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Alfonso PEDONE

Professore Associato
Dipartimento di Scienze Chimiche e Geologiche - Sede Dipartimento di Scienze Chimiche e Geologiche

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2024 - Accurate and Transferable Machine Learning Potential for Molecular Dynamics Simulation of Sodium Silicate Glasses [Articolo su rivista]
Bertani, Marco; Charpentier, Thibault; Faglioni, Francesco; Pedone, Alfonso

2024 - Decoding crystallization behavior of aluminoborosilicate glasses: From structural descriptors to Quantitative Structure – Property Relationship (QSPR) based predictive models [Articolo su rivista]
Zhang, Yingcheng; Bertani, Marco; Pedone, Alfonso; Youngman, Randall E.; Tricot, Gregory; Kumar, Aditya; Goel, Ashutosh

2024 - Iron nuclearity in mineral fibres: Unravelling the catalytic activity for predictive modelling of toxicity [Articolo su rivista]
Gualtieri, Alessandro F.; Cocchi, Marina; Muniz-Miranda, Francesco; Pedone, Alfonso; Castellini, Elena; Strani, Lorenzo

: Chronic inflammation induced in vivo by mineral fibres, such as asbestos, is sustained by the cyclic formation of cytotoxic/genotoxic oxidant species that are catalysed by iron. High catalytic activity is observed when iron atoms are isolated in the crystal lattice (nuclearity=1), whereas the catalytic activity is expected to be reduced or null when iron forms clusters of higher nuclearity. This study presents a novel approach for systematically measuring iron nuclearity across a large range of iron-containing standards and mineral fibres of social and economic importance, and for quantitatively assessing the relation between nuclearity and toxicity. The multivariate curve resolution (MCR) empirical approach and density functional theory (DFT) calculations were applied to the analysis of UV-Vis spectra to obtain information on the nature of iron and nuclearity. This approach led to the determination of the nuclearity of selected mineral fibres which was subsequently used to calculate a toxicity-related index. High nuclearity-related toxicity was estimated for chrysotile samples, fibrous glaucophane, asbestos tremolite, and fibrous wollastonite. Intermediate values of toxicity, corresponding to a mean nuclearity of 2, were assigned to actinolite asbestos, amosite, and crocidolite. Finally, a low nuclearity-related toxicity parameter, corresponding to an iron-cluster with a lower catalytic power to produce oxidants, was assigned to asbestos anthophyllite.

2024 - Quantum-Chemistry Study of the Hydrolysis Reaction Profile in Borate Networks: A Benchmark [Articolo su rivista]
Muniz-Miranda, Francesco; Occhi, Leonardo; Fontanive, Francesco; Menziani, Maria Cristina; Pedone, Alfonso

This investigation involved an ab initio and Density Functional Theory (DFT) analysis of the hydrolysis mechanism and energetics in a borate network. The focus was on understanding how water molecules interact with and disrupt the borate network, an area where the experimental data are scarce and unreliable. The modeled system consisted of two boron atoms, bridging oxygen atoms, and varying numbers of water molecules. This setup allows for an exploration of hydrolysis under different environmental conditions, including the presence of OH− or H+ ions to simulate basic or acidic environments, respectively. Our investigation utilized both ab initio calculations at the MP2 and CCSD(T) levels and DFT with a range of exchange–correlation functionals. The findings indicate that the borate network is significantly more susceptible to hydrolysis in a basic environment, with respect to an acidic or to a neutral pH setting. The inclusion of explicit water molecules in the calculations can significantly affect the results, depending on the nature of the transition state. In fact, some transition states exhibited closed-ring configurations involving water and the boron–oxygen–boron network; in these cases, there were indeed more water molecules corresponding to lower energy barriers for the reaction, suggesting a crucial role of water in stabilizing the transition states. This study provides valuable insights into the hydrolysis process of borate networks, offering a detailed comparison between different computational approaches. The results demonstrate that the functionals B3LYP, PBE0, and wB97Xd closely approximated the reference MP2 and CCSD(T) calculated reaction pathways, both qualitatively in terms of the mechanism, and quantitatively in terms of the differences in the reaction barriers within the 0.1–0.2 eV interval for the most plausible reaction pathways. In addition, CAM-B3LYP also yielded acceptable results in all cases except for the most complicated pathway. These findings are useful for guiding further computational studies, including those employing machine learning approaches, and experimental investigations requiring accurate reference data for hydrolysis reactions in borate networks.

2023 - Can DFT Calculations Provide Useful Information for SERS Applications? [Articolo su rivista]
Muniz-Miranda, Maurizio; Muniz-Miranda, Francesco; Menziani, Maria Cristina; Pedone, Alfonso

: Density functional theory (DFT) calculations allow us to reproduce the SERS (surface-enhanced Raman scattering) spectra of molecules adsorbed on nanostructured metal surfaces and extract the most information this spectroscopy is potentially able to provide. The latter point mainly concerns the anchoring mechanism and the bond strength between molecule and metal as well as the structural and electronic modifications of the adsorbed molecule. These findings are of fundamental importance for the application of this spectroscopic technique. This review presents and discusses some SERS-DFT studies carried out in Italy as a collaboration between the universities of Modena and Reggio-Emilia and of Florence, giving an overview of the information that we can extract with a combination of experimental SERS spectra and DFT modeling. In addition, a selection of the most recent studies and advancements on the DFT approach to SERS spectroscopy is reported with commentary.

2023 - Comparison of five empirical potential models for aluminosilicate systems: Albite and anorthite as test cases [Articolo su rivista]
Pallini, Annalisa; Bertani, Marco; Rustichelli, Daniel; Ziebarth, Benedikt; Mannstadt, Wolfgang; Pedone, Alfonso

2023 - Effects of magnesium on the structure of aluminoborosilicate glasses: NMR assessment of interatomic potentials models for molecular dynamics [Articolo su rivista]
Bertani, Marco; Bisbrouck, Nicolas; Delaye, Jean‐marc; Angeli, Frédéric; Pedone, Alfonso; Charpentier, Thibault

Classical molecular dynamics simulations have been used to investigate the structural role of Mg and its effect when it is incorporated in sodium aluminoborosilicate glasses. The simulations have been performed using three interatomic potentials; one is based on the rigid ionic model parameterized by Wang et al. (2018) and two slightly different parameterization of the core-shell model provided by Stevensson et al. (2018) and Pedone et al. (2020) The accuracies of these models have been assessed by detailed structural analysis and comparing the simulated nuclear magnetic resonance (NMR) spectra for spin active nuclei (Si-29, Al-27, B-11, O-17, Mg-25, and Na-23) with the experimental counterparts collected in a previous work. Our simulations reveal that the core-shell parameterizations provide better structural models. In fact, they better reproduce the NMR spectra of all the investigated nuclei and give better agreement with known experimental data. Magnesium is found to be five coordinated on average with distances with oxygen in between a network modifier (like Na) and an intermediate network formed (like Al). It prefers to lay closer to three-coordinated B atoms, forming B-NBO bonds, with respect to Si and especially Al. This can explain the formation of AlO5 and AlO6 units in the investigated Na-free glass, together with a Si clusterization.

2023 - Erratum for a new self‐consistent empirical potential model for multicomponent borate and borosilicate glasses (Journal of the American Ceramic Society, (2022), 105, 12, (7254-7271), 10.1111/jace.18681) [Articolo su rivista]
Bertani, M.; Pallini, A.; Lodesani, F.; Cocchi, M.; Menziani, M. C.; Pedone, A.

The manuscript contains a mistake in Equation (6) and an erroneous value of the B-ij term of B-O interaction in Table 2. An additional sentence is needed in paragraph 2.2. These errata acknowledge and correct the mistakes and add the needed information. The corrections do not lead to any changes in the results, discussion, and conclusion.

2023 - Evidence of Multiple Crystallization Pathways in Lithium Disilicate: A Metadynamics Investigation [Articolo su rivista]
Lodesani, F.; Menziani, M. C.; Urata, S.; Pedone, A.

Metadynamics simulations driven by using two X-ray diffraction peaks identified three alternative crystallization pathways of the lithium disilicate crystal from the melt. The most favorable one passes through the formation of disordered layered structures undergoing internal ordering in a second step. The second pathway involves the formation of phase-separated structures composed of nuclei of beta-cristobalite crystals surrounded by lithium -rich phases in which metasilicate chains are formed. The conversion of these structures to the stable lithium disilicate crystal involves an intermediate structure whose silicate layers are connected by silicate rings with the energy barrier of 2.5 kJ/mol per formula unit (f.u.). The third pathway is highly unlikely because of the huge energy barrier involved (20 kJ/mol per f.u.). This path also involves the passage through a phase-separated structure of an indefinite silica region surrounded mainly by amorphous lithium oxide.

2022 - A new self-consistent empirical potential model for multicomponent borate and borosilicate glasses [Articolo su rivista]
Bertani, M.; Pallini, A.; Cocchi, M.; Menziani, M. C.; Pedone, A.

A new self-consistent empirical potential model based on the BMP potential [Bertani et al., Phys. Rev. Mat. 5 (2021) 045602] has been developed for the simulation of multicomponent borate and borosilicate glasses. We exploited the Bayesian optimization approach to create a set of parameters for the B–O interaction, which depends on the glass composition, and in particular on the R = ([A2O]+[AEO])/[B2O3] (A = alkaline and AE alkaline-earth ions) and K = [SiO2]/[B2O3] ratios. The obtained force field (FF) has been applied to several borate and borosilicate glass series containing, as modifier oxide, Na2O, Li2O, CaO, and MgO and tested on experimental data, such as the fraction of BO4 (N4), density, non-bridging oxygen speciation, neutron diffraction spectra, 11B, 29Si, and 17O magic angle spinning nuclear magnetic resonance. A comparison with other interatomic potentials available in literature has also been performed. The results show that the FF reproduces well almost all the abovementioned properties, showing excellent agreement with experimental data in a wide range of compositions.

2022 - Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters [Articolo su rivista]
Lodesani, F.; Menziani, M. C.; Urata, S.; Pedone, A.

Metadynamics (MetaD) is a useful technique to study rare events such as crystallization. It has been only recently applied to study nucleation and crystallization in glass-forming liquids such as silicates, but the optimal set of parameters to drive crystallization and obtain converged free energy surfaces is still unexplored. In this work, we systematically investigated the effects of the simulation conditions to efficiently study the thermodynamics and mechanism of crystallization in highly viscous systems. As a prototype system, we used fused silica, which easily crystallizes to β-cristobalite through MetaD simulations, owing to its simple microstructure. We investigated the influence of the height, width, and bias factor used to define the biasing Gaussian potential, as well as the effects of the temperature and system size on the results. Among these parameters, the bias factor and temperature seem to be most effective in sampling the free energy landscape of melt to crystal transition and reaching convergence more quickly. We also demonstrate that the temperature rescaling from T > Tm is a reliable approach to recover free energy surfaces below Tm, provided that the temperature gap is below 600 K and the configurational space has been properly sampled. Finally, albeit a complete crystallization is hard to achieve with large simulation boxes, these can be reliably and effectively exploited to study the first stages of nucleation.

2022 - DFT and TD-DFT Study of the Chemical Effect in the SERS Spectra of Piperidine Adsorbed on Silver Colloidal Nanoparticles [Articolo su rivista]
Muniz-Miranda, Francesco; Pedone, Alfonso; Menziani, Maria Cristina; Muniz-Miranda, Maurizio

2022 - H2O2 adsorption and dissociation on various CeO2(111) surface models: a first-principles study [Articolo su rivista]
Brugnoli, L.; Urata, S.; Pedone, A.

Periodic density functional theory (DFT) calculations using the hybrid PBE0 functional and atom-centered Gaussian functions as basis sets were carried out to investigate the absorption and the first steps involved in the decomposition of hydrogen peroxide (H2O2) on three different models of the ceria (111) surface. One of the models is a clean surface, and the others are defective and partially hydroxylated ceria surfaces. On the clean surface, we found that the minimum energy path of hydrogen peroxide decomposition involves a three-step process, i.e., adsorption, deprotonation, and formation of the peroxide anion, stabilized through its interaction with the surface at a Ce (IV) site, with activation barriers of less than about 0.5 eV. The subsequent formation of superoxide anions and molecular oxygen species is attributed to electron transfer from the reactants to the Ce (IV) ions underneath. On the defective surface, H2O2dissociation is an energetically downhill reaction thermodynamically driven by the healing of the O vacancies, after the reduction and decomposition of H2O2into oxygen and water. On the hydroxylated surface, H2O2is first adsorbed by forming a favorable H-bond and then undergoes heterolytic dissociation, forming two hydroxyl groups at two vicinal Ce sites.

2022 - Interatomic potentials for oxide glasses: Past, present, and future [Articolo su rivista]
Pedone, A.; Bertani, M.; Brugnoli, L.; Pallini, A.

The continuous development and improvement of interatomic potential models for oxide glasses have made classical molecular dynamics a powerful computational technique routinely used for studying the structure and properties of such materials on a par with the more advanced experimental techniques. In this brief review, we retrace the development of the most used interatomic potential models from the earliest MD simulations up to now with a look at the possible future developments in this field due to the advent of the machine learning era and data-driven methods.

2022 - Structure Analysis and Properties Calculations [Capitolo/Saggio]
Presti, D.; Muniz-Miranda, F.; Tavanti, F.; Pedone, A.

2022 - Synthesis and characterization of polymethine dyes carrying thiobarbituric and carboxylic acid moieties [Articolo su rivista]
Desvals, A.; Fortino, M.; Lefebvre, C.; Rogier, J.; Michelin, C.; Alioui, S.; Rousset, E.; Pedone, A.; Lemercier, G.; Hoffmann, N.

An efficient synthesis of polymethine dyes carrying thiobarbituric and a carboxylic acid moiety has been developed. Such compounds play a key role in many photometric detections and quantifications of enzyme activities. In such tests, the metabolite of the enzyme activities is transformed into a β-dicarbonyl derivative. In the present study, this compound was prepared from furfural through organic synthesis. Its in situ transformation with thiobarbituric acid derivatives yields the target compounds on a gram-scale (0.4 to 0.6 g). A combined experimental and theoretical study of the photophysical properties of the synthesized compounds was carried out. Absorption and emission spectroscopy measurements highlighted a slight solvatochromism effect. The luminescence was quenched by molecular oxygen, indicating the partial triplet multiplicity character of the lowest excited state. Density Functional Theory (DFT) calculations have been applied for the evaluation of favoured conformations for these new compounds and the study of their optical properties. Within the Franck Condon principle, the vibrationally resolved electronic one-photon absorption spectrum has been simulated. This simulation shows the presence of a major band followed by a vibronic sideband, typical of organic chromophores in solution. The performed computational study revealed that the transition from the ground to the first excited electronic state has a π-π* character. Finally, TD-DFT energy level diagram calculations highlighted the presence of triplet states very close to the first singlet excited one, suggesting probable access to the triplet-excited state.

2022 - The effect of the incorporation of catalase mimetic activity cations on the structural, thermal and chemical durability properties of the 45S5 Bioglass® [Articolo su rivista]
Malavasi, G.; Pedone, A.

Understanding the effect of the incorporation of doping ions into the structure, thermal properties and chemical durability of bioactive glasses is fundamental for the design of new compositions with tailored biological functions and applications. In this work, we have applied a combined experimental and computational approach to unravel the effect of adding metal oxides of Ce, Ti, V, Mn, Fe, Co, Cu, and Zr that impart catalase mimetic activity to the 45S5 Bioglass® on its density, thermal properties and chemical durability. UV-Vis-NIR spectroscopy and temperature-programmed reduction (TPR) experiments allowed us to determine the oxidation states of the doping cations in the bulk of the glasses, Differential Thermal Analysis has been used to determine the glass transition and crystallization temperature, whereas the chemical durability in water was determined by following the hydrolytic resistance of glass grains at 98 °C standard method. The experimental results have been interpreted at the atomic level by exploiting reliable bulk and surface structural models of the investigated glasses generated by using Molecular Dynamics Simulations. Structure-property relationships helpful for the rational design of new glass compositions have also been inferred.

2021 - Development and Application of a ReaxFF Reactive Force Field for Cerium Oxide/Water Interfaces [Articolo su rivista]
Brugnoli, L.; Menziani, M. C.; Urata, S.; Pedone, A.

Ceria (CeO2) is a well-known catalytic oxide with many environmental, energy production, and industrial applications, most of them involving water as a reactant, byproduct, solvent, or simple spectator. In this work, we parameterized a Ce/O/H ReaxFF for the study of ceria and ceria/water interfaces. The parameters were fitted to anab initiotraining set obtained at the DFT/PBE0 level, including the structures, cohesive energies, and elastic properties of the crystalline phases Ce, CeO2, and Ce2O3; the O-defective structures and energies of vacancy formation on CeO2bulk and CeO2(111) surface, as well as the absorption and reaction energies of H2and H2O molecules on CeO2(111). The new potential reproduced reasonably well all the fitted properties as well as the relative stabilities of the different ceria surfaces, the oxygen vacancies formation, and the energies and structures of associative and dissociative water molecules on them. Molecular dynamics simulations of the liquid water on the CeO2(111) and CeO2(100) surfaces were carried out to study the coverage and the mechanism of water dissociation. After equilibration, on average, 35% of surface sites of CeO2(111) are hydroxylated whereas 15% of them are saturated with molecular water associatively adsorbed. As for the CeO2(100) surface, we observed that water preferentially dissociates covering 90% of the available surface sites in excellent agreement with recent experimental findings.

2021 - Disclosing the interaction of gold nanoparticles with aβ(1–40) monomers through replica exchange molecular dynamics simulations [Articolo su rivista]
Tavanti, F.; Pedone, A.; Menziani, M. C.

Amyloid-β aggregation is one of the principal causes of amyloidogenic diseases that lead to the loss of neuronal cells and to cognitive impairments. The use of gold nanoparticles treating amyloidogenic diseases is a promising approach, because the chemistry of the gold surface can be tuned in order to have a specific binding, obtaining effective tools to control the aggregation. In this paper, we show, by means of Replica Exchange Solute Tempering Molecular Simulations, how electrostatic interactions drive the absorption of Amyloid-β monomers onto citrates-capped gold nanoparticles. Importantly, upon binding, amyloid monomers show a reduced propensity in forming β-sheets secondary structures that are characteristics of mature amyloid fibrils.

2021 - Exploring the crystallization path of lithium disilicate through metadynamics simulations [Articolo su rivista]
Lodesani, F.; Tavanti, F.; Menziani, M. C.; Maeda, K.; Takato, Y.; Urata, S.; Pedone, A.

Understanding the crystallization mechanism in silica-based materials is of paramount importance to comprehend geological phenomena and to design novel materials for a variety of technological and industrial applications. In this work, we show that metadynamics simulations can effectively overcome a large energy barrier to crystallize from viscous oxide glass melts and can be used to identify the melt-to-crystal transition path of the lithium disilicate system. The accelerated atomistic simulation revealed of a two-step mechanism of the nanoscale crystal formation. First, a partially layered silica embryo appeared, and then a more ordered crystalline layer with size larger than the critical nucleus size was formed. Subsequently, lithium ions piled up around the silicate layer and triggered stacking of adjacent silicate layers, which eventually built a perfect crystal. Contrarily to previous hypotheses, no lithium metasilicate crystal was observed as a precursor of the homogeneous crystallization of lithium disilicate.

2021 - Improved empirical force field for multicomponent oxide glasses and crystals [Articolo su rivista]
Bertani, M.; Menziani, M. C.; Pedone, A.

In this paper, the self-consistent PMMCS force fields (FFs) [Pedone et al., J. Phys. Chem. B 110, 11780 (2006)10.1021/jp0611018] widely used for the simulation of a large variety of silicates, aluminosilicate and phosphate crystals, and multicomponent oxide glasses have been revised and improved by the inclusion of two types of three-body interactions acting between T-O-T bridges (T=Si and P) and network former-network former repulsive interactions. The FFs named Bertani-Menziani-Pedone (BMP)-harm and BMP-shrm better reproduce the T-O-T bond angle distributions (BADs) and network former-oxygen distances. Consequently, the prediction of Qn distributions (Q stands for quaternary species, and n is the number of bridging oxygens around it), neutron total distribution functions, solid-state nuclear magnetic resonance spectra of spin active nuclei (Si29, O17, P31, Al27), and the density have also been hugely improved with respect to the previous version of our FF. These results also highlight the strong correlation between the T-O-T BADs and the other short and intermediate structural properties in oxide glasses, which have been largely neglected in the past. In addition to the improvement of the structure, the FF has been revealed to reproduce well the ionic conductivity in mixed alkali aluminosilicate glasses and the elastic properties. The systematic comparison with other interatomic potential models, including the polarizable core-shell model, carried out in this paper showed that our potential model is more balanced and effective for simulating a vast family of crystalline and amorphous oxide-based systems.

