The Color and Stability of Maya Blue: TDDFT Calculations

Car-Parrinello structural optimizations of realistic models of the Maya Blue (MB) hybrid material are combined with TDDFT calculations of the electronic excitation spectra to identify the nature of the fundamental guest-host interactions leading to the unusual stability of this pigment. The comparison with the features of the experimental visible spectrum reveals that the main mode of interaction between the host solid (the palygorskite clay) and the guest molecule (the organic indigo dye) involves the coordination of the carbonyl group of the dye by Al3+ ions exposed at the edge of the palygorskite tunnels. Analogous Mg2+-dye interactions which do not strongly affect the MB visible spectrum can also be present. Thermal treatment used in the preparation of the pigment appears therefore essential to release some of the structural water molecules tightly bound to the Al3+ ions in the internal clay surface, thus leaving them available to coordinate the organic molecule. Moderate heating also favors the oxidation of indigo to dehydroindigo (DHI): the spectral features of the latter complex with Al3+ are in remarkable agreement with the experimental spectrum, thus confirming the substantial role of DHI in the properties of Maya Blue

The antioxidant properties of Ce-containing bioactive glass nanoparticles explained by Molecular Dynamics simulations

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 biodegradatio

Analysis of a Lennard-Jones fcc structure melting to the corresponding frozen liquid: differences between the bulk and the surface

We computed a Lennard Jones frozen liquid with a free surface using classical molecular dynamics. The structure factor curves on the free surface of this sample was calculated for different depths knowing that we have periodic boundary conditions on the other parts of the sample. The resulting structure factor curves show an horizontal shift of their first peak depending on how deep in the sample the curves are computed. We analyze our resulting curves in the light of spatial correlation functions during melting and at when the liquid is frozen. The conclusion is that near the free surface the sample is less dense than in the bulk and that the frozen liquid surface has a spatial correlation which does not differ very much from that of the bulk. This result is intrinsic to the melting of the Lennard Jones liquid and does not depend on any other parameter.Comment: 18 pages 9 figure

Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses

Several research lines are currently ongoing to address the multitude of facets of the pandemic COVID-19. In line with the One-Health concept, extending the target of the studies to the animals which humans are continuously interacting with may favor a better understanding of the SARS-CoV-2 biology and pathogenetic mechanisms; thus, helping to adopt the most suitable containment measures. The last two decades have already faced severe manifestations of the coronavirus infection in both humans and animals, thus, circulating epitopes from previous outbreaks might confer partial protection from SARS-CoV-2 infections. In the present study, we provide an in-silico survey of the major nucleocapsid protein epitopes and compare them with the homologues of taxonomically-related coronaviruses with tropism for animal species that are closely inter-related with the human beings population all over the world. Protein sequence alignment provides evidence of high sequence homology for some of the investigated proteins. Moreover, structural epitope mapping by homology modelling revealed a potential immunogenic value also for specific sequences scoring a lower identity with SARS-CoV-2 nucleocapsid proteins. These evidence provide a molecular structural rationale for a potential role in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic-oriented strategies

Gut–brain axis and neurodegeneration : State-of-the-art of meta-omics sciences for microbiota characterization

Recent advances in the field of meta-omics sciences and related bioinformatics tools have allowed a comprehensive investigation of human-associated microbiota and its contribution to achieving and maintaining the homeostatic balance. Bioactive compounds from the microbial community harboring the human gut are involved in a finely tuned network of interconnections with the host, orchestrating a wide variety of physiological processes. These includes the bidirectional crosstalk between the central nervous system, the enteric nervous system, and the gastrointestinal tract (i.e., gut\u2013brain axis). The increasing accumulation of evidence suggest a pivotal role of the composition and activity of the gut microbiota in neurodegeneration. In the present review we aim to provide an overview of the state-of-the-art of meta-omics sciences including metagenomics for the study of microbial genomes and taxa strains, metatranscriptomics for gene expression, metaproteomics and metabolomics to identify and/or quantify microbial proteins and metabolites, respectively. The potential and limitations of each discipline were highlighted, as well as the advantages of an integrated approach (multi-omics) to predict microbial functions and molecular mechanisms related to human diseases. Particular emphasis is given to the latest results obtained with these approaches in an attempt to elucidate the link between the gut microbiota and the most common neurodegenerative diseases, such as multiple sclerosis (MS), Alzheimer\u2019s disease (AD), Parkinson\u2019s disease (PD), and amyotrophic lateral sclerosis (ALS)

Computational Modeling of Silicate Glasses: A Quantitative Structure-Property Relationship Perspective

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

Atomic structure of Mg-based metallic glasses from molecular dynamics and neutron diffraction

We use a combination of classical molecular dynamics simulation and neutron diffraction to identify the atomic structure of five different Mg–Zn–Ca bulk metallic glasses, covering a range of compositions with substantially different behaviour when implanted in vitro. There is very good agreement between the structures obtained from computer simulation and those found experimentally. Bond lengths and the total correlation function do not change significantly with composition. The zinc and calcium bonding shows differences between composition: the distribution of Zn–Ca bond lengths becomes narrower with increasing Zn content, and the preference for Zn and Ca to avoid bonding to themselves or each other becomes less strong, and, for Zn–Ca, transforms into a positive preference to bond to each other. This transition occurs at about the same Zn content at which the behaviour on implantation changes, hinting at a possible structural connection. A very broad distribution of Voronoi polyhedra are also found, and this distribution broadens with increasing Zn content. The efficient cluster packing model, which is often used to describe the structure of bulk metallic glasses, was found not to describe these systems well