Chemical Reaction Equilibrium Research Articles

A thermodynamic approach to PCR primer design

We developed a primer design method, Pythia, in which state of the art DNA binding affinity computations are directly integrated into the primer design process. We use chemical reaction equilibrium analysis to integrate multiple binding energy calculations into a conservative measure of polymerase chain reaction (PCR) efficiency, and a precomputed index on genomic sequences to evaluate primer specificity. We show that Pythia can design primers with success rates comparable with those of current methods, but yields much higher coverage in difficult genomic regions. For example, in RepeatMasked sequences in the human genome, Pythia achieved a median coverage of 89% as compared with a median coverage of 51% for Primer3. For parameter settings yielding sensitivities of 81%, our method has a recall of 97%, compared with the Primer3 recall of 48%. Because our primer design approach is based on the chemistry of DNA interactions, it has fewer and more physically meaningful parameters than current methods, and is therefore easier to adjust to specific experimental requirements. Our software is freely available at http://pythia.sourceforge.net.

Density functional study of chemical reaction equilibrium for dimerization reactions in slit and cylindrical nanopores

We present a theoretical study of the effects of confinement on chemical reaction equilibrium in slit and cylindrical nanopores. We use a density functional theory (DFT) to investigate the effects of temperature, pore geometry, bulk pressure, transition layering, and capillary condensation on a dimerization reaction that mimics the nitric oxide dimerization reaction, 2NO <==> (NO)(2), in carbonlike slit and cylindrical nanopores in equilibrium with a vapor reservoir. In addition to the DFT calculations, we also utilize the reaction ensemble Monte Carlo method to supplement the DFT results for reaction conversion. This work is an extension of the previous DFT study by Tripathi and Chapman [J. Chem. Phys. 118, 7993 (2003)] on the dimerization reactions confined in the planar slits.

β-FeOOH thin film as positive electrode for lithium-ion cells

β-FeOOH thin film was prepared on the surface of a foamed Ni substrate by liquid phase deposition (LPD) method with a chemical equilibrium reaction between metal-fluoro complex and oxyhydroxide to make a low-cost and environmentally friendly positive electrode for high-power batteries. The new film electrode, with a thickness of 316 nm, was found out to give a large discharge capacity of 260 mAh g −1 at 0.05 C rate even without an electro-conductive material. Furthermore, the electrode also showed good discharge performance with the retention of 69.9% at 10–0.05 C current rate, which means a promising positive active material for high-power use.

The negative adsorption of chromium atoms on alloy-oxide film boundaries during oxidation in air and anodic passivation of Fe-Cr and Ni-Cr alloys

Equilibrium of Cr atoms between the surface layer and bulk of a binary alloy was analyzed. The Gibbs adsorption equation was used to obtain the dependence of the adsorption activity of atoms in the surface layer on their activity in the bulk. An approximate thermodynamic method was used to calculate the adsorption of Fe (Ni) and Cr atoms in the surface layers of Fe-Cr and Ni-Cr alloys. According to calculations, there was negative adsorption, XCr ≪ 1, in the surface layer of the alloys caused by a large difference between the Gibbs surface energies of Cr and Fe (or Ni). The negative adsorption of Cr shifted chemical reaction equilibria on the alloy-oxide film boundary both in oxidation in air and in anodic passivation, 3FeO (NiO) + 2Cr = Cr2O3 + 3Fe(Ni), toward oxide film enrichment in the FeO (or NiO) oxide. A unified method for calculating the composition of oxide films on alloys was used for both processes. The method was based on the use of the initial data on the Gibbs surface energy of metals constituting alloys. The calculated oxide film compositions were close to the experimental X-ray photoelectron spectroscopy data.

Analytical approximate solution of competitive facilitated transport of acid gases through liquid membranes

An analytical approximate solution for the competitive facilitation factor of components A and E across a liquid membrane is developed in the case of instantaneous reactions inside the liquid membranes. This analytical solution solves the dimensionless, nonlinear diffusion-reaction transport problem governing the competitive facilitated transport of two gaseous components through liquid membranes. Prediction of the facilitation factors has been obtained for the equilibrium chemical reaction regime, considering the unequal complexes diffusivities and cases of zero and nonzero permeate side solute concentrations. This mathematical solution leads to analytical expressions for the concentration profiles of the species across the liquid membrane. In comparison with the present numerical solution and also numerical calculations and experimental data from the open literature, the difference between the analytical predictions and those obtained from the numerical solution were found to be in well agreement.