2021 - Toward the understanding of crystallization, mechanical properties and reactivity of multicomponent bioactive glasses [Articolo su rivista]
Pedone, Alfonso; Cannillo, Valeria; Menziani, Maria Cristina

2021 - Unraveling the internal conversion process within the Q-bands of a chlorophyll-like-system through surface-hopping molecular dynamics simulations [Articolo su rivista]
Fortino, M.; Collini, E.; Bloino, J.; Pedone, A.

The non-radiative relaxation process within the Q-bands of chlorophylls represents a crucial preliminary step during the photosynthetic mechanism. Despite several experimental and theoretical efforts performed in order to clarify the complex dynamics characterizing this stage, a complete understanding of this mechanism is still far to be reached. In this study, non-adiabatic excited-state molecular dynamic simulations have been performed to model the non-radiative process within the Q-bands for a model system of chlorophylls. This system has been considered in the gas phase and then, to have a more representative picture of the environment, with implicit and mixed implicit-explicit solvation models. In the first part of this analysis, absorption spectra have been simulated for each model in order to guide the setup for the non-adiabatic excited-state molecular dynamic simulations. Then, non-adiabatic excited-state molecular dynamic simulations have been performed on a large set of independent trajectories and the population of the Qx and Qy states has been computed as the average of all the trajectories, estimating the rate constant for the process. Finally, with the aim of investigating the possible role played by the solvent in the Qx-Qy crossing mechanism, an essential dynamic analysis has been performed on the generated data, allowing one to find the most important motions during the simulated dynamics.

2020 - Combined Experimental and Computational Approach toward the Structural Design of Borosilicate-Based Bioactive Glasses [Articolo su rivista]
Stone-Weiss, N.; Bradtmuller, H.; Fortino, M.; Bertani, M.; Youngman, R. E.; Pedone, A.; Eckert, H.; Goel, A.

Transitioning beyond a trial-and-error based approach for the compositional design of next-generation borosilicate-based bioactive glasses requires a fundamental understanding of the underlying compositional and structural drivers controlling their degradation and ion release in vitro and in vivo. Accordingly, the present work combines magic-angle spinning (MAS) NMR techniques, MD simulations, and DFT calculations based on GIPAW and PAW algorithms, to build a comprehensive model describing the short-to-medium-range structure of potentially bioactive glasses in the Na2O-P2O5-B2O3-SiO2 system over a broad compositional space. P2O5 preferentially tends to attract network modifier species, thus resulting in a repolymerization of the silicate network and a restructuring of the borate component. 11B{31P} and 31P{11B} dipolar recoupling experiments suggest that the ability of glasses to incorporate P2O5 without phase separation is related to the formation of P-O-B(IV) linkages integrated into the borosilicate glass network. An analogous approach is used for elucidating the local environments of the Na+ network modifiers. This work, along with future studies aimed at elucidating composition-structure-solubility/bioactivity relationships, will lay the foundation for the development of quantitative structure-property relationship (QSPR) models, thus representing a leap forward in the design of functional borosilicate bioactive glasses with controlled ionic release behavior.

2020 - Computational insights into the binding of monolayer-capped gold nanoparticles onto amyloid-β fibrils [Articolo su rivista]
Tavanti, F.; Pedone, A.; Menziani, M. C.; Alexander-Katz, A.

Amyloids-β (Aβ) fibrils are involved in several neurodegenerative diseases. In this study, atomistic molecular dynamics simulations have been used to investigate how monolayer-protected gold nanoparticles interact with Aβ(1-40) and Aβ(1-42) fibrils. Our results show that small gold nanoparticles bind with the external side of amyloid-β fibrils that is involved in the fibrillation process. The binding affinity, studied for both kinds of fibrils as a function of the monolayer composition and the nanoparticle diameter, is modulated by hydrophobic interactions and ligand monolayer conformation. Our findings thus show that monolayer-protected nanoparticles are good candidates to prevent fibril aggregation and secondary nucleation or to deliver drugs to specific fibril regions.

2020 - Disclosing crystal nucleation mechanism in lithium disilicate glass through molecular dynamics simulations and free-energy calculations [Articolo su rivista]
Lodesani, F.; Menziani, M. C.; Maeda, K.; Takato, Y.; Urata, S.; Pedone, A.

Unraveling detailed mechanism of crystal nucleation from amorphous materials is challenging for both experimental and theoretical approaches. In this study, we have examined two methods to understand the initial stage of crystal precipitation from lithium disilicate glasses using molecular dynamics simulations. One of the methods is a modified exploring method to find structurally similar crystalline clusters in the glass models, enabling us to find three different embryos, such as Li2Si2O5 (LS2), Li2SiO3 (LS) and Li3PO4 (LP), in the 33Li2O·66SiO2·1P2O5 glass (LS2P1), in which P2O5 is added as a nucleating agent. Interestingly, LS2 and LP crystals were found inside the LS2P1 glass while LS crystal appeared on the glass surface, which agrees with experimental observations. The other method is free energy calculation using a subnano-scale spherical crystal embedded in the glass model. This method, which we called Free-Energy Seeding Method (FESM), allows us to evaluate free energy change as a function of crystal radius and to identify critical size of the crystal precipitation. The free energy profiles for LS and LS2 crystal nuclei in the LS2 glass models possess maximum energy at a critical radius as expected by classical nucleation theory. Furthermore, the critical radius and the energy barrier height agree well with recent experimental investigation, proving the applicability of this method to design glass–ceramics by atomistic modeling.

2020 - Insights into the effect of curcumin and (–)-epigallocatechin-3-gallate on the aggregation of aβ(1–40) monomers by means of molecular dynamics [Articolo su rivista]
Tavanti, F.; Pedone, A.; Menziani, M. C.

In this study, we compared the effects of two well-known natural compounds on the early step of the fibrillation process of amyloid-β (1–40), responsible for the formation of plaques in the brains of patients affected by Alzheimer’s disease (AD). The use of extensive replica exchange simulations up to the µs scale allowed us to characterize the inhibition activity of (–)-epigallocatechin-3-gallate (EGCG) and curcumin (CUR) on unfolded amyloid fibrils. A reduced number of β-strands, characteristic of amyloid fibrils, and an increased distance between the amino acids that are responsible for the intra-and interprotein aggregations are observed. The central core region of the amyloid-β (Aβ(1–40)) fibril is found to have a high affinity to EGCG and CUR due to the presence of hydrophobic residues. Lastly, the free binding energy computed using the Poisson Boltzmann Surface Ares suggests that EGCG is more likely to bind to unfolded Aβ(1–40) fibrils and that this molecule can be a good candidate to develop new and more effective congeners to treat AD.

2020 - O2Activation over Ag-Decorated CeO2(111) and TiO2(110) Surfaces: A Theoretical Comparative Investigation [Articolo su rivista]
Brugnoli, L.; Pedone, A.; Menziani, M. C.; Adamo, C.; Labat, F.

Periodic spin-polarized hybrid density functional theory calculations have been performed to investigate the reactivity of pristine, O-defective, and Ag-decorated CeO2(111) and TiO2(110) surfaces with a small Ag10 cluster toward O2. The adsorption of O2 and its subsequent dissociation have been studied in order to provide a better understanding of the role of the oxide, the metallic nanoparticle, and their interaction in the reactivity of composite metal/metal oxide materials toward O2, as potential catalysts to this reaction. Structural, energetic, electronic, and vibrational properties of all species involved in the different reaction paths considered have been fully characterized. On the stoichiometric surfaces, Ag10 is oxidized and reduces surface Ce4+/Ti4+ ions, while on the O-defective surfaces, the adhesion of silver is promoted only on CeO2 but unfavored on TiO2. On the other hand, on the silver-free supports, O2 strongly adsorbs at vacancies and preferentially reduces to peroxide. When no O vacancies are considered on the Ag10-decorated supports, the net positive charge on Ag10 actually prevents the adsorption and reduction of O2. Instead, when O vacancies are included, two reaction pathways are observed; oxygen molecules can weakly absorb on the silver cluster as a superoxide moiety or strongly adsorb at the vacancy as peroxide. The dissociation of the O-O bond of the peroxide is favored both from the thermodynamic and kinetic points of view in silver-decorated surfaces, in contrast with the silver-free cases. In addition, Ag10/CeO2 shows higher activity toward the O2 adsorption and dissociation than Ag10/TiO2, which can be related both to the higher ionicity and superior electron storage/release ability of ceria with respect to titania, thus leading to the weakening of the O-O bond and providing lower activation barriers for oxygen reduction. These results deepen the current understanding of the reactivity of metal/metal oxide composites toward O2, especially elucidating how the surface stoichiometry affects the charge state of the metal clusters, and hence the reactivity of these interfaces toward O2, with potential important consequences when such composites are considered for catalytic applications.

2020 - Role of specific solute-solvent interactions on the photophysical properties of distyryl substituted BODIPY derivatives [Articolo su rivista]
Fortino, M.; Collini, E.; Pedone, A.; Bloino, J.

Computational spectroscopy is now a valuable tool to better understand experimental spectroscopic data. Recent advancements in computational methods allow the study of electronic excited states of medium-large molecular systems with greater accuracy, simulating spectra directly comparable with experiments. Besides the system of interest, proper modelling of the environment effects is essential to reach a sufficient level of accuracy. This is especially important for solvents with high polarity or those able to establish specific interactions with the solute. One of the most straightforward and fastest ways to deal with solvent effects is the use of implicit models, like the polarizable continuum model (PCM). However, these models cannot describe specific solute-solvent interactions. In this case, one possible solution is the adoption of a mixed model that includes the solute and few solvent molecules within a PCM cavity. With the aim of investigating the role played by specific solute-solvent interactions, the behaviour of styryl substituted BODIPY systems in methanol has been studied at a theoretical level, considering both implicit and mixed implicit-explicit models. In the first part of our analysis, vibrationally resolved electronic spectra for absorption and emission processes have been simulated, using several sets of coordinates to represent normal modes, and compared with experiments. Then, to verify if specific solute-solvent interactions play a crucial role during the ultrafast intraband relaxation processes, 2D electronic spectra were also simulated, which could provide valuable information on the complex ultrafast dynamics.

2020 - Structural origins of the Mixed Alkali Effect in Alkali Aluminosilicate Glasses: Molecular Dynamics Study and its Assessment [Articolo su rivista]
Lodesani, Federica; Menziani, Maria Cristina; Hijiya, Hiroyuki; Takato, Yoichi; Urata, Shingo; Pedone, Alfonso

The comprehension of the nonlinear effects provided by mixed alkali effect (MAE) in oxide glasses is useful to optimize glass compositions to achieve specific properties that depend on the mobility of ions, such as the chemical durability, glass transition temperature, viscosity and ionic conductivity. Although molecular dynamics (MD) simulations have already been applied to investigate the MAE on silicates, less effort has been devoted to study such phenomenon in mixed alkali aluminosilicate glasses where alkali cations can act both as modifiers, forming non-bridging oxygens and percolation channels, and as charge compensator of the AlO4− units present in the network. Moreover, the ionic conductivity has not been computed yet; thus, the accuracy of the atomistic simulations in reproducing the MAE on the property is still open to question. In this work, we have validated five major interatomic potentials for the classical MD simulations by modelling the structure, density, glass transition temperature and ionic conductivity for three aluminosilicate glasses, (25 − x)Na2O − x(K2O) − 10(Al2O3) − 65(SiO2) (x = 0, 12.5, 25). It was observed that only the core-shell (CS) polarizable force field well reproduces the experimentally measured MAE on Tg and the ionic conductivity as well as the higher conductivity of single sodium aluminosilicate glass at low temperature and the higher conductivity of single potassium aluminosilicate glass at high temperature. The MAE is related to the suppression of jump events of the alkaline ions between dissimilar sites in the percolation channels consisting of both sodium and potassium ions as in the case of alkaline silicates. The superior reproducibility of the CS potential is originated from the larger and the flexible ring structures due to the smaller Si-O-Si inter-tetrahedra angle, creating appropriate percolation channels for ion conductivity. We also report detailed assessments for using the potential models including the CS potential for investigating MAE on aluminosilicates.

2019 - Adsorption of Trans-Zeatin on Laser-Ablated Gold Nanoparticles for Transport into Plant Cells and Growth Stimulation [Articolo su rivista]
Zoppi, A.; Caporali, S.; Muniz-Miranda, F.; Pedone, A.; Muniz-Miranda, M.

Gold nanoparticles can serve as nanovectors for trans-zeatin, a natural cytokinin used in plant culture to stimulate growth and bud formation. Here, we have used Raman scattering, X-ray photoelectron spectroscopy, UV-vis absorption, transmission electron microscopy, and density functional theory calculations to explain the role of citrate anions in both the formation and the reactivity of the gold colloidal nanoparticles obtained by laser ablation and to go deeper inside into the interaction between metal and zeatin. In particular, the SERS (surface-enhanced Raman scattering) spectroscopy has been employed to study the adsorption of zeatin on different gold colloidal substrates. It is established that the molecule links to gold as tautomer N7(H), predominant in the aqueous suspension, in close similarity with adenine adsorbed on gold. Moreover, the laser ablation of a gold target in citrate solution results in small, stable, and reactive Au nanoparticles, able to transport zeatin inside plant cells, where it can act as a growth hormone.

2019 - Assessment of interatomic parameters for the reproduction of borosilicate glass structures via DFT‐GIPAW calculations [Articolo su rivista]
Fortino, Mariagrazia; Berselli, Alessandro; Stone‐weiss, Nicholas; Deng, Lu; Goel, Ashutosh; Du, Jincheng; Pedone, Alfonso

Borates and borosilicates are potential candidates for the design and development of glass formulations with important industrial and technological applications. A major challenge that retards the pace of development of borate/borosilicate based glasses using predictive modeling is the lack of reliable computational models to predict the structure‐property relationships in these glasses over a wide compositional space. A major hindrance in this pursuit has been the complexity of boron‐oxygen bonding due to which it has been difficult to develop adequate B–O interatomic potentials. In this article, we have evaluated the performance of three B–O interatomic potential models recently developed by Bauchy et al [J. Non‐Cryst. Solids, 2018, 498, 294–304], Du et al [J. Am. Ceram. Soc.] and Edèn et al [Phys. Chem. Chem. Phys., 2018, 20, 8192–8209] aiming to reproduce the short‐to‐medium range structures of sodium borosilicate glasses in the system 25 Na2O x B2O3 (75 − x) SiO2 (x = 0‐75 mol%). To evaluate the different force fields, we have computed at the density functional theory level the NMR parameters of 11B, 23Na, and 29Si of the models generated with the three potentials and the simulated MAS NMR spectra compared with the experimental counterparts. It was observed that the rigid ionic models proposed by Bauchy and Du can both reliably reproduce the partitioning between BO3 and BO4 species of the investigated glasses, along with the local environment around sodium in the glass structure. However, they do not accurately reproduce the second coordination sphere of silicon ions and the Si–O–T (T = Si, B) and B‐O‐T distribution angles in the investigated compositional space which strongly affect the NMR parameters and final spectral shape. On the other hand, the core‐shell parameterization model proposed by Edén underestimates the fraction of BO4 species of the glass with composition 25Na2O 18.4B2O3 56.6SiO2 but can accurately reproduce the shape of the 11B and 29Si MAS‐NMR spectra of the glasses investigations due to the narrower B–O–T and Si‐O‐T bond angle distributions. Finally, the effect of the number of boron atoms (also distinguishing the BO3 and BO4 units) in the second coordination sphere of the network former cations on the NMR parameters have been evaluated.

2019 - H2 Dissociation and Water Evolution on Silver-Decorated CeO2(111): A Hybrid Density Functional Theory Investigation [Articolo su rivista]
Brugnoli, L.; Pedone, A.; Menziani, M. C.; Adamo, C.; Labat, F.

We present a theoretical investigation of the reactivity of both a pristine CeO2 surface and a small Ag cluster adsorbed on a CeO2 surface toward H2, using a periodic spin-polarized hybrid density functional theory approach. The dissociation of H2 and subsequent formation of H2O have been considered to highlight the role of the metal structure and its underlying metal oxide support as a potential candidate as a catalyst to the above-mentioned reactions. The structural, energetic, electronic, and vibrational properties of all species involved in different reaction paths considered have been fully characterized. The cluster-oxide surface interface has been found to involve the reduction of up to 3Ce4+ to Ce3+, by direct electron transfer from the cluster to the oxide. When comparing the reducibility of the Ag-CeO2 and clean CeO2 systems, O vacancy formation has been found to be hindered along the perimeter of the cluster, while it is promoted underneath the cluster, and is almost unaffected on the surface sites close to the cluster. On the other hand, barriers for the H2 dissociation and the formation of water by H and HO association are lowered with respect to the most favored reaction path found on clean CeO2. These results highlight the key role of metal structures and their underlying oxide support, and especially the three-phase boundary between the gas phase, Ag, and CeO2 as catalysts to such reactions, suggesting potential application as anodic electrocatalysts in fuel cells for example.

2019 - Multiscale Molecular Dynamics Simulation of Multiple Protein Adsorption on Gold Nanoparticles [Articolo su rivista]
Tavanti, F.; Pedone, A.; Menziani, M. C.

A multiscale molecular dynamics simulation study has been carried out in order to provide in-depth information on the adsorption of hemoglobin, myoglobin, and trypsin over citrate-capped AuNPs of 15 nm diameter. In particular, determinants for single proteins adsorption and simultaneous adsorption of the three types of proteins considered have been studied by Coarse-Grained and Meso-Scale molecular simulations, respectively. The results, discussed in the light of the controversial experimental data reported in the current experimental literature, have provided a detailed description of the (i) recognition process, (ii) number of proteins involved in the early stages of corona formation, (iii) protein competition for AuNP adsorption, (iv) interaction modalities between AuNP and protein binding sites, and (v) protein structural preservation and alteration.

2019 - On the simulation of vibrationally resolved electronic spectra of medium-size molecules: the case of styryl substituted BODIPYs [Articolo su rivista]
Fortino, Mariagrazia; Bloino, Julien; Collini, Elisabetta; Bolzonello, Luca; Trapani, Mariachiara; Faglioni, Francesco; Pedone, Alfonso

BODIPY dyes are used in a variety of applications because of their peculiar spectroscopic and photo-physical properties that vary depending on the stereochemistry of the functional groups attached to the boron-dipyrromethene core structure. In this work, we have applied several computational methods, adapted for semi-rigid molecules based on the Franck-Condon principle, for the study of the optical properties of BODIPY systems and for the understanding of the influence of functional groups on their spectroscopic features. We have analyzed the electronic spectra of two styryl substituted BODIPY molecules of technological interest, properly taking into account the vibronic contribution. For comparison with recently recorded experimental data in methanol, the vibrationally resolved electronic spectra of these systems were computed using both Time-Independent (TI) and Time-Dependent (TD) formalisms. The first step toward the analysis of optical properties of the styryl modified BODIPYs was a benchmark of several density functionals, to select the most appropriate one. We have found that all benchmarked functionals provide good results in terms of band shape but some of them show strong discrepancies in terms of band position. Beyond the issue of the electronic structure calculation method, different levels of sophistication can be adopted for the calculation of vibronic transitions. In this study, the effect of mode couplings and the influence of the Herzberg-Teller terms on the theoretical spectra has been investigated. It has been found that all levels of theory considered give reproducible results for the investigated systems: band positions and shapes are similar at all levels and little improvements have been found in terms of band shape with the inclusion of Herzberg-Teller effect. Inclusion of temperature effects proved to be challenging due to the important impact of large amplitude motions. Better agreement can be achieved by adopting a suitable set of coordinates coupled with a reduced-dimensionality scheme.

2019 - Reducibility of Ag- and Cu-Modified Ultrathin Epitaxial Cerium Oxide Films [Articolo su rivista]
Gasperi, G.; Brugnoli, L.; Pedone, A.; Menziani, M. C.; Valeri, S.; Luches, P.

The functionality of cerium oxide, and in particular its reactivity, can be significantly altered by the addition of diluted cationic species with different electronic properties as compared to cerium. We investigate the modifications induced by Ag and Cu as modifier cations in cerium oxide ultrathin epitaxial films. The reducibility is assessed by following the modifications of the oxidation state of surface Ce ions by X-ray photoemission spectroscopy, during thermal treatments in ultrahigh vacuum and oxygen partial pressure. A significantly higher reducibility is observed in Ag- and Cu-modified films as compared to pure CeO2 films of the same thickness. The thermal stability of the cation modifier concentration and the changes of the surface structure with the reducing treatments are also discussed. The modifications induced in the material are explained by comparison with density functional theory calculations, which indicate that the oxygen vacancy formation energy is significantly modified by the addition of Ag or Cu in the cerium oxide matrix. The obtained results are of help in view of a rational design of catalysts with optimized performance.

