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The 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.

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.

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.

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 an ab initio training 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 CeO2 bulk and CeO2 (111) surface, as well as the absorption and reaction energies of H2 and 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.

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 ...

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.

Amyloid-&beta, 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-&beta, monomers onto citrates-capped gold nanoparticles. Importantly, upon binding, amyloid monomers show a reduced propensity in forming &beta, sheets secondary structures that are characteristics of mature amyloid fibrils.

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.

In this paper, the self-consistent PMMCS force fields (FFs) [Pedone et al., J. Phys. Chem. B 110, 11780 (2006)] 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 ($T=\mathrm{Si}$ 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 ${Q}^{n}$ 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 ($^{29}\mathrm{Si}$, $^{17}\mathrm{O}$, $^{31}\mathrm{P}$, $^{27}\mathrm{Al}$), 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.

In this study, we have applied Molecular Dynamics (MD) simulations to obtain reliable structural models of the bulk and surfaces of the 45S5 Bioglass® and three recently designed glasses in the system Na2O-K2O-CaO-MgO-SrO-P2O5-SiO2 and interpreting their different behaviour and properties. In fact, the substitution of sodium oxide with alkaline earth oxides (Ca, Mg and Sr) in the traditional 45S5 Bioglass® has been shown to be beneficial for improving the sinterability and mechanical properties of the glass maintaining optimal biocompatibility.The reduced tendency of crystallization has been associated to the increased chemical disorder around network former cations, the reduced mobility of alkaline earth cations with respect to sodium and the reduced coordination number of magnesium, which hamper the large structural re-organization necessary to the precipitation of the Na2Ca2Si3O9 crystal phase. In all the compositions, fragmented chains dominate the silica network and the network connectivity is similar. However, the increased interconnection of such chains by Mg, Ca and Sr cations makes the substituted glasses stiffer and harder than the 45S5 Bioglass®. The different reactivity of the glasses is due to the different amount of alkali cations and undercoordinated species at the glass surfaces.The approach presented provides deeper insights on the structure-properties relationships in bioactive glasses, and can be used to find precious guidelines for compositional tuning and designing innovative bioactive glass compositions with desired behaviour or property for a specific application.

Translocator protein 18 kDa [TSPO or peripheral-type benzodiazepine receptor (PBR)] was identified in the search of binding sites for benzodiazepine anxiolytic drugs in peripheral regions. In these areas, binding sites for TSPO ligands were recognized in steroid-producing tissues. TSPO plays an important role in many cellular functions, and its coding sequence is highly conserved across species. TSPO is located predominantly on the membrane of mitochondria and is overexpressed in several solid cancers. TSPO basal expression in the CNS is low, but it becomes high in neurodegenerative conditions. Thus, TSPO constitutes not only as an outstanding drug target but also as a valuable marker for the diagnosis of a number of diseases. The aim of the present article is to show the lesson we have learned from our activity in TSPO medicinal chemistry and in approaching the targeted delivery to mitochondria by means of TSPO ligands.

Protein 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.

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.

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 w...

In this study, we compared the effects of two well-known natural compounds on the early step of the fibrillation process of amyloid-&beta, (1&ndash, 40), responsible for the formation of plaques in the brains of patients affected by Alzheimer&rsquo, s disease (AD). The use of extensive replica exchange simulations up to the &micro, s scale allowed us to characterize the inhibition activity of (&ndash, )-epigallocatechin-3-gallate (EGCG) and curcumin (CUR) on unfolded amyloid fibrils. A reduced number of &beta, 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-&beta, (A&beta, 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 A&beta, 40) fibrils and that this molecule can be a good candidate to develop new and more effective congeners to treat AD.

