allowed significant reversion of S. Side reactions (decomposition of oxide components) were observed, and these were considered to be coupled to the transfer of S. An electrochemical reaction mechanism was proposed based on the experimental observations found in the present study.

Sub-Ensemble Monitoring of DNA Strand Displacement Using Multiparameter Single-Molecule FRET.

PubMed

Baltierra-Jasso, Laura E; Morten, Michael J; Magennis, Steven W

2018-03-05

Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here, we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constant of 10 m -1  s -1 . We also followed the displacement from a DNA three-way junction (3WJ) by ssDNA. The presence of three internal mismatched bases in the middle of the invading strand did not prevent displacement from the 3WJ, but reduced the second-order rate constant by about 50 %. We attribute strand exchange in the dsDNA and 3WJ to a zero-toehold pathway from the blunt-ended duplex arms. The single-molecule approach demonstrated here will be useful for studying complex DNA networks. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets

PubMed Central

Kotera, Masaaki; Tabei, Yasuo; Yamanishi, Yoshihiro; Tokimatsu, Toshiaki; Goto, Susumu

2013-01-01

Motivation: The metabolic pathway is an important biochemical reaction network involving enzymatic reactions among chemical compounds. However, it is assumed that a large number of metabolic pathways remain unknown, and many reactions are still missing even in known pathways. Therefore, the most important challenge in metabolomics is the automated de novo reconstruction of metabolic pathways, which includes the elucidation of previously unknown reactions to bridge the metabolic gaps. Results: In this article, we develop a novel method to reconstruct metabolic pathways from a large compound set in the reaction-filling framework. We define feature vectors representing the chemical transformation patterns of compound–compound pairs in enzymatic reactions using chemical fingerprints. We apply a sparsity-induced classifier to learn what we refer to as ‘enzymatic-reaction likeness’, i.e. whether compound pairs are possibly converted to each other by enzymatic reactions. The originality of our method lies in the search for potential reactions among many compounds at a time, in the extraction of reaction-related chemical transformation patterns and in the large-scale applicability owing to the computational efficiency. In the results, we demonstrate the usefulness of our proposed method on the de novo reconstruction of 134 metabolic pathways in Kyoto Encyclopedia of Genes and Genomes (KEGG). Our comprehensively predicted reaction networks of 15 698 compounds enable us to suggest many potential pathways and to increase research productivity in metabolomics. Availability: Softwares are available on request. Supplementary material are available at http://web.kuicr.kyoto-u.ac.jp/supp/kot/ismb2013/. Contact: goto@kuicr.kyoto-u.ac.jp PMID:23812977

A density functional theory study of the decomposition mechanism of nitroglycerin.

PubMed

Pei, Liguan; Dong, Kehai; Tang, Yanhui; Zhang, Bo; Yu, Chang; Li, Wenzuo

2017-08-21

The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition was investigated at the B3LYP/6-31G(d,p) level of theory. Five possible decomposition pathways involving NG were identified and the rate constants for the pathways at temperatures ranging from 200 to 1000 K were calculated using CVT/SCT. There was found to be a lower energy barrier to the β-H abstraction reaction than to the α-H abstraction reaction during the initial step in the autocatalytic decomposition of NG. The decomposition pathways for CHOCOCHONO 2 (a product obtained following the abstraction of three H atoms from NG by NO 2 ) include O-NO 2 cleavage or isomer production, meaning that the autocatalytic decomposition of NG has two reaction pathways, both of which are exothermic. The rate constants for these two reaction pathways are greater than the rate constants for the three pathways corresponding to unimolecular NG decomposition. The overall process of NG decomposition can be divided into two stages based on the NO 2 concentration, which affects the decomposition products and reactions. In the first stage, the reaction pathway corresponding to O-NO 2 cleavage is the main pathway, but the rates of the two autocatalytic decomposition pathways increase with increasing NO 2 concentration. However, when a threshold NO 2 concentration is reached, the NG decomposition process enters its second stage, with the two pathways for NG autocatalytic decomposition becoming the main and secondary reaction pathways.

Numerical Problem Solving Using Mathcad in Undergraduate Reaction Engineering

ERIC Educational Resources Information Center

Parulekar, Satish J.

2006-01-01

Experience in using a user-friendly software, Mathcad, in the undergraduate chemical reaction engineering course is discussed. Example problems considered for illustration deal with simultaneous solution of linear algebraic equations (kinetic parameter estimation), nonlinear algebraic equations (equilibrium calculations for multiple reactions and…

Solitosynthesis: Cosmological evolution of non-topological solitons

NASA Technical Reports Server (NTRS)

Griest, Kim; Kolb, Edward W.

1989-01-01

The thermal creation, fusion, evaporation, and destruction of non-topological solitons (NTS) after a phase transition in the early universe is considered. By defining and following NTS statistical equilibrium and departures from it, and depending on particle physics parameters, one of three possible scenarios occurs. If reaction rates are high enough, a period of equilibrium occurs and relic abundances are determined by the freeze-out temperature. Equilibrium first drives most NTS's into their constituents (free phi particles) and then causes rapid fusion into large NTS's. If freeze-out occurs during the first phase, the NTS's are almost entirely destroyed, while if it occurs during the second phase, solitosynthesis occurs and NTS's may be cosmically relevant. For slow reaction rates the NTS's are born frozen out and have the abundance determined by the phase transition. Analytic approximations for determining the abundances are developed, and tested by numerically integrating a reaction network in an expanding universe. Unfortunately, for most of the parameter space considered, solito-destruction/evaporation occurs.

Assessment of tautomer distribution using the condensed reaction graph approach

NASA Astrophysics Data System (ADS)

Gimadiev, T. R.; Madzhidov, T. I.; Nugmanov, R. I.; Baskin, I. I.; Antipin, I. S.; Varnek, A.

2018-03-01

We report the first direct QSPR modeling of equilibrium constants of tautomeric transformations (logK T ) in different solvents and at different temperatures, which do not require intermediate assessment of acidity (basicity) constants for all tautomeric forms. The key step of the modeling consisted in the merging of two tautomers in one sole molecular graph ("condensed reaction graph") which enables to compute molecular descriptors characterizing entire equilibrium. The support vector regression method was used to build the models. The training set consisted of 785 transformations belonging to 11 types of tautomeric reactions with equilibrium constants measured in different solvents and at different temperatures. The models obtained perform well both in cross-validation (Q2 = 0.81 RMSE = 0.7 logK T units) and on two external test sets. Benchmarking studies demonstrate that our models outperform results obtained with DFT B3LYP/6-311 ++ G(d,p) and ChemAxon Tautomerizer applicable only in water at room temperature.

How important is thermodynamics for identifying elementary flux modes?

PubMed Central

Peres, Sabine; Jolicœur, Mario; Moulin, Cécile

2017-01-01

We present a method for computing thermodynamically feasible elementary flux modes (tEFMs) using equilibrium constants without need of internal metabolite concentrations. The method is compared with the method based on a binary distinction between reversible and irreversible reactions. When all reactions are reversible, adding the constraints based on equilibrium constants reduces the number of elementary flux modes (EFMs) by a factor of two. Declaring in advance some reactions as irreversible, based on reliable biochemical expertise, can in general reduce the number of EFMs by a greater factor. But, even in this case, computing tEFMs can rule out some EFMs which are biochemically irrelevant. We applied our method to two published models described with binary distinction: the monosaccharide metabolism and the central carbon metabolism of Chinese hamster ovary cells. The results show that the binary distinction is in good agreement with biochemical observations. Moreover, the suppression of the EFMs that are not consistent with the equilibrium constants appears to be biologically relevant. PMID:28222104

Latent curing systems stabilized by reaction equilibrium in homogeneous mixtures of benzoxazine and amine

PubMed Central

Wang, Jun; Xu, Ya Zhen; Fu, Ya Fei; Liu, Xiang Dong

2016-01-01

Latent curing systems are widely used in industrial thermosets in applications such as adhesion, coating, and composites. Despite many attempts to improve the practicality of this dormant reaction system, the majority of commercially available latent products still use particulate hardeners or liquid compounds with blocked active groups. These formulations generally lack fluidity or rapid reaction characteristics and thus are problematic in some industry applications. Here we describe a novel concept that stabilizes highly reactive benzoxazine/amine mixtures by reaction equilibrium. These new latent benzoxazine curing systems have a long storable lifetime but very short gel time at 150 °C. The reversible reaction between benzoxazine and amine is further demonstrated by FT-IR spectral measurements and rheological experiments, and it is shown that the overall characteristics of the latent system are promising for many industrial applications. PMID:27917932

Deoxygenation of Palmitic and Lauric Acids over Pt/ZIF-67 Membrane/Zeolite 5A Bead Catalysts.

PubMed

Yang, Liqiu; Carreon, Moises A

2017-09-20

The deoxygenation of palmitic and lauric acids over 0.5 wt % Pt/ZIF-67 membrane/zeolite 5A bead catalysts is demonstrated. Almost complete conversion (% deoxygenation of ≥95%) of these two fatty acids was observed over both fresh and recycled catalyst after a 2 h reaction time. The catalysts displayed high selectivity to pentadecane and undecane via decarboxylation reaction pathway even at low 0.5 wt % Pt loading. Selectivity to pentadecane and undecane as high as ∼92% and ∼94% was observed under CO 2 atmosphere when palmitic and lauric acids were used respectively as reactants. Depending on the reaction gas atmosphere, two distinctive reaction pathways were observed: decarboxylation and hydrodeoxygenation. Specifically, it was found that decarboxylation reaction pathway was more favorable in the presence of helium and CO 2 , while hydrodeoxygenation pathway strongly competed against the decarboxylation pathway when hydrogen was employed during the deoxygenation reactions. Esters were identified as the key reaction intermediates leading to decarboxylation and hydrodeoxygenation pathways.

The use of analytical sedimentation velocity to extract thermodynamic linkage.

PubMed

Cole, James L; Correia, John J; Stafford, Walter F

2011-11-01

For 25 years, the Gibbs Conference on Biothermodynamics has focused on the use of thermodynamics to extract information about the mechanism and regulation of biological processes. This includes the determination of equilibrium constants for macromolecular interactions by high precision physical measurements. These approaches further reveal thermodynamic linkages to ligand binding events. Analytical ultracentrifugation has been a fundamental technique in the determination of macromolecular reaction stoichiometry and energetics for 85 years. This approach is highly amenable to the extraction of thermodynamic couplings to small molecule binding in the overall reaction pathway. In the 1980s this approach was extended to the use of sedimentation velocity techniques, primarily by the analysis of tubulin-drug interactions by Na and Timasheff. This transport method necessarily incorporates the complexity of both hydrodynamic and thermodynamic nonideality. The advent of modern computational methods in the last 20 years has subsequently made the analysis of sedimentation velocity data for interacting systems more robust and rigorous. Here we review three examples where sedimentation velocity has been useful at extracting thermodynamic information about reaction stoichiometry and energetics. Approaches to extract linkage to small molecule binding and the influence of hydrodynamic nonideality are emphasized. These methods are shown to also apply to the collection of fluorescence data with the new Aviv FDS. Copyright © 2011 Elsevier B.V. All rights reserved.

The use of analytical sedimentation velocity to extract thermodynamic linkage

PubMed Central

Cole, James L.; Correia, John J.; Stafford, Walter F.

2011-01-01

For 25 years, the Gibbs Conference on Biothermodynamics has focused on the use of thermodynamics to extract information about the mechanism and regulation of biological processes. This includes the determination of equilibrium constants for macromolecular interactions by high precision physical measurements. These approaches further reveal thermodynamic linkages to ligand binding events. Analytical ultracentrifugation has been a fundamental technique in the determination of macromolecular reaction stoichiometry and energetics for 85 years. This approach is highly amenable to the extraction of thermodynamic couplings to small molecule binding in the overall reaction pathway. In the 1980’s this approach was extended to the use of sedimentation velocity techniques, primarily by the analysis of tubulin-drug interactions by Na and Timasheff. This transport method necessarily incorporates the complexity of both hydrodynamic and thermodynamic nonideality. The advent of modern computational methods in the last 20 years has subsequently made the analysis of sedimentation velocity data for interacting systems more robust and rigorous. Here we review three examples where sedimentation velocity has been useful at extracting thermodynamic information about reaction stoichiometry and energetics. Approaches to extract linkage to small molecule binding and the influence of hydrodynamic nonideality are emphasized. These methods are shown to also apply to the collection of fluorescence data with the new Aviv FDS. PMID:21703752

The mechanism for enhanced oxidation degradation of dioxin-like PCBs (PCB-77) in the atmosphere by the solvation effect.

PubMed

Xin, Mei-Ling; Yang, Jia-Wen; Li, Yu

2017-07-11

The reaction pathways of PCB-77 in the atmosphere with ·OH, O 2 , NO x , and 1 O 2 were inferred based on density functional theory calculations with the 6-31G* basis set. The structures the reactants, transition states, intermediates, and products were optimized. The energy barriers and reaction heats were obtained to determine the energetically favorable reaction pathways. To study the solvation effect, the energy barriers and reaction rates for PCB-77 with different polar and nonpolar solvents (cyclohexane, benzene, carbon tetrachloride, chloroform, acetone, dichloromethane, ethanol, methanol, acetonitrile, dimethylsulfoxide, and water) were calculated. The results showed that ·OH preferentially added to the C5 atom of PCB-77, which has no Cl atom substituent, to generate the intermediate IM5. This intermediate subsequently reacted with O 2 via pathway A to generate IM5a, with an energy barrier of 7.27 kcal/mol and total reaction rate of 8.45 × 10 -8  cm 3 /molecule s. Pathway B involved direct dehydrogenation of IM5 to produce the OH-PCBs intermediate IM5b, with an energy barrier of 28.49 kcal/mol and total reaction rate of 1.15 × 10 -5  cm 3 /molecule s. The most likely degradation pathway of PCB-77 in the atmosphere is pathway A to produce IM5a. The solvation effect results showed that cyclohexane, carbon tetrachloride, and benzene could reduce the reaction energy barrier of pathway A. Among these solvents, the solvation effect of benzene was the largest, and could reduce the total reaction energy barrier by 25%. Cyclohexane, carbon tetrachloride, benzene, dichloromethane, acetone, and ethanol could increase the total reaction rate of pathway A. The increase in the reaction rate of pathway A with benzene was 8%. The effect of solvents on oxidative degradation of PCB-77 in the atmosphere is important. Graphical abstract The reaction pathways of PCB-77 in the atmosphere with •OH, O2, NOx, and 1O2 were inferred based on density functional theory calculations with the 6-31G* basis set. Different polar and nonpolar solvents: cyclohexane, benzene, carbon tetrachloride, chloroform, acetone, dichloromethane, ethanol, methanol, acetonitrile, dimethylsulfoxide, and water were selected to study the solvation effect on the favorable reaction pathways. The investigated results showed what kind of pathway was most likely to occur and the solvent effect on the reaction pathway.

An overlapping region between the two terminal folding units of the outer surface protein A (OspA) controls its folding behavior.

PubMed

Makabe, Koki; Nakamura, Takashi; Dhar, Debanjan; Ikura, Teikichi; Koide, Shohei; Kuwajima, Kunihiro

2018-04-27

Although many naturally occurring proteins consist of multiple domains, most studies on protein folding to date deal with single-domain proteins or isolated domains of multi-domain proteins. Studies of multi-domain protein folding are required for further advancing our understanding of protein folding mechanisms. Borrelia outer surface protein A (OspA) is a β-rich two-domain protein, in which two globular domains are connected by a rigid and stable single-layer β-sheet. Thus, OspA is particularly suited as a model system for studying the interplays of domains in protein folding. Here, we studied the equilibria and kinetics of the urea-induced folding-unfolding reactions of OspA probed with tryptophan fluorescence and ultraviolet circular dichroism. Global analysis of the experimental data revealed compelling lines of evidence for accumulation of an on-pathway intermediate during kinetic refolding and for the identity between the kinetic intermediate and a previously described equilibrium unfolding intermediate. The results suggest that the intermediate has the fully native structure in the N-terminal domain and the single layer β-sheet, with the C-terminal domain still unfolded. The observation of the productive on-pathway folding intermediate clearly indicates substantial interactions between the two domains mediated by the single-layer β-sheet. We propose that a rigid and stable intervening region between two domains creates an overlap between two folding units and can energetically couple their folding reactions. Copyright © 2018. Published by Elsevier Ltd.

Understanding the interplay of weak forces in [3,3]-sigmatropic rearrangement for stereospecific synthesis of diamines.

PubMed

So, Soon Mog; Mui, Leo; Kim, Hyunwoo; Chin, Jik

2012-08-21

Chiral diamines are important building blocks for constructing stereoselective catalysts, including transition metal based catalysts and organocatalysts that facilitate oxidation, reduction, hydrolysis, and C-C bond forming reactions. These molecules are also critical components in the synthesis of drugs, including antiviral agents such as Tamiflu and Relenza and anticancer agents such as oxaliplatin and nutlin-3. The diaza-Cope rearrangement reaction provides one of the most versatile methods for rapidly generating a wide variety of chiral diamines stereospecifically and under mild conditions. Weak forces such as hydrogen bonding, electronic, steric, oxyanionic, and conjugation effects can drive this equilibrium process to completion. In this Account, we examine the effect of these individual weak forces on the value of the equilibrium constant for the diaza-Cope rearrangement reaction using both computational and experimental methods. The availability of a wide variety of aldehydes and diamines allows for the facile synthesis of the diimines needed to study the weak forces. Furthermore, because the reaction generally takes place cleanly at ambient temperature, we can easily measure equilibrium constants for rearrangement of the diimines. We use the Hammett equation to further examine the electronic and oxyanionic effects. In addition, computations and experiments provide us with new insights into the origin and extent of stereospecificity for this rearrangement reaction. The diaza-Cope rearrangement, with its unusual interplay between weak forces and the equilibrium constant of the reaction, provides a rare opportunity to study the effects of the fundamental weak forces on a chemical reaction. Among these many weak forces that affect the diaza-Cope rearrangement, the anion effect is the strongest (10.9 kcal/mol) followed by the resonance-assisted hydrogen-bond effect (7.1 kcal/mol), the steric effect (5.7 kcal/mol), the conjugation effect (5.5 kcal/mol), and the electronic effect (3.2 kcal/mol). Based on both computation and experimental data, the effects of these weak forces are additive. Understanding the interplay of the weak forces in the [3,3]-sigmatropic reaction is interesting in its own right and also provides valuable insights for the synthesis of chiral diamine based drugs and catalysts in excellent yield and enantiopurity.

The Art of the Lecture Revisited.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1983

1983-01-01

Lecturing hints, periodic table, mechanistic approach to predicting inorganic reaction products for substitution reactions, reaction rates, spectroscopy, and entropy role change in establishing position of equilibrium for vaporization of water and synthesis of ammonia were topics of lectures presented at the Seventh Biennial Conference on Chemical…

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics.

PubMed

Chapman, Brian

2017-06-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis-Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis- substrate binding, cis → trans bound enzyme shuttling, trans -substrate dissociation and trans → cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive 'tuning' of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force-flux relations, with only a minority of cases having their quasi -linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically 'tuned' to its particular task, dependent on the cis- and trans- substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics

PubMed Central

2017-01-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis–Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis-substrate binding, cis→trans bound enzyme shuttling, trans-substrate dissociation and trans→cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive ‘tuning’ of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force–flux relations, with only a minority of cases having their quasi-linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically ‘tuned’ to its particular task, dependent on the cis- and trans-substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport. PMID:28680687

Energy spectrum of 208Pb(n,x) reactions

NASA Astrophysics Data System (ADS)

Tel, E.; Kavun, Y.; Özdoǧan, H.; Kaplan, A.

2018-02-01

Fission and fusion reactor technologies have been investigated since 1950's on the world. For reactor technology, fission and fusion reaction investigations are play important role for improve new generation technologies. Especially, neutron reaction studies have an important place in the development of nuclear materials. So neutron effects on materials should study as theoretically and experimentally for improve reactor design. For this reason, Nuclear reaction codes are very useful tools when experimental data are unavailable. For such circumstances scientists created many nuclear reaction codes such as ALICE/ASH, CEM95, PCROSS, TALYS, GEANT, FLUKA. In this study we used ALICE/ASH, PCROSS and CEM95 codes for energy spectrum calculation of outgoing particles from Pb bombardment by neutron. While Weisskopf-Ewing model has been used for the equilibrium process in the calculations, full exciton, hybrid and geometry dependent hybrid nuclear reaction models have been used for the pre-equilibrium process. The calculated results have been discussed and compared with the experimental data taken from EXFOR.

Formation of nitric acid hydrates - A chemical equilibrium approach

NASA Technical Reports Server (NTRS)

Smith, Roland H.

1990-01-01

Published data are used to calculate equilibrium constants for reactions of the formation of nitric acid hydrates over the temperature range 190 to 205 K. Standard enthalpies of formation and standard entropies are calculated for the tri- and mono-hydrates. These are shown to be in reasonable agreement with earlier calorimetric measurements. The formation of nitric acid trihydrate in the polar stratosphere is discussed in terms of these equilibrium constants.

Spontaneity and Equilibrium: Why "?G < 0 Denotes a Spontaneous Process" and "?G = 0 Means the System Is at Equilibrium" Are Incorrect

ERIC Educational Resources Information Center

Raff, Lionel M.

2014-01-01

The fundamental criteria for chemical reactions to be spontaneous in a given direction are generally incorrectly stated as ?G < 0 or ?A < 0 in most introductory chemistry textbooks and even in some more advanced texts. Similarly, the criteria for equilibrium are also misstated as being ?G = 0 or ?A = 0. Following a brief review of the…

The Role of Glutamine Synthetase and Glutamate Dehydrogenase in Cerebral Ammonia Homeostasis

PubMed Central

Cooper, Arthur J. L.

2012-01-01

In the brain, glutamine synthetase (GS), which is located predominantly in astrocytes, is largely responsible for the removal of both blood-derived and metabolically generated ammonia. Thus, studies with [13N]ammonia have shown that about 25% of blood-derived ammonia is removed in a single pass through the rat brain and that this ammonia is incorporated primarily into glutamine (amide) in astrocytes. Major pathways for cerebral ammonia generation include the glutaminase reaction and the glutamate dehydrogenase (GDH) reaction. The equilibrium position of the GDH-catalyzed reaction in vitro favors reductive amination of α-ketoglutarate at pH 7.4. Nevertheless, only a small amount of label derived from [13N]ammonia in rat brain is incorporated into glutamate and the α-amine of glutamine in vivo. Most likely the cerebral GDH reaction is drawn normally in the direction of glutamate oxidation (ammonia production) by rapid removal of ammonia as glutamine. Linkage of glutamate/α-ketoglutarate-utilizing aminotransferases with the GDH reaction channels excess amino acid nitrogen toward ammonia for glutamine synthesis. At high ammonia levels and/or when GS is inhibited the GDH reaction coupled with glutamate/α-ketoglutarate-linked aminotransferases may, however, promote the flow of ammonia nitrogen toward synthesis of amino acids. Preliminary evidence suggests an important role for the purine nucleotide cycle (PNC) as an additional source of ammonia in neurons (Net reaction: L-Aspartate + GTP + H2O → Fumarate + GDP + Pi + NH3) and in the beat cycle of ependyma cilia. The link of the PNC to aminotransferases and GDH/GS and its role in cerebral nitrogen metabolism under both normal and pathological (e.g. hyperammonemic encephalopathy) conditions should be a productive area for future research. PMID:22618691

Techniques used to study the DNA polymerase reaction pathway

PubMed Central

Joyce, Catherine M.

2009-01-01

Summary A minimal reaction pathway for DNA polymerases was established over 20 years ago using chemical quench methods. Since that time there has been considerable interest in noncovalent steps in the reaction pathway, conformational changes involving the polymerase or its DNA substrate that may play a role in substrate specificity. Fluorescence-based assays have been devised in order to study these conformational transitions and the results obtained have added new detail to the reaction pathway. PMID:19665596

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.

Confinement Effects on Carbon Dioxide Methanation: A Novel Mechanism for Abiotic Methane Formation

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

Le, Thu; Striolo, Alberto; Turner, C. Heath

An important scientific debate focuses on the possibility of abiotic synthesis of hydrocarbons during oceanic crust-seawater interactions. While on-site measurements near hydrothermal vents support this possibility, laboratory studies have provided data that are in some cases contradictory. At conditions relevant for sub-surface environments it has been shown that classic thermodynamics favour the production of CO 2 from CH 4, while abiotic methane synthesis would require the opposite. However, confinement effects are known to alter reaction equilibria. This report shows that indeed thermodynamic equilibrium can be shifted towards methane production, suggesting that thermal hydrocarbon synthesis near hydrothermal vents and deeper inmore » the magma-hydrothermal system is possible. We report reactive ensemble Monte Carlo simulations for the CO 2 methanation reaction. We compare the predicted equilibrium composition in the bulk gaseous phase to that expected in the presence of confinement. In the bulk phase we obtain excellent agreement with classic thermodynamic expectations. When the reactants can exchange between bulk and a confined phase our results show strong dependency of the reaction equilibrium conversions, X CO2, on nanopore size, nanopore chemistry, and nanopore morphology. Some physical conditions that could shift significantly the equilibrium composition of the reactive system with respect to bulk observations are discussed.« less

Confinement Effects on Carbon Dioxide Methanation: A Novel Mechanism for Abiotic Methane Formation

DOE PAGES

Le, Thu; Striolo, Alberto; Turner, C. Heath; ...

2017-08-21

An important scientific debate focuses on the possibility of abiotic synthesis of hydrocarbons during oceanic crust-seawater interactions. While on-site measurements near hydrothermal vents support this possibility, laboratory studies have provided data that are in some cases contradictory. At conditions relevant for sub-surface environments it has been shown that classic thermodynamics favour the production of CO 2 from CH 4, while abiotic methane synthesis would require the opposite. However, confinement effects are known to alter reaction equilibria. This report shows that indeed thermodynamic equilibrium can be shifted towards methane production, suggesting that thermal hydrocarbon synthesis near hydrothermal vents and deeper inmore » the magma-hydrothermal system is possible. We report reactive ensemble Monte Carlo simulations for the CO 2 methanation reaction. We compare the predicted equilibrium composition in the bulk gaseous phase to that expected in the presence of confinement. In the bulk phase we obtain excellent agreement with classic thermodynamic expectations. When the reactants can exchange between bulk and a confined phase our results show strong dependency of the reaction equilibrium conversions, X CO2, on nanopore size, nanopore chemistry, and nanopore morphology. Some physical conditions that could shift significantly the equilibrium composition of the reactive system with respect to bulk observations are discussed.« less

State-to-state modeling of non-equilibrium air nozzle flows

NASA Astrophysics Data System (ADS)

Nagnibeda, E.; Papina, K.; Kunova, O.

2018-05-01

One-dimensional non-equilibrium air flows in nozzles are studied on the basis of the state-to-state description of vibrational-chemical kinetics. Five-component mixture N2/O2/NO/N/O is considered taking into account Zeldovich exchange reactions of NO formation, dissociation, recombination and vibrational energy transitions. The equations for vibrational and chem-ical kinetics in a flow are coupled to the conservation equations of momentum and total energy and solved numerically for different conditions in a nozzle throat. The vibrational distributions of nitrogen and oxygen molecules, number densities of species as well as the gas temperature and flow velocity along a nozzle axis are analysed using the detailed state-to-state flow description and in the frame of the simplified one-temperature thermal equilibrium kinetic model. The comparison of the results showed the influence of non-equilibrium kinetics on macroscopic nozzle flow parameters. In the state-to-state approach, non-Boltzmann vibrational dis-tributions of N2 and O2 molecules with a plateau part at intermediate levels are found. The results are found with the use of the complete and simplified schemes of reactions and the impact of exchange reactions, dissociation and recombination on variation of vibrational level populations, mixture composition, gas velocity and temperature along a nozzle axis is shown.

Reactive solute transport in streams: 1. Development of an equilibrium- based model

USGS Publications Warehouse

Runkel, Robert L.; Bencala, Kenneth E.; Broshears, Robert E.; Chapra, Steven C.

1996-01-01

An equilibrium-based solute transport model is developed for the simulation of trace metal fate and transport in streams. The model is formed by coupling a solute transport model with a chemical equilibrium submodel based on MINTEQ. The solute transport model considers the physical processes of advection, dispersion, lateral inflow, and transient storage, while the equilibrium submodel considers the speciation and complexation of aqueous species, precipitation/dissolution and sorption. Within the model, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (water-borne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach.

DSMC modeling of flows with recombination reactions

NASA Astrophysics Data System (ADS)

Gimelshein, Sergey; Wysong, Ingrid

2017-06-01

An empirical microscopic recombination model is developed for the direct simulation Monte Carlo method that complements the extended weak vibrational bias model of dissociation. The model maintains the correct equilibrium reaction constant in a wide range of temperatures by using the collision theory to enforce the number of recombination events. It also strictly follows the detailed balance requirement for equilibrium gas. The model and its implementation are verified with oxygen and nitrogen heat bath relaxation and compared with available experimental data on atomic oxygen recombination in argon and molecular nitrogen.

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.

New constraints on kinetic isotope effects during CO2(aq) hydration and hydroxylation: Revisiting theoretical and experimental data

NASA Astrophysics Data System (ADS)

Sade, Ziv; Halevy, Itay

2017-10-01

CO2 (de)hydration (i.e., CO2 hydration/HCO3- dehydration) and (de)hydroxylation (i.e., CO2 hydroxylation/HCO3- dehydroxylation) are key reactions in the dissolved inorganic carbon (DIC) system. Kinetic isotope effects (KIEs) during these reactions are likely to be expressed in the DIC and recorded in carbonate minerals formed during CO2 degassing or dissolution of gaseous CO2. Thus, a better understanding of KIEs during CO2 (de)hydration and (de)hydroxylation would improve interpretations of disequilibrium compositions in carbonate minerals. To date, the literature lacks direct experimental constraints on most of the oxygen KIEs associated with these reactions. In addition, theoretical estimates describe oxygen KIEs during separate individual reactions. The KIEs of the related reverse reactions were neither derived directly nor calculated from a link to the equilibrium fractionation. Consequently, KIE estimates of experimental and theoretical studies have been difficult to compare. Here we revisit experimental and theoretical data to provide new constraints on oxygen KIEs during CO2 (de)hydration and (de)hydroxylation. For this purpose, we provide a clearer definition of the KIEs and relate them both to isotopic rate constants and equilibrium fractionations. Such relations are well founded in studies of single isotope source/sink reactions, but they have not been established for reactions that involve dual isotopic sources/sinks, such as CO2 (de)hydration and (de)hydroxylation. We apply the new quantitative constraints on the KIEs to investigate fractionations during simultaneous CaCO3 precipitation and HCO3- dehydration far from equilibrium.

Noise-induced modulation of the relaxation kinetics around a non-equilibrium steady state of non-linear chemical reaction networks.

PubMed

Ramaswamy, Rajesh; Sbalzarini, Ivo F; González-Segredo, Nélido

2011-01-28

Stochastic effects from correlated noise non-trivially modulate the kinetics of non-linear chemical reaction networks. This is especially important in systems where reactions are confined to small volumes and reactants are delivered in bursts. We characterise how the two noise sources confinement and burst modulate the relaxation kinetics of a non-linear reaction network around a non-equilibrium steady state. We find that the lifetimes of species change with burst input and confinement. Confinement increases the lifetimes of all species that are involved in any non-linear reaction as a reactant. Burst monotonically increases or decreases lifetimes. Competition between burst-induced and confinement-induced modulation may hence lead to a non-monotonic modulation. We quantify lifetime as the integral of the time autocorrelation function (ACF) of concentration fluctuations around a non-equilibrium steady state of the reaction network. Furthermore, we look at the first and second derivatives of the ACF, each of which is affected in opposite ways by burst and confinement. This allows discriminating between these two noise sources. We analytically derive the ACF from the linear Fokker-Planck approximation of the chemical master equation in order to establish a baseline for the burst-induced modulation at low confinement. Effects of higher confinement are then studied using a partial-propensity stochastic simulation algorithm. The results presented here may help understand the mechanisms that deviate stochastic kinetics from its deterministic counterpart. In addition, they may be instrumental when using fluorescence-lifetime imaging microscopy (FLIM) or fluorescence-correlation spectroscopy (FCS) to measure confinement and burst in systems with known reaction rates, or, alternatively, to correct for the effects of confinement and burst when experimentally measuring reaction rates.

Assessment of Stable Isotope Distribution in Complex Systems

NASA Astrophysics Data System (ADS)

He, Y.; Cao, X.; Wang, J.; Bao, H.

2017-12-01

Biomolecules in living organisms have the potential to approach chemical steady state and even apparent isotope equilibrium because enzymatic reactions are intrinsically reversible. If an apparent local equilibrium can be identified, enzymatic reversibility and its controlling factors may be quantified, which helps to understand complex biochemical processes. Earlier research on isotope fractionation tends to focus on specific process and compare mostly two different chemical species. Using linear regression, "Thermodynamic order", which refers to correlated δ13C and 13β values, has been proposed to be present among many biomolecules by Galimov et al. However, the concept "thermodynamic order" they proposed and the approach they used has been questioned. Here, we propose that the deviation of a complex system from its equilibrium state can be rigorously described as a graph problem as is applied in discrete mathematics. The deviation of isotope distribution from equilibrium state and apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference matrix (|Δα|). Applying the |Δα| matrix analysis to earlier published data of amino acids, we show the existence of apparent local equilibrium among different amino acids in potato and a kind of green alga. The existence of apparent local equilibrium is in turn consistent with the notion that enzymatic reactions can be reversible even in living systems. The result also implies that previous emphasis on external carbon source intake may be misplaced when studying isotope distribution in physiology. In addition to the identification of local equilibrium among biomolecules, the difference matrix approach has the potential to explore chemical or isotope equilibrium state in extraterrestrial bodies, to distinguish living from non-living systems, and to classify living species. This approach will benefit from large numbers of systematic data and advanced pattern recognition techniques.

Tested Demonstrations: Thermodynamic Changes, Kinetics, Equilibrium, and LeChatelier's Principle.

ERIC Educational Resources Information Center

Gilbert, George L., Ed.

1984-01-01

Procedures for demonstrating thermodynamic changes, kinetics and reaction mechanisms, equilibrium, and LeChatelier's principle are presented. The only materials needed for these demonstrations are beakers, water, assorted wooden blocks of varying thickness, assorted rubber tubing, and a sponge. The concepts illustrated in each demonstration are…

A Study of Interactions between Mixing and Chemical Reaction Using the Rate-Controlled Constrained-Equilibrium Method

NASA Astrophysics Data System (ADS)

Hadi, Fatemeh; Janbozorgi, Mohammad; Sheikhi, M. Reza H.; Metghalchi, Hameed

2016-10-01

The rate-controlled constrained-equilibrium (RCCE) method is employed to study the interactions between mixing and chemical reaction. Considering that mixing can influence the RCCE state, the key objective is to assess the accuracy and numerical performance of the method in simulations involving both reaction and mixing. The RCCE formulation includes rate equations for constraint potentials, density and temperature, which allows taking account of mixing alongside chemical reaction without splitting. The RCCE is a dimension reduction method for chemical kinetics based on thermodynamics laws. It describes the time evolution of reacting systems using a series of constrained-equilibrium states determined by RCCE constraints. The full chemical composition at each state is obtained by maximizing the entropy subject to the instantaneous values of the constraints. The RCCE is applied to a spatially homogeneous constant pressure partially stirred reactor (PaSR) involving methane combustion in oxygen. Simulations are carried out over a wide range of initial temperatures and equivalence ratios. The chemical kinetics, comprised of 29 species and 133 reaction steps, is represented by 12 RCCE constraints. The RCCE predictions are compared with those obtained by direct integration of the same kinetics, termed detailed kinetics model (DKM). The RCCE shows accurate prediction of combustion in PaSR with different mixing intensities. The method also demonstrates reduced numerical stiffness and overall computational cost compared to DKM.

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

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

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a ``glass like`` material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

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

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a glass like'' material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

Entropy Generation in a Chemical Reaction

ERIC Educational Resources Information Center

Miranda, E. N.

2010-01-01

Entropy generation in a chemical reaction is analysed without using the general formalism of non-equilibrium thermodynamics at a level adequate for advanced undergraduates. In a first approach to the problem, the phenomenological kinetic equation of an elementary first-order reaction is used to show that entropy production is always positive. A…

Chemical Reactions of Molecules Promoted and Simultaneously Imaged by the Electron Beam in Transmission Electron Microscopy.

PubMed

Skowron, Stephen T; Chamberlain, Thomas W; Biskupek, Johannes; Kaiser, Ute; Besley, Elena; Khlobystov, Andrei N

2017-08-15

The main objective of this Account is to assess the challenges of transmission electron microscopy (TEM) of molecules, based on over 15 years of our work in this field, and to outline the opportunities in studying chemical reactions under the electron beam (e-beam). During TEM imaging of an individual molecule adsorbed on an atomically thin substrate, such as graphene or a carbon nanotube, the e-beam transfers kinetic energy to atoms of the molecule, displacing them from equilibrium positions. Impact of the e-beam triggers bond dissociation and various chemical reactions which can be imaged concurrently with their activation by the e-beam and can be presented as stop-frame movies. This experimental approach, which we term ChemTEM, harnesses energy transferred from the e-beam to the molecule via direct interactions with the atomic nuclei, enabling accurate predictions of bond dissociation events and control of the type and rate of chemical reactions. Elemental composition and structure of the reactant molecules as well as the operating conditions of TEM (particularly the energy of the e-beam) determine the product formed in ChemTEM processes, while the e-beam dose rate controls the reaction rate. Because the e-beam of TEM acts simultaneously as a source of energy for the reaction and as an imaging tool monitoring the same reaction, ChemTEM reveals atomic-level chemical information, such as pathways of reactions imaged for individual molecules, step-by-step and in real time; structures of illusive reaction intermediates; and direct comparison of catalytic activity of different transition metals filmed with atomic resolution. Chemical transformations in ChemTEM often lead to previously unforeseen products, demonstrating the potential of this method to become not only an analytical tool for studying reactions, but also a powerful instrument for discovery of materials that can be synthesized on preparative scale.

Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model

NASA Astrophysics Data System (ADS)

Glowacki, David R.; Orr-Ewing, Andrew J.; Harvey, Jeremy N.

2015-07-01

We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ˜23 kcal mol-1 localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral blue shift, while relaxation of the post-reaction solvation environment results in a red shift. These two competing effects mean that the post-reaction relaxation profile is distinct from what is observed when Franck-Condon vibrational excitation of DF occurs within a microsolvation environment initially at equilibrium. Our conclusions, along with the theoretical and parallel software framework presented in this paper, should be more broadly applicable to a range of complex reactive systems.