2019 - SERS, XPS and DFT study of xanthine adsorbed on citrate-stabilized gold nanoparticles [Articolo su rivista]
Caporali, S.; Muniz-Miranda, F.; Pedone, A.; Muniz-Miranda, M.

We have studied the adsorption of xanthine, a nucleobase present in human tissue and fluids that is involved in important metabolic processes, on citrate-reduced gold colloidal nanoparticles by means of surface-enhanced Raman scattering (SERS), absorption, and X-ray photoelectron spectroscopy (XPS) measurements, along with density functional theory (DFT) calculations. The citrate anions stabilize the colloidal suspensions by strongly binding the gold nanoparticles. However, these anions do not impair the adsorption of xanthine on positively-charged active sites present on the metal surface. We have obtained the Fourier transform (FT)-SERS spectra of adsorbed xanthine by laser excitation in the near infrared spectral region, where interference due to fluorescence emission does not usually occur. In fact, the addition of chloride ions to the Au/xanthine colloid induces the aggregation of the gold nanoparticles, whose plasmonic band is shifted to the near infrared region where there is the exciting laser line of the FT–Raman instrument. Hence, this analytical approach is potentially suitable for spectroscopic determination of xanthine directly in body fluids, avoiding fluorescence phenomena induced by visible laser irradiation.

2019 - Structure Model and Toxicity of the Product of Biodissolution of Chrysotile Asbestos in the Lungs [Articolo su rivista]
Gualtieri, A. F.; Lusvardi, G.; Pedone, A.; Di Giuseppe, D.; Zoboli, A.; Mucci, A.; Zambon, A.; Filaferro, M.; Vitale, G.; Benassi, M.; Avallone, R.; Pasquali, L.; Lassinantti Gualtieri, M.

Asbestos is a commercial term indicating six natural silicates with asbestiform crystal habit. Of these, five are double-chain silicates (amphibole) and one is a layer silicate (serpentine asbestos or chrysotile). Although all species are classified as human carcinogens, their degree of toxicity is still a matter of debate. Amphibole asbestos species are biopersistent in the human lungs and exert their chronic toxic action for decades, whereas chrysotile is not biopersistent and transforms into an amorphous silica structure prone to chemical/physical clearance when exposed to the acidic environment created by the alveolar macrophages. There is evidence in the literature of the toxicity of chrysotile, but its limited biopersistence is thought to explain the difference in toxicity with respect to amphibole asbestos. To date, no comprehensive model describing the toxic action of chrysotile in the lungs is available, as the structure and toxic action of the product formed by the biodissolution of chrysotile are unknown. This work is aimed at fulfilling this gap and explaining the toxic action in terms of structural, chemical, and physical properties. We show that chrysotile's fibrous structure induces cellular damage, mainly through physical interactions. Based on our previous work and novel findings, we propose the following toxicity model: inhaled chrysotile fibers exert their toxicity in the alveolar space by physical and biochemical action. The fibers are soon leached by the intracellular acid environment into a product with residual toxicity, and the dissolution process liberates toxic metals in the intracellular and extracellular environment.

2018 - An atomic-level look at the structure-property relationship of cerium-doped glasses using classical molecular dynamics [Articolo su rivista]
Pedone, Alfonso; Tavanti, Francesco; Malavasi, Gianluca; Menziani, Maria Cristina

Ce-containing bioactive glasses are of great interest in biomedical field since they exert antioxidant properties associated with low toxicity and a broad spectrum of bacteriostatic activities. The results obtained by classical molecular dynamics simulations allow the elucidation of the correlations between the effect of the inclusion of cerium doping ions into the structure of phosphosilicate and silicate bioactive glasses and their properties. The addition of small quantities of Ce to the silicate bioglass favours the depolymerisation of the silicate network with a positive effect on the ability to dissolve in body fluid. Moreover, the under coordination of both the Ce3+ and Ce4+ species in these glasses enhances their catalytic activity towards hydrogen peroxide. Conversely, the formation of cerium phosphate domains in the phosphosilicate glasses leads to detrimental effects for both the solubility and the catalytic activity of the glasses. Finally, a new quantitative view of the structure-activity relationships governing the macroscopic properties of these glasses has been obtained by means of structural descriptor that takes into account the fragmentation of the Si network and the consequent rearrangement of the modifier ions and the network destruction per cerium unit descriptor.

2018 - Assessment of Density Functional Approximations for Highly Correlated Oxides: The Case of CeO2 and Ce2O3 [Articolo su rivista]
Brugnoli, Luca; Ferrari, Anna Maria; Civalleri, Bartolomeo; Pedone, Alfonso; Menziani, Maria Cristina

CeO2 based materials are very attractive as catalytic components for industrial processes and environmentally friendly technologies; therefore, a reliable and computationally affordable theoretical description of the main properties of ceria is needed. In particular, the description of the interconversion between the Ce(IV) and Ce(III) oxidation states, on which lies the main chemical features of the cerium oxide, results in quite a challenge at the Density Functional Theory level. Here, we tested several density functional approximations, spanning from GGA to hybrid (Global, Meta-Global, and Range Separated Corrected) functionals, on the structural, vibrational, electronic, and thermochemical properties of bulk CeO2 and Ce2O3. GGA and Meta-GGA xc best predict the thermochemical data, while the discrepancies increase with the introduction of the exact exchange in hybrid functionals. Overall, the Short Range Corrected and Global Hybrid functionals with a percentage of Exact Exchange between 16 and 25 give the best description of the crystal properties. Then, a group of the best performing functionals has been tested on the formation energy of an oxygen vacancy at the (111) CeO2 surface. In general, increasing the amount of exact exchange in the hybrid functionals leads to a better description of the localized Ce 4f states, while the energy of formation of the O vacancy decreases, worsening compared to the experiment.

2018 - Computational Insight into the Effect of Natural Compounds on the Destabilization of Preformed Amyloid-β(1⁻40) Fibrils [Articolo su rivista]
Tavanti, Francesco; Pedone, Alfonso; Menziani, Maria Cristina

One of the principal hallmarks of Alzheimer's disease (AD) is related to the aggregation of amyloid-β fibrils in an insoluble form in the brain, also known as amyloidosis. Therefore, a prominent therapeutic strategy against AD consists of either blocking the amyloid aggregation and/or destroying the already formed aggregates. Natural products have shown significant therapeutic potential as amyloid inhibitors from in vitro studies as well as in vivo animal tests. In this study, the interaction of five natural biophenols (curcumin, dopamine, (-)-epigallocatechin-3-gallate, quercetin, and rosmarinic acid) with amyloid-β(1⁻40) fibrils has been studied through computational simulations. The results allowed the identification and characterization of the different binding modalities of each compounds and their consequences on fibril dynamics and aggregation. It emerges that the lateral aggregation of the fibrils is strongly influenced by the intercalation of the ligands, which modulates the double-layered structure stability.

2018 - Molecular Dynamics Investigation of Halide-Containing Phospho-Silicate Bioactive Glasses [Articolo su rivista]
Pedone, Alfonso; Chen, Xiaojing; Hill, Robert G.; Karpukhina, Natalia

Oxyhalide-containing silicate glasses have been receiving increasing attention in recent years due to their extensive medical and dental applications. This manuscript reports the first detailed structural investigation using MD simulations in the context of chloride- and mixed-fluoride/chloride-containing phospho-silicate bioactive glasses. It is shown that adding fluoride, chloride, and mixed fluoride and chloride has not altered the Qn silicate distribution and phosphorus speciation significantly in all of the glasses investigated. The Q2 silicon species is the predominant species with smaller and nearly equal proportions of Q1 and Q3 species, whereas phosphorus is largely present as orthophosphate Q0 units. No Si-F/Cl and P-F/Cl bonds have been observed at room temperature. Both F and Cl anions are present as F-Ca(n) and Cl-Ca(n). MD simulations also indicate opposite effects of fluoride and chloride on the crystallization ability of the glasses. The environment of Cl in chloride-containing glass series is quite different from the chlorapatite and CaCl2 crystals, and a significant structural reorganization is required to observe the appearance of the crystal nuclei. Instead, the environment of fluoride ions in the glasses is quite similar to that present in the FAP and CaF2 crystals and thus F-containing glasses manifest a high crystallization tendency. Moreover, in the mixed-fluoride/chloride-containing glasses, fluorine tends to surround phosphate, whereas chloride moves toward the silicate network. Finally, it was observed that a good correlation exists between the glass transition temperature and the overall strength of the glass network quantified by the Fnet factor.

2018 - New Insight into Mixing Fluoride and Chloride in Bioactive Silicate Glasses [Articolo su rivista]
Chen, Xiaojing; Chen, Xiaohui; Pedone, Alfonso; Apperley, David; Hill, Robert G.; Karpukhina, Natalia

Adding fluoride into bioactive glasses leads to fluorapatite formation and a decrease in glass transition temperature. Recently, chloride has been introduced into glasses as an alternative to fluoride. The presence of the large chloride ion lowers glass crystallisation tendency and increases glass molar volume, which effectively facilitates glass degradation and bone-bonding apatite-like layer formation. However, there is no information regarding the effect of mixing fluoride and chloride on the glass structure and properties. This study aims to synthesize mixed fluoride and chloride containing bioactive glasses; investigate the structural role of fluoride and chloride and their effects on glass properties. The chloride content measurements reveal that 77-90% of chloride was retained in these Q2type glasses. Glass transition temperature reduced markedly with an increase in CaX2(X = F + Cl) content, while the glass molar volume increased.29Si MAS-NMR results show that the incorporation of mixed fluoride and chloride did not cause significant change in the polymerization of the silicate network and no detectable concentration of Si-F/Cl bands were present. This agrees with19F NMR spectra showing that F existed as F-Ca(n) species.

2018 - Raman and Computational Study on the Adsorption of Xanthine on Silver Nanocolloids [Articolo su rivista]
Muniz-Miranda, Francesco; Pedone, Alfonso; Muniz-Miranda, Maurizio

Xanthine is a nucleobase, deriving from adenine and guanine by deamination and oxidation processes, which may deposit in the human body causing diseases, similar to uric acid. Here, we have investigated the adsorption of xanthine on silver colloidal nanoparticles by means of surface-enhanced Raman scattering (SERS) with an exciting radiation in the near-infrared spectral region, where interference due to fluorescence does not occur, along with density functional theory calculations of molecule/metal model systems. By adopting a combined experimental and computational approach, we have identified the "marker" SERS bands of xanthine and the tautomer that preferentially binds the silver particles, as well as the molecular group involved in the interaction with metal. This investigation allows using the FT-SERS spectroscopy for biosensory and diagnostic purposes in body fluids, detecting abnormal levels of xanthine, and preventing metabolic diseases.

2018 - SERS active Ag-SiO2 nanoparticles obtained by laser ablation of silver in colloidal silica [Articolo su rivista]
Gellini, Cristina; Muniz-Miranda, Francesco; Pedone, Alfonso; Muniz-Miranda, Maurizio

Highly stable Ag-SiO2 nanoparticle composites were first obtained by laser ablation of a silver target in an aqueous colloidal dispersion of silica and examined by UV-vis absorption spectroscopy, transmission electron microscopy and Raman spectroscopy. The surface enhanced Raman scattering (SERS) activity of these nanocomposites was tested using 2,2'-bipyridine as a molecular reporter and excitation in the visible and near-IR spectral regions. The computational DFT approach provided evidence of ligand adsorption on positively charged adatoms of the silver nanostructured surface, in a very similar way to the metal/molecule interaction occurring in the corresponding Ag(I) coordination compound.

2018 - SERS and DFT investigation on push-pull molecules: 4-Dimethylamino- 4’-nitrostilbene adsorbed on silver colloidal nanoparticles [Articolo su rivista]
Muniz-Miranda, Maurizio; Muniz-Miranda, Francesco; Pedone, Alfonso

The adsorption of 4-dimethylamino-4’-nitrostilbene, a typical push-pull chromophore, on Ag colloidal nanoparticles has been studied for the first time by SERS spectroscopy with different exciting lines and interpreted by the help of density functional theory calculations. This study allowed ascertaining the adsorption of DANS on silver via nitro-group and collecting information on the structural changes of the molecule induced by the interaction with the metal surface, leading to augmented nonlinear optical properties. In addition, under blue-green light irradiation the adsorbed molecules undergo a photoreduction of the nitro-group by a plasmon-induced catalyzing effect of the nanostructured silver surface.

2018 - SERS, XPS and DFT investigation on palladium surfaces coated with 2,2′-bipyridine monolayers [Articolo su rivista]
Muniz-Miranda, Maurizio; Muniz-Miranda, Francesco; Caporali, Stefano; Calisi, Nicola; Pedone, Alfonso

Palladium surfaces, pretreated with a solution of 2,2′-bipyridine (bpy) as ligand molecule, were SERS-activated by means of laser-ablated Ag colloidal nanoparticles. XPS and Raman measurements, along with DFT simulations, evidenced the species formed on the metal surface as bpy-Pd(OH) 2 , which appears quite similar, from both structural and spectroscopic points of view, to the bpy-PdCl 2 coordination compound, whose catalytic activity is well known. Based on these observations, the use of Pd substrates coated with bpy is proposed for reactions of heterogeneous catalysis, instead of using bpy-PdCl 2 as homogeneous catalyst. Moreover, palladium nanoparticles could be prepared by laser ablation in aqueous solution of bpy, exhibiting both colloidal stability and catalytic activity.

2018 - Spectroscopic and Computational Studies on Ligand-Capped Metal Nanoparticles and Clusters [Capitolo/Saggio]
Muniz-Miranda, M.; Muniz-Miranda, F.; Pedone, A.

Metal nanoparticles represent a bridge between single atoms and bulk materials, presenting peculiar chemical and optical properties. Under irradiation with an appropriate electromagnetic wave, the conduction electrons do not oscillate freely, because they are trapped in the nanometric size of the metal particles, which exhibit collective excitations called “localized plasmons.” These latter are needed to promote enhancements for both the Raman signal and the fluorescence emission of molecules adhering to the metal surface, when the exciting radiation wavelengths match those of the plasmon bands. Hence, Raman enhancements up to 107 factors are generally observed for molecules adsorbed on silver or gold nanoparticles in the SERS (surface-enhanced Raman scattering) measurements. When, instead, metal particles have sizes below about 2 nm, they do not have metallic properties owing to the existence of discrete electronic energy levels and the loss of overlapping electronic bands. These metal clusters exhibit a typical quantum size behavior, with optical and electronic properties different from those relative to plasmons. In this work, the spectroscopic properties of silver and gold nanoparticles and clusters, capped with organic ligands, are investigated by Raman scattering, absorption, and fluorescence measurements and interpreted by different computational approaches.

2018 - Spectroscopic and DFT investigation on the photo-chemical properties of a push-pull chromophore: 4-Dimethylamino-4′-nitrostilbene [Articolo su rivista]
Muniz-Miranda, Francesco; Pedone, Alfonso; Muniz-Miranda, Maurizio

4-Dimethylamino-4′-nitrostilbene (DANS), a π-conjugated push-pull molecule, has been investigated by means of a combined spectroscopic and computational approach. When the Raman excitation is close to the visible electronic transition of DANS, vibrational bands not belonging to DANS appear in the spectra, increasing with the laser power. These bands are observed at room temperature in the solid phase, but not at low temperature or in solution, and we interpret them as due to a thermally-activated photoreaction occurring under laser irradiation in the visible spectral region. Density-functional calculations correctly reproducing the electronic and vibrational spectra of DANS, describe the charge-transfer process, indicate that an azo-derivative is the product of the photoreaction of DANS and provide a reasonable interpretation of this process.

2018 - The Effect of Alkaline Cations on the Intercalation of Carbon Dioxide in Sepiolite Minerals: A Molecular Dynamics Investigation [Articolo su rivista]
Tavanti, F.; Muniz-Miranda, F.; Pedone, A.

The ability of the sepiolite mineral to intercalate CO2 molecules inside its channels in the presence of different alkaline cations (K+, Na+, and Li+) has been studied by classical molecular dynamics simulations. Starting from an alkaline-free sepiolite crystalline model, we built three models with stoichiometry Mg320Si440Al40O1200(OH)160X+40·480H2O. On these models, we gradually replaced the water molecules present in the channels with carbon dioxide and determined the energy of this exchange reaction as well as the structural organization and dynamics of carbon dioxide in the channels. The adsorption energy shows that the Li-containing sepiolite mineral retains more carbon dioxide with respect to those with sodium and potassium cations in the channels. Moreover, the ordered patterns of CO2 molecules observed in the alkaline-free sepiolite mineral are in part destabilized by the presence of cations decreasing the adsorption capacity of this clay mineral.

2018 - Two-Dimensional Electronic Spectroscopy Reveals Dynamics and Mechanisms of Solvent-Driven Inertial Relaxation in Polar BODIPY Dyes [Articolo su rivista]
Bolzonello, Luca; Polo, Annalisa; Volpato, Andrea; Meneghin, Elena; Cordaro, Massimiliano; Trapani, Mariachiara; Fortino, Mariagrazia; Pedone, Alfonso; Castriciano, Maria Angela; Collini, Elisabetta

In this work, we demonstrate the use of two-dimensional electronic spectroscopy (2DES) to study the mechanism and time scale of the femtosecond Stokes shift dynamics in molecules characterized by intramolecular charge transfer, such as distyryl-functionalized boron dipyrromethene (BODIPY) molecules. The obtained results demonstrate that 2DES allows clear and direct visualization of the phenomenon. The analysis of the 2D data in terms of 2D frequency-frequency decay associated maps provides indeed not only the time scale of the relaxation process but also the starting and the final point of the energy flow and the associated reorganization energy, identified by looking at the coordinates of a negative signature below the diagonal. The sensitivity of the 2DES technique to vibrational coherence dynamics also allowed the identification of a possible relaxation mechanism involving specific interaction between a vibrational mode of the dye and the solvent.

2017 - A Modular Implementation for the Simulation of 1D and 2D Solid-State NMR Spectra of Quadrupolar Nuclei in the Virtual Multifrequency Spectrometer-Draw Graphical Interface [Articolo su rivista]
Presti, Davide; Pedone, Alfonso; Licari, Daniele; Barone, Vincenzo

We present the implementation of the solid state (SoS)NMR module for the simulation of several 1D and 2D NMR spectra of all the elements in the periodic table in the virtual multifrequency spectrometer (VMS). This module is fully integrated with the graphical user interface of VMS (VMS-Draw) [Licari et al., J. Comput. Chem. 36, 2015, 321-334], a freeware tool which allows a user-friendly handling of structures and analyses of advanced spectroscopical properties of chemical compounds-from model systems to real-world applications. Besides the numerous modules already available in VMS for the study of electronic, optical, vibrational, vibronic, and EPR properties, here the simulation of NMR spectra is presented with a particular emphasis on those techniques usually employed to investigate solid state systems. The SoSNMR module benefits from its ability to work under both periodic and nonperiodic conditions, such that small molecules/molecular clusters can be treated, as well as extended three-dimensional systems enforcing (or not) translational periodicity. These features allow VMS to simulate spectra resulting from NMR calculations by some popular quantum chemistry codes, namely Gaussian09/16, Castep, and Quantum Espresso. The effectiveness of the SoSNMR module of VMS is examined throughout the manuscript, and applied to simulate 1D static, MAS, and VAS NMR spectra as well as 2D correlation (90°, MAS) and MQMAS spectra of active NMR nuclei embedded in different amorphous and crystalline systems of actual interest in chemistry and material science. Finally, the program is able to simulate the spectra of both the total ensemble of spin-active nuclei present in the system and of subensembles differentiated depending on the chemical environment of the first and second coordination sphere in a very general way applicable to any kind of systems.

2017 - Computational Insight into the Interaction of Cytochrome C with Wet and PVP-Coated Ag Surfaces [Articolo su rivista]
Tavanti, Francesco; Pedone, Alfonso; Matteini, Paolo; Menziani, Maria Cristina

In this work, the adsorption of cytochrome C (CytC) on wet 100, 111, 110, and 120 silver surfaces has been investigated by computational simulations. The effect of polyvinylpyrrolidone (PVP) coating has also been studied. The main results obtained can be summarized as follow: (a) CytC strongly interacts with wet bare high index facets, while the adsorption over the 100 surface is disfavored due to the strong water structuring at the surface; (b) a nonselective protein adsorption mechanism is highlighted; (c) the native structure of CytC is well preserved during adsorption; (d) the heme group of CytC is never found to interact directly with the surface; (e) the interactions with the PVP-capped 100 surface is weak and specific. These results can be exploited to better control biological responses at engineered nanosurface, allowing the development of improved diagnostic tools.

