Obtuse Steps Research Articles

Microbial-mineral interaction experiments and density functional theory calculations revealing accelerating effects for the dolomitization of calcite surfaces by organic components

Carbonates represent major sedimentary rocks in on the continental and oceanic crust of Earth and are often closely related to microbial activities. However, the origin of magnesium-containing carbonates, such as dolomites, has not yet been fully resolved and was debated for many years. In order to reveal the specific role of organic components and microbes on the precipitation of magnesium ions, different dolomitization experiments were carried out with various setups for the presence of eight amino acids and microbes. The Gibbs free energy for dehydration of Mg[6(H2O)]2+ and organic‑magnesium complexes (OMC) at the calcite (101¯4) step edges were calculated by density functional theory (DFT). Combined results of X-ray diffraction (XRD), scanning electron microscope-energy disperse spectroscopy (SEM-EDS), transmission electron microscope (TEM), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR) and high resolution transmission electron microscopy (HRTEM) indicated that magnesium ions were incorporated into the crystal lattice of calcite after calcite reacting with organic‑magnesium solutions (OMS). Dolomite was formed on the surface of calcite under the presence of microbes. The Gibbs free energy barrier of asp, glu, gly, thr, tyr, lys, ser, and ala bonding to Mg[6(H2O)]2+ were 17.8, 16.2, 14.8, 16.5, 19.2, 14.5, 19.0, 17.0 kcal/mol, those are lower than that of the direct dehydration of Mg[6(H2O)]2+ of 19.45 kcal/mol. The Gibbs free barrier of OMC bonding at the acute step ([481¯] and [4¯41]) of 29.7/34.25 kcal/mol are lower than that of Mg[6(H2O)]2+ of 32.45/36.7 kcal/mol and the Gibbs free barrier of OMC bonding at the obtuse step ([481¯] and [4¯41]) of 42.07/47.6 kcal/mol are lower than that of Mg[6(H2O)]2+ of 55.4/60.34 kcal/mol. The enhancing effects of organic components and microbes on the precipitation of magnesium ions were collectively determined through experimental and theoretical calculation, thus setting up a new direction for future studies of dolomitization with a focus on microbial- mineral interactions.

Atomic-scale structures and dynamics at the growing calcite step edge investigated by high-speed frequency modulation atomic force microscopy.

We have investigated the calcite growth mechanism by directly imaging atomic-scale structural changes at the growing step edges with high-speed frequency modulation atomic force microscopy (HS-FM-AFM). We compared the results with those previously obtained during dissolution, where a transition region (TR) consisting of a Ca(OH)2 monolayer was found to be formed along the step edges as an intermediate state. We found that the TR is created not only during dissolution but also during the growth process. Steps with and without a TR coexist with a ratio of 7 : 3 in both dissolution and growth, implying that their primary reaction pathways should involve TR formation. While all the dissolving steps show a linear shape, the growing steps additionally present a complex non-linear shape with many kinks. The TRs formed along the linear steps present a fixed and uniform width, while those along the complex steps present a non-uniform and dynamically varying width. The acute and obtuse steps show similar TR formation probability, TR width, and step velocity during growth, while a TR is preferentially formed along an acute step during dissolution. For both step types, TRs during growth are wider than those during dissolution. Based on these findings, we present possible reaction pathways triggered by the adsorption of either CO2 or HCO3- for the elementary steps in calcite growth.

Pb2+ Uptake by Magnesite: The Competition between Thermodynamic Driving Force and Reaction Kinetics