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

The biochemical basis for thermoregulation in heat-producing flowers

PubMed Central

Umekawa, Yui; Seymour, Roger S.; Ito, Kikukatsu

2016-01-01

Thermoregulation (homeothermy) in animals involves a complex mechanism involving thermal receptors throughout the body and integration in the hypothalamus that controls shivering and non-shivering thermogenesis. The flowers of some ancient families of seed plants show a similar degree of physiological thermoregulation, but by a different mechanism. Here, we show that respiratory control in homeothermic spadices of skunk cabbage (Symplocarpus renifolius) is achieved by rate-determining biochemical reactions in which the overall thermodynamic activation energy exhibits a negative value. Moreover, NADPH production, catalyzed by mitochondrial isocitrate dehydrogenase in a chemically endothermic reaction, plays a role in the pre-equilibrium reaction. We propose that a law of chemical equilibrium known as Le Châtelier’s principle governs the homeothermic control in skunk cabbage. PMID:27095582

Ab initio study of the chlorine nitrate protonation reaction - Implications for loss of ClONO2 in the stratosphere

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1993-01-01

Ab initio quantum mechanical methods, including coupled-cluster theory, are used to determine the equilibrium geometries, dipole moments, and harmonic vibrational frequencies of ClONO2, NO2(+), and four isomers of protonated ClONO2. It was found that, for the equilibrium structures and harmonic frequencies of ClONO2, HOCl, and NO2(+), the highest-level theoretical predictions are consistent with the available experimental information concerning the reactions of ClONO2 and HOCl with HCl on the surface of polar stratospheric clouds (PSCs). The study supports a recent hypothesis that the reaction of ClONO2 on the surface of PSCs is proton catalyzed, although the mechanism is different.

The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

PubMed

Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

2017-12-01

The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.

The Extraction of Metals from Their Oxides and Sulphides.

ERIC Educational Resources Information Center

Price, Alun H.

1980-01-01

Briefly describes the application of thermodynamics (system at equilibrium) to the study of the extraction of metals from their oxides (dynamic situation). It is more relevant to study the temperature variation of the equilibrium constants of the reaction than to study the free energy approach. (Author/SK)

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

PubMed

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

2016-10-04

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

Direct Monte Carlo simulation of chemical reaction systems: Simple bimolecular reactions

NASA Astrophysics Data System (ADS)

Piersall, Shannon D.; Anderson, James B.

1991-07-01

In applications to several simple reaction systems we have explored a ``direct simulation'' method for predicting and understanding the behavior of gas phase chemical reaction systems. This Monte Carlo method, originated by Bird, has been found remarkably successful in treating a number of difficult problems in rarefied dynamics. Extension to chemical reactions offers a powerful tool for treating reaction systems with nonthermal distributions, with coupled gas-dynamic and reaction effects, with emission and adsorption of radiation, and with many other effects difficult to treat in any other way. The usual differential equations of chemical kinetics are eliminated. For a bimolecular reaction of the type A+B→C+D with a rate sufficiently low to allow a continued thermal equilibrium of reactants we find that direct simulation reproduces the expected second order kinetics. Simulations for a range of temperatures yield the activation energies expected for the reaction models specified. For faster reactions under conditions leading to a depletion of energetic reactant species, the expected slowing of reaction rates and departures from equilibrium distributions are observed. The minimum sample sizes required for adequate simulations are as low as 1000 molecules for these cases. The calculations are found to be simple and straightforward for the homogeneous systems considered. Although computation requirements may be excessively high for very slow reactions, they are reasonably low for fast reactions, for which nonequilibrium effects are most important.

Reduced Equations for Calculating the Combustion Rates of Jet-A and Methane Fuel

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2003-01-01

Simplified kinetic schemes for Jet-A and methane fuels were developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) that is being developed at Glenn. These kinetic schemes presented here result in a correlation that gives the chemical kinetic time as a function of initial overall cell fuel/air ratio, pressure, and temperature. The correlations would then be used with the turbulent mixing times to determine the limiting properties and progress of the reaction. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentration of carbon monoxide as a function of fuel air ratio, pressure, and temperature. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates and the values obtained from the equilibrium correlations were then used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide, and NOx were obtained for both Jet-A fuel and methane.

Recent advances in modeling Hugoniots with Cheetah

NASA Astrophysics Data System (ADS)

Glaesemann, Kurt

2005-07-01

The detonation of an energetic material is the result of a complex interaction between kinetic chemical reactions and thermodynamic chemical equilibrium. Unfortunately, little is known concerning the detailed chemical kinetics of reacting energetic materials. Cheetah uses rate laws to treat species with the slowest chemical reactions, while assuming other chemical species are in equilibrium. Cheetah supports a wide range of elements and condensed detonation products and can also be applied to gas phase reactions. Improvements have been made to Cheetah's equilibrium solver, that allow it to find a wider range of thermodynamic states. Many of the difficulties experienced by users in earlier versions of Cheetah have been fixed. New capabilities have also been added. The ultimate result is a code that can be applied to a wide range of shock problems involving both energetic and non-energetic materials. New experimental validations of Cheetah's equation of state methodology have been performed, including both reacted and unreacted Hugoniots. This work was performed under the auspices of the U.S. Department of Energy by the University of California Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

Physical Properties and CO2 Reaction Pathway of 1-Ethyl-3-Methylimidazolium Ionic Liquids with Aprotic Heterocyclic Anions

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

Seo, S; DeSilva, MA; Brennecke, JF

2014-12-25

Ionic liquids (ILs) with aprotic heterocyclic anions (AHA) are attractive candidates for CO2 capture technologies. In this study, a series of AHA ILs with 1-ethyl-3-methylimidazolium ([emim](+)) cations were synthesized, and their physical properties (density, viscosity, and ionic conductivity) were measured. In addition, CO2 solubility in each IL was determined at room temperature using a volumetric method at pressures between 0 and 1 bar. The AHAs are basic anions that are capable of reacting stoichiometrically with CO2 to form carbamate species. An interesting CO2 uptake isotherm behavior was observed, and this may be attributed to a parallel, equilibrium proton exchange processmore » between the imidazolium cation and the basic AHA in the presence of CO2, followed by the formation of "transient" carbene species that react rapidly with CO2. The presence of the imidazolium-carboxylate species and carbamate anion species was verified using H-1 and C-13 NMR spectroscopy. While the reaction between CO2 and the proposed transient carbene resulted in cation-CO2 binding that is stronger than the anion-CO2 reaction, the reactions of the imidazolium AHA ILs were fully reversible upon regeneration at 80 degrees C with nitrogen purging. The presence of water decreased the CO2 uptake due to the inhibiting effect of the neutral species (protonated form of AHA) that is formed.« less

Reactive Transport of Petroleum Hydrocarbon Constituents in a Shallow Aquifer: Modeling Geochemical Interactions Between Organic and Inorganic Species

NASA Astrophysics Data System (ADS)

McNab, W. W.; Narasimhan, T. N.

1995-08-01

Dissolved organic contaminants such as petroleum hydrocarbon constituents are often observed to degrade in groundwater environments through biologically mediated transformation reactions into carbon dioxide, methane, or intermediate organic compounds. Such transformations are closely tied to local geochemical conditions. Favorable degradation pathways depend upon local redox conditions through thermodynamic constraints and the availability of appropriate mediating microbial populations. Conversely, the progress of the degradation reactions may affect the chemical composition of groundwater through changes in electron donor/acceptor speciation and pH, possibly inducing mineral precipitation/dissolution reactions. Transport of reactive organic and inorganic aqueous species through open systems may enhance the reaction process by mixing unlike waters and producing a state of general thermodynamic disequilibrium. In this study, field data from an aquifer contaminated by petroleum hydrocarbons have been analyzed using a mathematical model which dynamically couples equilibrium geochemistry of inorganic constituents, kinetically dominated sequential degradation of organic compounds, and advective-dispersive chemical transport. Simulation results indicate that coupled geochemical processes inferred from field data, such as organic biodegradation, iron reduction and dissolution, and methanogenesis, can be successfully modeled using a partial-redox-disequilibrium approach. The results of this study also suggest how the modeling approach can be used to study system sensitivity to various physical and chemical parameters, such as the effect of dispersion on the position of chemical fronts and the impact of alternative buffering mineral phases (e.g., goethite versus amorphous Fe(OH)3) on water chemistry.

The Gaseous Explosive Reaction : The Effect of Inert Gases

NASA Technical Reports Server (NTRS)

Stevens, F W

1928-01-01

Attention is called in this report to previous investigations of gaseous explosive reactions carried out under constant volume conditions, where the effect of inert gases on the thermodynamic equilibrium was determined. The advantage of constant pressure methods over those of constant volume as applied to studies of the gaseous explosive reaction is pointed out and the possibility of realizing for this purpose a constant pressure bomb mentioned. The application of constant pressure methods to the study of gaseous explosive reactions, made possible by the use of a constant pressure bomb, led to the discovery of an important kinetic relation connecting the rate of propagation of the zone of explosive reaction within the active gases, with the initial concentrations of those gases: s = K(sub 1)(A)(sup n1)(B)(sup n2)(C)(sup n3)------. By a method analogous to that followed in determining the effect of inert gases on the equilibrium constant K, the present paper records an attempt to determine their kinetic effect upon the expression given above.

The Metallurgical Design of Steels for Optimum Mechanical Properties

DTIC Science & Technology

1945-10-22

to’casting and working), and to some extent, during deforma- tion. Th,. vwr{oua alloying elements have little effect upon the nature of the...procoed, tWho so-ca~lled "equilibrium~ states". This topic lies in thc fiold of thcr- modynrunics. When the equilibrium conditions are( understood, it...is ~o[ssi- ble to considnr thc rates Pand the moch~rmisms of the tra.-nsforr-Wtins: ton- ice in the field of reaction kinetics. Equilibrium Conditions

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 Heterogeneous Chemical Reactions on the Köhler Activation of Aqueous Organic Aerosols.

PubMed

Djikaev, Yuri S; Ruckenstein, Eli

2018-05-03

We study some thermodynamic aspects of the activation of aqueous organic aerosols into cloud droplets considering the aerosols to consist of liquid solution of water and hydrophilic and hydrophobic organic compounds, taking into account the presence of reactive species in the air. The hydrophobic (surfactant) organic molecules on the surface of such an aerosol can be processed by chemical reactions with some atmospheric species; this affects the hygroscopicity of the aerosol and hence its ability to become a cloud droplet either via nucleation or via Köhler activation. The most probable pathway of such processing involves atmospheric hydroxyl radicals that abstract hydrogen atoms from hydrophobic organic molecules located on the aerosol surface (first step), the resulting radicals being quickly oxidized by ubiquitous atmospheric oxygen molecules to produce surface-bound peroxyl radicals (second step). These two reactions play a crucial role in the enhancement of the Köhler activation of the aerosol and its evolution into a cloud droplet. Taking them and a third reaction (next in the multistep chain of relevant heterogeneous reactions) into account, one can derive an explicit expression for the free energy of formation of a four-component aqueous droplet on a ternary aqueous organic aerosol as a function of four independent variables of state of a droplet. The results of numerical calculations suggest that the formation of cloud droplets on such (aqueous hydrophilic/hydrophobic organic) aerosols is most likely to occur as a Köhler activation-like process rather than via nucleation. The model allows one to determine the threshold parameters of the system necessary for the Köhler activation of such aerosols, which are predicted to be very sensitive to the equilibrium constant of the chain of three heterogeneous reactions involved in the chemical aging of aerosols.

Equilibrium Polymerization of Butyl Methacrylate in Bulk and in Nanopore Confinement

NASA Astrophysics Data System (ADS)

Tian, Qian; Simon, Sindee

The equilibrium between monomer and polymer in free radical polymerization can be shifted towards monomer under nanoconfinement. This decrease in ceiling temperature is due to a decrease in the entropy associated with the constrained polymer chains, resulting in a larger negative change in entropy of reaction. Here, we investigate the equilibrium polymerization of butyl methacrylate (BMA) in bulk and in nanopore confinement with differential scanning calorimetry (DSC) using di-tert-butyl peroxide (DTBP) as initiator. This system has several advantages compare to the previously studied system of methyl methacrylate (MMA) initiated with 2,2'-azo-bis-isobutyronitrile (AIBN), namely, a reduced rate of reaction, higher boiling point of monomer, and higher initiator utilization temperature range, all of which facilitate the study of the reaction at high temperatures near the ceiling temperature. Interestingly, for BMA, there is no change in limiting conversion between material reacted in bulk and that in controlled pore glass having pore diameters of 7.5 and 50 nm. This unexpected result may be due to the greater flexibility of the PBMA chains compared to PMMA, suggesting that in the BMA/PBMA system, the degree of confinement is relatively low. Future studies will continue to investigate how the entropy change on reaction is affected by confinement.

In Situ Tracking Kinetic Pathways of Li + /Na + Substitution during Ion-Exchange Synthesis of Li xNa 1.5–x VOPO 4 F 0.5

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

Park, Young-Uk; Bai, Jianming; Wang, Liping

Ion exchange is a ubiquitous phenomenon central to wide industrial applications, ranging from traditional (bio)chemical separation to the emerging chimie douce synthesis of materials for batteries and other energy applications. The exchange process is complex, involving substitution and transport of different ions under non-equilibrium conditions, and thus difficult to probe, leaving a gap in mechanistic understanding of kinetic exchange pathways toward final products. Herein, we report in situ tracking kinetic pathways of Li +/Na + substitution during solvothermal ion-exchange synthesis of Li xNa 1.5-xVOPO 4F 0.5 (0 ≤ x ≤ 1.5), a promising multi-Li polyanionic cathode for batteries. The real-timemore » observation, corroborated by first-principles calculations, reveals a selective replacement of Na + by Li +, leading to peculiar Na +/Li +/vacancy orderings in the intermediates. Contradicting the traditional belief of facile topotactic substitution via solid solution reaction, an abrupt two-phase transformation occurs and predominantly governs the kinetics of ion exchange and transport in the 1D polyanionic framework, consequently leading to significant difference of Li stoichiometry and electrochemical properties in the exchanged products. The findings may help to pave the way for rational design of ion exchange synthesis for making new materials.« less

In Situ Tracking Kinetic Pathways of Li + /Na + Substitution during Ion-Exchange Synthesis of Li xNa 1.5–x VOPO 4 F 0.5

DOE PAGES

Park, Young-Uk; Bai, Jianming; Wang, Liping; ...

2017-08-29

Ion exchange is a ubiquitous phenomenon central to wide industrial applications, ranging from traditional (bio)chemical separation to the emerging chimie douce synthesis of materials for batteries and other energy applications. The exchange process is complex, involving substitution and transport of different ions under non-equilibrium conditions, and thus difficult to probe, leaving a gap in mechanistic understanding of kinetic exchange pathways toward final products. Herein, we report in situ tracking kinetic pathways of Li +/Na + substitution during solvothermal ion-exchange synthesis of Li xNa 1.5-xVOPO 4F 0.5 (0 ≤ x ≤ 1.5), a promising multi-Li polyanionic cathode for batteries. The real-timemore » observation, corroborated by first-principles calculations, reveals a selective replacement of Na + by Li +, leading to peculiar Na +/Li +/vacancy orderings in the intermediates. Contradicting the traditional belief of facile topotactic substitution via solid solution reaction, an abrupt two-phase transformation occurs and predominantly governs the kinetics of ion exchange and transport in the 1D polyanionic framework, consequently leading to significant difference of Li stoichiometry and electrochemical properties in the exchanged products. The findings may help to pave the way for rational design of ion exchange synthesis for making new materials.« less

Using Computer-Based "Experiments" in the Analysis of Chemical Reaction Equilibria

ERIC Educational Resources Information Center

Li, Zhao; Corti, David S.

2018-01-01

The application of the Reaction Monte Carlo (RxMC) algorithm to standard textbook problems in chemical reaction equilibria is discussed. The RxMC method is a molecular simulation algorithm for studying the equilibrium properties of reactive systems, and therefore provides the opportunity to develop computer-based "experiments" for the…

Spontaneity and Equilibrium III: A History of Misinformation

ERIC Educational Resources Information Center

Raff, Lionel M.

2014-01-01

Necessary and sufficient criteria for reaction spontaneity in a given direction and for spontaneity of finite transformations in single-reaction, closed systems are developed. The criteria are general in that they hold for reactions conducted under either conditions of constant T and p or constant T and V. These results are illustrated using a…

Misconceptions regarding basic thermodynamics and enzyme kinetics have led to erroneous conclusions regarding the metabolic importance of lactate dehydrogenase isoenzyme expression.

PubMed

Bak, Lasse K; Schousboe, Arne

2017-11-01

Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate involving the coenzyme NAD + . Part of the foundation for the proposed shuttling of lactate from astrocytes to neurons during brain activation is the differential distribution of LDH isoenzymes between the two cell types. In this short review, we outline the basic kinetic properties of the LDH isoenzymes expressed in neurons and astrocytes, and argue that the distribution of LDH isoenzymes does not in any way govern directional flow of lactate between the two cellular compartments. The two main points are as follows. First, in line with the general concept of chemical catalysis, enzymes do not influence the thermodynamic equilibrium of a chemical reaction but merely the speed at which equilibrium is obtained. Thus, differential distribution of LDH isoenzymes with different kinetic parameters does not predict which cells are producing and which are consuming lactate. Second, the thermodynamic equilibrium of the reaction is toward the reduced substrate (i.e., lactate), which is reflected in the concentrations measured in brain tissue, suggesting that the reaction is at near-equilibrium at steady state. To conclude, the cellular distribution of LDH isoenzymes is of little if any consequence in determining any directional flow of lactate between neurons and astrocytes. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Quantifying Differences in the Impact of Variable Chemistry on Equilibrium Uranium(VI) Adsorption Properties of Aquifer Sediments

PubMed Central

2011-01-01

Uranium adsorption–desorption on sediment samples collected from the Hanford 300-Area, Richland, WA varied extensively over a range of field-relevant chemical conditions, complicating assessment of possible differences in equilibrium adsorption properties. Adsorption equilibrium was achieved in 500–1000 h although dissolved uranium concentrations increased over thousands of hours owing to changes in aqueous chemical composition driven by sediment-water reactions. A nonelectrostatic surface complexation reaction, >SOH + UO22+ + 2CO32- = >SOUO2(CO3HCO3)2–, provided the best fit to experimental data for each sediment sample resulting in a range of conditional equilibrium constants (logKc) from 21.49 to 21.76. Potential differences in uranium adsorption properties could be assessed in plots based on the generalized mass-action expressions yielding linear trends displaced vertically by differences in logKc values. Using this approach, logKc values for seven sediment samples were not significantly different. However, a significant difference in adsorption properties between one sediment sample and the fines (<0.063 mm) of another could be demonstrated despite the fines requiring a different reaction stoichiometry. Estimates of logKc uncertainty were improved by capturing all data points within experimental errors. The mass-action expression plots demonstrate that applying models outside the range of conditions used in model calibration greatly increases potential errors. PMID:21923109

Quantifying differences in the impact of variable chemistry on equilibrium Uranium(VI) adsorption properties of aquifer sediments.

PubMed

Stoliker, Deborah L; Kent, Douglas B; Zachara, John M

2011-10-15

Uranium adsorption-desorption on sediment samples collected from the Hanford 300-Area, Richland, WA varied extensively over a range of field-relevant chemical conditions, complicating assessment of possible differences in equilibrium adsorption properties. Adsorption equilibrium was achieved in 500-1000 h although dissolved uranium concentrations increased over thousands of hours owing to changes in aqueous chemical composition driven by sediment-water reactions. A nonelectrostatic surface complexation reaction, >SOH + UO₂²⁺ + 2CO₃²⁻ = >SOUO₂(CO₃HCO₃)²⁻, provided the best fit to experimental data for each sediment sample resulting in a range of conditional equilibrium constants (logK(c)) from 21.49 to 21.76. Potential differences in uranium adsorption properties could be assessed in plots based on the generalized mass-action expressions yielding linear trends displaced vertically by differences in logK(c) values. Using this approach, logK(c) values for seven sediment samples were not significantly different. However, a significant difference in adsorption properties between one sediment sample and the fines (< 0.063 mm) of another could be demonstrated despite the fines requiring a different reaction stoichiometry. Estimates of logK(c) uncertainty were improved by capturing all data points within experimental errors. The mass-action expression plots demonstrate that applying models outside the range of conditions used in model calibration greatly increases potential errors.

Effect of Acid-Base Equilibrium on Absorption Spectra of Humic acid in the Presence of Copper Ions

NASA Astrophysics Data System (ADS)

Lavrik, N. L.; Mulloev, N. U.

2014-03-01

The reaction between humic acid (HA, sample IHSS) and a metal ion (Cu2+) that was manifested as absorption bands in the range 210-350 nm was recorded using absorption spectroscopy. The reaction was found to be more effective as the pH increased. These data were interpreted in the framework of generally accepted concepts about the influence of acid-base equilibrium on the dissociation of salts, according to which increasing the solution pH increases the concentration of HA anions. It was suggested that [HA-Cu2+] complexes formed.

Development of an alkaline/surfactant/polymer compositional reservoir simulator

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

Bhuyan, D.

1989-01-01

The mathematical formulation of a generalized three-dimensional compositional reservoir simulator for high-pH chemical flooding processes is presented in this work. The model assumes local thermodynamic equilibrium with respect to both reaction chemistry and phase behavior and calculates equilibrium electrolyte and phase compositions as a function of time and position. The reaction chemistry considers aqueous electrolytic chemistry, precipitation/dissolution of minerals, ion exchange reactions on matrix surface, reaction of acidic components of crude oil with the bases in the aqueous solution and cation exchange reactions with the micelles. The simulator combines this detailed reaction chemistry associated with these processes with the extensivemore » physical and flow property modeling schemes of an existing chemical flood simulator (UTCHEM) to model the multiphase, multidimensional displacement processes. The formulation of the chemical equilibrium model is quite general and is adaptable to simulate a variety of chemical descriptions. In addition to its use in the simulation of high-pH chemical flooding processes, the model will find application in the simulation of other reactive flow problems like the ground water contamination, reinjection of produced water, chemical waste disposal, etc. in one, two or three dimensions and under multiphase flow conditions. In this work, the model is used to simulate several hypothetical cases of high-pH chemical floods, which include cases from a simple alkaline preflush of a micellar/polymer flood to surfactant enhanced alkaline-polymer flooding and the results are analyzed. Finally, a few published alkaline, alkaline-polymer and surfactant-alkaline-polymer corefloods are simulated and compared with the experimental results.« less

Bioproducts and environmental quality: Biofuels, greenhouse gases, and water quality

NASA Astrophysics Data System (ADS)

Ren, Xiaolin

Promoting bio-based products is one oft-proposed solution to reduce GHG emissions because the feedstocks capture carbon, offsetting at least partially the carbon discharges resulting from use of the products. However, several life cycle analyses point out that while biofuels may emit less life cycle net carbon emissions than fossil fuels, they may exacerbate other parts of biogeochemical cycles, notably nutrient loads in the aquatic environment. In three essays, this dissertation explores the tradeoff between GHG emissions and nitrogen leaching associated with biofuel production using general equilibrium models. The first essay develops a theoretical general equilibrium model to calculate the second-best GHG tax with the existence of a nitrogen leaching distortion. The results indicate that the second-best GHG tax could be higher or lower than the first-best tax rates depending largely on the elasticity of substitution between fossil fuel and biofuel. The second and third essays employ computable general equilibrium models to further explore the tradeoff between GHG emissions and nitrogen leaching. The computable general equilibrium models also incorporate multiple biofuel pathways, i.e., biofuels made from different feedstocks using different processes, to identify the cost-effective combinations of biofuel pathways under different policies, and the corresponding economic and environmental impacts.

Analysis of non-equilibrium phenomena in inductively coupled plasma generators

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

Zhang, W.; Panesi, M., E-mail: mpanesi@illinois.edu; Lani, A.

This work addresses the modeling of non-equilibrium phenomena in inductively coupled plasma discharges. In the proposed computational model, the electromagnetic induction equation is solved together with the set of Navier-Stokes equations in order to compute the electromagnetic and flow fields, accounting for their mutual interaction. Semi-classical statistical thermodynamics is used to determine the plasma thermodynamic properties, while transport properties are obtained from kinetic principles, with the method of Chapman and Enskog. Particle ambipolar diffusive fluxes are found by solving the Stefan-Maxwell equations with a simple iterative method. Two physico-mathematical formulations are used to model the chemical reaction processes: (1) Amore » Local Thermodynamics Equilibrium (LTE) formulation and (2) a thermo-chemical non-equilibrium (TCNEQ) formulation. In the TCNEQ model, thermal non-equilibrium between the translational energy mode of the gas and the vibrational energy mode of individual molecules is accounted for. The electronic states of the chemical species are assumed in equilibrium with the vibrational temperature, whereas the rotational energy mode is assumed to be equilibrated with translation. Three different physical models are used to account for the coupling of chemistry and energy transfer processes. Numerical simulations obtained with the LTE and TCNEQ formulations are used to characterize the extent of non-equilibrium of the flow inside the Plasmatron facility at the von Karman Institute. Each model was tested using different kinetic mechanisms to assess the sensitivity of the results to variations in the reaction parameters. A comparison of temperatures and composition profiles at the outlet of the torch demonstrates that the flow is in non-equilibrium for operating conditions characterized by pressures below 30 000 Pa, frequency 0.37 MHz, input power 80 kW, and mass flow 8 g/s.« less

Analysis of non-equilibrium phenomena in inductively coupled plasma generators

NASA Astrophysics Data System (ADS)

Zhang, W.; Lani, A.; Panesi, M.

2016-07-01

This work addresses the modeling of non-equilibrium phenomena in inductively coupled plasma discharges. In the proposed computational model, the electromagnetic induction equation is solved together with the set of Navier-Stokes equations in order to compute the electromagnetic and flow fields, accounting for their mutual interaction. Semi-classical statistical thermodynamics is used to determine the plasma thermodynamic properties, while transport properties are obtained from kinetic principles, with the method of Chapman and Enskog. Particle ambipolar diffusive fluxes are found by solving the Stefan-Maxwell equations with a simple iterative method. Two physico-mathematical formulations are used to model the chemical reaction processes: (1) A Local Thermodynamics Equilibrium (LTE) formulation and (2) a thermo-chemical non-equilibrium (TCNEQ) formulation. In the TCNEQ model, thermal non-equilibrium between the translational energy mode of the gas and the vibrational energy mode of individual molecules is accounted for. The electronic states of the chemical species are assumed in equilibrium with the vibrational temperature, whereas the rotational energy mode is assumed to be equilibrated with translation. Three different physical models are used to account for the coupling of chemistry and energy transfer processes. Numerical simulations obtained with the LTE and TCNEQ formulations are used to characterize the extent of non-equilibrium of the flow inside the Plasmatron facility at the von Karman Institute. Each model was tested using different kinetic mechanisms to assess the sensitivity of the results to variations in the reaction parameters. A comparison of temperatures and composition profiles at the outlet of the torch demonstrates that the flow is in non-equilibrium for operating conditions characterized by pressures below 30 000 Pa, frequency 0.37 MHz, input power 80 kW, and mass flow 8 g/s.

Modeling of uncertainties in biochemical reactions.

PubMed

Mišković, Ljubiša; Hatzimanikatis, Vassily

2011-02-01

Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual reactions. However, kinetic data acquired from experimental observations bring along uncertainties due to various experimental conditions and measurement methods. In this contribution, we propose a novel way to model the uncertainty in the enzyme kinetics and to predict quantitatively the responses of metabolic reactions to the changes in enzyme activities under uncertainty. The proposed methodology accounts explicitly for mechanistic properties of enzymes and physico-chemical and thermodynamic constraints, and is based on formalism from systems theory and metabolic control analysis. We achieve this by observing that kinetic responses of metabolic reactions depend: (i) on the distribution of the enzymes among their free form and all reactive states; (ii) on the equilibrium displacements of the overall reaction and that of the individual enzymatic steps; and (iii) on the net fluxes through the enzyme. Relying on this observation, we develop a novel, efficient Monte Carlo sampling procedure to generate all states within a metabolic reaction that satisfy imposed constrains. Thus, we derive the statistics of the expected responses of the metabolic reactions to changes in enzyme levels and activities, in the levels of metabolites, and in the values of the kinetic parameters. We present aspects of the proposed framework through an example of the fundamental three-step reversible enzymatic reaction mechanism. We demonstrate that the equilibrium displacements of the individual enzymatic steps have an important influence on kinetic responses of the enzyme. Furthermore, we derive the conditions that must be satisfied by a reversible three-step enzymatic reaction operating far away from the equilibrium in order to respond to changes in metabolite levels according to the irreversible Michelis-Menten kinetics. The efficient sampling procedure allows easy, scalable, implementation of this methodology to modeling of large-scale biochemical networks. © 2010 Wiley Periodicals, Inc.

Consistent post-reaction vibrational energy redistribution in DSMC simulations using TCE model

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Alexeenko, Alina

2016-10-01

The direct simulation Monte Carlo (DSMC) method has been widely applied to study shockwaves, hypersonic reentry flows, and other nonequilibrium flow phenomena. Although there is currently active research on high-fidelity models based on ab initio data, the total collision energy (TCE) and Larsen-Borgnakke (LB) models remain the most often used chemistry and relaxation models in DSMC simulations, respectively. The conventional implementation of the discrete LB model, however, may not satisfy detailed balance when recombination and exchange reactions play an important role in the flow energy balance. This issue can become even more critical in reacting mixtures involving polyatomic molecules, such as in combustion. In this work, this important shortcoming is addressed and an empirical approach to consistently specify the post-reaction vibrational states close to thermochemical equilibrium conditions is proposed within the TCE framework. Following Bird's quantum-kinetic (QK) methodology for populating post-reaction states, the new TCE-based approach involves two main steps. The state-specific TCE reaction probabilities for a forward reaction are first pre-computed from equilibrium 0-D simulations. These probabilities are then employed to populate the post-reaction vibrational states of the corresponding reverse reaction. The new approach is illustrated by application to exchange and recombination reactions relevant to H2-O2 combustion processes.

Systematic Approach to Calculate the Concentration of Chemical Species in Multi-Equilibrium Problems

ERIC Educational Resources Information Center

Baeza-Baeza, Juan Jose; Garcia-Alvarez-Coque, Maria Celia

2011-01-01

A general systematic approach is proposed for the numerical calculation of multi-equilibrium problems. The approach involves several steps: (i) the establishment of balances involving the chemical species in solution (e.g., mass balances, charge balance, and stoichiometric balance for the reaction products), (ii) the selection of the unknowns (the…

Inventory Control: A Small Electronic Device for Studying Chemical Kinetics.

ERIC Educational Resources Information Center

Perez-Rodriguez, A. L.; Calvo-Aguilar, J. L.

1984-01-01

Shows how the rate of reaction can be studied using a simple electronic device that overcomes the difficulty students encounter in solving the differential equations describing chemical equilibrium. The device, used in conjunction with an oscilloscope, supplies the voltages that represent the chemical variables that take part in the equilibrium.…

Hammett analyses of halocarbene-halocarbanion equilibria.

PubMed

Wang, Lei; Moss, Robert A; Krogh-Jespersen, Karsten

2013-04-19

Substituted arylchlorocarbenes (X = H, p-Cl, p-CF3, p-F, m-Cl) reacted reversibly with Cl(-) in dichloroethane to form the corresponding aryldichloromethide carbanions. Equilibrium constants and rate constants for the forward and reverse reactions were correlated by the Hammett equation. DFT methods were used to compute equilibrium constants and electronic absorption spectra.

VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera)

PubMed Central

Naithani, Sushma; Raja, Rajani; Waddell, Elijah N.; Elser, Justin; Gouthu, Satyanarayana; Deluc, Laurent G.; Jaiswal, Pankaj

2014-01-01

We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to (i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, (ii) compare grapevine metabolic networks with other publicly available plant metabolic networks, and (iii) upload, visualize and analyze high-throughput data such as transcriptomes, proteomes, metabolomes etc. using OMICs-Viewer tool. VitisCyc is based on the genome sequence of the nearly homozygous genotype PN40024 of Vitis vinifera “Pinot Noir” cultivar with 12X v1 annotations and was built on BioCyc platform using Pathway Tools software and MetaCyc reference database. Furthermore, VitisCyc was enriched for plant-specific pathways and grape-specific metabolites, reactions and pathways. Currently VitisCyc harbors 68 super pathways, 362 biosynthesis pathways, 118 catabolic pathways, 5 detoxification pathways, 36 energy related pathways and 6 transport pathways, 10,908 enzymes, 2912 enzymatic reactions, 31 transport reactions and 2024 compounds. VitisCyc, as a community resource, can aid in the discovery of candidate genes and pathways that are regulated during plant growth and development, and in response to biotic and abiotic stress signals generated from a plant's immediate environment. VitisCyc version 3.18 is available online at http://pathways.cgrb.oregonstate.edu. PMID:25538713

Ferric sulphate catalysed esterification of free fatty acids in waste cooking oil.

PubMed

Gan, Suyin; Ng, Hoon Kiat; Ooi, Chun Weng; Motala, Nafisa Osman; Ismail, Mohd Anas Farhan

2010-10-01

In this work, the esterification of free fatty acids (FFA) in waste cooking oil catalysed by ferric sulphate was studied as a pre-treatment step for biodiesel production. The effects of reaction time, methanol to oil ratio, catalyst concentration and temperature on the conversion of FFA were investigated on a laboratory scale. The results showed that the conversion of FFA reached equilibrium after an hour, and was positively dependent on the methanol to oil molar ratio and temperature. An optimum catalyst concentration of 2 wt.% gave maximum FFA conversion of 59.2%. For catalyst loadings of 2 wt.% and below, this catalysed esterification was proposed to follow a pseudo-homogeneous pathway akin to mineral acid-catalysed esterification, driven by the H(+) ions produced through the hydrolysis of metal complex [Fe(H(2)O)(6)](3+) (aq). Copyright 2010 Elsevier Ltd. All rights reserved.

Design, Synthesis, and Chemical and Biological Properties of Cyclic ADP-4-Thioribose as a Stable Equivalent of Cyclic ADP-Ribose.

PubMed

Tsuzuki, Takayoshi; Takano, Satoshi; Sakaguchi, Natsumi; Kudoh, Takashi; Murayama, Takashi; Sakurai, Takashi; Hashii, Minako; Higashida, Haruhiro; Weber, Karin; Guse, Andreas H; Kameda, Tomoshi; Hirokawa, Takatsugu; Kumaki, Yasuhiro; Arisawa, Mitsuhiro; Potter, Barry V L; Shuto, Satoshi

2014-01-01

Here we describe the successful synthesis of cyclic ADP-4-thioribose (cADPtR, 3 ), designed as a stable mimic of cyclic ADP-ribose (cADPR, 1 ), a Ca 2+ -mobilizing second messenger, in which the key N1-β-thioribosyladenosine structure was stereoselectively constructed by condensation between the imidazole nucleoside derivative 8 and the 4-thioribosylamine 7 via equilibrium in 7 between the α-anomer ( 7α ) and the β-anomer ( 7β ) during the reaction course. cADPtR is, unlike cADPR, chemically and biologically stable, while it effectively mobilizes intracellular Ca 2+ like cADPR in various biological systems, such as sea urchin homogenate, NG108-15 neuronal cells, and Jurkat T-lymphocytes. Thus, cADPtR is a stable equivalent of cADPR, which can be useful as a biological tool for investigating cADPR-mediated Ca 2+ -mobilizing pathways.

Significance of vapor phase chemical reactions on CVD rates predicted by chemically frozen and local thermochemical equilibrium boundary layer theories

NASA Technical Reports Server (NTRS)

Gokoglu, Suleyman A.

1988-01-01

This paper investigates the role played by vapor-phase chemical reactions on CVD rates by comparing the results of two extreme theories developed to predict CVD mass transport rates in the absence of interfacial kinetic barrier: one based on chemically frozen boundary layer and the other based on local thermochemical equilibrium. Both theories consider laminar convective-diffusion boundary layers at high Reynolds numbers and include thermal (Soret) diffusion and variable property effects. As an example, Na2SO4 deposition was studied. It was found that gas phase reactions have no important role on Na2SO4 deposition rates and on the predictions of the theories. The implications of the predictions of the two theories to other CVD systems are discussed.

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

PubMed

Kulasiri, Don

2011-01-01

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

Equilibrium of particle nitrite with gas phase HONO: Tropospheric measurements in the high Arctic during polar sunrise

NASA Astrophysics Data System (ADS)

Li, Shao-Meng

1994-12-01

Gas phase HONO(g) and nitrite in particles of <5-μm size were measured in the troposphere during the Polar Sunrise Experiment at Alert, Northwest Territories, Canada, during January 19 to April 20, 1992, using denuder-filter pack sampling and IC-UV detection. The measurements indicated that HONO(g) existed at concentrations of up to 70 ppt before polar sunrise but gradually decreased to 5-10 ppt after sunrise. The calculated OH formation rate from HONO(g) photolysis was greater than from the photolysis of both O3 and CH2O by more than one order of magnitude during the sunlit period and led to moderately high levels of OH, e.g., 3×105 molecules cm-3 OH at noontime on April 5. Particle nitrite measurements showed a gradual increase in concentrations with increasing solar insolation, but the concentrations were generally less than 10 ppt. The pH and the sulfate molar concentrations of the particles and the water vapor mixing ratio indicate that the particles were highly acidic being approximately 70% (W/W) H2SO4 solution. In such highly concentrated H2SO4 solution, most particle nitrite should exist as hydrated nitrosonium ion H2ONO+. Taking this into consideration, the particle nitrite was in an approximate equilibrium with the measured HONO(g). This equilibrium, with HONO(g) rapidly photolyzed, was a good indication that the particles were effective sources of HONO(g) and implied rapid production of particle N(+III) during this period. Two possible pathways leading to the formation of particle N(+III) species are suggested, i.e., reduction of HNO3(aq) by SO2(g) and reduction of NO3-; (aq) by Br- (aq). However, N2O5 reaction with NaBr cannot be ruled out as the alternative HONO(g) formation mechanism which bypasses the equilibrium.

Phi-value analysis of a linear, sequential reaction mechanism: theory and application to ion channel gating.

PubMed

Zhou, Yu; Pearson, John E; Auerbach, Anthony

2005-12-01

We derive the analytical form of a rate-equilibrium free-energy relationship (with slope Phi) for a bounded, linear chain of coupled reactions having arbitrary connecting rate constants. The results confirm previous simulation studies showing that Phi-values reflect the position of the perturbed reaction within the chain, with reactions occurring earlier in the sequence producing higher Phi-values than those occurring later in the sequence. The derivation includes an expression for the transmission coefficients of the overall reaction based on the rate constants of an arbitrary, discrete, finite Markov chain. The results indicate that experimental Phi-values can be used to calculate the relative heights of the energy barriers between intermediate states of the chain but provide no information about the energies of the wells along the reaction path. Application of the equations to the case of diliganded acetylcholine receptor channel gating suggests that the transition-state ensemble for this reaction is nearly flat. Although this mechanism accounts for many of the basic features of diliganded and unliganded acetylcholine receptor channel gating, the experimental rate-equilibrium free-energy relationships appear to be more linear than those predicted by the theory.

Stochastic approach to equilibrium and nonequilibrium thermodynamics.

