Volume 89, Issue 5

Numerical simulations were carried out for determining the chemical reactions relevant for the sequestration of CO 2 in basaltic rock formations. The mineralogy of natural geological systems consists of silicate minerals such as the phyllosilicates and zeolites that form complex solid solutions. Using the GEMS code package based on Gibbs energy minimization, combined with the new MINES database, we can now simulate the solubility of these multicomponent and multisite mineral solid solutions in basaltic rocks. This study explores the varying effects of CO 2 partial pressures, basaltic glass dissolution kinetics and reaction time on the complex chemistry of the overall CO 2 -water-basalt reaction path. The simulations indicate four reaction progress stages with the competing reactions between smectites (di- and trioctahedral) and Ca-Fe-Mg-carbonates controlling the amount of CO 2 mineralized. A better understanding of these key mineral-fluid reactions and improvement of their thermodynamic models is critical for making more acurate predictive calculations. This comprises the basis for extending the simulations to reactive transport models, and for the assessment of the feasibility of long-term CO 2 storage in basaltic rock formations.

We present an overview of novel numerical methods for chemical equilibrium and kinetic calculations for complex non-ideal multiphase systems. The methods we present for equilibrium calculations are based either on Gibbs energy minimization (GEM) calculations or on solving the system of extended law of mass-action (xLMA) equations. In both methods, no a posteriori phase stability tests, and thus no tentative addition or removal of phases during or at the end of the calculations, are necessary. All potentially stable phases are considered from the beginning of the calculation, and stability indices are immediately available at the end of the computation to determine which phases are actually stable at equilibrium. Both GEM and xLMA equilibrium methods are tailored for computationally demanding applications that require many rapid local equilibrium calculations, such as reactive transport modeling. The numerical method for chemical kinetic calculations we present supports both closed and open systems, and it considers a partial equilibrium simplification for fast reactions. The method employs an implicit integration scheme that improves stability and speed when solving the often stiff differential equations in kinetic calculations. As such, it requires compositional derivatives of the reaction rates to assemble the Jacobian matrix of the resultant implicit algebraic equations that are solved at every time step. We present a detailed procedure to calculate these derivatives, and we show how the partial equilibrium assumption affects their computation. These numerical methods have been implemented in Reaktoro (reaktoro.org), an open-source software for modeling chemically reactive systems. We finish with a discussion on the comparison of these methods with others in the literature.

Intracellular inclusions of amorphous Ba- and Sr-rich calcium carbonates – referred to as “micropearls”– have recently been detected in Lake Geneva. These micropearls are formed under conditions of pronounced Ba and Sr undersaturation in the lake waters. Their formation can be explained by the ability of certain microorganisms to preconcentrate these trace elements in tandem with a non-equilibrium solid-solution growing mechanism.

Procedures are proposed for the naming of individual atoms, P, O, F, N, and S in phosphate esters, amidates, thiophosphates, polyphosphates, their mimics, and analogues of transition states for enzyme-catalyzed phosphoryl transfer reactions. Their purpose is to enable scientists in very different fields, e.g. biochemistry, biophysics, chemistry, computational chemistry, crystallography, and molecular biology, to share standard protocols for the labelling of individual atoms in complex molecules. This will facilitate clear and unambiguous descriptions of structural results, as well as scientific intercommunication concerning them. At the present time, perusal of the Protein Data Bank (PDB) and other sources shows that there is a limited degree of commonality in nomenclature, but a large measure of irregularity in more complex structures. The recommendations described here adhere to established practice as closely as possible, in particular to IUPAC and IUBMB recommendations and to “best practice” in the PDB, especially to its atom labelling of amino acids, and particularly to Cahn-Ingold-Prelog rules for stereochemical nomenclature. They are designed to work in complex enzyme sites for binding phosphates but also to have utility for non-enzymatic systems. Above all, the recommendations are designed to be easy to comprehend and user-friendly.