Alfonso Pedone

ABSTRACT Molecular dynamics, density functional theory calculations and Na-23 NMR experiments have been used to inspect the chemical and structural characteristics of the Na environment in soda-lime silicate (CSN) and aluminosilicate (CASN) glasses. The use of an improved 3QMAS pulse sequence has allowed a clear identification of different Na sites. Average coordination numbers have been extracted by fitting the Na-23 3QMAS spectra with the computed NMR parameters. The results show that the Na-23 delta(iso) values correlate with the average < Na-O > distances only when the different coordination numbers are explicitly taken into account.

(43)Ca MQMAS NMR spectra of three silica-based glasses in which Ca(2+) ions play different structural roles have been collected and processed in order to extract the underlying NMR parameter distributions. The NMR parameters have been interpreted with the help of molecular dynamics simulations and DFT-GIPAW calculations. This synergetic experimental-computational approach has allowed us to investigate the Ca environment, to estimate Ca coordination numbers from MD-derived models, and to push further the discussion about (43)Ca NMR sensitivity to the first and second coordination spheres: (43)Ca δiso and Ca-O distance can be successfully correlated as a function of Ca coordination number.

An extensive benchmark of exchange-correlation functionals on the structure of the X-ray resolved phosphine and thiolate-protected Ag14-based nanocluster, named XMC1, is reported. Calculations were performed both on simplified model systems, with the complexity of the ligands greatly reduced, and on the complete XMC1 particle. Most of the density functionals that yielded good relaxed structures on analogous calculations on gold nanoclusters (viz. those employing the generalized gradient approximation) significantly deform the structure of XMC1. On the contrary, some of the exchange-correlation functionals including part of the exact Hartree-Fock exchange (hybrid functionals) reproduce the experimental geometry with minimal errors. In particular, the widely adopted B3LYP yields fairly accurate structures for XMC1, whereas it is outperformed by many other functionals (both hybrids and generalized gradient corrected) in similar calculations on analogous gold-based systems. Time-depende...

A computational protocol that combines periodic and QM/QM' calculations has been applied to investigate the structural (geometrical and electronic) and photophysical absorption properties of the salicylidene aniline (SA) thermochromic molecular crystal. The protocol consists of three different steps, namely (i) the description of the molecular crystal using a periodic approach taking into account dispersion interactions, (ii) the identification of reliable finite models (clusters), and (iii) the calculation of vertical transition energies including environmental effects through the use of an electronic embedding model (QM/QM' ONIOM approach). The encouraging results obtained in this work for the β polymorph of SA, both in terms of accuracy and computational cost, open the way to the simulation and the prediction of the photophysical behavior of other molecular crystals, especially those much less well characterized experimentally.

ABSTRACT In this study, coarse-grained computational simulations of the ubiquitin corona around gold nanoparticles have been carried out, and the effect of the nanoparticle size (10, 16, 20, and 24 nm diameter) and environment (bare nanoparticle surface, and citrate-coated surface, where citrate are treated with implicit and explicit models) has been analysed. The results showed that the corona is obtained after a slow reorientation step that occurs at the nanoparticle surface in order to optimize the nanoparticle–ubiquitins interaction. The ubiquitin binding modalities depend on the nanoparticle environment, while conformational changes of ubiquitins upon binding and their aggregation propensity slightly depend on nanoparticle size.

ABSTRACT Classical molecular dynamics simulations, density functional theory calculations, and spin-effective Hamiltonians have been used to simulate the 17O MAS and 3QMAS NMR spectra of Ca–Na silicate and aluminosilicate glasses and melts employed as simplified models for basaltic, andesitic, and rhyolitic magmas. The direct comparison of the theoretical NMR spectra of molecular dynamics derived structural models with the experimental counterparts available in the literature has allowed the investigation of the nature of nonframework cation mixing and the extent of intermixing among framework units in Na–Ca aluminosilicate glasses. In particular, in agreement with previous experimental evidence, the results show a nonrandom distribution of the network-modifying Ca and Na in soda-lime glasses with the prevalence of dissimilar Na–Ca pairs around nonbridging oxygens. The oxygen sites are not completely resolved in the MAS spectra of the aluminosilicate glasses. On the contrary, in the 17O 3QMAS spectra the multiple oxygen sites, in particular the Si–O–Si, Al–O–Al, Al–O–Si, and the nonbridging oxygen peaks, are distinguishable. The small amount of Al–O–Al sites found in the investigated glasses reveals that the Al avoidance rule is not respected in amorphous solids. The Si–O–Al sites are surrounded by Na ions, which play a preferential role as a charge-balancing cation, while Ca can act as a network-modifying cation. Finally, correlations between the structural characteristic and the values of the NMR parameters have been attempted with the aim of helping the interpretation of NMR spectra of glasses with similar compositions.

