Free Energy Change Of Reaction Research Articles

Reaction thermodynamics as a constraint on piscine steroidogenesis flux distributions

While a considerable amount is known of the dynamics of piscine steroidogenesis during reproduction, the influence of thermodynamics constraints on its control has not been studied. In this manuscript, Gibbs free energy change of reactions was calculated for piscine steroidogenesis using the in silico eQuilibrator thermodynamics calculator. The analysis identified cytochrome P450 (cyp450) oxidoreductase reactions to have more negative Gibbs free energy changes relative to hydroxysteroid (HSD) and transferase reactions. In addition, a more favorable Gibbs free energy change was predicted for the Δ5 (cyp450 catalyzed) vs. Δ4 (HSD catalyzed) steroidogenesis branch-point, which converts pregnenolone to 17α-hydroxypregnenolone or progesterone respectively. Comparison of in silico predictions with in vivo experimentally measured flux across the Δ5 vs. Δ4 branch-point showed higher flux through the thermodynamically more favorable Δ5 pathway in reproducing or spawning vs. non-spawning fathead minnows (Pimephales promelas). However, the exposure of fish to endocrine stressors such as hypoxia or the synthetic estrogen 17α-ethinylestradiol (EE2), resulted in increased flux through both Δ5 and Δ4 pathways, indicating an adaptive response to increase steroidogenic redundancy. The correspondence of elevated flux through the Δ5 branch-point in spawning fish indicated the use of a thermodynamically favorable pathway to optimize steroid hormone productions during reproduction. We hypothesize that such selective use of a thermodynamically favorable steroidogenesis pathway may conserve reduced equivalents or transcriptional costs for investment to other biosynthetic or catabolic reactions to support reproduction. If generalizable, such an approach can provide novel insights into the structural principles and regulation of steroidogenesis or other metabolic pathways.

In Silico Simulations Reveal Molecular Mechanism of Uranyl Ion Toxicity towards DNA-Binding Domain of PARP-1 Protein.

The molecular toxicity of the uranyl ion (UO22+) in living cells is primarily determined by its high affinity to both native and potential metal-binding sites that commonly occur in the structure of biomolecules. Recent advances in computational and experimental research have shed light on the structural properties and functional impacts of uranyl binding to proteins, organic ligands, nucleic acids, and their complexes. In the present work, we report the results of the computational investigation of the uranyl-mediated loss of DNA-binding activity of PARP-1, a eukaryotic enzyme that participates in DNA repair, cell differentiation, and the induction of inflammation. The latest experimental studies have shown that the uranyl ion directly interacts with its DNA-binding subdomains, zinc fingers Zn1 and Zn2, and alters their tertiary structure. Here, we propose an atomistic mechanism underlying this process and compute the free energy change along the suggested pathway. Our Quantum Mechanics/Molecular Mechanics (QM/MM) simulations of the Zn2-UO22+ complex indicate that the uranyl ion replaces zinc in its native binding site. However, the resulting state is destroyed due to the spontaneous internal hydrolysis of the U-Cys162 coordination bond. Despite the enthalpy of hydrolysis being +2.8 kcal/mol, the overall reaction free energy change is -0.6 kcal/mol, which is attributed to the loss of domain's native tertiary structure originally maintained by a zinc ion. The subsequent reorganization of the binding site includes the association of the uranyl ion with the Glu190/Asp191 acidic cluster and significant perturbations in the domain's tertiary structure driven by a further decrease in the free energy by 6.8 kcal/mol. The disruption of the DNA-binding interface revealed in our study is consistent with previous experimental findings and explains the loss of PARP-like zinc fingers' affinity for nucleic acids.

