Benchmarking dispersion-corrected DFT methods for the evaluation of materials with anisotropic properties: structural, electronic, dielectric, optical and vibrational analysis of calcite (CaCO3, space group R3[combining macron]c).

Calcite (CaCO3, space group R3[combining macron]c) is a solid phase whose well-known highly anisotropic physical properties can be exploited to compare and calibrate various theoretical simulation methods. In this work, to benchmark different ab initio Density Functional Theory approaches that include for the first time corrections for dispersive forces, a systematic analysis of structural, electronic, dielectric, optical and vibrational properties of calcite is performed. The simulations considered the generalized-gradient approximation functional PBE and the hybrid B3LYP and PBE0, whereas the DFT-D2 and DFT-D3 schemes were adopted to account for the long-range interactions. This study suggests an overall better agreement between the theoretical results obtained with the DFT functionals corrected for the dispersive forces, with a better performance of hybrid functionals over PBE.

Growth factor sustained delivery from poly-lactic-co-glycolic acid microcarriers and its mass transfer modeling by finite element in a dynamic and static three-dimensional environment bioengineered with stem cells.

Poly-lactic-co-glycolic acid (PLGA) microcarriers (0.8 ± 0.2 µm) have been fabricated with a load of 20 µg/gPLGA by an emulsion-based-proprietary technology to sustained deliver human bone morphogenetic protein 2 (hBMP2), a growth factor largely used for osteogenic induction. hBMP2 release profile, measured in vitro, showed a moderate "burst" release of 20% of the load in first 3 days, followed by a sustained release of 3% of the load along the following 21 days. PLGA microbeads loaded with fluorescent marker (8 mg/gPLGA ) and hydroxyapatite (30 mg/gPLGA ) were also fabricated and successfully dispersed within three-dimensional (3D) alginate scaffold (Ca-alginate 2% wt/wt) in a range between 50 and 200 mg/cm3 ; the presence of microcarriers within the scaffold induced a variation of its stiffness between 0.03 and 0.06 MPa; whereas the scaffold surface area was monitored always in the range of 190-200 m2 /g. Uniform microcarriers dispersion was obtained up to 200 mg/cm3 ; higher loading values in the 3D scaffold produced large aggregates. The release data and the surface area were, then, used to simulate by finite element modeling the hBMP2 mass transfer within the 3D hydrogel bioengineered with stem cells, in dynamic and static cultivations. The simulation was developed with COMSOL Multiphysics® giving a good representation of hBMP2 mass balances along microbeads (bulk eroded) and on cell surface (cell binding). hBMP2 degradation rate was also taken into account in the simulations. hBMP2 concentration of 20 ng/cm3 was set as a target because it has been described as the minimum effective value for stem cells stimulation versus the osteogenic phenotype. The sensitivity analysis suggested the best microbeads/cells ratio in the 3D microenvironment, along 21 days of cultivations in both static and dynamic cultivation (perfusion) conditions. The simulated formulation was so assembled experimentally using human mesenchymal stem cells and an improved scaffold stiffness up to 0.09 MPa (n = 3; p ≤ 0.01) was monitored after 21 days of cultivation; moreover a uniform extracellular matrix deposition within the 3D system was detected by Von Kossa staining, especially in dynamic conditions. The results indicated that the described tool can be useful for the design of 3D bioengineered microarchitecture by quantitative understanding.

Single Molecule Investigation of Glycine-Chlorite Interaction by Cross-Correlated Scanning Probe Microscopy and Quantum Mechanics Simulations.