2017 - Effects of substituents on transport properties of molecular materials for organic solar cells: A theoretical investigation [Articolo su rivista]
Alberga, Domenico; Ciofini, Ilaria; Mangiatordi, Giuseppe Felice; Pedone, Alfonso; Lattanzi, Gianluca; Roncali, Jean; Adamo, Carlo

We present a theoretical investigation of the effects of substitution of the triphenylamine (TPA) block on the overall properties of materials based on small push.pull molecules designed as donors for organic photovoltaics (OPV). In particular, we exploit modern computational techniques such as density functional theory (DFT), timedependent DFT, molecular dynamics, and the Marcus theory to analyze the charge and exciton transport properties in crystalline and amorphous phases of four compounds in which one phenyl ring of the TPA block of 2-[(5-4-[methyl-(phenyl)amino]phenylthiophen-2-yl)methylene]- malononitrile is replaced with a methyl, an α-naphthyl, and a β-naphthyl. Our calculations unveil the molecular rationale behind the different transport properties observed in the experiments. We show that, although the effects of the substituents on the electronic and optical properties are negligible, they have an impact on the molecular packing of the crystalline structure, thus explaining the different macroscopic transport properties (observed and calculated). In particular, the substitution of a phenyl with a methyl favors face-to-face π-π packing in the crystal structure and allows a good π-orbital overlap and high hopping rates. On the other hand, the introduction of an α-naphthyl group generates a steric hindrance that negatively affects the transport properties. Moreover, the investigated substitutions do not significantly influence the degree of local order in the amorphous bulks displaying complete disorder and low hole mobilities. These results, in agreement with the experimental findings, suggest that our computational approach is able to account for the macroscopic effect of subtle transformations of a molecular structure on transport properties and thus can be further employed to obtain valuable insights into the molecular design of optimized active materials for OPV.

2017 - Experimental and Molecular Dynamics Investigation Proves That Montmorillonite Traps the Biogenic Amines Histamine and Tyramine [Articolo su rivista]
Malferrari, Daniele; Bernini, Fabrizio; Tavanti, Francesco; Tuccio, Luca; Pedone, Alfonso

Biogenic amines present in high concentrations in foods obtained through fermentation could have toxic effects and contribute to the arising of allergies. For this reason, their removal is of great importance. In this work, we used an experimental and computational approach to investigate the interaction between a calcium montmorillonite, a layered silicate very common in clays, and the two biogenic amines histamine and tyramine, obtaining deep insight into their binding modalities and structural organization. Calcium montmorillonite can exchange almost all its interlayer Ca2+with the protonated histamine and tyramine, thus reducing their concentration in water solution. The adopted multianalytical approach allowed classification of the interaction mechanism as an intercalation. Molecular dynamics simulations showed that the intercalated histamine and tyramine preferentially interact, through the protonated amino nitrogen, with tetrahedral aluminum bearing a net negative charge, whereas interactions with neutral tetrahedral silica is less favorable. We observed that most of histamine molecules bind in the center and above the 6T net of the silica sheet, but for electrostatic constraints they cannot occupy the center of two adjacent 6T nets as occurs for tyramine.

2017 - Magneto-Plasmonic Colloidal Nanoparticles Obtained by Laser Ablation of Nickel and Silver Targets in Water [Articolo su rivista]
Gellini, Cristina; Deepak, Francis Leonard; Muniz Miranda, Maurizio; Caporali, Stefano; Muniz Miranda, Francesco; Pedone, Alfonso; Innocenti, Claudia; Sangregorio, Claudio

Stable magneto-plasmonic nanoparticles in colloidal suspensions are fabricated by two-step nanosecond pulsed laser ablation of nickel and silver targets in pure water and characterized by UV-visible absorption, Raman, X-ray photoelectron spectroscopic, and magnetic measurements, along with high-resolution electron microscopy analysis. These systems are constituted by a low-crystallinity matrix of ferromagnetic nickel hydroxide, where nickel oxide nanocrystals are embedded,, with silver nanoparticles intimately linked to them. The surface enhanced Raman scattering activity is assessed by adsorption of adenine as probe ligand. Spectroscopic investigation and density functional theory calculations revealed that adenine is linked to nickel oxide, while nanosilver essentially plays the role of ensuring the Raman enhancement for the adsorbed organic ligand. Both magnetic and plasmonic properties allow using these nanostructured bimetallic platforms as catalysts in chemical reactions or nanosensors in biomedicine as well as in environmental research.

2017 - Models of Aged Magnesium–Silicate–Hydrate Cements Based on the Lizardite and Talc Crystals: A Periodic DFT-GIPAW Investigation [Articolo su rivista]
Pedone, Alfonso; Palazzetti, Federico; Barone, Vincenzo

Classical MD simulations and periodic DFT-GIPAW calculations have been employed to investigate possible structural models of aged magnesium−silicate−hydrate (M−S−H) cements. Four models were built, two based, respectively, on the lizardite Mg3Si2O5(OH)4 and talc Mg3Si4O10(OH)2 crystals in which we have modified the Mg/Si ratio and distribution of Qn silicon species (n is the number of bridging oxygens for each quaternary silicon atom) according to previous experimental evidence. The other two models were still based on the lizardite and talc crystals, but the original Mg/Si ratios were retained. The latter two models were used to simulate MSH binders containing different proportions of talc- and lizardite-based amorphous phases as proposed in several experimental works. From these initial models, additional structures were generated by adding increasing amounts of water molecules to investigate its effect on the structure and on the 29Si and 25Mg MAS NMR spectra. Our results demonstrate that MSH phases with an Mg/Si ratio close to 1 can be described as a defective talc-based model or as the combination of talc and lizardite amorphous models with the former being the dominant phase. In both cases, the hydrated models provide the best agreement with NMR experiments.

2017 - Structure of active cerium sites within bioactive glasses [Articolo su rivista]
Benedetti, Francesco; Luches, Paola; D'Addato, Sergio; Valeri, Sergio; Nicolini, Valentina; Pedone, Alfonso; Menziani, Maria Cristina; Malavasi, Gianluca

The inclusion of small amounts of cerium within the matrix of bioactive glasses, a class of materials used for bone tissue reparation and regeneration, adds a very important antioxidant property. In this work we investigate the local structure around cerium ions in cerium oxide doped bioactive phosphosilicate and silicate glasses, by X-ray absorption fine structure at the Ce K-edge, combined with classical molecular dynamics (MD) simulations. The local structure of the active Ce sites results significantly different from the one in bulk cerium oxide phases. A contracted Ce–O first shell distance with respect to bulk oxides is detected, in full agreement with the results of MD simulations. The cerium environment in the glass matrix at different stages of the reaction with H2O2 does not show significant modifications, in spite of the very high catalytic activity. The accurate description of the active Ce sites within bioactive glasses reported in this work is an important step toward an atomic scale understanding of the material functionalities.

2017 - Understanding Aggregation-Induced Emission in Molecular Crystals: Insights from Theory [Articolo su rivista]
Presti, Davide; Wilbraham, Liam; Targa, Cecilia; Labat, Frédéric; Pedone, Alfonso; Menziani, Maria Cristina; Ciofini, Ilaria; Adamo, Carlo

Aggregation-induced emission can often be explained via the restriction of intramolecular rotation paradigm and/or excimer formation. The enhanced luminescence recently observed for aggregates of fluorenone derivatives are no exception. In this work, however, we use a recently developed excited-state electrostatic embedding technique to demonstrate that enhanced emission in diphenylfluorenone can be rationalized by considering a single-molecule process, in which the field induced by the crystalline environment at the excited state enhances the relative brightness of otherwise poorly emissive states, resulting in both enhanced fluorescence and a substantial bathochromic shift in comparison with emission in dilute solution.

2016 - Assessment of the basis set effect on the structural and electronic properties of organic-protected gold nanoclusters [Articolo su rivista]
MUNIZ MIRANDA, Francesco; Menziani, Maria Cristina; Pedone, Alfonso

We have investigated the structural and optical properties of five monolayer-protected gold nanoclusters with a combination of exchange–correlation functionals, namely B-PBE for the geometry relaxation and CAM-B3LYP for the time-dependent calculations. We have tested the accuracy of five different basis sets in reproducing the experimental structures of these nanoclusters, and we have found that even a rather small basis set (single zeta) can outperform a significantly larger one (double zeta) if some selected atoms are treated with polarization functions. Namely, the sulfur and phosphorous atoms of the capping thiols and phosphines usually are hypervalent when bonded to the gold inner core; therefore, polarization functions allow them significantly more structural flexibility. With the two best performing basis sets, we carried out optical calculations and found that the resulting UV–Vis profiles are largely similar, in particular the energy and orbital contributions of the optical gaps are very close. The results support the use of the small basis set proposed here to investigate larger nanoclusters with general hybrid and range-corrected hybrid functionals.

Malavasi, Gianluca; Nicolini, Valentina; Gambuzzi, Elisa; Menabue, Ledi; Lusvardi, Gigliola; Pedone, Alfonso; Benedetti, Francesco; Luches, Paola; D'Addato, Sergio; Valeri, Sergio

The ability of a Ce-containing bioactive glasses to inhibit oxidative stress in terms of reduction of H2O2, by mimicking the catalase enzyme activity is demonstrated for the first time. The antioxidant properties of bioactive glasses containing CeO2 have been evaluated by following the degradation of hydrogen peroxide with time after immersion in H2O2 aqueous solutions with different concentration. XPS, UV-Vis and magnetic measurements allowed us to determine the Ce3+/Ce4+ ratio (bulk and surface) and to correlate it with the ability of the samples to show catalase mimetic activity. We have found that the bioactive glass (23.2Na2O-25.7CaO-43.4SiO2-2.4P2O5-5.3CeO2) immersed in 0.1M H2O2 aqueous solution is able to degrade 90% of it in one week.

2016 - Electronic and optical properties of the Au22[1,8-bis(diphenylphosphino) octane]6 nanoclusters disclosed by DFT and TD-DFT calculations [Articolo su rivista]
MUNIZ MIRANDA, Francesco; Presti, Davide; Menziani, Maria Cristina; Pedone, Alfonso

Time-dependent density functional theory calculations have been used to investigate the electronic and optical properties of a nanocluster composed of two directly bonded Au11 subunits, held together by six bidentate diphosphine ligands: 1,8-bis(diphenylphosphino) octane. Three exchange–correlation functionals have been adopted, a general hybrid (PBE0) and two range-separated hybrids (ωB97X and CAM-B3LYP). The results obtained show that the aforementioned properties are significantly different from those of a previously studied Au11-based nanocluster formed by just one single subunit. In particular, charge transfer excitations from the inner metal core to the outer ligands affect most of the UV–visible spectrum and occur for both alkyl and aromatic ligands. This is particularly evident when thiazole molecules are bonded to the gold core: In this case Au → ligand transitions affect also the first HOMO → LUMO excitation. Moreover, the gold core of this Au22 nanocluster has eight under-coordinated Au surface atoms not engaged in bonds with the ligands. No other known organic-protected gold nanocluster has a similar feature. These gold atoms can be considered as potential in situ active sites for catalysis, their catalytic efficiency and selectivity being modulated by charge distribution.

2016 - Experimental and DFT Characterization of Halloysite Nanotubes Loaded with Salicylic Acid [Articolo su rivista]
Spepi, Alessio; Duce, Celia; Pedone, Alfonso; Presti, Davide; Rivera, José Gonzalez; Ierardi, Vincenzo; Tiné, Maria Rosaria

Halloysite nanotubes (HNTs) and salicylic acid (SA) are natural substances widely used in different fields. HNTs are very promising as nanocarriers because of their biocompatibility, atoxicity, anti-inflammatory properties and capacity to maintain the biological activity of immobilized enzymes. Because of its bactericidal and antiseptic properties, salicylic acid (SA) is used in pharmaceutical formulations, and as an additive for preserving foods and cosmetics. In this study, we set up a procedure for the loading of HNTs with SA for their possible application in active food packaging. Pristine HNTs were studied together with acidic etched HNTs with enlarged internal lumen, and various pH values for the loading solutions were tested in order to obtain the maximum loading. The HNTs-empty and loaded with SA-were characterized by TG-FTIR, FTIR SEM, STEM, and nitrogen adsorption/desorption isotherms measurements. We obtained a maximum loading of 10.5% (w/w), using HNTs pretreated with H2SO4 2 M at 25 degrees C for 48h and a solution of sodium salicylate at pH 8. We also characterized the interaction of SA-HNTs at a molecular level by combining ATR-FTIR measurements and periodic density functional theory (DFT) calculations. We believe that the information on the SA-HNT complexes derived from our research should help to improve the current knowledge of SA clay interactions. In addition, it should be of interest for environmental and earth sciences since SA is used to model natural organic matter (NOM) in both experimental and theoretical studies of NOM adsorption on different kinds of mineral surfaces.

2016 - Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations [Articolo su rivista]
Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral–octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water–clay interfaces, which are of fundamental importance for both natural processes and industrial applications.

2016 - Modeling emission features of salicylidene aniline molecular crystals: A QM/QM' approach [Articolo su rivista]
Presti, Davide; Labat, Frédéric; Pedone, Alfonso; Frisch, Michael J.; Hratchian, Hrant P.; Ciofini, Ilaria; Menziani, Maria Cristina; Adamo, Carlo

A new computational protocol relying on the use of electrostatic embedding, derived from QM/QM' ONIOM calculations, to simulate the effect of the crystalline environment on the emission spectra of molecular crystals is here applied to the beta-form of salicylidene aniline (SA). The first singlet excited states (S-1) of the SA cis-keto and trans-keto conformers, surrounded by a cluster of other molecules representing the crystalline structure, were optimized by using a QM/QM' ONIOM approach with and without electronic embedding. The model system consisting of the central salicylidene aniline molecule was treated at the DFT level by using either the B3LYP, PBE0, or the CAM-B3LYP functional, whereas the real system was treated at the HF level. The CAM-B3LYP/HF level of theory provides emission energies in good agreement with experiment with differences of 220/232 nm (cis-keto form) and 28/214 nm (trans-keto form), respectively, whereas notably larger differences are obtained using global hybrids. Though such differences on the optical properties arise from the density functional choice, the contribution of the electronic embedding is rather independent of the functional used. This plays in favor of a more general applicability of the present protocol to other crystalline molecular systems.

2016 - Optical properties of the dibenzothiazolylphenol molecular crystals through ONIOM calculations: the effect of the electrostatic embedding scheme [Articolo su rivista]
Presti, Davide; Pedone, Alfonso; Ciofini, Ilaria; Labat, Frédéric; Menziani, Maria Cristina; Adamo, Carlo

Periodic density functional theory (DFT) and hybrid ONIOM time-dependent DFT/MM cluster calculations have been carried out to investigate the ground- and excited-state properties of the crystalline structures of the enolic and ketonic tautomeric forms of a propoxy-substituted dibenzothiazolylphenol molecule (OPr), a prototype for systems undergoing the excited-state intramolecular proton transfer process. The crystalline structures of the tautomeric forms are well reproduced and, as expected, at the ground state, the enol polymorph is predicted to be more stable than the keto one. At the excited state, the effect of the environment on time-dependent DFT calculations has been accounted for by including a charge embedding scheme, and the influence of different kinds of point charges (Mulliken, CM5, RESP and QEq) in determining the optical properties of the central molecule has been investigated. The results reveal that, in fair agreement with experimental data, the absorption (emission) energies of the enol (keto) OPr molecule is red-shifted of about 3 (3) nm going from the gas phase to chloroform and blue-shifted of 10 (23) nm going from the gas to the crystal phase when the electronic embedding with Mulliken charges is employed. The electrostatic embedding influences the excited-state properties more severely than the ground-state properties, and apart the QEq charges, all other models provide Stokes shifts in reasonable agreement with experimental data.

2016 - Raman and DFT study of methimazole chemisorbed on gold colloidal nanoparticles [Articolo su rivista]
Muniz Miranda, Maurizio; Muniz Miranda, Francesco; Pedone, Alfonso

The adsorption of methimazole on gold colloidal nanoparticles was investigated using a combination of surface-enhanced Raman scattering and density functional theory calculations, which allowed identifying the thiolate anion as the molecular species chemically interacting with the active sites of the gold surface, modeled as zero-charge metal adatoms, only through the sulfur atom. This result can be important for the use of these ligand/metal nanohybrids in the process of drug delivery. Moreover, functionalized gold nanoparticles are able to promote the Raman enhancement in the red-light region as well as in the near-infrared, where generally no fluorescence emission occurs. This paves the way for the use of these nanosystems in a biological environment, even in vivo experiments.

2016 - Recent advances in solid-state NMR computational spectroscopy: The case of alumino-silicate glasses [Articolo su rivista]
Pedone, Alfonso

Solid-state NMR spectroscopy and computational approaches such as Molecular Dynamics (MD) simulations and Density Functional Theory have proven to be very useful and versatile techniques for studying the structure and the dynamics of noncrystalline materials if a direct comparison between experiment and theory is established. In this review, the basic concepts in first-principle modeling of solid-state NMR spectra of oxide glasses are presented. There are three theoretical ingredients in the computational recipe. First, classical or ab initio molecular dynamics simulations are employed to generate the structural models of the glasses of interest. Second, periodic Density Functional Theory calculations coupled with the gauge including projector augmented-wave (GIPAW) algorithm form the basis for the ab initio calculations of NMR parameters (chemical shielding and quadrupolar parameters). Finally, Spin-effective Hamiltonian are employed to simulate the solid-state NMR spectra directly comparable with the experimental counterparts. As an example of this methodology, the investigation of the local and medium range structure of Na-Ca silicate and aluminosilicate glasses that are usually employed as simplified models for basaltic, andesitic and rhyolitic magmas will be reported. We will show how the direct comparison of the theoretical NMR spectra of MD derived structural models with the experimental counterparts allows gaining new insights into the atomistic structure of very complex oxide glasses.

2016 - Supercritical CO2 Confined in Palygorskite and Sepiolite Minerals: A Classical Molecular Dynamics Investigation [Articolo su rivista]
MUNIZ MIRANDA, Francesco; Lodesani, Federica; Tavanti, Francesco; Presti, Davide; Malferrari, Daniele; Pedone, Alfonso

We have investigated the ability of two modular phyllosilicates (palygorskite and sepiolite) to store CO2 molecules inside their structural channels by means of classical molecular dynamics. Several models containing an increasing supercritical-CO2/H2O ratio into the phyllosilicate channels have been built and the structural and dynamic properties of carbon dioxide and water molecules investigated in detail. We found that both clay minerals can achieve this goal, with sepiolite being able to store more carbon dioxide molecules (and more stably) than palygorskite, due to the larger channels of the former. Interestingly, with the increase of CO2 molecules inside the minerals, the diffusivity of both water and carbon dioxide drastically decreases and carbon dioxide molecules tend to arrange themselves in an ordered pattern. (Figure Presented).

2016 - The antioxidant properties of Ce-containing bioactive glass nanoparticles explained by Molecular Dynamics simulations [Articolo su rivista]
Pedone, Alfonso; MUNIZ MIRANDA, Francesco; Menziani, Maria Cristina; Tilocca, Antonio

Molecular dynamics simulations of two glass nanoparticles with composition 25Na2O·25CaO 50SiO2 mol% (Ce-K NP) and 46.1SiO2·24.4Na2O·26.9CaO· 2.6P2O5 mol.% (Ce-BG NP) doped with 3.6 mol% of CeO2 have been carried out in order to explain the enhanced antioxidant properties of the former glass with respect to the latter. The present models show that the different catalase mimetic activity of the two NPs is related to the Ce3+/Ce4+ ratio exposed at their surface. In fact, this ratio is about 3.5 and 13 in the bulk and at the surface of the Ce-BG NP, and 1.0 and 2.1 in the bulk and at the surface of the Ce-K NPs, respectively. Since both oxidation states are necessary for the catalysis of the dismutation reaction of hydrogen peroxides, NPs with a very high Ce3+/Ce4+ ratio possess poorer antioxidant properties. Moreover, our simulations reveal that the already low silicate connectivity found in the bulk glasses examined here is further reduced on the nanoparticle surface, whereas the Na+/Ca2+ ratio rapidly increases. Sodium, calcium and cerium sites in proximity of the surface are found to be under-coordinated, prone to quickly react with water present in physiological environments, thus accelerating the glass biodegradation

2016 - The effect of composition on structural, thermal, redox and bioactive properties of Ce-containing glasses [Articolo su rivista]
Nicolini, Valentina; Varini, Elena; Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; Lusvardi, Gigliola; Pedone, Alfonso; Benedetti, Francesco; Luches, Paola

The effect of phosphate on the ability of Ce-containing bioactive glasses to inhibit oxidative stress was studied on compositions based on Hench (46.2%SiO224.3%Na2O26.9ÊO2.6P2O5, mol%) and Kokubo (50.0%SiO225.0%Na2O25.0ÊO) glasses. In particular, the reduction of catalase mimetic activity of Ce-containing glasses due to the presence: i) of P2O5 in the glass compositions, and ii) of phosphate groups in the solution employed for catalase mimetic activity tests was explained and rationalized by combining SEM, XPS, XRD, DTA, FT-IR and UV-vis experiments with Molecular Dynamics simulations.The results suggest that the Ce ions play a different structural role in the two series of glasses. In particular, in phosphate free glasses Ce is coordinated by non-bridging oxygens (NBOs) originated from the disruption of the silicate network, whereas in phosphate containing glasses the NBOs around Ce ions belong to orthophosphate groups. The latter groups stabilize the Ce3+ species subtracting them from the interconversion process between Ce3+ and Ce4+, which is of fundamental importance for the exhibition of the catalase mimetic activity.