In-situ phase evolution of multi-component boride to high-entropy ceramic upon ultra-high temperature ablation

Multi-component boride (Hf0.5Zr0.5)B2-SmB6-ErB4-YB6 (HZRB) utilized as a coating on SiC-coated carbon/carbon (C/C) composite was prepared by supersonic atmosphere plasma spraying. In-situ phase evolution of HZRB into (Hf0.2Zr0.2Sm0.2Er0.2Y0.2)O2-δ high-entropy oxide (HEO) was investigated after oxyacetylene ablation for 120 s. The first-principles calculations were applied to analyze the in-situ formation mechanism of HEO. The mixing Gibbs free energy change (∆Gmix) of HEO was calculated to be negative at 2573 K, indicating that the HEO can be generated upon the ablation temperature. Due to the lower Gibbs free energy change of reaction (∆RGm), (Hf0.5Zr0.5)B2 will be oxidized to generate HfO2 firstly, and other elements dissolved into the HfO2 lattice to form HEO. The solution energies of Zr, Sm, Er and Y atoms are − 0.01, 6.28, 8.55 and 4.46 eV/atom, and corresponding solution reactions possess negative ∆RGm, indicating the possible solution sequence of these elements is Zr > Y > Sm > Er.

Experimental investigation and validation on the effect of nickel addition on properties of the pressureless sintered boron carbide composites using machine learning models

This research work aims to investigate the effect of a low amount of nickel (<0.6 wt%) on the properties of the boron carbide. The samples are synthesized through pressureless sintering at 2150 °C under an argon atmosphere (1 bar). Firstly, the thermodynamic simulation is carried out using the HSC software to determine the free energy change of reactions and their viability. The prepared samples are analyzed by employing various characterization techniques such as XRD, FESEM, and EDS. It is concluded that the presence of nickel (i.e., a low melting point than the boron carbide) results in the formation of the liquid phase during the sintering process. Thus, the sinterability of the samples is significantly enhanced. Moreover, the optimum sample is obtained by adding the 4 wt% of nickel in boron carbide. The maximum density, hardness, elastic modulus, and fracture toughness for the sample containing 4 wt% nickel are obtained as 91.00%, 21.83 GPa, 374.45 GPa, and 3.11 MPa m0.5, respectively. Furthermore, machine learning (ML) techniques (i.e., M5P tree model, random tree, REPTree (Reduced-Error Pruning), and artificial neural network (ANN)) are also utilized to check the adequacy of the results. It is concluded that the maximum value of CC, i.e., 0.9929, is obtained for the REPTree technique with a minimum value of MAE (i.e., 0.0869) and RMSE (i.e., 0.0968). It is observed that the ML technique showed the validation of experimental results.

Effect of the particle size on the reactivity of MgO-Al2O3 hydrating mixtures: A long-term kinetic investigation of hydrotalcite synthesis

Hydrotalcite-like compounds (HTlc) are commonly known anionic clay that may potentially be used as hydraulic binder component for refractory materials, ion exchangers, catalyst or carrier of bioactive molecules. According to current state of knowledge LDH (Layered Double Hydroxides) can be synthesized using various methods including mechanochemical synthesis, hydrothermal precipitation, sol–gel syntheses and coprecipitation method. Research on the synthesis of hydrotalcite in the mixture of oxide powders of Al2O3 and MgO cured under specific conditions is particularly important in case of the determination of the relationship between the type (susceptibility to hydration, grain size and specific surface area) of initial powders and reaction kinetics. As a result, the hydration of an equimolar mixture of magnesium and alumina oxides nano- or micro-powders has been proven to be an effective low temperature method of synthesis well crystallized MgAl LDH with highly ordered structures. This investigations clearly show that the kinetics of hydration is influenced only by properties of aluminium oxide as initial powder. The synthesis of Mg6Al2CO3(OH)16∙4H2O as a result of hydration is associated with composite matrix formation which firstly consist of partly reacted initial powders bonded by hydration products. The synthesis of Mg6Al2CO3(OH)16∙4H2O was discussed in terms of molar Gibbs free energy change of reactions within the MgO-Al2O3-CO2-H2O system. The calculated formation Gibbs energy was negative, when Mg(OH)2 was formed as an intermediate product. The standard Gibbs free energies of hydrotalcite formation was estimated based on the simple mechanical mixture model that treats Mg6Al2CO3(OH)16∙4H2O as mixtures of simple oxides. Thermodynamic calculations were performed assuming an equilibrium state between aqueous solutions and corresponding precipitates after synthesis.

