Periodic Ab Initio Calculations Research Articles

Critical assessment of the x-ray restrained wave function approach: Advantages, drawbacks, and perspectives for density functional theory and periodic abinitio calculations.

The x-ray restrained wave function (XRW) method is a quantum crystallographic technique to extract wave functions compatible with experimental x-ray diffraction data. The approach looks for wave functions that minimize the energies of the investigated systems and also reproduce sets of x-ray structure factors. Given the strict relationship between x-ray structure factors and electron distributions, the strategy practically allows determining wave functions that correspond to given (usually experimental) electron densities. In this work, the capabilities of the XRW approach were further tested. The aim was to evaluate whether the XRW technique could serve as a tool for suggesting new exchange-correlation functionals for density functional theory or refining existing ones. Additionally, the ability of the method to address the influences of the crystalline environment was also assessed. The outcomes of XRW computations were thus compared to those of traditional gas-phase, embedding quantum mechanics/molecular mechanics, and fully periodic calculations. The results revealed that, irrespective of the initial conditions, the XRW computations practically yield a consensus electron density, in contrast to the currently employed density functional approximations (DFAs), which tend to give a too large range of electron distributions. This is encouraging in view of exploiting the XRW technique to develop improved functionals. Conversely, the calculations also emphasized that the XRW method is limited in its ability to effectively address the influences of the crystalline environment. This underscores the need for a periodic XRW technique, which would allow further untangling the shortcomings of DFAs from those inherent to the XRW approach.

Non-orthogonal Configuration Interaction Study on the Effect of Thermal Distortions on the Singlet Fission Process in Photoexcited Pure and B,N-Doped Pentacene Crystals.

The present computational work analyzes singlet fission (SF) as a pathway for multiplication of photogenerated excitons in crystalline polyacenes. Our study explores the well-known crystalline pentacene (C22H14) and the prospective and potentially interesting doped B,N-pentacene (BC20NH14). At the molecular level, the singlet fission process involves a pair of neighboring molecules and is based on the coupling between an excited singlet state (S1S0) and two singlet-coupled triplets (1T1T1), which, typically, is influenced by an intermolecular charge transfer state. Taking data from periodic density functional theory and ab initio wave function calculations, we applied the non-orthogonal configuration interaction method to determine electronic coupling parameters. The comparison of the results for both equilibrium structures reveal smaller SF coupling for pentacene than for B,N-pentacene by a factor of ∼5. Introduction of the dynamic behavior to the crystals (vibrations, thermal motion) provides a more realistic picture of the effect of the disorder at the molecular level on the SF efficiency. The coupling values associated to out-of-equilibrium structures show that most of the S1S0/1T1T1 couplings remain virtually constant or slightly increase for pentacene when molecular disorder is introduced. Homologous calculations on B,N-pentacene show a generalized decrease in the coupling values, notably if large phonon displacements are considered. A few of the structures analyzed feature much larger SF coupling if some distortion results in (nearly) degenerate charge transfer and excited singlet and triplet states. For these particular situations, an acceleration of the SF process could occur although in competition with electron-hole separation as an alternative pathway.

Progressive Structural Complexity in Ferroelectric 1,2,4-Triazolium Hexabromoantimonate(III): Interplay of "Order-Disorder" and "Displacive" Contributions to the Structural Phase Transitions.

Halobismuthates(III) and haloantimonates(III) with the R3MX6 chemical composition create a new and broadly unexplored class of ferroelectric compounds. In this paper, we report the haloantimonate(III) ferroelectric comprising an aromatic (1,2,4-triazolium) cation, i.e., (C2N3H4)3[SbBr6] (TBA). Temperature-resolved structural and spectroscopic studies indicate that TBA undergoes two solid-solid phase transitions between tetragonal [P42/m (I)] and monoclinic [P21/n (II) and P21 (III)] phases. TBA experiences a paraelectric-ferroelectric phase transition at 271/268 K (II-III) driven by "order-disorder" and "displacive" molecular mechanisms. The ferroelectric properties of phase III have been confirmed by hysteresis loop measurement, and additionally, the acentric order has been further supported by second-harmonic generation measurements. Insight into the molecular origins of the ferroelectric polarization was provided by periodic ab initio calculations using the Berry phase approach at the density functional theory (DFT-D3) method level employed for calculations of spontaneous polarization.