Mathematical modelling of CO2 facilitated transport through liquid membranes containing amines as carrier

AbstractAn approximate analytical solution for the facilitated transport of carbon dioxide across a liquid membrane containing aqueous primary and secondary amine solutions has been developed in which the reversible reaction A(CO2) + 2B(amine) $\Leftrightarrow$ AB(carbamate) + BH(protonated amine) occurs inside the liquid membranes. The current approximate analytical solution predicts the facilitated factor of CO2 through the membrane and is based on the dimensionless, nonlinear diffusion‐reaction transport problem. The approximate analytical solution predicts the facilitation factors for the range from the moderate reaction rate to the equilibrium chemical reaction regime, allowing unequal diffusivities of complexes and carrier and cases of zero and nonzero permeate side solute concentrations. In the present mathematical model, a constant free carrier concentration is assumed throughout the membrane phase. In comparison with the numerically calculated results, the results obtained were found to be in well agreement.

순산소 및 배가스 재순환 연소 기술

Oxy-fuel combustion is a reliable way for the reduction of pollutants, the higher combustion efficiency and the separation of carbon dioxide. The review of recent research trends and the prospects of oxy-fuel combustion were presented. The difference in characteristics among oxy-fuel combustion, conventional air combustion, oxy-fuel combustion with flue gas recirculation (FGR) technique was investigated. Recent experiments of oxy-fuel combustion with/without FGR were surveyed in various ways which are optimized burner design, flame characteristics, the soot emission, the radiation effect, the NOx reduction and the corrosion of combustor. Numerical simulation is more important in oxy-fuel combustion because flame temperature is so high that conventional measurement devices have a restricted application. Equilibrium and non-equilibrium chemical reaction mechanisms for oxy-fuel combustion were investigated. Combustion models suitable for the numerical simulation of non-premixed oxy-fuel flame were surveyed.

Liquid phase deposition of iron and cobalt doped TiO2 epitaxial thin films

Liquid phase deposition (LPD) is a wet process in which metal oxide thin films can be deposited on substrates via a chemical equilibrium reaction between a metal fluoro-complex and a metal oxide in aqueous solution. In this study, iron and cobalt doped TiO2 anatase thin films were deposited on (001) oriented SrTiO3 single crystal substrates using liquid phase deposition. The process involves the reaction of ammonium hexafluorotitanate and boric acid, in the presence of FeOOH–HF and Co(NO3)2–ethylenediamine (en) for the iron and cobalt doped TiO2 films respectively. Cobalt doping was also attempted by immersing a non-doped TiO2 film in a solution of Co-en ions. XRD shows that the films are c-axis oriented and films epitaxy was confirmed using pole figure measurements. No metallic secondary phases were detected by XRD and XPS. The iron and cobalt doped films are observed to yield room temperature ferromagnetism. The insulating nature of the films suggests that bound magnetic polarons are responsible for the observed ferromagnetism. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Injection of seawater and mixtures with produced water into North Sea chalk formation: Impact of fluid–rock interactions on wettability and scale formation