In this work, we studied the interaction of glycine with the (001) surface of chlorite mineral at a single molecule level by cross-correlating scanning probe microscopy (SPM) and ab initio quantum mechanics (QM) investigations. Chlorite mineral is particularly interesting and peculiar for the interaction with organic molecules because it presents an alternated stacking of brucite-like (hydrophobic) and talc-like (hydrophilic) layers of different polarities. Brucite-like is positive, whereas talc-like is negative. The experimental atomic force microscopy (AFM) observations show that glycine is stably and selectively adsorbed on the brucite-like layer, organized in monolayers with different patterns. The sizes of single molecules of glycine measured by AFM are in agreement with those calculated by QM. Glycine molecules were found to align both at the edges and on the terraces of the brucitic surface. QM simulations confirmed the AFM observations that glycine molecule is adsorbed with high adsorption energy preferentially with its plane parallel to the (001) brucite-like surface. QM also provided the geometry conformation of the molecule and the bonding scheme between glycine and brucite surface. This kind of data can be very helpful both to biotechnological applications of this substrate and to depict some important processes that might have been occurred in prebiotic environments.

Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: talc [Mg3Si4O10(OH)2] as model system.

The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg3Si4O10(OH)2], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO∕B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.

The effect of long-range interactions on the infrared and Raman spectra of aragonite (CaCO3, Pmcn) up to 25 GPa.

Long-range interactions are relevant in the physical description of materials, even for those where other stronger bonds give the leading contributions. In this work, we demonstrate this assertion by simulating the infrared and Raman spectra of aragonite, an important calcium carbonate polymorph (space group Pmcn) in geological, biological and materials science fields. To this aim, we used Density Functional Theory methods and two corrections to include long-range interactions (DFT-D2 and DFT-D3). The results were correlated to IR spectroscopy and confocal Raman spectrometry data, finding a very good agreement between theory and experiments. Furthermore, the evolution of the IR/Raman modes up to 25 GPa was described in terms of mode-Grüneisen's parameters, which are useful for geological and materials science applications of aragonite. Our findings clearly show that weak interactions are of utmost importance when modelling minerals and materials, even when they are not the predominant forces.

Dataset on the crystallographic, vibrational, and electronic properties of 1M-phlogopite K(Mg,Fe)3(Si3Al)O10(OH)2 obtained from Density Functional Theory investigations.

The present work reports a dataset on the crystal structure, optical properties (complex dielectric function and refractive index), infrared, reflectance and Raman spectra, and electronic properties (band structure and density of states) of the 1M-polytype of phlogopite [1]. This phyllosilicate presents chemical formula K(Mg,Fe)3(Si3Al)O10(OH)2, with Mg/Fe ratio ≥ 2. The dataset was obtained from Density Functional Theory (DFT) simulations at B3LYP-D* level, i.e., with the hybrid functional B3LYP corrected with an ad hoc DFT-D2 scheme, and all-electron Gaussian-type orbitals basis sets for all atoms in the unit cell. Furthermore, experimental confocal Raman micro-spectrometry data (spectra) collected on a single crystal phlogopite specimen are reported. The quality of the dataset was assessed by comparing the results with available X-ray diffraction and IR/Raman spectroscopy data reported in literature. The reported complete dataset is a reference for future studies in fundamental georesource exploration and exploitation, applied mineralogy, geology, and material science.

Structural, elastic, electronic, optical and vibrational properties of single-layered, bilayered and bulk molybdenite MoS2-2H.

In recent years, transition metal dichalcogenides have received great attention since they can be prepared as two-dimensional semiconductors, presenting heterodesmic structures incorporating strong in-plane covalent bonds and weak out-of-plane interactions, with an easy cleavage/exfoliation in single or multiple layers. In this context, molybdenite, the mineralogical name of molybdenum disulfide, MoS2, has drawn much attention because of its very promising physical properties for optoelectronic applications, in particular a band gap that can be tailored with the material's thickness, optical absorption in the visible region and strong light-matter interactions due to the planar exciton confinement effect. Despite this wide interest and the numerous experimental and theoretical articles in the literature, these report on just one or two specific features of bulk and layered MoS2 and sometimes provide conflicting results. For these reasons, presented here is a thorough theoretical analysis of the different aspects of bulk, monolayer and bilayer MoS2 within the density functional theory (DFT) framework and with the DFT-D3 correction to account for long-range interactions. The crystal chemistry, stiffness, and electronic, dielectric/optical and phonon properties of single-layered, bilayered and bulk molybdenite have been investigated, to obtain a consistent and detailed set of data and to assess the variations and cross correlation from the bulk to single- and double-layer units. The simulations show the indirect-direct transition of the band gap (K-K' in the first Brillouin zone) from the bulk to the single-layer structure, which however reverts to an indirect transition when a bilayer is considered. In general, the optical properties are in good agreement with previous experimental measurements using spectroscopic ellipsometry and reflectivity, and with preliminary theoretical simulations.