Dynamics and disorder: on the stability of pyrazinamide polymorphs.

This article focuses on the structure and relative stability of four pyrazinamide polymorphs. New single crystal X-ray diffraction data collected for all forms at 10 K and 122 K are presented. By combining periodic ab initio DFT calculations with normal-mode refinement against X-ray diffraction data, both enthalpic and entropic contributions to the free energy of all polymorphs are calculated. On the basis of the estimated free energies, the stability order of the polymorphs as a function of temperature and the corresponding solid state phase transition temperatures are anticipated. It can be concluded that the α and γ forms have higher vibrational entropy than that of the β and δ forms and therefore they are significantly more stabilized at higher temperatures. Due to the entropy which arises from the disorder in γ form, it overcomes form α and is the most stable form at temperatures above ∼500 K. Our findings are in qualitative agreement with the experimental calorimetry results.

0D Bismuth(III)-Based Hybrid Ferroelectric: Tris(acetamidinium) Hexabromobismuthate(III)

Ferroelectric properties of haloantimonates(III) and halobismuthates(III) have been detected for as much as 40 structures belonging to 7 different types of anionic networks, with RMX4, R2MX5, R3M2X9, and R5M2X11 stoichiometries being the most frequently reported to host these properties. We report on the first ferroelectric of the halobismuthate(III) family with a R3MX6 stoichiometry, that is, tris(acetamidinium)hexabromobismuthate(III), (CH3C(NH2)2)3[BiBr6] (ABB), characterized by a one-component organic network. While the stoichiometry and crystal packing of ABB might seem uncomplicated, the temperature-resolved structural and spectroscopic studies paint a different picture in which rich polymorphism in the solid state occurs between tetragonal (paraelastic) and triclinic (ferroelastic) crystal phases: I (P42/n) → II (P1̅) at 272/277 K (cooling/heating), II (P1̅) → III (P1̅) at 207 K, and III (P1̅) → IV (P1) at 98/127 K. The ferroelectric properties of phase IV have been confirmed by the pyroelectric current and hysteresis loop measurements; additionally, the acentric symmetry has been further supported by second harmonic generation measurements. Crystallographic analysis of phase III reveals the antiparallel alignment of acetamidinium dipoles, pointing to the antiferrroelectric nature of this phase. In turn, the character of the ferroelectric transition (III → IV) should be considered as “displacive” for both cationic and anionic substructures.) In this report, we also explore the two-photon absorption property of ABB at 800 nm, a property that is unexplored for any halobismuthate(III) thus far. We also present periodic ab initio calculations for ABB crystals. The Berry-phase approach at the Hartree–Fock and density functional theory (DFT-D3) method levels is employed for spontaneous polarization calculations. The origin of ferroelectric polarization is studied using DFT-D3 and RHF electronic structure calculations, emphasizing the relationship between Ps and the relative orientation of organic/inorganic components.

Solvates of New Arylpiperazine Salicylamide Derivative-a Multi-Technique Approach to the Description of 5 HTR Ligand Structure and Interactions.

A new ligand for 5-HT1A and 5-HT7 receptors, an arylpiperazine salicylamide derivative with an inflexible spacer, is investigated to identify preferred fragments capable of creating essential intermolecular interactions in different solvates. To fully identify and characterize the obtained crystalline materials, various methods including powder and single-crystal X-ray diffraction, solid-state NMR, and thermal analysis were employed, supplemented by periodic ab initio calculations. The molecular conformation in different solvates, types, and hierarchy of intermolecular interactions as well as the crystal packing were investigated to provide data for future research focused on studying protein–ligand interactions. Based on various methods of crystal structure analysis, including the interaction energy calculation and programs using an artificial neural network, a salicylamide fragment was found to be crucial for intermolecular contacts, mostly of dispersion and electrostatic character. A supramolecular 2D kite-type layer of {4,4} topology was found to form in crystals. The closed voids between layers contain disordered solvents, very weakly interacting with the molecule and the layer. It has been postulated that the separation of the layers might be influenced by an increase in temperature or the size of the solvent; hence, only methanol and ethanol hemi-solvates could be obtained from a series of various alcohols.

