Reactive Transport: A Review of Basic Concepts with Emphasis on Biochemical Processes

Reactive transport (RT) couples bio-geo-chemical reactions and transport. RT is important to understand numerous scientific questions and solve some engineering problems. RT is highly multidisciplinary, which hinders the development of a body of knowledge shared by RT modelers and developers. The goal of this paper is to review the basic conceptual issues shared by all RT problems, so as to facilitate advance along the current frontier: biochemical reactions. To this end, we review the basic equations to point that chemical systems are controlled by the set of equilibrium reactions, which are easy to model, but whose rate is controlled by mixing. Since mixing is not properly represented by the standard advection-dispersion equation (ADE), we conclude that this equation is poor for RT. This leads us to review alternative transport formulations, and the methods to solve RT problems using both the ADE and alternative equations. Since equilibrium is easy, difficulties arise for kinetic reactions, which is especially true for biochemistry, where numerous frontiers are open (how to represent microbial communities, impact of genomics, effect of biofilms on flow and transport, etc.). We conclude with the basic 10 issues that we consider fundamental for any conceptually sound RT effort.

Rh-Catalyzed Reductive Amination of Undecanal in an Aqueous Microemulsion System Using a Non-Ionic Surfactant

The homogeneously catalyzed reductive amination of the long-chain aldehyde undecanal with diethylamine was performed in an aqueous microemulsion system using the non-ionic surfactant Marlophen NP8. The experiments showed that the used water-soluble rhodium/SulfoXantphos catalyst system is suitable for this reaction. The Rh-catalyzed formation of the alcohol by-product can be completely suppressed by the use of carbon monoxide with its stabilizing effect of the catalyst system. In addition to pressure and temperature, the most important parameters for the reaction performance of the reductive amination are the concentrations of reactants. Especially, the initial concentration of the aldehyde has a strong impact on the chemoselectivity, and the formation of aldol by-product due to the fact that both, the enamine condensation and the aldol condensation are equilibrium reactions.

GeoChemFoam: Direct Modelling of Multiphase Reactive Transport in Real Pore Geometries with Equilibrium Reactions

GeoChemFoam is an open-source OpenFOAM-based toolbox that includes a range of additional packages that solve various flow processes from multiphase transport with interface transfer, to single-phase flow in multiscale porous media, to reactive transport with mineral dissolution. In this paper, we present a novel multiphase reactive transport solver for simulations on complex pore geometries, including microfluidic devices and micro-CT images, and its implementation in GeoChemFoam. The geochemical model includes bulk and surface equilibrium reactions. Multiphase flow is solved using the Volume-Of-Fluid method, and the transport of species is solved using the continuous species transfer method. The reactive transport equations are solved using a sequential operator splitting method, with the transport step solved using GeoChemFoam, and the reaction step solved using Phreeqc, the US geological survey’s geochemical software. The model and its implementation are validated by comparison with analytical solutions in 1D and 2D geometries. We then simulate multiphase reactive transport in two test pore geometries: a 3D pore cavity and a 3D micro-CT image of Bentheimer sandstone. In each case, we show the pore-scale simulation results can be used to develop upscaled models that are significantly more accurate than standard macro-scale equilibrium models.

Correlation Between Reduced Mass and Gibbs Energy Change of Reaction

<p>The correlation between the Gibbs free energy change of reaction and the reduced mass was clarified. In the case of bond formation reactions, the computed Gibbs energy change of reaction increased in the positive direction as the reduced mass increased. In the case of dissociation equilibrium reactions, such as the dissociation of tetrahedral carbonyl addition compound, the computed Gibbs energy change of reaction also increased in the positive direction as the reducing mass increased, but the extent of the change was smaller than in the case of bond formation reactions. The results were in good agreement with those derived from the relationship between yield and reduced mass, indicating that was originated from the correlation between the Gibbs energy change and the reduced mass.</p>

Correlation Between Reduced Mass and Gibbs Energy Change of Reaction

<p>The correlation between the Gibbs free energy change of reaction and the reduced mass was clarified. In the case of bond formation reactions, the computed Gibbs energy change of reaction increased in the positive direction as the reduced mass increased. In the case of dissociation equilibrium reactions, such as the dissociation of tetrahedral carbonyl addition compound, the computed Gibbs energy change of reaction also increased in the positive direction as the reducing mass increased, but the extent of the change was smaller than in the case of bond formation reactions. The results were in good agreement with those derived from the relationship between yield and reduced mass, indicating that was originated from the correlation between the Gibbs energy change and the reduced mass.</p>