2016 - What can we learn from atomistic simulations of bioactive glasses? [Capitolo/Saggio]
Pedone, A.; Menziani, M. C.

In the last decades, most experimental efforts have been devoted to design bioactive glasses (please consult the Editor’s note in order to clarify the usage of the terms bioglass, bioactive glass and biocompatible glasses) with enhanced biological and mechanical properties by adding specific ions to known bioactive compositions. Concurrently, computational research has been focused to the understanding of the relationships between bioactivity and composition by rationalization of the role of the doping ions. Thus, a deep knowledge of the structural organization of the constituent atoms of the bioactive glasses has been gained by the employment of ab initio and classical molecular dynamics simulations techniques. This chapter reviews the recent successes in this field by presenting, in a concise way, the structure–properties relationships of silicate, phospho-silicate and phosphate glasses with potential bioactive properties.

2015 - A closer look into the ubiquitin corona on gold nanoparticles by computational studies [Articolo su rivista]
Tavanti, Francesco; Pedone, Alfonso; Menziani, Maria Cristina

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.

2015 - Benchmarking TD-DFT against vibrationally resolved absorption spectra at room temperature: 7-aminocoumarins as test cases [Articolo su rivista]
MUNIZ MIRANDA, Francesco; Pedone, Alfonso; Battistelli, Giulia; Montalti, Marco; Bloino, Julien; Barone, Vincenzo

Time-dependent density functional theory (TD-DFT) is usually benchmarked by evaluating how the vertical excitation energies computed by using different exchange-correlation (XC) functionals compare with the maximum of the absorption spectra. However, the latter does not necessarily coincide with the vertical energies because it is affected by the vibronic band structure that has to be properly taken into account. In this work, we have evaluated the performance of several functionals belonging to different families in reproducing the vibronic structure (band shape) of four 7-aminocoumarin molecules of technological interest, whose spectra have been recorded in methylcyclohexane and acetonitrile solvents. In order to compare the computed vibronic spectra with the experimental ones in the most consistent way, the effect of temperature, often neglected, was also taken into account. We have found that no single functional provides simultaneously accurate band positions and shapes, but the combination of ωB97X vibronic couplings with PBE0 vertical energies can lead to very satisfactory results. In addition to the assessment of XC functionals, several adiabatic and vertical models proposed in the literature to compute vibrationally resolved electronic spectra have been tested and validated with respect to experiments. On these grounds, the adiabatic Hessian model has been used to perform a complete analysis of the ωB97X/PBE0 vibronic transitions contributing to the final band shapes of the investigated aminocoumarin molecules.

2015 - Calcium environment in silicate and aluminosilicate glasses probed by (43)Ca MQMAS NMR experiments and MD-GIPAW calculations [Articolo su rivista]
Gambuzzi, Elisa; Pedone, Alfonso; Menziani, Maria Cristina; Angeli, Frédéric; Florian, Pierre; Charpentier, Thibault

(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.

2015 - Competitive Binding of Proteins to Gold Nanoparticles Disclosed by Molecular Dynamics Simulations [Articolo su rivista]
Tavanti, Francesco; Pedone, Alfonso; Menziani, Maria Cristina

Abstract This work reports the results of coarse-grained molecular dynamics simulations of citrate-coated gold nanoparticles (AuNPs) in interaction with insulin and fibrinogen, two of the most abundant proteins in the plasma. The following have been found: (a) The corona of citrate-coated AuNP of 5 nm core diameter is composed by a single layer of proteins comprising a maximum of 20 insulins, whereas only 3 fibrinogens are contemporaneously present. (b) The binding site for insulin is specific and independent from the number of insulins considered in the computational simulations, whereas fibrinogen presents different binding modes, as a function of protein concentration and composition. Moreover, fibrinogen is able to accommodate two citrate-coated AuNPs in independent binding sites localized at the ending nodes. (c) A competitve process for AuNP binding is observed when insulins and fibrinogens are contemporaneously present in the simulations. (d) The overall protein secondary structure is maintained upon binding to a single citrate-coated AuNP, but small changes in helix and sheet percentages are observed for both proteins. (e) A partial unfolding of the α-helix bundle is found for fibrinogen bound to two AuNPs. This may provide a molecular level understanding of the inflammatory response to nanoparticles. © 2015 American Chemical Society.

2015 - Computational Modeling of Silicate Glasses: A Quantitative Structure-Property Relationship Perspective [Capitolo/Saggio]
Pedone, Alfonso; Menziani, Maria Cristina

This article reviews the present state of Quantitative Structure-Property Relationships (QSPR) in glass design and gives an outlook into future developments. First an overview is given of the statistical methodology, with particular emphasis to the integration of QSPR with molecular dynamics simulations to derive informative structural descriptors. Then, the potentiality of this approach as a tool for interpretative and predictive purposes is highlighted by a number of recent inspiring applications.

2015 - DFT and TD-DFT assessment of the structural and optoelectronic properties of an organic-Ag14 nanocluster [Articolo su rivista]
Muniz-Miranda, F.; Menziani, M. C.; Pedone, A.

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-dependent density functional calculations have been employed to recover the experimental UV-vis spectrum. The present investigation shows that to correctly reproduce the optical feature of XMC1 the ligands cannot be omitted, because they interact with the metal core at energies much closer to the optical gap than in the case of gold-based nanoclusters of similar sizes. Due to this fact, a functional that accurately describes charge-transfer electronic transitions (such as the long-range corrected CAM-B3LYP) has to be adopted.

2015 - Dynamics of Fracture in Silica and Soda-Silicate Glasses: From Bulk Materials to Nanowires [Articolo su rivista]
Pedone, Alfonso; Menziani, Maria Cristina; Cormack, Alastair N.

Classical molecular dynamics simulations are used to investigate the fracture mechanism, intrinsic strength, strain at failure and elastic modulus of silica and soda-silicate bulk glasses and nanowires. The latter have been generated by using a new casting approach described in this paper for the first time. The results show that large systems have to be used to reproduce the brittle fracture mechanism of silicate glasses; the appropriate dimensions of the simulation boxes depend on the glass composition. Whereas for silica glass an ideal brittle fracture is observed with models containing 30k atoms, for soda-silicate glasses models with more than 60k atoms should be used. Glasses containing nanovoids and atomic defects (such as under- and overcoordinated silicon and oxygen atoms) are less brittle than flaw-free bulk glasses. The main finding, shown here for the first time, is that the presence of atomic defects and/or modifier cations allows the material to rearrange its structure and absorb the stresses caused by mechanical deformation, the former by transforming from high energy point defects to more stable configurations and the latter by saturating NBOs formed during the gradual breaking of the Si–O bonds that starts soon after the strain at failure is reached. In general, silica nanowires are characterized by lower mechanical properties with respect to bulk models because of the slightly higher amount of atomic defects (3-fold Si, nonbridging oxygens, and small rings) on their surfaces compared to that found in bulk glasses. These defects are not present in soda-silicate nanowires whose surfaces are rich in sodium ions that compensate the negative charge of nonbridging oxygens.

2015 - Evidence of catalase mimetic activity in ce(3+)/ce(4+) doped bioactive glasses [Articolo su rivista]
Nicolini, Valentina; Gambuzzi, Elisa; Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; Lusvardi, Gigliola; Pedone, Alfonso; Benedetti, Francesco; Luches, Paola; D'Addato, Sergio; Valeri, Sergio

The ability of Ce-containing bioactive glasses to inhibit oxidative stress in terms of reduction of hydrogen peroxide, by mimicking the catalase enzyme activity is demonstrated here for the first time. The antioxidant properties of three bioactive glasses containing an increasing amount of CeO2 have been evaluated by following the degradation of hydrogen peroxide with time after immersion in H2O2 aqueous solutions with different concentration. XPS and UV-vis measurements allowed us to determine the Ce(3+)/Ce(4+) ratio in the bulk and on the glass surface, and to correlate it with the ability of the samples to show catalase mimetic activity. Interestingly, we have found that the bioactive glass with composition 23.2Na2O-25.7CaO-43.4SiO2-2.4P2O5-5.3CeO2 immersed in 0.1 M H2O2 aqueous solution is able to degrade 90% of it in 1 week. The reduction in bioactivity of the glasses with increasing CeO2 content is here rationalized in terms of a lower amount of phosphate groups available for the hydroxyapatite layer formation, after binding with cerium ions. In fact, classical molecular dynamics simulations revealed that the addition of CeO2 leads to the formation of cerium phosphate rich regions. The formation of an insoluble CePO4 crystalline phase is also observed by XRD analysis after thermal treatment of the glass samples.

2015 - Influence of Silver Doping on the Photoluminescence of Protected AgnAu25–n Nanoclusters: A Time-Dependent Density Functional Theory Investigation [Articolo su rivista]
Muniz Miranda, Francesco; Menziani, Maria Cristina; Pedone, Alfonso

The effect of silver doping on the electronic properties and photoluminescence of a class of structurally similar AgnAu25–n2+ nanoclusters (0 ≤ n ≤ 13) has been investigated here by means of time-dependent density functional calculations. As very recently reported in the literature, a mixture of these clusters showed an unexpected 200-fold fluorescence quantum yield boost with respect to Au252+, but no mechanism has been proposed to date to explain this phenomenon. The results presented here suggest that the origin of this boost lies in the nature of the first excited state (S1), which is affected differently by the increasing presence of Ag atoms into the network of Au atoms. In fact, doping the cluster with silver atoms has the effect of shifting the lowest-energy “dark” excited states to higher energy, leaving a very “bright” highest occupied molecular orbital → lowest unoccupied molecular orbital (HOMO → LUMO) transition as the lowest-energy excitation. We propose that when fluorescence occurs from “bright” S1 states, it receives a boost in the quantum yield because of the high oscillator strength of these HOMO → LUMO transitions.

2014 - Assessment of Exchange-Correlation Functionals in Reproducing the Structure and Optical Gap of Organic-Protected Gold Nanoclusters [Articolo su rivista]
Francesco Muniz, Miranda; Menziani, Maria Cristina; Pedone, Alfonso

Extensive benchmarks of exchange-correlation functionals on real X-ray resolved nanoclusters have been carried out and reported here for the first time. The systems investigated and used for the tests are two undecagold and one Au24+-based nanoclusters stabilized by thiol and phosphine ligands. Time-dependent density-functional theory has been used to compare calculations with experimental data on optical gaps. It has been observed that GGA functionals employing PBE-like correlation (viz., PBE itself, B-PBE, B-P86, and B-PW91) coupled with an improved version of the LANL2DZ pseudopotential and basis set provide accurate results for both the structure and optical gap of gold nanoclusters, at a reasonable computational cost. Good geometries have been also obtained using some global hybrid (e.g., PBE0, B3-P86, mPW1-PW91) and range-separated hybrid (e.g., HSE06) functionals making use of PBE-like correlation, even though they yield optical gaps overestimating the experimental findings up to 0.5 eV. Popular exchange-correlation combinations such as B-LYP and B3-LYP deform cluster geometry during structural optimization, probably due to the LYP correlation. Effects of the stabilizing organic ligands on the properties of metal cores have been probed simulating the nanoclusters at the density-functional level of theory retaining the organic coating. This paper provides a useful contribution to the simulations of structural and optoelectronic properties of larger metal–organic particles suitable for a wide range of nanotechnological applications.

2014 - Computational Protocol for Modeling Thermochromic Molecular Crystals: Salicylidene Aniline As a Case Study [Articolo su rivista]
Presti, Davide; Fréderic, Labat; Pedone, Alfonso; Michael J., Frisch; Hrant P., Hratchian; Ilaria, Ciofini; Menziani, Maria Cristina; Carlo, Adamo

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.

2014 - Computational interpretation of 23Na MQMAS NMR Spectra: a comprehensive investigation of the Na environment in silicate glasses [Articolo su rivista]
Gambuzzi, Elisa; Thibault, Chapentier; Menziani, Maria Cristina; Pedone, Alfonso

Molecular Dynamics, Density Functional Theory calculations and 23Na 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 23Na 3QMAS spectra with the computed NMR parameters. The results show that the 23Na δiso values correlate with the average <Na-O> distances only when the different coordination numbers are explicitly taken into account.

2014 - Environmental and dynamical effects on the optical properties of molecular systems by time-independent and time-dependent approaches: Coumarin derivatives as test cases [Articolo su rivista]
Vincenzo, Barone; Malgorzata, Biczysko; Julien, Bloino; Luciano, Carta; Pedone, Alfonso

The main building blocks of a virtual spectrometer aimed at the vis-à-vis comparison between computed and experimental electronic spectra of large-size molecules in condensed phases are shortly analyzed with special attention to stereo-electronic, dynamic and environmental effects. The combined use of time-dependent and time-independent models allows to deal effectively with both high- and low-resolution spectra involving several electronic states at finite temperatures and in different environments ranging from isotropic solutions to surfaces and interiors of nanoparticles. The most salient features of virtual spectrometer are next illustrated by studying absorption and emission spectra of several coumarin derivatives in different environments.

2014 - Large-Scale B3LYP Simulations of Ibuprofen Adsorbed in MCM-41 Mesoporous Silica as Drug Delivery System [Articolo su rivista]
Massimo Delle, Piane; Marta, Corno; Pedone, Alfonso; Roberto, Dovesi; Piero, Ugliengo

The atomistic details of the interaction between ibuprofen (one of the most common nonsteroidal anti-inflammatory drugs) and a realistic model of MCM-41 (one of the most studied mesoporous silica materials for drug delivery) were elucidated by quantum mechanical modeling inclusive of London forces. Calculations are based on periodic density functional theory adopting all-electron Gaussian-type basis functions of polarized double-ζ quality and the B3LYP hybrid functional. By docking the drug on different sites of the MCM-41 pore walls, we have sampled different local features of the potential energy surface of the drug–silica system, both for low and high loadings (one and seven drug molecules per unit cell, respectively). For all cases, ibuprofen adsorption in MCM-41 is exothermic (average ΔH = −99 kJ·mol–1) and exergonic (average ΔG = −33 kJ·mol–1), exclusively when London interactions are taken into account due to their dominant role in dictating all features of this system. The comparison between simulated IR and NMR spectra suggests that static disorder of the adsorbed ibuprofen due to surface sites heterogeneity can also be invoked together with the current interpretation based on a dynamic behavior of the adsorbed ibuprofen to interpret the spectral features. Analysis of H-bond patterns exhibited by the drug interacting with the MCM-41 surface silanol (SiOH) groups revealed the importance of cooperativity in the H-bond strength. The present work shows that large-scale all-electron full quantum mechanical simulations employing accurate hybrid functionals can soon become competitive over modeling studies based on molecular mechanics methods, both in terms of superior accuracy and absence of the problematic parametrization, due to organic/inorganic interface.

2014 - On the opto-electronic properties of phosphine and thiolate-protected undecagold nanoclusters [Articolo su rivista]
Francesco Muniz, Miranda; Menziani, Maria Cristina; Pedone, Alfonso

We present here a detailed time-dependent density-functional theory investigation aimed at systematically dissecting the electronic spectra of two thiolate and phosphine protected undecagold nanoclusters. Calculations performed on the experimental structures of Au11(PPh3)7Cl3 and Au11(PPh3)7(SPyr)3 show that ligands have negligible contributions in the visible region. Metal → ligand charge transfer transitions appear at energies well above the visible threshold, while transitions with some small ligand → metal and ligand → ligand character occur sporadically at even higher energies. Thus, the conjugation effect between the π-electrons of the ligand and electrons of gold, recently hypothesized to interpret the spectra of phosphine and thiolate-protected nanoclusters, is not confirmed by the results of this study.

2014 - On the structure of Ce-containing silicophosphate glasses: a core–shell molecular dynamics investigation [Articolo su rivista]

Classical molecular dynamics simulations have been used to investigate the local and medium range structure of Ce-containing silicophosphate glasses widely used in optical and photonic devices because of their enhanced UV absorption and radiation damage resistance properties. New Ce3+–O and Ce4+–O parameters for a force-field based on the core–shell model were developed by fitting on the crystalline structures of Ce-containing crystal phases, and used to get insights into the structure of five silicophosphate glasses with increasing Ce2O3 and P2O5 content. An excellent agreement between experimental and computational data was found for the local environment around cerium ions and network former cations. The Ce3+–O bond lengths are generally longer than Ce4+–O, which shows higher coordination numbers. Both P and Si are four-fold coordinated; their allocation in the network is not uniform: the increasing Ce content leads to the formation of silica-rich domains and phosphate-rich domains, which entrap Ce cations increasing their solubility in the glass. We found that both the Qn distributions of phosphorous and Ce clustering depend on the Ce/P ratio in the glass. In particular, Ce clustering begins for Ce/P ratios between 0.17 and 0.29 in the glass series investigated.

2014 - Oxalyl Dihydrazide Polymorphism: a Periodic Dispersion-Corrected DFT and MP2 Investigation. [Articolo su rivista]
Presti, Davide; Pedone, Alfonso; Menziani, Maria Cristina; B., Civalleri; Lorenzo, Maschio

The molecular crystal of oxalyl dihydrazide differentiates into five polymorphs that are governed by inter- and intramolecular hydrogen bonds. The complex mixture of such interactions with long range dispersive forces makes its computational characterization very challenging; thus it represents an ideal benchmark for ab initio methods when striving for a description of polymorphism in molecular crystals. Indeed, a complete experimental energetic profile of this system is still lacking, and it is here investigated by means of periodic dispersion-corrected DFT and Local second order Møller–Plesset Perturbation theory (LMP2) calculations. In this work, the empirical dispersion correction schemes proposed by Tkatchenko and Scheffler (TS) [Tkatchenko et al., Phys. Rev. Lett., 2009, 102, 073005] and Grimme (D2) [Grimme, J. Comput. Chem., 2006, 27, 1787] have been used in combination with the PBE semilocal functional for geometry optimizations. We observed that PBE-TS provides a remarkable improvement in predicting the crystal structure of oxalyl dihydrazide polymorphs with respect to commonly used DFT-D functionals. The relative stabilities of the five forms have then been computed at the PBE-TS/D2, PBE0-D2, B3LYP-D2 and B3LYP-D3(BJ)+gCP level on the PBE-TS hydrogen-optimized geometries and benchmarked against high level periodic LMP2 calculations. PBE-TS, B3LYP-D2 and B3LYP-D3(BJ)+E(3) (that is including three-body corrections) achieve good predictions of the stability ordering, though the broadness of the energy range is slightly larger than in the case of LMP2.

2014 - Probing silicon and aluminium chemical environments in silicate and aluminosilicate glasses by solid state NMR spectroscopy and accurate first-principles calculations [Articolo su rivista]
Gambuzzi, Elisa; Pedone, Alfonso; Menziani, Maria Cristina; Frédéric, Angeli; Daniel, Caurant; Thibault, Charpentier

Silicon and aluminium chemical environments in silicate and aluminosilicate glasses with compositions 60SiO(2)center dot 20Na(2)O center dot 20CaO (CSN), 60SiO(2)center dot 20Al(2)O(3)center dot 20CaO (CAS), 78SiO(2)center dot 11Al(2)O(3)center dot 11Na(2)O (NAS) and 60SiO(2)center dot 10Al(2)O(3)center dot 10Na(2)O center dot 20CaO (CASN) have been investigated by Al-27 and Si-29 solid state magic angle spinning (MAS) and multiple quantum MAS (MQMAS) nuclear magnetic resonance (NMR) experiments. To interpret the NMR data, first-principles calculations using density functional theory were performed on structural models of these glasses. These models were generated by Shell-model molecular dynamics (MD) simulations. The theoretical NMR parameters and spectra were computed using the gauge including projected augmented wave (GIPAW) method and spin-effective Hamiltonians, respectively. This synergetic computational-experimental approach offers a clear structural characterization of these glasses, particularly in terms of network polymerization, chemical disorder (i.e. Si and Al distribution in second coordination sphere) and modifier cation distributions. The relationships between the local structural environments and the Si-29 and Al-27 NMR parameters are highlighted, and show that: (i) the isotropic chemical shift of both Si-29 and Al-27 increases of about +5 ppm for each Al added in the second sphere and (ii) both the Al-27 and Si-29 isotropic chemical shifts linearly decrease with the reduction of the average Si/Al-O-T bond angle. Conversely, Al-27 and Si-29 NMR parameters are much less sensitive to the connectivity with triple bridging oxygen atoms, precluding their indirect detection from Al-27 and Si-29 NMR. (C) 2013 Elsevier Ltd. All rights reserved.

