Computational Insights into Mg2+ Dehydration in the Presence of Carbonate

Water exchange around a free magnesium ion and magnesium paired with carbonate in aqueous solution was studied using free energy methods. Both a rigid-ion and a polarizable force field based on the AMOEBA model were examined. The parameters were adjusted to accurately reproduce the hydration structures of magnesium and carbonate in aqueous solution. The magnesium carbonate ion pairing free energies calculated with both force fields were found to be in excellent agreement with experimental data. Metadynamics simulations of the water exchange conducted with both models revealed that the formation of a contact magnesium carbonate ion pair significantly decreases the energy barrier for water exchange relative to the free magnesium ion in solution. This finding suggests that the presence of carbonate could accelerate the water exchange around magnesium and constitutes a first step toward a better understanding of the atomic-scale mechanisms involved in the nucleation of magnesium-bearing carbonate minerals

Determining the Adsorption Free Energies of Small Organic Molecules and Intrinsic Ions at the Terrace and Steps of Calcite

The adsorption of small molecules containing two different organic functional groups at terrace and step sites on the {101¯ 4} surface of calcite at the interface with aqueous solution was studied using free energy methods. For comparison, the adsorption free energies of the component ions of calcium carbonate were also determined at the same sites. Polarizability was taken into account through using a force field developed for calcium carbonate based on the AMOEBA model that contains static multipoles and self-consistent induced dipoles. The influence of including polarization was examined by comparing to data obtained with a fixed charge rigid-ion model. The strong hydration layers above the basal plane of calcite were shown to hinder the direct attachment of the small species studied, including the constituent ions of the mineral. Only the species bearing an amino group, namely, methylammonium and glycine, demonstrated favorable adsorption free energies. The ability of amino groups to more readily pass through the hydration layers than carboxylate and carbonate groups can be explained by their weaker solvation free energies, while the carbonate ions within the calcite surface with which they bind are also less strongly hydrated than calcium ions. Acetate, glycine, and methylammonium were all found to be able to directly bind to one growth site at the acute step of calcite. This is at variance with results obtained with a rigid-ion model in which all binding free energies are endergonic. Thus, including polarization allows for a description of the adsorption process that is more consistent with experimental observations, particularly at calcite steps, and for determination of more reliable atomic-scale mechanisms for calcite growth and its modification by organic additives. Even with polarization, the organic functional groups considered only exhibit moderate binding to calcite steps with adsorption free energies not exceeding -13 kJ/mol

Simulating the binding of key organic functional groups to aqueous calcium carbonate species

The interaction of organic molecules with mineral systems is relevant to a wide variety of scientific problems both in the environment and minerals processing. In this study, the coordination of small organics that contain the two most relevant functional groups for biomineralisation of calcium carbonate, namely carboxylate and ammonium, with the corresponding mineral ions are examined in aqueous solution. Specifically, two force fields have been examined based on rigid-ion or polarisable models, with the latter being within the AMOEBA formalism. Here the parameters for the rigid-ion model are determined to target the accurate reproduction of the hydration structure and solvation thermodynamics, while both force fields are designed to be compatible with the corresponding recently published models for aqueous calcium carbonate. The application of these force fields to ion pairing in aqueous solution is studied in order to quantitatively determine the extent of association

Fossilisation des apatites biologiques : approche cristallochimique et applications géochimiques

