1,721,072 research outputs found
Method dependence of proline ring flexibility in the poly-L-proline type II polymer
Full text linkWe studied the sensitivity of the energetic and geometrical features of the proline ring (pyrrolidine) to the quantum mechanical computational approach by adopting the proline monomer, trimer, and polymer, as simplified collagen protein models. Within the Density Functional Theory (DFT) approach, we tested the ability of different functionals (GGA PBE and the hybrid B3LYP), added with a posteriori empirical dispersion corrections (D), to predict the conformational potential energy surface of the five-membered heterocycle pyrrolidine ring for the above models, dictating the collagen main features. We also compared the DFT-D results with those from the recently proposed cost-effective HF-3c method and our variant HF-3c-027, both based on Hartree-Fock Hamiltonian and Gaussian minimal basis set properly corrected for basis set superposition error, structure deficiencies, and dispersion interactions. We found that dispersion interactions are essential to destabilize specific conformers. While the HF-3c and its HF-3c-027 variant are unreliable to predict accurately the energy of the ring conformers, structures are accurate. Indeed, the cost-effective DFT-D//HF-3c-027 approach in which the energetic is from the accurate DFT-D method on HF-3c-027 structures provides energetic in line with that derived by the costly DFT-D//DFT-D approach, paving the way to simulate more realistic collagen models of much larger size. The adoption of either PBE or B3LYP functional for the electronic part of the DFTD method gives very similar results, recommending the first as the most cost-effective method for simulating large collagen models. The predicted most stable conformation computed for the periodic poly proline (type II) model allows for a higher flexibility, in agreement with experimental studies on collagen protein. The present results open the way to large-scale calculations of the collagen/hydroxyapatite system, crucial for understanding the atomistic details in bones and teeth
Propionic acid derivatives confined in mesoporous silica: monomers or dimers? The case of ibuprofen investigated by static and dynamic ab initio simulations
No full textConfinement in mesoporous silica can greatly increase the solubility of pharmaceutical compounds. Propionic acid derivatives (a very popular class of drugs that include ibuprofen and ketoprofen) would greatly benefit from such technology, given their common apolar character. However, it is still debated whether, after confinement, these drugs are adsorbed on the pore walls as individual molecules or they keep the H-bonded dimeric structure that exists in their crystalline form. Their physical state inside the mesopores could have important consequences on the final performances of the drug delivery system. We employed accurate periodic density functional theory simulations, both static and dynamic, to investigate the issue. We simulated ibuprofen, as a model for all propionic acid derivatives, adsorbed both as a monomer and as a dimer inside a realistic model for the MCM-41 mesoporous silica. We found that adsorption is energetically favored in both cases, driven by both vdW and H-bond interactions. However, through ab initio molecular dynamics, we observed a continuous forming, breaking and reforming of these interactions. In the end, by comparing computed energetics, vibrational spectra and mobility, we were able to provide some important clues on the physical state of this class of drugs inside mesoporous silica, helping to define which drug family (monomer or dimer) is more probable after confinement
Stability of the Dipolar (001) Surface of Hydroxyapatite
No full textThe features of the ferroelectric (proton ordered) hydroxyapatite HA (001) surface as derived from the P63 hexagonal HA bulk have been studied by periodic density functional calculations using the hybrid B3LYP functional and Gaussian basis set of polarized double-ζ quality. Geometry, surface energy, and electronic features of HA (001) slab models of thickness from 1 nm to almost 50 nm have been computed, by keeping under careful control numerical errors due to the very large system size. The present results reveal that the ferroelectric OH– alignment does not compromise the stability of the HA (001) surface up to the nanometric scale. Indeed, a slab thickness of 43 nm, containing 2640 atoms in the unit cell, exhibits a dipole moment across the slab of 0.73 D, a wide band gap of 7.60 eV, and a surface energy of 1.344 J·m–2. No sign of “metallization” occurs as for the classical macroscopic polar zinc- or oxygen-terminated ZnO (0001) surfaces, due to counterpolarization of the electronic density of the Ca2+ and PO43– moieties surrounding the monodimensional OH– polar arrays. These findings may be relevant to explain why, experimentally, HA nanocrystals orient along the main axis of the proto-collagen fibrils with their crystallographic c axis (perpendicular to the {001} crystal plane family)
Water at hydroxyapatite surfaces: the effect of coverage and surface termination as investigated by all-electron B3LYP-D* simulations
