The Onset of Calcium Carbonate Nucleation: A Density Functional Theory Molecular Dynamics and Hybrid Microsolvation/Continuum Study

Ion association behaviors in the initial stage of calcium carbonate formation: An ab initio study

In this work, we performed static density functional theory calculations and ab initio metadynamics simulations to systematically investigate the association mechanisms and dynamic structures of four kinds of ion pairs that could be formed before the nucleation of CaCO3. For Ca2+-HCO3- and Ca2+-CO32- pairs, the arrangement of ligands around Ca2+ evolves between the six-coordinated octahedral structure and the seven-coordinated pentagonal bipyramidal structure. The formation of ion pairs follows an associative ligand substitution mechanism. Compared with HCO3-, CO32- exhibits a stronger affinity to Ca2+, leading to the formation of a more stable precursor phase in the prenucleation stage, which promotes the subsequent CaCO3 nucleation. In alkaline environments, excessive OH- ions decrease the coordination preference of Ca2+. In this case, the formation of Ca(OH)+-CO32- and Ca(OH)2-CO32- pairs favors the dissociative ligand substitution mechanism. The inhibiting effects of OH- ion on the CaCO3 association can be interpreted from two aspects, i.e., (1) OH- neutralizes positive charges on Ca2+, decreases the electrostatic interactions between Ca2+ and CO32-, and thus hinders the formation of the CaCO3 monomer, and (2) OH- decreases the capacity of Ca2+ for accommodating O, making it easier to separate Ca2+ and CO32- ions. Our findings on the ion association behaviors in the initial stage of CaCO3 formation not only help scientists evaluate the impact of ocean acidification on biomineralization but also provide theoretical support for the discovery and development of more effective approaches to manage undesirable scaling issues.

Precision Covalent Organic Frameworks for Surface Nucleation Control

Unwanted accumulation of ice and lime scale crystals on surfaces is a long-standing challenge with major economic and sustainability implications. Passive inhibition of icing and scaling by liquid-repellent surfaces are often inadequate, susceptible to surface failure under harsh conditions, and unsuitable for long-term/real-life usages. Such surfaces often require a multiplicity of additional features such as optical transparency, robust impact resistance, and ability to prevent contamination from low surface energy liquids. Unfortunately, most promising advances have relied on using perfluoro compounds, which are bio-persistent and/or highly toxic. Here it is shown that organic, reticular mesoporous structures, covalent organic frameworks (COFs), may offer a solution. By exploiting simple and scalable synthesis of defect-free COFs and rational post-synthetic functionalization, nanocoatings with precision nanoporosity (morphology) are prepared that can inhibit nucleation at the molecular level without compromising the related contamination prevention and robustness. The results offer a simple strategy to exploit the nanoconfinement effect, which remarkably delays the nucleation of ice and scale formation on surfaces. Ice nucleation is suppressed down to -28 °C, scale formation is avoided for >2 weeks in supersaturated conditions, and jets of organic solvents impacting at Weber numbers >105 are resisted with surfaces that also offer optical transparency (>92%).

CO2-mineralization and carbonation reactor rig: Design and validation for in situ neutron scattering experiments-Engineering and lessons learned

CO2 mineralization via aqueous Mg/Ca/Na-carbonate (MgCO3/CaCO3/Na2CO3) formation represents a huge opportunity for the utilization of captured CO2. However, large-scale mineralization is hindered by slow kinetics due to the highly hydrated character of the cations in aqueous solutions (Mg2+ in particular). Reaction conditions can be optimized to accelerate carbonation kinetics, for example, by the inclusion of additives that promote competitive dehydration of Mg2+ and subsequent agglomeration, nucleation, and crystallization. For tracking mineralization and these reaction steps, neutron scattering presents unprecedented advantages over traditional techniques for time-resolved in situ measurements. However, a setup providing continuous solution circulation to ensure reactant system homogeneity for industrially relevant CO2-mineralization is currently not available for use on neutron beamlines. We, therefore, undertook the design, construction, testing and implementation of such a self-contained reactor rig for use on selected neutron beamlines at the ISIS Neutron and Muon Source (Harwell, UK). The design ensured robust attachment via suspension from the covering Tomkinson flange to stabilize the reactor assembly and all fittings (~25 kg), as well as facilitating precise alignment of the entire reactor and sample (test) cell with respect to beam dimension and direction. The assembly successfully accomplished the principal tasks of providing a continuous flow of the reaction mixture (~500 mL) for homogeneity, quantitative control of CO2 flux into the mixture, and temperature and pressure regulation throughout the reaction and measurements. The design is discussed, with emphasis placed on the reactor, including its geometry, components, and all technical specifications. Descriptions of the off-beamline bench tests, safety, and functionality, as well as the installation on beamlines and trial experimental procedure, are provided, together with representative raw neutron scattering results.