X-ray charge density study of the 6-methyluracil derivative in the crystal: Revealing, consequences, and multipole refinement of minor static disorder

The accurate X-ray diffraction experiment was performed on the crystal of 1,6-dimethyl-3-propargyl-2,4-pyrimidinedione at 100 K. The static electron density (ED) was obtained via multipole refinement against these data. The presence of low-intense but nonrandom positive residual density peaks revealed that the structure was complicated by the minor conformational static disorder. Further analysis of the number and positions of critical points (CPs) (3, +3) of Laplacian of ED ∇2ρ(r) and the ratio of eigenvalues of its Hessian matrix unambiguously proved that the multipole-modeled ED of the main disorder component was contaminated by the second one. A method of visualizing the Laplacian minima as CP-ellipsoids with semiaxes inversely proportional to the eigenvalues of Hessian matrix of ∇2ρ(r) was applied to evaluate the correctness of modeled ED. Extra Laplacian CPs (3, +3) were attributed to the incorrect multipole populations, while the elongated shape of the corresponding discoid CP-ellipsoids was mainly considered to be the effect of troublesome kappa-parameters. A number of different multipole models were constructed in order to minimize the undesirable effects of disorder on the multipole ED. The two-component multipole model showed that the heterocyclic moiety of the minor component with an occupancy of 2% underwent the 180° rotation about the N3–C7 bond axis. Furthermore, the partial transfer of multipole parameters from the model refined against theoretical structure factors was utilized on the most problematic atoms, which massively contributed to disorder treatment. This approach allowed us to restore the ED of the main component in the crystal environment, which quality was gauged by the quantum-topological analysis as well as by its conformity to the data obtained from ab initio periodic calculations. Attempts to speculate on reasons for the limited disordering observed were made: theoretical calculations suggest that moderate hydrogen bonds support the disordering in the structure, while multiple weak noncovalent contacts, e.g., pi interactions, may provide the restrictions on the 50:50 disorder.

Inferring the one-electron reduced density matrix of molecular crystals from experimental data sets through semidefinite programming.

Constructing a quantum description of crystals from scattering experiments is of great significance to explain their macroscopic properties and to evaluate the pertinence of theoretical ab initio models. While reconstruction methods of the one-electron reduced density matrix have already been proposed, they are usually tied to strong assumptions that limit and may introduce bias in the model. The goal of this paper is to infer a one-electron reduced density matrix (1-RDM) with minimal assumptions. It has been found that the mathematical framework of semidefinite programming can achieve this goal. Additionally, it conveniently addresses the nontrivial constraints on the 1-RDM which were major hindrances for the existing models. The framework established in this work can be used as a reference to interpret experimental results. This method has been applied to the crystal of dry ice and provides very satisfactory results when compared with periodic ab initio calculations.

Strain-tunable orbital, spin-orbit, and optical properties of monolayer transition-metal dichalcogenides

When considering transition-metal dichalcogenides (TMDCs) in van der Waals (vdW) heterostructures for periodic ab-initio calculations, usually, lattice mismatch is present, and the TMDC needs to be strained. In this study we provide a systematic assessment of biaxial strain effects on the orbital, spin-orbit, and optical properties of the monolayer TMDCs using ab-initio calculations. We complement our analysis with a minimal tight-binding Hamiltonian that captures the low-energy bands of the TMDCs around K and K' valleys. We find characteristic trends of the orbital and spin-orbit parameters as a function of the biaxial strain. Specifically, the orbital gap decreases linearly, while the valence (conduction) band spin splitting increases (decreases) nonlinearly in magnitude when the lattice constant increases. Furthermore, employing the Bethe-Salpeter equation and the extracted parameters, we show the evolution of several exciton peaks, with biaxial strain, on different dielectric surroundings, which are particularly useful for interpreting experiments studying strain-tunable optical spectra of TMDCs.

Electronic properties and vibrational spectra of (NH4)2M″(SO4)2·6H2O (M = Ni, Cu) Tutton's salt: DFT and experimental study.