2014 - Reprint of "Environmental and dynamical effects on the optical properties of molecular systems by time-independent and time-dependent approaches: Coumarin derivatives as test cases" [Articolo su rivista]
Barone, V.; Biczysko, M.; Bloino, J.; Carta, L.; Pedone, A.

The main building blocks of a virtual spectrometer aimed at the vis-à-vis comparison between computed and experimental electronic spectra of large-size molecules in condensed phases are shortly analyzed with special attention to stereo-electronic, dynamic and environmental effects. The combined use of time-dependent and time-independent models allows to deal effectively with both high- and low-resolution spectra involving several electronic states at finite temperatures and in different environments ranging from isotropic solutions to surfaces and interiors of nanoparticles. The most salient features of virtual spectrometer are next illustrated by studying absorption and emission spectra of several coumarin derivatives in different environments. © 2014.

2014 - Unraveling the Polymorphism of [(p-cymene)Ru(κN-INA)Cl2] through Dispersion-Corrected DFT and NMR GIPAW Calculations [Articolo su rivista]
Presti, Davide; Pedone, Alfonso; Menziani, Maria Cristina

The structural and 13C/1H NMR parameters of the four crystal forms (1α, 1·H2O, 1β, and 1γ) of the solid wheel-and-axle (WAA) metal–organic compound [(p-cymene)Ru(κN-INA)Cl2] have been studied by means of periodic DFT calculations. The quality of the results obtained strongly depends on a correct description of long-range interactions; thus, in the geometry refinement protocol used, the pure DFT functionals need to be coupled with a dispersion-correction term (B3LYP-D2, B3LYP-D*). The solid-state 13C/1H NMR δiso parameters and 13C MAS NMR spectra, calculated by means of the PBE-GIPAW method, agree well with the experimental data for the four crystal forms (mean absolute deviations of the 13C and 1H δiso data values lie in the ranges 1.3–2.9 and 0.3–1.0 ppm, respectively). In this context, some revisions in the experimental assignment of the 13C/1H NMR δiso parameters of the 1·H2O, 1β, and 1γ crystal forms can be suggested. The mismatch in the assignment seems to be due to the rotation of the −COOH moiety, which occurs at the 1α–1·H2O transition and was not considered in the experiments. Finally, the results obtained suggest the presence of two COOH···Cl hydrogen bonds of comparable strength established by the two molecules in the asymmetric unit of the 1γ polymorph, in partial disagreement with previous findings.

2013 - Bioglasses: glasses for medical applications [Capitolo/Saggio]
Lusvardi, Gigliola; Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; Pedone, Alfonso

bioglasses for medical applications

2013 - Computational simulations of solid state NMR spectra: a new era in structure determination of oxide glasses [Articolo su rivista]
Thibault, Charpentier; Menziani, Maria Cristina; Pedone, Alfonso

The application of the MD-GIPAW approach to the calculation of NMR parameters, line widths and shapes of the spectra of oxide glasses is reviewed. Emphasis is given to the decisive role of this approach both as an interpretative tool for a deeper understanding of the spectral behavior of complex systems and as a predictive instrument to map NMR data in a distribution of structural parameters and vice versa (structural inversion method). After a brief overview of the basic features of oxide glasses and the experimental techniques routinely employed to investigate their structure, a general description of the computational methods usually adopted to generate sound structural models of amorphous materials is offered. The computational recipe used to compute the solid state NMR spectra of oxide glasses and to establish quantitative structural-NMR property relationships is then described. Finally, these concepts are applied to 'simple' network former glasses and more complex silicates, aluminosilicate, phosphosilicate and borosilicate glasses of scientific relevance. The final section is dedicated to the future developments that will hopefully improve the computational approach described overcoming some of the current limitations.

2013 - DFT Modeling of 45S5 and 77S Soda-Lime Phospho-Silicate Glass Surfaces: Clues on Different Bioactivity Mechanism [Articolo su rivista]
Enrico, Berardo; Pedone, Alfonso; Piero, Ugliengo; Marta, Corno

The reactivity of bioglasses, which is related to the dissolution of cations and orthosilicate groups in the physiological fluid, strongly depends on the key structural features present at the glass surfaces. On the basis of the composition and the synthetic routes employed to make the glass, surfaces with very different characteristics and thus presenting different mechanisms of dissolution can be observed. In this paper, the surface structures of two very different bioglass compositions, namely 45S5 (46.1 SiO2, 24.4 Na2O, 26.9 CaO, and 2.6 P2O5 mol %) and 77S (80.0 SiO2, 16.0 CaO, and 4.0 P2O5 mol %), have been investigated by means of periodic DFT calculations based on a PBE functional and localized Gaussian basis set as encoded in the CRYSTAL code. Our calculations show that the two glass surfaces differ by the relative amount of key structural sites such as NBOs, exposed ions, orthosilicate units, and small rings. We have demonstrated how the number of these sites affects the surface stability and reactivity (bioactivity).

2013 - Local versus Average Structure in LaSrAl3O7: A NMR and DFT Investigation [Articolo su rivista]
Chiara, Ferrara; Cristina, Tealdi; Pedone, Alfonso; Menziani, Maria Cristina; Aaron J., Rossini; Guido, Pintacuda; Piercarlo, Mustarelli

LaSrAl3O7 belongs to the family of (M2T(1)T(2)O7)-T-1-O-2 compounds with tetragonal melilite-like layered structure. In such compounds the local structure and properties may be very different from the average ones, mainly due to cationic disorder on the M site. In this work, solid-state Al-27 NMR spectroscopy and periodic density functional theory calculations were used to highlight the differences between local and average order in the LaSrAl3O7 crystal. The Al-27 isotropic chemical shifts and quadrupolar coupling constants were computed by employing the gauge including projector augmented wave (GIPAW) and PAW formalisms, respectively. An impressive linear relationship between the computed quadrupolar coupling constant C-Q and the Al tetrahedra (T-1, T-2) distortion was observed. In particular, our calculations showed that the distortion of the T-2 environment is determined by the La/Sr speciation around the apical nonbridging oxygen.

2013 - New insights into the bioactivity of SiO2–CaO and SiO2–CaO–P2O5 sol–gel glasses by molecular dynamics simulations [Articolo su rivista]
Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; Pedone, Alfonso; A. J., Salinas; M., Vallet Regı

The structures of binary xCaO . (100 - x)SiO2glasses with x = 10, 20 and 30 mol-% and ternary(20 - x)CaO . xP2O5 . 80SiO2 glasses with x = 3, 10, 15,17 and 20 mol-% have been studied by means of classicalmolecular dynamics simulations using both the melt-quenchedand the sol–gel protocols. The structural picturederived correlates the bioactive behaviour to the combinedeffects of the connectivity of the extended silicate networkand to the tendency to form (or not to form) non-homogeneousdomains. In this context, a mathematical relationshipthat relates the Ca/P ratio in the Ca phosphatemicro-segregation zones to the P2O5 content in ternaryglasses has been developed and this has been used to finetuningthe optimum amount of P in a glass for its highest invitro bioactivity. The composition with optimal Ca/P ratio,80SiO2 . 14.8CaO . 5.2P2O5 has been synthesized and the results of bioactivity tests have confirmed the prediction.

2013 - Role of Solvent on Charge Transfer in 7-Aminocoumarin Dyes: New Hints from TD-CAM-B3LYP and State Specific PCM Calculations [Articolo su rivista]
Pedone, Alfonso

Time-dependent B3LYP and CAM-B3LYP calculations have been used to investigate the absorption and emission energies as well as to shed light on the formation of the twisted intramolecular charge transfer state (TICT) in Coumarin-152 (C152) embedded in cyclohexane, acetonitrile, and water solvents. The bulk solvent effects have been included by using the linear-response (LR) and State-Specific (SS) models in the framework of the so-called polarizable continuum method (PCM). The results demonstrate that the choice of the exchangecorrelation functional and of the PCM model is critical to reproduce the experimental data in the most accurate way. In particular, it has been observed that both the solvatochromic and Stokes’ shifts are well reproduce by CAM-B3LYP/SSPCM calculations performed on the S0 and S1 geometries of C152 optimized at the B3LYP/LRPCM level of theory, whereas not accurate Stokes’ shifts are computed with CAM-B3LYP/SSPCM calculations carried out on the CAMB3LYP/ LRPCM optimized structures. This is attributed to the incorrect (underestimated) solvation energy provided by LRPCM, which could lead to misleading results especially for charge-transfer excited state structures in polar solvents. Instead, B3LYP/LRPCM excited state optimizations seem to provide a reasonable geometry for a simple ‘error cancellation’ effect due to the balance among the B3LYP overstabilization of charge transfer states and the LRPCM underestimation of the solute−solvent binding energy when the former is in a polar solvent. Finally, CAM-B3LYP/SSPCM calculations, in very good agreement with experimental evidence, show that the formation of an accessible TICT state is possible for C152 and that the crossing between S0 and S1 states at a dihedral angle of around 70° occurs only in polar solvents.

2013 - Study of the Structural Role of Gallium and Aluminum in 45S5 Bioactive Glasses by Molecular Dynamics Simulations [Articolo su rivista]
Malavasi, Gianluca; Pedone, Alfonso; Menziani, Maria Cristina

The structural properties of phosphosilicate glasses based on the 45S5 Bioglass doped with gallium and aluminum (46.2SiO(2)center dot 24.3Na(2)O center dot 26.9CaO center dot 2.6P(2)O(5)center dot 1.0X(2)O(3), 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 Biog,lass 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 Ca2+ and PO43- 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

2013 - Understanding the photophysical properties of coumarin-based Pluronic–silica (PluS) nanoparticles by means of time-resolved emission spectroscopy and accurate TDDFT/stochastic calculations [Articolo su rivista]
Pedone, Alfonso; Gambuzzi, Elisa; Vincenzo, Barone; Sara, Bonacchi; Damiano, Genovese; Enrico, Rampazzo; Luca, Prodi; Marco, Montalti

The photophysical properties of two 7-aminocoumarin molecules with flexible and rigid alkyl moieties at the 7-nitrogen atom have been investigated in ethanol and in Pluronic–silica nanoparticles (PluS NPs) by means of time-resolved emission spectroscopy (TRES) and time-dependent density functional theory (TDDFT). Although the two coumarin derivatives have very different photophysical properties in solution, they show quite similar photophysical behaviour when embedded into the NPs, where an increase in the fluorescence quantum yield of about 10 times was observed for the more flexible molecule. TDDFT calculations employing long-range corrected functionals and with proper account of environmental effects reveal that the formation of an accessible twisted-intramolecular charge transfer state (TICT) is possible for 7-aminocoumarin molecules with flexible alkyl groups in fluid solution, where a conical intersection between the S1 and S0 states is observed at a dihedral angle of about 801. The excited state dynamics of the population density of this reaction coordinate in ethanol and in silica NPs investigated through the resolution of a generalized Smoulochowsky equation shows that this deactivation mechanism is drastically hampered in a silica matrix, in good agreement with experimental evidence. Steady state and time resolved measurements also suggest that at high concentration for both the dyes intermolecular interactions into the silica matrix lead to fluorescence quenching. TDDFT/PCM calculations clearly indicate that the strong quenching and red shift observed is imputable to the formation of excimers with CT character after absorption of the monomeric species.

2012 - Extension of the AMBER force field to cyclic a,a dialkylated peptides [Articolo su rivista]
S., Grubisic; G., Brancato; Pedone, Alfonso; V., Barone

The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing a,a dialkylated residues with cyclic side chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino, M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4- amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational minima of the Ac–Ac6C–NMe (Ac = acetyl, Ac6C = 1-aminocyclohexaneacetic acid, NMe = methylamino) and Ac–TOAC–NMe dipeptides have been examined in terms of geometry and relative energy stability by Quantum Mechanical (QM) computations employing an hybrid density functional (PBE0) for an extended training set of conformers with various folds. A very good agreement between QM and MM (molecular mechanics) data has been obtained in most of the investigated properties, including solvent effects. Finally, the new set of parameters has been validated by comparing the conformational and dynamical behavior of TOAC-labeled polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM data and experimental evidence. The new FF accurately describes the tuning of conformational and dynamical behavior of the Ac–TOAC–NMe dipeptide and double spin-labeled heptapeptide Fmoc–(Aib–Aib–TOAC)2–Aib–OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, a-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found that the 310 helical structure of heptapeptide is the most stable one in vacuo, with a geometry very similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the 310- and a-helical structures is established in aqueous solution, in agreement with EPR data.

2012 - First-principles simulations of the 27Al and 17O solid-state NMR spectra of the CaAl2Si3O10 glass [Articolo su rivista]
Pedone, Alfonso; Gambuzzi, Elisa; Malavasi, Gianluca; Menziani, Maria Cristina

The local and medium-range structure of the 20CaO·20Al2O3·60SiO2 glass generated by classical molecular dynamics simulations has been compared to NMR experiments by computing the 27Al and 17O NMR parameters and NMR spectra from first-principles simulations. The calculation of the NMR parameters (chemical shielding and quadrupolar parameters), which are then used to simulate solid-state MAS and 3QMAS NMR spectra, is achieved by the gauge including projector augmented-wave and the projector augmented-wave methods on the DFT-PBE relaxed structure. The NMR spectra calculated with the present approach are found to be in excellent agreement with the experimental data, providing an unambiguous view of the local and medium-range structure of aluminosilicate glasses.

2012 - Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: pyrimidine as a test case. [Articolo su rivista]
M., Biczysko; J., Bloino; G., Brancato; I., Cacelli; C., Cappelli; A., Ferretti; A., Lami; S., Monti; Pedone, Alfonso; G., Prampolini; C., Puzzarini; F., Santoro; F., Trani; G., Villani

An integrated computational approach built on quantum mechanical (QM) methods, purposely tailored interand intra-molecular force fields and continuum solvent models combined with time-independent and timedependent schemes to account for nuclear motion effects is applied to the spectroscopic investigation of pyrimidine in the gas phase as well as in aqueous and CCl4 solutions. Accurate post-Hartree–Fock methodologies are employed to compute molecular structure, harmonic vibrational frequencies, energies and oscillator strengths for electronic transitions in order to validate the accuracy of approaches rooted into density functional theory with emphasis also on hybrid QM/QM′ models. Within the time-independent approaches,IR spectra are computed including anharmonicities through perturbative corrections while UV–vis line-shapes are simulated accounting for the vibrational structure; in both cases, the environmental effects are described by continuum models. The effects of conformational flexibility, including solvent dynamics, are describedthrough time-dependent models based on purposely DFT-tailored force fields applied to molecular dynamics simulations and on QM computations of spectroscopic properties. Such procedures are exploited to simulate IR and UV–vis spectra of pyrimidine in the gas phase and in solutions, leading in all cases to good agreementwith experimental observations and allowing to dissect different effects underlying spectral phenomena.

2012 - On the ability of Periodic Dispersion-Corrected DFT Calculations to Predict Molecular Crystal Polymorphism in para-diiodobenzene [Articolo su rivista]
Pedone, Alfonso; Presti, Davide; Menziani, Maria Cristina

Periodic DFT calculations employing the PBE, PBE0 and B3LYP functionals coupled with different dispersion correction schemes have been applied to para-diiodobenzene molecular crystal in order to determine how they perform in reproducing the energetic and crystal geometry of its two well known polymorphs.Our results demonstrate that, provided that the dispersion correction scheme proposed by Tkatchenko and Scheffler [Phys. Rev. Lett. 102 (2009) 073005] is used, DFT can be successfully employed to predictthe geometric structure and energy ordering of the a and b forms of para-diiodobenzene molecular crystal, with an accuracy comparable to that yielded by diffusion Monte Carlo calculations.

2012 - Role of Host-Guest Interactions in Tuning the Optical Properties of Coumarin Derivatives Incorporated in MCM-41: A TD-DFTInvestigation [Articolo su rivista]
Pedone, Alfonso; J., Bloino; V., Barone

The encapsulation of organic dye molecules insilica-based nanostructures leads to composite materials withnovel optical properties and a wide range of applications in thefield of nanotechnology. The design of new dye-doped silicabaseddevices requires a deep understanding of how host−guest interactions affect the optical properties and stability ofthe dye/silica assembly. In this work, density functional theory(DFT) and time-dependent DFT (TD-DFT) calculations havebeen employed to investigate the effect of the host−guestinteractions on the structural, optical, and electronic propertiesof two 7-aminocoumarin dyes (labeled C339 and C340) incorporated into MCM-41. Our calculations show that the interactionof the carbonyl groups of the coumarin molecules with the silanol groups on the silica surface is responsible for the dyestabilization and is strengthened upon photoexcitation. As a result, the computed absorption and emission spectra of theincorporated dyes are red-shifted compared to those in toluene, in perfect agreement with experimental measurements. Thecomputed electronic spectra reproduce well both the solvatochromic and Stokes shifts of the dye molecule in toluene and MCM-41, and also, the band-shape can be reconstructed by simply including the vibrational fine structure associated to the electronictransition.

2012 - The electronic structure of the lutein triplet state in plant light-harvesting complex II [Articolo su rivista]
E., Salvadori; M., Di Valentin; C. W. M., Kay; Pedone, Alfonso; V., Barone; D., Carbonera

Carotenoid molecules are essential for the life of photosynthetic organisms in that they protect the cell from the photo-oxidative damage induced by light-stress conditions. One of the photoprotectivemechanisms involves triplet–triplet energy transfer from the chlorophyll molecules to the carotenoids: a process that is strongly dependent on the electronic properties of the triplet states involved. Here, we obtain a clear description of the triplet state of lutein in LHCII from higher plants for the first time by density functional theory (DFT) calculations. DFT predictions have been validated by comparison with hyperfine couplings obtained with pulsed-ENDORspectroscopy. Knowledge of the spin density distribution, the frontier orbitals and orbital excitations forms a basis for discussing the requirements for an efficient triplet–triplet energy transfer. The results obtained for the lutein in LHCII are compared with those of the highlysubstituted carotenoid peridinin in PCP from Amphidinium carterae [Di Valentin et al., Biochim. Biophys. Acta, 2008, 1777, 295–307]. The presence of substituents in the peridinin molecule doesnot alter significantly the triplet state electronic structure compared to lutein. Despite the unusual spectroscopic behaviour of the peridinin excited singlet state, lutein and peridinin have similar triplet state properties. In both molecules the unpaired spins are delocalized uniformly over the whole p-conjugated system in an alternating even–odd pattern.

2012 - The structure of fluoride-containing bioactive glasses: new insights from first-principles calculations and solid state NMR spectroscopy. [Articolo su rivista]
Pedone, Alfonso; T., Charpentier; Menziani, Maria Cristina

Fluoride-containing bioactive glasses are attracting particular interest in many fields of dentistry and orthopedic because they combine the bone-bonding ability of bioactive glasses with the anticariogenic protection provided by fluoride ions. Since the biomedical applications of these materials critically depend on the release of ionic species in the surrounding physiological environment, a deep knowledge of their environments is required. In this paper, Density Functional Theory calculations and Spin Effective Hamiltonians have been employed to analyse the NMR signatures of the various environments of 19F, 29Si, 31P and 23Na atoms in fluorinated bioglasses structural models previously generated by Car-Parrinello Molecular Dynamics simulations. Comparison with experimental spectra expressly recorded in this work shows a good agreement and allows the enlightenment of some longstanding issues about the atomic structure of fluorinated bioglasses, such as the presence of Si-F and Si-O-P bonds. In particular, it is shown that Si-F bonds cannot be resolved by using MAS NMR experiments only, and 29Si{19F} REDOR experiments, that probes directly spatial proximities among atoms, must be employed. Our results show that F is coordinated entirely to the modifier ions Na and Ca, and that no Si-F bonds are present in the real glass structure. Thus, addition of fluorine to the 45S5 Bioglass® increases the polymerization of the silicate network by removing modifiers from the siliceous matrix and reducing its reactivity. Finally, the computed isotropic chemical shifts of the various environments of phosphorous show that, if present, Si-O-P bonds should be clearly noticeable in the 31P static NMR experimental spectrum. Instead, the latter shows that P is present as isolated orthophosphate units and does not enter into the siliceous matrix by forming Si-O-P bonds as conjectured by Molecular Dynamics simulations.

2012 - Unambiguous Description of the Oxygen Environment in Multicomponent Aluminosilicate Glasses from 17O Solid State NMR Computational Spectroscopy [Articolo su rivista]
Pedone, Alfonso; Gambuzzi, Elisa; Menziani, Maria Cristina

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 nonrandomdistribution 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 theinvestigated glasses reveals that the Al avoidance rule is not respected in amorphous solids. The Si−O−Al sites are surrounded byNa 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.

