Structural evolution of amino acid crystals under stress from a non-empirical density functional

Observation of the most H2-dense filled ice under high pressure

Hydrogen hydrates are among the basic constituents of our solar system's outer planets, some of their moons, as well Neptune-like exo-planets. The details of their high-pressure phases and their thermodynamic conditions of formation and stability are fundamental information for establishing the presence of hydrogen hydrates in the interior of those celestial bodies, for example, against the presence of the pure components (water ice and molecular hydrogen). Here, we report a synthesis path and experimental observation, by X-ray diffraction and Raman spectroscopy measurements, of the most H[Formula: see text]-dense phase of hydrogen hydrate so far reported, namely the compound 3 (or C[Formula: see text]). The detailed characterisation of this hydrogen-filled ice, based on the crystal structure of cubic ice I (ice I[Formula: see text]), is performed by comparing the experimental observations with first-principles calculations based on density functional theory and the stochastic self-consistent harmonic approximation. We observe that the extreme (up to 90 GPa and likely beyond) pressure stability of this hydrate phase is due to the close-packed geometry of the hydrogen molecules caged in the ice I[Formula: see text] skeleton.

Review of Applications of Density Functional Theory (DFT) Quantum Mechanical Calculations to Study the High-Pressure Polymorphs of Organic Crystalline Materials

Since its inception, chemistry has been predominated by the use of temperature to generate or change materials, but applications of pressure of more than a few tens of atmospheres for such purposes have been rarely observed. However, pressure is a very effective thermodynamic variable that is increasingly used to generate new materials or alter the properties of existing ones. As computational approaches designed to simulate the solid state are normally tuned using structural data at ambient pressure, applying them to high-pressure issues is a highly challenging test of their validity from a computational standpoint. However, the use of quantum chemical calculations, typically at the level of density functional theory (DFT), has repeatedly been shown to be a great tool that can be used to both predict properties that can be later confirmed by experimenters and to explain, at the molecular level, the observations of high-pressure experiments. This article's main goal is to compile, analyze, and synthesize the findings of works addressing the use of DFT in the context of molecular crystals subjected to high-pressure conditions in order to give a general overview of the possibilities offered by these state-of-the-art calculations.

Terahertz Spectroscopy and Ab-Initio Vibrational Analysis of Two Crystalline Forms of 5,5-Diethylbarbituric Acid

Terahertz (THz) absorption spectra of the two crystalline forms of 5,5-diethylbarbituric acid (barbital) were measured with THz time-domain spectroscopy (THz-TDS). The spectra exhibited the dissimilarity between the two forms. Identification of the polymorphs and quantitative analysis of the two forms are possible by THz-TDS. Further, we performed ab-initio calculations of the vibrational modes considering the crystal structures of the two forms, and the results were in good agreement with the experimental data. We discuss the difference between the THz absorption spectra of the two forms.

Carbon dioxide adsorption and conversion to methane and ethane on hydrogen boride sheets

Hydrogen boride (HB) sheets are metal-free two-dimensional materials comprising boron and hydrogen in a 1:1 stoichiometric ratio. In spite of the several advancements, the fundamental interactions between HB sheets and discrete molecules remain unclear. Here, we report the adsorption of CO2 and its conversion to CH4 and C2H6 using hydrogen-deficient HB sheets. Although fresh HB sheets did not adsorb CO2, hydrogen-deficient HB sheets reproducibly physisorbed CO2 at 297 K. The adsorption followed the Langmuir model with a saturation coverage of 2.4 × 10-4 mol g-1 and a heat of adsorption of approximately 20 kJ mol-1, which was supported by density functional theory calculations. When heated in a CO2 atmosphere, hydrogen-deficient HB began reacting with CO2 at 423 K. The detection of CH4 and C2H6 as CO2 reaction products in a moist atmosphere indicated that hydrogen-deficient HB promotes C-C coupling and CO2 conversion reactions. Our findings highlight the application potential of HB sheets as catalysts for CO2 conversion.