In this study, we have applied Molecular Dynamics (MD) simulations to obtain reliable structural models of the bulk and surfaces of the 45S5 Bioglass® and three recently designed glasses in the system Na2O-K2O-CaO-MgO-SrO-P2O5-SiO2 and to interpret their different behaviour and properties. In fact, the substitution of sodium oxide with alkaline earth oxides (Ca, Mg and Sr) in the traditional 45S5 Bioglass® has been shown to be beneficial for improving the sinterability and mechanical properties of the glass maintaining optimal biocompatibility. The reduced tendency of crystallization has been associated to the increased chemical disorder around network former cations, the reduced mobility of alkaline earth cations with respect to sodium and the reduced coordination number of magnesium, which hamper the large structural re-organization necessary to the precipitation of the Na2Ca2Si3O9 crystal phase. In all the compositions, fragmented chains dominate the silica network and the network connectivity is similar. However, the increased interconnection of such chains by Mg, Ca and Sr cations makes the substituted glasses stiffer and harder than the 45S5 Bioglass®. The different reactivity of the glasses is due to the different amount of alkali cations and undercoordinated species at the glass surfaces. The approach presented provides deeper insights on the structure-properties relationships in bioactive glasses, and can be used to find precious guidelines for compositional tuning and designing innovative bioactive glass compositions with desired behaviour or property for a specific application.

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 atoms 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 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 towards an atomic scale understanding of the material functionalities. This article is protected by copyright. All rights reserved.

Significance The ability of proteins to self-assemble into different types of fibrils with distinct morphologies has been linked to the pathological and clinical heterogeneity of amyloid diseases such as Alzheimer’s disease and Parkinson’s disease. Here, we describe nanoparticles (NPs) that efficiently label amyloid fibrils produced in vitro or isolated from postmortem tissues, under hydrating conditions and in such a way as to unmask their polymorphism and morphological features. Using these NPs, we show that pathological aggregates exhibit exceptional morphological homogeneity compared with amyloid fibrils produced in vitro, consistent with the emerging view that the physiologic milieu is a key determinant of amyloid fibril strains. These advances pave the way for elucidating the structural basis of amyloid strains and toxicity., Increasing evidence suggests that amyloid polymorphism gives rise to different strains of amyloids with distinct toxicities and pathology-spreading properties. Validating this hypothesis is challenging due to a lack of tools and methods that allow for the direct characterization of amyloid polymorphism in hydrated and complex biological samples. Here, we report on the development of 11-mercapto-1-undecanesulfonate-coated gold nanoparticles (NPs) that efficiently label the edges of synthetic, recombinant, and native amyloid fibrils derived from different amyloidogenic proteins. We demonstrate that these NPs represent powerful tools for assessing amyloid morphological polymorphism, using cryogenic transmission electron microscopy (cryo-EM). The NPs allowed for the visualization of morphological features that are not directly observed using standard imaging techniques, including transmission electron microscopy with use of the negative stain or cryo-EM imaging. The use of these NPs to label native paired helical filaments (PHFs) from the postmortem brain of a patient with Alzheimer’s disease, as well as amyloid fibrils extracted from the heart tissue of a patient suffering from systemic amyloid light-chain amyloidosis, revealed a high degree of homogeneity across the fibrils derived from human tissue in comparison with fibrils aggregated in vitro. These findings are consistent with, and strongly support, the emerging view that the physiologic milieu is a key determinant of amyloid fibril strains. Together, these advances should not only facilitate the profiling and characterization of amyloids for structural studies by cryo-EM, but also pave the way to elucidate the structural basis of amyloid strains and toxicity, and possibly the correlation between the pathological and clinical heterogeneity of amyloid diseases.

We have demonstrated that designed ankyrin repeat protein (DARPin) _9-29, which specifically targets human epidermal growth factor receptor 2 (HER2), binds tightly to gold mini nanorods (GNRs). Molecular dynamic simulations showed that a single layer of DARPin_9-29 molecules is formed on the surface of the nanorod and that conjugation with the nanorod does not involve the protein's domain responsible for specific binding to HER2. The nanorod-DARPin (DARPin-GNR) conjugate is specifically bound (in nanomolar concentrations) to human breast adenocarcinoma SK-BR-3 cells overexpressing HER2. Illumination by near-infrared light (850 nm) led to almost complete eradication of the conjugate-treated SK-BR-3 cells; the viability of epithelial human breast cancer cells expressing normal amounts of the receptor was much less affected by the illumination. The results reported here pave the way toward application of DARPin-GNR conjugates in phototherapy of cancer.