Facile band gap tuning in graphene-brucite heterojunctions.

The zero band gap of pure graphene is a well-known issue that limits some specific applications of graphene in opto- and microelectronics. This led to several research studies in the so-called van der Waals composites (known as heterostructures, or heterojunctions), where two monolayers of different materials are stacked and held together by dispersive interactions. In this paper, we introduced and considered a single layer of brucite Mg(OH)2, an overlooked 2D material that can be easily produced by exfoliation (like graphene from graphite), for the creation of the heterojunction. First principles simulations showed that brucite/graphene composites can modify the electronic properties (position of the Dirac cone with respect to the Fermi level and band gap) according to the crystallographic stacking and the presence of point defects. The present work represents then an important step forward in understanding and finding new ways to design two-dimensional materials with tailored electronic and physical properties.

Study of the variation of the optical properties of calcite with applied stress, useful for specific rock and material mechanics.

Calcite (CaCO3, trigonal crystal system, space group [Formula: see text]) is a ubiquitous carbonate phase commonly found on the Earth's crust that finds many useful applications in both scientific (mineralogy, petrology, geology) and technological fields (optics, sensors, materials technology) because of its peculiar anisotropic physical properties. Among them, photoelasticity, i.e., the variation of the optical properties of the mineral (including birefringence) with the applied stress, could find usefulness in determining the stress state of a rock sample containing calcite by employing simple optical measurements. However, the photoelastic tensor is not easily available from experiments, and affected by high uncertainties. Here we present a theoretical Density Functional Theory approach to obtain both elastic and photoelastic properties of calcite, considering realistic experimental conditions (298 K, 1 atm). The results were compared with those available in literature, further extending the knowledge of the photoelasticity of calcite, and clarifying an experimental discrepancy in the sign of the p41 photoelastic tensor component measured in past investigations. The methods here described and applied to a well-known crystalline material can be used to obtain the photoelastic properties of other minerals and/or materials at desired pressure and temperature conditions.

QUANTAS: a Python software for the analysis of thermodynamics and elastic behavior of solids from ab initio quantum mechanical simulations and experimental data.

Mineralogy, petrology and materials science are fundamental disciplines not only for the basic knowledge and classification of solid phases but also for their technological applications, which are becoming increasingly demanding and challenging. Characterization and design of materials are of utmost importance and usually need knowledge of the thermodynamics and mechanical stability of solids. Alongside well known experimental approaches, in recent years the advances in both quantum mechanical methods and computational power have placed theoretical investigations as a complementary useful and powerful tool in this kind of study. In order to aid both theoreticians and experimentalists, an open-source Python-based software, QUANTAS, has been developed. QUANTAS provides a fast, flexible, easy-to-use and extensible platform for calculating the thermodynamics and elastic behavior of crystalline solid phases, starting from both experimental and ab initio data.

Photodegradation of Bamboo: A Study on Changes in Mechanical Performances.

One of the main concerns in using natural materials in construction, such as bamboo, regards their durability. Ultra violet (UV)irradiation is claimed as a damaging agent; therefore, it is important to study its effect. Several studies have shown that bamboo components such as lignin are subjected to photochemical degradation, but it is not well understood how this affects the mechanical properties of bamboo. The aim of this paper is to explore the correlation between photodegradation and bamboo mechanical performance. Bamboo samples were exposed to accelerated UV ageing for different times (from 6 to 360 h) and then subjected to a four-point bending test. Since one of the ways to stabilize bamboo is to thermally treat it, the tests were conducted on natural untreated bamboo and treated bamboo with a traditional flame treatment. Modifications of the chemical features of the material were analyzed with Fourier Trasform Infra Red (FTIR) spectroscopy, while modifications of the morphological features were analyzed byEnvironmental Scanning Electron Microscopy ESEM and optical microscopy observations. The results show that the bending behavior of bamboo is not compromised by UV exposure up to 360 h. In fact, although a progressive degradation of lignin is reported and cracks in the fiber walls are highlighted from micrographs, no effects were found on the fiber length.