PubMed

Tomé, Tânia; de Oliveira, Mário J

2015-04-01

We develop the stochastic approach to thermodynamics based on stochastic dynamics, which can be discrete (master equation) and continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of entropy itself and the second the definition of entropy production rate, which is non-negative and vanishes in thermodynamic equilibrium. Based on these assumptions, we study interacting systems with many degrees of freedom in equilibrium or out of thermodynamic equilibrium and how the macroscopic laws are derived from the stochastic dynamics. These studies include the quasiequilibrium processes; the convexity of the equilibrium surface; the monotonic time behavior of thermodynamic potentials, including entropy; the bilinear form of the entropy production rate; the Onsager coefficients and reciprocal relations; and the nonequilibrium steady states of chemical reactions.

Experimental Study of Abiotic Organic Synthesis at High Temperature and Pressure Conditions: Carbon Isotope and Mineral Surface Characterizations

NASA Astrophysics Data System (ADS)

Fu, Q.; Socki, R. A.; Niles, P. B.

2010-12-01

Abiotic organic synthesis processes have been proposed as potential mechanisms for methane generation in subseafloor hydrothermal systems on Earth, and on other planets. To better understand the detailed reaction pathways and carbon isotope fractionations in this process under a wide range of physical and chemical conditions, hydrothermal experiments at high temperature (750 °C) and pressure (0.55 GPa) were performed using piston cylinder apparatus. Formic acid was used as the source of CO2 and H2, and magnetite was the mineral catalyst. The chemical and carbon isotopic compositions of dissolved organic products were determined by GC-C-MS-IRMS, while organic intermediaries on the mineral catalyst were characterized by Pyrolysis-GC-MS. Among experimental products, dissolved CO2 was the dominant carbon species with a relative abundance of 88 mol%. Dissolved CH4 and C2H6 were also identified with a mole ratio of CH4 over C2H6 of 15:1. No dissolved CO was detected in the experiment, which might be attributable to the loss of H2 through the Au capsule used in the experiments at high temperature and pressure conditions and corresponding conversion of CO to CO2 by the water-gas shift reaction. Carbon isotope results showed that the δ13C values of CH4 and C2H6 were -50.3‰ and -39.3‰ (V-PDB), respectively. CO2 derived from decarboxylation of formic acid had a δ13C value of -19.2‰, which was 3.2‰ heavier than its source, formic acid. The δ13C difference between CO2 and CH4 was 31.1‰, which was higher than the value of 9.4‰ calculated from theoretical isotopic equilibrium predictions at experimental conditions, suggesting the presence of a kinetic isotope effect. This number was also higher than the values (4.6 to 27.1‰) observed in similar experiments previously performed at 400 °C and 50 MPa with longer reaction times. CH4 is 11.0‰ less enriched in 13C than C2H6. Alcohols were observed as carbon compounds on magnetite surfaces by Pyrolysis-GC-MS, which confirms the hypothesis regarding the reaction pathways of hydrothermal abiotic organic synthesis proposed by Fu et al. (2007, 2008). In this proposed pathway, hydroxymethylene (-CHOH) groups serve as organic intermediaries on mineral surfaces while dissolved H2 serves as a chain terminator/breaker to generate short chain hydrocarbons and oxygenated compounds. This pathway is different from the carbide polymerization theory of Fischer-Tropsch-type (FTT) synthesis in a gas phase. The observed increase of δ13C values of C1 and C2 alkanes with carbon number in our hydrothermal experiments can be readily interpreted by hydroxymethylene pathway, and might be used to differentiate between hydroxymethylene and carbide polymerization pathways. Carbon isotope analysis of alcohols on mineral catalyst surfaces is under way to provide further constraints on formation of organic compounds by FTT in hydrothermal systems.

Experimental Study of Abiotic Organic Synthesis at High Temperature and Pressure Conditions: Carbon Isotope and Mineral Surface Characterizations

NASA Technical Reports Server (NTRS)

Fu, Qi; Socki, R. A.; Niles, P. B.

2010-01-01

Abiotic organic synthesis processes have been proposed as potential mechanisms for methane generation in subseafloor hydrothermal systems on Earth, and on other planets. To better understand the detailed reaction pathways and carbon isotope fractionations in this process under a wide range of physical and chemical conditions, hydrothermal experiments at high temperature (750 C) and pressure (0.55 GPa) were performed using piston cylinder apparatus. Formic acid was used as the source of CO2 and H2, and magnetite was the mineral catalyst. The chemical and carbon isotopic compositions of dissolved organic products were determined by GC-C-MS-IRMS, while organic intermediaries on the mineral catalyst were characterized by Pyrolysis-GC-MS. Among experimental products, dissolved CO2 was the dominant carbon species with a relative abundance of 88 mol%. Dissolved CH4 and C2H6 were also identified with a mole ratio of CH4 over C2H6 of 15:1. No dissolved CO was detected in the experiment, which might be attributable to the loss of H2 through the Au capsule used in the experiments at high temperature and pressure conditions and corresponding conversion of CO to CO2 by the water-gas shift reaction. Carbon isotope results showed that the 13C values of CH4 and C2H6 were -50.3% and -39.3% (V-PDB), respectively. CO2 derived from decarboxylation of formic acid had a (sigma)C-13 value of -19.2%, which was 3.2% heavier than its source, formic acid. The (sigma)C-13 difference between CO2 and CH4 was 31.1%, which was higher than the value of 9.4% calculated from theoretical isotopic equilibrium predictions at experimental conditions, suggesting the presence of a kinetic isotope effect. This number was also higher than the values (4.6 to 27.1%) observed in similar experiments previously performed at 400 C and 50 MPa with longer reaction times. CH4 is 11.0% less enriched in C-13 than C2H6. Alcohols were observed as carbon compounds on magnetite surfaces by Pyrolysis-GC-MS, which confirms the hypothesis regarding the reaction pathways of hydrothermal abiotic organic synthesis proposed by Fu et al. (2007, 2008). In this proposed pathway, hydroxymethylene (-CHOH) groups serve as organic intermediaries on mineral surfaces while dissolved H2 serves as a chain terminator/breaker to generate short chain hydrocarbons and oxygenated compounds. This pathway is different from the carbide polymerization theory of Fischer- Tropsch-type (FTT) synthesis in a gas phase. The observed increase of (sigma)C-13 values of C1 and C2 alkanes with carbon number in our hydrothermal experiments can be readily interpreted by hydroxymethylene pathway, and might be used to differentiate between hydroxymethylene and carbide polymerization pathways. Carbon isotope analysis of alcohols on mineral catalyst surfaces is under way to provide further constraints on formation of organic compounds by FTT in hydrothermal systems.

Computational methods for reactive transport modeling: An extended law of mass-action, xLMA, method for multiphase equilibrium calculations

NASA Astrophysics Data System (ADS)

Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg; Saar, Martin O.

2016-10-01

We present an extended law of mass-action (xLMA) method for multiphase equilibrium calculations and apply it in the context of reactive transport modeling. This extended LMA formulation differs from its conventional counterpart in that (i) it is directly derived from the Gibbs energy minimization (GEM) problem (i.e., the fundamental problem that describes the state of equilibrium of a chemical system under constant temperature and pressure); and (ii) it extends the conventional mass-action equations with Lagrange multipliers from the Gibbs energy minimization problem, which can be interpreted as stability indices of the chemical species. Accounting for these multipliers enables the method to determine all stable phases without presuming their types (e.g., aqueous, gaseous) or their presence in the equilibrium state. Therefore, the here proposed xLMA method inherits traits of Gibbs energy minimization algorithms that allow it to naturally detect the phases present in equilibrium, which can be single-component phases (e.g., pure solids or liquids) or non-ideal multi-component phases (e.g., aqueous, melts, gaseous, solid solutions, adsorption, or ion exchange). Moreover, our xLMA method requires no technique that tentatively adds or removes reactions based on phase stability indices (e.g., saturation indices for minerals), since the extended mass-action equations are valid even when their corresponding reactions involve unstable species. We successfully apply the proposed method to a reactive transport modeling problem in which we use PHREEQC and GEMS as alternative backends for the calculation of thermodynamic properties such as equilibrium constants of reactions, standard chemical potentials of species, and activity coefficients. Our tests show that our algorithm is efficient and robust for demanding applications, such as reactive transport modeling, where it converges within 1-3 iterations in most cases. The proposed xLMA method is implemented in Reaktoro, a unified open-source framework for modeling chemically reactive systems.

The equilibrium of the reaction catalysed by citrate oxaloacetate-lyase

PubMed Central

Tate, S. S.; Datta, S. P.

1965-01-01

1. A method of preparation and purification of citrate oxaloacetate-lyase (EC 4.1.3.6) from Aerobacter aerogenes is described. 2. The equilibrium of this reaction has been determined at pH 8·4 and 25°. It has been shown that K, i.e. [citrate3−]/[oxaloacetateketo2−][acetate −], is 3·08±0·72, but that Kapp., i.e. [total citrate]/[total oxaloacetate][total acetate], is markedly affected by the initial concentrations of the reactants and magnesium. 3. The free-energy change during the cleavage of citrate has been calculated and compared with data from other sources. 4. The free energy of hydrolysis of acetyl-CoA has been evaluated from the present data. 5. A detailed knowledge of the interactions of the reactants with metal ions has been shown to be important in the calculation of the equilibrium constant and related thermodynamic functions. PMID:14348207

Microstructures and formation history of melilite-rich calcium-aluminum-rich inclusions from the ALHA77307 CO3.0 chondrite

NASA Astrophysics Data System (ADS)

Han, Jangmi; Brearley, Adrian J.

2017-03-01

We have studied four melilite-rich calcium-aluminum-rich inclusions (CAIs) from the Allan Hills A77307 CO3.0 chondrite using transmission electron microscopy with the focused ion beam sample preparation technique. This type of CAI represents one of the dominant types of refractory inclusions in CO3 chondrites. Individual melilite-rich CAIs 04-07 record complex formational histories involving high-temperature gas-solid condensation that occurred under both equilibrium and disequilibrium conditions. CAI 04 contains two texturally- and compositionally-distinct occurrences of perovskite: fine-grained perovskite within a melilite-rich core and aggregates of perovskite grains that surround the core. The perovskite in the core was probably involved in a disequilibrium reaction with early equilibrium condensates (e.g., melilite and spinel) and a nebular gas to form Al-Ti-rich diopside, followed by a later condensation of the perovskite aggregates under equilibrium conditions. CAI 05 has a compact melilite-rich core surrounded by a porous mantle, and likely formed by at least two different condensation events under equilibrium and disequilibrium conditions. In CAI 06, complex intergrowth layers of spinel and diopside surrounding a melilite-rich core indicate disequilibrium reaction of spinel and melilite with a nebular gas to form Al-Ti-rich diopside following core formation by equilibrium condensation. CAI 07 is dominated by melilite with a narrow compositional range and equilibrated textures, suggesting its formation by equilibrium condensation over a limited temperature range. Collectively, we infer that the melilite-rich inclusions formed by a generalized sequence of high-temperature gas-solid condensation that involved: (1) formation of CAI cores by aggregation of primary equilibrium condensates (i.e., perovskite, spinel, and melilite), (2) back-reactions of the primary core minerals with a nebular gas under disequilibrium conditions, forming diopside that evolves in composition from Al-Ti-rich at the interface with the inclusion core to Al-Ti-poor on the exterior of the inclusions. The change in formation conditions may have been achieved by transport and injection of the core materials into a region of a partially-condensed gas that still contained refractory elements in the gas phase.

Permanganate oxidation of α-amino acids: kinetic correlations for the nonautocatalytic and autocatalytic reaction pathways.

PubMed

Perez-Benito, Joaquin F

2011-09-08

The reactions of permanganate ion with seven α-amino acids in aqueous KH(2)PO(4)/K(2)HPO(4) buffers have been followed spectrophotometrically at two different wavelengths: 526 nm (decay of MnO(4)(-)) and 418 nm (formation of colloidal MnO(2)). All of the reactions studied were autocatalyzed by colloidal MnO(2), with the contribution of the autocatalytic reaction pathway decreasing in the order glycine > l-threonine > l-alanine > l-glutamic acid > l-leucine > l-isoleucine > l-valine. The rate constants corresponding to the nonautocatalytic and autocatalytic pathways were obtained by means of either a differential rate law or an integrated one, the latter requiring the use of an iterative method for its implementation. The activation parameters for the two pathways were determined and analyzed to obtain statistically significant correlations for the series of reactions studied. The activation enthalpy of the nonautocatalytic pathway showed a strong, positive dependence on the standard Gibbs energy for the dissociation of the protonated amino group of the α-amino acid. Linear enthalpy-entropy correlations were found for both pathways, leading to isokinetic temperatures of 370 ± 21 K (nonautocatalytic) and 364 ± 28 K (autocatalytic). Mechanisms in agreement with the experimental data are proposed for the two reaction pathways.

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

PubMed Central

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

2013-01-01

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

Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods

PubMed Central

2014-01-01

Automatic reconstruction of metabolic pathways for an organism from genomics and transcriptomics data has been a challenging and important problem in bioinformatics. Traditionally, known reference pathways can be mapped into an organism-specific ones based on its genome annotation and protein homology. However, this simple knowledge-based mapping method might produce incomplete pathways and generally cannot predict unknown new relations and reactions. In contrast, ab initio metabolic network construction methods can predict novel reactions and interactions, but its accuracy tends to be low leading to a lot of false positives. Here we combine existing pathway knowledge and a new ab initio Bayesian probabilistic graphical model together in a novel fashion to improve automatic reconstruction of metabolic networks. Specifically, we built a knowledge database containing known, individual gene / protein interactions and metabolic reactions extracted from existing reference pathways. Known reactions and interactions were then used as constraints for Bayesian network learning methods to predict metabolic pathways. Using individual reactions and interactions extracted from different pathways of many organisms to guide pathway construction is new and improves both the coverage and accuracy of metabolic pathway construction. We applied this probabilistic knowledge-based approach to construct the metabolic networks from yeast gene expression data and compared its results with 62 known metabolic networks in the KEGG database. The experiment showed that the method improved the coverage of metabolic network construction over the traditional reference pathway mapping method and was more accurate than pure ab initio methods. PMID:25374614

Ionic Liquid Droplet Microreactor for Catalysis Reactions Not at Equilibrium.

PubMed

Zhang, Ming; Ettelaie, Rammile; Yan, Tao; Zhang, Suojiang; Cheng, Fangqin; Binks, Bernard P; Yang, Hengquan

2017-12-06

We develop a novel strategy to more effectively and controllably process continuous enzymatic or homogeneous catalysis reactions based on nonaqueous Pickering emulsions. A key element of this strategy is "bottom-up" construction of a macroscale continuous flow reaction system through packing catalyst-containing micron-sized ionic liquid (IL) droplet in oil in a column reactor. Due to the continuous influx of reactants into the droplet microreactors and the continuous release of products from the droplet microreactors, catalysis reactions in such a system can take place without limitations arising from establishment of the reaction equilibrium and catalyst separation, inherent in conventional batch reactions. As proof of the concept, enzymatic enantioselective trans-esterification and CuI-catalyzed cycloaddition reactions using this IL droplet-based flow system both exhibit 8 to 25-fold enhancement in catalysis efficiency compared to their batch counterparts, and a durability of at least 4000 h for the enantioselective trans-esterification of 1-phenylethyl alcohol, otherwise unattainable in their batch counterparts. We further establish a theoretical model for such a catalysis system working under nonequilibrium conditions, which not only supports the experimental results but also helps to predict reaction progress at a microscale level. Being operationally simple, efficient, and adaptive, this strategy provides an unprecedented platform for practical applications of enzymes and homogeneous catalysts even at a controllable level.

Some Considerations on the Fundamentals of Chemical Kinetics: Steady State, Quasi-Equilibrium, and Transition State Theory

ERIC Educational Resources Information Center

Perez-Benito, Joaquin F.

2017-01-01

The elementary reaction sequence A ? I ? Products is the simplest mechanism for which the steady-state and quasi-equilibrium kinetic approximations can be applied. The exact integrated solutions for this chemical system allow inferring the conditions that must fulfill the rate constants for the different approximations to hold. A graphical…

Utilization of a Microcomputer for the Study of an Iodine Oxidation and Equilibrium Reaction: A Physical Chemistry Experiment.

ERIC Educational Resources Information Center

Julien, L. M.

1984-01-01

Describes a physical chemistry experiment which incorporates the use of a microcomputer to enhance understanding of combined kinetic and equilibrium phenomena, to increase experimental capabilities when working with large numbers of students and limited equipment, and for the student to develop a better understanding of experimental design. (JN)

A Nonlinear, Multiinput, Multioutput Process Control Laboratory Experiment

ERIC Educational Resources Information Center

Young, Brent R.; van der Lee, James H.; Svrcek, William Y.

2006-01-01

Experience in using a user-friendly software, Mathcad, in the undergraduate chemical reaction engineering course is discussed. Example problems considered for illustration deal with simultaneous solution of linear algebraic equations (kinetic parameter estimation), nonlinear algebraic equations (equilibrium calculations for multiple reactions and…

Brucine diol-copper-catalyzed asymmetric synthesis of endo-pyrrolidines: the mechanistic dichotomy of imino esters.

PubMed

Li, Jian-Yuan; Kim, Hun Young; Oh, Kyungsoo

2015-03-06

Enantio- and diastereodivergent approaches to pyrrolidines are described by using catalyst- and substrate-controlled reaction pathways. A concerted endo-selective [3 + 2]-cycloaddition pathway is developed for the reaction of methyl imino ester, whereas endo-pyrrolidines with an opposite absolute stereochemical outcome are prepared by using the stepwise reaction pathway of tert-butyl imino ester. The development of catalyst- and substrate-controlled stereodivergent approaches highlights the inherent substrate-catalyst interactions in the [3 + 2]-cycloaddition reactions of metalated azomethine ylides.

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

PubMed

Ricard, Jacques

2010-01-01

The present article discusses the possibility that catalysed chemical networks can evolve. Even simple enzyme-catalysed chemical reactions can display this property. The example studied is that of a two-substrate proteinoid, or enzyme, reaction displaying random binding of its substrates A and B. The fundamental property of such a system is to display either emergence or integration depending on the respective values of the probabilities that the enzyme has bound one of its substrate regardless it has bound the other substrate, or, specifically, after it has bound the other substrate. There is emergence of information if p(A)>p(AB) and p(B)>p(BA). Conversely, if p(A)

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.

Molecular finite-size effects in stochastic models of equilibrium chemical systems.

PubMed

Cianci, Claudia; Smith, Stephen; Grima, Ramon

2016-02-28

The reaction-diffusion master equation (RDME) is a standard modelling approach for understanding stochastic and spatial chemical kinetics. An inherent assumption is that molecules are point-like. Here, we introduce the excluded volume reaction-diffusion master equation (vRDME) which takes into account volume exclusion effects on stochastic kinetics due to a finite molecular radius. We obtain an exact closed form solution of the RDME and of the vRDME for a general chemical system in equilibrium conditions. The difference between the two solutions increases with the ratio of molecular diameter to the compartment length scale. We show that an increase in the fraction of excluded space can (i) lead to deviations from the classical inverse square root law for the noise-strength, (ii) flip the skewness of the probability distribution from right to left-skewed, (iii) shift the equilibrium of bimolecular reactions so that more product molecules are formed, and (iv) strongly modulate the Fano factors and coefficients of variation. These volume exclusion effects are found to be particularly pronounced for chemical species not involved in chemical conservation laws. Finally, we show that statistics obtained using the vRDME are in good agreement with those obtained from Brownian dynamics with excluded volume interactions.

Direct numerical simulation of turbulent H2-O2 combustion using reduced chemistry

NASA Technical Reports Server (NTRS)

Montgomery, Christopher J.; Kosaly, George; Riley, James J.

1993-01-01

Results of direct numerical simulations of hydrogen-oxygen combustion using a partial-equilibrium chemistry scheme in constant density, decaying, isotropic turbulence are reported. The simulations qualitatively reproduce many features of experimental results, such as superequilibrium radical species mole fractions, with temperature and major species mole fractions closer to chemical equilibrium. It was also observed that the peak reaction rates occur in narrow zones where the stoichiometric surface intersects regions of high scalar dissipation, as might be expected for combustion conditions close to chemical equilibrium. Another finding was that high OH mole fraction correspond more closely to the stoichiometric surface than to areas of high reaction rate for conditions of the simulations. Simulation results were compared to predictions of the Conditional Moment Closure model. This model was found to give good results for all quantities of interest when the conditionally averaged scalar dissipation was used in the prediction. When the nonconditioned average dissipation was used, the predictions compared well to the simulations for most of the species and temperature, but not for the reaction rate. The comparison would be expected to improve for higher Reynolds number flows, however.

Self-organization in precipitation reactions far from the equilibrium

PubMed Central

Nakouzi, Elias; Steinbock, Oliver

2016-01-01

Far from the thermodynamic equilibrium, many precipitation reactions create complex product structures with fascinating features caused by their unusual origins. Unlike the dissipative patterns in other self-organizing reactions, these features can be permanent, suggesting potential applications in materials science and engineering. We review four distinct classes of precipitation reactions, describe similarities and differences, and discuss related challenges for theoretical studies. These classes are hollow micro- and macrotubes in chemical gardens, polycrystalline silica carbonate aggregates (biomorphs), Liesegang bands, and propagating precipitation-dissolution fronts. In many cases, these systems show intricate structural hierarchies that span from the nanometer scale into the macroscopic world. We summarize recent experimental progress that often involves growth under tightly regulated conditions by means of wet stamping, holographic heating, and controlled electric, magnetic, or pH perturbations. In this research field, progress requires mechanistic insights that cannot be derived from experiments alone. We discuss how mesoscopic aspects of the product structures can be modeled by reaction-transport equations and suggest important targets for future studies that should also include materials features at the nanoscale. PMID:27551688

Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

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

Ovacik, Meric A.; Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu; Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854

2013-09-15

Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogeneticmore » relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.« less

Thermodynamic Driving Force of Hydrogen on Rumen Microbial Metabolism: A Theoretical Investigation

PubMed Central

van Lingen, Henk J.; Plugge, Caroline M.; Fadel, James G.; Kebreab, Ermias; Bannink, André; Dijkstra, Jan

2016-01-01

Hydrogen is a key product of rumen fermentation and has been suggested to thermodynamically control the production of the various volatile fatty acids (VFA). Previous studies, however, have not accounted for the fact that only thermodynamic near-equilibrium conditions control the magnitude of reaction rate. Furthermore, the role of NAD, which is affected by hydrogen partial pressure (PH2), has often not been considered. The aim of this study was to quantify the control of PH2 on reaction rates of specific fermentation pathways, methanogenesis and NADH oxidation in rumen microbes. The control of PH2 was quantified using the thermodynamic potential factor (FT), which is a dimensionless factor that corrects a predicted kinetic reaction rate for the thermodynamic control exerted. Unity FT was calculated for all glucose fermentation pathways considered, indicating no inhibition of PH2 on the production of a specific type of VFA (e.g., acetate, propionate and butyrate) in the rumen. For NADH oxidation without ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity to zero for different NAD+ to NADH ratios and pH of 6.2 and 7.0, which indicates thermodynamic control of PH2. For NADH oxidation with ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity at pH of 7.0 only. For the acetate to propionate conversion, FT increased from 0.65 to unity with increasing PH2, which indicates thermodynamic control. For propionate to acetate and butyrate to acetate conversions, FT decreased to zero below the rumen range of PH2, indicating full thermodynamic suppression. For methanogenesis by archaea without cytochromes, FT differed from unity only below the rumen range of PH2, indicating no thermodynamic control. This theoretical investigation shows that thermodynamic control of PH2 on individual VFA produced and associated yield of hydrogen and methane cannot be explained without considering NADH oxidation. PMID:27783615

The annealing mechanism of the radiation-induced vacancy-oxygen defect in silicon

NASA Astrophysics Data System (ADS)

Voronkov, V. V.; Falster, R.; Londos, C. A.

2012-06-01

Annealing experiments on the VO defect (the A-centre) produced by radiation in silicon—reported long ago—have been re-examined in order to deduce the two most important properties of VO: its diffusivity and the equilibrium constant for VO dissociation into V + O. The loss rate of VO is accounted for by two major reactions. One is the conventional reaction of the trapping of mobile VO by oxygen, thus producing VO2. The other is an annihilation of vacancies, which coexist in an equilibrium ratio with VO, by radiation-produced interstitial point defects. In some cases, a minor reaction, VO + V, should also be taken into account. The emerging minor defects V2O are also highly mobile. They partially dissociate back and partially get trapped by oxygen producing stable V2O2 defects.

A chain reaction approach to modelling gene pathways.

PubMed

Cheng, Gary C; Chen, Dung-Tsa; Chen, James J; Soong, Seng-Jaw; Lamartiniere, Coral; Barnes, Stephen

2012-08-01

BACKGROUND: Of great interest in cancer prevention is how nutrient components affect gene pathways associated with the physiological events of puberty. Nutrient-gene interactions may cause changes in breast or prostate cells and, therefore, may result in cancer risk later in life. Analysis of gene pathways can lead to insights about nutrient-gene interactions and the development of more effective prevention approaches to reduce cancer risk. To date, researchers have relied heavily upon experimental assays (such as microarray analysis, etc.) to identify genes and their associated pathways that are affected by nutrient and diets. However, the vast number of genes and combinations of gene pathways, coupled with the expense of the experimental analyses, has delayed the progress of gene-pathway research. The development of an analytical approach based on available test data could greatly benefit the evaluation of gene pathways, and thus advance the study of nutrient-gene interactions in cancer prevention. In the present study, we have proposed a chain reaction model to simulate gene pathways, in which the gene expression changes through the pathway are represented by the species undergoing a set of chemical reactions. We have also developed a numerical tool to solve for the species changes due to the chain reactions over time. Through this approach we can examine the impact of nutrient-containing diets on the gene pathway; moreover, transformation of genes over time with a nutrient treatment can be observed numerically, which is very difficult to achieve experimentally. We apply this approach to microarray analysis data from an experiment which involved the effects of three polyphenols (nutrient treatments), epigallo-catechin-3-O-gallate (EGCG), genistein, and resveratrol, in a study of nutrient-gene interaction in the estrogen synthesis pathway during puberty. RESULTS: In this preliminary study, the estrogen synthesis pathway was simulated by a chain reaction model. By applying it to microarray data, the chain reaction model computed a set of reaction rates to examine the effects of three polyphenols (EGCG, genistein, and resveratrol) on gene expression in this pathway during puberty. We first performed statistical analysis to test the time factor on the estrogen synthesis pathway. Global tests were used to evaluate an overall gene expression change during puberty for each experimental group. Then, a chain reaction model was employed to simulate the estrogen synthesis pathway. Specifically, the model computed the reaction rates in a set of ordinary differential equations to describe interactions between genes in the pathway (A reaction rate K of A to B represents gene A will induce gene B per unit at a rate of K; we give details in the "method" section). Since disparate changes of gene expression may cause numerical error problems in solving these differential equations, we used an implicit scheme to address this issue. We first applied the chain reaction model to obtain the reaction rates for the control group. A sensitivity study was conducted to evaluate how well the model fits to the control group data at Day 50. Results showed a small bias and mean square error. These observations indicated the model is robust to low random noises and has a good fit for the control group. Then the chain reaction model derived from the control group data was used to predict gene expression at Day 50 for the three polyphenol groups. If these nutrients affect the estrogen synthesis pathways during puberty, we expect discrepancy between observed and expected expressions. Results indicated some genes had large differences in the EGCG (e.g., Hsd3b and Sts) and the resveratrol (e.g., Hsd3b and Hrmt12) groups. CONCLUSIONS: In the present study, we have presented (I) experimental studies of the effect of nutrient diets on the gene expression changes in a selected estrogen synthesis pathway. This experiment is valuable because it allows us to examine how the nutrient-containing diets regulate gene expression in the estrogen synthesis pathway during puberty; (II) global tests to assess an overall association of this particular pathway with time factor by utilizing generalized linear models to analyze microarray data; and (III) a chain reaction model to simulate the pathway. This is a novel application because we are able to translate the gene pathway into the chemical reactions in which each reaction channel describes gene-gene relationship in the pathway. In the chain reaction model, the implicit scheme is employed to efficiently solve the differential equations. Data analysis results show the proposed model is capable of predicting gene expression changes and demonstrating the effect of nutrient-containing diets on gene expression changes in the pathway. One of the objectives of this study is to explore and develop a numerical approach for simulating the gene expression change so that it can be applied and calibrated when the data of more time slices are available, and thus can be used to interpolate the expression change at a desired time point without conducting expensive experiments for a large amount of time points. Hence, we are not claiming this is either essential or the most efficient way for simulating this problem, rather a mathematical/numerical approach that can model the expression change of a large set of genes of a complex pathway. In addition, we understand the limitation of this experiment and realize that it is still far from being a complete model of predicting nutrient-gene interactions. The reason is that in the present model, the reaction rates were estimated based on available data at two time points; hence, the gene expression change is dependent upon the reaction rates and a linear function of the gene expressions. More data sets containing gene expression at various time slices are needed in order to improve the present model so that a non-linear variation of gene expression changes at different time can be predicted.

The A [plus] B [double arrow] C of Chemical Thermodynamics.

ERIC Educational Resources Information Center

Gerhartl, F. J.

1994-01-01

Basic chemical thermodynamics usually treats non-p,T reactions in a stepmotherly fashion. This paper covers the main aspects of the theoretical principles of reactions (p,T; V,T; p,H; and V,U) and offers results from the ABC computer program, which was designed to show the validity of the equilibrium theory to all types of reaction modes. (PVD)

Energy conservation and maximal entropy production in enzyme reactions.

PubMed

Dobovišek, Andrej; Vitas, Marko; Brumen, Milan; Fajmut, Aleš

2017-08-01

A procedure for maximization of the density of entropy production in a single stationary two-step enzyme reaction is developed. Under the constraints of mass conservation, fixed equilibrium constant of a reaction and fixed products of forward and backward enzyme rate constants the existence of maximum in the density of entropy production is demonstrated. In the state with maximal density of entropy production the optimal enzyme rate constants, the stationary concentrations of the substrate and the product, the stationary product yield as well as the stationary reaction flux are calculated. The test, whether these calculated values of the reaction parameters are consistent with their corresponding measured values, is performed for the enzyme Glucose Isomerase. It is found that calculated and measured rate constants agree within an order of magnitude, whereas the calculated reaction flux and the product yield differ from their corresponding measured values for less than 20 % and 5 %, respectively. This indicates that the enzyme Glucose Isomerase, considered in a non-equilibrium stationary state, as found in experiments using the continuous stirred tank reactors, possibly operates close to the state with the maximum in the density of entropy production. Copyright © 2017 Elsevier B.V. All rights reserved.

Interplay between Reaction and Phase Behaviour in Carbon Dioxide Hydrogenation to Methanol.

PubMed

Reymond, Helena; Amado-Blanco, Victor; Lauper, Andreas; Rudolf von Rohr, Philipp

2017-03-22

Condensation promotes CO 2 hydrogenation to CH 3 OH beyond equilibrium through in situ product separation. Although primordial for catalyst and reactor design, triggering conditions as well as the impact on sub-equilibrium reaction behaviour remain unclear. Herein we used an in-house designed micro-view-cell to gain chemical and physical insights into reaction and phase behaviour under high-pressure conditions over a commercial Cu/ZnO/Al 2 O 3 catalyst. Raman microscopy and video monitoring, combined with online gas chromatography analysis, allowed the complete characterisation of the reaction bulk up to 450 bar (1 bar=0.1 MPa) and 350 °C. Dew points of typical effluent streams related to a parametric study suggest that the improving reaction performance and reverting selectivities observed from 230 °C strongly correlate with (i) a regime transition from kinetic to thermodynamic, and (ii) a phase transition from a single supercritical to a biphasic reaction mixture. Our results advance a rationale behind transitioning CH 3 OH selectivities for an improved understanding of CO 2 hydrogenation under high pressure. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermodynamic Analysis of Chemically Reacting Mixtures-Comparison of First and Second Order Models.

PubMed

Pekař, Miloslav

2018-01-01

Recently, a method based on non-equilibrium continuum thermodynamics which derives thermodynamically consistent reaction rate models together with thermodynamic constraints on their parameters was analyzed using a triangular reaction scheme. The scheme was kinetically of the first order. Here, the analysis is further developed for several first and second order schemes to gain a deeper insight into the thermodynamic consistency of rate equations and relationships between chemical thermodynamic and kinetics. It is shown that the thermodynamic constraints on the so-called proper rate coefficient are usually simple sign restrictions consistent with the supposed reaction directions. Constraints on the so-called coupling rate coefficients are more complex and weaker. This means more freedom in kinetic coupling between reaction steps in a scheme, i.e., in the kinetic effects of other reactions on the rate of some reaction in a reacting system. When compared with traditional mass-action rate equations, the method allows a reduction in the number of traditional rate constants to be evaluated from data, i.e., a reduction in the dimensionality of the parameter estimation problem. This is due to identifying relationships between mass-action rate constants (relationships which also include thermodynamic equilibrium constants) which have so far been unknown.

Visualizing Chemistry: Investigations for Teachers.

ERIC Educational Resources Information Center

Ealy, Julie B.; Ealy, James L., Jr.

This book contains 101 investigations for chemistry classrooms. Topics include: (1) Physical Properties; (2) Reactions of Some Elements; (3) Reactions Involving Gases; (4) Energy Changes; (5) Solutions and Solubility; (6) Transition Metals and Complex Ions; (7) Kinetics and Equilibrium; (8) Acids and Bases; (9) Oxidation-Reduction; (10)…

Tested Demonstrations.

ERIC Educational Resources Information Center

Gilbert, George L., Ed.

1987-01-01

Describes two laboratory demonstrations in chemistry. One uses dry ice, freon, and freezer bags to demonstrate volume changes, vapor-liquid equilibrium, a simulation of a rain forest, and vaporization. The other uses the clock reaction technique to illustrate fast reactions and kinetic problems in releasing carbon dioxide during respiration. (TW)

Suppression of Ostwald Ripening by Chemical Reactions

NASA Astrophysics Data System (ADS)

Zwicker, David; Hyman, Anthony A.; Jülicher, Frank

2015-03-01

Emulsions consisting of droplets immersed in a fluid are typically unstable and coarsen over time. One important coarsening process is Ostwald ripening, which is driven by the surface tension of the droplets. Ostwald ripening must thus be suppressed to stabilize emulsions, e.g. to control the properties of pharmaceuticals, food, or cosmetics. Suppression of Ostwald ripening is also important in biological cells, which contain stable liquid-like compartments, e.g. germ granules, Cajal-bodies, and centrosomes. Such systems are often driven away from equilibrium by chemical reactions and can thus be called active emulsions. Here, we show that non-equilibrium chemical reactions can suppress Ostwald Ripening, leading to stable, monodisperse emulsions. We derive analytical approximations of the typical droplet size, droplet count, and time scale of the dynamics from a coarse-grained description of the droplet dynamics. We also compare these results to numerical simulations of the continuous concentration fields. Generally, we thus show how chemical reactions can be used to stabilize emulsions and to control their properties in technology and nature.

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

PubMed Central

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

2015-01-01

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

Elucidation of metabolic pathways from enzyme classification data.

PubMed

McDonald, Andrew G; Tipton, Keith F

2014-01-01

The IUBMB Enzyme List is widely used by other databases as a source for avoiding ambiguity in the recognition of enzymes as catalytic entities. However, it was not designed for metabolic pathway tracing, which has become increasingly important in systems biology. A Reactions Database has been created from the material in the Enzyme List to allow reactions to be searched by substrate/product, and pathways to be traced from any selected starting/seed substrate. An extensive synonym glossary allows searches by many of the alternative names, including accepted abbreviations, by which a chemical compound may be known. This database was necessary for the development of the application Reaction Explorer ( http://www.reaction-explorer.org ), which was written in Real Studio ( http://www.realsoftware.com/realstudio/ ) to search the Reactions Database and draw metabolic pathways from reactions selected by the user. Having input the name of the starting compound (the "seed"), the user is presented with a list of all reactions containing that compound and then selects the product of interest as the next point on the ensuing graph. The pathway diagram is then generated as the process iterates. A contextual menu is provided, which allows the user: (1) to remove a compound from the graph, along with all associated links; (2) to search the reactions database again for additional reactions involving the compound; (3) to search for the compound within the Enzyme List.

Absolute rate of the reaction of Cl(p-2) with molecular hydrogen from 200 - 500 K

NASA Technical Reports Server (NTRS)

Whytock, D. A.; Lee, J. H.; Michael, J. V.; Payne, W. A.; Stief, L. J.

1976-01-01

Rate constants for the reaction of atomic chlorine with hydrogen are measured from 200 - 500 K using the flash photolysis-resonance fluorescence technique. The results are compared with previous work and are discussed with particular reference to the equilibrium constant for the reaction and to relative rate data for chlorine atom reactions. Theoretical calculations, using the BEBO method with tunneling, give excellent agreement with experiment.

Sequestration of dyes from artificially prepared textile effluent using RSM-CCD optimized hybrid backbone based adsorbent-kinetic and equilibrium studies.

PubMed

Sukriti; Sharma, Jitender; Chadha, Amritpal Singh; Pruthi, Vaishali; Anand, Prerna; Bhatia, Jaspreet; Kaith, B S

2017-04-01

Present work reports the synthesis of semi-Interpenetrating Network Polymer (semi-IPN) using Gelatin-Gum xanthan hybrid backbone and polyvinyl alcohol in presence of l-tartaric acid and ammonium persulphate as the crosslinker-initiator system. Reaction parameters were optimized with Response Surface Methodology (RSM) in order to maximize the percent gel fraction of the synthesized sample. Polyvinyl alcohol, l-Tartaric acid, ammonium persulphate, reaction temperature, time and pH of the reaction medium were found to make an impact on the percentage gel fraction obtained. Incorporation of polyvinyl alcohol chains onto hybrid backbone and crosslinking between the different polymer chains were confirmed through techniques like FTIR, SEM-EDX and XRD. Semi-IPN was found to be very efficient in the removal of cationic dyes rhodamine-B (70%) and auramine-O (63%) from a mixture with an adsorbent dose of 700 mg, initial concentration of rhodamine-B 6 mgL -1 and auramine-O 26 mgL -1 , at an time interval of 22-25 h and 30 °C temp. Further to determine the nature of adsorption Langmuir and Freundlich adsorption isotherm models were studied and it was found that Langmuir adsorption isotherm was the best fit model for the removal of mixture of dyes. Kinetic studies for the sorption of dyes favored the reaction mechanism to occur via a pseudo second order pathway with R 2 value about 0.99. Copyright © 2017 Elsevier Ltd. All rights reserved.

REACTIONS OF MERCAPTANS. I. FORMATION OF 2-METHYL-2-THIAZOLINE-4- CARBOXYLIC ACID FROM N-ACETYLCYSTEINE. II. A SPECTROPHOTOMETRIC METHOD FOR STUDY OF THE REACTION OF RADIATION-PROTECTIVE MERCAPTANS WITH ARYL DISULFIDES

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

Smith, H.A. Jr.