The thermodynamic properties of carbonate minerals suggest a possibility for the use of the abundant materials (e.g., magnesite) for removing harmful divalent heavy metals (e.g., Pb2+). Despite the favourable thermodynamic condition for such transformation, batch experiments performed in this work indicate that the kinetic of the magnesite dissolution at room temperature is very slow. Another set of co-precipitation experiments from homogenous solution in the Mg-PbII-CO2-H2O system reveal that the solids formed can be grouped into two categories depending on the Pb/Mg ratio. The atomic ratio Pb/Mg is about 1 and 10 in the Mg-rich and Pb-rich phases, respectively. Both phases show a significant enrichment in Pb if compared with the initial stoichiometry of the aqueous solutions (Pb/Mg initial = 1 × 10 − 2–1 × 10−4). Finally, the growth of {10.4} magnesite surfaces in the absence and in the presence of Pb2+ was studied by in situ atomic force microscopy (AFM) measurements. In the presence of the foreign ion, a ten-fold increase in the spreading rate of the obtuse steps was observed. Further, the effect of solution ageing was also tested. We observed the nucleation of a secondary phase that quickly grows on the {10.4} surfaces of magnesite. The preferential incorporation of Pb2+ into the solid phase observed during precipitation and the catalytic effect of Pb2+ on magnesite growth are promising results for the development of environmental remediation processes. These processes, different from the transformation of magnesite into cerussite, are not limited by the slow dissolution rate of magnesite. Precipitation and growth require an external carbon source, thus they could be combined with carbon sequestration techniques.

Specific Ion Effects at Calcite Surface Defects Impact Nanomaterial Adhesion

Motivated by applications in subsurface hydrocarbon reservoirs such as colloidal instability and nanomaterial adhesion to mineral surfaces, we report atomistic molecular dynamics simulations to study the adhesion of carboxylate functionalized atomic force microscopy (AFM) tips (as surrogates of nanomaterials) on calcite surface line and point defects in deionized water, seawater, and brine. The line defects include acute and obtuse steps, and the point defects include Ca2+ and CO32– vacancies. The accumulations of specific ions on both functionalized AFM tips and calcite surface defects result in reduced adhesion. The specific ions in fluids played the dominant roles to modulate adhesion, yet the surface defects also had distinct characteristics. We believe the molecular insights put forward in this work may have important implications for stabilizing nanomaterials in harsh subsurface oil and gas reservoirs. In addition, the differential affinities of the calcite surface defects with the presence of specific ions observed in this work may further the understanding of the wettability alteration mechanism of calcium carbonates in high salinity geologic settings. To the best of our knowledge, this is the first study showing the interaction of nanomaterials on different calcite surface defects, mediated by specific ions.

Skin-Deep Surface Patterning of Calcite

The influence of soluble additives on the growth of calcite (CaCO3) is usually rationalized based on changes in crystal morphologies, where preferential association of the additives with either the acute or obtuse steps on the crystal surface gives rise to specific growth forms. In this work we investigate the influence of a highly acidic organic additive with calcite, cp20k from the barnacle Megabalanus rosa, and demonstrate that in addition to modifying the crystal morphology, additives can be used to generate calcite crystals with different surface architectures. These can potentially rise to interesting optical effects that may be important in applications such as in coatings and paints. These surface features form during dissolution/reprecipitation at the crystal surface during the incubation of crystals in solution, and confocal fluorescence microscopy confirmed they are limited to the surface of the crystal only. The surface patterning can also be tuned using alternative additives, mixtures of additives and by varying the solution conditions. Notably, we also show that surface structures can be used to determine the mode of interaction of additives with the microscopic surface steps under conditions where only minor changes in morphology have occurred. Introduction.

Variations in Atomic-Scale Step Edge Structures and Dynamics of Dissolving Calcite in Water Revealed by High-Speed Frequency Modulation Atomic Force Microscopy

Calcite dissolution plays critical roles in the global carbon cycle in the Earth, biomineralizations, and weathering of buildings. However, in spite of the importance, the atomistic events at the step edges during the dissolution have remained elusive because of the difficulties in their direct visualization. In this study, we used high-speed frequency modulation atomic force microscopy (FM-AFM) for visualizing various atomic-scale step edge structures and dynamics during the calcite dissolution in water. The obtained images reveal the coexistence of the steps with and without a transition region (TR); a Ca(OH)2 monolayer formed along the step edge as an intermediate state in the dissolution. The TRs are more frequently observed along the slowly dissolving acute steps than along the rapidly dissolving obtuse steps. This finding and our imaging of the TR formation process suggest that the free energy to form a TR is comparable to that for removing ions directly from the step edge and an increase in the loc...

Uncovering the Atomistic Mechanism for Calcite Step Growth.