2011 - Absorption and Emission Spectra of Fluorescent Silica Nanoparticles from TD-DFT/MM/PCM calculations [Articolo su rivista]
Pedone, Alfonso; G., Prampolini; S., Monti; V., Barone

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

2011 - Fluorescence Spectra of Organic Dyes in Solution: A Time Dependent Multilevel Approach [Articolo su rivista]
V., Barone; J., Bloino; S., Monti; Pedone, Alfonso; G., Prampolini

Classical all-atom molecular dynamics (MD) simulations and quantum mechanical (QM) time-dependent density functional theory (TD-DFT) calculations are employed to study the conformational and photophysical properties of the first emitter excited state of tetramethyl-rhodamine iso-thiocyanate fluorophore in aqueous solution. For this purpose, a specific and accurate force field has been parameterised from QM data to model the fluorophore’s first bright excited state. During the MD simulations, the consequences of the π → π* electronic transition on the structure and microsolvation sphere of the dye has been analysed in some detail and compared to the ground state behaviour. Thereafter, fluorescence has been calculated at the TD-DFT level on configurations sampled from the simulated MD trajectories, allowing us to include time dependent solvent effects in the computed emission spectrum. The latter, when compared with the absorption spectrum, reproduces well the experimental Stokes shift, further validating the proposed multilevel computational procedure.

2011 - Fluorine environment in bioactive glasses: ab initio molecular dynamics simulations. [Articolo su rivista]
J. K., Christie; PEDONE, Alfonso; MENZIANI, Maria Cristina; A., Tilocca

Car-Parrinello molecular dynamics (CPMD) simulations have been performed on a 45S5Bioglass composition in which 10 mol% of the CaO has been replaced with CaF2. The veryaccurate characterization of the fluorine environment in this system has allowed us to resolvesome longstanding issues about the atomic structure of fluorinated bioglasses. F is coordinatedalmost entirely to the modifier ions Na and Ca, with a very small amount of residual Si-Fbonds, whose fraction only becomes significant in the melt precursor. There is no evidencefor preferential bonding of F to either modifier ion: almost all F atoms are coordinated toboth calcium and sodium in a “mixed state”, rather than exclusively to either, as had beenconjectured. We discuss the consequences of these findings on the properties of fluorinecontainingbioglasses.

2011 - In-silico study of Hydroxyapatite and Bioglass® : how computational science sheds light on biomaterials [Capitolo/Saggio]
M., Corno; F., Chiatti; Pedone, Alfonso; P., Ugliengo

In the present Chapter it has been explained how crucial the computational techniques arewhen applied together with experimentalist measurements in the understanding ofbiological complex systems and mechanisms dealing with biomaterials for a large numberof reasons. Indeed, computational methods are extremely powerfully applied to predictstructure formation and crystal growth as well as to describe at a molecular level the realinteractions responsible of the attachment of the inorganic biomaterial to the organic tissue.In the investigation of phenomena related to a complex system such as the human body,many approximations are required, so a reductionist approach is employed also in thecomputational analysis

2011 - Insight into the Structure of Vanadium containing Glasses: a Molecular Dynamics Study [Articolo su rivista]
Ori, Guido; Montorsi, Monia; Pedone, Alfonso; Siligardi, Cristina

In this manuscript, classical molecular dynamics simulations (MD) have been applied to study the short and medium range order of very complex vanadium containing glasses with the aim of improving the first microscopic picture of such materials. A rigid ionic force-field has been extended to include the V5+-O, V4+-O and Cu2+-O interatomic pair parameters and tested to reproduce structural properties of known crystal phases with quite good accuracy. Then the structure of Na2O-SiO2, CaO-MgO-Al2O3-SiO2 and Na2O-P2O5 glass compositions in which vanadium is present in the range 1-72 wt% (0.3-60 mol.%) have been fully described in terms of vanadium local structure and Qn distributions. A fairly good agreement was found with experimental data further validating our computational models and providing a computational approach that could be used and extend to investigate in detail the structural information (V-V distances, V-O-V linkages and BO/NBO) directly correlated to macroscopic properties of application interest.

2011 - Magnetic Resonance Spectroscopy: Singlet and Doublet Electronic States [Capitolo/Saggio]
Pedone, Alfonso; O., Crescenzi

The aim of this chapter has been to provide an overview of current computational approaches in some specific areas of Magnetic Resonance Spectroscopy. Apart from theoretical considerations, the focus on singlet and doublet electronic states reflects the fact that in these specific fields computational spectroscopy has nowadays reached the stage of a mature technique. Thus, for example, comparisons between measured and computed values of chemical shifts are becoming an important tool for experimental studies in structural organic chemistry; likewise, hyperfine coupling constant are routinely calculated to gain insight into the behavior of spin-probes. Even more demanding computational applications, e.g. those involving the estimation of spin-spin coupling constants, are on their way to enter into routine use even by non specialists. In this spirit, the theoretical presentation has been kept at a reasonably accessible level, and a number “case studies” have been provided in order to illustrate the potentiality of the techniques introduced: this plan should contribute to further promote the introduction of computational approaches within standard experimental studies, which, in this as in many other fields of research, allows for enhanced understanding of phenomena, faster and more efficient characterization protocols, and innovative chemical results.

2011 - Realistic Modeling of Fluorescent Dye-Doped Silica Nanoparticles: A Step Toward the Understanding of their Enhanced Photophysical Properties. [Articolo su rivista]
Pedone, Alfonso; G., Prampolini; S., Monti; V., Barone

The very high brightness and photo-stability of silica nanoparticles (NPs) encapsulating organic fluorophores have been demonstrated recently and have opened up new exciting opportunities for a number of biotechnological and information technological applications. However, a systematic theoretical study of fluorescent core-shell NPs remains a challenge, and as a result, the understanding of the fundamental interaction and microscopic dynamics of the dye/NPs assembly is still lacking. In the present work, different computational methods, as classical molecular dynamics simulations based on purposely tailored force-fields and TDDFT quantum mechanical calculations, are combined in an integrated strategy to elucidate the mechanisms behind the brightness enhancement of realistic models of rhodamine (TRITC) based C-dots (Cornell dots) for the first time. TD-B3LYP/MM calculations on the S1 excited state dynamics of the dye show that crossing between the low lying (bright) ππ* and (dark) nπ* states occurs both in solution and in silica NPs albeit in the latter case it is reduced by the caging and screening effect played by the silica matrix. Moreover, our calculations show that the negligible solvatochromic shift between free-TRITC in solution and TRITC-based C-dots observed experimentally is due to seizure and incorporation of water molecules during the synthetic process that mediate the dye-silica interaction.

2010 - A Theoretical Multi-level Approach for the Study of Optical Properties of Organic Dyes in Solution. [Articolo su rivista]
V., Barone; J., Bloino; S., Monti; PEDONE, Alfonso; G., Prampolini

Classical all-atom molecular dynamics (MD) simulations and quantum mechanicaltime-dependent density functional theory (TD-DFT) calculations are employed to study theconformational and photophysical properties of tetramethylrhodamine iso-thiocyanate (TRITC)in solution. The potential energy surface (PES) is explored and the minimum energy structure isidentified both in water and ethanol. An accurate force-field is parameterized on the computedquantum mechanical data and used in the classical dynamics to take into account solutevibrations and solvent effects. Several configurations, extracted from the MD trajectories,are employed to investigate absorbance spectra in a time dependent approach, consideringsolvation models of increasing complexity. Explicit- and implicit-solvent approaches, as well ascombinations of them are used to predict and explain the absorption properties and the electronicstructure of the dye. The defined theoretical methodology succeeds in reproducing correctly theavailable experimental data.

2010 - Absorption and Emission UV-Vis Spectra of the TRITC Fluorophore molecule in solution: a quantum mechanical study. [Articolo su rivista]
Pedone, Alfonso; J., Bloino; S., Monti; G., Prampolini; V., Barone

The absorption and emission properties as well as the electronic structure in the ground (S0) andexcited (S1) states of tetramethylrhodamine isothiocyanate (TRITC) fluorophore molecule havebeen investigated by time-dependent density functional theory (TD-DFT). The effect of waterand ethanol solvents on the structure and optical properties of the dye was taken into accountby using both explicit and implicit solvent models, as well as combinations of them.Different hybrid and long range corrected functionals have been tested in reproducing absorptionand emission transition energies. It has been found that the B3LYP functional coupled with mixedexplicit/implicit solvent models reproduces correctly experimental data concerning both the solventand Stokes shifts. This work presents a first step to a more challenging project devoted to thedevelopment of integrated multiscale approaches and protocols for studying optical propertiesof fluoroprobes embedded in biological systems and/or encapsulated in nanoparticles oftechnological interest.

2010 - An integrated computational protocol for the accurate prediction of EPR and PNMR parameters of nitroxide radicals in solution. [Articolo su rivista]
V., Barone; P., Cimino; Pedone, Alfonso

Magnetic spectroscopic techniques such as electron paramagnetic resonance (EPR) and paramagneticNMR(PNMR) are valuabletools for understanding the structure and dynamics of complex systems such as, for example, biomolecules or nanomaterialslabeled with suitable free radicals. Unfortunately, such spectra do not give direct access to the radical structure because of thesubtle interplay between several different effects not easily separable and evaluable by experimentalists alone. In this respect,computational spectroscopy is becoming an essential and versatile tool for the assignment and interpretation of experimentalspectra. In this article, the new integrated computational approaches developed in the recent years in our research groupare reviewed. Such approaches have been applied to two widely used spin probes showing that proper account of stereoelectronic,environmental and dynamical effects leads to magnetic properties in remarkable agreement with experimentalresults.

2010 - Computer Simulations Techniques for Modelling Biomaterials [Articolo su rivista]
Pedone, Alfonso; M., Corno

Computational simulation of biomaterials constitutes a fundamental and fascinating research area, constantly growing thanks tothe increasing availability of computational resources. The combined approach of classical and ab-initio methods has allowedthe modelling of bioceramics (both bioactive glasses as the 45S5 Bioglass® and hydroxyapatite) and their complex interactionswith the biological environment.

2010 - Environmental Effects in Computational Chemistry: Accuracy and Interpretations. [Articolo su rivista]
Pedone, Alfonso; M., Biczysko; V., Barone

Spectroscopic techniques are valuable tools for understandingthe structure and dynamics of complex systems, such as biomolecules or nanomaterials. Most of the current research is devotedto the development of new experimental techniques forimproving the intrinsic resolution of different spectra. However,the subtle interplay of several different effects acting at differentlength and time scales still makes the interpretation andanalysis of such spectra a very difficult task. In this respect,computational spectroscopy is becoming a needful and versatiletool for the assignment and interpretation of experimentalspectra. It is in fact possible nowadays to model with relativelyhigh accuracy the physical–chemical properties of complexmolecules in different environments, and to link spectroscopicevidence directly to the structural and dynamical properties ofoptically or magnetically active solvated probes. In this Review,significant steps toward the simulation of entire spectra in condensedphases are presented together with some basic aspectsof computational spectroscopy, which highlight how intramolecularand intermolecular degrees of freedom influenceseveral spectroscopic parameters.

2010 - Extension of the AMBER force-field for the study of large nitroxides incondensed phases: an ab initio parameterization [Articolo su rivista]
E., Stendardo; Pedone, Alfonso; P., Cimino; Menziani, Maria Cristina; O., Crescenzi; V., Barone

The popular AMBER force-field has been extended to provide an accurate description of largeand flexible nitroxide free-radicals in condensed phases. New atom types have been included, andrelevant parameters have been fitted based on geometries, vibrational frequencies and potentialenergy surfaces computed at the DFT level for several different classes of nitroxides, bothin vacuo and in different solvents. The resulting computational tool is capable of providingreliable structures, vibrational frequencies, relative energies and spectroscopic observables forlarge and flexible nitroxide systems, including those typically used as spin labels. The modifiedforce field has been employed in the context of an integrated approach, based on classicalmolecular dynamics and discrete–continuum solvent models, for the investigation ofenvironmental and short-time dynamic effects on the hyperfine and gyromagnetic tensors ofPROXYL, TEMPO and INDCO spin probes. The computed magnetic parameters are in verygood agreement with the available experimental values, and the procedure allows for an unbiasedevaluation of the role of different effects in tuning the overall EPR observables.

2010 - Interplay of stereo-electronic, environmental, and dynamical effects in determining the EPR parameters of aromatic spin-probes: INDCO as a test case. [Articolo su rivista]
P., Cimino; Pedone, Alfonso; E., Stendardo; V., Barone

An integrated computational strategy for the evaluation of reliable structures and magneticproperties of spin probes and spin labels has been extended to aromatic species. From anelectronic point of view, delocalization of the unpaired electron density over aromatic moietiesreduces significantly the computed nitrogen isotropic hyperfine coupling constant (AN) withrespect to values characteristic of aliphatic nitroxides. Solvent effects in not too high polaritymedia are quite small, but not negligible. At this stage computed AN are lower than theirexperimental counterparts by more than 1 G. Inclusion of vibrational averaging effects bymolecular dynamics simulations with a new reliable force field restores full agreement withexperiment pointing out the limits of static approaches irrespective of the sophistication of theelectronic quantum mechanical method. The generality and computational effectiveness of theproposed integrated approach paves the route toward a reliable analysis of the interplay ofstereo-electronic, environmental, and dynamical effects in tuning the properties of large flexiblemagnetic systems of biological and technological interest.

2010 - Molecular Dynamics Simulations of Sodium Silicate Glasses:Optimization and Limits of the Computational Procedure [Articolo su rivista]
Pota, Marco; Pedone, Alfonso; Malavasi, Gianluca; Durante, Caterina; Cocchi, Marina; Menziani, Maria Cristina

The performance of the molecular dynamics (MD) simulations to obtain the structure of silica glasses containing different concentrations of alkali oxides has been tested. An optimal MD simulation procedure (including cooling cycle, MD constants and ensemble used) has been developed by means of experimental design methodologies (DOE), firstly restricting the study to the 30% Na2O silica glass for which experimental data are available to allow the comparison of the results. The optimization procedure led to simulations that well predict experimental density and short-range structure of glasses with different sodium content. On the contrary, the medium-range structure has been badly reproduced and it was not possible to determine a reliable correlation with the parameters of the simulation procedures used. Therefore, the correlation of medium-range properties with the structure has been studied by means of the PLS methods. The results showed to be useful to highlight the relationships among structural elements, such as radial distribution functions of specific bonds and angles, and Qn species, suggesting possible directions in order to improve the force field.

2010 - Multinuclear NMR of CaSiO3 Glass: Simulation from First-Principles [Articolo su rivista]
Pedone, Alfonso; T., Charpentier; Menziani, Maria Cristina

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 CaSiO3. Two CaSiO3 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 CaSiO3 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.

2010 - New Insights into the Atomic Structure of 45S5 Bioglass byMeans of Solid-State NMR Spectroscopy and AccurateFirst-Principles Simulations [Articolo su rivista]
Pedone, Alfonso; T., Charpentier; Malavasi, Gianluca; Menziani, Maria Cristina

An integrated computational method that couples classical molecular dynamics simulations withdensity functional theory calculations has been used to simulate the solid-state 17O and 23NaMQMAS, 29Si, 31P, and 23Na static and MAS NMR spectra of the 45S5 Bioglass structural modelswith up to 248 atoms. Comparison with the experimental spectra collected in this work (the 17OMQMAS spectrum of the 45S5 Bioglass is reported for the first time in the literature) shows anexcellent agreement. The results provide deep insights into fundamental open questions regarding theatomic-scale structural details of this glass of great medical interest. In particular, the host silicanetwork, described by theQn distribution (aQn species is a network-forming ion bonded to n bridgingoxygens), consists of chains and rings ofQ2Si (67.2%) SiO4 tetrahedra cross-linked with Q3Si (22.3%)species and terminated by a low quantity of Q1Si (10.1%) species. No Si-O-P bridges have beendetected by both 31P NMR and 17O MQMAS experiments, and therefore isolated orthophosphateunits are able to form nanodomains that subtract sodium and calcium cations from their networkmodifying role into the silicate network. Finally, both the experimental and theoretical results show amixture of dissimilar cations (Na,Ca) around NBO, according to a nonrandom distribution of thesespecies.

2010 - Unraveling Solvent Effects on the Electronic Absorption Spectra of TRITC Fluorophore in Solution: a Theoretical TD-DFT/PCM study [Articolo su rivista]
Pedone, Alfonso; V., Barone

In this paper the equilibrium between the two ground state forms of TRITC in solvents ofdifferent polarity has been studied by means of state of the art DFT calculations using thepolarizable continuum model (PCM) for including bulk solvent effects. TD-DFT/PCMcalculations have been used to calculate vertical excitation energies and the UV-Vis spectra ofTRITC has been interpreted in terms of the equilibrium between different forms, which ismodulated by the microenvironment embedding the molecule. We show that the most intenseabsorption bands are sensitive to solute–solvent interactions and provide a distinctive signature ofspecific interactions. The good agreement with experimental data makes our approach suitable tostudy and monitor modifications of the chemical environment of fluorophores in differentsolutions as well as in interaction with biological systems and nanoparticles.

2009 - Computational insight into the effect of CaO/MgO Substitution on the Structural Properties of Phospho-Silicate Bioactive Glasses. [Articolo su rivista]
Pedone, Alfonso; Malavasi, Gianluca; Menziani, Maria Cristina

The effect of the replacement of CaO for MgO on the structural properties of the 45S5 Bioglass with composition 46.2SiO2·24.3Na2O·(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 46.2SiO2·24.3Na2O·16.9CaO·2.6P2O5·10MgO 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.

2009 - Properties Calculations of Silica-Based Glasses by Atomistic Simulations Techniques: A review [Articolo su rivista]
Pedone, Alfonso

Silica-based glasses are of great importance in various technological fields ranging from fiber optic waveguides, laser optics for initiating fusion reactions, to containers for radioactive waste and biomedical applications.In the past, several works have been devoted to the modeling of structural properties of such materials, andintuitive relationships with experimental macroscopic properties have been addressed. However, the abilityto predict properties such as mechanical strength, elastic constants, chemical durability, and conductivity,which are of particular interest since they dictate whether a specific need or application can be met, is becomingan essential tool for glass manufactures. In this review, the results of classical atomistic simulations of thestructure, elastic properties, stress-strain diagrams, fracture mechanisms, and transport properties of silicateglasses are presented

2009 - Quantitative Structure−Property Relationships of Potentially Bioactive Fluoro Phospho-silicate Glasses [Articolo su rivista]
Lusvardi, Gigliola; Malavasi, Gianluca; F., Tarsitano; Menabue, Ledi; Menziani, Maria Cristina; Pedone, Alfonso

In this work, the glass transition temperature and chemical durability of bioactive phospho-silicate glasses were experimentally determined and correlated to the structural descriptor Fnet derived from classical molecular dynamics simulations. The replacement of CaF2 for Na2O in the parent glass 45S5 enhances both chemical durability and density, while the replacement of CaF2 for CaO lowers chemical durability. The proposed descriptor, Fnet, provides satisfactorily correlations with glass transition temperature and chemical durability over a wide range of compositions.

2009 - Vibrational features of phosphor-silicate glasses: Periodic B3LYP Simulations. [Articolo su rivista]
M., Corno; Pedone, Alfonso

B3LYP periodic calculations with double-f polarised basis set using CRYSTAL06 code have been run on a bioactivephospho-silicate glass similar in composition to Bioglass 45S5 (46.1 SiO2, 24.4 Na2O, 26.9 CaO and2.6 P2O5 mol%) and a phosphorous-free soda-lime glass (49.5 SiO2, 24.2 Na2O and 26.4 CaO mol%). Initialstructures have been obtained through a melt-quench process by classical molecular dynamics techniquesand the effect of phosphorous on the glass network structure and dynamics have been assessedby B3LYP vibrational spectra.

2008 - Accurate First-Principle Prediction of 29Si and 17O NMR Parameters in SiO2 Polymorphs: The Cases of Zeolites Sigma-2 and Ferrierite [Articolo su rivista]
Pedone, Alfonso; Pavone, M; Menziani, Maria Cristina; Barone, V.

Abstract: The magnetic shielding tensors of silica polymorphs have been investigated by meansof quantum chemical calculations. Several levels of theory, from Hartree-Fock to the lastgeneration of Density Functional Theory based approaches, have been tested on predicting29Si and 17O isotropic and principal components of the chemical shift tensors together with 17Oquadrupolar coupling constants. The NMR parameters have been computed on all known silicasystems, namely, R-quartz, R-cristobalite, coesite, Sigma-2, and ferrierite zeolites. Besides, clusterbased approaches have been compared to a hybrid Quantum-Mechanics/Molecular-Mechanics(QM/MM) method, within the ONIOM scheme. The convergence of computed 17O NMRparameters with respect to cluster size is found to be system-dependent. Excellent agreementbetween computed and experimental data has been found for 29Si NMR parameters of thedifferent Si sites of silica polymorphs and of Sigma-2 and ferrierite zeolites.