Recalibrating the calcium trap in amino acid carboxyl groups via classical molecular dynamics simulations

In order to use classical molecular dynamics to complement experiments accurately, it is important to use robust descriptions of the system. The interactions between biomolecules, like aspartic and glutamic acid, and dissolved ions are often studied using standard biomolecular force-fields, where the interactions between biomolecules and cations are often not parameterized explicitly. In this study, we have employed metadynamics simulations to investigate different interactions of Ca with aspartic and glutamic acid and constructed the free energy profiles of Ca²⁺-carboxylate association. Starting from a generally accepted, AMBER-based force field, the association was substantially over and under-estimated, depending on the choice of water model (TIP3P and SPC/fw, respectively). To rectify this discrepancy, we have replaced the default calcium parameters. Additionally, we modified the σ_ij value in the hetero-atomic Lennard-Jones interaction by 0.5% to further improve the interaction between Ca and carboxylate, based on comparison with the experimentally determined association constant for Ca with the carboxylate group of L-aspartic acid. The corrected description retrieved the structural properties of the ion pair in agreement with the original biomolecule - Ca²⁺ interaction in AMBER, whilst also producing an association constant comparable to experimental observations. This refined force field was then used to investigate the interactions between amino acids, calcium and carbonate ions during biogenic and biomimetic calcium carbonate mineralisation.

A Database of Solution Additives Promoting Mg2+ Dehydration and the Onset of MgCO3 Nucleation

Formed via aqueous carbonation of Mg²⁺ ions, the crystallization of magnesite (MgCO₃) is a promising route to carbon capture and reuse, albeit limited by the slow precipitation of MgCO₃. Although magnesite is naturally abundant, forming at low temperature conditions, its industrial production is an energy-intensive process due to the temperatures required to prevent the formation of hydrated phases. The principal difficulty in aqueous conditions arises from the very strong Mg²⁺···H₂O interaction, with high barriers to Mg²⁺ dehydration. Using atomistic simulations, we have investigated the influence of 30 additive anions (X ^n-, n = 1-3), ranging from simple halides to more complex molecules, on the first two steps of MgCO₃ aggregation from solution, as follows: Mg²⁺ dehydration and subsequent prenucleative Mg²⁺···CO₃ ^2- pairing. We have computed the thermodynamic stabilities of solvent shared ion pairs (Mg²⁺···H₂O···X ^n-) and contact ion pairs (Mg²⁺···X ^n-) to reveal the propensity of solution additives to inhibit or promote Mg²⁺···CO₃ ^2- formation. We have determined the stabilization of undercoordinated hydrated Mg²⁺ states with a vacant coordination site to which CO₃ ^2- can bind, subsequently initiating MgCO₃ nucleation or Mg²⁺ incorporation into the crystal lattice. Extensive molecular dynamics simulations of electrolyte solutions containing Na₂CO₃ with different sources of Mg²⁺ (i.e., MgCl₂, MgSO₄, and Mg(CH₃COO)₂) further show that the degree of dehydration of Mg²⁺ and the structure of prenucleation MgCO₃ clusters change depending on the counterion identity. Through a fundamental understanding of the role of solution additives in the mechanism of Mg²⁺ dehydration, our results help to rationalize previously reported experimental observation of the effect of solvation environments on the growth of magnesite. This understanding may contribute to identifying the solution composition and conditions that could promote the low-temperature CO₂ conversion into MgCO₃ at industrially relevant scales.