Shear response of nanoconfined water on muscovite mica: role of cations.

By monitoring the thermal noise of a vertically oriented micromechanical force sensor, we detect the viscoelastic response to shear for water in a subnanometer confinement. Measurements in pure water as well as under acidic and high-ionic-strength conditions relate this response to the effect of surface-adsorbed cations, which, because of their hydration, act as pinning centers restricting the mobility of the confined water molecules.

Hydroxylapatite and Related Minerals in Bone and Dental Tissues: Structural, Spectroscopic and Mechanical Properties from a Computational Perspective.

Hard tissues (e.g., bone, enamel, dentin) in vertebrates perform various and different functions, from sustaining the body to haematopoiesis. Such complex and hierarchal tissue is actually a material composite whose static and dynamic properties are controlled by the subtle physical and chemical interplay between its components, collagen (main organic part) and hydroxylapatite-like mineral. The knowledge needed to fully understand the properties of bony and dental tissues and to develop specific applicative biomaterials (e.g., fillers, prosthetics, scaffolds, implants, etc.) resides mostly at the atomic scale. Among the different methods to obtains such detailed information, atomistic computer simulations (in silico) have proven to be both corroborative and predictive tools in this subject. The authors have intensively worked on quantum mechanical simulations of bioapatite and the present work reports a detailed review addressed to the crystal-chemical, physical, spectroscopic, mechanical, and surface properties of the mineral phase of bone and dental tissues. The reviewed studies were conducted at different length and time scales, trying to understand the features of hydroxylapatite and biological apatite models alone and/or in interaction with simplified collagen-like models. The reported review shows the capability of the computational approach in dealing with complex biological physicochemical systems, providing accurate results that increase the overall knowledge of hard tissue science.

Thermally Treated Waste Silt as Filler in Geopolymer Cement.

This study aims to investigate the feasibility of including silt, a by-product of limestone aggregate production, as a filler in geopolymer cement. Two separate phases were planned: The first phase aimed to determine the optimum calcination conditions of the waste silt obtained from Società Azionaria Prodotti Asfaltico Bituminosi Affini (S.A.P.A.B.A. s.r.l.). A Design of Experiment (DOE) was produced, and raw silt was calcined accordingly. Geopolymer cement mixtures were made with sodium or potassium alkali solutions and were tested for compressive strength and leaching. Higher calcination temperatures showed better compressive strength, regardless of liquid type. By considering the compressive strength, leaching, and X-ray diffraction (XRD) analysis, the optimum calcination temperature and time was selected as 750 °C for 2 h. The second phase focused on determining the optimum amount of silt (%) that could be used in a geopolymer cement mixture. The results suggested that the addition of about 55% of silt (total solid weight) as filler can improve the compressive strength of geopolymers made with Na or K liquid activators. Based on the leaching test, the cumulative concentrations of the released trace elements from the geopolymer specimens into the leachant were lower than the thresholds for European standards.

Climate variation during the Holocene influenced the skeletal properties of Chamelea gallina shells in the North Adriatic Sea (Italy).