Seawater has been injected into high temperature and natural fractured North Sea chalk reservoirs to improve oil recovery with great success. Previous studies have shown that seawater will improve the water wetness and cause enhanced compaction of the matrix. The composition of the produced water will be quite similar to initial formation water at the start of the water injection. The formation water contains various amounts of divalent cations like Mg 2+, Ca 2+, Sr 2+, and Ba 2+. Later on, the composition will change due to the interaction between seawater and the chalk formation and some mixing with formation water. The fluid–rock interaction will involve dissolution of CaCO 3, substitution of Ca 2+ by Mg 2+ at the chalk surface, precipitation of CaSO 4, SrSO 4 and BaSO 4 depending on the reservoir temperature. Because of environmental reasons, it is desirable to re-inject produced water together with seawater. In the forthcoming research, we will study experimentally the effect of this re-injection on oil recovery and chalk compaction by using mixtures of produced water and seawater as injection fluid. Based on model studies using the OLI software package, the compatibility of mixtures of produced water and seawater has been studied at different temperatures by looking at the precipitation of CaSO 4, SrSO 4 and BaSO 4. Also the impact of changes in the concentrations of Ca 2+ and Mg 2+ due to surface substitution is modelled. The results are discussed in terms of possible scale formation in the producer and injector. In addition, actual chemical equilibrium reactions in the chalk matrix are discussed in relation to variation in temperature during continuous injection of seawater. Special focus is made on wettability modification, irreversible thermodynamics, and impact on the mechanical strength of the chalk matrix.

Molecular-level simulations of chemical reaction equilibrium for nitric oxide dimerization reaction in disordered nanoporous carbons

We report a molecular-level simulation study of the effects of confinement on chemical reaction equilibrium for the NO dimerization reaction, 2NO ⇌ (NO) 2, in disordered nanoporous carbons. We use the Reaction Ensemble Monte Carlo (RxMC) method [W.R. Smith, B. Tříska, J. Chem. Phys. 100 (1994) 3019–3027; J.K. Johnson, A.Z. Panagiotopoulos, K.E. Gubbins, Mol. Phys. 81 (1994) 717–733] to investigate the effects of temperature and bulk pressure on the reaction conversion in three models of disordered nanoporous carbons obtained from sucrose in equilibrium with a vapor reservoir. Atomistic models of the carbons used [S.K. Jain, R.J.-M. Pellenq, J.P. Pikunic, K.E. Gubbins, Langmuir 22 (2006) 9942–9948] were constructed using the Hybrid Reverse Monte Carlo method, differing by the processing conditions used in the preparation of the corresponding real material. In addition to the RxMC simulations, we test conventional macroscopic adsorption models, such as the Langmuir–Freundlich, multisite Langmuir, vacancy solution and ideal adsorption solution models, in connection with the ideal-gas model for the vapor reservoir to model the reaction equilibrium. Pure fluid adsorption isotherms needed as input to the macroscopic models for mixture adsorption are generated using the Gibbs Ensemble Monte Carlo or Grand Canonical Monte Carlo simulations. We analyze the effects of the confinement, temperature and bulk pressure on the NO dimerization reaction equilibrium in terms of the reactive adsorption isotherms. The RxMC simulations and thermodynamic modeling show that the sucrose-based carbons substantially increase the conversion of NO to (NO) 2 with respect to the vapor reservoir, where the conversion is less than a few percent.

GM and Mascoma in cellulosic venture

I developed a combined model of the thermal and chemical evolution of the Earth’s core and investigated its influence on a thermochemically stable region beneath the core-mantle boundary (CMB). The chemical effects of the growing stable region are caused by the equilibrium chemical reaction between silicate and the metallic core. The thermal effects can be characterized by the growth of the sub-isentropic shell, which may have a rapid growth rate compared to that of the chemically stable region. When the present-day CMB heat flow was varied, the origin of the stable region changed from chemical to thermochemical to purely thermal because the rapid growth of the sub-isentropic shell can replace the chemically stable region. Physically reasonable values of the present-day CMB heat flow that can maintain the geodynamo action over 4 billion years should be between 8 and 11 TW. To constrain the thickness of the thermochemically stable region beneath the CMB, the chemical diffusivity is important and should be ∼O(10−8) m2/s to obtain a thickness of the thermochemically stable region beneath the CMB consistent with that inferred from geomagnetic secular variations (140 km). However, the strength of the stable region found in this study is too high to be consistent with the constraint on the stability of the stable region inferred from geomagnetic secular variations.