Solvent-mediated isotope effects strongly influence the early stages of calcium carbonate formation: exploring D2O vs. H2O in a combined computational and experimental approach

In experimental studies, heavy water (D₂O) is employed, e.g., so as to shift the spectroscopic solvent background, but any potential effects of this solvent exchange on reaction pathways are often neglected. While the important role of light water (H₂O) during the early stages of calcium carbonate formation has been realized, studies into the actual effects of aqueous solvent exchanges are scarce. Here, we present a combined computational and experimental approach to start to fill this gap. We extended a suitable force field for molecular dynamics (MD) simulations. Experimentally, we utilised advanced titration assays and time-resolved attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. We find distinct effects in various mixtures of the two aqueous solvents, and in pure H₂O or D₂O. Disagreements between the computational results and experimental data regarding the stabilities of ion associates might be due to the unexplored role of HDO, or an unprobed complex phase behaviour of the solvent mixtures in the simulations. Altogether, however, our data suggest that calcium carbonate formation might proceed "more classically" in D₂O. Also, there are indications for the formation of new structures in amorphous and crystalline calcium carbonates. There is huge potential towards further improving the understanding of mineralization mechanisms by studying solvent-mediated isotope effects, also beyond calcium carbonate. Last, it must be appreciated that H₂O and D₂O have significant, distinct effects on mineralization mechanisms, and that care has to be taken when experimental data from D₂O studies are used, e.g., for the development of H₂O-based computer models.

Development and application of ReaxFF methodology for understanding the chemical dynamics of metal carbonates in aqueous solutions

A new ReaxFF reactive force field has been developed for metal carbonate systems including Na⁺, Ca²⁺, and Mg²⁺ cations and the CO₃^2- anion. This force field is fully transferable with previous ReaxFF water and water/electrolyte descriptions. The Me-O-C (Me = metal) three-body valence angle parameters and Me-C non-reactive parameters of the force field have been optimized against quantum mechanical calculations including equations of state, heats of formation, heats of reaction, angle distortions and vibrational frequencies. The new metal carbonate force field has been validated using molecular dynamics simulations to study the solvation and reactivity of metal and carbonate ions in water at 300 K and 700 K. The coordination radius and self-diffusion coefficient show good consistency with existing experimental and simulation results. The angular distribution analysis explains the structural preference of carbonate ions to form carbonates and bicarbonates, where Na⁺ predominantly forms carbonates due to weaker angular strain, while Ca²⁺ and Mg²⁺ prefer to form bicarbonate monodentate in nature. Residence time distribution analyses on different systems reveal the role of ions in accelerating and decelerating the dynamics of water and carbonate ions under different thermodynamic conditions. The formation and dissolution of bicarbonates and carbonates in solution were explored on the basis of the protonation capability in different systems. The nucleation phenomenon of metal carbonates at ambient and supercritical conditions is explained from the perspective of cluster formation over time: Ca²⁺ ions can form prenucleation clusters at ambient temperature but show saturation with increasing temperature, whereas Na⁺ and Mg²⁺ ions show a rapid increase in cluster size and amount upon increasing time and temperature.

The preparation, structure and luminescent properties of Mg–CaCO3:Eu3+ phosphors

Morphology and luminescence properties of Mg–CaCO₃:Eu³⁺ phosphors are found to change with the initial magnesium ion concentration.

Effect of Greenhouse Gases Dissolved in Seawater

A molecular dynamics simulation has been performed on the greenhouse gases carbon dioxide and methane dissolved in a sodium chloride aqueous solution, as a simple model of seawater. A carbon dioxide molecule is also treated as a hydrogen carbonate ion. The structure, coordination number, diffusion coefficient, shear viscosity, specific heat, and thermal conductivity of the solutions have been discussed. The anomalous behaviors of these properties, especially the negative pressure dependence of thermal conductivity, have been observed in the higher-pressure region.

Ab Initio Studies of Calcium Carbonate Hydration

Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance.