Current Density Calculations of an Octahedral Fe Nanocluster for Selective Electrocatalytic for Nitrogen Reduction

In this work, an octahedral-shaped iron nanocluster (NC) electrocatalyst has been modeled to examine the pathways of electrochemical nitrogen reduction reaction (NRR) and analyze the catalytic activity over the (110) surface. The Heyrovsky-type associative and dissociative NRR mechanisms on the (110) facet and edge of the NC are systematically elucidated by calculating reaction free energies for all the possible elementary reaction steps in NRR. Our results show that the most of the NRR intermediates (*N2, *N2H, *N2H2, *N, *NH, *NH2, and *NH3) bind weakly on different sites of the NC in comparison to that on the periodic Fe(110) surface. Importantly, the reaction free energy change for the potential determining step (PDS) in the distal associative mechanism with the formation of *NNH on the NC facet is lower than the edge of NC and periodic Fe(110) surface. Our study also indicates that the PDS (*NH2 formation) associated with the periodic Fe(110) surface is no longer the same as the reaction is catalyzed by the NC. The calculated value of working potential is observed lower for Fe85 NC in comparison to that of the periodic Fe(110) surface. Furthermore, the current density plot indicates that the NC shows less hydrogen evolution reaction (HER) activity compared to other considered Fe based systems. Apart from the working potential study, the positive shift of dissolution potential has also been considered for dissolution behavior of Fe from the NC with respect to surface, confirming its stability in an electrochemical environment. The Fe85 NC electrocatalyst possess quite a low overpotential of 0.29 V for NRR with reduced HER activity, which is further lower compared to that of the well-established Re(111) and enhanced stability toward Fe dissolution in comparison to that of the periodic Fe(110) surface. Therefore, such an NC system may perform as an efficient catalyst for an electrochemical NRR.

A precise, simple and general Basic Le Châtelier Principle based on elementary calculus: What Le Châtelier had in mind?

The Le Châtelier Principle is one of the most important concepts in chemistry, and it has been the topic of many publications over the years. However, its meaning and application are often fraught with misunderstanding and confusion. As a suggested replacement, we present herein a precise general statement that we call the Basic Le Châtelier Principle (BLCP), which is in keeping with a common thread in Le Châtelier’s original statements. The BLCP is formulated as a consequence of well-known properties of a simple but general optimization problem, which elevates its range of application beyond chemistry to any phenomenon governed by such an optimization principle. We show applications of the BLCP to simple example problems in economics and in physics, in addition to the usual chemistry problems,. Following a brief outline of Le Châtelier’s original statements, we formulate the BLCP, which incorporates the notion of “de signe contraire” (of opposite sign), common to all his statements. It arises by abstracting the chemical reaction equilibrium problem (CREP) in the single-reaction case to the general problem of minimizing a differentiable function $$f(x;\{p_j\})$$ , where x is the single independent variable and $$\{p_j\}$$ is a set of parameters. The BLCP arises from an exact expression for the dependence of the sign of the incremental change in the optimal solution $$x^*$$ on the sign of the incremental change in a parameter, which is derived using techniques taught in an early undergraduate calculus course. When translated back to the CREP, this yields unambiguous expressions for the sign of the incremental change in the equilibrium reaction extent, $$\xi ^*$$ , arising from an incremental change in each of T, P, the initial species amounts, $$\{n_i^0\}$$ , and the standard reaction free energy change, $$\varDelta G^{\Box }$$ . Special emphasis is placed on the requirement that f must satisfy a positive definite second derivative condition, for which we present a proof in the case of multiple reactions in an ideal solution model system. We also briefly consider the extension of the single-variable BLCP derived herein to the case of multiple independent variables and to finite parameter perturbations.