1962-08-01

I. Methyl 2-methyl-2-thiazoline-4-carboxylate was synthesized and converted to the corresponding acid. The behavior of the carboxythiazoline in various concentrations of mineral acids was studied spectrophotometrically. The cyclization of N-acetylcysteine to form a thiazoline-ring compound in concentrated mineral acids was also studied by this means. N-Acetylcysteine in concentrated mineral acid solutions yielded 2-methyl-2-thiazoline-4-carboxylic acid, which also was obtained by controlied hydrolysis of the corresponding methyl ester. Hydrolysis of methyl 2-methyl2-thiazoline-4-carboxylate, pK 3.05, in 0.1M sodium hydroxide yielded the corresponding carboxythiazoline in solution, pK 2.20 and 4.95. The carboxythiazoline was hydrolyzed very slowly in 7M hydrochloric acid, but the velocity of reactionmore » increased with decreasing acid concentration to a maximum at about pH 1.7; the products were N- and Sacetylcysteine, as well as cysteine and acetic acid. At acid concentrations below 0.2M, the last two products were formed slowly, and a pseudo-equilibrium could be established between thiazolinium ion, N-, and S-acetylcysteine. Equilibrium constants were determined. II. 4,4'-Dithiobis (benzenesulfonic acid) (I) and 4,4'-dithiobis(1-naphthalenesulfonic acid) (II) were synthesized from sulfanilic and naphthionic acids, respectively. The absorption spectra of I and II and of the corresponding mercaptans were determined. The thiol-disuifide interchange reactions were studied by spectrophotometric means for the reactions of cysteine with I and with II, and the equilibrium constants were determined. The systems had spectra very similar to those of the respective mixed disuifides with cysteine, and it was not possible to determine the concentrations from absorbancy measurements. On the other hand, the mercaptide ions had spectra different from the other species, with maxima at 285 and 348 m mu , respectively, and the concentrations of the corresponding mercaptans could be calculated from the absorbancies at these wavelengths. By appropriate choice of the initial concentrations and of pH, the equilibrium concentrations could be made negligible, and the equilibrium constants determined.« less

Amorphous ices explained in terms of nonequilibrium phase transitions in supercooled water

NASA Astrophysics Data System (ADS)

Limmer, David; Chandler, David

2013-03-01

We analyze the phase diagram of supercooled water out-of-equilibrium using concepts from space-time thermodynamics and the dynamic facilitation theory of the glass transition, together with molecular dynamics simulations. We find that when water is driven out-of-equilibrium, it can exist in multiple amorphous states. In contrast, we find that when water is at equilibrium, it can exist in only one liquid state. The amorphous non-equilibrium states are solids, distinguished from the liquid by their lack of mobility, and distinguished from each other by their different densities and local structure. This finding explains the experimentally observed polyamorphism of water as a class of nonequilibrium phenomena involving glasses of different densities. While the amorphous solids can be long lived, they are thermodynamically unstable. When allowed to relax to equilibrium, they crystallize with pathways that pass first through liquid state configurations and then to ordered ice.

Saturation kinetics in phenolic O-H bond oxidation by a mononuclear Mn(III)-OH complex derived from dioxygen.

PubMed

Wijeratne, Gayan B; Corzine, Briana; Day, Victor W; Jackson, Timothy A

2014-07-21

The mononuclear hydroxomanganese(III) complex, [Mn(III)(OH)(dpaq)](+), which is supported by the amide-containing N5 ligand dpaq (dpaq = 2-[bis(pyridin-2-ylmethyl)]amino-N-quinolin-8-yl-acetamidate) was generated by treatment of the manganese(II) species, [Mn(II)(dpaq)](OTf), with dioxygen in acetonitrile solution at 25 °C. This oxygenation reaction proceeds with essentially quantitative yield (greater than 98% isolated yield) and represents a rare example of an O2-mediated oxidation of a manganese(II) complex to generate a single product. The X-ray diffraction structure of [Mn(III)(OH)(dpaq)](+) reveals a short Mn-OH distance of 1.806(13) Å, with the hydroxo moiety trans to the amide function of the dpaq ligand. No shielding of the hydroxo group is observed in the solid-state structure. Nonetheless, [Mn(III)(OH)(dpaq)](+) is remarkably stable, decreasing in concentration by only 10% when stored in MeCN at 25 °C for 1 week. The [Mn(III)(OH)(dpaq)](+) complex participates in proton-coupled electron transfer reactions with substrates with relatively weak O-H and C-H bonds. For example, [Mn(III)(OH)(dpaq)](+) oxidizes TEMPOH (TEMPOH = 2,2'-6,6'-tetramethylpiperidine-1-ol), which has a bond dissociation free energy (BDFE) of 66.5 kcal/mol, in MeCN at 25 °C. The hydrogen/deuterium kinetic isotope effect of 1.8 observed for this reaction implies a concerted proton-electron transfer pathway. The [Mn(III)(OH)(dpaq)](+) complex also oxidizes xanthene (C-H BDFE of 73.3 kcal/mol in dimethylsulfoxide) and phenols, such as 2,4,6-tri-t-butylphenol, with BDFEs of less than 79 kcal/mol. Saturation kinetics were observed for phenol oxidation, implying an initial equilibrium prior to the rate-determining step. On the basis of a collective body of evidence, the equilibrium step is attributed to the formation of a hydrogen-bonding complex between [Mn(III)(OH)(dpaq)](+) and the phenol substrates.

An Easy and Effective Demonstration of Enzyme Stereospecificity and Equilibrium Thermodynamics

ERIC Educational Resources Information Center

Herdman, Chelsea; Dickman, Michael

2011-01-01

Enzyme stereospecificity and equilibrium thermodynamics can be demonstrated using the coupling of two amino acid derivatives by Thermoase C160. This protease will catalyze peptide bond formation between Z-L-AspOH and L-PheOMe to form the Aspartame precursor Z-L-Asp-L-PheOMe. Reaction completion manifests itself by precipitation of the product. As…

Methanol synthesis on ZnO(0001{sup ¯}). IV. Reaction mechanisms and electronic structure

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

Frenzel, Johannes, E-mail: johannes.frenzel@theochem.rub.de; Marx, Dominik

2014-09-28

Methanol synthesis from CO and H{sub 2} over ZnO, which requires high temperatures and high pressures giving rise to a complex interplay of physical and chemical processes over this heterogeneous catalyst surface, is investigated using ab initio simulations. The redox properties of the surrounding gas phase are known to directly impact on the catalyst properties and thus, set the overall catalytic reactivity of this easily reducible oxide material. In Paper III of our series [J. Kiss, J. Frenzel, N. N. Nair, B. Meyer, and D. Marx, J. Chem. Phys. 134, 064710 (2011)] we have qualitatively shown that for the partiallymore » hydroxylated and defective ZnO(0001{sup ¯}) surface there exists an intricate network of surface chemical reactions. In the present study, we employ advanced molecular dynamics techniques to resolve in detail this reaction network in terms of elementary steps on the defective surface, which is in stepwise equilibrium with the gas phase. The two individual reduction steps were investigated by ab initio metadynamics sampling of free energy landscapes in three-dimensional reaction subspaces. By also sampling adsorption and desorption processes and thus molecular species that are in the gas phase but close to the surface, our approach successfully generated several alternative pathways of methanol synthesis. The obtained results suggest an Eley-Rideal mechanism for both reduction steps, thus involving “near-surface” molecules from the gas phase, to give methanol preferentially over a strongly reduced catalyst surface, while important side reactions are of Langmuir-Hinshelwood type. Catalyst re-reduction by H{sub 2} stemming from the gas phase is a crucial process after each reduction step in order to maintain the catalyst's activity toward methanol formation and to close the catalytic cycle in some reaction channels. Furthermore, the role of oxygen vacancies, side reactions, and spectator species is investigated and mechanistic details are discussed based on extensive electronic structure analysis.« less

Spreading out of perturbations in reversible reaction networks

NASA Astrophysics Data System (ADS)

Maslov, Sergei; Sneppen, Kim; Ispolatov, I.

2007-08-01

Using an example of physical interactions between proteins, we study how a perturbation propagates in the equilibrium of a network of reversible reactions governed by the law of mass action. We introduce a matrix formalism to describe the linear response of all equilibrium concentrations to shifts in total abundances of individual reactants, and reveal its heuristic analogy to the flow of electric current in a network of resistors. Our main conclusion is that, on average, the induced changes in equilibrium concentrations decay exponentially as a function of network distance from the source of perturbation. We analyze how this decay is influenced by such factors as the topology of a network, binding strength, and correlations between concentrations of neighboring nodes. We find that the minimal branching of the network, small values of dissociation constants, and low equilibrium free (unbound) concentrations of reacting substances all decrease the decay constant and thus increase the range of propagation. Exact analytic expressions for the decay constant are obtained for the case of equally strong interactions and uniform as well as oscillating concentrations on the Bethe lattice. Our general findings are illustrated using a real network of protein-protein interactions in baker's yeast with experimentally determined protein concentrations.

Determination of enzyme thermal parameters for rational enzyme engineering and environmental/evolutionary studies.

PubMed

Lee, Charles K; Monk, Colin R; Daniel, Roy M

2013-01-01

Of the two independent processes by which enzymes lose activity with increasing temperature, irreversible thermal inactivation and rapid reversible equilibration with an inactive form, the latter is only describable by the Equilibrium Model. Any investigation of the effect of temperature upon enzymes, a mandatory step in rational enzyme engineering and study of enzyme temperature adaptation, thus requires determining the enzymes' thermodynamic parameters as defined by the Equilibrium Model. The necessary data for this procedure can be collected by carrying out multiple isothermal enzyme assays at 3-5°C intervals over a suitable temperature range. If the collected data meet requirements for V max determination (i.e., if the enzyme kinetics are "ideal"), then the enzyme's Equilibrium Model parameters (ΔH eq, T eq, ΔG (‡) cat, and ΔG (‡) inact) can be determined using a freely available iterative model-fitting software package designed for this purpose.Although "ideal" enzyme reactions are required for determination of all four Equilibrium Model parameters, ΔH eq, T eq, and ΔG (‡) cat can be determined from initial (zero-time) rates for most nonideal enzyme reactions, with substrate saturation being the only requirement.

Quantifying differences in the impact of variable chemistry on equilibrium uranium(VI) adsorption properties of aquifer sediments

USGS Publications Warehouse

Stoliker, Deborah L.; Kent, Douglas B.; Zachara, John M.

2011-01-01

Uranium adsorption-desorption on sediment samples collected from the Hanford 300-Area, Richland, WA varied extensively over a range of field-relevant chemical conditions, complicating assessment of possible differences in equilibrium adsorption properties. Adsorption equilibrium was achieved in 500-1000 h although dissolved uranium concentrations increased over thousands of hours owing to changes in aqueous chemical composition driven by sediment-water reactions. A nonelectrostatic surface complexation reaction, >SOH + UO22+ + 2CO32- = >SOUO2(CO3HCO3)2-, provided the best fit to experimental data for each sediment sample resulting in a range of conditional equilibrium constants (logKc) from 21.49 to 21.76. Potential differences in uranium adsorption properties could be assessed in plots based on the generalized mass-action expressions yielding linear trends displaced vertically by differences in logKc values. Using this approach, logKc values for seven sediment samples were not significantly different. However, a significant difference in adsorption properties between one sediment sample and the fines (Kc uncertainty were improved by capturing all data points within experimental errors. The mass-action expression plots demonstrate that applying models outside the range of conditions used in model calibration greatly increases potential errors.

Shock and Laser Induced Non-Equilibrium Chemistry in Molecular Energetics

NASA Astrophysics Data System (ADS)

Wood, Mitchell; Cherukara, Mathew; Kober, Edward; Strachan, Alejandro

2015-06-01

In this study, we have used large scale reactive molecular dynamics (MD) simulations to study how contrasting initiation mechanisms from either shock or electromagnetic insults compare to traditional thermal initiation. We will show how insults of equal strength but different character can yield vastly different reaction profiles and thus the evolution of hot-spots. For shocked RDX (Up = 2km/s), we find that the collapse of a cylindrical 40 nm diameter pore leads to a significant amount of non-equilibrium reactions followed by the formation of a sustained deflagration wave. In contrast, a hot spot that is seeded into a statically compressed crystal with matching size and temperature will quench over the same timescale, highlighting the importance of insult type. Furthermore, MD simulations of electromagnetic insults coupled to intramolecular vibrations have shown, in some cases, mode specific initial chemistry and altered kinetics of the subsequent decomposition. By leveraging spectroscopic and chemical information gathered in our MD simulations, we have been able to identify and track non-equilibrium vibrational states of these materials and correlate them to these observed changes. Implications of insult dependent reactivity and non-equilibrium chemistry will be discussed.

Protein Folding Mechanism of the Dimeric AmphiphysinII/Bin1 N-BAR Domain

PubMed Central

Gruber, Tobias; Balbach, Jochen

2015-01-01

The human AmphyphisinII/Bin1 N-BAR domain belongs to the BAR domain superfamily, whose members sense and generate membrane curvatures. The N-BAR domain is a 57 kDa homodimeric protein comprising a six helix bundle. Here we report the protein folding mechanism of this protein as a representative of this protein superfamily. The concentration dependent thermodynamic stability was studied by urea equilibrium transition curves followed by fluorescence and far-UV CD spectroscopy. Kinetic unfolding and refolding experiments, including rapid double and triple mixing techniques, allowed to unravel the complex folding behavior of N-BAR. The equilibrium unfolding transition curve can be described by a two-state process, while the folding kinetics show four refolding phases, an additional burst reaction and two unfolding phases. All fast refolding phases show a rollover in the chevron plot but only one of these phases depends on the protein concentration reporting the dimerization step. Secondary structure formation occurs during the three fast refolding phases. The slowest phase can be assigned to a proline isomerization. All kinetic experiments were also followed by fluorescence anisotropy detection to verify the assignment of the dimerization step to the respective folding phase. Based on these experiments we propose for N-BAR two parallel folding pathways towards the homodimeric native state depending on the proline conformation in the unfolded state. PMID:26368922

Insights into the Adsorption of Carbon Dioxide in the Presence of Water Vapor Utilizing a Low Molecular Weight Polyethylenimine-Impregnated CARiACT Silica Sorbent

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

Monazam, Esmail R.; Breault, Ronald W.; Fauth, Daniel J.

Thermogravimetric analysis was employed to investigate the CO 2 and H 2O adsorption rates and water vapor equilibrium on anhydrous and pre-hydrate linear polyethylenimine (LPEI) sorbent impregnated within a commercially functional CARiACT G10 (HPV) silica support. Water vapor experiments utilizing specific humidity of 2%, 8%, and 16% in contact with an anhydrous PEI sorbent resulted in proportional quantities of water vapor uptake. Subsequently, both anhydrous and pre-hydrated PEI-impregnated sorbents were made available to identical humidified gaseous streams containing a CO 2 concentration of 10% at 60oC. CO 2 capacity increased dramatically in the presence of different levels of humidity. Variousmore » kinetic models were systematically employed to interpret the experimental data including single and multiple-step models. The rate data was best represented by a reaction mechanism pathway involving the interplay of CO 2 with PEI-impregnated sorbents exhibited a quick adsorption phase followed by a slow approach to equilibrium. Moreover, a phenomenological rate model was developed to describe the dynamic H 2O and CO 2 uptakes at specific humidity levels studied. The kinetic study showed good agreement with experimental data. Furthermore, the effects observed during the adsorption and hydration are shown to be complementary to known chemical and physical transformations within the polyethylenimine’s macromolecule.« less

Insights into the Adsorption of Carbon Dioxide in the Presence of Water Vapor Utilizing a Low Molecular Weight Polyethylenimine-Impregnated CARiACT Silica Sorbent

DOE PAGES

Monazam, Esmail R.; Breault, Ronald W.; Fauth, Daniel J.; ...

2017-07-20

Thermogravimetric analysis was employed to investigate the CO 2 and H 2O adsorption rates and water vapor equilibrium on anhydrous and pre-hydrate linear polyethylenimine (LPEI) sorbent impregnated within a commercially functional CARiACT G10 (HPV) silica support. Water vapor experiments utilizing specific humidity of 2%, 8%, and 16% in contact with an anhydrous PEI sorbent resulted in proportional quantities of water vapor uptake. Subsequently, both anhydrous and pre-hydrated PEI-impregnated sorbents were made available to identical humidified gaseous streams containing a CO 2 concentration of 10% at 60oC. CO 2 capacity increased dramatically in the presence of different levels of humidity. Variousmore » kinetic models were systematically employed to interpret the experimental data including single and multiple-step models. The rate data was best represented by a reaction mechanism pathway involving the interplay of CO 2 with PEI-impregnated sorbents exhibited a quick adsorption phase followed by a slow approach to equilibrium. Moreover, a phenomenological rate model was developed to describe the dynamic H 2O and CO 2 uptakes at specific humidity levels studied. The kinetic study showed good agreement with experimental data. Furthermore, the effects observed during the adsorption and hydration are shown to be complementary to known chemical and physical transformations within the polyethylenimine’s macromolecule.« less

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.

Coupled alkali feldspar dissolution and secondary mineral precipitation in batch systems: 4. Numerical modeling of kinetic reaction paths

NASA Astrophysics Data System (ADS)

Zhu, Chen; Lu, Peng; Zheng, Zuoping; Ganor, Jiwchar

2010-07-01

This paper explores how dissolution and precipitation reactions are coupled in batch reactor experimental systems at elevated temperatures. This is the fourth paper in our series of "Coupled Alkali Feldspar Dissolution and Secondary Mineral Precipitation in Batch Systems". In our third paper, we demonstrated via speciation-solubility modeling that partial equilibrium between secondary minerals and aqueous solutions was not attained in feldspar hydrolysis batch reactors at 90-300 °C and that a strong coupling between dissolution and precipitation reactions follows as a consequence of the slower precipitation of secondary minerals ( Zhu and Lu, 2009). Here, we develop this concept further by using numerical reaction path models to elucidate how the dissolution and precipitation reactions are coupled. Modeling results show that a quasi-steady state was reached. At the quasi-steady state, dissolution reactions proceeded at rates that are orders of magnitude slower than the rates measured at far from equilibrium. The quasi-steady state is determined by the relative rate constants, and strongly influenced by the function of Gibbs free energy of reaction ( ΔG) in the rate laws. To explore the potential effects of fluid flow rates on the coupling of reactions, we extrapolate a batch system ( Ganor et al., 2007) to open systems and simulated one-dimensional reactive mass transport for oligoclase dissolution and kaolinite precipitation in homogeneous porous media. Different steady states were achieved at different locations along the one-dimensional domain. The time-space distribution and saturation indices (SI) at the steady states were a function of flow rates for a given kinetic model. Regardless of the differences in SI, the ratio between oligoclase dissolution rates and kaolinite precipitation rates remained 1.626, as in the batch system case ( Ganor et al., 2007). Therefore, our simulation results demonstrated coupling among dissolution, precipitation, and flow rates. Results reported in this communication lend support to our hypothesis that slow secondary mineral precipitation explains part of the well-known apparent discrepancy between lab measured and field estimated feldspar dissolution rates ( Zhu et al., 2004). Here we show how the slow secondary mineral precipitation provides a regulator to explain why the systems are held close to equilibrium and show how the most often-quoted "near equilibrium" explanation for an apparent field-lab discrepancy can work quantitatively. The substantiated hypothesis now offers the promise of reconciling part of the apparent field-lab discrepancy.

New force replica exchange method and protein folding pathways probed by force-clamp technique.

PubMed

Kouza, Maksim; Hu, Chin-Kun; Li, Mai Suan

2008-01-28

We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. This new approach was applied to obtain the force-temperature phase diagram and other thermodynamical quantities of the three-domain ubiquitin. Using the C(alpha)-Go model and the Langevin dynamics, we have shown that the refolding pathways of single ubiquitin depend on which terminus is fixed. If the N end is fixed then the folding pathways are different compared to the case when both termini are free, but fixing the C terminal does not change them. Surprisingly, we have found that the anchoring terminal does not affect the pathways of individual secondary structures of three-domain ubiquitin, indicating the important role of the multidomain construction. Therefore, force-clamp experiments, in which one end of a protein is kept fixed, can probe the refolding pathways of a single free-end ubiquitin if one uses either the polyubiquitin or a single domain with the C terminus anchored. However, it is shown that anchoring one end does not affect refolding pathways of the titin domain I27, and the force-clamp spectroscopy is always capable to predict folding sequencing of this protein. We have obtained the reasonable estimate for unfolding barrier of ubiquitin, using the microscopic theory for the dependence of unfolding time on the external force. The linkage between residue Lys48 and the C terminal of ubiquitin is found to have the dramatic effect on the location of the transition state along the end-to-end distance reaction coordinate, but the multidomain construction leaves the transition state almost unchanged. We have found that the maximum force in the force-extension profile from constant velocity force pulling simulations depends on temperature nonlinearly. However, for some narrow temperature interval this dependence becomes linear, as have been observed in recent experiments.

Hydrogen oxidation mechanisms on Ni/yttria stabilized zirconia anodes: Separation of reaction pathways by geometry variation of pattern electrodes

NASA Astrophysics Data System (ADS)

Doppler, M. C.; Fleig, J.; Bram, M.; Opitz, A. K.

2018-03-01

Nickel/yttria stabilized zirconia (YSZ) electrodes are affecting the overall performance of solid oxide fuel cells (SOFCs) in general and strongly contribute to the cell resistance in case of novel metal supported SOFCs in particular. The electrochemical fuel conversion mechanisms in these electrodes are, however, still only partly understood. In this study, micro-structured Ni thin film electrodes on YSZ with 15 different geometries are utilized to investigate reaction pathways for the hydrogen electro-oxidation at Ni/YSZ anodes. From electrodes with constant area but varying triple phase boundary (TPB) length a contribution to the electro-catalytic activity is found that does not depend on the TPB length. This additional activity could clearly be attributed to a yet unknown reaction pathway scaling with the electrode area. It is shown that this area related pathway has significantly different electrochemical behavior compared to the TPB pathway regarding its thermal activation, sulfur poisoning behavior, and H2/H2O partial pressure dependence. Moreover, possible reaction mechanisms of this reaction pathway are discussed, identifying either a pathway based on hydrogen diffusion through Ni with water release at the TPB or a path with oxygen diffusion through Ni to be a very likely explanation for the experimental results.

Incorporation of a Chemical Equilibrium Equation of State into LOCI-Chem

NASA Technical Reports Server (NTRS)

Cox, Carey F.

2005-01-01

Renewed interest in development of advanced high-speed transport, reentry vehicles and propulsion systems has led to a resurgence of research into high speed aerodynamics. As this flow regime is typically dominated by hot reacting gaseous flow, efficient models for the characteristic chemical activity are necessary for accurate and cost effective analysis and design of aerodynamic vehicles that transit this regime. The LOCI-Chem code recently developed by Ed Luke at Mississippi State University for NASA/MSFC and used by NASA/MSFC and SSC represents an important step in providing an accurate, efficient computational tool for the simulation of reacting flows through the use of finite-rate kinetics [3]. Finite rate chemistry however, requires the solution of an additional N-1 species mass conservation equations with source terms involving reaction kinetics that are not fully understood. In the equilibrium limit, where the reaction rates approach infinity, these equations become very stiff. Through the use of the assumption of local chemical equilibrium the set of governing equations is reduced back to the usual gas dynamic equations, and thus requires less computation, while still allowing for the inclusion of reacting flow phenomenology. The incorporation of a chemical equilibrium equation of state module into the LOCI-Chem code was the primary objective of the current research. The major goals of the project were: (1) the development of a chemical equilibrium composition solver, and (2) the incorporation of chemical equilibrium solver into LOCI-Chem. Due to time and resource constraints, code optimization was not considered unless it was important to the proper functioning of the code.

Modeling of molecular nitrogen collisions and dissociation processes for direct simulation Monte Carlo.

PubMed

Parsons, Neal; Levin, Deborah A; van Duin, Adri C T; Zhu, Tong

2014-12-21

The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision cross sections and reaction probabilities. However, total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic flows. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For hypersonic flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the N2(Σg+1)-N2(Σg+1) collision pair for conditions expected in hypersonic shocks using a new potential energy surface developed using a ReaxFF fit to recent advanced ab initio calculations. The MD/QCT-computed reaction probabilities were found to exhibit better physical behavior and predict less dissociation than the baseline total collision energy reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model compared well with computed equilibrium reaction rates and shock-tube data. In addition, the MD/QCT-computed total cross sections were found to agree well with established variable hard sphere total cross sections.

ReactPRED: a tool to predict and analyze biochemical reactions.

PubMed

Sivakumar, Tadi Venkata; Giri, Varun; Park, Jin Hwan; Kim, Tae Yong; Bhaduri, Anirban

2016-11-15

Biochemical pathways engineering is often used to synthesize or degrade target chemicals. In silico screening of the biochemical transformation space allows predicting feasible reactions, constituting these pathways. Current enabling tools are customized to predict reactions based on pre-defined biochemical transformations or reaction rule sets. Reaction rule sets are usually curated manually and tailored to specific applications. They are not exhaustive. In addition, current systems are incapable of regulating and refining data with an aim to tune specificity and sensitivity. A robust and flexible tool that allows automated reaction rule set creation along with regulated pathway prediction and analyses is a need. ReactPRED aims to address the same. ReactPRED is an open source flexible and customizable tool enabling users to predict biochemical reactions and pathways. The tool allows automated reaction rule creation from a user defined reaction set. Additionally, reaction rule degree and rule tolerance features allow refinement of predicted data. It is available as a flexible graphical user interface and a console application. ReactPRED is available at: https://sourceforge.net/projects/reactpred/ CONTACT: anirban.b@samsung.com or ty76.kim@samsung.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Sparse Partial Equilibrium Tables in Chemically Resolved Reactive Flow

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

Vitello, P; Fried, L E; Pudliner, B

2003-07-14

The detonation of an energetic material is the result of a complex interaction between kinetic chemical reactions and hydrodynamics. Unfortunately, little is known concerning the detailed chemical kinetics of detonations in energetic materials. CHEETAH uses rate laws to treat species with the slowest chemical reactions, while assuming other chemical species are in equilibrium. CHEETAH supports a wide range of elements and condensed detonation products and can also be applied to gas detonations. A sparse hash table of equation of state values, called the ''cache'' is used in CHEETAH to enhance the efficiency of kinetic reaction calculations. For large-scale parallel hydrodynamicmore » calculations, CHEETAH uses MPI communication to updates to the cache. We present here details of the sparse caching model used in the CHEETAH. To demonstrate the efficiency of modeling using a sparse cache model we consider detonations in energetic materials.« less

Thermochemistry and Kinetics of the Cl+O2 Association Reaction

NASA Technical Reports Server (NTRS)

Nicovich, J. M.; Kreutter, K. D.; Shackelford, C. J.; Wine, P. H.

1997-01-01

Laser flash photolysis of Cl2/O2 mixtures has been employed in conjunction with Cl((sup 2)P(sub 3/2)) detection by time-resolved fluorescence spectroscopy to investigate equilibration kinetics for the reactions Cl + O2 + O is in equilibrium with ClOO + O2 at temperatures of 181-200 K and O2 pressures of 15-40 Torr. The third-order rate coefficient for the association reaction at 186.5 +/- 5.5 K is (8.9 +/- 2.9) x 10(exp -33) cm(exp 6) molecule(exp -2) s(exp -1) and the equilibrium constant (K(p)) at 185.4 K is 18.9 atm(exp -1) (factor of 1.7 uncertainty). A third law analysis of our data leads to a value for the Cl-OO bond dissociation energy of 4.76 +/- 0.49 kcal mol(exp -1).

Sparse Partial Equilibrium Tables in Chemically Resolved Reactive Flow

NASA Astrophysics Data System (ADS)

Vitello, Peter; Fried, Laurence E.; Pudliner, Brian; McAbee, Tom

2004-07-01

The detonation of an energetic material is the result of a complex interaction between kinetic chemical reactions and hydrodynamics. Unfortunately, little is known concerning the detailed chemical kinetics of detonations in energetic materials. CHEETAH uses rate laws to treat species with the slowest chemical reactions, while assuming other chemical species are in equilibrium. CHEETAH supports a wide range of elements and condensed detonation products and can also be applied to gas detonations. A sparse hash table of equation of state values is used in CHEETAH to enhance the efficiency of kinetic reaction calculations. For large-scale parallel hydrodynamic calculations, CHEETAH uses parallel communication to updates to the cache. We present here details of the sparse caching model used in the CHEETAH coupled to an ALE hydrocode. To demonstrate the efficiency of modeling using a sparse cache model we consider detonations in energetic materials.

Enhanced reaction kinetics in biological cells

NASA Astrophysics Data System (ADS)

Loverdo, C.; Bénichou, O.; Moreau, M.; Voituriez, R.

2008-02-01

The cell cytoskeleton is a striking example of an `active' medium driven out-of-equilibrium by ATP hydrolysis. Such activity has been shown to have a spectacular impact on the mechanical and rheological properties of the cellular medium, as well as on its transport properties: a generic tracer particle freely diffuses as in a standard equilibrium medium, but also intermittently binds with random interaction times to motor proteins, which perform active ballistic excursions along cytoskeletal filaments. Here, we propose an analytical model of transport-limited reactions in active media, and show quantitatively how active transport can enhance reactivity for large enough tracers such as vesicles. We derive analytically the average interaction time with motor proteins that optimizes the reaction rate, and reveal remarkable universal features of the optimal configuration. We discuss why active transport may be beneficial in various biological examples: cell cytoskeleton, membranes and lamellipodia, and tubular structures such as axons.

The effect of photochemical models on calculated equilibria and cooling rates in the stratosphere

NASA Technical Reports Server (NTRS)

Blake, D.; Lindzen, R. S.

1973-01-01

Simplified models were developed for radiative heating and cooling and for ozone photochemistry in the region 22-60 km. The latter permit the inclusion of nitrogen and hydrogen reactions in addition to simple oxygen reactions. The simplicity of the scheme facilitates the use of a wide variety of cooling and reaction rates. It is shown that joint radiative-photochemical equilibrium is appropriate to the mean state of the atmosphere between 35 and 60 km. The relaxation of perturbations from joint radiative-photochemical equilibrium was also investigated. In all cases the coupling between temperature dependent ozone photochemistry and radiation lead to a reduction of the thermal relaxation time from its purely radiative value. The latter, which amounts to about 10 days, is reduced to 2-4 days at heights of 31-35 km. This greatly enhances the dissipation of waves traveling through the stratosphere.

Interaction between fiscal and monetary policy in a dynamic nonlinear model.

PubMed

Bertella, Mario A; Rego, Henio A; Neris, Celso; Silva, Jonathas N; Podobnik, Boris; Stanley, H Eugene

2015-01-01

The objective of this study is to verify the dynamics between fiscal policy, measured by public debt, and monetary policy, measured by a reaction function of a central bank. Changes in monetary policies due to deviations from their targets always generate fiscal impacts. We examine two policy reaction functions: the first related to inflation targets and the second related to economic growth targets. We find that the condition for stable equilibrium is more restrictive in the first case than in the second. We then apply our simulation model to Brazil and United Kingdom and find that the equilibrium is unstable in the Brazilian case but stable in the UK case.

Interaction between Fiscal and Monetary Policy in a Dynamic Nonlinear Model

PubMed Central

Bertella, Mario A.; Rego, Henio A.; Neris, Celso; Silva, Jonathas N.; Podobnik, Boris; Stanley, H. Eugene

2015-01-01

The objective of this study is to verify the dynamics between fiscal policy, measured by public debt, and monetary policy, measured by a reaction function of a central bank. Changes in monetary policies due to deviations from their targets always generate fiscal impacts. We examine two policy reaction functions: the first related to inflation targets and the second related to economic growth targets. We find that the condition for stable equilibrium is more restrictive in the first case than in the second. We then apply our simulation model to Brazil and United Kingdom and find that the equilibrium is unstable in the Brazilian case but stable in the UK case. PMID:25799581

Kinetics of Acid Reactions: Making Sense of Associated Concepts

ERIC Educational Resources Information Center

Tan, Kim Chwee Daniel; Treagust, David F.; Chandrasegaran, A. L.; Mocerino, Mauro

2010-01-01

In chemical kinetics, in addition to the concepts related to kinetics, stoichiometry, chemical equilibrium and the characteristics of the reactants are often involved when comparing the rates of different reactions, making such comparisons very challenging for students at all levels, as well as for pre-service science teachers. Consequently, four…

Mixed Potentials: Experimental Illustrations of an Important Concept in Practical Electrochemistry.

ERIC Educational Resources Information Center

Power, G. P.; Ritchie, I. M.

1983-01-01

Presents a largely experimental approach to the concept of mixed potentials, pointing out the close parallel that exists between equilibrium potentials. Describes several important examples of mixed potentials, providing current-voltage and polarization curves and half reactions as examples. Includes a discussion of corrosion reactions and…

Origin of fatty acid synthesis - Thermodynamics and kinetics of reaction pathways

NASA Technical Reports Server (NTRS)

Weber, Arthur L.

1991-01-01

The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modern pathway is not primitive because it requires sophisticated enzymatic catalysis, an alternative pathway of primitive fatty acid synthesis is proposed that uses glycolaldehyde as a substrate. In contrast to the modern pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy. Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.

Rethinking pattern formation in reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Halatek, J.; Frey, E.

2018-05-01

The present theoretical framework for the analysis of pattern formation in complex systems is mostly limited to the vicinity of fixed (global) equilibria. Here we present a new theoretical approach to characterize dynamical states arbitrarily far from (global) equilibrium. We show that reaction-diffusion systems that are driven by locally mass-conserving interactions can be understood in terms of local equilibria of diffusively coupled compartments. Diffusive coupling generically induces lateral redistribution of the globally conserved quantities, and the variable local amounts of these quantities determine the local equilibria in each compartment. We find that, even far from global equilibrium, the system is well characterized by its moving local equilibria. We apply this framework to in vitro Min protein pattern formation, a paradigmatic model for biological pattern formation. Within our framework we can predict and explain transitions between chemical turbulence and order arbitrarily far from global equilibrium. Our results reveal conceptually new principles of self-organized pattern formation that may well govern diverse dynamical systems.

Effects of •OH and •NO radicals in the aqueous phase on H2O2 and \\text{NO}_{2}^{-} generated in plasma-activated medium

NASA Astrophysics Data System (ADS)

Kurake, Naoyuki; Tanaka, Hiromasa; Ishikawa, Kenji; Takeda, Keigo; Hashizume, Hiroshi; Nakamura, Kae; Kajiyama, Hiroaki; Kondo, Takashi; Kikkawa, Fumitaka; Mizuno, Masaaki; Hori, Masaru

2017-04-01

A plasma-activated medium (PAM), which means a cell-culture medium irradiated with cold atmospheric plasmas or non-equilibrium atmospheric pressure plasma (NEAPP), has shown strong antitumor effects on various kinds of cells such as gastric cancer cells, human lung adenocarcinoma cells, human breast cancer cells and so on. In order to clarify the mechanism, it is extremely important to investigate the behaviors of stable and unstable reactive oxygen nitrogen species in culture medium irradiated by NEAPP. The roles of hydroxyl radicals (•OH) and nitric oxide (•NO) were studied to understand the dominant synthetic pathways of H2O2 and \\text{NO}2- in culture medium irradiated with NEAPP. In the PAM, •OH in the aqueous phase was generated predominantly by photo-dissociation. However, most of the H2O2 nor \\text{NO}2- generated in the PAM did not originate from aqueous •OH and •NO. Pathways for the generation of H2O2 and \\text{NO}2- are suggested based on the high concentrations of intermediates generated at the gas/aqueous-phase interface following NEAPP irradiation. On the basis of these results, the reaction model of chemical species in the culture medium is proposed.

The mechanism and thermodynamics of transesterification of acetate-ester enolates in the gas phase

NASA Astrophysics Data System (ADS)

Haas, George W.; Giblin, Daryl E.; Gross, Michael L.

1998-01-01

In solution, base-catalyzed hydrolysis and transesterification of esters are initiated by hydroxide- or alkoxide-ion attack at the carbonyl carbon. At low pressures in the gas phase, however, transesterification proceeds by an attack of the enolate anion of an acetate ester on an alcohol. Fourier transform mass spectrometry (FTMS) indicates that the reaction is the second-order process: -CH2-CO2-R + R'-OH --> - CH2-CO2-R' + R-OH and there is little to no detectable production of either alkoxide anion. Labeling studies show that the product and reactant enolate anion esters undergo exchange of hydrogens located [alpha] to the carbonyl carbon with the deuterium of R'-OD. The extent of the H/D exchange increases with reaction time, pointing to a short-lived intermediate. The alcoholysis reaction rate constants increase with increasing acidity of the primary, straight-chained alkyl alcohols, whereas steric effects associated with branched alcohols cause the rate constants to decrease. Equilibrium constants, which were determined directly from measurements at equilibrium and which were calculated from the forward and reverse rate constants, are near unity and show internal consistency. In the absence of steric effects, the larger enolate is always the favored product at equilibrium. The intermediate for the transesterification reaction, which can be generated at a few tenths of a torr in a tandem mass spectrometer, is tetrahedral, but other adducts that are collisionally stabilized under these conditions are principally loosely bound complexes.

Organic Acids: The Pools of Fixed Carbon Involved in Redox Regulation and Energy Balance in Higher Plants

PubMed Central

Igamberdiev, Abir U.; Eprintsev, Alexander T.

2016-01-01

Organic acids are synthesized in plants as a result of the incomplete oxidation of photosynthetic products and represent the stored pools of fixed carbon accumulated due to different transient times of conversion of carbon compounds in metabolic pathways. When redox level in the cell increases, e.g., in conditions of active photosynthesis, the tricarboxylic acid (TCA) cycle in mitochondria is transformed to a partial cycle supplying citrate for the synthesis of 2-oxoglutarate and glutamate (citrate valve), while malate is accumulated and participates in the redox balance in different cell compartments (via malate valve). This results in malate and citrate frequently being the most accumulated acids in plants. However, the intensity of reactions linked to the conversion of these compounds can cause preferential accumulation of other organic acids, e.g., fumarate or isocitrate, in higher concentrations than malate and citrate. The secondary reactions, associated with the central metabolic pathways, in particularly with the TCA cycle, result in accumulation of other organic acids that are derived from the intermediates of the cycle. They form the additional pools of fixed carbon and stabilize the TCA cycle. Trans-aconitate is formed from citrate or cis-aconitate, accumulation of hydroxycitrate can be linked to metabolism of 2-oxoglutarate, while 4-hydroxy-2-oxoglutarate can be formed from pyruvate and glyoxylate. Glyoxylate, a product of either glycolate oxidase or isocitrate lyase, can be converted to oxalate. Malonate is accumulated at high concentrations in legume plants. Organic acids play a role in plants in providing redox equilibrium, supporting ionic gradients on membranes, and acidification of the extracellular medium. PMID:27471516

Aqueous geochemistry of low molecular weight hydrocarbons at elevated temperatures and pressures: constraints from mineral buffered laboratory experiments

NASA Astrophysics Data System (ADS)

Seewald, Jeffrey S.