Diatom-inspired skeletonisation of insulin - Mechanistic insights into crystallisation and extracellular bioactivity

In this paper, we encage insulin within calcium carbonate by means of a biomineralisation process. We find that both dogbone and crossbone morphologies develop during the crystallisation process. The crystals break down into small nanocrystals after prolonged immersion in phosphate buffer solution, which adhere extracellularly to mammalian cells without causing any observable damage or early cell-death. The mechanisms behind calcium carbonate encaging of single insulin monomers are detailed. This communication elucidates a novel, diatom-inspired approach to the mineral skeletonisation of insulin.

Modelling the effects of salt solutions on the hydration of calcium ions

Classical molecular dynamics simulations of several aqueous alkali halide salt solutions have been used to determine the effect of electrolytes on the structure of water and the hydration properties of calcium ions. Compared with the simulations of Ca(2+) ions in pure liquid water, the frequency of water exchange in the first hydration shell of calcium, which is a fundamental process in controlling the reactivity of calcium(ii) aqua-ions, is drastically reduced in the presence of other electrolytes in solution. The strong stabilization of the hydration shell of Ca(2+) occurs not only when the halide anions are directly coordinated to calcium, but also when the alkali and halide ions are placed at or outside the second coordination shell of Ca(2+), suggesting that the reactivity of the first solvation shell of the calcium ion can be influenced by the specific affinity of other ions in solution for the water molecules coordinated to Ca(2+). Analysis of the hydrogen-bonded structure of water in the vicinity of the calcium ion shows that the average number of hydrogen bonds per water molecules, which is 1.8 in pure liquid water, decreases as the concentration of alkali-halide salts in solution increases, and that the temporal fluctuations of hydrogen bonds are significantly larger than those obtained for Ca(2+) in pure liquid water. This effect has been explained in terms of the dynamics of reorganization of the O-H···X(-) (X = F, Cl and Br) hydrogen bond. This work shows the importance of solution composition in determining the hydrogen-bonding network and ligand-exchange dynamics around metal ions, both in solution and at the mineral-water interfaces, which in turn has implications for interactions occurring at the mineral-water interface, ultimately controlling the mobilization of ions in the environment as well as in industrial processes.

Density functional theory study of the oligomerization of carboxylic acids

We present a density functional theory [M06-2X/6-31+G(d,p)] study of the structures and free energies of formation of oligomers of four carboxylic acids (formic acid, acetic acid, tetrolic acid, and benzoic acid) in water, chloroform, and carbon tetrachloride. Solvation effects were treated using the SMD continuum solvation model. The low-lying energy structures of molecular complexes were located by adopting an efficient search procedure to probe the potential energy surfaces of the oligomers of carboxylic acids (CA)n (n = 2-6). The free energies of the isomers of (CA)n in solution were determined as the sum of the electronic energy, vibrational-rotational-translational gas-phase contribution, and solvation free energy. The assessment of the computational protocol adopted in this study with respect to the dimerization of acetic acid, (AA)2, and formic acid, (FA)2, located new isomers of (AA)2 and (FA)2 and gave dimerization constants in good agreement with the experimental values. The calculation of the self-association of acetic acid, tetrolic acid, and benzoic acid shows the following: (i) Classic carboxylic dimers are the most stable isomer of (CA)2 in both the gas phase and solution. (ii) Trimers of carboxylic acid are stable in apolar aprotic solvents. (iii) Molecular clusters consisting of two interacting classic carboxylic dimers (CA)4,(D+D) are the most stable type of tetramers, but their formation from the self-association of classic carboxylic dimers is highly unfavorable. (iv) For acetic acid and tetrolic acid the reactions (CA)2 + 2CA → (CA)4,(D+D) and (CA)3 + CA → (CA)4,(D+D) are exoergonic, but these aggregation pathways go through unstable clusters that could hinder the formation of tetrameric species. (v) For tetrolic acid the prenucleation species that are more likely to form in solution are dimeric and trimeric structures that have encoded structural motifs resembling the α and β solid forms of tetrolic acid. (vi) Stable tetramers of benzoic acid could form in carbon tetrachloride from the aggregation of trimers and monomers. (vii) Higher order clusters such as acetic acid pentamers and tetrolic acid hexamers are highly unstable in all solvation environments.