Chemical and stable isotope compositions of fossil remains of vertebrates provide unique palaeo-environmental information. However, its reliability depends on the preservation of the biogenic geochemical record during the fossilisation process. This work aims to undersand how the geochemical record is acquired and preserved by studying the isotopic fractionation properties of apatite, the main inorganic constituent of vertebrates bones and teeth, and the crystal-chemical transformations occuring during fossilisation. These transformations are probed at the atomic scale using ATR-FTIR and solid-state NMR spectroscopies and their interpretation is supported by the modelling of ATR-FTIR spectra and DFT calculations of theoretical equilibrium isotopic fractionation properties. Atomic scale transformations of bones altered in aqueous solutions consist of partial dissolution of the biogenic apatite and formation of secondary carbonated fluor- or hydroxy- apatite, depending on the presence or absence of fluoride in the solution. These results were then applied to the study of the transformation of fossil bones from the karstic environments of Bolt’s Farm cave system (Cradle of Humankind, South Africa) and from the fluvio-lacustrine environments of the Tugen Hills (Gregory Rift, Kenya). Systematic formation of secondary carbonated fluorapatite is observed, as well as formation of secondary carbonated hydroxyapatite in the less fluorinated Bolt’s Farm fossils, highlighting the potentiality of fossil bones to record local physical-chemical conditions prevailing in fossilisation environments. The ~ 60 % maximum fraction of secondary apatite observed in fossils and modern bones altered under controlled conditions suggests it has a protective role against further dissolution of the primary apatite.Les fragments de squelettes de vertébrés préservés sous forme de fossiles fournissent des informations paléo-environnementales uniques via leur composition isotopique et leur teneur en éléments traces. Toutefois la validité de ces informations dépend crucialement de la préservation de l’enregistrement géochimique biogénique au cours de la fossilisation. Ce travail a pour objectif de comprendre comment s’effectue l’acquisition de l’information géochimique puis sa préservation en étudiant les propriétés de fractionnement isotopique de l’apatite, constituant inorganique majeur des os et dents de vertébrés, et les mécanismes de transformations cristallochimiques impliqués par la fossilisation. Celles-ci sont sondées à l’échelle atomique à l’aide des spectroscopies ATR-FTIR et RMN du solide, leur interprétation s’appuyant sur la modélisation des spectres ATR-FTIR et le calcul ab initio (DFT) des propriétés de fractionnement isotopique à l’équilibre de l’apatite. Les transformations à l’échelle atomique observées suite à l’altération d’os actuel en solution aqueuse attestent d’un processus de dissolution partielle de l’apatite biogénique et de formation de fluor- ou hydroxy- apatite carbonatée secondaire à la surface des cristallites, selon la présence ou non de fluor en solution. Ces résultats ont ensuite été appliqués à l’étude de la transformation d’os fossiles issus des environnements karstiques de Bolt’s Farm dans le Berceau de l’Humanité (Afrique du Sud) et des environnements fluvio-lacustres volcano-sédimentaires des collines Tugen dans la vallée du Rift Grégory (Kenya). La formation de fluorapatite carbonatée est systématiquement observée, de l’hydroxyapatite carbonatée est également formée dans les fossiles de Bolt’s Farm moins fluorés, soulignant ainsi le potentiel des ossements fossiles à révéler les conditions précoces de fossilisation. Un degré maximal de transformation, aussi bien des os fossiles que des os actuels altérés, est observé à environ 60 % d’apatite secondaire, suggérant l’idée d’un rôle protecteur de cette phase contre la dissolution totale de l’apatite primaire

Fossilization of biological apatites : crystal-chemical approach and geochemical applications

Les fragments de squelettes de vertébrés préservés sous forme de fossiles fournissent des informations paléo-environnementales uniques via leur composition isotopique et leur teneur en éléments traces. Toutefois la validité de ces informations dépend crucialement de la préservation de l’enregistrement géochimique biogénique au cours de la fossilisation. Ce travail a pour objectif de comprendre comment s’effectue l’acquisition de l’information géochimique puis sa préservation en étudiant les propriétés de fractionnement isotopique de l’apatite, constituant inorganique majeur des os et dents de vertébrés, et les mécanismes de transformations cristallochimiques impliqués par la fossilisation. Celles-ci sont sondées à l’échelle atomique à l’aide des spectroscopies ATR-FTIR et RMN du solide, leur interprétation s’appuyant sur la modélisation des spectres ATR-FTIR et le calcul ab initio (DFT) des propriétés de fractionnement isotopique à l’équilibre de l’apatite. Les transformations à l’échelle atomique observées suite à l’altération d’os actuel en solution aqueuse attestent d’un processus de dissolution partielle de l’apatite biogénique et de formation de fluor- ou hydroxy- apatite carbonatée secondaire à la surface des cristallites, selon la présence ou non de fluor en solution. Ces résultats ont ensuite été appliqués à l’étude de la transformation d’os fossiles issus des environnements karstiques de Bolt’s Farm dans le Berceau de l’Humanité (Afrique du Sud) et des environnements fluvio-lacustres volcano-sédimentaires des collines Tugen dans la vallée du Rift Grégory (Kenya). La formation de fluorapatite carbonatée est systématiquement observée, de l’hydroxyapatite carbonatée est également formée dans les fossiles de Bolt’s Farm moins fluorés, soulignant ainsi le potentiel des ossements fossiles à révéler les conditions précoces de fossilisation. Un degré maximal de transformation, aussi bien des os fossiles que des os actuels altérés, est observé à environ 60 % d’apatite secondaire, suggérant l’idée d’un rôle protecteur de cette phase contre la dissolution totale de l’apatite primaire.Chemical and stable isotope compositions of fossil remains of vertebrates provide unique palaeo-environmental information. However, its reliability depends on the preservation of the biogenic geochemical record during the fossilisation process. This work aims to undersand how the geochemical record is acquired and preserved by studying the isotopic fractionation properties of apatite, the main inorganic constituent of vertebrates bones and teeth, and the crystal-chemical transformations occuring during fossilisation. These transformations are probed at the atomic scale using ATR-FTIR and solid-state NMR spectroscopies and their interpretation is supported by the modelling of ATR-FTIR spectra and DFT calculations of theoretical equilibrium isotopic fractionation properties. Atomic scale transformations of bones altered in aqueous solutions consist of partial dissolution of the biogenic apatite and formation of secondary carbonated fluor- or hydroxy- apatite, depending on the presence or absence of fluoride in the solution. These results were then applied to the study of the transformation of fossil bones from the karstic environments of Bolt’s Farm cave system (Cradle of Humankind, South Africa) and from the fluvio-lacustrine environments of the Tugen Hills (Gregory Rift, Kenya). Systematic formation of secondary carbonated fluorapatite is observed, as well as formation of secondary carbonated hydroxyapatite in the less fluorinated Bolt’s Farm fossils, highlighting the potentiality of fossil bones to record local physical-chemical conditions prevailing in fossilisation environments. The ~ 60 % maximum fraction of secondary apatite observed in fossils and modern bones altered under controlled conditions suggests it has a protective role against further dissolution of the primary apatite