Understanding how marine taxa will respond to near-future climate changes is one of the main challenges for management of coastal ecosystem services. Ecological studies that investigate relationships between the environment and shell properties of commercially important marine species are commonly restricted to latitudinal gradients or small-scale laboratory experiments. This paper aimed to explore the variations in shell features and growth of the edible bivalve Chamelea gallina from the Holocene sedimentary succession to present-day thanatocoenosis of the Po Plain-Adriatic Sea system (Italy). Comparing the Holocene sub-fossil record to modern thanatocoenoses allowed obtaining an insight of shell variations dynamics on a millennial temporal scale. Five shoreface-related assemblages rich in C. gallina were considered: two from the Middle Holocene, when regional sea surface temperatures were higher than today, representing a possible analogue for the near-future global warming, one from the Late Holocene and two from the present-day. We investigated shell biometry and skeletal properties in relation to the valve length of C. gallina. Juveniles were found to be more porous than adults in all horizons. This suggested that C. gallina promoted an accelerated shell accretion with a higher porosity and lower density at the expense of mechanically fragile shells. A positive correlation between sea surface temperature and both micro-density and bulk density were found, with modern specimens being less dense, likely due to lower aragonite saturation state at lower temperature, which could ultimately increase the energetic costs of shell formation. Since no variation was observed in shell CaCO3 polymorphism (100% aragonite) or in compositional parameters among the analyzed horizons, the observed dynamics in skeletal parameters are likely not driven by a diagenetic recrystallization of the shell mineral phase. This study contributes to understand the response of C. gallina to climate-driven environmental shifts and offers insights for assessing anthropogenic impacts on this economic relevant species.

Thermodynamic and thermoelastic data of georesources raw minerals: Zinc sulphide and apatite.

This article reports a dataset on the thermodynamic and elastic properties of two important raw minerals exploited in georesources and ore mining. The presented data refers to two zinc sulphide polymorphs, namely zinc-blende (low-pressure polymorph, space group F 4 - 3 m ) and rock-salt (high-pressure polymorph, space group F m 3 - m ) [1], and of type-A carbonated apatite, [CAp, Ca10(PO4)6CO3, space group P1] [2]. The data here reported were calculated from ab initio quantum mechanical simulations at the DFT/B3LYP level, all-electron Gaussian-type orbitals basis sets and from the analysis of the phonon properties of the zinc sulphide polymorphs and of type-A CAp by means of the quasi-harmonic approximation. In addition, a correction to take into account the effects of dispersive forces was considered to obtain the dataset of type-A carbonated apatite. This dataset, which was validated against experimental thermodynamic data reported in literature, has been employed to construct the phase diagram between the two zinc sulphide polymorphs and discuss their stability over the temperature and pressure range 0-800 K and 0-25 GPa. The thermodynamic and thermoelastic data of CAp were obtained between 0 and 600 K and 0-3 GPa, below the temperature of thermal decomposition of the mineral. The reported data can be of use in several application fields, for instance fundamental georesource exploration and exploitation, and also in applied mineralogy, geology, material science, and as a reference to assess the quality of other theoretical approaches. Furthermore, the data of type-A carbonated apatite could be useful for designing and processing new biomaterials with tailored properties.

Simulated infrared and Raman spectroscopy, complex dielectric function and refractive index dataset of monoclinic C2/m stoichiometric clinochlore Mg6Si4O10(OH)8 as obtained from Density Functional Theory.

This article reports a simulated dataset of the vibrational (infrared and Raman) and optical properties (complex dielectric function and refractive index) of clinochlore, an important mineral belonging to the phyllosilicate family [1]. The data here reported were calculated from ab initio Density Functional Theory (DFT) simulations at B3LYP level, including a correction for the dispersive forces (B3LYP-D* approach) and all-electron Gaussian-type orbitals basis sets. This dataset was calculated between 0 cm-1 and 4000 cm-1 and comprises infrared, reflectance and Raman spectra, frequency-dependent complex dielectric function and complex refractive index of clinochlore. The data was validated against available experimental spectroscopic results reported in literature and can be of help in several application fields, for instance fundamental georesource exploration and exploitation, in applied mineralogy, geology, material science, and as a reference to assess the quality of other theoretical approaches.

Stannous Fluoride Preventive Effect on Enamel Erosion: An In Vitro Study.