An automatic tool (named CLUSTER) for the prediction of the most probable crystal phases that can separate from glasses has been developed. The program analyzes the output of molecular dynamics simulations of glasses or glass ceramics, systematically sampling the ratios of the ions in different portions of the simulation box and comparing them to the stoichiometric ratio of compositionally equivalent crystalline phases retrieved from a crystal structure database. The efficacy of the similarity index elaborated has been judged by comparing the results obtained with the crystal phases identified by XRD analysis after thermal treatment in a series of multicomponent potential bioactive glasses and glass ceramics for which the advantages of rational-designed erosion-controlled release is straightforward.

ABSTRACT The effect of the replacement of CaO for MgO on the structural properties of the 45S5 Bioglass with composition 46.2SiO2·24.3Na 2O·(26.9 - x)CaO·2.6P2O5· xMgO where x = 0, 5, 10, 15, 20, and 26.9 mol has been studied by means of molecular dynamics simulations. The results confirmed the complexity of the local environment of Mg ions which are coordinated by 5 nonbridging oxygens of different TO4 tetrahedra (T = Si/P) leading to large rings in the structures. A rough correlation between the average dimension of the rings found in the structure and the computed Young's modulus is obtained. The Young's modulus decrease at low Mg-content reaching a minimum for the 46.2SiO 2·24.3Na2O·16.9CaO·2.6P 2O5·10MgO glass. At this composition, Mg is homogeneously distributed in the silica rich region together with Ca and Na ions but is almost totally absent from the Ca-Na-phosphate rich regions. The results suggest that the ideal glass composition for lowering the Young's modulus preserving a specific bioactivity can be found below 10% of MgO content.

Glasses belonging to the Na(2)O-CaO-P(2)O(5)-SiO(2) system and modified by CaF(2) substitution for CaO and Na(2)O alternatively, were synthesized and characterized experimentally and computationally. The results of molecular dynamics simulations show that fluorine is almost exclusively bonded to modifier cations (Ca and Na) with coordination number close to 4. A similar mean coordination number value is found in the crystal phases obtained by means of thermal treatment at fixed temperature. Addition of fluorine increases the polymerization of silicate tetrahedra by removing modifiers from the siliceous matrix. No appreciable amount of Si-F bonds are detected.

The structural properties of phosphosilicate glasses based on the 45S5 Bioglass doped with gallium and aluminum (46.2 SiO2·24.3Na2O·26.9CaO·2.6P2O5·1.0X2O3, X = Ga or Al) are investigated by means of classical molecular dynamics simulations. Structural features of the two compositions are compared with those of the original 45S5 Bioglass in order to relate them to the different known bioactivities of these materials. Differences in the coordination environments of Ga and Al, network connectivity, and ion aggregation reveal a microscopic model of these glasses which supports the interpretation of the experimental data and provides new insight into the different biological behaviors of Ga- and Al-containing phosphosilicate glasses. Although Ga is found predominantly in a 4-fold coordination environment, small amounts of 5- and 6-fold coordinated atoms have been detected depending on the interatomic potential model employed. This suggests its possible intermediate role in phosphosilicate glasses. On the contrary, Al plays a network former role and leads to glasses with a more polymerized structure. Interestingly, the results show an increased propensity for aggregation of the Ca(2+) and PO4(3-) ions in the Al-containing phosphosilicate glasses with respect to the Ga-containing ones. This leads to insoluble calcium-phosphate-rich regions not detected in the bioactive glasses.

A new empirical pairwise potential model for ionic and semi-ionic oxides has been developed. Its transferability and reliability have been demonstrated by testing the potentials toward the prediction of structural and mechanical properties of a wide range of silicates of technological and geological importance. The partial ionic charge model with a Morse function is used, and it allows the modeling of the quenching of melts, silicate glasses, and inorganic crystals at high-pressure and high-temperature conditions. The results obtained by molecular dynamics and free energy calculations are discussed in relation to the prediction of structural and mechanical properties of a series of soda lime silicate glasses.

Fluorinated bioactive glasses (FBGs) combine the antibacterial properties of fluorine with the biological activity of phosphosilicate glasses. Because their biomedical application depends on the release of fluorine, the detailed characterization of the fluorine environment in FBGs is the key to understand their properties. Car-Parrinello molecular dynamics (CPMD) simulations have been performed on a 45S5 Bioglass composition in which 10 mol % of the CaO has been replaced with CaF(2), and have allowed us to resolve some longstanding issues about the atomic structure of fluorinated bioglasses, with particular regard to the structural role of fluorine. F is coordinated almost entirely to the modifier ions Na and Ca, with a very small amount of residual Si-F bonds, whose fraction only becomes significant in the melt precursor. High temperature leads to Si-F bonds in both tetra- (SiO(3)F) and, less frequently, penta-coordinated (SiO(4)F and SiO(3)F(2)) complexes, showing that formation of these bonds through the expansion of the SiO(4) coordination shell is generally less favored. There is no evidence for preferential bonding of F to either modifier ion: almost all F atoms are coordinated to both calcium and sodium in a "mixed state", rather than exclusively to either, as had been conjectured. We discuss the consequences of these findings on the properties of fluorine-containing bioglasses.