Determination of Proton-Coupled Electron Transfer Reorganization Energies with Application to Water Oxidation Catalysts.

The reorganization energy, λ, for interfacial electron transfer (ET) and for proton-coupled electron transfer (PCET) between a water oxidation catalyst and a conductive In2O3:Sn (ITO) oxide were extracted from kinetic data by application of Marcus-Gerischer theory. Specifically, light excitation of the water oxidation catalyst [RuII(tpy)(4,4'-(PO3H2)2-bpy)OH2]2+ (RuII-OH2), where tpy is 2,2':6',2″-terpyridine and bpy is 2,2'-bipyridine, anchored to a mesoporous thin film of ITO nanocrystallites resulted in rapid excited-state injection ( kinj > 108 s-1). The subsequent reaction of the injected electron (ITO(e-)) and the oxidized catalyst was quantified spectroscopically on nanosecond and longer time scales. The metallic character of ITO allowed potentiostatic control of the reaction free energy change -Δ Go over a 1 eV range. At pH values below the p Ka = 1.7 of the oxidized catalyst, ET was the primary reaction. Within the pH range 2 ≤ pH ≤ 5, an interfacial PCET reaction (ITO(e-) + RuIII-OH + H+→ RuII-OH2) occurred with smaller rate constants. Plots of the rate constants versus -Δ Go provided a reorganization energy of λPCET = 0.9 eV and λET = 0.5 eV. A second water oxidation catalyst provided similar values and demonstrated generality. The utilization of conductive oxides is shown to be a powerful tool for quantifying PCET reorganization energies at oxide surfaces for the first time.

Thermochemical Measurements of Cation Exchange in CdSe Nanocrystals Using Isothermal Titration Calorimetry.

Among the various reported post synthetic modifications of colloidal nanocrystals, cation exchange (CE) is one of the most promising and versatile approaches for the synthesis of nanostructures that cannot be directly synthesized from their constitutive precursors. Numerous studies have reported on the qualitative analysis of these reactions, but rigorous quantitative study of the thermodynamics of CE in colloidal nanoparticles is still lacking. We demonstrate using isothermal titration calorimetry (ITC), the thermodynamics of the CE between cadmium selenide (CdSe) nanocrystals and silver in solution can be quantified. We survey the influence of CdSe nanocrystal diameter, capping ligands and temperature on the thermodynamics of the exchange reaction. Results obtained from ITC provide a detailed description of overall thermodynamic parameters-equilibrium constant ( K eq), enthalpy (Δ H), entropy (Δ S) and stoichiometry ( n)-of the exchange reaction. We compared the free energy change of reaction (Δ G) between CdSe and Ag+ obtained directly from ITC for both CdSe bulk and nanoparticles with values calculated from previously reported methods. While the calculated value is closer to the experimentally obtained Δ G rxn for bulk particles, nanocrystals show an additional Gibbs free energy stabilization of ∼-14 kJ/mol Se. We discuss a thermochemical cycle elucidating the steps involved in the overall cation exchange process. This work demonstrates the application of ITC to probe the thermochemistry of nanoscale transformations under relevant solution conditions.

Theoretical Study on Hydrogenolytic Cleavage of Intermonomer Linkages in Lignin

Hydrogenolysis is an important approach for depolymerization of lignin, which provides attractive new sustainable platforms of fuels, chemicals, and materials. The theory of lignin hydrogenolysis is, however, still unsound, which limits the development of this approach and causes inconsistencies among experimental studies. In this paper, density functional theory is employed to investigate the initial hydrogenolytic cleavages of recognized five different types of interaromatic unit linkages of lignin, assuming the presence of hydrogen free radicals. The relative free energies of reactant complexes, reaction free energy changes, and rate constants for candidate reactions are calculated comprehensively at 298-538 K. On the basis of the results of calculation and a rapid equilibrium hypothesis, the major reaction channel is decided for each linkage, and its kinetics is assessed. It is concluded that the hydrogenolysis occurs at β-O-4 ether, diphenyl ether 4-O-5', and β-1' diphenylmethane linkages instantaneously if these are accessible to hydrogen free radicals, while β-5 phenylcoumaran and β-β' pinoresinol linkages are virtually inert to hydrogenolysis.