The aim of this in vitro study was to evaluate the effects of a single dose application of two daily toothpastes on enamel exposed to acid attack. The research was conducted on human molars enamel fragments (n = 72). The two different toothpastes active ingredients were sodium fluoride (NaF) and stannous fluoride (SnF2). They were compared in protecting the surface of the enamel exposed to three acids: citric acid, lactic acid and hydrochloric acid. A spectrophotometer was used to measure the calcium ions and phosphate released in the solutions by the enamel specimens. Afterward, ionic concentrations were analyzed through the t-Student test, in order to estimate the significance level (p < 0.05) of the solubility differences obtained between the treatment and control groups. Finally, sample surfaces were analyzed with scanning electron microscopy and X-ray energy dispersive spectroscopy (SEM/EDX). The two analyzed toothpastes did not reveal any statistically significant variation in the release of calcium and phosphate (p > 0.05). Nevertheless, acid-resistant deposits were detected in samples treated with stannous fluoride and exposed to lactic acid, though the presence of tin ion deposits on samples treated with stannous fluoride was not shown. A single dose of a fluoride-based toothpaste before different acids attack, in simulated oral cavity conditions, did not show a significant preventive effect.

Electrochemical data on redox properties of human Cofilin-2 and its Mutant S3D.

The reported data are related to a research paper entitled "Phosphorylated cofilin-2 is more prone to oxidative modifications on Cys39 and favors amyloid fibril formation" [1]. Info about the formation and redox properties of the disulfide bridge of a protein is quite difficult to obtain and only in a few cases was it possible to observe a cyclic voltammetry (CV) signal [2,3]. Human cofilin-2 contains two cysteines (Cys39 and Cys80) which can be oxidized in suitable conditions and form a disulfide bridge [1]. For this purpose, CV measurements were carried out on human cofilin-2 WT and its mutant S3D immobilized on a gold electrode coated by an anionic self-assembled monolayer (SAM), after a pre-oxidation time which was fundamental for observing a CV signal relating to the oxidation/reduction process of the disulfide bridge of the proteins. The data include CV curves obtained with and without electrochemical pre-oxidation and after oxidation with H2O2. In addition, the plot of the cathodic peak current vs. electrochemical pre-oxidation time and the pH dependence of the formal potential (E°') are reported. The data obtained by CV measurements were used to determine the time required to form the disulfide bridge for the immobilized proteins and, consequently, to observe the CV signal, to calculate the E°' values and analyse the pH dependence of E°'. The electrochemical data were provided which will be useful for further electrochemical investigations regarding proteins bearing disulfide bridge(s) or cysteines prone to oxidation.

Phosphorylated cofilin-2 is more prone to oxidative modifications on Cys39 and favors amyloid fibril formation.

Cofilins are small protein of the actin depolymerizing family. Actin polymerization/depolymerization is central to a number of critical cellular physiological tasks making cofilin a key protein for several physiological functions of the cell. Cofilin activity is mainly regulated by phosphorylation on serine residue 3 making this post-translational modification key to the regulation of myofilament integrity. In fact, in this form, the protein segregates in myocardial aggregates in human idiopathic dilated cardiomyopathy. Since myofilament network is an early target of oxidative stress we investigated the molecular changes induced by oxidation on cofilin isoforms and their interplay with the protein phosphorylation state to get insight on whether/how those changes may predispose to early protein aggregation. Using different and complementary approaches we characterized the aggregation properties of cofilin-2 and its phosphomimetic variant (S3D) in response to oxidative stress in silico, in vitro and on isolated cardiomyocytes. We found that the phosphorylated (inactive) form of cofilin-2 is mechanistically linked to the formation of an extended network of fibrillar structures induced by oxidative stress via the formation of a disulfide bond between Cys39 and Cys80. Such phosphorylation-dependent effect is likely controlled by changes in the hydrogen bonding network involving Cys39. We found that the sulfide ion inhibits the formation of such structures. This might represent the mechanism for the protective effect of the therapeutic agent Na2S on ischemic injury.