In situ probing calcium carbonate formation by combining fast controlled precipitation method and small-angle X-ray scattering

The initial stage of calcium carbonate nucleation and growth, found usually in "natural" precipitation conditions, is still not well understood. The calcium carbonate formation for moderate supersaturation level could be achieved by an original method called the fast controlled precipitation (FCP) method. FCP was coupled with SAXS (small-angle X-ray scattering) measurements to get insight into the nucleation and growth mechanisms of calcium carbonate particles in Ca(HCO3)2 aqueous solutions. Two size distributions of particles were observed. The particle size evolutions of these two distributions were obtained by analyzing the SAXS data. A nice agreement was obtained between the total volume fractions of CaCO3 obtained by SAXS analysis and by pH-resistivity curve modeling (from FCP tests).

Pre-nucleation clusters as solute precursors in crystallisation

Crystallisation is at the heart of various scientific disciplines, but still the understanding of the molecular mechanisms underlying phase separation and the formation of the first solid particles in aqueous solution is rather limited. In this review, classical nucleation theory, as well as established concepts of spinodal decomposition and liquid-liquid demixing, is introduced together with a description of the recently proposed pre-nucleation cluster pathway. The features of pre-nucleation clusters are presented and discussed in relation to recent modifications of the classical and established models for phase separation, together with a review of experimental work and computer simulations on the characteristics of pre-nucleation clusters of calcium phosphate, calcium carbonate, iron(oxy)(hydr)oxide, silica, and also amino acids as an example of small organic molecules. The role of pre-nucleation clusters as solute precursors in the emergence of a new phase is summarized, and the link between the chemical speciation of homogeneous solutions and the process of phase separation via pre-nucleation clusters is highlighted.

Predicting pKa in Implicit Solvents: Current Status and Future Directions

Computational prediction of condensed phase acidity is a topic of much interest in the field today. We introduce the methods available for predicting gas phase acidity and pKas in aqueous and non-aqueous solvents including high-level electronic structure methods, empirical linear free energy relationships (LFERs), implicit solvent methods, explicit solvent statistical free energy methods, and hybrid implicit–explicit approaches. The focus of this paper is on implicit solvent methods, and we review recent developments including new electronic structure methods, cluster-continuum schemes for calculating ionic solvation free energies, as well as address issues relating to the choice of proton solvation free energy to use with implicit solvation models, and whether thermodynamic cycles are necessary for the computation of pKas. A comparison of the scope and accuracy of implicit solvent methods with ab initio molecular dynamics free energy methods is also presented. The present status of the theory and future directions are outlined.

Carbonate-coordinated metal complexes precede the formation of liquid amorphous mineral emulsions of divalent metal carbonates

During the mineralisation of metal carbonates MCO3 (M=Ca, Sr, Ba, Mn, Cd, Pb) liquid-like amorphous intermediates emerge. These intermediates that form via a liquid/liquid phase separation behave like a classical emulsion and are stabilized electrostatically. The occurrence of these intermediates is attributed to the formation of highly hydrated networks whose stability is mainly based on weak interactions and the variability of the metal-containing pre-critical clusters. Their existence and compositional freedom are evidenced by electrospray ionization mass spectrometry (ESI-MS). Liquid intermediates in non-classical crystallisation pathways seem to be more common than assumed.

Accuracy of the microsolvation-continuum approach in computing the pK(a) and the free energies of formation of phosphate species in aqueous solution