A Surface-Enhanced Raman Scattering (SERS) spectrum of 4-cyanopyridine (4CNPy) was recorded on silver plasmonic nanoparticles and analyzed by using Density Functional Theory (DFT) calculations. Two simple molecular models of the metal&ndash, 4CNPy surface complex with a single silver cation or with a neutral dimer (Ag+&ndash, 4CNPy, Ag2&ndash, 4CNPy), linked through the two possible interacting sites of 4CNPy (aromatic nitrogen, N, and nitrile group, CN), were considered. The calculated vibrational wavenumbers and intensities of the adsorbate and the isolated species are compared with the experimental Raman and SERS results. The analysis of the DFT predictions and the experimental data indicates that 4CNPy adsorbs preferentially on neutral/charged active sites of the silver nanoparticles through the nitrogen atom of the aromatic ring with a perpendicular orientation.

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.

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 Agand 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 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.

A water-soluble Morita–Baylis–Hillman adduct (MBHA) derivative (3) was previously shown to self-assemble in a water environment into functional nanoreactors capable of performing multiple attacks and functionalization of N-acetylhexahistidine. In order to challenge this intriguing reactivity in a model protein more complex than N-acetylhexahistidine, the single-chain Fv antibody CRB0137 was characterized from the point of view of its structure and made to react with 3 in kinetics experiments. The results of these studies suggested that MBHA derivative 3 reacted typically with the amino acid residues of the CRB0137 hexahistidine tag leading to the formation of multi-PEGylated species. Overall, they demonstrate the viability of a new methodology for the site-specific PEGylation of engineered proteins bearing poly-histidine tags.

Water-soluble MBHA derivatives were found to self-assemble in a water environment to generate aggregates showing core–shell architectures. The aggregates appeared to be capable of working as nanoreactors performing a multi-functionalization of poly-histidine fragments, which after an initial interaction with the solvated oligo(ethylene glycol) shell reach the reactive core.

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%SiO224.3%Na2O26.9%CaO2.6P2O5, mol%) and Kokubo (50.0%SiO225.0%Na2O25.0%CaO) 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. Keywords: Bioactive glasses, Cerium, Catalase mimetic activity, Bioactivity, SEM-EDS, XPS, Molecular dynamics simulations

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 β-form of salicylidene aniline (SA). The first singlet excited states (S1) 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 −20/−32 nm (cis-keto form) and −8/−14 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 Wiley Periodicals, Inc.

CeO

One of the principal hallmarks of Alzheimer&rsquo, s disease (AD) is related to the aggregation of amyloid-&beta, 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-&beta, (1&ndash, 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.

Several neurodegenerative diseases, like Alzheimer’s (AD), are characterized by amyloid fibrillar deposition of misfolded proteins, and this feature can be exploited for both diagnosis and therapy design. In this paper, structural modifications of curcumin scaffold were examined in order to improve its bioavailability and stability in physiological conditions, as well as its ability to interfere with β-amyloid fibrils and aggregates. The acid-base behaviour of curcumin derivatives, their pharmacokinetic stability in physiological conditions, and in vitro ability to interfere with Aβ fibrils at different incubation time were investigated. The mechanisms governing these phenomena have been studied at atomic level by means of molecular docking and dynamic simulations. Finally, biological activity of selected curcuminoids has been investigated in vitro to evaluate their safety and efficiency in oxidative stress protection on hippocampal HT-22 mouse cells. Two aromatic rings, π-conjugated structure and H-donor/acceptor substituents on the aromatic rings showed to be the sine qua non structural features to provide interaction and disaggregation activity even at very low incubation time (2h). Computational simulations proved that upon binding the ligands modify the conformational dynamics and/or interact with the amyloidogenic region of the protofibril facilitating disaggregation. Significantly, in vitro results on hippocampal cells pointed out protection against glutamate toxicity and safety when administered at low concentrations (1 μM). On the overall, in view of its higher stability in physiological conditions with respect to curcumin, of his rapid binding to fibrillar aggregates and strong depolymerizing activity, phtalimmide derivative K2F21 appeared a good candidate for both AD diagnostic and therapeutic purposes.

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 ...

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 bindin...

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 “b...