Determining a complete atomic-level picture of how minerals grow from aqueous solution remains a challenge as macroscopic rates can be a convolution of many reactions. For the case of calcite (CaCO3 ) in water, computer simulations have been used to map the complex thermodynamic landscape leading to growth of the two distinct steps, acute and obtuse, on the basal surface. The carbonate ion is found to preferentially adsorb at the upper edge of acute steps while Ca2+ only adsorbs after CO32- . In contrast to the conventional picture, ion pairs prefer to bind at the upper edge of the step with only one ion, at most, coordinated to the step and lower terrace. Migration of the first carbonate ion to a growth site is found to be rate-limiting for kink nucleation, with this process having a lower activation energy on the obtuse step.

Uncovering the Atomistic Mechanism for Calcite Step Growth

AbstractDetermining a complete atomic‐level picture of how minerals grow from aqueous solution remains a challenge as macroscopic rates can be a convolution of many reactions. For the case of calcite (CaCO3) in water, computer simulations have been used to map the complex thermodynamic landscape leading to growth of the two distinct steps, acute and obtuse, on the basal surface. The carbonate ion is found to preferentially adsorb at the upper edge of acute steps while Ca2+ only adsorbs after CO32−. In contrast to the conventional picture, ion pairs prefer to bind at the upper edge of the step with only one ion, at most, coordinated to the step and lower terrace. Migration of the first carbonate ion to a growth site is found to be rate‐limiting for kink nucleation, with this process having a lower activation energy on the obtuse step.

Structure and Dynamics of Water at Step Edges on the Calcite {101̅4} Surface

The behavior of liquid water around obtuse and acute steps parallel to ⟨441⟩ on the {1014} cleavage surface of calcite has been investigated by means of classical molecular dynamics simulations performed with a force-field fitted against thermodynamic properties. Water density maps, radial distribution functions, and water average residence times have been investigated. The structure and dynamics of the first two ordered hydration layers, which have been previously observed for the basal surface of calcite, are found to be disrupted by the presence of the steps over a range of five molecular rows either side of the step edge. Calcium sites along the step top edge can coordinate up to three water molecules, as compared with just the single water that can be adsorbed per calcium ion on the flat surface. Water residence times at calcium sites in the vicinity of the step span greater than 2 orders of magnitude, from tenths to several tens of ns, as compared to 2 and 0.2 ns for the flat surface and a calcium...

Calcite Growth Kinetics: Dependence on Saturation Index, Ca2+:CO32–Activity Ratio, and Surface Atomic Structure

It is becoming increasingly clear that the rate of crystal growth, even at constant saturation, varies with pH, ionic strength, and solution stoichiometry. Here, we contribute to the limited data set on experimentally obtained calcite step velocities from solutions with strictly controlled parameters. We measured growth on obtuse and acute edges in solutions with five Ca2+:CO32– activity ratios (r): 0.1, 1.0, 10, 25, and 50, at three saturation indices: SI = 0.6, 0.8, and 1.0. The curve describing rate as a function of r is not centered at r = 1, and the maximum velocity is different for each step. Obtuse steps generally grow faster in Ca2+-rich solutions, i.e., r > 1, whereas the acute rates dominate when CO32– is in excess, i.e., r < 1. We show that the local arrangement of every second carbonate at the acute steps can help explain these rate differences. To further analyze the differences in growth rates, we fitted four currently used growth models to our data set, to derive growth parameters for each ...

Hydrothermal atomic force microscopy observations of barite step growth rates as a function of the aqueous barium-to-sulfate ratio