A mechanistic treatment of the dominant soil nitrogen cycling processes: Model development, testing, and application

The development and initial application of a mechanistic model (TOUGHREACT‐N) designed to characterize soil nitrogen (N) cycling and losses are described. The model couples advective and diffusive nutrient transport, multiple microbial biomass dynamics, and equilibrium and kinetic chemical reactions. TOUGHREACT‐N was calibrated and tested against field measurements to assess pathways of N loss as either gas emission or solute leachate following fertilization and irrigation in a Central Valley, California, agricultural field as functions of fertilizer application rate and depth, and irrigation water volume. Our results, relative to the period before plants emerge, show that an increase in fertilizer rate produced a nonlinear response in terms of N losses. An increase of irrigation volume produced NO2− and NO3− leaching, whereas an increase in fertilization depth mainly increased leaching of all N solutes. In addition, nitrifying bacteria largely increased in mass with increasing fertilizer rate. Increases in water application caused nitrifiers and denitrifiers to decrease and increase their mass, respectively, while nitrifiers and denitrifiers reversed their spatial stratification when fertilizer was applied below 15 cm depth. Coupling aqueous advection and diffusion, and gaseous diffusion with biological processes, closely captured actual conditions and, in the system explored here, significantly clarified interpretation of field measurements.

Equilibrium shift in membrane reactors: A thermodynamic analysis of the dehydrogenative conversion of alkanes

The shift in equilibrium conversion for dehydrogenation and dehydroalkylation reactions as a result of selective extraction of hydrogen in a membrane reactor has been evaluated by a simple model based on thermodynamics taking into account chemical reaction equilibrium and hydrogen equilibrium across a 100% hydrogen-selective membrane. There is a limit to which the equilibrium can be shifted in a membrane reactor, depending on the thermodynamics of given reactions. The effects of temperature, pressure and sweep gas flow rate on equilibrium conversion and selectivity in a membrane reactor have been demonstrated.

Analysis of jet fuel reforming for solid oxide fuel cell applications in auxiliary power units

Jet fuel reforming was analyzed for both partial oxidation and autothermal reforming processes based on the chemical-reaction equilibria with possible use of solid oxide fuel cells in the auxiliary power units of aircraft to reduce pollutant emissions. Parameters considered in this paper were the oxygen-to-carbon ratio (0–0.7), the steam-to-carbon ratio (0–1), and the reformer temperature (500– 1200 ∘ C ). The product compositions and energy change of the reforming process were calculated for 12 hydrocarbons of a surrogate jet fuel under the isothermal conditions and the jet fuel under the adiabatic conditions. Solid carbon in the form of graphite was included as one of the products. The effect of 12 hydrocarbons on the oxygen-to-carbon ratio at the carbon formation boundary was negligible above 700 ∘ C . Under isothermal conditions, the maximum yield of hydrogen, carbon monoxide, or syngas was at the carbon formation boundary. Under adiabatic conditions, the minimum required oxygen-to-carbon ratio to avoid carbon formation was decreased from 0.52 to 0.38 and the corresponding temperature was reduced from 844 to 617 ∘ C with the increase of steam-to-carbon ratio from 0 to 1 for the jet fuel reforming. The maximum reforming efficiency based on the synthesis gas was about 83% for the considered steam-to-carbon ratios.

A New Approach to Estimate Ion Distribution between the Exchanger and Solution Phases

Currently there are two approaches to treat ion exchange equilibrium between the exchanger phase and solution phase: the chemical reaction equilibrium and the Donnan equilibrium. Nevertheless, theoretical calculation of the ion distribution between these two phases remains impossible using these two approaches because of the difficulty in obtaining the activity coefficient of an ion in the exchanger phase for a solution mixture containing two or more types of electrolytes. Our analysis of ion diffusion in an electric field showed that the exchange process of electrostatic adsorption can be treated as a diffusion process. A new equilibrium equation was obtained by treating ion exchange as a diffusion process. The new equation can be used to predict the ion distribution between the exchanger and solution phases without knowing the activity coefficients of the adsorbed ions. The new approach was tested and verified using published experimental data for a Na–Ca‐illite system. The experimental data and the theoretical predictions matched very well. The new ion distribution equation can provide another way to calculate ion exchange equilibrium for a well‐dispersed suspension of dilute bulk solution containing two types of electrolytes.