2001-05-01

Organic matter, water, and minerals coexist at elevated temperatures and pressures in sedimentary basins and participate in a wide range of geochemical processes that includes the generation of oil and natural gas. A series of laboratory experiments were conducted at 300 to 350°C and 350 bars to examine chemical interactions involving low molecular weight aqueous hydrocarbons with water and Fe-bearing minerals under hydrothermal conditions. Mineral buffers composed of hematite-magnetite-pyrite, hematite-magnetite, and pyrite-pyrrhotite-magnetite were added to each experiment to fix the redox state of the fluid and the activity of reduced sulfur species. During each experiment the chemical system was externally modified by addition of ethene, ethane, propene, 1-butene, or n-heptane, and variations in the abundance of aqueous organic species were monitored as a function of time and temperature. Results of the experiments indicate that decomposition of aqueous n-alkanes proceeds through a series of oxidation and hydration reactions that sequentially produce alkenes, alcohols, ketones, and organic acids as reaction intermediaries. Organic acids subsequently undergo decarboxylation and/or oxidation reactions to form carbon dioxide and shorter chain saturated hydrocarbons. This alteration assemblage is compositionally distinct from that produced by thermal cracking under anhydrous conditions, indicating that the presence of water and minerals provide alternative reaction pathways for the decomposition of hydrocarbons. The rate of hydrocarbon oxidation decreases substantially under reducing conditions and in the absence of catalytically active aqueous sulfur species. These results represent compelling evidence that the stability of aqueous hydrocarbons at elevated temperatures in natural environments is not a simple function of time and temperature alone. Under the appropriate geochemical conditions, stepwise oxidation represents a mechanism for the decomposition of low molecular weight hydrocarbons and the production of methane-rich ("dry") natural gas. Evaluation of aqueous reaction products generated during the experiments within a thermodynamic framework indicates that alkane-alkene, alkene-ketone, and alkene-alcohol reactions attained metastable thermodynamic equilibrium states. This equilibrium included water and iron-bearing minerals, demonstrating the direct involvement of inorganic species as reactants during organic transformations. The high reactivity of water and iron-bearing minerals suggests that they represent abundant sources of hydrogen and oxygen available for the formation of hydrocarbons and oxygenated alteration products. Thus, variations in elemental kerogen composition may not accurately reflect the timing and extent of hydrocarbon, carbon dioxide, and organic acid generation in sedimentary basins. This study demonstrates that the stabilities of aqueous hydrocarbons are strongly influenced by inorganic sediment composition at elevated temperatures. Incorporation of such interactions into geochemical models will greatly improve prediction of the occurrence of hydrocarbons in natural environments over geologic time.

Facile chemical synthesis and equilibrium unfolding properties of CopG

PubMed Central

Wales, Thomas E.; Richardson, Jane S.; Fitzgerald, Michael C.

2004-01-01

The 45-amino acid polypeptide chain of the homodimeric transcriptional repressor, CopG, was chemically synthesized by stepwise solid phase peptide synthesis (SPPS) using a protocol based on Boc-chemistry. The product obtained from the synthesis was readily purified by reversed-phase HPLC to give a good overall yield (21% by weight). Moreover, the synthetic CopG constructs prepared in this work folded into three-dimensional structures similar to the wild-type protein prepared using conventional recombinant methods as judged by far UV-CD spectroscopy. A fluorescent CopG analog, (Y39W)CopG, was also designed and chemically synthesized to facilitate biophysical studies of CopG’s protein folding and assembly reaction. The guanidinium chloride-induced equilibrium unfolding properties of the wild-type CopG and (Y39W)CopG constructs in this work were characterized and used to develop a model for CopG’s equilibrium unfolding reaction. Our results indicate that CopG’s folding and assembly reaction is well modeled by a two-state process involving folded dimer and unfolded monomer. Using this model, ΔGf and m-values of −13.42 ± 0.04 kcal/mole dimer and 1.92 ± 0.01 kcal/(mole M) were calculated for CopG. PMID:15169951

O/S-1/ interactions - The product channels. [collisional electron quenching and chemical reaction pathway frequencies

NASA Technical Reports Server (NTRS)

Slanger, T. G.; Black, G.

1978-01-01

The first measurements are reported of the reaction pathways for the interaction between oxygen atoms in the 4.19 eV S-1 state, and four molecules, N2O, CO2, H2O, and NO. Distinction is made between three possible paths - quenching to O(D-1), quenching to O(P-3), and chemical reaction. With N2O, the most reasonable interpretation of the data indicates that there no reaction, in sharp contrast with the interaction between O(D-1) and N2O, which proceeds entirely by reaction. Similarly, there is no reaction with CO2. With H2O, the reactive pathway is the dominant one, although electronic quenching is not negligible. With NO, O(D-1) is the preferred product.

Extension of CE/SE method to non-equilibrium dissociating flows

NASA Astrophysics Data System (ADS)

Wen, C. Y.; Saldivar Massimi, H.; Shen, H.

2018-03-01

In this study, the hypersonic non-equilibrium flows over rounded nose geometries are numerically investigated by a robust conservation element and solution element (CE/SE) code, which is based on hybrid meshes consisting of triangular and quadrilateral elements. The dissociating and recombination chemical reactions as well as the vibrational energy relaxation are taken into account. The stiff source terms are solved by an implicit trapezoidal method of integration. Comparison with laboratory and numerical cases are provided to demonstrate the accuracy and reliability of the present CE/SE code in simulating hypersonic non-equilibrium flows.

The effects of finite-rate reactions at the gas/surface interface in support of thermal protection system design

NASA Astrophysics Data System (ADS)

Beerman, Adam Farrell

2011-12-01

Gas-surface modeling is dependent on material type and atmospheric reentry conditions. Lower molecular collisions at the low pressure trajectories make it more likely for occurrences of nonequilibrium, or finite-rate, reactions. Equilibrium is often assumed at the surface of a material as it is a subset of nonequilibrium and is easier to compute, though it can lead to overly conservative predictions. A case where a low density material experiences a low pressure trajectory and designed for equilibrium is the Stardust Return Capsule (SRC) with the Phenolic Impregnated Carbon Ablator (PICA) as its heatshield. Post-flight analysis of the recession on the SRC found that the prediction from the equilibrium model can be more than 50% larger than the measured recession. The Modified Park Model was chosen as the finite-rate model as it contains simple four reactions (oxidation, sublimation, and nitridation) and has been previously used to study individual points of the SRC trajectory. The Modified Park Model cannot model equilibrium so a model BFIAT was developed that allows finite-rate reactions to be applied to the surface for a certain length of time. Finite-rate sublimation was determined to be reaction of importance in the Park Model for SRC-like conditions. The predicted recession on the SRC heatshield experienced a reduction in its overprediction; the finite-rate predictions fall with the measurement error of the recession at three points on the heatshield. The recession reduction was driven by a significant reduction in char formation. There was little change in the pyrolysis gas rate. The finite-rate model was also applied to simulations of various arc-jet tests that covered a range of heating conditions on the surface of the PICA material. Comparison to this experimental data further showed the role of finite-rate reactions and sublimation in the Park Model and conditions that favor the nonequilibrium assumption (heating over 1000 W/cm2). For the emerging PICA material, used for the Mars Science Laboratory and one of two material choices for the Crew Exploration Vehicle, and SRC-like trajectories, a finite-rate model was developed such that the more robust nonequilibrium assumption can be applied to design processes to reduce heatshield mass.

Modeling Bimolecular Reactive Transport With Mixing-Limitation: Theory and Application to Column Experiments

NASA Astrophysics Data System (ADS)

Ginn, T. R.

2018-01-01

The challenge of determining mixing extent of solutions undergoing advective-dispersive-diffusive transport is well known. In particular, reaction extent between displacing and displaced solutes depends on mixing at the pore scale, that is, generally smaller than continuum scale quantification that relies on dispersive fluxes. Here a novel mobile-mobile mass transfer approach is developed to distinguish diffusive mixing from dispersive spreading in one-dimensional transport involving small-scale velocity variations with some correlation, such as occurs in hydrodynamic dispersion, in which short-range ballistic transports give rise to dispersed but not mixed segregation zones, termed here ballisticules. When considering transport of a single solution, this approach distinguishes self-diffusive mixing from spreading, and in the case of displacement of one solution by another, each containing a participant reactant of an irreversible bimolecular reaction, this results in time-delayed diffusive mixing of reactants. The approach generates models for both kinetically controlled and equilibrium irreversible reaction cases, while honoring independently measured reaction rates and dispersivities. The mathematical solution for the equilibrium case is a simple analytical expression. The approach is applied to published experimental data on bimolecular reactions for homogeneous porous media under postasymptotic dispersive conditions with good results.

The underlying pathway structure of biochemical reaction networks

PubMed Central

Schilling, Christophe H.; Palsson, Bernhard O.

1998-01-01

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying biochemical pathways that are fundamental to the corresponding biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying biochemical pathways from the rapidly growing information on cellular function. PMID:9539712

Toll-like receptor polymorphisms in malaria-endemic populations

PubMed Central

Greene, Jennifer A; Moormann, Ann M; Vulule, John; Bockarie, Moses J; Zimmerman, Peter A; Kazura, James W

2009-01-01

Background Toll-like receptors (TLR) and related downstream signaling pathways of innate immunity have been implicated in the pathogenesis of Plasmodium falciparum malaria. Because of their potential role in malaria pathogenesis, polymorphisms in these genes may be under selective pressure in populations where this infectious disease is endemic. Methods A post-PCR Ligation Detection Reaction-Fluorescent Microsphere Assay (LDR-FMA) was developed to determine the frequencies of TLR2, TLR4, TLR9, MyD88-Adaptor Like Protein (MAL) single nucleotide polymorphisms (SNPs), and TLR2 length polymorphisms in 170 residents of two regions of Kenya where malaria transmission is stable and high (holoendemic) or episodic and low, 346 residents of a malaria holoendemic region of Papua New Guinea, and 261 residents of North America of self-identified ethnicity. Results The difference in historical malaria exposure between the two Kenyan sites has significantly increased the frequency of malaria protective alleles glucose-6-phoshpate dehydrogenase (G6PD) and Hemoglobin S (HbS) in the holoendemic site compared to the episodic transmission site. However, this study detected no such difference in the TLR2, TLR4, TLR9, and MAL allele frequencies between the two study sites. All polymorphisms were in Hardy Weinberg Equilibrium in the Kenyan and Papua New Guinean populations. TLR9 SNPs and length polymorphisms within the TLR2 5' untranslated region were the only mutant alleles present at a frequency greater than 10% in all populations. Conclusion Similar frequencies of TLR2, TLR4, TLR9, and MAL genetic polymorphisms in populations with different histories of malaria exposure suggest that these innate immune pathways have not been under strong selective pressure by malaria. Genotype frequencies are consistent with Hardy-Weinberg Equilibrium and the Neutral Theory, suggesting that genetic drift has influenced allele frequencies to a greater extent than selective pressure from malaria or any other infectious agents in these populations. PMID:19317913

Recycling Frank: Spontaneous emergence of homochirality in noncatalytic systems

PubMed Central

Plasson, Raphaël; Bersini, Hugues; Commeyras, Auguste

2004-01-01

In this work, we introduce a prebiotically relevant protometabolic pattern corresponding to an engine of deracemization by using an external energy source. The spontaneous formation of a nonracemic mixture of chiral compounds can be observed in out-of-equilibrium systems via a symmetry-breaking phenomenon. This observation is possible thanks to chirally selective autocatalytic reactions (Frank's model) [Frank, F. C. (1953) Biochim. Biophys. Acta 11, 459–463]. We show that the use of a Frank-like model in a recycled system composed of reversible chemical reactions, rather than the classical irreversible system, allows for the emergence of a synergetic autoinduction from simple reactions, without any autocatalytic or even catalytic reaction. This model is described as a theoretical framework, based on the stereoselective reactivity of preexisting chiral monomeric building blocks (polymerization, epimerization, and depolymerization) maintained out of equilibrium by a continuous energy income, via an activation reaction. It permits the self-conversion of all monomeric subunits into a single chiral configuration. Real prebiotic systems of amino acid derivatives can be described on this basis. They are shown to be able to spontaneously reach a stable nonracemic state in a few centuries. In such systems, the presence of epimerization reactions is no more destructive, but in contrast is the central driving force of the unstabilization of the racemic state. PMID:15548617

Insight into reaction pathways in CO hydrogenation reactions over K/MoS 2 supported catalysts via alcohol/olefin co-feed experiments

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

Taborga Claure, Micaela; Morrill, Michael R.; Goh, Jin Wai

2016-01-01

Reaction pathways for higher alcohol synthesis from syngas are studied over K/MoS 2domains supported on mesoporous carbon (C) and mixed MgAl oxide (MMO)viaaddition of methanol, ethanol, and ethylene co-feeds.

Relationships between CO 2, thermodynamic limits on silicate weathering, and the strength of the silicate weathering feedback

DOE PAGES

Winnick, Matthew J.; Maher, Kate

2018-01-27

Recent studies have suggested that thermodynamic limitations on chemical weathering rates exert a first-order control on riverine solute fluxes and by extension, global chemical weathering rates. As such, these limitations may play a prominent role in the regulation of carbon dioxide levels (pCO 2) over geologic timescales by constraining the maximum global weathering flux. In this study, we develop a theoretical scaling relationship between equilibrium solute concentrations and pCO 2 based on equilibrium constants and reaction stoichiometry relating primary mineral dissolution and secondary mineral precipitation. Here, we test this theoretical scaling relationship against reactive transport simulations of chemical weathering profilesmore » under open-and closed-system conditions, representing partially and fully water-saturated regolith, respectively. Under open-system conditions, equilibrium bicarbonate concentrations vary as a power-law function of pCO 2(y =kx n)where nis dependent on reaction stoichiometry and kis dependent on both reaction stoichiometry and the equilibrium constant. Under closed-system conditions, bicarbonate concentrations vary linearly with pCO 2 at low values and approach open-system scaling at high pCO 2. To describe the potential role of thermodynamic limitations in the global silicate weathering feedback, we develop a new mathematical framework to assess weathering feedback strength in terms of both (1) steady-state atmospheric pCO 2 concentrations, and (2) susceptibility to secular changes in degassing rates and transient carbon cycle perturbations, which we term 1st and 2nd order feedback strength, respectively. Finally, we discuss the implications of these results for the effects of vascular land plant evolution on feedback strength, the potential role of vegetation in controlling modern solute fluxes, and the application of these frameworks to a more complete functional description of the silicate weathering feedback. Most notably, the dependence of equilibrium solute concentrations on pCO 2 may represent a direct weathering feedback largely independent of climate and modulated by belowground organic carbon respiration.« less

Relationships between CO 2, thermodynamic limits on silicate weathering, and the strength of the silicate weathering feedback

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

Winnick, Matthew J.; Maher, Kate

Recent studies have suggested that thermodynamic limitations on chemical weathering rates exert a first-order control on riverine solute fluxes and by extension, global chemical weathering rates. As such, these limitations may play a prominent role in the regulation of carbon dioxide levels (pCO 2) over geologic timescales by constraining the maximum global weathering flux. In this study, we develop a theoretical scaling relationship between equilibrium solute concentrations and pCO 2 based on equilibrium constants and reaction stoichiometry relating primary mineral dissolution and secondary mineral precipitation. Here, we test this theoretical scaling relationship against reactive transport simulations of chemical weathering profilesmore » under open-and closed-system conditions, representing partially and fully water-saturated regolith, respectively. Under open-system conditions, equilibrium bicarbonate concentrations vary as a power-law function of pCO 2(y =kx n)where nis dependent on reaction stoichiometry and kis dependent on both reaction stoichiometry and the equilibrium constant. Under closed-system conditions, bicarbonate concentrations vary linearly with pCO 2 at low values and approach open-system scaling at high pCO 2. To describe the potential role of thermodynamic limitations in the global silicate weathering feedback, we develop a new mathematical framework to assess weathering feedback strength in terms of both (1) steady-state atmospheric pCO 2 concentrations, and (2) susceptibility to secular changes in degassing rates and transient carbon cycle perturbations, which we term 1st and 2nd order feedback strength, respectively. Finally, we discuss the implications of these results for the effects of vascular land plant evolution on feedback strength, the potential role of vegetation in controlling modern solute fluxes, and the application of these frameworks to a more complete functional description of the silicate weathering feedback. Most notably, the dependence of equilibrium solute concentrations on pCO 2 may represent a direct weathering feedback largely independent of climate and modulated by belowground organic carbon respiration.« less

Relationships between CO2, thermodynamic limits on silicate weathering, and the strength of the silicate weathering feedback

NASA Astrophysics Data System (ADS)

Winnick, Matthew J.; Maher, Kate

2018-03-01

Recent studies have suggested that thermodynamic limitations on chemical weathering rates exert a first-order control on riverine solute fluxes and by extension, global chemical weathering rates. As such, these limitations may play a prominent role in the regulation of carbon dioxide levels (pCO2) over geologic timescales by constraining the maximum global weathering flux. In this study, we develop a theoretical scaling relationship between equilibrium solute concentrations and pCO2 based on equilibrium constants and reaction stoichiometry relating primary mineral dissolution and secondary mineral precipitation. We test this theoretical scaling relationship against reactive transport simulations of chemical weathering profiles under open- and closed-system conditions, representing partially and fully water-saturated regolith, respectively. Under open-system conditions, equilibrium bicarbonate concentrations vary as a power-law function of pCO2 (y = kxn) where n is dependent on reaction stoichiometry and k is dependent on both reaction stoichiometry and the equilibrium constant. Under closed-system conditions, bicarbonate concentrations vary linearly with pCO2 at low values and approach open-system scaling at high pCO2. To describe the potential role of thermodynamic limitations in the global silicate weathering feedback, we develop a new mathematical framework to assess weathering feedback strength in terms of both (1) steady-state atmospheric pCO2 concentrations, and (2) susceptibility to secular changes in degassing rates and transient carbon cycle perturbations, which we term 1st and 2nd order feedback strength, respectively. Finally, we discuss the implications of these results for the effects of vascular land plant evolution on feedback strength, the potential role of vegetation in controlling modern solute fluxes, and the application of these frameworks to a more complete functional description of the silicate weathering feedback. Most notably, the dependence of equilibrium solute concentrations on pCO2 may represent a direct weathering feedback largely independent of climate and modulated by belowground organic carbon respiration.

Can a fractured caprock self-heal?

NASA Astrophysics Data System (ADS)

Elkhoury, Jean E.; Detwiler, Russell L.; Ameli, Pasha

2015-05-01

The ability of geologic seals to prevent leakage of fluids injected into the deep subsurface is critical for mitigating risks associated with greenhouse-gas sequestration and natural-gas production. Fractures caused by tectonic or injection-induced stresses create potential leakage pathways that may be further enhanced by mineral dissolution. We present results from reactive-flow experiments in fractured caprock (dolomitic anhydrite), where additional dissolution occurs in the rock matrix adjacent to the fracture surfaces. Preferential dissolution of anhydrite left a compacted layer of dolomite in the fractures. At lower flow rate, rock-fluid reactions proceeded to near equilibrium within the fracture with preferential flow paths persisting over the 6-month duration of the experiment and a negligible change in permeability. At higher flow rate, permeability decreased by a dramatic two orders of magnitude. This laboratory-scale observation of self-healing argues against the likelihood of runaway permeability growth in fractured porous caprock composed of minerals with different solubilities and reaction kinetics. However, scaling arguments suggest that at larger length scales this self-healing process may be offset by the formation of dissolution channels. Our results have relevance beyond the greenhouse-gas sequestration problem. Chemical disequilibrium at waste injection sites and in hydrothermal reservoirs will lead to reactive flows that may also significantly alter formation permeability.

Ignition conditions relaxation for central hot-spot ignition with an ion-electron non-equilibrium model

NASA Astrophysics Data System (ADS)

Fan, Zhengfeng; Liu, Jie

2016-10-01

We present an ion-electron non-equilibrium model, in which the hot-spot ion temperature is higher than its electron temperature so that the hot-spot nuclear reactions are enhanced while energy leaks are considerably reduced. Theoretical analysis shows that the ignition region would be significantly enlarged in the hot-spot rhoR-T space as compared with the commonly used equilibrium model. Simulations show that shocks could be utilized to create and maintain non-equilibrium conditions within the hot spot, and the hot-spot rhoR requirement is remarkably reduced for achieving self-heating. In NIF high-foot implosions, it is observed that the x-ray enhancement factors are less than unity, which is not self-consistent and is caused by assuming Te =Ti. And from this non-consistency, we could infer that ion-electron non-equilibrium exists in the high-foot implosions and the ion temperature could be 9% larger than the equilibrium temperature.

Self-assembly and transformation of hybrid nano-objects and nanostructures under equilibrium and non-equilibrium conditions

NASA Astrophysics Data System (ADS)

Mann, Stephen

2009-10-01

Understanding how chemically derived processes control the construction and organization of matter across extended and multiple length scales is of growing interest in many areas of materials research. Here we review present equilibrium and non-equilibrium self-assembly approaches to the synthetic construction of discrete hybrid (inorganic-organic) nano-objects and higher-level nanostructured networks. We examine a range of synthetic modalities under equilibrium conditions that give rise to integrative self-assembly (supramolecular wrapping, nanoscale incarceration and nanostructure templating) or higher-order self-assembly (programmed/directed aggregation). We contrast these strategies with processes of transformative self-assembly that use self-organizing media, reaction-diffusion systems and coupled mesophases to produce higher-level hybrid structures under non-equilibrium conditions. Key elements of the constructional codes associated with these processes are identified with regard to existing theoretical knowledge, and presented as a heuristic guideline for the rational design of hybrid nano-objects and nanomaterials.

Light charged clusters emitted in 32 MeV/nucleon Xe,124136+Sn,112124 reactions: Chemical equilibrium and production of 3He and 6He

NASA Astrophysics Data System (ADS)

Bougault, R.; Bonnet, E.; Borderie, B.; Chbihi, A.; Dell'Aquila, D.; Fable, Q.; Francalanza, L.; Frankland, J. D.; Galichet, E.; Gruyer, D.; Guinet, D.; Henri, M.; La Commara, M.; Le Neindre, N.; Lombardo, I.; Lopez, O.; Manduci, L.; Marini, P.; Pârlog, M.; Roy, R.; Saint-Onge, P.; Verde, G.; Vient, E.; Vigilante, M.; Indra Collaboration

2018-02-01

Background: The isovector part of the nuclear equation of state remains partly unknown and is the subject of many studies. The degree of equilibration between the two main collision partners in heavy ion reactions may be used to study the equation of state since it is connected to isospin (N /Z ) transport properties of nuclear matter. Purpose: We aim to test chemical equilibrium attainment by measuring isotopic characteristics of emitted elements as a function of impact parameter. Method: We study four Xe,124136+Sn,112124 reactions at 32 MeV/nucleon. The data were acquired with the INDRA detector at the GANIL (Caen, France) facility. Combined (projectile+target) systems are identical for two studied reactions, therefore it is possible to study the path towards chemical equilibrium from different neutron to proton ratio (N /Z ) entrance channels. The study is limited to identified isotopes detected in the forward part of the center of mass in order to focus on the evolution of projectile-like fragment isotopic content and the benefit of excellent detection performances of the forward part of the apparatus. Results: Light charged particle productions, multiplicities, and abundance ratios dependence against impact parameter are studied. It is measured to almost identical mean characteristics for the two 124Xe+124Sn and 136Xe+112Sn systems for central collisions. Comparing all four studied systems it is shown that mean values evolve from projectile N /Z to projectile+target N /Z dependence. Those identical mean characteristics concern all light charged particles except 3He whose mean behavior is strongly different. Conclusions: Our inclusive analysis (no event selection) shows that N /Z equilibration between the projectile-like and the target-like is realized to a high degree for central collisions. The light charged particle production mean value difference between 124Xe+124Sn and 136Xe+112Sn systems for central collisions is of the order of a few %. This slight difference could be explained by pre-equilibrium particle emission whose intensity may differ for the two reactions. This point is demonstrated using 3He mean characteristics whose production takes place before chemical equilibrium attainment. The realized N /Z balance between projectile-like and target-like does not imply a pure two-body mechanism. Indeed a midrapidity production of light charged particle does exist and its N /Z is different as compared to the projectile-like one: it is n enriched. This point is touched using 6He midrapidity production which is favored by the drift phenomenon.

Modeling the optimal central carbon metabolic pathways under feedback inhibition using flux balance analysis.

PubMed

De, Rajat K; Tomar, Namrata

2012-12-01

Metabolism is a complex process for energy production for cellular activity. It consists of a cascade of reactions that form a highly branched network in which the product of one reaction is the reactant of the next reaction. Metabolic pathways efficiently produce maximal amount of biomass while maintaining a steady-state behavior. The steady-state activity of such biochemical pathways necessarily incorporates feedback inhibition of the enzymes. This observation motivates us to incorporate feedback inhibition for modeling the optimal activity of metabolic pathways using flux balance analysis (FBA). We demonstrate the effectiveness of the methodology on a synthetic pathway with and without feedback inhibition. Similarly, for the first time, the Central Carbon Metabolic (CCM) pathways of Saccharomyces cerevisiae and Homo sapiens have been modeled and compared based on the above understanding. The optimal pathway, which maximizes the amount of the target product(s), is selected from all those obtained by the proposed method. For this, we have observed the concentration of the product inhibited enzymes of CCM pathway and its influence on its corresponding metabolite/substrate. We have also studied the concentration of the enzymes which are responsible for the synthesis of target products. We further hypothesize that an optimal pathway would opt for higher flux rate reactions. In light of these observations, we can say that an optimal pathway should have lower enzyme concentration and higher flux rates. Finally, we demonstrate the superiority of the proposed method by comparing it with the extreme pathway analysis.

Nonequilibrium Phase Transitions in Supercooled Water

NASA Astrophysics Data System (ADS)

Limmer, David; Chandler, David

2012-02-01

We present results of a simulation study of water driven out of equilibrium. Using transition path sampling, we can probe stationary path distributions parameterize by order parameters that are extensive in space and time. We find that by coupling external fields to these parameters, we can drive water through a first order dynamical phase transition into amorphous ice. By varying the initial equilibrium distributions we can probe pathways for the creation of amorphous ices of low and high densities.

Reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma

NASA Astrophysics Data System (ADS)

Zhao, Yuefeng; Wang, Chao; Li, Li; Wang, Lijuan; Pan, Jie

2018-03-01

In this work, a two-dimensional fluid model is built up to numerically investigate the reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma. The calculation results indicate that the electron collisions with CH4 are the key pathways to produce the neutral particles CH2 and CH as well as the charged particles e and CH3+. CH3, H2, H, C2H2, and C2H4 primarily result from the reactions between the neutral particles and CH4. The charge transfer reactions are the significant pathways to produce CH4+, C2H2+, and C2H4+. As to the neutral species CH and H and the charged species CH3+, the reactions between themselves and CH4 contribute to substantial losses of these particles. The ways responsible for losing CH3, H2, C2H2, and C2H4 are CH3 + H → CH4, H2 + CH → CH2 + H, CH4+ + C2H2 → C2H2+ + CH4, and CH4+ + C2H4 → C2H4+ + CH4, respectively. Both electrons and C2H4+ are consumed by the dissociative electron-ion recombination reactions. The essential reaction pathways of losing CH4+ and C2H2+ are the charge transfer reactions.

Mixing and non-equilibrium chemical reaction in a compressible mixing layer. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Steinberger, Craig J.

1991-01-01

The effects of compressibility, chemical reaction exothermicity, and non-equilibrium chemical modeling in a reacting plane mixing layer were investigated by means of two dimensional direct numerical simulations. The chemical reaction was irreversible and second order of the type A + B yields Products + Heat. The general governing fluid equations of a compressible reacting flow field were solved by means of high order finite difference methods. Physical effects were then determined by examining the response of the mixing layer to variation of the relevant non-dimensionalized parameters. The simulations show that increased compressibility generally results in a suppressed mixing, and consequently a reduced chemical reaction conversion rate. Reaction heat release was found to enhance mixing at the initial stages of the layer growth, but had a stabilizing effect at later times. The increased stability manifested itself in the suppression or delay of the formation of large coherent structures within the flow. Calculations were performed for a constant rate chemical kinetics model and an Arrhenius type kinetic prototype. The choice of the model was shown to have an effect on the development of the flow. The Arrhenius model caused a greater temperature increase due to reaction than the constant kinetic model. This had the same effect as increasing the exothermicity of the reaction. Localized flame quenching was also observed when the Zeldovich number was relatively large.

Simulations for Teaching Chemical Equilibrium

NASA Astrophysics Data System (ADS)

Huddle, Penelope A.; White, Margaret Dawn; Rogers, Fiona

2000-07-01

This paper outlines a systematic approach to teaching chemical equilibrium using simulation experiments that address most known alternate conceptions in the topic. Graphs drawn using the data from the simulations are identical to those obtained using real experimental data for reactions that go to equilibrium. This allows easy mapping of the analogy to the target. The requirements for the simulations are simple and inexpensive, making them accessible to even the poorest schools. The simulations can be adapted for all levels, from pupils who are first encountering equilibrium through students in tertiary education to qualified teachers who have experienced difficulty in teaching the topic. The simulations were piloted on four very different audiences. Minor modifications were then made before the Equilibrium Games as reported in this paper were tested on three groups of subjects: a Grade 12 class, college students, and university Chemistry I students. Marked improvements in understanding of the concept were shown in two of the three sets of subjects.

Phase Transitions and Scaling in Systems Far from Equilibrium

NASA Astrophysics Data System (ADS)

Täuber, Uwe C.

2017-03-01

Scaling ideas and renormalization group approaches proved crucial for a deep understanding and classification of critical phenomena in thermal equilibrium. Over the past decades, these powerful conceptual and mathematical tools were extended to continuous phase transitions separating distinct nonequilibrium stationary states in driven classical and quantum systems. In concordance with detailed numerical simulations and laboratory experiments, several prominent dynamical universality classes have emerged that govern large-scale, long-time scaling properties both near and far from thermal equilibrium. These pertain to genuine specific critical points as well as entire parameter space regions for steady states that display generic scale invariance. The exploration of nonstationary relaxation properties and associated physical aging scaling constitutes a complementary potent means to characterize cooperative dynamics in complex out-of-equilibrium systems. This review describes dynamic scaling features through paradigmatic examples that include near-equilibrium critical dynamics, driven lattice gases and growing interfaces, correlation-dominated reaction-diffusion systems, and basic epidemic models.

The Chemical Basis of Thiol Addition to Nitro-conjugated Linoleic Acid, a Protective Cell-signaling Lipid*♦

PubMed Central

Turell, Lucía; Vitturi, Darío A.; Coitiño, E. Laura; Lebrato, Lourdes; Möller, Matías N.; Sagasti, Camila; Salvatore, Sonia R.; Woodcock, Steven R.; Alvarez, Beatriz; Schopfer, Francisco J.

2017-01-01

Nitroalkene fatty acids are formed in vivo and exert protective and anti-inflammatory effects via reversible Michael addition to thiol-containing proteins in key signaling pathways. Nitro-conjugated linoleic acid (NO2-CLA) is preferentially formed, constitutes the most abundant nitrated fatty acid in humans, and contains two carbons that could potentially react with thiols, modulating signaling actions and levels. In this work, we examined the reactions of NO2-CLA with low molecular weight thiols (glutathione, cysteine, homocysteine, cysteinylglycine, and β-mercaptoethanol) and human serum albumin. Reactions followed reversible biphasic kinetics, consistent with the presence of two electrophilic centers in NO2-CLA located on the β- and δ-carbons with respect to the nitro group. The differential reactivity was confirmed by computational modeling of the electronic structure. The rates (kon and koff) and equilibrium constants for both reactions were determined for different thiols. LC-UV-Visible and LC-MS analyses showed that the fast reaction corresponds to β-adduct formation (the kinetic product), while the slow reaction corresponds to the formation of the δ-adduct (the thermodynamic product). The pH dependence of the rate constants, the correlation between intrinsic reactivity and thiol pKa, and the absence of deuterium solvent kinetic isotope effects suggested stepwise mechanisms with thiolate attack on NO2-CLA as rate-controlling step. Computational modeling supported the mechanism and revealed additional features of the transition states, anionic intermediates, and final neutral products. Importantly, the detection of cysteine-δ-adducts in human urine provided evidence for the biological relevance of this reaction. Finally, human serum albumin was found to bind NO2-CLA both non-covalently and to form covalent adducts at Cys-34, suggesting potential modes for systemic distribution. These results provide new insights into the chemical basis of NO2-CLA signaling actions. PMID:27923813

Reliable Mechanochemistry: Protocols for Reproducible Outcomes of Neat and Liquid Assisted Ball-mill Grinding Experiments.

PubMed

Belenguer, Ana M; Lampronti, Giulio I; Sanders, Jeremy K M

2018-01-23

The equilibrium outcomes of ball mill grinding can dramatically change as a function of even tiny variations in the experimental conditions such as the presence of very small amounts of added solvent. To reproducibly and accurately capture this sensitivity, the experimentalist needs to carefully consider every single factor that can affect the ball mill grinding reaction under investigation, from ensuring the grinding jars are clean and dry before use, to accurately adding the stoichiometry of the starting materials, to validating that the delivery of solvent volume is accurate, to ensuring that the interaction between the solvent and the powder is well understood and, if necessary, a specific soaking time is added to the procedure. Preliminary kinetic studies are essential to determine the necessary milling time to achieve equilibrium. Only then can exquisite phase composition curves be obtained as a function of the solvent concentration under ball mill liquid assisted grinding (LAG). By using strict and careful procedures analogous to the ones here presented, such milling equilibrium curves can be obtained for virtually all milling systems. The system we use to demonstrate these procedures is a disulfide exchange reaction starting from the equimolar mixture of two homodimers to obtain at equilibrium quantitative heterodimer. The latter is formed by ball mill grinding as two different polymorphs, Form A and Form B. The ratio R = [Form B] / ([Form A] + [Form B]) at milling equilibrium depends on the nature and concentration of the solvent in the milling jar.

Exploring the use of multiple analogical models when teaching and learning chemical equilibrium

NASA Astrophysics Data System (ADS)

Harrison, Allan G.; de Jong, Onno

2005-12-01

This study describes the multiple analogical models used to introduce and teach Grade 12 chemical equilibrium. We examine the teacher's reasons for using models, explain each model's development during the lessons, and analyze the understandings students derived from the models. A case study approach was used and the data were drawn from the observation of three consecutive Grade 12 lessons on chemical equilibrium, pre- and post-lesson interviews, and delayed student interviews. The key analogical models used in teaching were: the school dance; the sugar in a teacup; the pot of curry; and the busy highway. The lesson and interview data were subject to multiple, independent analyses and yielded the following outcomes: The teacher planned to use the students' prior knowledge wherever possible and he responded to student questions with stories and extended and enriched analogies. He planned to discuss where each analogy broke down but did not. The students enjoyed the teaching but built variable mental models of equilibrium and some of their analogical mappings were unreliable. A female student disliked masculine analogies, other students tended to see elements of the multiple models in isolation, and some did not recognize all the analogical mappings embedded in the teaching plan. Most students learned that equilibrium reactions are dynamic, occur in closed systems, and the forward and reverse reactions are balanced. We recommend the use of multiple analogies like these and insist that teachers always show where the analogy breaks down and carefully negotiate the conceptual outcomes.

Spectral Dependence of Chlorophyll Biosynthesis Pathways in Plant Leaves.

PubMed

Belyaeva, O B; Litvin, F F

2015-12-01

This review covers studies on the dependence of chlorophyll photobiosynthesis reactions from protochlorophyllide on the spectral composition of actinic light. A general scheme of the reaction sequence for the photochemical stage in chlorophyll biosynthesis for etiolated plant leaves is presented. Comparative analysis of the data shows that the use of light with varied wavelengths for etiolated plant illumination reveals parallel transformation pathways of different protochlorophyllide forms into chlorophyllide, including a pathway for early photosystem II reaction center P-680 pigment formation.

Chem Lab Simulation #3 and #4.

ERIC Educational Resources Information Center

Pipeline, 1983

1983-01-01

Two copy-protected chemistry simulations (for Apple II) are described. The first demonstrates Hess' law of heat reaction. The second illustrates how heat of vaporization can be used to determine an unknown liquid and shows how to find thermodynamic parameters in an equilibrium reaction. Both are self-instructing and use high-resolution graphics.…

Dynamic Nature of Atoms and Molecules, Science (Experimental): 5316.06.

ERIC Educational Resources Information Center

Buffaloe, Jacquelin F.

This unit of instruction deals with the study of both physical and chemical systems in equilibrium. It provides the student with instruction that will enable him to predict products in solubility, acid-base, and oxidation-reduction reactions and to write and balance equations for these reactions and solve problems involving equilibria constants.…

Diagnostics for the Analysis of Surface Chemistry Effects on Composite Energetic Material Reactions

DTIC Science & Technology

2015-10-30

integration time) and a NETZSCH STA 449 Jupiter that will allow for consistency and efficiency with its automatic 20 sample changer. (2) Together these...Purchase of the NETZSCH STA 449 Jupiter (DSC-TGA) to resolve reaction kinetics under equilibrium conditions. Images of this instrumentation are included in

A new network representation of the metabolism to detect chemical transformation modules.

PubMed

Sorokina, Maria; Medigue, Claudine; Vallenet, David

2015-11-14

Metabolism is generally modeled by directed networks where nodes represent reactions and/or metabolites. In order to explore metabolic pathway conservation and divergence among organisms, previous studies were based on graph alignment to find similar pathways. Few years ago, the concept of chemical transformation modules, also called reaction modules, was introduced and correspond to sequences of chemical transformations which are conserved in metabolism. We propose here a novel graph representation of the metabolic network where reactions sharing a same chemical transformation type are grouped in Reaction Molecular Signatures (RMS). RMS were automatically computed for all reactions and encode changes in atoms and bonds. A reaction network containing all available metabolic knowledge was then reduced by an aggregation of reaction nodes and edges to obtain a RMS network. Paths in this network were explored and a substantial number of conserved chemical transformation modules was detected. Furthermore, this graph-based formalism allows us to define several path scores reflecting different biological conservation meanings. These scores are significantly higher for paths corresponding to known metabolic pathways and were used conjointly to build association rules that should predict metabolic pathway types like biosynthesis or degradation. This representation of metabolism in a RMS network offers new insights to capture relevant metabolic contexts. Furthermore, along with genomic context methods, it should improve the detection of gene clusters corresponding to new metabolic pathways.

Exploring the combinatorial space of complete pathways to chemicals.

PubMed

Wang, Lin; Ng, Chiam Yu; Dash, Satyakam; Maranas, Costas D

2018-04-06

Computational pathway design tools often face the challenges of balancing the stoichiometry of co-metabolites and cofactors, and dealing with reaction rule utilization in a single workflow. To this end, we provide an overview of two complementary stoichiometry-based pathway design tools optStoic and novoStoic developed in our group to tackle these challenges. optStoic is designed to determine the stoichiometry of overall conversion first which optimizes a performance criterion (e.g. high carbon/energy efficiency) and ensures a comprehensive search of co-metabolites and cofactors. The procedure then identifies the minimum number of intervening reactions to connect the source and sink metabolites. We also further the pathway design procedure by expanding the search space to include both known and hypothetical reactions, represented by reaction rules, in a new tool termed novoStoic. Reaction rules are derived based on a mixed-integer linear programming (MILP) compatible reaction operator, which allow us to explore natural promiscuous enzymes, engineer candidate enzymes that are not already promiscuous as well as design de novo enzymes. The identified biochemical reaction rules then guide novoStoic to design routes that expand the currently known biotransformation space using a single MILP modeling procedure. We demonstrate the use of the two computational tools in pathway elucidation by designing novel synthetic routes for isobutanol. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Applicability of DFT model in reactive distillation

NASA Astrophysics Data System (ADS)

Staszak, Maciej

2017-11-01

The density functional theory (DFT) applicability to reactive distillation is discussed. Brief modeling techniques description of distillation and rectification with chemical reaction is provided as a background for quantum method usage description. The equilibrium and nonequilibrium distillation models are described for that purpose. The DFT quantum theory is concisely described. The usage of DFT in the modeling of reactive distillation is described in two parts. One of the fundamental and very important component of distillation modeling is vapor-liquid equilibrium description for which the DFT quantum approach can be used. The representative DFT models, namely COSMO-RS (Conductor like Screening Model for Real Solvents), COSMOSPACE (COSMO Surface Pair Activity Coefficient) and COSMO-SAC (SAC - segment activity coefficient) approaches are described. The second part treats the way in which the chemical reaction is described by means of quantum DFT method. The intrinsic reaction coordinate (IRC) method is described which is used to find minimum energy path of substrates to products transition. The DFT is one of the methods which can be used for that purpose. The literature data examples are provided which proves that IRC method is applicable for chemical reaction kinetics description.