2008 - B3LYP Simulation of the Full Vibrational Spectrum of 45S5 Bioactive Silicate Glass compared to v-Silica [Articolo su rivista]
M., Corno; Pedone, Alfonso; R., Dovesi; P., Ugliengo

The IR spectrum of the Bioglass 45S5 (of composition 46.1 SiO2, 24.4 Na2O, 26.9 CaO, and 2.6 P2O5mol %) has been simulated by means of periodic ab initio B3LYP calculations. The initial glass structureunit cell envisaging 78 atoms was generated through a melt quench process by means of classical moleculardynamics simulations. The molecular mechanics optimized unit cell has then been fully reoptimized(both unit-cell parameters and internal coordinates) at B3LYP level in a periodic approach using Gaussianbasis sets of double- quality by means of the CRYSTAL06 code. Although long-range structural propertiescannot be modeled by using this ab initio approach because of the intrinsic amorphous nature of theglass, the quantum mechanical simulation proved to be extremely effective in predicting and analyzingthe vibrational features of this biomaterial. The effect of modifiers Na and Ca cations on the networkdynamics has been assessed by comparing the 45S5 vibrational spectrum with that of amorphous V-SiO2,both simulated at the B3LYP level. A detailed assignment of each spectral peak to the correspondingvibrational mode of the two glasses has been addressed and the role of cation modifiers on the vibrationalfeatures has been analyzed in greater details. This may be useful to support further IR and Ramaninvestigations of the bulk structure of these materials.

2008 - Deflocculant effect on the surface properties of kaolinite investigated through malachite green adsorption [Articolo su rivista]
Castellini, Elena; Andreoli, Roberto; Malavasi, Gianluca; Pedone, Alfonso

The adsorption of malachite green (MG) on sodium-exchanged kaolinite and on the same clay treated with two widely used deflocculants, sodium hexametaphosphate (NaHMP) and sodium disilicate (NaDIS), was investigated. The results indicate that the deflocculants affect the adsorption process. In particular, DIS treatment increases physisorption, whereas HMP treatment almost completely prevents it. The Frumkin isotherm accurately describes MG adsorption for all of the adsorbents investigated and the Frumkin inter- action parameter is found to be repulsive, in keeping with the cationic nature of the adsorbed species. TheKeywords: temperature dependences of the adsorption constant and the related thermodynamic parameters H◦ adsAdsorption and S◦ ads were also determined and discussed.

2008 - Elastic and dynamical properties of alkali silicate glasses from computer simulations techniques [Articolo su rivista]
Pedone, Alfonso; Malavasi, Gianluca; CORMACK A., N; Segre, Ulderico; Menziani, Maria Cristina

This paper shows recent progresses in the field ofcomputer simulations of inorganic glasses. Moleculardynamics simulations and energy minimization methods havebeen applied to calculate the elastic and transport proper-ties of alkali silicate glasses of compositions xM2 O · (100 −x)SiO2 (with x = 0, 10, 15, 20, 25, 30 % mol for M = Li,Na and K) and of a soda-lime glass with composition 15Na2 O·10CaO · 75SiO2 , which has been employed to ascertain theeffect of the replacement of CaO for Na2 O. The excellentagreement of the computed results with the experimentaldata highlights the important predictive and interpretativerole reached by computer simulations techniques.

2008 - Elucidation of the Structural Role of Fluorine in Potentially Bioactive Glasses by Experimental and Computational Investigation [Articolo su rivista]
Lusvardi, Gigliola; Malavasi, Gianluca; M., Cortada; Menabue, Ledi; Menziani, Maria Cristina; Pedone, Alfonso; Segre, Ulderico

Glasses belonging to the Na2O-CaO-P2O5-SiO2 system and modified by CaF2 substitution for CaO and Na2Oalternatively, were synthesized and characterized experimentally and computationally. The results of moleculardynamics simulations show that fluorine is almost exclusively bonded to modifier cations (Ca and Na) withcoordination number close to 4. A similar mean coordination number value is found in the crystal phasesobtained by means of thermal treatment at fixed temperature. Addition of fluorine increases the polymerizationof silicate tetrahedra by removing modifiers from the siliceous matrix. No appreciable amount of Si-F bondsare detected.

2008 - FFSiOH: a New Force Field for Silica Polymorphs and Their Hydroxylated Surfaces Based on Periodic B3LYP Calculations [Articolo su rivista]
Pedone, Alfonso; Malavasi, Gianluca; Segre, Ulderico; Menziani, Maria Cristina; Musso, F; Corno, M; Civalleri, B; Ugliengo, P.

A partial charge shell-ion model potential for silica polymorphs and their hydroxylated surfaces(FFSiOH) was parametrized in a self-consistent way using periodic B3LYP results for bulk R-cristobaliteand the (100) and (001) hydroxylated surfaces. The reliability of the new potentials was checked bycomparing structures, vibrational frequencies and relative phase stabilities of dense bulk silica polymorphs,namely R-quartz, R-cristobalite, R-tridymite, and Stishovite with both experimental and B3LYP data.The FFSiOH was also checked for computing structural and vibrational features of representative all-silica microporous materials, namely edingtonite, chabazite, and faujasite. As a last step, FFSiOH wasadopted to predict OH stretching vibrational frequencies and relative thermodynamic stability of themost common fully hydroxylated surfaces of the dense silica polymorphs, the (100) and (001) facesof all-silica edingtonite, the features of the local Si-defect in chabazite and sodalite known as (SiOH)4hydrogarnet and the geometries of H-bonded silanol groups of an amorphous silica surface. In all casesexcellent agreement resulted between FFSiOH and B3LYP periodic data and experimental data, whenavailable. The new FFSiOH force field opens up the molecular simulation of materials in which thesurface hydroxyl groups play a key role, as is the case for amorphous silica surfaces, all-silica zeoliteexternal surfaces, and the internal walls of mesoporous materials.

2008 - Medium-range order in phosphosilicate bioactive glasses: Insights from MAS-NMR spectra, chemical durability experiments and molecular dynamics simulations [Articolo su rivista]
L., Linati; Lusvardi, Gigliola; Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; P., Mustarelli; Pedone, Alfonso; Segre, Ulderico

The medium-range order of phospho-silicate bioactive glasses (with compositions (2 p)SiO2 Æ 1Na2O Æ 1.1CaO Æ pP2O5, in whichp = 0.10, 0.20, 0.26) has been studied by means of a combined-experimental (MAS-NMR, chemical durability measurements) and computational(classical molecular dynamics (MD)) approach. The structural model obtained by MD is showed to be helpful in the interpretationof the NMR spectra. A small amount of Si–O–P link units has been detected in glasses with low P2O5-content, but at high P2O5concentration the percentage of Si–O–P bridges becomes important. However, Qn distributions show that the HP5 (p = 0.20) glass structureis less polymerized with respect to the H (p = 0.10) and HP6.5 (p = 0.26) glasses. These results provide useful explanation of thebehavior of these glasses in water and highlight the influence of the medium-range order on a very important property of potentialbioactive glasses such as the chemical durability.

2008 - Molecular dynamics of stress-strain behaviour of silica glass under tensile load. [Articolo su rivista]
Pedone, Alfonso; Malavasi, Gianluca; Menziani, Maria Cristina; Segre, Ulderico; Cormack, A. N.

Molecular dynamics (MD) simulations were carried out to study the stress-strain diagrams of crystallineand amorphous silica under different nonequilibrium conditions. The responses of a tensile load wererecorded in two cases. In one case, the system was not allowed to relax along the transverse direction(null Poisson’s ratio), while in the other case, the deformations were allowed in directions perpendicularto the strained one. The higher strength of crystalline silica as compared to amorphous silica resultedfrom a different distribution of ring sizes. The results obtained for the inert failure strains and intrinsicstrength of the silica glass were in good agreement with the experimental data, and the nonlinear elasticbehavior of the glass was reproduced along with the effects of strain rate and temperature variation.Elastic properties extracted from stress-strain diagrams also were compared with the properties calculatedby means of static methods and with experimental data.

2008 - Properties of zinc releasing surfaces for clinical applications [Articolo su rivista]
Lusvardi, Gigliola; Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; Pedone, Alfonso; Segre, Ulderico; Aina, V; Perardi, A; Morterra, C; Boccafoschi, F; Gatti, S; Bosetti, M; Cannas, M.

Two series of glasses of general formula (2-p) SiO21.1Na2OCaOpP2O5xZnO (p = 0.10, 0.20; x = 0.0, 0.16, 0.35, and 0.78) have been analyzed for physico-chem. surface features before and after contact with simulated body fluid, morphol. characteristics, and osteoblast-like cells behavior when cultured on them. The resulted good cell adhesion and growth, along with nonsignificant changes of the focal contacts, allow the authors to indicate HZ5 and HP5Z5 glasses as the ones having optimal ratio of Zn/P to maintain acceptable cell behavior, comparable to the bioactive glass (Bioglass) used as a control; results are also rationalized by means of three-dimensional models derived by mol. dynamic simulations, with decompn. and conversion rates optimized with respect to the parent Hench's Bioglass.

2008 - Role of Magnesium in Soda-Lime Glasses: Insight into Structural, Transport, and Mechanical Properties through Computer Simulations [Articolo su rivista]
Pedone, Alfonso; Malavasi, Gianluca; Menziani, Maria Cristina; Segre, Ulderico; Cormack, A. N.

The role of Mg in soda-lime glasses was elucidated by classical molecular dynamics (MD) simulations. Theeffect of the replacement of CaO for MgO on the structure, transport, and elastic properties of a series ofglasses with compositions 15Na2O · (10 - x)CaO · xMgO · 75SiO2 (x ) 0, 5, and 10 mol) was studied. Differentstructural roles were found for the Ca and Mg ions. The former, coordinated by six oxygen atoms, acts as anetwork modifier, while the latter, four-fold coordinated, participates in the silica network. Consequently, Naion diffusion is favored by the replacement of MgO for CaO in these glasses, as shown by variation in thecomputed diffusion coefficients and activation energy of the process in the series of glasses studied. Moreover,the consequences of these structural modifications on the elastic properties (Young’s modulus, shear modulus,bulk modulus, Poisson’s ratio, and compressibility) of the glasses were evaluated by means of energyminimization techniques carried out on the structures obtained by MD simulations.

2007 - A computational multiscale strategy of the study of amorphous materials [Articolo su rivista]
Malavasi, Gianluca; Menziani, Maria Cristina; Pedone, Alfonso; Civalleri, B; Corno, M; Ugliengo, P.

A first step towards a computational Si–O–P angles, respectively. Other geometrical featuresmultiscale approach has been adopted here to deal with are in excellent agreement within the two approaches.the computational simulation of the Hench bioglass Electronic properties of the Hench bioglass have been45S5, an amorphous material of 48.1% SiO2 , 25.9% reported at B3LYP for the first time and both Mullik-CaO, 22.2% Na2 O and 3.7% P2 O5 composition. Molec- en charges and electronic band structure show a ratherular dynamics simulations based on classical force fields ionic character of the material, whereas a band gap offollowed by static minimizations on quenched structures about 6.5 eV characterizes the bioglass as a strong insu-have been run on a unit cell size suitable for subsequent lator. Work presently in progress will soon allow theab initio calculations. The molecular mechanics opti- information to be transferred from the B3LYP calcu-mized unit cell envisaging 78 atoms of Na12 Ca7 P2 Si13 lations to the molecular mechanics engine in order toO44 composition and P1 symmetry has then been fully refine the presently available empirical force fields foroptimized (both unit cell parameters and internal coor- complex ionic systems and their surfaces.dinates) at B3LYP level in a periodic approach usinggaussian basis sets of double-ζ quality and the devel-opment version of the CRYSTAL03 code. Comparisonbetween the molecular mechanics and B3LYP optimizedstructures shows the latter to give a slightly higherdensity than the former, due to overestimation of theSi–O bonds and underestimation of the Si–O–Si and

2007 - An ab initio parameterized interatomic force field for hydroxyapatite [Articolo su rivista]
Pedone, Alfonso; M., Corno; B., Civalleri; Malavasi, Gianluca; Menziani, Maria Cristina; Segre, Ulderico; P., Ugliengo

A classical interatomic force field for hydroxyapatite has been parameterized from periodicab initio calculations carried out on the hexagonal structure (space group P63). The GULPprogram has been used for fitting geometry and phonon frequencies computed with theCRYSTAL06 program using the B3LYP hybrid functional and Gaussian-type basis set ofpolarized double zeta quality. Polarization effects and covalent bonding have been includedthrough the shell-ion model potential. Excellent agreement has been found in reproducingstructural features, lattice dynamics, the OH stretching vibrations and relative phase stabilitiesbetween the monoclinic structure (space group P21/b) and the hexagonal one. Transferability fromhydroxyapatite to other calcium phosphates has also been demonstrated.

2007 - Crystallization Kinetics of Bioactive Glasses in the ZnO-Na2O-CaO-SiO2 System [Articolo su rivista]
Malavasi, Gianluca; Lusvardi, Gigliola; Pedone, Alfonso; Menziani, Maria Cristina; M., Dappiaggi; Gualtieri, Alessandro; Menabue, Ledi

The crystallization kinetics of Na2OâCaOâ2SiO2 (x ) 0) and 0.68ZnOâNa2OâCaOâ2SiO2 (x ) 0.68, where xis the ZnO stoichiometric coefficient in the glass formula) bioactive glasses have been studied using bothnonisothermal and isothermal methods. The results obtained from isothermal XRPD analyses have showedthat the first glass crystallizes into the isochemical Na2CaSi2O6 phase, whereas the Na2ZnSiO4 crystallinephase is obtained from the Zn-rich glass, in addition to Na2CaSi2O6. The activation energy (Ea) for thecrystallization of the Na2OâCaOâ2SiO2 glass is 193 ( 10 and 203 ( 5 kJ/mol from the isothermal in situXRPD and nonisothermal DSC experiments, respectively. The Avrami exponent n determined from theisothermal method is 1 at low temperature (530 °C), and its value increases linearly with temperature increaseup to 2 at 607 °C. For the crystallization of Na2CaSi2O6 from the Zn-containing glass, higher values of boththe crystallization temperature (667 and 661 °C) and Ea (223 ( 10 and 211 ( 5 kJ/mol) have been foundfrom the isothermal and nonisothermal methods, respectively. The Na2ZnSiO4 crystalline phase crystallizesat lower temperature with respect to Na2CaSi2O6, and the Ea value is 266 ( 20 and 245 ( 15 kJ/mol fromthe isothermal and nonisothermal methods, respectively. The results of this work show that the addition ofZn favors the crystallization from the glass at lower temperature with respect to the Zn-free glass. In fact, itcauses an increase of Ea for the Na diffusion process, determined using MD simulations, and consequentlyan overall increase of Ea for the crystallization process of Na2CaSi2O6. Our results show good agreementbetween the Ea and n values obtained with the two different methods and confirm the reliability of thenonisothermal method applied to kinetic crystallization of glassy systems. This study allows the determinationof the temperature stability field of the crystalline phases with the view of creating a different glass ceramicuseful in the field of bioactive materials.

2007 - Density of multicomponent silica-based potential bioglasses: Quantitative structure-property relationships (QSPR) analysis [Articolo su rivista]
Lusvardi, Gigliola; Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; Pedone, Alfonso; Segre, Ulderico

The results of a quantitative structure-property relationships (QSPR) analysis of multicomponent silica-based potential bioglasses (containing Na2O, CaO, P2O5 and/or ZnO) are here presented. A quantitative model explaining the variation of the density data measured for series of glasses with different compositions has been obtained by means of a structural descriptor derived from molecular dynamics (MD) simulations. A descriptor able to rationalize the variation in density caused by the overall packing degree of the structural units in the glasses examined has been defined. It is worth noting that the descriptor used allows the fitting of glasses with different composition (presence-absence Of P2O5, ZnO, Na2O and CaO) in the same correlation. The validity of the QSPR approach, which has recently been introduced for the rationalization and prediction of the technology-related properties of a series of complex multicomponent glasses, is confirmed by this work on a larger series of glasses of various compositions. (c) 2006 Elsevier Ltd. All rights reserved.

2007 - Insight into elastic properties of binary alkali silicate glasses; prediction and interpretation through atomistic simulation techniques [Articolo su rivista]
Pedone, Alfonso; Malavasi, Gianluca; A. N., Cormack; Segre, Ulderico; Menziani, Maria Cristina

Molecular dynamics simulations and energy-minimization techniques have been applied for the firsttime to determine the whole set of elastic properties (Young’s modulus, shear modulus, bulk modulus,and Poisson’s ratio) of alkali silicate glasses with different ion modifiers (Li, Na, and K) in the range0-30 mol % alkaline oxide. Excellent agreement has been found between the simulation results and theexperimental data. The peculiar behavior of the Li-containing glasses with respect to the Na and K onesis extensively discussed in terms of the glass structural features. It is found that the elastic propertyvariation as a function of alkali addition can be explained by three concurrent factors: (1) depolymerizationof the silica network; (2) increasing the cohesion of the glass by the establishment of alkali-NBO bonds;and (3) decreasing the free volume with consequent increasing of the glass packing density.

2006 - A new self-consistent empirical interatomic potential model for oxides, silicates, and silica-based glasses [Articolo su rivista]
Pedone, Alfonso; Malavasi, Gianluca; Menziani, Maria Cristina; An, Cormack; Segre, Ulderico

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.

2006 - Cell configuration for focal adhesions in cells seeded onto Zinc-doped silicate-bioglasses [Capitolo/Saggio]
Lusvardi, Gigliola; Malavasi, Gianluca; Pedone, Alfonso; Menabue, Ledi; Menziani, Maria Cristina; V., Bolis; M., Borsetti; F., Boccafoschi; M., Cannas

2006 - Physico-chemical characterization and in vivo evaluation of zinc-glasses biocompatibility [Capitolo/Saggio]
Lusvardi, Gigliola; Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; Pedone, Alfonso; Zaffe, Davide

Study of soda-lime-phosphosilicate glasses based on Bioglass® and modified by zinc. "In vitro"(SBF) bioactivity was investigated through apatite forming ability and through a preliminary "in vivo" study. Zinc improves chemical durability but does not inhibit the apatite formation; a mixed-metal (Ca-Zn) phosphate-based crystalline layer is identified on the surface of HP5Z5. The improvement of the observed chemical durability can also be rationalized by Molecular Dynamics simulations

2006 - Towards a quantitative rationalization of multicomponent glass properties by means of molecular dynamics simulations [Articolo su rivista]
Malavasi, Gianluca; Pedone, Alfonso; Menziani, Maria Cristina

This review summarizes the achievements obtained by making use of molecular dynamics (MD) simulations in the elucidation of the structure of multicomponent glasses exerting bioactive properties. Emphasis on critical aspects of MD simulations for oxide glasses treatment is given. The potentiality of the quantitative structure-property relationships (QSPR) analysis as a tool for interpretative and predictive purposes is highlighted.

2006 - Void size distribution in MD-modelled silica glass structures [Articolo su rivista]
Malavasi, Gianluca; Menziani, Maria Cristina; Pedone, Alfonso; Segre, Ulderico

The void distribution of different models of the silica glass have been analyzed in terms of the Voronoi-Delaunay description of the void space into a disordered system. The silica glass has been modelled by making use of different pair-pair and three body potentials, previously proposed. The glass structural parameters (bond lengths and bond angles) are compared with known experimental data. A computer algorithm has been implemented to apply the Voronoi-Delaunay approach to a system of non-uniform spheres, and it is fully described. The algorithm furnishes the size distribution of interstices into the bulk structure. From this result, the solubility of noble gasses into the glass is computed, and the values obtained are successfully compared to known experimental data. The correlation between void size distribution and ring size distribution in silica glass is discussed. Both the glass structure and void distribution give better agreement to the experimental data when the pair pair interaction is modelled with the potential developed by Beest et al. [B.W.H. Beest, G.J. Kramer, R.A. Santen, Phys. Rev. Lett. 64 (1990) 1955].

2005 - A Computational Tool for the Prediction of Crystalline Phases Obtained from Controlled Crystallization of Glasses [Articolo su rivista]
Lusvardi, Gigliola; Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; Pedone, Alfonso; Segre, Ulderico

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

2004 - Vetri bioattivi contenenti zinco: comportamento in viotro ed in vivo [Relazione in Atti di Convegno]
Lusvardi, Gigliola; Zaffe, Davide; Bertoldi, Carlo; Malavasi, Gianluca; Menabue, Ledi; Menziani, Maria Cristina; Pedone, Alfonso

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