The crystallization kinetics of Na(2)O.CaO.2SiO(2) (x = 0) and 0.68ZnO.Na(2)O.CaO.2SiO(2) (x = 0.68, where x is the ZnO stoichiometric coefficient in the glass formula) bioactive glasses have been studied using both nonisothermal and isothermal methods. The results obtained from isothermal XRPD analyses have showed that the first glass crystallizes into the isochemical Na(2)CaSi(2)O(6) phase, whereas the Na(2)ZnSiO(4) crystalline phase is obtained from the Zn-rich glass, in addition to Na(2)CaSi(2)O(6). The activation energy (Ea) for the crystallization of the Na(2)O.CaO.2SiO(2) glass is 193 +/- 10 and 203 +/- 5 kJ/mol from the isothermal in situ XRPD and nonisothermal DSC experiments, respectively. The Avrami exponent n determined from the isothermal method is 1 at low temperature (530 degrees C), and its value increases linearly with temperature increase up to 2 at 607 degrees C. For the crystallization of Na(2)CaSi(2)O(6) from the Zn-containing glass, higher values of both the crystallization temperature (667 and 661 degrees C) and Ea (223 +/- 10 and 211 +/- 5 kJ/mol) have been found from the isothermal and nonisothermal methods, respectively. The Na(2)ZnSiO(4) crystalline phase crystallizes at lower temperature with respect to Na(2)CaSi(2)O(6), and the Ea value is 266 +/- 20 and 245 +/- 15 kJ/mol from the isothermal and nonisothermal methods, respectively. The results of this work show that the addition of Zn favors the crystallization from the glass at lower temperature with respect to the Zn-free glass. In fact, it causes an increase of Ea for the Na diffusion process, determined using MD simulations, and consequently an overall increase of Ea for the crystallization process of Na(2)CaSi(2)O(6). Our results show good agreement between the Ea and n values obtained with the two different methods and confirm the reliability of the nonisothermal method applied to kinetic crystallization of glassy systems. This study allows the determination of the temperature stability field of the crystalline phases with the view of creating a different glass ceramic useful in the field of bioactive materials.

A multi-scale computational protocol, which combines Quantum Mechanics and Molecular Mechanics (QM/MM) calculations with the polarisable continuum model (PCM), has been used to study the tetramethylrhodamine isothiocyanate (TRITC) fluorophore, embedded in three different environments, namely in water, on an amorphous silica surface and covalently encapsulated in a silica nanoparticle (C dot). Absorption and emission spectra have been simulated by using TD-B3LYP/PCM calculations, performed on the TRITC ground and excited state geometries, optimized at the QM/MM level. The results are in good agreement with experimental data confirming the caging effect played by the silica shell on the mobility of the TRITC molecule when covalently encapsulated in silica nanoparticles. This could result in a decrease of the nonradiative decay rate and thus an increase of the quantum yield of the molecule.

The popular AMBER force-field has been extended to provide an accurate description of large and flexible nitroxide free-radicals in condensed phases. New atom types have been included, and relevant parameters have been fitted based on geometries, vibrational frequencies and potential energy surfaces computed at the DFT level for several different classes of nitroxides, both in vacuo and in different solvents. The resulting computational tool is capable of providing reliable structures, vibrational frequencies, relative energies and spectroscopic observables for large and flexible nitroxide systems, including those typically used as spin labels. The modified force field has been employed in the context of an integrated approach, based on classical molecular dynamics and discrete-continuum solvent models, for the investigation of environmental and short-time dynamic effects on the hyperfine and gyromagnetic tensors of PROXYL, TEMPO and INDCO spin probes. The computed magnetic parameters are in very good agreement with the available experimental values, and the procedure allows for an unbiased evaluation of the role of different effects in tuning the overall EPR observables.

An integrated computational method which couples classical molecular dynamics simulations with density functional theory calculations is used to simulate the solid-state NMR spectra of amorphous CaSiO(3). Two CaSiO(3) glass models are obtained by shell-model molecular dynamics simulations, successively relaxed at the GGA-PBE level of theory. The calculation of the NMR parameters (chemical shielding and quadrupolar parameters), which are then used to simulate solid-state 1D and 2D-NMR spectra of silicon-29, oxygen-17 and calcium-43, is achieved by the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods. It is shown that the limitations due to the finite size of the MD models can be overcome using a Kernel Estimation Density (KDE) approach to simulate the spectra since it better accounts for the disorder effects on the NMR parameter distribution. KDE allows reconstructing a smoothed NMR parameter distribution from the MD/GIPAW data. Simulated NMR spectra calculated with the present approach are found to be in excellent agreement with the experimental data. This further validates the CaSiO(3) structural model obtained by MD simulations allowing the inference of relationships between structural data and NMR response. The methods used to simulate 1D and 2D-NMR spectra from MD GIPAW data have been integrated in a package (called fpNMR) freely available on request.