No full textHydroxyapatite [HA, Ca-10(PO4)(6)(OH)(2)], the main constituent of bones and teeth enamels, is a widely studied and employed biomaterial. Its applications span from dental to orthopedic implants, including bone tissue engineering scaffolds, coating, filler and many others. Previous theoretical and experimental studies have already characterized the physical-chemical foundations of water adsorption on a number of HA surfaces, an essential step in the mechanism of biomaterial integration. Here, we extend such knowledge by simulating, at a hybrid DFT level of theory, different HA surface terminations, both stoichiometric and non-stoichiometric, as free and in interaction with water. Such a goal is achieved at an unprecedented accuracy, with a large all-electron basis set and including dispersion forces contributions. The calculated results are then compared with experimental micro-calorimetric data, showing a good agreement in the loading trend of the (010) surfaces. More generally, this theoretical approach is confirmed to be an efficient tool to analyze these biomaterials, giving the possibility to investigate the HA behavior toward more complex molecules, from amino acids to collagen, at the here-presented level of theory, to shed some light on the complex biomineralization process of human bones and teeth
The vibrational features of hydroxylapatite and type A carbonated apatite: A first principle contribution
Full text linkIn 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 the density function method using the hybrid B3LYP functional and an all-electron polarized double-? quality Gaussian-type basis set using the CRYSTAL09 computer program. The effect on the vibrational properties due to improving the Ca pseudopotential, usually adopted in previous studies on hydroxylapatite, toward 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 presented in the literature and can be useful to experimental researchers to assign unequivocally the bands in infrared and Raman spectra to specific fundamental vibrational modes
Ab-initio modeling of protein/biomaterial interactions: influence of amino acid polar side chains on adsorption at hydroxyapatite surfaces
Full text linkThe adsorption from gas-phase of five different amino acids (AA), namely Gly, Ser,
Lys, Gln and Glu, on three surface models of hexagonal hydroxyapatite (HA) has been
studied at B3LYP level with Gaussian type basis set within a periodic approach. The
AA adsorption was simulated on the (001) and (010) stoichiometric surfaces, the latter
both in its pristine and water reacted form. Low/high AA coverage has been studied by
doubling the HA unit cell size. The AA have been docked to the HA surfaces following
the electrostatic complementarity between the electrostatic potentials of AA and the
bare HA. Gly adsorbs as a zwitterion at the (001) surface, whereas at the (010) ones the
proton of the COOH group is transferred to the surface resulting in an HA + /Gly - ion
pair. For the other AA the common COOH-CH-NH 2 moiety behaves like in Gly, while
the specific side-chain functionalities adsorb at the HA surfaces by maximizing
electrostatic and H-bond interactions. The interactions between the side chains and the
HA surface imparts a higher stability compared to the Gly case, with Glu being the
strongest adsorbate due to its high Ca affinity and H-bond donor propensity. For AA of
large size, the adsorption is more favorable in conditions of low coverage as repulsion
between adjacent AA is avoided. For all considered AA, the strongest interaction is
always established on the (010) faces rather than on the (001) one, therefore suggesting
an easier growth along the c-direction of hydroxyapatite crystals from AA solutions
Hydroxyapatite as a key biomaterial: quantum-mechanical simulation of its surfaces in interaction with biomolecules
No full textHow strong are H-bonds at the fully hydroxylated silica surfaces? Insights from the B3LYP electron density topological analysis
No full textThe calculation through the supermolecular approach of the hydrogen bond strength EHB between silanol groups at the surface of an ample class of silica-based materials is hindered by the intrinsic difficulty to define the “H-bond free” reference system. We propose, for the first time, to evaluate EHB by adopting the literature empirical correlation relating the Bader local electronic kinetic energy density Gb computed at the H⋅⋅⋅O bond critical point with EHB. Remarkably, EHB for the hydroxylated surfaces of quartz polymorphs correlates with surface formation energy, showing that the surface EHB is responsible of the surface stability. A number of correlations between hydrogen bond features are established, with that between EHB and the enhanced infrared intensity associated to surface hydrogen bond formation, obeying the literature formula semi-quantitatively. The present results are quite general and can be extended to other inorganic surfaces where hydrogen bonds between surface sites are the dominant features
Computational Studies of Magnesium and Strontium Substitution in Hydroxyapatite
No full textThe properties of hydroxyapatite can be improved by substitution of biologically relevant ions, such as magnesium (Mg) and strontium (Sr), into its structure. Previous work in the literature has not reached agreement as to site preferences in these substitutions, and there are suggestions that these may change with differing levels of substitution. The current work adopted a quantum mechanical approach based on density functional theory using the CRYSTAL09 code to investigate
the structural changes relating to, and site preferences of, magnesium and strontium substitution (to 10 mol%) in hydroxyapatites and also to predict the corresponding vibrational spectra in the harmonic approximation. The structures underwent full geometrical optimisation within the P63
space group, indicating an energetic site preference for the Ca(2) site in the case of Mg substitution, and the Ca(1) site in the case of Sr. Shrinkage of the unit cell was observed in the case of Mg substitution, and expansion in the case of Sr substitution, in agreement with the corresponding ionic
radii. Thermodynamic properties of the structures obtained from the harmonic vibrational frequency calculations confirmed that the structures were minima on the potential energy surface. Isotopic substitutions indicated that the main contribution of Sr and Mg to vibrational modes is at frequencies < 400 cm-1
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