Mechanistic information from the first volume profile analysis for a reversible intermolecular electron-transfer reaction involving pentaammine(isonicotinamide)ruthenium and cytochrome c

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

Baensch, B.; Meier, M.; Martinez, P.

1994-10-12

The reversible intermolecular electron-transfer reaction between pentaammine(isonicotinamide)ruthenium(II/III) and horse-heart cytochrome c iron(III/II) was subjected to a detailed kinetic and thermodynamic study as a function of temperature and pressure. Theoretical calculations based on the Marcus-Hush theory were employed to predict all rate and equilibrium constants as well as activation parameters. There is an excellent agreement between the kinetically and thermodynamically determined equilibrium constants and associated pressure parameters. These data are used to construct a volume profile for the overall process, from which it follows that the transition state lies halfway between the reactant and product states on a volume basis. Themore » reorganization in the transition state has reached a similar degree in both directions of the electron-transfer process and corresponds to a {lambda}{sup {double_dagger}} value of 0.44 for this reversible reaction. This is the first complete volume profile analysis for a reversible intermolecular electron-transfer reaction.« less

Development of a low-pressure materials pre-treatment process for improved energy efficiency

NASA Astrophysics Data System (ADS)

Lee, Kwanghee; You, Byung Don

2017-09-01

Low pressure materials pre-treatment process has been developed as an alternative to the existing high-temperature sludge drying, limestone calcination, and limonite dehydroxylation. Using the thermodynamic equilibrium relationship between temperature and pressure represented by the Clausius-Clapeyron equation, the operational temperature of these reactions could be lowered at reduced pressure for increased energy efficiency. For industrial sludge drying, the evaporation rate was controlled by interfacial kinetics showing a constant rate with time and significant acceleration in the reaction could be observed with reduced pressure. At this modified reaction rate under low pressure, the rate was also partially controlled by mass transfer. Temperature of limestone calcination was lowered, but the reaction was limited at the calculated equilibrium temperature of the Clausius-Clapeyron equation and slightly higher temperatures were required. The energy consumption during limestone calcination and limonite dehydroxylation were evaluated, where lower processing pressures could enhance the energy efficiency for limestone calcination, but limonite dehydroxylation could not achieve energy-savings due to the greater power consumption of the vacuum pump under lower pressure and reduced temperatures.

Numerical simulation of advective-dispersive multisolute transport with sorption, ion exchange and equilibrium chemistry

USGS Publications Warehouse

Lewis, F.M.; Voss, C.I.; Rubin, Jacob

1986-01-01

A model was developed that can simulate the effect of certain chemical and sorption reactions simultaneously among solutes involved in advective-dispersive transport through porous media. The model is based on a methodology that utilizes physical-chemical relationships in the development of the basic solute mass-balance equations; however, the form of these equations allows their solution to be obtained by methods that do not depend on the chemical processes. The chemical environment is governed by the condition of local chemical equilibrium, and may be defined either by the linear sorption of a single species and two soluble complexation reactions which also involve that species, or binary ion exchange and one complexation reaction involving a common ion. Partial differential equations that describe solute mass balance entirely in the liquid phase are developed for each tenad (a chemical entity whose total mass is independent of the reaction process) in terms of their total dissolved concentration. These equations are solved numerically in two dimensions through the modification of an existing groundwater flow/transport computer code. (Author 's abstract)

The Thermochemical and Kinetic Properties of Ascorbate are Tuned by its Local Environment: Solution Chemistry and Biochemical Implications

PubMed Central

Warren, Jeffrey J.; Mayer, James M.

2010-01-01

Ascorbate (Vitamin C) is a ubiquitous biological cofactor. While its aqueous solution chemistry has long been studied, many in vivo reactions of ascorbate occur in enzyme active sites or at membrane interfaces, which have varying local environments. This report shows that the rate and driving force of oxidations of two ascorbate derivatives by the TEMPO radical (2,2′-6,6′-tetramethylpiperidine-1-oxyl) in acetonitrile are very sensitive to the presence of various additives. These reactions proceed by the transfer of a proton and an electron (a hydrogen atom), as is typical of biological ascorbate reactions. The measured rate and equilibrium constants vary substantially with added water or other polar solutes in acetonitrile solutions, indicating large shifts in the reducing power of ascorbate. The correlation of rate and equilibrium constants indicates that this effect has a thermochemical origin rather than being a purely kinetic effect. This contrasts with previous examples of solvent effects on hydrogen atom transfer reactions. Potential biological implications of this apparently unique effect are discussed. PMID:20476757

Criegee intermediate-hydrogen sulfide chemistry at the air/water interface.

PubMed

Kumar, Manoj; Zhong, Jie; Francisco, Joseph S; Zeng, Xiao C

2017-08-01

We carry out Born-Oppenheimer molecular dynamic simulations to show that the reaction between the smallest Criegee intermediate, CH 2 OO, and hydrogen sulfide (H 2 S) at the air/water interface can be observed within few picoseconds. The reaction follows both concerted and stepwise mechanisms with former being the dominant reaction pathway. The concerted reaction proceeds with or without the involvement of one or two nearby water molecules. An important implication of the simulation results is that the Criegee-H 2 S reaction can provide a novel non-photochemical pathway for the formation of a C-S linkage in clouds and could be a new oxidation pathway for H 2 S in terrestrial, geothermal and volcanic regions.

Remarks on the chemical Fokker-Planck and Langevin equations: Nonphysical currents at equilibrium.

PubMed

Ceccato, Alessandro; Frezzato, Diego

2018-02-14

The chemical Langevin equation and the associated chemical Fokker-Planck equation are well-known continuous approximations of the discrete stochastic evolution of reaction networks. In this work, we show that these approximations suffer from a physical inconsistency, namely, the presence of nonphysical probability currents at the thermal equilibrium even for closed and fully detailed-balanced kinetic schemes. An illustration is given for a model case.

Cation disorder and gas phase equilibrium in an YBa 2Cu 3O 7- x superconducting thin film

NASA Astrophysics Data System (ADS)

Shin, Dong Chan; Ki Park, Yong; Park, Jong-Chul; Kang, Suk-Joong L.; Yong Yoon, Duk

1997-02-01

YBa 2Cu 3O 7- x superconducting thin films have been grown by in situ off-axis rf sputtering with varying oxygen pressure, Ba/Y ratio in a target, and deposition temperature. With decreasing oxygen pressure, increasing Ba/Y ratio, increasing deposition temperature, the critical temperature of the thin films decreased and the c-axis length increased. The property change of films with the variation of deposition variables has been explained by a gas phase equilibrium of the oxidation reaction of Ba and Y. Applying Le Chatelier's principle to the oxidation reaction, we were able to predict the relation of deposition variables and the resultant properties of thin films; the prediction was in good agreement with the experimental results. From the relation between the three deposition variables and gas phase equilibrium, a 3-dimensional processing diagram was introduced. This diagram has shown that the optimum deposition condition of YBa 2Cu 3O 7- x thin films is not a fixed point but can be varied. The gas phase equilibrium can also be applied to the explanation of previous results that good quality films were obtained at low deposition temperature using active species, such as O, O 3, and O 2+.

Preparing "Chameleon Balls" from Natural Plants: Simple Handmade pH Indicator and Teaching Material for Chemical Equilibrium

NASA Astrophysics Data System (ADS)

Kanda, Naoki; Asano, Takayuki; Itoh, Toshiyuki; Onoda, Makoto

1995-12-01

Anthocyanins are found in the flowers and fruits of natural plants. Since their color depends on pH, they are sometines used as a pH indicator. Since these sequences are reversible, they are also useful in demonstrating chemical equilibrium in the repetitive color changes of anthocyanins from flowers by controlling pH conditions. We prepared the polysaccharide beads conatining water extracts of red cabbage as calcium alginate. The beads showed a clear red color under acidic conditions, turned blue at neutral pH of 7, and orange-yellow at pH of 13. This color change could be demonstrated over and over. Because the color changes of these polysaccharide beads depended darmatically on pH, junior high students in science classes called them "chameleon balls" when we demonstrated this reaction for them. In this paper we describe how polysaccharide beads, which are made from calcium alginate with natural pigments, served as a teaching tool for the chemical equilibrium of anthocyanins under different pH conditions. Preparation of the chameleon ball is very easy. The most important thing is that making the chameleon ball is great fun. The ball should therefore be viewed not only as a handmade pH indicator but also an interesting teaching tool of the chemical equilibrium reaction.

Unfolding single RNA molecules: bridging the gap between equilibrium and non-equilibrium statistical thermodynamics.

PubMed

Bustamante, Carlos

2005-11-01

During the last 15 years, scientists have developed methods that permit the direct mechanical manipulation of individual molecules. Using this approach, they have begun to investigate the effect of force and torque in chemical and biochemical reactions. These studies span from the study of the mechanical properties of macromolecules, to the characterization of molecular motors, to the mechanical unfolding of individual proteins and RNA. Here I present a review of some of our most recent results using mechanical force to unfold individual molecules of RNA. These studies make it possible to follow in real time the trajectory of each molecule as it unfolds and characterize the various intermediates of the reaction. Moreover, if the process takes place reversibly it is possible to extract both kinetic and thermodynamic information from these experiments at the same time that we characterize the forces that maintain the three-dimensional structure of the molecule in solution. These studies bring us closer to the biological unfolding processes in the cell as they simulate in vitro, the mechanical unfolding of RNAs carried out in the cell by helicases. If the unfolding process occurs irreversibly, I show here that single-molecule experiments can still provide equilibrium, thermodynamic information from non-equilibrium data by using recently discovered fluctuation theorems. Such theorems represent a bridge between equilibrium and non-equilibrium statistical mechanics. In fact, first derived in 1997, the first experimental demonstration of the validity of fluctuation theorems was obtained by unfolding mechanically a single molecule of RNA. It is perhaps a sign of the times that important physical results are these days used to extract information about biological systems and that biological systems are being used to test and confirm fundamental new laws in physics.

Indirect electroreductive cyclization and electrohydrocyclization using catalytic reduced nickel(II) salen.

PubMed

Miranda, James A; Wade, Carolyn J; Little, R Daniel

2005-09-30

[Chemical reaction: See text] We describe efforts to achieve the electroreductive cyclization (ERC) and the electrohydrocyclization (EHC) reactions using catalytic nickel(II) salen as a mediator. While nickel(II) salen proved effective, the analogous cobalt complex as well as nickel(II) cyclam were not. The transformations were achieved in yields ranging from 60 to 94% using either a mercury pool or an environmentally preferable reticulated vitreous carbon (RVC) cathode. These examples represent the first instances wherein a nickel salen complex has been used in this manner. Clear differences between the voltammetric behavior of the ERC and EHC substrates were observed. The bisenoate 14, for example, displays a substantially larger catalytic current. When the structurally modified mediator 31 was used, the electron-transfer pathway shuts down. Instead, the reduced form of 31 behaves as an electrogenerated base, leading to the formation of the intramolecular Michael adduct 23. Presumably, the methyl groups of the modified ligand diminish the ability of the reduced form of the complex to serve as a nucleophile but not as a base. Aldehyde 23 was also characterized as a side product of the nickel(II) salen mediated electroreductive cyclization of 11. Given that it is absent from nonmediated processes, its formation is linked to the presence of the mediator. To account for the results, we favor the existence of a mechanistic continuum involving an equilibrium between nickel(II) salen (15) and two reduced forms, one being the metal-centered species 16, the other being a ligand-centered species 17. We postulate that one form may be more prominently involved with the chemistry than another, depending upon the electronic properties/requirements of the substrate, and suggest that the equilibrium will shift to accommodate the need. Thus, for a hard electrophile like an alkyl halide, the properties of 16 ought to dominate, whereas 17 ought to predominate as the reactive species accounting for the chemistry described herein since it properly matches a soft ligand-centered nucleophile with a soft electron deficient alkene.

Speciation in experimental C-O-H fluids produced by the thermal dissociation of oxalic acid dihydrate

NASA Astrophysics Data System (ADS)

Morgan, G. B., VI; Chou, I.-Ming; Pasteris, J. D.

1992-01-01

Fluid speciations and their related reaction pathways were studied in C-O-H-system fluids produced by the thermal dissociation of oxalic acid dihydrate (OAD: H 2C 2O 4 · 2H 2O) sealed in silica glass capsules. Experiments were conducted in the temperature range 230-750°C, with bulk fluid densities in the range 0.01-0.53 g/cm 3. Pressure was controlled by temperature and density in the isochoric systems. The quenched products of dissociation experiments were an aqueous liquid and one (supercritical fluid) or, rarely, two (vapor plus liquid) carbonic phase (s). In-situ Raman microanalyses were performed on the quenched carbonic phases at room temperature, at which fluid pressures ranged from about 50 to 340 bars. Bulk fluid speciations were reconstructed from the Raman analyses via mass balance constraints, and appear to monitor the true fluid speciations at run conditions. In experiments from the lowtemperature range (230-350°C), fluid speciations record the dissociation of OAD according to the reaction OAD = CO2 + CO + 3 H2O. A process of the form CO + H2O = CO2 + H2 is driven to the right with increasing temperature. The hydrogen gas produced tends to escape from the sample systems via diffusion into/through the silica glass capsules, shifting bulk compositions toward equimolar binary H 2O-CO 2 mixtures. The speciations of fluids in experiments with minimal hydrogen loss show poor agreement with speciations calculated for equilibrium fluids by the corresponding-states model of SAXENA and FEI (1988). Such disagreement suggests that the formations of CH 4 and graphite are metastably inhibited in the current experiments, which correlates with their absence or trivial abundances in experimental products. Moreover, calculations in which the stabilities of methane and graphite are suppressed suggest that such metastable equilibrium is approached only in experiments at temperatures greater than about 600-650°C. These results have applications to fluid processes in geological environments, in addition to considerations of using oxalate compounds as volatile sources in experimental studies. It is possible that disequilibrium or metastable fluids may be entrapped as inclusions; re-speciation (toward metastable or stable equilibrium) during P-T evolution of a given terrain would place the fluid inclusion on a new isochore that would not project through the original conditions of entrapment. Moreover, the disequilibrium to metastable nature of dissociation reactions, coupled with the diffusional mobility of hydrogen gas observed in the current experiments, suggests that the predominance of binary H 2O-CO 2 fluid mixtures in natural inclusions from medium- to high-grade metamorphic terrains may be more than a coincidence of similar initial bulk compositions.

Speciation in experimental C-O-H fluids produced by the thermal dissociation of oxalic acid dihydrate

USGS Publications Warehouse

Morgan, G.B.; Chou, I.-Ming; Pasteris, J.D.

1992-01-01

Fluid speciations and their related reaction pathways were studied in C-O-H-system fluids produced by the thermal dissociation of oxalic acid dihydrate (OAD: H2C2O4 ?? 2H2O) sealed in silica glass capsules. Experiments were conducted in the temperature range 230-750??C, with bulk fluid densities in the range 0.01-0.53 g/cm3. Pressure was controlled by temperature and density in the isochoric systems. The quenched products of dissociation experiments were an aqueous liquid and one (supercritical fluid) or, rarely, two (vapor plus liquid) carbonic phase (s). In-situ Raman microanalyses were performed on the quenched carbonic phases at room temperature, at which fluid pressures ranged from about 50 to 340 bars. Bulk fluid speciations were reconstructed from the Raman analyses via mass balance constraints, and appear to monitor the true fluid speciations at run conditions. In experiments from the lowtemperature range (230-350??C), fluid speciations record the dissociation of OAD according to the reaction OAD = CO2 + CO + 3H2O. A process of the form CO + H2O = CO2 + H2 is driven to the right with increasing temperature. The hydrogen gas produced tends to escape from the sample systems via diffusion into/through the silica glass capsules, shifting bulk compositions toward equimolar binary H2O-CO2 mixtures. The speciations of fluids in experiments with minimal hydrogen loss show poor agreement with speciations calculated for equilibrium fluids by the corresponding-states model of Saxena and Fei (1988). Such disagreement suggests that the formations of CH4 and graphite are metastably inhibited in the current experiments, which correlates with their absence or trivial abundances in experimental products. Moreover, calculations in which the stabilities of methane and graphite are suppressed suggest that such metastable equilibrium is approached only in experiments at temperatures greater than about 600-650??C. These results have applications to fluid processes in geological environments, in addition to considerations of using oxalate compounds as volatile sources in experimental studies. It is possible that disequilibrium or metastable fluids may be entrapped as inclusions; re-speciation (toward metastable or stable equilibrium) during P-T evolution of a given terrain would place the fluid inclusion on a new isochore that would not project through the original conditions of entrapment. Moreover, the disequilibrium to metastable nature of dissociation reactions, coupled with the diffusional mobility of hydrogen gas observed in the current experiments, suggests that the predominance of binary H2O-CO2 fluid mixtures in natural inclusions from medium- to high-grade metamorphic terrains may be more than a coincidence of similar initial bulk compositions. ?? 1992.

Analysis of the difference in color development in the dye-binding method due to the kind of buffer solution.

PubMed

Suzuki, Yuji

2006-06-01

In a dye-binding method using a pH indicator, color development has reportedly been affected by the kind of buffer solution used in the color reagent. This phenomenon was analyzed by using a calculation based on the assumption that the anion of the buffer solution also reacts with protein. Color development decreases with increases in the anion concentration of the buffer solution and in the equilibrium constant of the reaction between the anion and protein. The differences in color development due to the kind of buffer solution can be attributed to differences in the equilibrium constant of the reaction forming the anion-protein complex and to the concentration of the anion between the buffer solutions.

Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

NASA Technical Reports Server (NTRS)

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

1994-01-01

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

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.

Theoretical study on the identity ion pair SN2 reactions of LiX with CH3SX (X=Cl, Br, and I): structure, mechanism, and potential energy surface.

PubMed

Ren, Yi; Gai, Jing-Gang; Xiong, Yan; Lee, Kuo-Hsing; Chu, San-Yan

2007-07-26

Three archetypal ion pair nucleophilic substitution reactions at the methylsulfenyl sulfur atom LiX+CH3SX-->XSCH3+LiX (X=Cl, Br, and I) are investigated by the modified Gaussian-2 theory. Including lithium cation in the anionic models makes the ion pair reactions proceed along an SN2 mechanism, contrary to the addition-elimination pathway occurring in the corresponding anionic nucleophilic substitution reactions X-+CH3SX-->XSCH3+X-. Two reaction pathways for the ion pair SN2 reactions at sulfur, inversion and retention, are proposed. Results indicate the inversion pathway is favorable for all the halogens. Comparison of the transition structures and energetics for the ion pair SN2 at sulfur with the potential competition ion pair SN2 reactions at carbon LiX+CH3SX-->XCH3+LiXS shows that the SN2 reactions at carbon are not favorable from the viewpoints of kinetics and thermodynamics.

Esterification of palm fatty acid distillate with epychlorohydrin using cation exchange resin catalyst

NASA Astrophysics Data System (ADS)

Budhijanto, Budhijanto; Subagyo, Albertus F. P. H.

2017-05-01

Palm Fatty Acid Distillate (PFAD) is one of the wastes from the conversion of crude palm oil (CPO) into cooking oil. The PFAD is currently only utilized as the raw material for low grade soap and biofuel. To improve the economic value of PFAD, it was converted into monoglyceride by esterification process. Furthermore, the monoglyceride could be polymerized to form alkyd resin, which is a commodity of increasing importance. This study aimed to propose a kinetics model for esterification of PFAD with epichlorohydrin using cation exchange resin catalyst. The reaction was the first step from a series of reactions to produce the monoglyceride. In this study, the reaction between PFAD and epichlorohydirne was run in a stirred batch reactor. The stirrer was operated at a constant speed of 400 RPM. The reaction was carried out for 180 minutes on varied temperatures of 60°C, 70°C, 80°C, dan 90°C. Cation exchange resin was applied as solid catalysts. Analysis was conducted periodically by measuring the acid number of the samples, which was further used to calculate PFAD conversion. The data were used to determine the rate constants and the equilibrium constants of the kinetics model. The kinetics constants implied that the reaction was reversible and controlled by the intrinsic surface reaction. Despite the complication of the heterogeneous nature of the reaction, the kinetics data well fitted the elementary rate law. The effect of temperature on the equilibrium constants indicated that the reaction is exothermic.

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

PubMed

Buchner, Alexander; Tostevin, Filipe; Gerland, Ulrich

2013-05-17

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

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

PubMed

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

2010-05-06

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

Influences of growth parameters on the reaction pathway during GaN synthesis

NASA Astrophysics Data System (ADS)

Zhang, Zhi; Liu, Zhongyi; Fang, Haisheng

2018-01-01

Gallium nitride (GaN) film growth is a complicated physical and chemical process including fluid flow, heat transfer, species transport and chemical reaction. Study of the reaction mechanism, i.e., the reaction pathway, is important for optimizing the growth process in the actual manufacture. In the paper, the growth pathway of GaN in a closed-coupled showerhead metal-organic chemical vapor deposition (CCS-MOCVD) reactor is investigated in detail using computational fluid dynamics (CFD). Influences of the process parameters, such as the chamber pressure, the inlet temperature, the susceptor temperature and the pre-exponential factor, on the reaction pathway are examined. The results show that increases of the chamber pressure or the inlet temperature, as well as reductions of the susceptor temperature or the pre-exponential factor lead to the adduct route dominating the growth. The deposition rate contributed by the decomposition route, however, can be enhanced dramatically by increasing the inlet temperature, the susceptor temperature and the pre-exponential factor.

Geochemical evolution of groundwater in the Culebra dolomite near the Waste Isolation Pilot Plant, southeastern New Mexico, USA

USGS Publications Warehouse

Siegel, M.D.; Anderholm, S.

1994-01-01

The Culebra Dolomite Member of the Rustler Formation, a thin (10 m) fractured dolomite aquifer, lies approximately 450 m above the repository horizon of the Waste Isolation Pilot Plant (WIPP) in southeastern New Mexico, USA. Salinities of water in the Culebra range roughly from 10,000 to 200,000 mg/L within the WIPP site. A proposed model for the post-Pleistocene hydrochemical evolution of the Culebra tentatively identifies the major sources and sinks for many of the groundwater solutes. Reaction-path simulations with the PHRQPITZ code suggest that the Culebra dolomite is a partial chemical equilibrium system whose composition is controlled by an irreversible process (dissolution of evaporites) and equilibrium with gypsum and calcite. Net geochemical reactions along postulated modern flow paths, calculated with the NETPATH code, include dissolution of halite, carbonate and evaporite salts, and ion exchange. R-mode principal component analysis revealed correlations among the concentrations of Si, Mg, pH, Li, and B that are consistent with several clay-water reactions. The results of the geochemical calculations and mineralogical data are consistent with the following hydrochemical model: 1. (1) solutes are added to the Culebra by dissolution of evaporite minerals 2. (2) the solubilities of gypsum and calcite increase as the salinity increases; these minerals dissolve as chemical equilibrium is maintained between them and the groundwater 3. (3) equilibrium is not maintained between the waters and dolomite; sufficient Mg is added to the waters by dissolution of accessory carnallite or polyhalite such that the degree of dolomite supersaturation increases with ionic strength 4. (4) clays within the fractures and rock matrix exert some control on the distribution of Li, B, Mg, and Si via sorption, ion exchange, and dissolution. ?? 1994.

Erratum to "The mechanism and thermodynamics of transesterification of acetate-ester enolates in the gas phase" : [Int. J. Mass Spectrom. Ion Process. 172 (1998) 25

NASA Astrophysics Data System (ADS)

Haas, George W.; Giblin, Daryl E.; Gross, Michael L.

1998-02-01

In solution, base-catalyzed hydrolysis and transesterification of esters are initiated by hydroxide- or alkoxide-ion attack at the carbonyl carbon. At low pressures in the gas phase, however, transesterification proceeds by an attack of the enolate anion of an acetate ester on an alcohol. Fourier transform mass spectrometry (FTMS) indicates that the reaction is the second-order process: -CH2-CO2-R+R'-OH-->-CH2-CO2-R'+R-OH and there is little to no detectable production of either alkoxide anion. Labeling studies show that the product and reactant enolate anion esters undergo exchange of hydrogens located [alpha] to the carbonyl carbon with the deuterium of R'--OD. The extent of the H/D exchange increases with reaction time, pointing to a short-lived intermediate. The alcoholysis reaction rate constants increase with increasing acidity of the primary, straight-chained alkyl alcohols, whereas steric effects associated with branched alcohols cause the rate constants to decrease. Equilibrium constants, which were determined directly from measurements at equilibrium and which were calculated from the forward and reverse rate constants, are near unity and show internal consistency. In the absence of steric effects, the larger enolate is always the favored product at equilibrium. The intermediate for the transesterification reaction, which can be generated at a few tenths of a torr in a tandem mass spectrometer, is tetrahedral, but other adducts that are collisionally stabilized under these conditions are principally loosely bound complexes.

n-BuLi as a highly efficient precatalyst for hydrophosphonylation of aldehydes and unactivated ketones.

PubMed

Liu, Chengwei; Zhang, Yu; Qian, Qinqin; Yuan, Dan; Yao, Yingming

2014-12-05

It was found for the first time that organic alkali metal compounds serve as highly efficient precatalysts for the hydrophosphonylation reactions of aldehydes and unactivated ketones with dialkyl phosphite under mild conditions. For ketone substrates, a reversible reaction was observed, and the influence of catalyst loading and reaction temperature on the reaction equilibrium was studied in detail. Overall, the hydrophosphonylation reactions catalyzed by 0.1 mol % n-BuLi were completed within 5 min for a broad range of substrates and generated a series of α-hydroxy phosphonates in high yields.

Episodic fluid expulsion and fluid pathways during high-pressure dehydration of serpentinite

NASA Astrophysics Data System (ADS)

Padrón-Navarta, J.; Garrido, C. J.; López Sánchez-Vizcaíno, V.; Gómez-Pugnaire, M.; Tommasi, A.; Marchesi, C.

2011-12-01

Our understanding of subduction zone processes is tightly connected to our knowledge of the cycling of volatiles in the Earth, namely the loci of devolatilization reactions and the fluid migration mechanism. The exact nature of fluid pathways at high-pressure conditions is poorly known and still highly speculative. The study of metamorphic terrains that record main dehydration reaction are, thus, an invaluable tool to decipher the mechanism for fluid expulsion. Among other dehydration reactions in subduction zones, the antigorite (Atg) breakdown is rather discontinuous, releases the largest amount of fluids (ca. 9 wt. %) and is considered to have important seismological implications. The antigorite dehydration front in the Cerro del Almirez (Betic Cordillera, Spain) offers, thus, an unique opportunity to investigate the dynamics of fluid expulsion through the study of micro- and macrotextures recorded in the prograde assemblage (chlorite harzburgite). Chl-harzburgites show two textures interspersed in decameter-sized domains: granoblastic and spinifex-like. Both were formed under similar P-T conditions (~1.6-1.9 GPa and 680-710°C)). We ascribe the change in texture to shifts of the growth rate due to temporal and spatial fluctuations of the affinity of the Atg-breakdown reaction. These fluctuations are driven by cyclic variations of the excess fluid pressure which are ultimately controlled by the hydrodynamics of deserpentinization fluid expulsion. Crystallization at a low affinity of the reaction, correspondig to the granoblastic texture, may be attained if fluids are slowly drained out from the dehydration front. During the advancement of the dehydration front, overpressured domains are left behind preserving highly metastable Atg-serpentinite domains. Brittle failure results in a sudden drop of the fluid pressure, and a displacement of Atg equilibrium towards the prograde products that crystallizes at a high affinity of the reaction (spinifex-like texture). Evidences of brittle failure are found along grain-size reduction zones (GSRZ), a few mm to meters wide, which form roughly planar conjugate structures and crosscut the metamorphic texture. GSRZ are characterized by (1) sharp, irregular shapes and abrupt terminations contacts with undeformed metaperidotite, (2) an important reduction of the olivine grain size (60-250 μm), and (3) decrease in the opx modal amount. Analysis of olivine crystal-preferred orientations in GSRZ shows similar patterns, but a higher dispersion than in neighboring metaperidotite. These structures are interpreted as due to hydrofracturing allowing for the formation of high permeability channelways for overpressured fluids. This textural bimodality (granofels and spinifex-like) and the record of brittle failure witness a unique example of feedback between cyclic metamorphic fluid expulsion, reaction rates, and deformation in the Atg-dehydrating system.

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

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

King, Zachary A.; Drager, Andreas; Ebrahim, Ali

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).more » Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.« less

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

PubMed Central

King, Zachary A.; Dräger, Andreas; Ebrahim, Ali; Sonnenschein, Nikolaus; Lewis, Nathan E.; Palsson, Bernhard O.

2015-01-01

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools. PMID:26313928

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

DOE PAGES

King, Zachary A.; Drager, Andreas; Ebrahim, Ali; ...

2015-08-27

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).more » Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.« less

Elucidation of the Pathway to Astaxanthin in the Flowers of Adonis aestivalis[C][W

PubMed Central

Cunningham, Francis X.; Gantt, Elisabeth

2011-01-01

A few species in the genus Adonis are the only land plants known to produce the valuable red ketocarotenoid astaxanthin in abundance. Here, we ascertain the pathway that leads from the β-rings of β-carotene, a carotenoid ubiquitous in plants, to the 3-hydroxy-4-keto-β-rings of astaxanthin (3,3′-dihydroxy-β,β-carotene-4,4’-dione) in the blood-red flowers of Adonis aestivalis, an ornamental and medicinal plant commonly known as summer pheasant’s eye. Two gene products were found to catalyze three distinct reactions, with the first and third reactions of the pathway catalyzed by the same enzyme. The pathway commences with the activation of the number 4 carbon of a β-ring in a reaction catalyzed by a carotenoid β-ring 4-dehydrogenase (CBFD), continues with the further dehydrogenation of this carbon to yield a carbonyl in a reaction catalyzed by a carotenoid 4-hydroxy-β-ring 4-dehydrogenase, and concludes with the addition of an hydroxyl group at the number 3 carbon in a reaction catalyzed by the erstwhile CBFD enzyme. The A. aestivalis pathway is both portable and robust, functioning efficiently in a simple bacterial host. Our elucidation of the pathway to astaxanthin in A. aestivalis provides enabling technology for development of a biological production process and reveals the evolutionary origin of this unusual plant pathway, one unrelated to and distinctly different from those used by bacteria, green algae, and fungi to synthesize astaxanthin. PMID:21862704

Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape

PubMed Central

Street, Timothy O; Barrick, Doug

2009-01-01

The Notch ankyrin domain is a repeat protein whose folding has been characterized through equilibrium and kinetic measurements. In previous work, equilibrium folding free energies of truncated constructs were used to generate an experimentally determined folding energy landscape (Mello and Barrick, Proc Natl Acad Sci USA 2004;101:14102–14107). Here, this folding energy landscape is used to parameterize a kinetic model in which local transition probabilities between partly folded states are based on energy values from the landscape. The landscape-based model correctly predicts highly diverse experimentally determined folding kinetics of the Notch ankyrin domain and sequence variants. These predictions include monophasic folding and biphasic unfolding, curvature in the unfolding limb of the chevron plot, population of a transient unfolding intermediate, relative folding rates of 19 variants spanning three orders of magnitude, and a change in the folding pathway that results from C-terminal stabilization. These findings indicate that the folding pathway(s) of the Notch ankyrin domain are thermodynamically selected: the primary determinants of kinetic behavior can be simply deduced from the local stability of individual repeats. PMID:19177351

Demystifying Introductory Chemistry. Part 4: An Approach to Reaction Thermodynamics through Enthalpies, Entropies, and Free Energies of Atomization.

ERIC Educational Resources Information Center

Spencer, James N.; And Others

1996-01-01

Presents an alternative approach to teaching reaction thermodynamics in introductory chemistry courses using calculations of enthalpies, entropies, and free energies of atomization. Uses a consistent concept, that of decomposition of a compound to its gaseous atoms, to discuss not only thermodynamic parameters but also equilibrium and…

The H[subscript 3]PO[subscript 4] Acid Ionization Reactions: A Capstone Multiconcept Thermodynamics General Chemistry Laboratory Exercise

ERIC Educational Resources Information Center

Nyasulu, Frazier; Barlag, Rebecca; Wise, Lindy; McMills, Lauren

2013-01-01

The thermodynamic properties of weak acid ionization reactions are determined. The thermodynamic properties are corresponding values of the absolute temperature (T), the weak acid equilibrium constant (K[subscript a]), the enthalpy of ionization (delta[subscript i]H[degrees]), and the entropy of ionization (delta[subscript i]S[degrees]). The…

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).

Oxidative protein folding: from thiol-disulfide exchange reactions to the redox poise of the endoplasmic reticulum.

PubMed

Hudson, Devin A; Gannon, Shawn A; Thorpe, Colin

2015-03-01

This review examines oxidative protein folding within the mammalian endoplasmic reticulum (ER) from an enzymological perspective. In protein disulfide isomerase-first (PDI-first) pathways of oxidative protein folding, PDI is the immediate oxidant of reduced client proteins and then addresses disulfide mispairings in a second isomerization phase. In PDI-second pathways the initial oxidation is PDI-independent. Evidence for the rapid reduction of PDI by reduced glutathione is presented in the context of PDI-first pathways. Strategies and challenges are discussed for determination of the concentrations of reduced and oxidized glutathione and of the ratios of PDI(red):PDI(ox). The preponderance of evidence suggests that the mammalian ER is more reducing than first envisaged. The average redox state of major PDI-family members is largely to almost totally reduced. These observations are consistent with model studies showing that oxidative protein folding proceeds most efficiently at a reducing redox poise consistent with a stoichiometric insertion of disulfides into client proteins. After a discussion of the use of natively encoded fluorescent probes to report the glutathione redox poise of the ER, this review concludes with an elaboration of a complementary strategy to discontinuously survey the redox state of as many redox-active disulfides as can be identified by ratiometric LC-MS-MS methods. Consortia of oxidoreductases that are in redox equilibrium can then be identified and compared to the glutathione redox poise of the ER to gain a more detailed understanding of the factors that influence oxidative protein folding within the secretory compartment. Copyright © 2014 Elsevier Inc. All rights reserved.

High-Capacity and Long-Cycle Life Aqueous Rechargeable Lithium-Ion Battery with the FePO4 Anode.

PubMed

Wang, Yuesheng; Yang, Shi-Ze; You, Ya; Feng, Zimin; Zhu, Wen; Gariépy, Vincent; Xia, Jiexiang; Commarieu, Basile; Darwiche, Ali; Guerfi, Abdelbast; Zaghib, Karim

2018-02-28

Aqueous lithium-ion batteries are emerging as strong candidates for a great variety of energy storage applications because of their low cost, high-rate capability, and high safety. Exciting progress has been made in the search for anode materials with high capacity, low toxicity, and high conductivity; yet, most of the anode materials, because of their low equilibrium voltages, facilitate hydrogen evolution. Here, we show the application of olivine FePO 4 and amorphous FePO 4 ·2H 2 O as anode materials for aqueous lithium-ion batteries. Their capacities reached 163 and 82 mA h/g at a current rate of 0.2 C, respectively. The full cell with an amorphous FePO 4 ·2H 2 O anode maintained 92% capacity after 500 cycles at a current rate of 0.2 C. The acidic aqueous electrolyte in the full cells prevented cathodic oxygen evolution, while the higher equilibrium voltage of FePO 4 avoided hydrogen evolution as well, making them highly stable. A combination of in situ X-ray diffraction analyses and computational studies revealed that olivine FePO 4 still has the biphase reaction in the aqueous electrolyte and that the intercalation pathways in FePO 4 ·2H 2 O form a 2-D mesh. The low cost, high safety, and outstanding electrochemical performance make the full cells with olivine or amorphous hydrated FePO 4 anodes commercially viable configurations for aqueous lithium-ion batteries.

Representing metabolic pathway information: an object-oriented approach.

PubMed

Ellis, L B; Speedie, S M; McLeish, R

1998-01-01

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a website providing information and dynamic links for microbial metabolic pathways, enzyme reactions, and their substrates and products. The Compound, Organism, Reaction and Enzyme (CORE) object-oriented database management system was developed to contain and serve this information. CORE was developed using Java, an object-oriented programming language, and PSE persistent object classes from Object Design, Inc. CORE dynamically generates descriptive web pages for reactions, compounds and enzymes, and reconstructs ad hoc pathway maps starting from any UM-BBD reaction. CORE code is available from the authors upon request. CORE is accessible through the UM-BBD at: http://www. labmed.umn.edu/umbbd/index.html.

The measurable heat flux that accompanies active transport by Ca2+-ATPase.

PubMed

Bedeaux, Dick; Kjelstrup, Signe

2008-12-28

We present a new mesoscopic basis which can be used to derive flux equations for the forward and reverse mode of operation of ion-pumps. We obtain a description of the fluxes far from global equilibrium. An asymmetric set of transport coefficients is obtained, by assuming that the chemical reaction as well as the ion transports are activated, and that the enzyme has a temperature independent of the activation coordinates. Close to global equilibrium, the description reduces to the well known one from non-equilibrium thermodynamics with a symmetric set of transport coefficients. We show how the measurable heat flux and the heat production under isothermal conditions, as well as thermogenesis, can be defined. Thermogenesis is defined via the onset of the chemical reaction or ion transports by a temperature drop. A prescription has been given for how to determine transport coefficients on the mesocopic level, using the macroscopic coefficient obtained from measurements, the activation enthalpy, and a proper probability distribution. The method may give new impetus to a long-standing unsolved transport problem in biophysics.

On violations of Le Chatelier's principle for a temperature change in small systems observed for short times

NASA Astrophysics Data System (ADS)

Dasmeh, Pouria; Searles, Debra J.; Ajloo, Davood; Evans, Denis J.; Williams, Stephen R.

