Complex band structure with non-orthogonal basis set: analytical properties and implementation in the SIESTA code

The complex band structure, although not directly observable, determines many properties of a material where the periodicity is broken, such at surfaces, interfaces and defects. Furthermore, its knowledge helps in the interpretation of electronic transport calculations and in the study of topological materials. Here we extend the transfer matrix method, often used to compute the complex bands, to electronic structures constructed using an atomic non-orthogonal basis set. We demonstrate that when the overlap matrix is not the identity, the non-orthogonal case, spurious features appear in the analytic continuation of the band structure to the complex plane. The properties of these are studied both numerically and analytically and discussed in the context of existing literature. Finally, a numerical implementation to extract the complex band structure from periodic calculations carried out with the density functional theory code SIESTA is presented. This is constructed as a simple post-processing tool, and it is therefore amenable to high-throughput studies of insulators and semiconductors.

Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors

Alamethicin (ALM) is an antimicrobial peptide that is frequently employed in studies of the mechanism of action of pore-forming molecules. Advanced techniques of solid-state NMR spectroscopy (SSNMR) are important in these studies, as they are capable of describing the alignment of helical peptides, such as ALM, in lipid bilayers. Here, it is demonstrated how an analysis of the SSNMR measurements can benefit from fully periodic calculations, which employ the plane-wave density-functional theory (PW DFT) of the solid-phase geometry and related spectral parameters of ALM. The PW DFT calculations are used to obtain the structure of desolvated crystalline ALM and predict the NMR chemical shift tensors (CSTs) of its nuclei. A variation in the CSTs of the amidic nitrogens and carbonyl carbons along the ALM backbone is evaluated and included in simulations of the orientation-dependent anisotropic 15N and 13C chemical shift components. In this way, the influence of the site-specific structural effects on the experimentally determined orientation of ALM is shown in models of cell membranes.

Fast and Accurate Electric Field Gradient Calculations in Molecular Solids With Density Functional Theory

Modern approaches for calculating electric field gradient (EFF) tensors in molecular solids rely upon plane-wave calculations employing periodic boundary conditions (PBC). In practice, models employing PBCs are limited to generalized gradient approximation (GGA) density functionals. Hybrid density functionals applied in the context of gauge-including atomic orbital (GIAO) calculations have been shown to substantially improve the accuracy of predicted NMR parameters. Here we propose an efficient method that effectively combines the benefits of both periodic calculations and single-molecule techniques for predicting electric field gradient tensors in molecular solids. Periodic calculations using plane-wave basis sets were used to model the crystalline environment. We then introduce a molecular correction to the periodic result obtained from a single-molecule calculation performed with a hybrid density functional. Single-molecule calculations performed using hybrid density functionals were found to significantly improve the agreement of predicted 17O quadrupolar coupling constants (Cq) with experiment. We demonstrate a 31% reduction in the RMS error for the predicted 17O Cq values relative to standard plane-wave methods using a carefully constructed test set comprised of 22 oxygen-containing molecular crystals. We show comparable improvements in accuracy using five different hybrid density functionals and find predicted Cq values to be relatively insensitive to the choice of basis set used in the single molecule calculation. Finally, the utility of high-accuracy 17O Cq predictions is demonstrated by examining the disordered 4-Nitrobenzaldehyde crystal structure.

Analyzing Discrepancies in Chemical-Shift Predictions of Solid Pyridinium Fumarates

Highly accurate chemical-shift predictions in molecular solids are behind the success and rapid development of NMR crystallography. However, unusually large errors of predicted hydrogen and carbon chemical shifts are sometimes reported. An understanding of these deviations is crucial for the reliability of NMR crystallography. Here, recently reported large deviations of predicted hydrogen and carbon chemical shifts of a series of solid pyridinium fumarates are thoroughly analyzed. The influence of the geometry optimization protocol and of the computational level of NMR calculations on the accuracy of predicted chemical shifts is investigated. Periodic calculations with GGA, meta-GGA and hybrid functionals are employed. Furthermore, molecular corrections at the coupled-cluster singles-and-doubles (CCSD) level are calculated. The effect of nuclear delocalization on the structure and NMR shielding is also investigated. The geometry optimization with a computationally demanding hybrid functional leads to a substantial improvement in proton chemical-shift predictions.

A method to restore the intrinsic dielectric functions of 2D materials in periodic calculations

A highly feasible method to restore the intrinsic optical properties of 2D materials in supercell calculations was formulated and applied.

Synergy between Experimental and Theoretical Investigations Reveals the Anti‑Corrosion Efficiency of Imine-Chalcones

The inhibitory action of three imine-chalcones on carbon steel corrosion in HCl was investigated by theoretical and experimental methods. Quantum descriptors were calculated at the conductor-like polarizable continuum model (CPCM)-Becke-3 Parameter-Lee-Yang-Parr (B3LYP)‑D3/def2-TZVPP level allowing the prediction of efficiency inhibition ranking. Electrochemical techniques and mass loss experiments were employed to determine inhibition efficiencies and related experimental parameters. Scanning electron microscopy was employed for metal surface analysis. The N-[(1Z,2E)-1,3-diphenylprop-2-in-1-ylidene]-1-phenethylamine (IM‑F) was pointed out as the most efficient inhibitor in this group, with 96% of corrosion inhibition. Moreover, theoretical results obtained from periodic calculations for the adsorption on the Fe(110) surface corroborated the highest efficacy of IM‑F.