The complex crystals of the family of the Tutton's salt have been investigated through the numerous experimental and theoretical studies to understand their physical properties and their potential technological applications. In spite of the more than 60 years of research, there are very few studies about the electronic properties of Tutton's salt. In our present work, we have calculated the stability, electronic properties and the first theoretical study of band structure of the three different crystals of the Tutton's salt, ammonium nickel sulfate hexahydrate ((NH4)2Ni(SO4)2·6H2O), ammonium nickel-copper sulfate hexahydrate ((NH4)2Ni0.5Cu0.5(SO4)2·6H2O) and ammonium copper sulfate hexahydrate ((NH4)2Ni(SO4)2·6H2O) with the help of periodic ab-initio calculations based on density functional theory (DFT). In addition to this, the internal Raman and FTIR modes of the ionic fragments [Ni(H2O)6]2+, [Cu(H2O)6]2+ NH4+ and SO42- of the sample crystals were obtained by employing the ab initio and the orientation of the molecular vibrations of the ionic fragments have been presented in picturized form. Furthermore, the Raman and FTIR spectroscopy of the sample crystals were measured in the range 100-4000 cm-1 and 400-4000 cm-1 respectively, and the internal vibrational modes obtained from experimental measurement have been compared with those obtained from DFT calculations.

Controlling the Adsorption of Aromatic Compounds on Pt(111) with Oxygenate Substituents: From DFT to Simple Molecular Descriptors.

Aromatic chemistry on metallic surfaces is involved in many processes within the contexts of biomass valorization, pollutant degradation, or corrosion protection. Albeit theoretically and experimentally challenging, knowing the structure and the stability of aromatic compounds on such surfaces is essential to understand their properties. To gain insights on this topic, we performed periodic ab initio calculations on Pt(111) to determine a set of simple molecular descriptors that predict both the stability and the structure of aromatic adsorbates substituted with alkyl and alkoxy (or hydroxy) groups. While the van der Waals (vdW) interaction is controlled by the molecular weight and the deformation energy by both the nature and the relative position of the substituents to the surface, the chemical bonding can be correlated to the Hard and Soft Acids and Bases (HSAB) interaction energy. This work gives general insights on the interaction of aromatic compounds with the Pt(111) surface.

Source Function applied to experimental densities reveals subtle electron-delocalization effects and appraises their transferability properties in crystals.

The Source Function (SF), introduced in 1998 by Richard Bader and Carlo Gatti, is succinctly reviewed and a number of paradigmatic applications to in vacuo and crystal systems are illustrated to exemplify how the SF may be used to discuss chemical bonding in both conventional and highly challenging cases. The SF enables the electron density to be seen at a point determined by source contributions from the atoms or a group of atoms of a system, and it is therefore well linked to the chemist's awareness that any local property and chemical behaviour is to some degree influenced by all the remaining parts of a system. The key and captivating feature of the SF is that its evaluation requires only knowledge of the electron density (ED) of a system, thereby enabling a comparison of ab initio and X-ray diffraction derived electron density properties on a common and rigorous basis. The capability of the SF to detect electron-delocalization effects and to quantify their degree of transferability is systematically explored in this paper through the analysis and comparison of experimentally X-ray derived Source Function patterns in benzene, naphthalene and (±)-8'-benzhydrylideneamino-1,1'-binaphthyl-2-ol (BAB) molecular crystals. It is shown that the SF tool recovers the characteristic SF percentage patterns caused by π-electron conjugation in the first two paradigmatic aromatic molecules in almost perfect quantitative agreement with those obtained from ab initio periodic calculations. Moreover, the effect of chemical substitution on the degree of transferability of such patterns to the benzene- and naphthalene-like moieties of BAB is neatly shown and quantified by the observed systematic deviations, relative to benzene and naphthalene, of only those SF contributions from the substituted C atoms. Finally, the capability of the SF to reveal electron-delocalization effects is challenged by using a promolecule density, rather than the proper quantum mechanical density, to determine the changes in SF patterns along the cyclohexene, 1,3-cyclohexadiene and benzene molecule series. It is shown that, differently from the proper quantum density, the promolecular density is unable to reproduce the SF trends anticipated by the increase of electron delocalization along the series, therefore ruling out the geometrical effect as being the only cause for the observed SF patterns changes.

Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. I. Theory.

This study demonstrates and tests the refinement of a lattice-dynamical model derived from periodic ab initio calculations at the Γ point against elastic diffraction data (X-ray or neutron). Refinement of only a handful of parameters is sufficient to obtain a similar agreement with the data as the conventional crystallographic model using anisotropic displacement parameters. By refinement against X-ray data, H displacement parameters are obtained which compare favourably with those from neutron diffraction experiments. The approach opens the door for evaluating thermodynamic properties, and for refinement against multi-temperature data, against inelastic diffraction data, spectroscopic information and thermal diffuse scattering data.

Periodic DFT Study on the Adsorption and Catalytic Desulfurization of Thiophene over VC(001) and VN(001) via Hydrogenation and Direct Pathways

Periodic ab initio DFT calculations based on ultrasoft pseudopotentials and a plane-wave basis set were carried out to shed some light on the adsorption and reaction mechanisms of thiophene over vanadium carbide and vanadium nitride cubic face-centered (001) surfaces and its implications for hydrodesulfurization (HDS). Direct (DDS) and hydrogenating (HYD) routes were considered for further desulfurization reactions. Furthermore, to identify their role in the adsorption and desulfurization process, various initial configurations for the adsorption complexes were investigated. Our results suggest that ring hydrogenation does not necessarily lead to a preference for the HYD pathway of thiophene desulfurization. Moreover, surface and electronic effects due to adsorption were also evaluated. We have found that under ideal conditions, vanadium nitride and carbide surfaces present similar activity over desulfurization of thiophene, in qualitative agreement with experiments.

Adsorption of F2C[dbnd]CFCl on TiO2 nano-powder: Structures, energetics and vibrational properties from DRIFT spectroscopy and periodic quantum chemical calculations

Photodegradation over titanium dioxide (TiO2) is a very appealing technology for removing environmental pollutants from the air, the adsorption interaction being the first step of the whole reaction pathway. In the present work the adsorption of F2CCFCl (chlorotrifluoroethene, halon 1113), a compound used by industry and detected in the atmosphere, on a commercial TiO2 nano-powder is investigated experimentally by in situ DRIFT spectroscopy and theoretically through periodic ab initio calculations rooted in DFT. The spectra of the adsorbed molecule suggest that the anchoring to the surface mainly takes place through F atoms. Theoretically, five adsorption configurations for the molecule interacting with the anatase (101) surface are simulated at B3LYP level and for each of them, structures, binding energies and vibrational frequencies are derived. The interplay between theory and experiments shows the coexistence of different adsorption configurations, the foremost ones featuring the interaction of one F atom with a fivefold coordinated Ti4+ of the surface. These two adsorption models, which mostly differ for the orientation of the adsorbate with respect to the surface, feature a binding energy of −45.6 and −41.0kJmol−1 according to dispersion corrected DFT calculations. The favorable adsorption interaction appears as an important requirement toward the application of titanium dioxide technologies for the photocatalytic degradation of halon 1113.

Structural analysis of zeolite beta through periodic ab initio simulations of XRD and [formula omitted] and [formula omitted] NMR spectra

For large systems containing hundreds of atoms in the unit cell, as usually is observed in the zeolitic materials, the use of periodic ab initio calculations is limited by the requirement of huge computation resources. In this work, by using the primitive unit cell of the zeolite beta crystal, which is 50% smaller than its conventional crystallographic unit cell, we are able to perform periodic ab initio calculations for this system. Contrary to cluster-type calculations, the correct chemical environment of the entire zeolite beta crystal is taken into account, allowing for an accurate determination of this XRD pattern and the NMR spectra of the 29Si and 17O nuclei. In particular, we present a complete characterization of the distribution of quadrupole coupling constants (Cq), asymmetry parameter (η), and isotropic chemical shifts for the δisoSi and the δisoO, which have not yet been investigated experimentally.