Study elastic properties of the leucine and isoleuicine from first principles calculations

I studied the elastic properties of crystalline L- and DL-forms of leucine and isoleucine within the framework of density functional theory with van der Waals interactions. The energy gaps of the considered crystals are 7.48-7.60 eV. Chiral molecules have the same chemical composition. Therefore, the study of crystalline amino acids provides a better understanding of how the structure of molecules affects mechanical properties of molecular crystals. Complete set of elastic constants for L-leucine, L-isoleucine, DL-leucine and DL-isoleucine were calculated. Linear compressibility of crystals has high anisotropy. The crystalline L- and DL-forms of leucine and isoleucine have different mechanical properties. Linear compressibility has a negative value for DL-isoleucine. My calculations predict that L-leucine and L-isoleucine are ductile compounds, while DL-leucine and DL-isoleucine are brittle compounds.

Prediction of a Supersolid Phase in High-Pressure Deuterium

Supersolid is a mysterious and puzzling state of matter whose possible existence has stirred a vigorous debate among physicists for over 60 years. Its elusive nature stems from the coexistence of two seemingly contradicting properties, long-range order and superfluidity. We report computational evidence of a supersolid phase of deuterium under high pressure (p>800  GPa) and low temperature (T<1.0  K). In our simulations, that are based on bosonic path integral molecular dynamics, we observe a highly concerted exchange of atoms while the system preserves its crystalline order. The exchange processes are favored by the soft core interactions between deuterium atoms that form a densely packed metallic solid. At the zero temperature limit, Bose-Einstein condensation is observed as the permutation probability of N deuterium atoms approaches 1/N with a finite superfluid fraction. Our study provides concrete evidence for the existence of a supersolid phase in high-pressure deuterium and could provide insights on the future investigation of supersolid phases in real materials.

Study of the Elastic Properties of the Energetic Molecular Crystals Using Density Functionals with van der Waals Corrections

We studied the elastic properties of crystalline energetic materials within the framework of density functional theory with van der Waals interactions (DFT-D3(BJ) and rev-vdW-DF2). The full sets of elastic constants were computed. The computed parameters are in good agreement with the experimental data. Among the crystals studied in this work, FOX7 had the lowest compressibility value of 0.0034 GPa^-1 and had the highest anisotropy. Crystalline pentaerythritol tetranitrate had almost isotropic mechanical properties.

Physicochemical properties of L- and DL-valine: first-principles calculations

At present, physicochemical properties of amino acid molecular crystals are of the utmost interest. The compounds where molecules have different chirality are the focus of particular interest. This paper, presents a study on the structural and electronic properties of crystalline L- and DL-valine within the framework of density functional theory including van der Waals interactions. The results of this study showed that electronic properties of the two forms of valine are similar at zero pressure. Pressure leads to different responses in these crystals which is manifested as various deformations of molecules. The pressure effect on the infrared spectra and distribution of electron density of L- and DL-valine has been studied.

Theoretical investigations into the variability of the 15N solid-state NMR parameters within an antimicrobial peptide ampullosporin A

The solid-state NMR measurements play an indispensable role in studies of interactions between biological membranes and peptaibols, which are amphipathic oligopeptides with a high abundance of alpha-aminobutyric acid (Aib). The solid-state NMR investigations are important in establishing the molecular models of the pore forming and antimicrobial properties of peptaibols, but rely on certain simplifications. Some of the underlying assumptions concern the parameters describing the 15N NMR chemical shielding tensor (CST) of the amide nitrogens in Aib and in conventional amino acids. Here the density functional theory (DFT) based calculations were applied to the known crystal structure of one of peptaibols, Ampullosporin A, in order to explicitly describe the variation of the 15N NMR parameters within its backbone. Based on the DFT computational data it was possible to verify the validity of the assumptions previously made about the differences between Aib and other amino acids in the isotropic part of the CST. Also the trends in the magnitudes and orientations of the anisotropic components of the CST, as revealed by the DFT calculations of the full periodic structure of Ampullosporin A, were thoroughly analyzed, and may be employed in future studies of peptaibols.