The synergy effect and reaction pathway in the oxygen reduction reaction on the sulfur and nitrogen dual doped graphene catalyst

The first-principle calculations are performed to explore the synergy effects between two dopants (N, S) and the detailed reaction pathway of oxygen reduction reaction (ORR) on the graphene catalysts. The co-doping N and S induces the significant spin density and has a strong chemical bonding with oxygen molecule which is not observed on the mono-doped cases. Three different reaction pathways are revealed from the calculations. Due to the large barrier of the OO breaking, the hydrogenation of the adsorbed oxygen molecule is kinetically more favorable. The free energy change of reaction under different electrode potential is also evaluated.

Free radical scavenging and COX-2 inhibition by simple colon metabolites of polyphenols: A theoretical approach

Free radical scavenging and inhibitory potency against cyclooxygenase-2 (COX-2) by two abundant colon metabolites of polyphenols, i.e., 3-hydroxyphenylacetic acid (3-HPAA) and 4-hydroxyphenylpropionic acid (4-HPPA) were theoretically studied. Different free radical scavenging mechanisms are investigated in water and pentyl ethanoate as a solvent. By considering electronic properties of scavenged free radicals, hydrogen atom transfer (HAT) and sequential proton loss electron transfer (SPLET) mechanisms are found to be thermodynamically probable and competitive processes in both media. The Gibbs free energy change for reaction of inactivation of free radicals indicates 3-HPAA and 4-HPPA as potent scavengers. Their reactivity toward free radicals was predicted to decrease as follows: hydroxyl>>alkoxyls>phenoxyl≈peroxyls>>superoxide. Shown free radical scavenging potency of 3-HPAA and 4-HPPA along with their high μM concentration produced by microbial colon degradation of polyphenols could enable at least in situ inactivation of free radicals. Docking analysis with structural forms of 3-HPAA and 4-HPPA indicates dianionic ligands as potent inhibitors of COX-2, an inducible enzyme involved in colon carcinogenesis. Obtained results suggest that suppressing levels of free radicals and COX-2 could be achieved by 3-HPAA and 4-HPPA indicating that these compounds may contribute to reduced risk of colon cancer development.

Shifts in Rumen Fermentation and Microbiota Are Associated with Dissolved Ruminal Hydrogen Concentrations in Lactating Dairy Cows Fed Different Types of Carbohydrates

Background: Different carbohydrates ingested greatly influence rumen fermentation and microbiota and gaseous methane emissions. Dissolved hydrogen concentration is related to rumen fermentation and methane production.Objectives: We tested the hypothesis that carbohydrates ingested greatly alter the rumen environment in dairy cows, and that dissolved hydrogen concentration is associated with these changes in rumen fermentation and microbiota.Methods: Twenty-eight lactating Chinese Holstein dairy cows [aged 4–5 y, body weight 480 ± 37 kg (mean ± SD)] were used in a randomized complete block design to investigate effects of 4 diets differing in forage content (45% compared with 35%) and source (rice straw compared with a mixture of rice straw and corn silage) on feed intake, rumen fermentation, and microbial populations.Results: Feed intake (10.7–12.6 kg/d) and fiber degradation (0.584–0.692) greatly differed (P ≤ 0.05) between cows fed the 4 diets, leading to large differences (P ≤ 0.05) in gaseous methane yield (27.2–37.3 g/kg organic matter digested), dissolved hydrogen (0.258–1.64 μmol/L), rumen fermentation products, and microbiota. Ruminal dissolved hydrogen was negatively correlated (r < −0.40; P < 0.05) with molar proportion of acetate, numbers of fungi, abundance of Fibrobacter succinogenes, and methane yield, but positively correlated (r > 0.40; P < 0.05) with molar proportions of propionate and n-butyrate, numbers of methanogens, and abundance of Selenomonas ruminantium and Prevotella spp. Ruminal dissolved hydrogen was positively correlated (r = 0.93; P < 0.001) with Gibbs free energy changes of reactions producing greater acetate and hydrogen, but not correlated with those reactions producing more propionate without hydrogen.Conclusions: Changes in fermentation pathways from acetate toward propionate production and in microbiota from fibrolytic toward amylolytic species were closely associated with ruminal dissolved hydrogen in lactating dairy cows. An unresolved paradox was that greater dissolved hydrogen was associated with greater numbers of methanogens but with lower gaseous methane emissions.