First principles density functional theory (Perdew-Burke-Ernzerhof) calculations have been used to compute the hydration properties, aqueous-phase acid dissociation constants (pK(a)) and Gibbs free energies of formation of small polyphosphates in aqueous solution. The effect of the hydrated environment has been simulated through a hybrid microsolvation-continuum approach, where the phosphate species are simulated as microsolvated solutes, while the remainder of the bulk solvent is treated as a dielectric continuum using the COSMO solvation model. The solvation free energies of orthophosphates and pyrophosphates have been computed applying monomer and cluster thermodynamic cycles, and using the geometries optimised in the gas-phase as well as in the COSMO environment. The results indicate that the simple polarisable continuum or microsolvation-continuum models are unable to compute accurate free energies of solvation for charged species like phosphates. The calculation of the pK(a) shows that the computed values of acid dissociation constants are critically dependent on the number of water molecules n(H(2)O) included in the hydrated phosphate clusters. The optimal number n(H(2)O) is determined from the minimum value of the "incremental" water binding free energy associated with the process of adding a water molecule to a micro-solvated phosphate species. Analysis of the effect of n(H(2)O) on the free energies of orthophosphate condensation reactions shows that can vary by tenths of kcal mol(-1), depending on the particular choice of n(H(2)O) for the monomeric and dimeric species. We discuss a methodology for the determination of n(H(2)O); for the orthophosphates the "incremental" binding energy approach is used to determine n(H(2)O), whereas for the polyphosphates the number of explicit water molecules is simply equal to the effective charge of these anions. The application of this method to compute the free energy of formation of pyro- and tri-phosphates gives generally good agreement with the available experimental data.

How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics study using model peptides of different conformations

Bone sialoprotein (BSP) is a highly phosphorylated, acidic, noncollagenous protein in bone matrix. Although BSP has been proposed to be a nucleator of hydroxyapatite (Ca(5)(PO(4))(3)OH), the major mineral component of bone, no detailed mechanism for the nucleation process has been elucidated at the atomic level to date. In the present work, using a peptide model, we apply molecular dynamics (MD) simulations to study the conformational effect of a proposed nucleating motif of BSP (a phosphorylated, acidic, 10 amino-acid residue sequence) on controlling the distributions of Ca(2+) and inorganic phosphate (Pi) ions in solution, and specifically, we explore whether a nucleating template for orientated hydroxyapatite could be formed in different peptide conformations. Both the alpha-helical conformation and the random coil structure have been studied, and inorganic solutions without the peptide are simulated as reference. Ca(2+) distributions around the peptide surface and interactions between Ca(2+) and Pi in the presence of the peptide are examined in detail. From the MD simulations, although in some cases for the alpha-helical conformation, we observe that a Ca(2+) equilateral triangle forms around the surface of peptide, which matches the distribution of Ca(2+) ions on the (001) face of the hydroxyapatite crystal, we do not consistently find a stable nucleating template formation in general for either the helical conformation or the random coil structure. Therefore, independent of conformations, the BSP nucleating motif is more likely to help nucleate an amorphous calcium phosphate cluster, which ultimately converts to crystalline hydroxyapatite.

Structure and dynamics of the hydrated magnesium ion and of the solvated magnesium carbonates: insights from first principles simulations

We report first principles molecular dynamics simulations based on the density functional theory and the Car-Parrinello method to study the structures and dynamics of the hydrated Mg(2+) ion and of the solvated MgHCO(3)(+) and MgCO(3) complexes in aqueous solution. According to these simulations, the first hydration shell of the hydrated magnesium ion consists of six water molecules, whereas in the solvated magnesium bicarbonate and magnesium carbonate complexes the Mg(2+) is mostly five-coordinated, which indicates that when coordinated to magnesium the HCO(3)(-) and CO(3)(2-) anions reduce its the coordination sphere. Our simulations show that the structures of the most stable monomers of magnesium bi-carbonate and magnesium carbonate in solution are Mg[eta(1)-HCO(3)](H(2)O)(4)(+) and Mg[eta(1)-CO(3)](H(2)O)(4), i.e. the preferred hydration number is four, while the (bi-)carbonate is coordinated to the magnesium in a monodentate mode. The analysis of the exchange processes of the water molecules in the first and second hydration shell of Mg(2+) shows that the HCO(3)(-) or CO(3)(2-) ligands affect the dynamics of the magnesium coordination spheres by making its hydration shell more "labile". Furthermore, molecular dynamics simulations of the non-associated Mg(2+)/Cl(-) pair in water suggest that, despite negligible differences in the coordination spheres of Mg(2+), the chloride anion has a significant influence on the water exchange rates in the second hydration shell of Mg(2+).