Cost-Effective Quantum Mechanical Approach for Predicting Thermodynamic and Mechanical Stability of Pure-Silica Zeolites

Infrared harmonic features of collagen models at B3LYP-D3: From amide bands to the THz region

In this paper, we have studied the vibrational spectral features for the collagen triple helix using a dispersion corrected hybrid density functional theory (DFT-D) approach. The protein is simulated by an infinite extended polymer both in the gas phase and in a water micro-solvated environment. We have adopted proline-rich collagen models in line with the high content of proline in natural collagens. Our scaled harmonic vibrational spectra are in very good agreement with the experiments and allow for the peak assignment of the collagen amide I and III bands, supporting or questioning the experimental interpretation by means of vibrational normal modes analysis. Furthermore, we demonstrated that IR spectroscopy in the THz region can detect the small variations inherent to the triple helix helicity (10/3 over 7/2), thus elucidating the packing state of the collagen. So far, identifying the collagen helicity is only possible by means of crystal x-ray diffraction.

Ab initio description of oxygen vacancies in epitaxially strained [Formula: see text] at finite temperatures

Epitaxially grown [Formula: see text] (STO) thin films are material enablers for a number of critical energy-conversion and information-storage technologies like electrochemical electrode coatings, solid oxide fuel cells and random access memories. Oxygen vacancies ([Formula: see text]), on the other hand, are key defects to understand and tailor many of the unique functionalities realized in oxide perovskite thin films. Here, we present a comprehensive and technically sound ab initio description of [Formula: see text] in epitaxially strained (001) STO thin films. The novelty of our first-principles study lies in the incorporation of lattice thermal excitations on the formation energy and diffusion properties of [Formula: see text] over wide epitaxial strain conditions ([Formula: see text]%). We found that thermal lattice excitations are necessary to obtain a satisfactory agreement between first-principles calculations and the available experimental data for the formation energy of [Formula: see text]. Furthermore, it is shown that thermal lattice excitations noticeably affect the energy barriers for oxygen ion diffusion, which strongly depend on [Formula: see text] and are significantly reduced (increased) under tensile (compressive) strain. The present work demonstrates that for a realistic theoretical description of oxygen vacancies in STO thin films is necessary to consider lattice thermal excitations, thus going beyond standard zero-temperature ab initio approaches.

Balancing Cost and Accuracy in Quantum Mechanical Simulations on Collagen Protein Models

Collagen proteins are spread in almost every vertebrate's tissue with mechanical function. The defining feature of this fundamental family of proteins is its well-known collagen triple-helical domain. This helical domain can have different geometries, varying in helical elongation and interstrands contact, as a function of the amino acidic composition. The helical geometrical features play an important role in the interaction of the collagen protein with cell receptors, but for the vast majority of collagen compositions, these geometrical features are unknown. Quantum mechanical (QM) simulations based on the density functional theory (DFT) provide a robust approach to characterize the scenario on the collagen composition-structure relationships. In this work, we analyze the role of the adopted computational method in predicting the collagen structure for two purposes. First, we look for a cost-effective computational approach to apply to a large-scale composition-structure analysis. Second, we attempt to assess the robustness of the predictions by varying the QM methods. Therefore, we have run geometry optimization on periodic models of the collagen protein using a variety of approaches based on the most commonly used DFT functionals (PBE, HSE06, and B3LYP) with and without dispersion correction (D3^ABC). We have coupled these methods with several different basis sets, looking for the highest accuracy/cost ratio. Furthermore, we have studied the performance of the composite HF-3c method and the semiempirical GFN1-xTB method. Our results identify a computational recipe that is potentially capable of predicting collagen structural features in line with DFT simulations, with orders of magnitude reduced computational cost, encouraging further investigations on the topic.

Exfoliation Energy of Layered Materials by DFT-D: Beware of Dispersion!