Charge Density Analysis of 2,6-Dinitrophenol

The charge density of 2,6-dinitrophenol has been carefully determined from low temperature (20 K) single crystal X-ray diffraction data and periodic ab initio theoretical calculations. The topological analysis performed on the refined densities within the framework of the Quantum Theory of Atoms in Molecules (QTAIM), allowed us to characterize, both qualitatively and quantitatively, the various intra- and intermolecular interactions existing in the crystal structure of this compound. Notably two strong intramolecular noncovalent interactions have been characterized (O···H, De > 60 kJ/mol; O···O, De ∼ 19 kJ/mol). In addition, a series of weaker intermolecular interactions (O···N, O···O, O···C, and C···C) with estimated dissociation energies of 1–9 kJ/mol have been identified.

In silico infrared and Raman spectroscopy under pressure: the case of CaSnO3 perovskite.

The CaSnO3 perovskite is investigated under geochemical pressure, up to 25 GPa, by means of periodic ab initio calculations performed at B3LYP level with local Gaussian-type orbital basis sets. Structural, elastic, and spectroscopic (phonon wave-numbers, infrared and Raman intensities) properties are fully characterized and discussed. The evolution of the Raman spectrum of CaSnO3 under pressure is reported to remarkably agree with a recent experimental determination [J. Kung, Y. J. Lin, and C. M. Lin, J. Chem. Phys. 135, 224507 (2011)] as regards both wave-number shifts and intensity changes. All phonon modes are symmetry-labeled and bands assigned. The single-crystal total spectrum is symmetry-decomposed into the six directional spectra related to the components of the polarizability tensor. The infrared spectrum at increasing pressure is reported for the first time and its main features discussed. All calculations are performed using the Crystal14 program, taking advantage of the new implementation of analytical infrared and Raman intensities for crystalline materials.

SHADE3server: a streamlined approach to estimate H-atom anisotropic displacement parameters using periodicab initiocalculations or experimental information

A major update of theSHADEserver (http://shade.ki.ku.dk) is presented. In addition to all of the previous options for estimating H-atom anisotropic displacement parameters (ADPs) that were offered bySHADE2, the newest version offers two new methods. The first method combines the original translation–libration–screw analysis with input from periodicab initiocalculations. The second method allows the user to input experimental information from spectroscopic measurements or from neutron diffraction experiments on related structures and utilize this information to evaluate ADPs of H atoms. Tools are provided to set up theab initiocalculations and to derive the internal motion from the calculations. The new server was tested on a range of compounds where neutron diffraction data were available. In most cases, the results are significantly better than previous estimates, and for strong hydrogen bonds in proton sponges, theab initiocalculations become crucial.

A comprehensive DFT investigation of bulk and low-index surfaces of ZrO2 polymorphs.

The bulk structure, the relative stability, and the electronic properties of monoclinic, tetragonal, and cubic ZrO(2) have been studied from a theoretical point of view, through periodic ab initio calculations using different Gaussian basis sets together with Hartree-Fock (HF), pure Density Functional Theory (DFT), and mixed HF/DFT schemes as found in hybrid functionals. The role of a posteriori empirical correction for dispersion, according to the Grimme D2 scheme, has also been investigated. The obtained results show that, among the tested functionals, PBE0 not only provides the best structural description of the three polymorphs, but it also represents the best compromise to accurately describe both the geometric and electronic features of the oxide. The relative stability of the three phases can also be qualitatively reproduced, as long as thermal contributions to the energy are taken into account. Four low-index ZrO(2) surfaces [monoclinic (-111), tetragonal (101 and 111), and cubic (111)] have then been studied at this latter level of theory. Surface energies, atomic relaxations, and electronic properties of these surfaces have been computed. The most stable surface is the cubic one, which is associated to small relaxations confined to the outermost layers. It is followed by the monoclinic (-111) and the tetragonal (101), which have very similar surface energies and atomic displacements. The tetragonal (111) was instead found to be, by far, the less stable with large displacements not only for the outermost but also for deeper layers. Through the comparison of different methods and basis sets, this study allowed us to find a reliable and accurate computational protocol for the investigation of zirconia, both in its bulk and surfaces forms, in view of more complex technological applications, such as ZrO(2) doped with aliovalent oxides as found in solid oxide fuel cells.