The stable polyiodides: Experimental and theoretical studies of formation mechanism

The structures of polyiodides have been extensively studied for long time, but it was rarely involved of the mechanism of polyiodide species formation in preparation. The tetraethylammonium polyiodides were chosen as model chemicals and prepared with different molar ratios of reactants in ethanol solvent, the products were analyzed by titration, Raman spectra and TGA/DTG/DSC analysis, with the increase of the molar ratios of reactants, the iodine contents of the products reached a constant value. Finally, only two stable structures, Et4NI3 (1, space group Cmca) and Et4NI7 (2, space group Cmca), were isolated by recrystallization of slow evaporating solvent(s). The thermal analysis of tetraethylammonium polyiodides showed that all tetraethylammonium polyiodides lost I2 together to become Et4NI3 firstly and then continue to decompose. The decomposition of Et4NI3 was not a simple process which Et4NI3 lost one iodine molecule and then became Et4NI. In addition, the thermodynamical properties of species (I2 and Et4NIx, x=1, 3, 5, 7) and the molar standard Gibbs free energy changes of reactions (ΔrGmθ), as well as the mechanism of tetraethylammonium polyiodides formation were interpreted by density functional theory (DFT) calculations. The calculations show that the solvent effects have impact on the reactions. Accordingly, a comparative study was carried out on the solid phase synthesis of Et4NI5 at 80°C and at molten state. Furthermore, the solid synthesis of Et4NI5 was characterized by variable temperature (−25°C∼150°C) Raman Spectrometer. The polyiodide components interconversion showed the discrete I5- could be formed in molten state. In short, what species of polyiodides crystallized from reactions in solutions are decided by the synergy between ΔrGm of reactions and Coulombic interactions etc. of polyiodide crystals.

Application of computational chemistry methods to obtain thermodynamic data for hydrogen production from liquefied petroleum gas

The objective of this study was to estimate thermodynamic data, such as standard enthalpy, entropy and Gibbs free energy changes of reaction and, consequently, chemical equilibrium constants, for a reaction system describing the hydrogen production from Liquefied Petroleum Gas (LPG). The acquisition of those properties was made using computational chemistry methods and the results were compared with experimental data reported in the literature. The reaction system of steam reforming of LPG was reported as a set of seven independent reactions involving the chemical species n-C4H10, C3H8, C2H6, C2H4, CH4, CO2, CO, H2O, H2 and solid carbon. Six computational approaches were used: Density Functional Theory (DFT) employing Becke's three parameter hybrid exchange functional, and the Lee-Yang-Parr correlation functional (B3LYP) using the 6-31G++(d,p) basis set and the composite methods CBS-QB3, Gaussian-1 (G1), Gaussian-2 (G2), Gaussian-3 (G3) and Gaussian-4 (G4). Mole fractions of the system components were also determined between 873.15 and 1173.15 K, at 1 atm and a feed with a stoichiometric amount of water. Results showed that the hybrid functional B3LYP/6-31G++(d,p), G3 and G4 theories were the most appropriated methods to predict the properties of interest. Gaussian-3 and Gaussian-4 theories are expected to be good thermodynamic data predictors and the known efficient prediction of vibrational frequencies by B3LYP is probably the source of the good agreement found in this study. This last methodology is of special interest since it presents low computational cost, which is important when more complex molecular systems are considered.