2009-12-01

Le Chatelier's principle states that when a system is disturbed, it will shift its equilibrium to counteract the disturbance. However for a chemical reaction in a small, confined system, the probability of observing it proceed in the opposite direction to that predicted by Le Chatelier's principle, can be significant. This work gives a molecular level proof of Le Chatelier's principle for the case of a temperature change. Moreover, a new, exact mathematical expression is derived that is valid for arbitrary system sizes and gives the relative probability that a single experiment will proceed in the endothermic or exothermic direction, in terms of a microscopic phase function. We show that the average of the time integral of this function is the maximum possible value of the purely irreversible entropy production for the thermal relaxation process. Our result is tested against computer simulations of the unfolding of a polypeptide. We prove that any equilibrium reaction mixture on average responds to a temperature increase by shifting its point of equilibrium in the endothermic direction.

Kynurenine pathway metabolites and enzymes involved in redox reactions.

PubMed

González Esquivel, D; Ramírez-Ortega, D; Pineda, B; Castro, N; Ríos, C; Pérez de la Cruz, V

2017-01-01

Oxido-reduction reactions are a fundamental part of the life due to support many vital biological processes as cellular respiration and glucose oxidation. In the redox reactions, one substance transfers one or more electrons to another substance. An important electron carrier is the coenzyme NAD + , which is involved in many metabolic pathways. De novo biosynthesis of NAD + is through the kynurenine pathway, the major route of tryptophan catabolism, which is sensitive to redox environment and produces metabolites with redox capacity, able to alter biological functions that are controlled by redox-responsive signaling pathways. Kynurenine pathway metabolites have been implicated in the physiology process and in the physiopathology of many diseases; processes that also share others factors as dysregulation of calcium homeostasis, mitochondrial dysfunction, oxidative stress, inflammation and cell death, which impact the redox environment. This review examines in detail the available evidence in which kynurenine pathway metabolites participate in redox reactions and their effect on cellular redox homeostasis, since the knowledge of the main factors and mechanisms that lead to cell death in many neurodegenative disorders and other pathologies, such as mitochondrial dysfunction, oxidative stress and kynurenines imbalance, will allow to develop therapies using them as targets. This article is part of the Special Issue entitled 'The Kynurenine Pathway in Health and Disease'. Copyright © 2016 Elsevier Ltd. All rights reserved.

Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase

NASA Astrophysics Data System (ADS)

Tran, Diem-Trang T.; Le, Ly T.; Truong, Thanh N.

2013-08-01

Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called "pathway docking" in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.

Anomalous versus Slowed-Down Brownian Diffusion in the Ligand-Binding Equilibrium

PubMed Central

Soula, Hédi; Caré, Bertrand; Beslon, Guillaume; Berry, Hugues

2013-01-01

Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) that converges back to a Brownian motion with reduced diffusion coefficient at long times after the anomalous diffusion regime. Therefore, slowed-down Brownian motion could be considered the macroscopic limit of transient anomalous diffusion. On the other hand, membranes are also heterogeneous media in which Brownian motion may be locally slowed down due to variations in lipid composition. Here, we investigate whether both situations lead to a similar behavior for the reversible ligand-binding reaction in two dimensions. We compare the (long-time) equilibrium properties obtained with transient anomalous diffusion due to obstacle hindrance or power-law-distributed residence times (continuous-time random walks) to those obtained with space-dependent slowed-down Brownian motion. Using theoretical arguments and Monte Carlo simulations, we show that these three scenarios have distinctive effects on the apparent affinity of the reaction. Whereas continuous-time random walks decrease the apparent affinity of the reaction, locally slowed-down Brownian motion and local hindrance by obstacles both improve it. However, only in the case of slowed-down Brownian motion is the affinity maximal when the slowdown is restricted to a subregion of the available space. Hence, even at long times (equilibrium), these processes are different and exhibit irreconcilable behaviors when the area fraction of reduced mobility changes. PMID:24209851

Infrared and reflectron time-of-flight mass spectroscopic study on the synthesis of glycolaldehyde in methanol (CH3OH) and methanol-carbon monoxide (CH3OH-CO) ices exposed to ionization radiation.

PubMed

Maity, Surajit; Kaiser, Ralf I; Jones, Brant M

2014-01-01

We present conclusive evidence on the formation of glycolaldehyde (HOCH2CHO) synthesized within astrophysically relevant ices of methanol (CH3OH) and methanol-carbon monoxide (CH3OH-CO) upon exposure to ionizing radiation at 5.5 K. The radiation induced chemical processes of the ices were monitored on line and in situ via infrared spectroscopy which was complimented by temperature programmed desorption studies post irradiation, utilizing highly sensitive reflectron time-of-flight mass spectrometry coupled with single photon fragment free photoionization (ReTOF-PI) at 10.49 eV. Specifically, glycolaldehyde was observed via the v14 band and further enhanced with the associated frequency shifts of the carbonyl stretching mode observed in irradiated isotopologue ice mixtures. Furthermore, experiments conducted with mixed isotopic ices of methanol-carbon monoxide (13CH3OH-CO, CH3(18)OH-CO, CD3OD-13CO and CH3OH-C18O) provide solid evidence of at least three competing reaction pathways involved in the formation of glycolaldehyde via non-equilibrium chemistry, which were identified as follows: (i) radical-radical recombination of HCO and CH2OH formed via decomposition of methanol--the "two methanol pathway"; (ii) via the reaction of one methanol unit (CH2OH from the decomposition of CH3OH) with one carbon monoxide unit (HCO from the hydrogenation of CO)--the "one methanol, one carbon monoxide pathway"; and (iii) formation via hydrogenation of carbon monoxide resulting in radicals of HCO and CH2OH--the "two carbon monoxide pathway". In addition, temperature programmed desorption studies revealed an increase in the amount of glycolaldehyde formed, suggesting further thermal chemistry of trapped radicals within the ice matrix. Sublimation of glycolaldehyde during the warm up was also monitored via ReTOF-PI and validated via the mutual agreement of the associated isotopic frequency shifts within the infrared band positions and the identical sublimation profiles obtained from the ReTOF spectra and infrared spectroscopy of the corresponding isotopes. In addition, an isomer of glycolaldehyde (ethene-1,2-diol) was tentatively assigned. Confirmation of the identified pathways based on infrared spectroscopy was also obtained from the observed ion signals corresponding to isotopomers of glycolaldehyde. These coupled techniques provide clear, concise evidence of the formation of a complex and astrobiologically important organic, glycolaldehyde, relevant to the icy mantles observed in the interstellar medium.

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

NASA Astrophysics Data System (ADS)

García-Meseguer, Rafael; Martí, Sergio; Ruiz-Pernía, J. Javier; Moliner, Vicent; Tuñón, Iñaki

2013-07-01

Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We show that the structure of the protein provides an adequate environment for the progress of the reaction, although a certain degree of flexibility is needed to attain the full catalytic effect. However, these motions do not introduce significant dynamical corrections to the rate constant and can be described as equilibrium fluctuations.

Reversible Hydrogen Transfer Reactions in Thiyl Radicals From Cysteine and Related Molecules: Absolute Kinetics and Equilibrium Constants Determined by Pulse Radiolysis

PubMed Central

Koppenol, Willem H.

2013-01-01

The mercapto group of cysteine (Cys) is a predominant target for oxidative modification, where one-electron oxidation leads to the formation of Cys thiyl radicals, CysS•. These Cys thiyl radicals enter 1,2- and 1,3-hydrogen transfer reactions, for which rate constants are reported in this paper. The products of these 1,2- and 1,3-hydrogen transfer reactions are carbon-centered radicals at position C3 (α-mercaptoalkyl radicals) and C2 (•Cα radicals) of Cys, respectively. Both processes can be monitored separately in Cys analogues such as cysteamine (CyaSH) and penicillamine (PenSH). At acidic pH, thiyl radicals from CyaSH permit only the 1,2-hydrogen transfer according to equilibrium 12, +H3NCH2CH2S• ⇌ +H3NCH2 •CH–SH, where rate constants for forward and reverse reaction are k12 ≈ 105 s−1 and k−12 ≈ 1.5 × 105s−1, respectively. In contrast, only the 1,3-hydrogen transfer is possible for thiyl radicals from PenSH according to equilibrium 14, (+H3N/CO2H)Cα–C(CH3)2–S• ⇌ (+H3N/CO2H)•Cα–C(CH3)2–SH, where rate constants for the forward and the reverse reaction are k14 = 8 × 104 s−1 and k−14 = 1.4 × 106 s−1. The •Cα radicals from PenSH and Cys have the additional opportunity for β-elimination of HS•/S•−, which proceeds with k39 ≈ (3 ± 1) × 104 s−1 from •Cα radicals from PenSH and k−34 ≈ 5 × 103 s−1 from •Cα radicals from Cys. The rate constants quantified for the 1,2- and 1,3-hydrogen transfer reactions can be used as a basis to calculate similar processes for Cys thiyl radicals in proteins, where hydrogen transfer reactions, followed by the addition of oxygen, may lead to the irreversible modification of target proteins. PMID:22483034

Regulation of the PI3K pathway through a p85α monomer–homodimer equilibrium | Office of Cancer Genomics

Cancer.gov

The canonical action of the p85α regulatory subunit of phosphatidylinositol 3-kinase (PI3K) is to associate with the p110α catalytic subunit to allow stimuli-dependent activation of the PI3K pathway. We elucidate a p110α-independent role of homodimerized p85α in the positive regulation of PTEN stability and activity.

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.

Enzymatic oxidation of ethanol in the gaseous phase.

PubMed

Barzana, E; Karel, M; Klibanov, A M

1989-11-01

The enzymatic conversion of gaseous substrates represents a novel concept in bioprocessing. A critical parameter in such systems is the water activity, A(w) The present article reports the effect of A(w) on the catalytic performance of alcohol oxidase acting on ethanol vapors. Enzyme activity in the gas-phase reaction increases several orders of magnitude, whereas the thermostability decreases drastically when A(w) is increased from 0.11 to 0.97. The enzyme is active on gaseous substrates even at hydration levels below the monolayer coverage. Enhanced thermostability at lower hydrations results in an increase in the optimum temperature of the gas-phase reaction catalyzed by alcohol oxidase. The apparent activation energy decreases as A(w) increases, approaching the value obtained for the enzyme in aqueous solution. The formation of a pread-sorbed ethanol phase on the surface of the support is not a prerequisite for the reaction, suggesting that the reaction occurs by direct interaction of the gaseous substrate with the enzyme. The gas-phase reaction follows Michaelis-Menten kinetics, with a K(m) value almost 100 times lower than that in aqueous solution. Based on vapor-liquid equilibrium data and observed K(m) values, it is postulated that during the gas-phase reaction the ethanol on the enzyme establishes an equilibrium with the ethanol vapor similar to that between ethanol in water and ethanol in the gas phase.

A coupled mechanical-chemical model for reflecting the influence of stress on oxidation reactions in thermal barrier coating

NASA Astrophysics Data System (ADS)

Chen, Lin; Yueming, Li

2018-06-01

In this paper, a coupled mechanical-chemical model is established based on the thermodynamic framework, in which the contribution of chemical expansion to free energy is introduced. The stress-dependent chemical potential equilibrium at the gas-solid interface and the stress gradient-dependent diffusion equation as well as a so-called generalized force which is conjugate to the oxidation rate are derived from the proposed model, which could reflect the influence of stresses on the oxidation reaction. Based on the proposed coupled mechanical-chemical model, a user element subroutine is developed in ABAQUS. The numerical simulation of the high temperature oxidation in the thermal barrier coating is carried out to verify the accuracy of the proposed model, and then the influence of stresses on the oxidation reaction is investigated. In thermally grown oxide, the considerable stresses would be induced by permanent volumetric swelling during the oxidation. The stresses play an important role in the chemical potential equilibrium at the gas-solid interface and strongly affect the oxidation reaction. The gradient of the stresses, however, only occurs in the extremely thin oxidation front layer, which plays a very limited role in the oxidation reaction. The generalized force could be divided into the stress-dependent and the stress-independent parts. Comparing with the stress-independent part, the stress-dependent part is smaller, which has little influence on oxidation reaction.

Stochastic pumping of non-equilibrium steady-states: how molecules adapt to a fluctuating environment.

PubMed

Astumian, R D

2018-01-11

In the absence of input energy, a chemical reaction in a closed system ineluctably relaxes toward an equilibrium state governed by a Boltzmann distribution. The addition of a catalyst to the system provides a way for more rapid equilibration toward this distribution, but the catalyst can never, in and of itself, drive the system away from equilibrium. In the presence of external fluctuations, however, a macromolecular catalyst (e.g., an enzyme) can absorb energy and drive the formation of a steady state between reactant and product that is not determined solely by their relative energies. Due to the ubiquity of non-equilibrium steady states in living systems, the development of a theory for the effects of external fluctuations on chemical systems has been a longstanding focus of non-equilibrium thermodynamics. The theory of stochastic pumping has provided insight into how a non-equilibrium steady-state can be formed and maintained in the presence of dissipation and kinetic asymmetry. This effort has been greatly enhanced by a confluence of experimental and theoretical work on synthetic molecular machines designed explicitly to harness external energy to drive non-equilibrium transport and self-assembly.

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

PubMed Central

2017-01-01

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

Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse

PubMed Central

Perera, Lalith; Freudenthal, Bret D.; Beard, William A.; Shock, David D.; Pedersen, Lee G.; Wilson, Samuel H.

2015-01-01

DNA polymerases facilitate faithful insertion of nucleotides, a central reaction occurring during DNA replication and repair. DNA synthesis (forward reaction) is “balanced,” as dictated by the chemical equilibrium by the reverse reaction of pyrophosphorolysis. Two closely spaced divalent metal ions (catalytic and nucleotide-binding metals) provide the scaffold for these reactions. The catalytic metal lowers the pKa of O3′ of the growing primer terminus, and the nucleotide-binding metal facilitates substrate binding. Recent time-lapse crystallographic studies of DNA polymerases have identified an additional metal ion (product metal) associated with pyrophosphate formation, leading to the suggestion of its possible involvement in the reverse reaction. Here, we establish a rationale for a role of the product metal using quantum mechanical/molecular mechanical calculations of the reverse reaction in the confines of the DNA polymerase β active site. Additionally, site-directed mutagenesis identifies essential residues and metal-binding sites necessary for pyrophosphorolysis. The results indicate that the catalytic metal site must be occupied by a magnesium ion for pyrophosphorolysis to occur. Critically, the product metal site is occupied by a magnesium ion early in the pyrophosphorolysis reaction path but must be removed later. The proposed dynamic nature of the active site metal ions is consistent with crystallographic structures. The transition barrier for pyrophosphorolysis was estimated to be significantly higher than that for the forward reaction, consistent with kinetic activity measurements of the respective reactions. These observations provide a framework to understand how ions and active site changes could modulate the internal chemical equilibrium of a reaction that is central to genome stability. PMID:26351676

The equilibrium constant for N2O5 = NO2 + NO3 - Absolute determination by direct measurement from 243 to 397 K

NASA Technical Reports Server (NTRS)

Cantrell, C. A.; Davidson, J. A.; Mcdaniel, A. H.; Shetter, R. E.; Calvert, J. G.

1988-01-01

Direct determinations of the equilibrium constant for the reaction N2O5 = NO2 + NO3 were carried out by measuring NO2, NO3, and N2O5 using long-path visible and infrared absorption spectroscopy as a function of temperature from 243 to 397 K. The first-order decay rate constant of N2O5 was experimentally measured as a function of temperature. These results are in turn used to derive a value for the rate coefficient for the NO-forming channel in the reaction of NO3 with NO2. The implications of the results for atmospheric chemistry, the thermodynamics of NO3, and for laboratory kinetics studies are discussed.

A BGK model for reactive mixtures of polyatomic gases with continuous internal energy

NASA Astrophysics Data System (ADS)

Bisi, M.; Monaco, R.; Soares, A. J.

2018-03-01

In this paper we derive a BGK relaxation model for a mixture of polyatomic gases with a continuous structure of internal energies. The emphasis of the paper is on the case of a quaternary mixture undergoing a reversible chemical reaction of bimolecular type. For such a mixture we prove an H -theorem and characterize the equilibrium solutions with the related mass action law of chemical kinetics. Further, a Chapman-Enskog asymptotic analysis is performed in view of computing the first-order non-equilibrium corrections to the distribution functions and investigating the transport properties of the reactive mixture. The chemical reaction rate is explicitly derived at the first order and the balance equations for the constituent number densities are derived at the Euler level.

Practical Approaches to Protein Folding and Assembly

PubMed Central

Walters, Jad; Milam, Sara L.; Clark, A. Clay

2009-01-01

We describe here the use of several spectroscopies, such as fluorescence emission, circular dichroism, and differential quenching by acrylamide, in examining the equilibrium and kinetic folding of proteins. The first section regarding equilibrium techniques provides practical information for determining the conformational stability of a protein. In addition, several equilibrium-folding models are discussed, from two-state monomer to four-state homodimer, providing a comprehensive protocol for interpretation of folding curves. The second section focuses on the experimental design and interpretation of kinetic data, such as burst-phase analysis and exponential fits, used in elucidating kinetic folding pathways. In addition, simulation programs are used routinely to support folding models generated by kinetic experiments, and the fundamentals of simulations are covered. PMID:19289201

System-Wide Water Resources Program Nutrient Sub-Model (SWWRP-NSM) Version 1.1

DTIC Science & Technology

2008-09-01

species including crops, native grasses, and trees . The process descriptions utilize a single plant growth model to simulate all types of land covers...characteristics: • Multi- species , multi-phase, and multi-reaction system • Fast (equilibrium-based) and slow (non-equilibrium-based or rate- based...Transformation and loading of N and P species in the overland flow • Simulation of the N and P cycle in the water column (both overland and

OneG: A Computational Tool for Predicting Cryptic Intermediates in the Unfolding Kinetics of Proteins under Native Conditions

PubMed Central

Richa, Tambi; Sivaraman, Thirunavukkarasu

2012-01-01

Understanding the relationships between conformations of proteins and their stabilities is one key to address the protein folding paradigm. The free energy change (ΔG) of unfolding reactions of proteins is measured by traditional denaturation methods and native hydrogen-deuterium (H/D) exchange methods. However, the free energy of unfolding (ΔGU) and the free energy of exchange (ΔGHX) of proteins are not in good agreement, though the experimental conditions of both methods are well matching to each other. The anomaly is due to any one or combinations of the following reasons: (i) effects of cis-trans proline isomerisation under equilibrium unfolding reactions of proteins (ii) inappropriateness in accounting the baselines of melting curves (iii) presence of cryptic intermediates, which may elude the melting curve analysis and (iv) existence of higher energy metastable states in the H/D exchange reactions of proteins. Herein, we have developed a novel computational tool, OneG, which accounts the discrepancy between ΔGU and ΔGHX of proteins by systematically accounting all the four factors mentioned above. The program is fully automated and requires four inputs: three-dimensional structures of proteins, ΔGU, ΔGU * and residue-specific ΔGHX determined under EX2-exchange conditions in the absence of denaturants. The robustness of the program has been validated using experimental data available for proteins such as cytochrome c and apocytochrome b562 and the data analyses revealed that cryptic intermediates of the proteins detected by the experimental methods and the cryptic intermediates predicted by the OneG for those proteins were in good agreement. Furthermore, using OneG, we have shown possible existence of cryptic intermediates and metastable states in the unfolding pathways of cardiotoxin III and cobrotoxin, respectively, which are homologous proteins. The unique application of the program to map the unfolding pathways of proteins under native conditions have been brought into fore and the program is publicly available at http://sblab.sastra.edu/oneg.html PMID:22412877

A Method for Finding Metabolic Pathways Using Atomic Group Tracking.

PubMed

Huang, Yiran; Zhong, Cheng; Lin, Hai Xiang; Wang, Jianyi

2017-01-01

A fundamental computational problem in metabolic engineering is to find pathways between compounds. Pathfinding methods using atom tracking have been widely used to find biochemically relevant pathways. However, these methods require the user to define the atoms to be tracked. This may lead to failing to predict the pathways that do not conserve the user-defined atoms. In this work, we propose a pathfinding method called AGPathFinder to find biochemically relevant metabolic pathways between two given compounds. In AGPathFinder, we find alternative pathways by tracking the movement of atomic groups through metabolic networks and use combined information of reaction thermodynamics and compound similarity to guide the search towards more feasible pathways and better performance. The experimental results show that atomic group tracking enables our method to find pathways without the need of defining the atoms to be tracked, avoid hub metabolites, and obtain biochemically meaningful pathways. Our results also demonstrate that atomic group tracking, when incorporated with combined information of reaction thermodynamics and compound similarity, improves the quality of the found pathways. In most cases, the average compound inclusion accuracy and reaction inclusion accuracy for the top resulting pathways of our method are around 0.90 and 0.70, respectively, which are better than those of the existing methods. Additionally, AGPathFinder provides the information of thermodynamic feasibility and compound similarity for the resulting pathways.

A Method for Finding Metabolic Pathways Using Atomic Group Tracking

PubMed Central

Zhong, Cheng; Lin, Hai Xiang; Wang, Jianyi

2017-01-01

A fundamental computational problem in metabolic engineering is to find pathways between compounds. Pathfinding methods using atom tracking have been widely used to find biochemically relevant pathways. However, these methods require the user to define the atoms to be tracked. This may lead to failing to predict the pathways that do not conserve the user-defined atoms. In this work, we propose a pathfinding method called AGPathFinder to find biochemically relevant metabolic pathways between two given compounds. In AGPathFinder, we find alternative pathways by tracking the movement of atomic groups through metabolic networks and use combined information of reaction thermodynamics and compound similarity to guide the search towards more feasible pathways and better performance. The experimental results show that atomic group tracking enables our method to find pathways without the need of defining the atoms to be tracked, avoid hub metabolites, and obtain biochemically meaningful pathways. Our results also demonstrate that atomic group tracking, when incorporated with combined information of reaction thermodynamics and compound similarity, improves the quality of the found pathways. In most cases, the average compound inclusion accuracy and reaction inclusion accuracy for the top resulting pathways of our method are around 0.90 and 0.70, respectively, which are better than those of the existing methods. Additionally, AGPathFinder provides the information of thermodynamic feasibility and compound similarity for the resulting pathways. PMID:28068354

Non-equilibrium calculations of atmospheric processes initiated by electron impact.

NASA Astrophysics Data System (ADS)

Campbell, L.; Brunger, M. J.

2007-05-01

Electron impact in the atmosphere produces ionisation, dissociation, electronic excitation and vibrational excitation of atoms and molecules. The products can then take part in chemical reactions, recombination with electrons, or radiative or collisional deactivation. While most such processes are fast, some longer--lived species do not reach equilibrium. The electron source (photoelectrons or auroral electrons) also varies over time and longer-lived species can move substantially in altitude by molecular, ambipolar or eddy diffusion. Hence non-equilibrium calculations are required in some circumstances. Such time-step calculations need to have sufficiently short steps so that the fastest processes are still calculated correctly, but this can lead to computation times that are too large. Hence techniques to allow for longer time steps by incorporating equilibrium calculations are described. Examples are given for results of atmospheric non-equilibrium calculations, including the populations of the vibrational levels of ground state N2, the electron density and its dependence on vibrationally excited N2, predictions of nitric oxide density, and detailed processes during short duration auroral events.

Fast quench reactor and method

DOEpatents

Detering, Brent A.; Donaldson, Alan D.; Fincke, James R.; Kong, Peter C.

2002-01-01

A fast quench reaction includes a reactor chamber having a high temperature heating means such as a plasma torch at its inlet and a restrictive convergent-divergent nozzle at its outlet end. Reactants are injected into the reactor chamber. The resulting heated gaseous stream is then rapidly cooled by passage through the nozzle. This "freezes" the desired end product(s) in the heated equilibrium reaction stage.

Patchy reaction-diffusion and population abundance: the relative importance of habitat amount and arrangement

Treesearch

Curtis H. Flather; Michael Bevers

2002-01-01

A discrete reaction-diffusion model was used to estimate long-term equilibrium populations of a hypothetical species inhabiting patchy landscapes to examine the relative importance of habitat amount and arrangement in explaining population size. When examined over a broad range of habitat amounts and arrangements, population size was largely determined by a pure amount...

Fast quench reactor and method

DOEpatents

Detering, Brent A.; Donaldson, Alan D.; Fincke, James R.; Kong, Peter C.

1998-01-01

A fast quench reaction includes a reactor chamber having a high temperature heating means such as a plasma torch at its inlet and a restrictive convergent-divergent nozzle at its outlet end. Reactants are injected into the reactor chamber. The resulting heated gaseous stream is then rapidly cooled by passage through the nozzle. This "freezes" the desired end product(s) in the heated equilibrium reaction stage.

Fast quench reactor and method

DOEpatents

Detering, Brent A.; Donaldson, Alan D.; Fincke, James R.; Kong, Peter C.

2002-09-24

A fast quench reaction includes a reactor chamber having a high temperature heating means such as a plasma torch at its inlet and a restrictive convergent-divergent nozzle at its outlet end. Reactants are injected into the reactor chamber. The resulting heated gaseous stream is then rapidly cooled by passage through the nozzle. This "freezes" the desired end product(s) in the heated equilibrium reaction stage.

Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

NASA Astrophysics Data System (ADS)

Zaharieva, Roussislava; Hanagud, Sathya

2009-06-01

Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

Theory for rates, equilibrium constants, and Brønsted slopes in F1-ATPase single molecule imaging experiments

PubMed Central

Volkán-Kacsó, Sándor; Marcus, Rudolph A.

2015-01-01

A theoretical model of elastically coupled reactions is proposed for single molecule imaging and rotor manipulation experiments on F1-ATPase. Stalling experiments are considered in which rates of individual ligand binding, ligand release, and chemical reaction steps have an exponential dependence on rotor angle. These data are treated in terms of the effect of thermodynamic driving forces on reaction rates, and lead to equations relating rate constants and free energies to the stalling angle. These relations, in turn, are modeled using a formalism originally developed to treat electron and other transfer reactions. During stalling the free energy profile of the enzymatic steps is altered by a work term due to elastic structural twisting. Using biochemical and single molecule data, the dependence of the rate constant and equilibrium constant on the stall angle, as well as the Børnsted slope are predicted and compared with experiment. Reasonable agreement is found with stalling experiments for ATP and GTP binding. The model can be applied to other torque-generating steps of reversible ligand binding, such as ADP and Pi release, when sufficient data become available. PMID:26483483

Energetic study of 4(3H)-pyrimidinone: aromaticity of reactions, hydrogen bond rules, and support for an anomeric effect.

PubMed

Galvão, Tiago L P; Rocha, Inês M; Ribeiro da Silva, Maria D M C; Ribeiro da Silva, Manuel A V

2014-05-08

4(3H)-Pyrimidinone is observed in nature in equilibrium with other tautomeric forms, mimicking the tautomeric equilibrium in pyrimidine nucleobases. In this work, the enthalpy of formation in the gaseous phase of 4(3H)-pyrimidinone was derived from the combination of the enthalpy of formation in the crystalline phase, obtained by static bomb combustion calorimetry, and the enthalpy of sublimation, obtained by Knudsen effusion. The gaseous phase enthalpy of formation of 4(3H)-pyrimidinone was interpreted in terms of isodesmic reactions that consider the enthalpic effects of hydroxypyridines and pyrimidine. After comparison of the experimental and computational results, the same type of isodesmic reactions was used to study the substituent effects of the hydroxyl functional group of 2-, 4-, and 5-hydroxypyrimidines. The influence of aromaticity on the energetics of hydroxypyrimidines was evaluated using the variation of nucleus-independent chemical shifts for several reactions. The influence of intramolecular hydrogen bonds was investigated using the quantum theory of atoms in molecules and the geometric rule of Baker and Hubbard to identify hydrogen bonds. The energetic results obtained were also interpreted in terms of an in plane anomeric effect in the pyrimidine ring.

Aromatic sulfonation with sulfur trioxide: mechanism and kinetic model.

PubMed

Moors, Samuel L C; Deraet, Xavier; Van Assche, Guy; Geerlings, Paul; De Proft, Frank

2017-01-01

Electrophilic aromatic sulfonation of benzene with sulfur trioxide is studied with ab initio molecular dynamics simulations in gas phase, and in explicit noncomplexing (CCl 3 F) and complexing (CH 3 NO 2 ) solvent models. We investigate different possible reaction pathways, the number of SO 3 molecules participating in the reaction, and the influence of the solvent. Our simulations confirm the existence of a low-energy concerted pathway with formation of a cyclic transition state with two SO 3 molecules. Based on the simulation results, we propose a sequence of elementary reaction steps and a kinetic model compatible with experimental data. Furthermore, a new alternative reaction pathway is proposed in complexing solvent, involving two SO 3 and one CH 3 NO 2 .

Analysis of the reaction of carbachol with acetylcholinesterase using thioflavin T as a coupled fluorescence reporter.

PubMed

Rosenberry, Terrone L; Sonoda, Leilani K; Dekat, Sarah E; Cusack, Bernadette; Johnson, Joseph L

2008-12-09

Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acylated enzyme intermediate is produced. Carbamates are very poor substrates that, like other AChE substrates, form an initial enzyme-substrate complex with free AChE (E) and proceed to an acylated enzyme intermediate (EC), which is then hydrolyzed. However, the hydrolysis of EC is slow enough to resolve the acylation and deacylation steps on the catalytic pathway. Here, we focus on the reaction of carbachol (carbamoylcholine) with AChE. The kinetics and thermodynamics of this reaction are of special interest because carbachol is an isosteric analogue of the physiological substrate acetylcholine. We show that the reaction can be monitored with thioflavin T as a fluorescent reporter group. The fluorescence of thioflavin T is strongly enhanced when it binds to the P-site of AChE, and this fluorescence is partially quenched when a second ligand binds to the A-site to form a ternary complex. Analysis of the fluorescence reaction profiles was challenging because four thermodynamic parameters and two fluorescence coefficients were fitted from the combined data both for E and for EC. Respective equilibrium dissociation constants of 6 and 26 mM were obtained for carbachol binding to the A- and P-sites in E and of 2 and 32 mM for carbachol binding to the A- and P-sites in EC. These constants for the binding of carbachol to the P-site are about an order of magnitude larger (i.e., indicating lower affinity) than previous estimates for the binding of acetylthiocholine to the P-site.

Analysis of the reaction of carbachol with acetylcholinesterase with thioflavin T as a coupled fluorescence reporter†

PubMed Central

Rosenberry, Terrone L.; Sonoda, Leilani K.; Dekat, Sarah E.; Cusack, Bernadette; Johnson, Joseph L.

2009-01-01

Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acylated enzyme intermediate is produced. Carbamates are very poor substrates that, like other AChE substrates, form an initial enzyme-substrate complex with free AChE (E) and proceed to an acylated enzyme intermediate (EC) which is then hydrolyzed. However, the hydrolysis of EC is slow enough to resolve the acylation and deacylation steps on the catalytic pathway. Here we focus on the reaction of carbachol (carbamoylcholine) with AChE. The kinetics and thermodynamics of this reaction are of special interest because carbachol is an isosteric analog of the physiological substrate acetylcholine. We show that the reaction can be monitored with thioflavin T as a fluorescent reporter group. The fluorescence of thioflavin T is strongly enhanced when it binds to the P-site of AChE, and this fluorescence is partially quenched when a second ligand binds to the A-site to form a ternary complex. Analysis of the fluorescence reaction profiles was challenging, because four thermodynamic parameters and two fluorescence coefficients were fitted from the combined data both for E and for EC. Respective equilibrium dissociation constants of 6 and 26 mM were obtained for carbachol binding to the A- and P-sites in E and of 2 and 32 mM for carbachol binding to the A- and P-sites in EC. These constants for the binding of carbachol to the P-site are about an order of magnitude larger (i.e., indicating lower affinity) than previous estimates for the binding of acetylthiocholine to the P-site. PMID:19006330

Evidence for an intermediate in tau filament formation.

PubMed

Chirita, Carmen N; Kuret, Jeff

2004-02-17

Alzheimer's disease is defined in part by the intraneuronal accumulation of filaments comprised of the microtubule-associated protein tau. In vitro, fibrillization of full-length, unphosphorylated recombinant tau can be induced under near-physiological conditions by treatment with various agents, including anionic surfactants. Here we examine the pathway through which anionic surfactants promote tau fibrillization using a combination of electron microscopy and fluorescence spectroscopy. Protein and surfactant first interacted in solution to form micelles, which then provided negatively charged surfaces that accumulated tau aggregates. Surface aggregation of tau protein was followed by the time-dependent appearance of a thioflavin S reactive intermediate that accumulated over a period of hours. The intermediate was unstable in the absence of anionic surfaces, suggesting it was not filamentous. Fibrillization proceeded after intermediate formation with classic nucleation-dependent kinetics, consisting of lag phase followed by the exponential increase in filament lengths, followed by an equilibrium phase reached in approximately 24 h. The pathway did not require protein insertion into the micelle hydrophobic core or conformational change arising from mixed micelle formation, because anionic microspheres constructed from impermeable polystyrene were capable of qualitatively reproducing all aspects of the fibrillization reaction. It is proposed that the progression from amorphous aggregation through intermediate formation and fibrillization may underlie the activity of other inducers such as hyperphosphorylation and may be operative in vivo.

The Theory of Thermodynamics for Chemical Reactions in Dispersed Heterogeneous Systems

PubMed

Yongqiang; Baojiao; Jianfeng

1997-07-01

In this paper, the expressions of Gibbs energy change, enthalpy change, entropy change, and equilibrium constant for chemical reactions in dispersed heterogeneous systems are derived using classical thermodynamics theory. The thermodynamical relations for the same reaction system between the dispersed and the block state are also derived. The effects of degree of dispersion on thermodynamical properties, reaction directions, and chemical equilibria are discussed. The results show that the present equation of thermodynamics for chemical reactions is only a special case of the above-mentioned formulas and that the effect of the dispersity of a heterogeneous system on the chemical reaction obeys the Le Chatelier principle of movement of equilibria.

Controlling reactivity of nanoporous catalyst materials by tuning reaction product-pore interior interactions: Statistical mechanical modeling

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

Wang, Jing; Ackerman, David M.; Lin, Victor S.-Y.

2013-04-02

Statistical mechanical modeling is performed of a catalytic conversion reaction within a functionalized nanoporous material to assess the effect of varying the reaction product-pore interior interaction from attractive to repulsive. A strong enhancement in reactivity is observed not just due to the shift in reaction equilibrium towards completion but also due to enhanced transport within the pore resulting from reduced loading. The latter effect is strongest for highly restricted transport (single-file diffusion), and applies even for irreversible reactions. The analysis is performed utilizing a generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reactionmore » and restricted transport.« less

Interfacing Biocompatible Reactions with Engineered Escherichia coli.

PubMed

Wallace, Stephen; Balskus, Emily P

2017-01-01

Biocompatible chemistry represents a new way of merging chemical and biological synthesis by interfacing nonenzymatic reactions with metabolic pathways. This approach can enable the production of nonnatural molecules directly from renewable starting materials via microbial fermentation. When developing a new biocompatible reaction certain criteria must be satisfied, i.e., the reaction must be (1) functional in aqueous growth media at ambient temperature and pH, (2) nontoxic to the producing microorganism, and (3) have negligible effects on the targeted metabolic pathway. This chapter provides a detailed outline of two biocompatible reaction procedures (hydrogenation and cyclopropanation), and describes some of the chemical and microbiological experiments and considerations required during biocompatible reaction development.

Detonation Reaction Zones in Condensed Explosives

NASA Astrophysics Data System (ADS)

Tarver, Craig M.

2006-07-01

Experimental measurements using nanosecond time resolved embedded gauges and laser interferometric techniques, combined with Non-Equilibrium Zeldovich - von Neumann - Doling (NEZND) theory and Ignition and Growth reactive flow hydrodynamic modeling, have revealed the average pressure/particle velocity states attained in reaction zones of self-sustaining detonation waves in several solid and liquid explosives. The time durations of these reaction zone processes are discussed for explosives based on pentaerythritol tetranitrate (PETN), nitromethane, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), triaminitrinitrobenzene(TATB) and trinitrotoluene (TNT).

Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations

PubMed Central

Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M.

2011-01-01

We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, Transition Path Theory (TPT) for constructing folding pathways and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270K and 566K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the Weighted-Histogram-Analysis Method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (Pfold) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding “tubes”, a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways. PMID:21254767

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

PubMed

Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M

2011-02-17

We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, transition path theory (TPT) for constructing folding pathways, and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270 and 566 K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the weighted-histogram-analysis method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (P(fold)) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding "tubes", a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network, and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways.

Efficient reactive Brownian dynamics

DOE PAGES

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

2018-01-21

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

Efficient reactive Brownian dynamics

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Efficient reactive Brownian dynamics

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

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

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

Stochastic Kinetics on Networks: When Slow Is Fast

PubMed Central

2015-01-01

Most chemical and biological processes can be viewed as reaction networks in which different pathways often compete kinetically for transformation of substrates into products. An enzymatic process is an example of such phenomena when biological catalysts create new routes for chemical reactions to proceed. It is typically assumed that the general process of product formation is governed by the pathway with the fastest kinetics at all time scales. In contrast to the expectation, here we show theoretically that at time scales sufficiently short, reactions are predominantly determined by the shortest pathway (in the number of intermediate states), regardless of the average turnover time associated with each pathway. This universal phenomenon is demonstrated by an explicit calculation for a system with two competing reversible (or irreversible) pathways. The time scales that characterize this regime and its relevance for single-molecule experimental studies are also discussed. PMID:25140607

A General Method for Automatic Computation of Equilibrium Compositions and Theoretical Rocket Performance of Propellants

NASA Technical Reports Server (NTRS)

Gordon, Sanford; Zeleznik, Frank J.; Huff, Vearl N.

1959-01-01

A general computer program for chemical equilibrium and rocket performance calculations was written for the IBM 650 computer with 2000 words of drum storage, 60 words of high-speed core storage, indexing registers, and floating point attachments. The program is capable of carrying out combustion and isentropic expansion calculations on a chemical system that may include as many as 10 different chemical elements, 30 reaction products, and 25 pressure ratios. In addition to the equilibrium composition, temperature, and pressure, the program calculates specific impulse, specific impulse in vacuum, characteristic velocity, thrust coefficient, area ratio, molecular weight, Mach number, specific heat, isentropic exponent, enthalpy, entropy, and several thermodynamic first derivatives.

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.

The Reaction of Hydrogen Sulfide with Disulfides: Formation of a Stable Trisulfide and Implications to Biological Systems.

PubMed

Bianco, Christopher L; Akaike, Takaaki; Ida, Tomoaki; Nagy, Peter; Bogdandi, Virag; Toscano, John P; Kumagai, Yoshito; Henderson, Catherine F; Goddu, Robert N; Lin, Joseph; Fukuto, Jon M

2018-05-29

The signaling associated with hydrogen sulfide (H 2 S) remains to be established and recent studies have alluded to the possibility that H 2 S-derived species play important roles. Of particular interest are hydropersulfides (RSSH) and related polysulfides (RSS n R, n>1). This work elucidates the fundamental chemical relationship between these sulfur species as well as examine their biological effects. Using standard analytical techniques ( 1 H-NMR and mass spectrometry), the equilibrium reactions between H 2 S, disulfides (RSSR), RSSH, dialkyltrisulfides (RSSSR) and thiols (RSH) were examined. Their ability to protect cells from electrophilic and/or oxidative stress was also examined using cell culture. H 2 S, RSSR, RSSH, RSSSR and RSH are all in a dynamic equilibrium. In a biological system, these species can exist simultaneously and thus it is difficult to discern which species is (are) the biological effector (s). Treatment of cells with the dialkyl trisulfide cysteine trisulfide (Cys-SSS-Cys) results in high intracellular levels of hydropersulfides and protection from electrophilic stress. In aqueous systems, the reaction between H 2 S and RSSR results in the formation of equilbria whereby H 2 S, RSH, RSSR, RSSH and RSSSR are present. In a biological system, any of these species can be responsible for the observed biological activity. These equilibrium species can also be generated via the reaction of RSH with RSSSR. Due to these equilibria, Cys-SSS-Cys can be a method for generating any of the other species. Importantly, HEK293T cells treated with Cys-SSS-Cys results in increased levels of hydropersulfides, allowing examination of the biological effects of RSSH. This article is protected by copyright. All rights reserved.