The rate of growth of ionic minerals from solutions with varying aqueous cation:anion ratios may result in significant errors in mineralization rates predicted by commonly-used affinity-based rate equations. To assess the potential influence of solute stoichiometry on barite growth, step velocities on the barite (001) surface have been measured at 108°C using hydrothermal atomic force microscopy (HAFM) at moderate supersaturation and as a function of the aqueous barium:sulfate ratio (r). Barite growth hillocks at r∼1 were bounded by 〈120〉 steps, however at r<1, kink site densities increased, steps followed a direction vicinal to 〈120〉, and the [010] steps developed. At r>1, steps roughened and rounded as the kink site density increased. Step velocities peaked at r=1 and decreased roughly symmetrically as a function of r, indicating the attachment rates of barium and sulfate ions are similar under these conditions. We hypothesize that the differences in our observations at high and low r arise from differences in the attachment rate constants for the obtuse and acute 〈120〉 steps. Based on results at low r, the data suggests the attachment rate constant for barium ions is similar for obtuse and acute steps. Based on results at high r, the data suggests the attachment rate constant for sulfate is greater for obtuse steps than acute steps. Utilizing a step growth model developed by Stack and Grantham (2010) the experimental step velocities as a function of r were readily fit while attempts to fit the data using a model developed by Zhang and Nancollas (1998) were less successful.

On the effect of aqueous Ca on magnesite growth – Insight into trace element inhibition of carbonate mineral precipitation

Motivated by the strong effect of aqueous Mg on calcite growth rates, this study used hydrothermal atomic force microscopy (HAFM) and hydrothermal mixed-flow reactor (HMFR) experiments to explore the effect of aqueous Ca on magnesite growth kinetics at 100°C and pH ∼7.7. Obtuse step velocities on (104) surfaces during magnesite growth were measured to be 4±3nm/s at fluid saturation states, equal to the ion activity quotient divided by the equilibrium constant for the magnesite hydrolysis reaction, of 86–117. These rates do not vary systematically with aqueous Ca concentration up to 3×10−3mol/kg. Magnesite growth rates determined by HAFM are found to be negligibly affected by the presence of aqueous Ca at these saturation states and are largely consistent with those previously reported in aqueous Ca-free systems by Saldi et al. (2009) and Gautier et al. (2015). Similarly, magnesite growth rates measured by HMFR exhibit no systematic variation on aqueous Ca concentrations. Rates in this study, however, were extended to higher degrees of fluid supersaturation with respect to magnesite than previous studies. All measured HMFR rates can be accurately described taking account the combined effects of both the spiral growth and two dimensional nucleation/growth mechanisms. Despite the lack of a clear effect of aqueous Ca on magnesite growth rates, Raman spectroscopy confirmed the incorporation of up to 8mol percent of Ca2+ into the growing magnesite structure.

Is bicarbonate stable in and on the calcite surface?

We have used density functional theory with the COSMO-RS implicit solvent model to predict the pKa for the deprotonation of bicarbonate to carbonate, i.e. HCO3−<=>CO32−+H+, when HCO3− is included in, and adsorbed on, a calcite surface. We have used cluster models (80–100 atoms) to represent the flat {10.4} surface, acute steps, obtuse steps, two types of kinks on the acute step and two types of kinks on the obtuse steps. Based on the predicted pKa values, which range from −6.0 to 2.4 depending on the surface site, we conclude that bicarbonate deprotonates to carbonate when it is in calcite even when pH in solution is very low. This is true for all surface sites, even for solutions where 2.4<pH<6.35, where H2CO30 is the dominant dissolved species. When bicarbonate is adsorbed on calcite, the predicted pKa for deprotonation is 7.5, which is ∼3 pH units lower than in aqueous solution, 10.35. This means that adsorbed carbonate is stable even when the concentration of dissolved CO32− is several orders of magnitude lower. This has a significant effect on surface charge and thus the behaviour of the calcite surface. Our results help explain the potential determining behaviour of the carbonate species in calcite–water systems, particularly in the pH range where the bicarbonate species dominates in water and where the carbonate species dominates at the surface, i.e. when 7.5<pH<10.35. Our atomic scale data for the various calcite surface sites provide the needed input to improve and constrain surface complexation modelling and are especially useful for predicting behaviour in systems where experiments are difficult or impossible, such as at high temperature and pressure.