Vitiation Effects on Scramjet Engine Performance in Mach 6 Flight Conditions

Quasi-one-dimensional analyses with either chemical equilibrium or finite-rate reaction were conducted to evaluate the effects of contamination due to flow vitiation on engine performances, namely, thrust production. The incoming flow state was calculated based on measurements, and a higher total enthalpy for the freestream through a vitiation heater compared to that through a storage heater was found, the difference in the flow condition being responsible for two-thirds of the reduction in the thrust production with vitiation observed in the engine tests. With the finite-rate reaction calculation, the possibility of a further reduction due to the contamination effect on the combustion mechanism was found, which was responsible for one-third of the measured reduction. The one-dimensional analyses were further pursued to find matched test conditions with the storage heater to that with the vitiation heater in view of the thrust production and pressure distribution within the engine, and both freestream enthalpy and fuel equivalence ratio should be adjusted to attain the matched conditions.

Selective desorption of carbon dioxide from sewage sludge for in situ methane enrichment—Part II: modelling and evaluation of experiments

In situ methane enrichment in anaerobic digestion of sewage sludge has been investigated by experiments and by modelling. Sludge from a full scale digester was fed to a pilot scale bubble column having 0.3 m diameter for preferential desorption of carbon dioxide. In this second part, a model describing the steady-state performance of the bubble column for desorption of carbon dioxide and methane has been developed. The column is assumed to operate in the homogeneous flow regime, and with respect to carbon dioxide and methane both phases are described by the axial dispersion model. The model treats the chemical reaction equilibrium between carbon dioxide and bicarbonate as being slow and the bicarbonate concentration as being constant. The model is correlated to previously reported experimental results to determine the liquid side mass transfer coefficient in each experiment. A simple power law model is used to correlate the mass transfer coefficient to the gas flow rate. In general, the model allows for a reasonable qualitative description of the behaviour of the bubble column performance but the quantitative agreement with experimental results is not satisfactory. It is believed, though that the main problem is actually not in the model but is related to experimental uncertainties concerning inlet concentrations of liquid phase methane and bicarbonate.

A Method for Modeling Two- and Three-Phase Reactive Distillation Columns

An algorithm for the steady-state simulation of two- and three-phase multistage reactive distillation processes with equilibrium chemical reactions is developed. In the developed algorithm, the phase stability, phase equilibrium, and chemical reaction equilibrium calculations are preformed simultaneously. The algorithm was used to simulate a variety of two- and three-phase reactive distillation processes. The simulation results were compared against the available experimental data in the literature. Good agreement was observed between the simulation results and experimental data. A multistage reactive distillation process for the production of cyclohexanol from the hydration of cyclohexene with two liquid phases present on multiple stages was simulated. A high-purity cyclohexanol product with a high cyclohexene conversion was obtained for this process.

On the nature of crosslinks in thermoreversible gels

A review is given concerning the nature of crosslinks in thermoreversible gels. In these gels the crosslinks can be formed e.g. by means of crystallisation of parts of polymer molecules, by liquid-liquid phase separation in solution and in bulk, by hydrogen bridging, by complexation of polymer chains, by helix formation, by chemical equilibrium reaction or by interactions between side-chains. One example will be given for each of these eight possibilities of crosslink formation.

Chemical Equilibrium and Reaction Kinetics of Heterogeneously Catalyzed n-Hexyl Acetate Esterification

In the framework of a project on reactive distillation, reaction equilibrium and kinetics of the esterification of n-hexanol and acetic acid, yielding n-hexyl acetate and water, were investigated. Chemical equilibrium and auto-catalyzed reaction kinetics were measured using batch reactors whereas a plug flow reactor was chosen to study the heterogeneously catalyzed reaction. The catalyst was Amberlyst CSP2. Dihexyl ether and hexene were observed as byproducts. The study covers temperatures between 20 and 130 °C, with a focus on the technically important range of 80−120 °C. Feed compositions were varied so that the entire concentration range relevant for reactive distillation was covered. On the basis of the experimental results, a thermodynamically consistent reaction model is developed. Two model types are tested, a pseudo-homogeneous and an adsorption-based model, for which the adsorption constants were determined from independent adsorption experiments of the immersion type carried out in the present w...