Biochemical thermodynamics: applications of Mathematica.

PubMed

Alberty, Robert A

2006-01-01

The most efficient way to store thermodynamic data on enzyme-catalyzed reactions is to use matrices of species properties. Since equilibrium in enzyme-catalyzed reactions is reached at specified pH values, the thermodynamics of the reactions is discussed in terms of transformed thermodynamic properties. These transformed thermodynamic properties are complicated functions of temperature, pH, and ionic strength that can be calculated from the matrices of species values. The most important of these transformed thermodynamic properties is the standard transformed Gibbs energy of formation of a reactant (sum of species). It is the most important because when this function of temperature, pH, and ionic strength is known, all the other standard transformed properties can be calculated by taking partial derivatives. The species database in this package contains data matrices for 199 reactants. For 94 of these reactants, standard enthalpies of formation of species are known, and so standard transformed Gibbs energies, standard transformed enthalpies, standard transformed entropies, and average numbers of hydrogen atoms can be calculated as functions of temperature, pH, and ionic strength. For reactions between these 94 reactants, the changes in these properties can be calculated over a range of temperatures, pHs, and ionic strengths, and so can apparent equilibrium constants. For the other 105 reactants, only standard transformed Gibbs energies of formation and average numbers of hydrogen atoms at 298.15 K can be calculated. The loading of this package provides functions of pH and ionic strength at 298.15 K for standard transformed Gibbs energies of formation and average numbers of hydrogen atoms for 199 reactants. It also provides functions of temperature, pH, and ionic strength for the standard transformed Gibbs energies of formation, standard transformed enthalpies of formation, standard transformed entropies of formation, and average numbers of hydrogen atoms for 94 reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

Exploring the Reaction Pathways of Bioglycerol Hydrodeoxygenation to Propene over Molybdena-Based Catalysts.

PubMed

Zacharopoulou, Vasiliki; Vasiliadou, Efterpi S; Lemonidou, Angeliki A

2018-01-10

The one-step reaction of glycerol with hydrogen to form propene selectively is a particularly challenging catalytic pathway that has not yet been explored thoroughly. Molybdena-based catalysts are active and selective to C-O bond scission; propene is the only product in the gas phase under the standard reaction conditions, and further hydrogenation to propane is impeded. Within this context, this work focuses on the exploration of the reaction pathways and the investigation of various parameters that affect the catalytic performance, such as the role of hydrogen on the product distribution and the effect of the catalyst pretreatment step. Under a hydrogen atmosphere, propene is produced primarily via 2-propenol, whereas under an inert atmosphere propanal and glycerol dissociation products are formed mainly. The reaction most likely proceeds through a reverse Mars-van Krevelen mechanism as partially reduced Mo species drive the reaction to the formation of the desired product. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transcriptional Changes That Characterize the Immune Reactions of Leprosy

PubMed Central

Dupnik, Kathryn M.; Bair, Thomas B.; Maia, Andressa O.; Amorim, Francianne M.; Costa, Marcos R.; Keesen, Tatjana S. L.; Valverde, Joanna G.; Queiroz, Maria do Carmo A. P.; Medeiros, Lúcio L.; de Lucena, Nelly L.; Wilson, Mary E.; Nobre, Mauricio L.; Johnson, Warren D.; Jeronimo, Selma M. B.

2015-01-01

Background. Leprosy morbidity is increased by 2 pathologic immune reactions, reversal reaction (RR) and erythema nodosum leprosum (ENL). Methods. To discover host factors related to immune reactions, global transcriptional profiles of peripheral blood mononuclear cells were compared between 11 RR, 11 ENL, and 19 matched control patients, with confirmation by quantitative polymerase chain reaction. Encoded proteins were investigated in skin biopsy specimens by means of immunohistochemistry. Results. There were 275 genes differentially expressed in RR and 517 differentially expressed in ENL on the microarray. Pathway analysis showed immunity-related pathways represented in RR and ENL transcriptional profiles, with the “complement and coagulation” pathway common to both. Interferon γ was identified as a significant upstream regulator of the expression changes for RR and ENL. Immunohistochemical staining of skin lesions showed increased C1q in both RR and ENL. Conclusions. These data suggest a previously underrecognized role for complement in the pathogenesis of both RR and ENL, and we propose new hypotheses for reaction pathogenesis. PMID:25398459

Reaction pathways for the deoxygenation of vegetable oils and related model compounds.

PubMed

Gosselink, Robert W; Hollak, Stefan A W; Chang, Shu-Wei; van Haveren, Jacco; de Jong, Krijn P; Bitter, Johannes H; van Es, Daan S

2013-09-01

Vegetable oil-based feeds are regarded as an alternative source for the production of fuels and chemicals. Paraffins and olefins can be produced from these feeds through catalytic deoxygenation. The fundamentals of this process are mostly studied by using model compounds such as fatty acids, fatty acid esters, and specific triglycerides because of their structural similarity to vegetable oils. In this Review we discuss the impact of feedstock, reaction conditions, and nature of the catalyst on the reaction pathways of the deoxygenation of vegetable oils and its derivatives. As such, we conclude on the suitability of model compounds for this reaction. It is shown that the type of catalyst has a significant effect on the deoxygenation pathway, that is, group 10 metal catalysts are active in decarbonylation/decarboxylation whereas metal sulfide catalysts are more selective to hydrodeoxygenation. Deoxygenation studies performed under H2 showed similar pathways for fatty acids, fatty acid esters, triglycerides, and vegetable oils, as mostly deoxygenation occurs indirectly via the formation of fatty acids. Deoxygenation in the absence of H2 results in significant differences in reaction pathways and selectivities depending on the feedstock. Additionally, using unsaturated feedstocks under inert gas results in a high selectivity to undesired reactions such as cracking and the formation of heavies. Therefore, addition of H2 is proposed to be essential for the catalytic deoxygenation of vegetable oil feeds. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fundamental Reaction Pathway for Peptide Metabolism by Proteasome: Insights from First-principles Quantum Mechanical/Molecular Mechanical Free Energy Calculations

PubMed Central

Wei, Donghui; Fang, Lei; Tang, Mingsheng; Zhan, Chang-Guo

2013-01-01

Proteasome is the major component of the crucial nonlysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-Oγ. The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-Oγ, followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-Nz. Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-Nz to Thr1-Oγ. According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3b) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally-derived activation free energy of ~18.3–19.4 kcal/mol, suggesting that the computational results are reasonable. PMID:24111489

Kinetic modeling of non-ideal explosives with CHEETAH

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

Fried, L E; Howard, W M; Souers, P C

1998-08-06

We report an implementation of the Wood-Kirkwood kinetic detonation model based on multi-species equations of state and multiple reaction rate laws. Finite rate laws are used for the slowest chemical reactions. Other reactions are given infinite rates and are kept in constant thermodynamic equilibrium. We model a wide range of ideal and non-ideal composite energetic materials. We find that we can replicate experimental detonation velocities to within a few per cent, while obtaining good agreement with estimated reaction zone lengths. The detonation velocity as a function of charge radius is also correctly reproduced.

Exploring the reaction channels between arsine and the hydroxyl radical

NASA Astrophysics Data System (ADS)

Viana, Rommel B.

2017-10-01

The aim of this study was to present the reaction mechanism channels between arsine (AsH3) and hydroxyl (OH) which was evaluated at CCSD(T)/CBS//CCSD/cc-pVTZ level. One potential channel is the hydrogen abstraction pathway (R1), leading to AsH2 and H2O products, which occurs due to the formation of an entrance complex (AsH3OH) followed by a 1,2-hydrogen shift pathway (involving the proton transfer from the arsine group to hydroxyls, with one leading to the products). Additional channels are accessed via H-elimination pathways of the entrance complexes, forming arsinous acid (AsH2OH; R2) and arsine oxide (AsH3O; R3). In this respect, R2 is the only exoergic route of the three exit channels, representing the major branching ratio at 200-1000 K and, after 2000 K, R1 increases gradually becoming the major route of this reaction. In contrast, even at 4000 K, R3 is a highly unfeasible pathway. Therefore, the information predicted here provides new insights into the neutral-neutral chemical reaction dynamics regarding the Group V hydrides. On the other side, the R2 pathway may have some potential to solve the arsine oxidation puzzle as a possible primary pathway to the arsenic-oxygen species formation.

Evolution of atomic structure during nanoparticle formation

DOE PAGES

Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; ...

2014-04-14

Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structuremore » is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries.« less

Thermodynamic and transport combustion properties of hydrocarbons with air. Part 2: Compositions corresponding to Kelvin temperature schedules in part 1

NASA Technical Reports Server (NTRS)

Gordon, S.

1982-01-01

The equilibrium compositions that correspond to the thermodynamic and transport combustion properties for a wide range of conditions for the reaction of hydrocarbons with air are presented. Initially 55 gaseous species and 3 coin condensed species were considered in the calculations. Only 17 of these 55 gaseous species had equilibrium mole fractions greater than 0.000005 for any of the conditions studied and therefore these were the only ones retained in the final tables.

Liquid chromatographic determination of water

DOEpatents

Fortier, N.E.; Fritz, J.S.

1990-11-13

A sensitive method for the determination of water in the presence of common interferences is presented. The detection system is based on the effect of water on the equilibrium which results from the reaction aryl aldehydes, such as cinnamaldehyde and methanol in the eluent to form cinnamaldehyde dimethylacetal, plus water. This equilibrium is shifted in a catalytic atmosphere of a hydrogen ion form past column reactor. The extent of the shift and the resulting change in absorbance are proportional to the amount of water present. 1 fig.

Liquid chromatographic determination of water

DOEpatents

Fortier, Nancy E.; Fritz, James S.

1990-11-13

A sensitive method for the determination of water in the presence of common interferences is presented. The detection system is based on the effect of water on the equilibrium which results from the reaction aryl aldehydes, such as cinnamaldehyde and methanol in the eluent to form cinnamaldehyde dimethylacetal, plus water. This equilibrium is shifted in a catalytic atmosphere of a hydrogen ion form past column reactor. The extent of the shift and the resulting change in absorbance are proportional to the amount of water present.

Sulfur Radical-Induced Redox Modifications in Proteins: Analysis and Mechanistic Aspects.

PubMed

Schöneich, Christian

2017-03-10

The sulfur-containing amino acids cysteine (Cys) and methionine (Met) are prominent protein targets of redox modification during conditions of oxidative stress. Here, two-electron pathways have received widespread attention, in part due to their role in signaling processes. However, Cys and Met are equally prone to one-electron pathways, generating intermediary radicals and/or radial ions. These radicals/radical ions can generate various reaction products that are not commonly monitored in redox proteomic studies, but they may be relevant for the fate of proteins during oxidative stress. Recent Advances: Time-resolved kinetic studies and product analysis have expanded our mechanistic understanding of radical reaction pathways of sulfur-containing amino acids. These reactions are now studied in some detail for Met and Cys in proteins, and homocysteine (Hcy) chemically linked to proteins, and the role of protein radical reactions in physiological processes is evolving. Radical-derived products from Cys, Hcy, and Met can react with additional amino acids in proteins, leading to secondary protein modifications, which are potentially remote from initial points of radical attack. These products may contain intra- and intermolecular cross-links, which may lead to protein aggregation. Protein sequence and conformation will have a significant impact on the formation of such products, and a thorough understanding of reaction mechanisms and specifically how protein structure influences reaction pathways will be critical for identification and characterization of novel reaction products. Future studies must evaluate the biological significance of novel reaction products that are derived from radical reactions of sulfur-containing amino acids. Antioxid. Redox Signal. 26, 388-405.

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

NASA Astrophysics Data System (ADS)

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

2014-10-01

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

Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms.

PubMed

Stirling, András; Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele

2004-10-18

We studied the thermal intramolecular and radical rearrangement of azulene to naphthalene by employing a novel metadynamics method based on Car-Parrinello molecular dynamics. We demonstrate that relatively short simulations can provide us with several possible reaction mechanisms for the rearrangement. We show that different choices of the collective coordinates can steer the reaction along different pathways, thus offering the possibility of choosing the most probable mechanism. We consider herein three intramolecular mechanisms and two radical pathways. We found the norcaradiene pathway to be the preferable intramolecular mechanism, whereas the spiran mechanism is the favored radical route. We obtained high activation energies for all the intramolecular pathways (81.5-98.6 kcal mol(-1)), whereas the radical routes have activation energies of 24-39 kcal mol(-1). The calculations have also resulted in elementary steps and intermediates not yet considered. A few attractive features of the metadynamics method in studying chemical reactions are pointed out.

RhoA/ROCK Signaling Pathway Mediates Shuanghuanglian Injection-Induced Pseudo-allergic Reactions.

PubMed

Han, Jiayin; Zhao, Yong; Zhang, Yushi; Li, Chunying; Yi, Yan; Pan, Chen; Tian, Jingzhuo; Yang, Yifei; Cui, Hongyu; Wang, Lianmei; Liu, Suyan; Liu, Jing; Deng, Nuo; Liang, Aihua

2018-01-01

Background: Shuanghuanglian injection (SHLI) is a famous Chinese medicine used as an intravenous preparation for the treatment of acute respiratory tract infections. In the recent years, the immediate hypersensitivity reactions induced by SHLI have attracted broad attention. However, the mechanism involved in these reactions has not yet been elucidated. The present study aims to explore the characteristics of the immediate hypersensitivity reactions induced by SHLI and deciphers the role of the RhoA/ROCK signaling pathway in these reactions. Methods: SHLI-immunized mice or naive mice were intravenously injected (i.v.) with SHLI (600 mg/kg) once, and vascular leakage in the ears was evaluated. Passive cutaneous anaphylaxis test was conducted using sera collected from SHLI-immunized mice. Naive mice were administered (i.v.) with a single dose of 150, 300, or 600 mg/kg of SHLI, and vascular leakage, histamine release, and histopathological alterations in the ears, lungs, and intestines were tested. In vitro , human umbilical vein endothelial cell (HUVEC) monolayer was incubated with SHLI (0.05, 0.1, or 0.15 mg/mL), and the changes in endothelial permeability and cytoskeleton were observed. Western blot analysis was performed and ROCK inhibitor was employed to investigate the contribution of the RhoA/ROCK signaling pathway in SHLI-induced hypersensitivity reactions, both in HUVECs and in mice. Results: Our results indicate that SHLI was able to cause immediate dose-dependent vascular leakage, edema, and exudates in the ears, lungs, and intestines, and histamine release in mice. These were pseudo-allergic reactions, as SHLI-specific IgE was not elicited during sensitization. In addition, SHLI induced reorganization of actin cytoskeleton and disrupted the endothelial barrier. The administration of SHLI directly activated the RhoA/ROCK signaling pathway both in HUVECs and in the ears, lungs, and intestines of mice. Fasudil hydrochloride, a ROCK inhibitor, ameliorated the SHLI-induced hypersensitivity reactions in both endothelial cells and mice indicating its protective effect. SHLI-induced pseudo-allergic reactions were mediated by the activation of the RhoA/ROCK signaling pathway. Conclusion : This study presents a novel mechanism of SHLI-induced immediate hypersensitivity reactions and suggests a potential therapeutic strategy to prevent the associated adverse reactions.

Thermal plasticity of growth and development varies adaptively among alternative developmental pathways.

PubMed

Kivelä, Sami M; Svensson, Beatrice; Tiwe, Alma; Gotthard, Karl

2015-09-01

Polyphenism, the expression of discrete alternative phenotypes, is often a consequence of a developmental switch. Physiological changes induced by a developmental switch potentially affect reaction norms, but the evolution and existence of alternative reaction norms remains poorly understood. Here, we demonstrate that, in the butterfly Pieris napi (Lepidoptera: Pieridae), thermal reaction norms of several life history traits vary adaptively among switch-induced alternative developmental pathways of diapause and direct development. The switch was affected both by photoperiod and temperature, ambient temperature during late development having the potential to override earlier photoperiodic cues. Directly developing larvae had higher development and growth rates than diapausing ones across the studied thermal gradient. Reaction norm shapes also differed between the alternative developmental pathways, indicating pathway-specific selection on thermal sensitivity. Relative mass increments decreased linearly with increasing temperature and were higher under direct development than diapause. Contrary to predictions, population phenology did not explain trait variation or thermal sensitivity, but our experimental design probably lacks power for finding subtle phenology effects. We demonstrate adaptive differentiation in thermal reaction norms among alternative phenotypes, and suggest that the consequences of an environmentally dependent developmental switch primarily drive the evolution of alternative thermal reaction norms in P. napi. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Toward rational design of amines for CO2 capture: Substituent effect on kinetic process for the reaction of monoethanolamine with CO2.

PubMed

Xie, Hongbin; Wang, Pan; He, Ning; Yang, Xianhai; Chen, Jingwen

2015-11-01

Amines have been considered as promising candidates for post-combustion CO2 capture. A mechanistic understanding for the chemical processes involved in the capture and release of CO2 is important for the rational design of amines. In this study, the structural effects of amines on the kinetic competition among three typical products (carbamates, carbamic acids and bicarbonate) from amines+CO2 were investigated, in contrast to previous thermodynamic studies to tune the reaction of amines with CO2 based on desirable reaction enthalpy and reaction stoichiometry. We used a quantum chemical method to calculate the activation energies (Ea) for the reactions of a range of substituted monoethanolamines with CO2 covering three pathways to the three products. The results indicate that the formation of carbamates is the most favorable, among the three considered products. In addition, we found that the Ea values for all pathways linearly correlate with pKa of amines, and more importantly, the kinetic competition between carbamate and bicarbonate absorption pathways varies with pKa of the amines, i.e. stronger basicity results in less difference in Ea. These results highlight the importance of the consideration of kinetic competition among different reaction pathways in amine design. Copyright © 2015. Published by Elsevier B.V.

Computer program to solve two-dimensional shock-wave interference problems with an equilibrium chemically reacting air model

NASA Technical Reports Server (NTRS)

Glass, Christopher E.

1990-01-01

The computer program EASI, an acronym for Equilibrium Air Shock Interference, was developed to calculate the inviscid flowfield, the maximum surface pressure, and the maximum heat flux produced by six shock wave interference patterns on a 2-D, cylindrical configuration. Thermodynamic properties of the inviscid flowfield are determined using either an 11-specie, 7-reaction equilibrium chemically reacting air model or a calorically perfect air model. The inviscid flowfield is solved using the integral form of the conservation equations. Surface heating calculations at the impingement point for the equilibrium chemically reacting air model use variable transport properties and specific heat. However, for the calorically perfect air model, heating rate calculations use a constant Prandtl number. Sample calculations of the six shock wave interference patterns, a listing of the computer program, and flowcharts of the programming logic are included.

Computer program to solve two-dimensional shock-wave interference problems with an equilibrium chemically reacting air model

NASA Astrophysics Data System (ADS)

Glass, Christopher E.

1990-08-01

The computer program EASI, an acronym for Equilibrium Air Shock Interference, was developed to calculate the inviscid flowfield, the maximum surface pressure, and the maximum heat flux produced by six shock wave interference patterns on a 2-D, cylindrical configuration. Thermodynamic properties of the inviscid flowfield are determined using either an 11-specie, 7-reaction equilibrium chemically reacting air model or a calorically perfect air model. The inviscid flowfield is solved using the integral form of the conservation equations. Surface heating calculations at the impingement point for the equilibrium chemically reacting air model use variable transport properties and specific heat. However, for the calorically perfect air model, heating rate calculations use a constant Prandtl number. Sample calculations of the six shock wave interference patterns, a listing of the computer program, and flowcharts of the programming logic are included.

Adaptive Chemical Networks under Non-Equilibrium Conditions: The Evaporating Droplet.

PubMed

Armao, Joseph J; Lehn, Jean-Marie

2016-10-17

Non-volatile solutes in an evaporating drop experience an out-of-equilibrium state due to non-linear concentration effects and complex flow patterns. Here, we demonstrate a small molecule chemical reaction network that undergoes a rapid adaptation response to the out-of-equilibrium conditions inside the droplet leading to control over the molecular constitution and spatial arrangement of the deposition pattern. Adaptation results in a pronounced coffee stain effect and coupling to chemical concentration gradients within the drop is demonstrated. Amplification and suppression of network species are readily identifiable with confocal fluorescence microscopy. We anticipate that these observations will contribute to the design and exploration of out-of-equilibrium chemical systems, as well as be useful towards the development of point-of-care medical diagnostics and controlled deposition of small molecules through inkjet printing. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectral Quasi-Equilibrium Manifold for Chemical Kinetics.

PubMed

Kooshkbaghi, Mahdi; Frouzakis, Christos E; Boulouchos, Konstantinos; Karlin, Iliya V

2016-05-26

The Spectral Quasi-Equilibrium Manifold (SQEM) method is a model reduction technique for chemical kinetics based on entropy maximization under constraints built by the slowest eigenvectors at equilibrium. The method is revisited here and discussed and validated through the Michaelis-Menten kinetic scheme, and the quality of the reduction is related to the temporal evolution and the gap between eigenvalues. SQEM is then applied to detailed reaction mechanisms for the homogeneous combustion of hydrogen, syngas, and methane mixtures with air in adiabatic constant pressure reactors. The system states computed using SQEM are compared with those obtained by direct integration of the detailed mechanism, and good agreement between the reduced and the detailed descriptions is demonstrated. The SQEM reduced model of hydrogen/air combustion is also compared with another similar technique, the Rate-Controlled Constrained-Equilibrium (RCCE). For the same number of representative variables, SQEM is found to provide a more accurate description.

Grain formation in astronomical systems: A critical review of condensation processes

NASA Technical Reports Server (NTRS)

Donn, B.

1978-01-01

An analysis is presented of the assumption and the applicability of the three theoretical methods for calculating condensations in cosmic clouds where no pre-existing nuclei exist. The three procedures are: thermodynamic equilibrium calculations, nucleation theory, and a kinetic treatment which would take into account the characteristics of each individual collision. Thermodynamics provide detailed results on the composition temperature and composition of the condensate provided the system attains equilibrium. Because of the cosmic abundance mixture of elements, large supersaturations in some cases and low pressures, equilibrium is not expected in astronomical clouds. Nucleation theory, a combination of thermodynamics and kinetics, has the limitations of each scheme. Kinetics, not requiring equilibrium, avoids nearly all the thermodynamics difficulties but requires detailed knowledge of many reactions which thermodynamics avoids. It appears to be the only valid way to treat grain formation in space. A review of experimental studies is given.

Dynamics Sampling in Transition Pathway Space.

PubMed

Zhou, Hongyu; Tao, Peng

2018-01-09

The minimum energy pathway contains important information describing the transition between two states on a potential energy surface (PES). Chain-of-states methods were developed to efficiently calculate minimum energy pathways connecting two stable states. In the chain-of-states framework, a series of structures are generated and optimized to represent the minimum energy pathway connecting two states. However, multiple pathways may exist connecting two existing states and should be identified to obtain a full view of the transitions. Therefore, we developed an enhanced sampling method, named as the direct pathway dynamics sampling (DPDS) method, to facilitate exploration of a PES for multiple pathways connecting two stable states as well as addition minima and their associated transition pathways. In the DPDS method, molecular dynamics simulations are carried out on the targeting PES within a chain-of-states framework to directly sample the transition pathway space. The simulations of DPDS could be regulated by two parameters controlling distance among states along the pathway and smoothness of the pathway. One advantage of the chain-of-states framework is that no specific reaction coordinates are necessary to generate the reaction pathway, because such information is implicitly represented by the structures along the pathway. The chain-of-states setup in a DPDS method greatly enhances the sufficient sampling in high-energy space between two end states, such as transition states. By removing the constraint on the end states of the pathway, DPDS will also sample pathways connecting minima on a PES in addition to the end points of the starting pathway. This feature makes DPDS an ideal method to directly explore transition pathway space. Three examples demonstrate the efficiency of DPDS methods in sampling the high-energy area important for reactions on the PES.

RAPID COMMUNICATION: Formation of MgB2 at ambient temperature with an electrochemical process: a plausible mechanism

NASA Astrophysics Data System (ADS)

Jadhav, A. B.; Subhedar, K. M.; Hyam, R. S.; Talaptra, A.; Sen, Pintu; Bandyopadhyay, S. K.; Pawar, S. H.

2005-06-01

The binary intermetallic MgB2 superconductor has been synthesized by many research groups. However, the mechanism of its formation is not clearly understood. In this communication, a comprehensive mechanism of the formation of MgB2 from Le Chatelier's principle of equilibrium reaction has been explained both for solid-state reaction and electrodeposition methods.

Production of bismuth-204 for medical use

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

Kinsley, M.T.; Lebowitz, E.; Baranosky, J.

1973-11-01

A method is described for producing practical quantities of highpuriti, / sup 204/Bi by, the /sup 206/Pb(p,3n)/sup 204/Bi reaction. A simple elec trolytic separation method with good yield has been developed. The cross section for the above reaction was calculated for 32,MeV protons. Decay data for /supb 204/Bi-/ sup 204m/Pb equilibrium samples are also reported. (auth)

Separation of the isotopes of boron by chemical exchange reactions

DOEpatents

McCandless, Frank P.; Herbst, Ronald S.

1995-01-01

The isotopes of boron, .sup.10 B and .sup.11 B, are separated by means of a gas-liquid chemical exchange reaction involving the isotopic equilibrium between gaseous BF.sub.3 and a liquid BF.sub.3 . donor molecular addition complex formed between BF.sub.3 gas and a donor chosen from the group consisting of: nitromethane, acetone, methyl isobutyl ketone, or diisobutyl ketone.

Dissociation cross section for high energy O2-O2 collisions

NASA Astrophysics Data System (ADS)

Mankodi, T. K.; Bhandarkar, U. V.; Puranik, B. P.

2018-04-01

Collision-induced dissociation cross section database for high energy O2-O2 collisions (up to 30 eV) is generated and published using the quasiclassical trajectory method on the singlet, triplet, and quintet spin ground state O4 potential energy surfaces. At equilibrium conditions, these cross sections predict reaction rate coefficients that match those obtained experimentally. The main advantage of the cross section database based on ab initio computations is in the study of complex flows with high degree of non-equilibrium. Direct simulation Monte Carlo simulations using the reactive cross section databases are carried out for high enthalpy hypersonic oxygen flow over a cylinder at rarefied ambient conditions. A comparative study with the phenomenological total collision energy chemical model is also undertaken to point out the difference and advantage of the reported ab initio reaction model.

Validation of chemistry models employed in a particle simulation method

NASA Technical Reports Server (NTRS)

Haas, Brian L.; Mcdonald, Jeffrey D.

1991-01-01

The chemistry models employed in a statistical particle simulation method, as implemented in the Intel iPSC/860 multiprocessor computer, are validated and applied. Chemical relaxation of five-species air in these reservoirs involves 34 simultaneous dissociation, recombination, and atomic-exchange reactions. The reaction rates employed in the analytic solutions are obtained from Arrhenius experimental correlations as functions of temperature for adiabatic gas reservoirs in thermal equilibrium. Favorable agreement with the analytic solutions validates the simulation when applied to relaxation of O2 toward equilibrium in reservoirs dominated by dissociation and recombination, respectively, and when applied to relaxation of air in the temperature range 5000 to 30,000 K. A flow of O2 over a circular cylinder at high Mach number is simulated to demonstrate application of the method to multidimensional reactive flows.

Modeling Ignition of HMX with the Gibbs Formulation

NASA Astrophysics Data System (ADS)

Lee, Kibaek; Stewart, D. Scott

2017-06-01

We present a HMX model with the Gibbs formulation in which stress tensor and temperature are assumed to be in local equilibrium, but phase/chemical changes are not assumed to be in equilibrium. We assume multi-components for HMX including beta- and delta-phase, liquid, and gas phase of HMX and its gas products. Isotropic small strain solid model, modified Fried Howard liquid EOS, and ideal gas EOS are used for its relevant component. Phase/chemical changes are characterized as reactions and are in individual reaction rate. Maxwell-Stefan model is used for diffusion. Excited gas products in the local domain lead unreacted HMX solid to the ignition event. Density of the mixture, stress, strain, displacement, mass fractions, and temperature are considered in 1D domain with time histories. Office of Naval Research and Air Force Office of Scientific Research.

Products and kinetics of the liquid-phase reaction of glyoxal catalyzed by ammonium ions (NH4(+)).

PubMed

Nozière, Barbara; Dziedzic, Pawel; Córdova, Armando

2009-01-08

Glyoxal, a common atmospheric gas, has been reported to be depleted in some regions of the atmosphere. The corresponding sink could be accounted for by reactions in or at the surface of atmospheric particles, but these reactions were not identified. Recently, we showed that inorganic ammonium ions, NH(4)(+), are efficient catalysts for reactions of carbonyl compounds, including glyoxal, in the liquid phase. To determine whether ammonium-catalyzed reactions can contribute to depletion of glyoxal in the atmosphere, the reactivity of this compound in aqueous solutions containing ammonium salts (ammonium sulfate, chloride, fluoride, and phosphate) at 298 K has been studied. The products identified by LC-HRMS and UV absorption revealed a mechanism involving two distinct pathways: a Bronsted acid pathway and an iminium pathway. The kinetics of the iminium pathway was studied by monitoring formation of a specific product. This pathway was second order in glyoxal in most of the solutions studied and should therefore be second order in most ammonium-containing aerosols in the atmosphere. The corresponding rate constant, k(II) (M(-1) s(-1)), increased strongly with ammonium ion activity, a(NH(4)(+)), and pH: k(II) (M(-1) s(-1)) = (2 +/- 1) x 10(-10) exp((1.5 +/- 0.8)aNH(4)(+)) exp((2.5 +/- 0.2)pH). This iminium pathway is a lower limit for the ammonium-catalyzed consumption of glyoxal, but the contribution of the acid pathway is expected to be small in tropospheric aerosols. With these results the reactive uptake of glyoxal on ammonium-containing aerosols was estimated and shown to be a possible explanation for depletion of this compound in Mexico City.

Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network.

PubMed

Culyba, Matthew J; Kubiak, Jeffrey M; Mo, Charlie Y; Goulian, Mark; Kohli, Rahul M

2018-06-01

Biochemical pathways are often genetically encoded as simple transcription regulation networks, where one transcription factor regulates the expression of multiple genes in a pathway. The relative timing of each promoter's activation and shut-off within the network can impact physiology. In the DNA damage repair pathway (known as the SOS response) of Escherichia coli, approximately 40 genes are regulated by the LexA repressor. After a DNA damaging event, LexA degradation triggers SOS gene transcription, which is temporally separated into subsets of 'early', 'middle', and 'late' genes. Although this feature plays an important role in regulating the SOS response, both the range of this separation and its underlying mechanism are not experimentally defined. Here we show that, at low doses of DNA damage, the timing of promoter activities is not separated. Instead, timing differences only emerge at higher levels of DNA damage and increase as a function of DNA damage dose. To understand mechanism, we derived a series of synthetic SOS gene promoters which vary in LexA-operator binding kinetics, but are otherwise identical, and then studied their activity over a large dose-range of DNA damage. In distinction to established models based on rapid equilibrium assumptions, the data best fit a kinetic model of repressor occupancy at promoters, where the drop in cellular LexA levels associated with higher doses of DNA damage leads to non-equilibrium binding kinetics of LexA at operators. Operators with slow LexA binding kinetics achieve their minimal occupancy state at later times than operators with fast binding kinetics, resulting in a time separation of peak promoter activity between genes. These data provide insight into this remarkable feature of the SOS pathway by demonstrating how a single transcription factor can be employed to control the relative timing of each gene's transcription as a function of stimulus dose.

Effect of Temperature to Adsorption Capacity and Coefficient Distribution on Rare Earth Elements Adsorption (Y, Gd, Dy) Using SIR

NASA Astrophysics Data System (ADS)

Aziz, N.; Mindaryani, A.; Supranto; Taftazani, A.; Biyantoro, D.

2018-04-01

The use of REE like element of Yttrium (Y) as a superconducting material requires a purity of more than 90%, so it needs to increase the purity of Y from the settling process. The purpose of this research is to study the separation process of REE that is Y, Gd, Dy elements from REE hydroxide (REE(OH)3) using SIR method are consisting of Amberlite XAD-16 resin impregnated with Di-(2-ethylhexyl) phosphate ( D2EHPA) and Tributyl Phosphate (TBP) and determine the isotherm model on REE adsorption and determine the kinetic model of pseudo adsorption reaction. This research was started by activating XAD-16 resin and is mixed with TBP-D2EHPA solvents so it will form SIR, then it is conducted on variation of SIR composition, temperature variation of adsorption process, determination of equilibrium equation and kinetic sorption occurring in SIR adsorption based on experimental data of liquid concentration as function of time. Based on the calculation result, the most effective SIR composition for REE separation is 0.75 g, the equilibrium equation for Y, Gd and Dy follows the Henry equilibrium model and the pseudo kinetic model of the reaction order Y, Gd, and Dy is followed by the pseudo reaction of order 2 The result of separation of LTJ with SIR is said to be effective from another method because purity is obtained that is 96.73% and qualify as a super conductor material.

Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium.

PubMed

Soula, Hédi; Caré, Bertrand; Beslon, Guillaume; Berry, Hugues

2013-11-05

Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) that converges back to a Brownian motion with reduced diffusion coefficient at long times after the anomalous diffusion regime. Therefore, slowed-down Brownian motion could be considered the macroscopic limit of transient anomalous diffusion. On the other hand, membranes are also heterogeneous media in which Brownian motion may be locally slowed down due to variations in lipid composition. Here, we investigate whether both situations lead to a similar behavior for the reversible ligand-binding reaction in two dimensions. We compare the (long-time) equilibrium properties obtained with transient anomalous diffusion due to obstacle hindrance or power-law-distributed residence times (continuous-time random walks) to those obtained with space-dependent slowed-down Brownian motion. Using theoretical arguments and Monte Carlo simulations, we show that these three scenarios have distinctive effects on the apparent affinity of the reaction. Whereas continuous-time random walks decrease the apparent affinity of the reaction, locally slowed-down Brownian motion and local hindrance by obstacles both improve it. However, only in the case of slowed-down Brownian motion is the affinity maximal when the slowdown is restricted to a subregion of the available space. Hence, even at long times (equilibrium), these processes are different and exhibit irreconcilable behaviors when the area fraction of reduced mobility changes. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

One-Dimensional Transport with Equilibrium Chemistry (OTEQ) - A Reactive Transport Model for Streams and Rivers

USGS Publications Warehouse

Runkel, Robert L.

2010-01-01

OTEQ is a mathematical simulation model used to characterize the fate and transport of waterborne solutes in streams and rivers. The model is formed by coupling a solute transport model with a chemical equilibrium submodel. The solute transport model is based on OTIS, a model that considers the physical processes of advection, dispersion, lateral inflow, and transient storage. The equilibrium submodel is based on MINTEQ, a model that considers the speciation and complexation of aqueous species, acid-base reactions, precipitation/dissolution, and sorption. Within OTEQ, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (waterborne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach. The model's ability to simulate pH, precipitation/dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between instream chemistry and hydrologic transport at the field scale. This report details the development and application of OTEQ. Sections of the report describe model theory, input/output specifications, model applications, and installation instructions. OTEQ may be obtained over the Internet at http://water.usgs.gov/software/OTEQ.

Mechanism of single metal exchange in the reactions of [M4(SPh)10]2- (M = Zn or Fe) with CoX2 (X = Cl or NO3) or FeCl2.

PubMed

Autissier, Valerie; Henderson, Richard A

2008-07-21

The kinetics of the reactions between [Zn4(SPh)10](2-) and an excess of MX2 (M = Co, X = NO3 or Cl; M = Fe, X = Cl), in which a Zn(II) is replaced by M(II), have been studied in MeCN at 25.0 degrees C. (1)H NMR spectroscopy shows that the ultimate product of the reactions is an equilibrium mixture of clusters of composition [Zn(n)M(4-n)(SPh)10](2-), and this is reflected in the multiphasic absorbance-time curves observed over protracted times (several minutes) using stopped-flow spectrophotometry to study the reactions. The kinetics of only the first phase have been determined, corresponding to the equilibrium formation of [Zn3M(SPh)10](2-). The effects of varying the concentrations of cluster, MX2, and ZnCl2 on the kinetics have been investigated. The rate law is consistent with the equilibrium nature of the metal exchange process and indicates a mechanism for the formation of [Zn3M(SPh)10](2-) involving two coupled equilibria. In the initial step binding of MX2 to a bridging thiolate in [Zn4(SPh)10](2-) results in breaking of a Zn-bridging thiolate bond. In the second step replacement of the cluster Zn involves transfer of the bridging thiolates from the Zn to M, with breaking of a Zn-bridged thiolate bond being rate-limiting. The kinetics for the reaction of ZnCl2 with [Zn3M(SPh)10](2-) (M = Fe or Co)} depends on the identity of M. This behavior indicates attack of ZnCl2 at a M-mu-SPh-Zn bridged thiolate. Similar studies on the analogous reactions between [Fe4(SPh)10](2-) and an excess of CoX2 (X = NO3 or Cl) in MeCN exhibit simpler kinetics but these are also consistent with the same mechanism.

BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases.

PubMed

Jamialahmadi, Oveis; Motamedian, Ehsan; Hashemi-Najafabadi, Sameereh

2016-10-18

Development of an interface tool between the Biochemical, Genetic and Genomic (BiGG) and KEGG databases is necessary for simultaneous access to the features of both databases. For this purpose, we present the BiKEGG toolbox, an open source COBRA toolbox extension providing a set of functions to infer the reaction correspondences between the KEGG reaction identifiers and those in the BiGG knowledgebase using a combination of manual verification and computational methods. Inferred reaction correspondences using this approach are supported by evidence from the literature, which provides a higher number of reconciled reactions between these two databases compared to the MetaNetX and MetRxn databases. This set of equivalent reactions is then used to automatically superimpose the predicted fluxes using COBRA methods on classical KEGG pathway maps or to create a customized metabolic map based on the KEGG global metabolic pathway, and to find the corresponding reactions in BiGG based on the genome annotation of an organism in the KEGG database. Customized metabolic maps can be created for a set of pathways of interest, for the whole KEGG global map or exclusively for all pathways for which there exists at least one flux carrying reaction. This flexibility in visualization enables BiKEGG to indicate reaction directionality as well as to visualize the reaction fluxes for different static or dynamic conditions in an animated manner. BiKEGG allows the user to export (1) the output visualized metabolic maps to various standard image formats or save them as a video or animated GIF file, and (2) the equivalent reactions for an organism as an Excel spreadsheet.