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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Thermomechanical, electronic and thermodynamic properties of ZnS cubic polymorphs: an ab initio investigation on the zinc-blende-rock-salt phase transition.

In the present work, an extensive and detailed theoretical investigation is reported on the thermomechanical, electronic and thermodynamic properties of zinc-blende (sphalerite, zb-ZnS) and rock-salt zinc sulfide (rs-ZnS) over a wide range of pressure, by means of ab initio Density Functional Theory, Gaussian type orbitals and the well known B3LYP functional. For the first time, vibrational frequencies, phonon dispersion relations, elasto-piezo-dielectric tensor, thermodynamic and thermomechanical properties of rs-ZnS were calculated with a consistent approach that allows a direct comparison with the low-pressure polymorph. Special attention was paid to the evaluation of the thermodynamic pressure-temperature stability of the mineral phases between 0-25 GPa and 0-800 K. The static (T = 0 K) bulk moduli of sphalerite and rock-salt ZnS were 72.63 (3) GPa and 84.39 (5) GPa, respectively. The phase transition in static conditions calculated from the equation of state was about 15.5 GPa, whereas the elastic constants data resulted in Ptrans = 14.6 GPa. At room temperature (300 K), the zb-rs transition occurs at 14.70 GPa and a negative Clapeyron slope (dP)/(dT) = 0.0023 was observed up to 800 K. The electronic band structure showed a direct band gap for zb-ZnS (Eg = 4.830 eV at equilibrium geometry), which became an indirect one by increasing pressure above 11 GPa. The results were found to be in good agreement with the available experimental and theoretical data, further extending the knowledge of important properties of zinc sulfide, in particular the thermomechanical ones of the rock-salt polymorph here extensively explored for the first time.

Crystal-chemical and structural data related to the equation of state and second-order elastic constants of portlandite Ca(OH)2 and brucite Mg(OH)2.

This data article reports crystal-chemical and structural data (unit cell parameters and internal coordinates) of two hydroxyl minerals, namely brucite [magnesium hydroxide, Mg(OH)2] and portlandite [calcium hydroxide, Ca(OH)2], which were calculated and employed to derive the mechanical behavior of these solid phases under hydrostatic compression (Ulian and Valdrè, 2018). The dataset has been obtained by ab initio quantum mechanical means, by employing Density Functional Theory methods, in particular the B3LYP hybrid functional, all-electron Gaussian-type orbitals basis sets and a correction to take into account the effects of dispersive forces. Equilibrium and expanded/compressed models of both minerals were realized and geometrically optimized within two space group settings, P 3 ¯ m1 and P 3 ¯ .

Anisotropy and directional elastic behavior data obtained from the second-order elastic constants of portlandite Ca(OH)2 and brucite Mg(OH)2.

This article reports data on the anisotropy and directional elastic behavior, namely Young׳s modulus E, linear compressibility ß, shear modulus µ, Poisson׳s ratio ν and wave velocities Vs1, Vs2 and Vp, of brucite (magnesium hydroxide, Mg(OH)2) and portlandite (calcium hydroxide, Ca(OH)2), calculated from their second order elastic constants at different hydrostatic compressions (Ulian and Valdrè, in press). The dataset has been obtained by ab initio quantum mechanical means, by employing density functional theory methods, in particular the B3LYP hybrid functional, all-electron Gaussian-type orbitals basis sets and a correction to take into account the effects of dispersive forces.

Dataset on the piezo-spectroscopic behaviour of hydroxylapatite: Effect of mechanical stress on the Raman and Infrared vibrational bands from ab initio quantum mechanical simulations.

This article reports data on the vibrational (Raman and Infrared) behavior of hydroxylapatite [OHAp, Ca10(PO4)6(OH)2, space group P63] under mechanical stress, which were discussed in details in the work of Ulian and Valdrè (2017) [1]. The dataset has been obtained by ab initio quantum mechanical means, by employing Density Functional Theory methods, in particular the B3LYP hybrid functional, all-electron Gaussian-type orbitals basis sets and a correction to take into account the effects of dispersive forces.

Effect of mechanical stress on the Raman and infrared bands of hydroxylapatite: A quantum mechanical first principle investigation.

The calcium apatite minerals are among the most studied in the biomaterial field because of their similarity with the mineral phase of bone tissues, which is mainly the hexagonal polymorph of hydroxylapatite. Given the growing interest both in the microscopic processes governing the behaviour of these natural biomaterials and in recent experimental methods to investigate the Raman response of hydroxylapatite upon mechanical loading, we report in the present work a detailed quantum mechanical analysis by DFT/B3LYP-D* approach on the Raman and infrared responses of hydroxylapatite upon deformation of its unit cell. From the vibrational results, the piezo-spectroscopic components Δν = Πijσij were calculated. For the first time to the authors' knowledge quantum mechanics (QM) was applied to resolve the piezo-spectroscopic response of hydroxylapatite. The QM results on the uniaxial stress responses of this phase on the piezo-spectroscopic components Π11 and Π33 of the symmetric P-O stretching mode were 2.54 ± 0.09cm-1/GPa and 2.56 ± 0.06cm-1/GPa, respectively (Raman simulation) and 2.48 ± 0.15cm-1/GPa and Π33 = 2.74 ± 0.08cm-1/GPa, respectively, of the asymmetric P-O stretching (infrared spectroscopy simulation). These results are in excellent agreement with previous experimental data reported in literature. The quantum mechanical analysis of the other vibrational bands (not present in literature) shed more light on this new and very important application of both Raman and IR spectroscopies and extend the knowledge of the behaviour of hydroxylapatite, suggesting and addressing further experimental research and analytic strategy.

Raman spectroscopic investigation on the molecular structure of apatite and collagen in osteoporotic cortical bone.

This study employed highly spectrally resolved Raman spectroscopy to examine the molecular composition of cortical bone tissue obtained from murine females in their healthy and ovariectomy- (OVX-) induced osteoporotic states. The aim of the study was to identify structural differences at the molecular scale both in apatite mineral and collagen fibrils between the two groups of samples. Raman spectroscopy was used to determine the chemical composition of cortical bone in regions including characteristic bands of both bone mineral and bone matrix. The results demonstrated that the mineral apatite of bone did not undergo significant amorphization in its diseased state, with the Raman microprobe also failing in recognizing a direct role of carbonate content in the embrittlement of OVX-diseased bone. On the other hand, complex off-stoichiometry variations could be detected in the columnar Ca-structure of the bony hydroxyapatite according to morphological variations of the Raman band belonging to the symmetric phosphate stretching (A1) band at ~959cm-1. A fundamental role was also recognized for collagen quality on the process of bone embrittlement. The so-called matrix maturity ratio, as systematically measured on Raman spectra in the Amide I region, increased with statistical significance in OVX-treated samples as compared to control samples. An 8% increase could be associated to a 115% increase in elastic stress intensification in the mineral phase of OVX-diseased tissue as compared to the control one, thus proving a degradation in the (elastic) energy-dissipative capacity of a diseased bone matrix.

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.