Polymorphism of methyl 4-amino-3-phenylisothiazole-5-carboxylate: an experimental and theoretical study

Being a close analogue of amflutizole, methyl 4-amino-3-phenylisothiazole-5-carboxylate (C11H10N2O2S) was assumed to be capable of forming polymorphic structures. Noncentrosymmetric and centrosymmetric polymorphs have been obtained by crystallization from a series of more volatile solvents and from denser tetrachloromethane, respectively. Identical conformations of the molecule are found in both structures. The two polymorphs differ mainly in the intermolecular interactions formed by the amino group and in the type of stacking interactions between the π-systems. The most effective method for revealing packing motifs in structures with intermolecular interactions of different types (hydrogen bonding, stacking, dispersion, etc.) is to study the pairwise interaction energies using quantum chemical calculations. Molecules form a column as the primary basic structural motif due to stacking interactions in both polymorphic structures under study. The character of a column (straight or zigzag) is determined by the orientations of the stacked molecules (in a `head-to-head' or `head-to-tail' manner). Columns bound by intermolecular N—H...O and N—H...N hydrogen bonds form a double column as the main structural motif in the noncentrosymmetric structure. Double columns in the noncentrosymmetric structure and columns in the centrosymmetric structure interact strongly within the ab crystallographic plane, forming a layer as a secondary basic structural motif. The noncentrosymmetric structure has a lower density and a lower (by 0.59 kJ mol−1) lattice energy, calculated using periodic calculations, compared to the centrosymmetric structure.

Importance of the Oxyl Character on the IrO2 Surface Dependent Catalytic Activity for the Oxygen Evolution Reaction

The oxygen evolution reaction (OER) is considered to be the limiting step for the water splitting process. OER catalyst optimization is hindered because in the desirable acidic conditions the sole active catalysts are the expensive RuO2 and IrO2-based materials. Thus, the understanding of the factors controlling the reactivity of IrO2 is mandatory. In this contribution, we carried out spin polarized DFT (PBE-D2) periodic calculations to analyze the catalytic activities of the main ((110), (011), (100) and (001)) IrO2 surfaces. We considered the oxo-coupling (I2M) and water nucleophilic attack (WNA) mechanisms and computed the energy barriers of the chemical processes. Results show that the oxo-coupling and the water attack should be viewed as homolytic couplings and thus, the two processes only occur if the Ir=O species on the surfaces exhibit oxyl character. In these cases, the WNA mechanism is always easy and it becomes the most favorable pathway on the (110), (100) and (001) surfaces. In contrast, for the (011) facet the oxo-coupling is preferred. The required overpotentials for the four IrO2 surfaces depends on the feasibility to oxidize the Ir-OH to Ir-O species. However, if the oxidation is too favorable the resulting Ir=O species has no oxyl character and thus it does not further react. Therefore, the optimal catalyst shows a trade-off between the Ir-OH oxidation feasibility and the oxyl character of the surface Ir=O species. These two factors are tuned by the coordination of the unsaturated iridium sites: the (100) and (001) surfaces are more active than the (110) and (011). The key role of oxyl species has been shown to be important for molecular catalysts. However, the implications of oxyl species on IrO2 have rarely been mentioned. Present results show that the homogeneous and heterogeneous processes seem to have important similarities, thus suggesting that strategies used in one of the two fields could be transferred to the other.

Importance of the Oxyl Character on the IrO2 Surface Dependent Catalytic Activity for the Oxygen Evolution Reaction

The oxygen evolution reaction (OER) is considered to be the limiting step for the water splitting process. OER catalyst optimization is hindered because in the desirable acidic conditions the sole active catalysts are the expensive RuO2 and IrO2-based materials. Thus, the understanding of the factors controlling the reactivity of IrO2 is mandatory. In this contribution, we carried out spin polarized DFT (PBE-D2) periodic calculations to analyze the catalytic activities of the main ((110), (011), (100) and (001)) IrO2 surfaces. We considered the oxo-coupling (I2M) and water nucleophilic attack (WNA) mechanisms and computed the energy barriers of the chemical processes. Results show that the oxo-coupling and the water attack should be viewed as homolytic couplings and thus, the two processes only occur if the Ir=O species on the surfaces exhibit oxyl character. In these cases, the WNA mechanism is always easy and it becomes the most favorable pathway on the (110), (100) and (001) surfaces. In contrast, for the (011) facet the oxo-coupling is preferred. The required overpotentials for the four IrO2 surfaces depends on the feasibility to oxidize the Ir-OH to Ir-O species. However, if the oxidation is too favorable the resulting Ir=O species has no oxyl character and thus it does not further react. Therefore, the optimal catalyst shows a trade-off between the Ir-OH oxidation feasibility and the oxyl character of the surface Ir=O species. These two factors are tuned by the coordination of the unsaturated iridium sites: the (100) and (001) surfaces are more active than the (110) and (011). The key role of oxyl species has been shown to be important for molecular catalysts. However, the implications of oxyl species on IrO2 have rarely been mentioned. Present results show that the homogeneous and heterogeneous processes seem to have important similarities, thus suggesting that strategies used in one of the two fields could be transferred to the other.