Magnesium Impurities Decide the Structure of Calcium Carbonate Hemihydrate

International audienc

Analyse en IRM digestive des sténoses fibreuses et inflammatoires dans la maladie de Crohn

MONTPELLIER-BU Médecine UPM (341722108) / SudocMONTPELLIER-BU Médecine (341722104) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Modeling the attenuated total reflectance infrared (ATR-FTIR) spectrum of apatite

International audienceAttenuated total reflectance (ATR) infrared spectra were measured on a synthetic and a natural fluorapatite sample. A modeling approach based on the computation of the Fresnel reflection coefficient between the ATR crystal and the powder sample was used to analyze the line shape of the spectra. The dielectric properties of the samples were related to those of pure fluorapatite using an effective medium approach, based on Maxwell–Garnett and Bruggeman models. The Bruggeman effective medium model leads to a very good agreement with the experimental data recorded on the synthetic fluorapatite sample. The poorer agreement observed on the natural sample suggests a more significant heterogeneity of the sample at a characteristic length scale larger than the mid-infrared characteristic wavelength, i.e., about 10 micrometers. The results demonstrate the prominent role of macroscopic electrostatic effects over fine details of the microscopic structure in determining the line shape of strong ATR bands

Line-broadening and anharmonic effects in the attenuated total reflectance infrared spectra of calcite

International audienceThe attenuated total reflectance (ATR) spectra of two calcite samples have been measured using Ge and diamond internal reflection elements. One of the samples was obtained by precipitation from solution and displays sub-micrometer sized particles. The second sample was obtained by grinding a single-crystal of calcite (''Iceland spar'' variety). Theoretical spectra were obtained by computing the reflection coefficient of the interface between the ATR internal reflection element and a homogeneous effective medium representing the powder sample. The dielectric properties of the effective medium have been determined from those of bulk calcite using the Bruggeman approach which is adequate for standard powders with intermediate fractions of solid and empty porosity. Although this modeling approach provides a quantitative interpretation of the broadening of strong absorption bands in the calcite ATR spectra, it fails to reproduce the apparent splitting of the strong nu3 CO3 band. This problem was solved by combining the electrostatic modeling approach with a semi-quantum model of the dielectric tensor of bulk calcite, which allows for a frequency-dependent damping of the nu3 CO3 excitation. The frequency-dependence is ascribed to a multiphonon-related resonance in the nu3 CO3 phonon self-energy at a frequency close to its transverse optical frequency. The combination of approaches exposed in the present study makes it possible to discriminate among physically different processes affecting the powder infrared spectra of calcite, some being related to the long-range nature of electrostatic interactions in polar materials and others being related to atomic-scale anharmonic interactions between vibrational modes