Advanced capabilities for materials modelling with Quantum ESPRESSO

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

ζ-Glycine: insight into the mechanism of a polymorphic phase transition

Glycine is the simplest and most polymorphic amino acid, with five phases having been structurally characterized at atmospheric or high pressure. A sixth form, the elusive ζ phase, was discovered over a decade ago as a short-lived intermediate which formed as the high-pressure ∊ phase transformed to the γ form on decompression. However, its structure has remained unsolved. We now report the structure of the ζ phase, which was trapped at 100 K enabling neutron powder diffraction data to be obtained. The structure was solved using the results of a crystal structure prediction procedure based on fully ab initio energy calculations combined with a genetic algorithm for searching phase space. We show that the fate of ζ-glycine depends on its thermal history: although at room temperature it transforms back to the γ phase, warming the sample from 100 K to room temperature yielded β-glycine, the least stable of the known ambient-pressure polymorphs.

Hydrostatic Pressure Effects on Structural and Electronic Properties of ETN and PETN from First-Principles Calculations

We studied the structural and electronic properties of pentaerythritol tetranitrate (PETN) and erythritol tetranitrate (ETN) crystals within the framework of density functional theory with van der Waals interactions. The computed lattice parameters have good agreement with experimental data. Electronic and structural properties of the crystals under 0-20 GPa hydrostatic pressure were studied. The parameters of equations of state calculated from the theoretical data show good agreement with experiment within the studied pressure intervals. We have also calculated the detonation velocity and pressure.

van der Waals forces in density functional theory: a review of the vdW-DF method

A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.

van der Waals density functionals built upon the electron-gas tradition: facing the challenge of competing interactions

The theoretical description of sparse matter attracts much interest, in particular for those ground-state properties that can be described by density functional theory. One proposed approach, the van der Waals density functional (vdW-DF) method, rests on strong physical foundations and offers simple yet accurate and robust functionals. A very recent functional within this method called vdW-DF-cx [K. Berland and P. Hyldgaard, Phys. Rev. B 89, 035412 (2014)] stands out in its attempt to use an exchange energy derived from the same plasmon-based theory from which the nonlocal correlation energy was derived. Encouraged by its good performance for solids, layered materials, and aromatic molecules, we apply it to several systems that are characterized by competing interactions. These include the ferroelectric response in PbTiO3, the adsorption of small molecules within metal-organic frameworks, the graphite/diamond phase transition, and the adsorption of an aromatic-molecule on the Ag(111) surface. Our results indicate that vdW-DF-cx is overall well suited to tackle these challenging systems. In addition to being a competitive density functional for sparse matter, the vdW-DF-cx construction presents a more robust general-purpose functional that could be applied to a range of materials problems with a variety of competing interactions.

Interaction of silicene with β-Si3N4(0001)/Si(111) substrate; energetics and electronic properties

The free-standing, quasi-2D layer of Si is known as silicene, in analogy with graphene. Much effort is devoted in the study of silicene, since, similarly to graphene, it shows a very high electron mobility. The interaction of silicene with a hybrid substrate, β-Si3N4(0001)/Si(111), exposing the β-Si3N4(0001) surface, has been studied by means of Density Functional calculations, with van der Waals interactions included. Once deepened the most important structural and electronic features of the hybrid substrate, we demonstrated that an electron transfer occurs from the substrate to the silicene layer. In turn, such an electron transfer can be modulated by the doping of the substrate. The β-Si3N4/silicene interaction appears to be strong enough to ensure adequate adsorption stability. It is also shown that electronic states of substrate and adsorbate still remain decoupled, paving the way for the exploitation of the peculiar electron mobility properties of the silicene layer. A detailed analysis in both direct and reciprocal space is reported.

Mechanical properties of hydrogenated bilayer graphene

Using first principle methods, we study the mechanical properties of monolayer and bilayer graphene with 50% and 100% coverage of hydrogen. We employ the vdW-DF, vdW-DF-C09x, and vdW-DF2-C09x van der Waals functionals for the exchange correlation interactions that give significantly improved interlayer spacings and energies. We also use the PBE form for the generalized gradient corrected exchange correlation functional for comparison. We present a consistent theoretical framework for the in-plane layer modulus and the out-of-plane interlayer modulus and we calculate, for the first time, these properties for these systems. This gives a measure of the change of the strength properties when monolayer and bilayer graphene are hydrogenated. Moreover, comparing the relative performance of these functionals in describing hydrogenated bilayered graphenes, we also benchmark these functionals in how they calculate the properties of graphite.