In this work, we have computed the exfoliation energy (the energy required to separate a single layer from the bulk structure), the interlayer distance, and the thermodynamic state functions for representative layered inorganic minerals such as Brucite, Portlandite, and Kaolinite, while leaving the more classical 2D transition-metal dichalcogenides (like MoS₂) for future work. Such materials are interesting for several applications in the field of adsorption and in prebiotic chemistry. Their peculiar features are directly controlled by the exfoliation energy. In materials without cations/anions linking different layers, the interactions keeping the layers together are of weak nature, mainly dispersion London interactions and hydrogen bonds, somehow challenging to deal with computationally. We used Hartree-Fock (HF) and density functional theory (DFT) approaches focusing on the role of dispersion forces using the popular and widespread Grimme's pairwise dispersion schemes (-D2 and -D3) and, as a reference method, the periodic MP2 approach based on localized orbitals (LMP2). The results are highly dependent on the choice of the scheme adopted to account for dispersion interactions. D2 and D3 schemes combined with either HF or DFT lead to overestimated exfoliation energies (about 2.5 and 1.7 times higher than LMP2 data for Brucite/Portlandite and Kaolinite) and underestimated interlayer distances (by about 3.5% for Brucite/Portlandite). The reason is that D2 and D3 corrections are based on neutral atomic parameters for each chemical element which, instead, behave as cations in the considered layered material (Mg, Ca, and Al), causing overattractive interaction between layers. More sophisticated dispersion corrections methods, like those based on nonlocal vdW functionals, many body dispersion model, and exchange-hole dipole moment not relying on atom-typing, are, in principle, better suited to describe the London interaction of ionic species. Nonetheless, we demonstrate that good results can be achieved also within the simpler D2 and D3 schemes, in agreement with previous literature suggestions, by adopting the dispersion coefficients of the preceding noble gas for the ionic species, leading to energetics in good agreement with LMP2 and structures closer to the experiments.

Efficient and accurate description of adsorption in zeolites

Accurate theoretical methods are needed to correctly describe adsorption on solid surfaces or in porous materials. The random phase approximation (RPA) with singles corrections scheme and the second order Møller-Plesset perturbation theory (MP2) are two schemes, which offer high accuracy at affordable computational cost. However, there is little knowledge about their applicability and reliability for different adsorbates and surfaces. Here, we calculate adsorption energies of seven different molecules in zeolite chabazite to show that RPA with singles corrections is superior to MP2, not only in terms of accuracy but also in terms of computer time. Therefore, RPA with singles is a suitable scheme for obtaining highly accurate adsorption energies in porous materials and similar systems.

Extending and assessing composite electronic structure methods to the solid state

A hierarchy of simplified Hartree-Fock (HF), density functional theory (DFT) methods, and their combinations has been recently proposed for the fast electronic structure computation of large systems. The covered methods are a minimal basis set Hartree-Fock (HF-3c), a small basis set global hybrid functional (PBEh-3c), and its screened exchange variant (HSE-3c), all augmented with semiclassical correction potentials. Here, we extend their applicability to inorganic covalent and ionic solids as well as layered materials. The new methods have been dubbed HFsol-3c, PBEsol0-3c, and HSEsol-3c, respectively, to indicate their parent functional as well as the correction potentials. They have been implemented in the CRYSTAL code to enable routine application for molecular as well as solid materials. We validate the new methods on diverse sets of solid state benchmarks that cover more than 90 solids ranging from covalent, ionic, semi-ionic, layered, and molecular crystals. While we focus on structural and energetic properties, we also test bandgaps, vibrational frequencies, elastic constants, and dielectric and piezoelectric tensors. HSEsol-3c appears to be most promising with mean absolute error for cohesive energies and unit cell volumes of molecular crystals of 1.5 kcal/mol and 2.8%, respectively. Lattice parameters of inorganic solids deviate by 3% from the references, and vibrational frequencies of α-quartz have standard deviations of 10 cm^-1. Overall, this shows an accuracy competitive to converged basis set dispersion corrected DFT with a substantial increase in computational efficiency.

Crystal-energy landscapes of active pharmaceutical ingredients using composite approaches

Composite methods employing dispersion-corrected DFT consistently identify experimentally isolated polymorphs as the lowest-energy crystal structures of common APIs.