Influence of organic ligands on magnesite growth: A hydrothermal atomic force microscopy study

In order to understand the effects of carboxylic ligands on magnesite growth at low hydrothermal conditions, the growth processes on the (104) surface have been investigated using hydrothermal atomic force microscopy (HAFM). Experiments were performed with various concentrations of oxalate, citrate and EDTA at T=100°C and a pH value of about 8.We show that the ligands influence magnesite growth in different manners. At concentrations of 1–10mM, citrate and oxalate both exert a significant, but different, effect on the morphology of growth islands, while EDTA has little influence. The shape modifications can be understood as a consequence of modified kink-reactivities due to ligand adsorption at particular kink-sites at the island steps, depending on the ligand conformation and chemical functionalities. However, none of the three investigated ligands significantly modifies obtuse steps velocities. On acute step velocity, HAFM resolution was unfortunately too low for a precise quantification of their influence.Bulk crystal growth rates calculated from step generation frequencies through spiral growth are in good agreement with precipitation rates retrieved from mixed-flow reactor experiments and confirm that citrate significantly inhibits magnesite growth at concentrations higher than 1mM. Based on these new surface scale observations, we propose that observed growth inhibition stems from a decreased rotation frequency of growth spirals, which may originate either from a decrease of the acute step velocity or from an increase of the critical step length. EDTA appears to have a negligible influence on magnesite growth kinetics at the investigated conditions. This may be due to the fact that in solution it is mostly present in form of the MgEDTA2− aqueous complex, which has a low surface adsorption constant and therefore interacts little with the magnesite surface. Finally, an effect of oxalate on bulk growth rates could not be detected at the chosen conditions.

Importance of water in the control of calcite crystal growth by organic molecules

The binding conformation of aspartic acid (Asp) at the calcite surface is strongly affected by the structure of the surrounding water. On the {104} plane, Asp binds directly to the acute step edge, but not to the obtuse step edge, reflecting a difference in the structure of water near the step edge. This selective binding to the acute step edge causes a change in the step morphology on the {104} plane when Asp is added to real systems.

Implications of solution chemistry effects: Direction-specific restraints on the step kinetics of calcite growth

Classical crystallization models successfully depict the dependence of growth kinetics on thermodynamic driving force but cannot predict the roles of solution chemistry. Yet, it has become increasingly clear that crystal growth rate at fixed supersaturations depends on pH, ionic strength, and the relative abundance of cations and anions in the parent solutions. We conducted experiments to isolate the effect of individual solution-chemistry parameters on calcite step growth kinetics. Our results revealed a distinct correlation between step velocity and pH in acute and obtuse directions and a simultaneous trend change at pH ∼9.5. Step speeds varied with solution stoichiometry, and each direction reached its maximal rate at a different [Ca2+]/[CO32-] value. In addition, the solution cation/anion at which maximal step speed occurred appeared to be pH dependent as well. Limited effect of ionic strength on step growth was observed in the obtuse direction at low background electrolyte concentrations, but no obvious change was found for growth at the acute side. We proposed a growth model based upon independent incorporation of cations and anions and interpreted these observations as: (1) solute constituents enter kinks through direct solution diffusion at obtuse steps but surface diffusion at acute steps; (2) growth is limited by Ca2+ dehydration at the obtuse side, but by surface adsorption and reorientation and rearrangement of CO32− in the acute direction; and (3) background electrolyte (NaCl in our study) competes with solutes for surface sites at more easily accessible kinks.

Difference in the Conformation and Dynamics of Aspartic Acid on the Flat Regions, Step Edges, and Kinks of a Calcite Surface: A Molecular Dynamics Study

Molecular dynamics simulations were conducted to investigate the conformation and dynamics of an aspartic acid molecule near the {104} and {110} planes of a CaCO3 calcite crystal, near the acute and obtuse [114] step edges on the {104} plane, and near kinks formed at the step edges. The simulations indicate that the amino acid binds indirectly to the {104} plane, whereas it binds directly to the {110} plane. The simulations also indicate that the acid binds directly to the acute step edge but does not bind to the obtuse step edge. These differences in the binding of the acid to the planes and the step edges were attributed to a difference in the structure of the surrounding water. The simulations also indicate that the acid binds to the kink formed at both the acute and the obtuse step edges, if a Ca2+ ion is placed at the corner of the kink. The binding was much stronger at the kink than at the planes and the step edges.