Identification and analysis of synthesis routes in complex catalytic reaction networks for biomass upgrading

In this paper, we present a method to construct and query the spectrum (>15,000) of potential biomass-derived compounds that can be synthesized using heterogeneous catalysis. Specifically, it involves the construction of an exhaustive network of reactions using RING, a rule-based network generator that we have developed, to identify potentially synthesizable compounds from biomass. Subsequently, we: (a) employ quantitative structure–property relationships to query compounds with desired properties, (b) seek different synthesis routes to these compounds, and (c) evaluate these routes in terms of stoichiometric, energetics, and physical parameters such as atom efficiency, enthalpy and free energy change of reactions, and aqueous-organic partition coefficients (LogP) of intermediates. Thermochemistry and LogP are both estimated using group additivity methods, and all property estimations are performed on-the-fly during network generation. We present this method in context of identifying and evaluating heterogeneous catalytic routes from biomass to fatty alcohols that are potential constituents of nonionic surfactants. We also show that group additivity-based estimates of enthalpy of reaction are accurate to within 10kJ/mol and LogP values reliably predict the relative hydrophobicity of compounds. This method is generic, flexible, reliable and fast in terms of the scope of chemistry that can be considered, properties that can be included, predictive accuracy, and speed of execution; it can, therefore, be used to rapidly screen a large spectrum of compounds and synthesis routes in biomass conversion.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

BackgroundConstraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used.ResultsIn this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism.ConclusionsThis study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets.

Molecular mechanisms of cobalt-catalyzed hydrogen evolution.

Several cobalt complexes catalyze the evolution of hydrogen from acidic solutions, both homogeneously and at electrodes. The detailed molecular mechanisms of these transformations remain unresolved, largely owing to the fact that key reactive intermediates have eluded detection. One method of stabilizing reactive intermediates involves minimizing the overall reaction free-energy change. Here, we report a new cobalt(I) complex that reacts with tosylic acid to evolve hydrogen with a driving force of just 30 meV/Co. Protonation of Co(I) produces a transient Co(III)-H complex that was characterized by nuclear magnetic resonance spectroscopy. The Co(III)-H intermediate decays by second-order kinetics with an inverse dependence on acid concentration. Analysis of the kinetics suggests that Co(III)-H produces hydrogen by two competing pathways: a slower homolytic route involving two Co(III)-H species and a dominant heterolytic channel in which a highly reactive Co(II)-H transient is generated by Co(I) reduction of Co(III)-H.

Determination of the Thermodynamically Dominant Metabolic Pathways

An effective strategy comprising two phases is proposed to determine the thermodynamically dominant pathways in a metabolic network of a given phenotype, involving several metabolic reactions. In the first phase, stoichiometrically feasible metabolic pathways are exhaustively identified through the flux balance analysis and the graph-theoretic method based on P-graphs. In the second phase, thermodynamically dominant pathways are selected from these stoichiometrically feasible metabolic pathways on the basis of the Gibbs free energy change of reaction. The proposed strategy’s efficacy is demonstrated by applying it to two E. coli models: one is for maximal acetate and ethanol production, and the other is for maximalpoly(3-hydroxybutyrate) production.

Influence of La and Ce on Microstructure and Properties of Cu-Cr-Zr Alloy

The degassing and dedusting mechanism of La and Ce during non-vacuum melting process of Cu-Cr-Zr alloy were analyzed by thermodynamics. The gibbs free energy changes of reactions of La and Ce with some impurties such as O2, H2, S, P and Si, were calculated to discriminate the possibility of reaction during the melting process, respectively. In addition, the effect of La and Ce on microstructure and properties were studied. The results show that La and Ce can react with O2, H2, S, P and Si, which improves the effect of degassing and dedusting remarkably; the addition of La and Ce can eliminate pine-tree crystal, fine grain and clear grain bourdary.