111 research outputs found
Improved empirical force field for multicomponent oxide glasses and crystals
No full textIn 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
Computational insight on the interaction of common blood proteins with gold nanoparticles
No full textProtein interactions with engineered gold nanoparticles (AuNPs) and the consequent formation of the protein corona are very relevant and poorly understood biological phenomena. The nanoparticle coverage affects protein binding modalities, and the adsorbed protein sites influence interactions with other macromolecules and cells. Here, we studied four common blood proteins, i.e., hemoglobin, serum albumin, α1-antiproteinase, and complement C3, interacting with AuNPs covered by hydrophobic 11-mercapto-1-undecanesulfonate (MUS). We use Molecular Dynamics and the Martini coarse−grained model to gain quantitative insight into the kinetics of the interaction, the physico-chemical characteristics of the binding site, and the nanoparticle adsorption capacity. Results show that proteins bind to MUS−capped AuNPs through strong hydrophobic interactions and that they adapt to the AuNP surfaces to maximize the contact surface, but no dramatic change in the secondary structure of the proteins is observed. We suggest a new method to calculate the maximum adsorption capacity of capped AuNPs based on the effective surface covered by each protein, which better represents the realistic behavior of these systems
What can we learn from atomistic simulations of bioactive glasses?
No full textIn 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
Multiscale Molecular Dynamics Simulation of Multiple Protein Adsorption on Gold Nanoparticles
No full textA 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
Novel Pet‐Degrading Enzymes: Structure‐Function from a Computational Perspective
No full textThe bacterium strain Ideonella sakaiensis 201-F6 is able to hydrolyze low-crystallinity PET films at 30 °C due to two enzymes named PETase and MHETase. Since its discovery, many efforts have been dedicated to elucidating the structure and features of those two enzymes, and various authors have highlighted the necessity to optimize both the substrate binding site and the global structure in order to enhance the stability and catalytic activity of these PET biocatalysts so as to make them more suitable for industrial applications. In this review, the strategies adopted by different research groups to investigate the structure and functionality of both PETase and MHETase in depth are described, emphasizing the advantages provided by the use of computational methods to complement and drive experiments. Subsequently, the modifications implemented with protein engineering are discussed. The versatility of the enzymes secreted by I. sakaiensis enables the prediction that they will find several applications in the disposal of PET debris, encouraging a prioritization of efforts in this prolific research field
Disclosing the interaction of gold nanoparticles with aβ(1–40) monomers through replica exchange molecular dynamics simulations
No full textAmyloid-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
Insights into the effect of curcumin and (–)-epigallocatechin-3-gallate on the aggregation of aβ(1–40) monomers by means of molecular dynamics
No full textIn 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
Accurate First-Principle Prediction of 29Si and 17O NMR Parameters in SiO2 Polymorphs: The Cases of Zeolites Sigma-2 and Ferrierite
No full textAbstract: 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
DFT and TD-DFT assessment of the structural and optoelectronic properties of an organic-Ag14 nanocluster
No full textAn 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
Evidence of Multiple Crystallization Pathways in Lithium Disilicate: A Metadynamics Investigation
No full textMetadynamics 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
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