Hydromagnesite solubility product and growth kinetics in aqueous solution from 25 to 75 °C

Hydromagnesite Mg5(CO3)4(OH)2·4H2O is the most widespread form of hydrated Mg-carbonate minerals. To better understand the factors controlling the precipitation of hydrated Mg-carbonates, we measured hydromagnesite solubility product at 25 and 50°C and its growth rate between 25 and 75°C, using natural hydromagnesite from a cave as seed material.The solubility products values derived in this study, Ksp–Hmgs=−37.08±0.50 and −38.90±0.54 at 25 and 50°C, respectively, are in the upper range of published values. Hydromagnesite growth rate normalized to the BET surface area at 8⩽pH⩽10 is consistent with the direct and reversible attachment of the reactants at the solid surface being rate-limiting. It may be described by:RHmgs=A0·e-Ea/RT(ΩHmgs1/5-1)where A0, the pre-exponential factor, and Ea, the activation energy, are equal to 5.12×10−7mol/cm2/s and 45.5±9kJ/mol, respectively, and ΩHmgs stands for the saturation state of the solution with respect to hydromagnesite. Comparison of hydromagnesite growth rates with recently published magnesite growth rates (Saldi et al., 2009, 2012) show that: (1) hydromagnesite apparent growth activation energy is lower by more than 100kJ/mol compared to the activation energy for magnesite obtuse step advancement, and (2) hydromagnesite growth rate constant extrapolated to 90°C is 2.5 orders of magnitude higher than corresponding magnesite growth rate constant. Thus, our results confirm the long-standing hypothesis that the slow dehydration kinetics of the Mg2+ cation is responsible for the sluggish magnesite formation at low temperature, and that the kinetic barrier for hydromagnesite growth is much lower. Nevertheless, simulation of hydromagnesite and magnesite growth rates as a function of solution composition at 50 and 90°C, and pH 7 and 9 reveal that, because of its much higher solubility, hydromagnesite would grow more quickly than magnesite in natural or industrial environments only at 50°C and pH 9. This is consistent with the formation of hydromagnesite during the surface alteration of ultramafic rocks.

Upscaling Calcite Growth Rates from the Mesoscale to the Macroscale

Quantitative prediction of mineral reaction rates in the subsurface remains a daunting task partly because a key parameter for macroscopic models, the reactive site density, is poorly constrained. Here we report atomic force microscopy (AFM) measurements on the {1014} calcite surface of monomolecular step densities, treated as equivalent to the reactive site density, as a function of aqueous calcium-to-carbonate ratio and saturation index. Data for the obtuse step orientation are combined with existing step velocity measurements to generate a model that predicts overall macroscopic calcite growth rates. The model is quantitatively consistent with several published macroscopic rates under a range of alkaline solution conditions, particularly for two of the most comprehensive data sets, without the need for additional fit parameters. The model reproduces peak growth rates, and its functional form is simple enough to be incorporated into reactive transport or other macroscopic models designed for predictions in porous media. However, it currently cannot model equilibrium or pH effects and it may overestimate rates at high aqueous calcium-to-carbonate ratios. The discrepancies in rates at high calcium-to-carbonate ratios may be due to differences in pretreatment, such as exposing the seed material to SI ≥ 1.0 to generate/develop growth hillocks, or other factors.

How acidic is water on calcite?

We have used density functional theory in combination with the COSMO-RS implicit solvent model to calculate the pKa for water adsorbed on various sites on a calcite surface. The mineral surfaces were modeled using 80 atom clusters. We found that, on kink sites, water is acidic with pKa as low as 3.5, implying that, at equilibrium, the kink sites are associated with one hydroxyl ion in addition to water. We also calculated pKa for ethanol and phenol adsorbed on calcite and compared the free energies of adsorption for ethanol and water. Ethanol was found to bind more strongly on the {10.4} terrace and on the obtuse step, whereas on kink sites, water (in the form of hydroxyl ions) binds more strongly than ethanol (in the form of ethoxide). Our results are relevant for modeling the dissolution and precipitation of minerals and show how the OH functional group behaves in the interaction between organic molecules and mineral surfaces.