In this work, the vibrational spectra of hexagonal hydroxylapatite OHAp (space group P63) and type A carbonated apatite [Ca10(PO4)6(CO3), space group P1] have been calculated with an ab initio approach by density function method using the hybrid B3LYP functional and an all-electron polarized double-zeta quality Gaussian-type basis set using CRYSTAL09 computer program. The effect on the vibrational properties due to improving the Ca pseudopotential, usually adopted in previous studies on hydroxylapatite, towards the present all-electron basis set has also been briefly addressed. The anharmonic correction for hydroxyl groups in OHAp has also been considered. The results of the modeling are in good agreement with the available FTIR and Raman data present in literature and can be useful to experimental researchers to assign unequivocally the bands in infrared and Raman spectra to specific fundamental vibrational modes.

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The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg3Si4O10(OH)2], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO∕B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.

In this work, we studied the interaction of glycine with the (001) surface of chlorite mineral at a single molecule level by cross-correlating scanning probe microscopy (SPM) and ab initio quantum mechanics (QM) investigations. Chlorite mineral is particularly interesting and peculiar for the interaction with organic molecules because it presents an alternated stacking of brucite-like (hydrophobic) and talc-like (hydrophilic) layers of different polarities. Brucite-like is positive, whereas talc-like is negative. The experimental atomic force microscopy (AFM) observations show that glycine is stably and selectively adsorbed on the brucite-like layer, organized in monolayers with different patterns. The sizes of single molecules of glycine measured by AFM are in agreement with those calculated by QM. Glycine molecules were found to align both at the edges and on the terraces of the brucitic surface. QM simulations confirmed the AFM observations that glycine molecule is adsorbed with high adsorption energy preferentially with its plane parallel to the (001) brucite-like surface. QM also provided the geometry conformation of the molecule and the bonding scheme between glycine and brucite surface. This kind of data can be very helpful both to biotechnological applications of this substrate and to depict some important processes that might have been occurred in prebiotic environments.

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Carbonate apatite is a material of the utmost importance as it represents the inorganic fraction of biological hard tissues in bones and teeth. Here we study the static and dynamic features of CO3 2– ion in the apatitic channel of carbonate apatite (A-type substitution), by applying both static and dynamic quantum mechanical calculations based on density functional methods with B3LYP-D* and PBE functionals. The static calculations reveal a number of almost energetically equivalent carbonate configurations in the channel, leading to cell parameters compatible with the P 3̅ space group assigned by the experimental X-ray structure determination. Ab initio isothermal–isobaric molecular dynamics simulations provide insights on the CO3 2– mobility, showing that at the temperature of the experimental structural determination the CO3 2– moiety undergoes a dynamic disorder, as the carbonate group is almost free to move within the apatitic channel enhancing its exchangeability with other anions.

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