Thermodynamic constraints on the diversity of microbial ecosystems

Most biological processes are driven by non-equilibrium thermodynamics, but despite significant progress in theoretical ecology the constraints this places on ecosystem dynamics has been barely considered. Microbial ecosystems represent a natural place to begin this consideration, as many of the ways they interact, such as metabolite production and cross-feeding, can be described in thermodynamic terms. Previous work considered the impact of thermodynamics such as the rate-yield trade-off on individual species' competitive ability, but restrained from analyzing complex dynamical systems. To address this gap we developed a thermodynamic microbial consumer-resource model with fully reversible reaction kinetics, which allows direct consideration of free-energy dissipation. Using this model, we show that ecosystem diversity increases with supplied free energy, because greater availability of free energy allows for faster ecosystem development. Thus, when species from the initial community begin to go extinct more possible niches have been formed, facilitating increased diversity. Our model also shows that the inclusion of species utilising near-to-equilibrium reactions increases diversity under conditions of low free-energy supply. At low free energy supply thermodynamic interaction types reach comparable strength to the conventional (competition and facilitation) interactions yielding a more nuanced classification of interactions, and emphasising the key role thermodynamics plays in the dynamics. Though our model is valid for all microbial ecosystems where diversification from an initial substrate occurs it is of particular use when the initial substrate is recalcitrant (low-free energy).

Modeling of the BOF Tapping Process: The Reactions in the Ladle

A tapping process model of the steel from the basic oxygen furnace (BOF) addressing the reactions in the ladle is proposed. In the model, the effective equilibrium reaction zone (EERZ) method is applied to describe the steel/slag interfacial reaction. The equilibrium reactions in the bulk steel (steel/inclusion/lining wear) and slag (liquid slag/slag additions/lining wear) are considered. The thermodynamic library—ChemApp is used to perform thermodynamic calculation. The process model includes most of the actions during the tapping process, such as the additions of ferroalloys and slag formers, carryover slag entrapment and air pick-up. After the calibration by the industrial measurements of two plants, the model is applied to study the influence of the amount of carryover slag.

Production cross-section calculations of 111In via proton and alpha-induced nuclear reactions

[Formula: see text], a known gamma emitter, is used for many medical purposes such as imaging of myocardial metastases. It can be produced by using different nuclear reactions. In this study, the reactions of [Formula: see text]Ag([Formula: see text]2n)[Formula: see text], [Formula: see text](p,[Formula: see text]n)[Formula: see text], [Formula: see text](p,[Formula: see text]2n)[Formula: see text], [Formula: see text](p,[Formula: see text]3n)[Formula: see text] and [Formula: see text](p,[Formula: see text]4n)[Formula: see text], which are the production routes of [Formula: see text], were investigated. Production cross-section calculations were performed by using equilibrium and pre-equilibrium models of TALYS 1.95 and EMPIRE 3.2 nuclear reaction codes. Hauser–Feshbach Model was appointed in both codes for calculations of equilibrium approximations. Exciton and Hybrid Monte Carlo Simulation (HMS) models were used in the EMPIRE 3.2, whereas Two-Component Exciton and Geometry Dependent Hybrid Model, which is implemented to TALYS code, has been used in the TALYS 1.95 for pre-equilibrium reactions. Also, a weighting matrix of the nuclear models was obtained by using statistical variance analysis. The optimum beam energy to obtain [Formula: see text] has been determined by using the results obtained from this weighting matrix.

Efficient Construction of the Hexacyclic Ring Core of Palau’amine: The pKa Concept for Proceeding with Unfavorable Equilibrium Reactions

Palau’amine has received a great deal of attention as an attractive synthetic target due to its intriguing molecular architecture and significant immunosuppressive activity, and we achieved its total synthesis in...

Squeezing out the Catalysts: The Disulphide Bond Exchange in Aryl Disulphides at High Hydrostatic Pressure

Exchange of the disulphide bond is a prominent example of equilibrium reactions. Therefore, the wide library of disulphide exchange reactions requires the application of catalysts, such as reducing agents, strong bases, ultraviolet light, or ultrasounds to stimulate higher conversion yields. We employed the pressure between 100 and 400 MPa, for promoting the exchange reactions between various homodimeric aryl disulphides and for optimized conditions obtained 100 % yields and pure single-crystal form of the heterodimer. The reactions were performed in a diamond-anvil cell, as well as in a hydraulic piston-and-cylinder press, and the products were characterized by X-ray diffraction, mass and NMR spectroscopy. <br>