Five structural domains in chain A and partial charge distribution in RBD with same orientation as of chain A.

Clay mineral materials have attracted attention due to their many properties and applications. The applications of clay minerals are closely linked to their structure and composition. In this paper, we studied the electronic structure properties of kaolinite, muscovite, and montmorillonite crystals, which are classified as clay minerals, by using DFT-based ab initio packages VASP and the OLCAO. The aim of this work is to have a deep understanding of clay mineral materials, including electronic structure, bond strength, mechanical properties, and optical properties. It is worth mentioning that understanding these properties may help continually result in new and innovative clay products in several applications, such as in pharmaceutical applications using kaolinite for their potential in cancer treatment, muscovite used as insulators in electrical appliances, and engineering applications that use montmorillonite as a sealant. In addition, our results show that the role played by hydrogen bonds in O-H bonds has an impact on the hydration in these crystals. Based on calculated total bond order density, it is concluded that kaolinite is slightly more cohesive than montmorillonite, which is consistent with the calculated mechanical properties.

The most recent Omicron variant of SARS-CoV-2 has caused global concern and anxiety. The only thing certain about this strain, with a large number of mutations in the spike protein, is that it spreads quickly, seems to evade immune defense, and mitigates the benefits of existing vaccines. Based on the ultra-large-scale ab initio computational modeling of the receptor binding motif (RBM) and the human angiotensin-converting enzyme-2 (ACE2) interface, we provide the details of the effect of Omicron mutations at the fundamental atomic scale level. In-depth analysis anchored in the novel concept of amino acid-amino acid bond pair units (AABPU) indicates that mutations in the Omicron variant are connected with (i) significant changes in the shape and structure of AABPU components, together with (ii) significant increase in the positive partial charge, which facilitates the interaction with ACE2. We have identified changes in bonding due to mutations in the RBM. The calculated bond order, based on AABPU, reveals that the Omicron mutations increase the binding strength of RBM to ACE2. Our findings correlate with and are instrumental to explain the current observations and can contribute to the prediction of next potential new variant of concern.

The relation between amino acid (AA) sequence and biologically active conformation controls the process of polypeptide chains folding into three-dimensional (3d) protein structures. The recent achievements in the resolution achieved in cryo-electron microscopy coupled with improvements in computational methodologies have accelerated the analysis of structures and properties of proteins. However, the detailed interaction between AAs has not been fully elucidated. Herein, we present a de novo method to evaluate inter-amino acid interactions based on the concept of accurately evaluating the amino acid bond pairs (AABP). The results obtained enabled the identification of complex 3d long-range interconnected AA interacting network in proteins. The method is applied to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. We show that although nearest-neighbor AAs in the primary sequence have large AABP, other nonlocal AAs make substantial contribution to AABP with significant participation of both covalent and hydrogen bonding. Detailed analysis of AABP in RBD reveals the pivotal role they play in sequence conservation with profound implications on residue mutations and for therapeutic drug design. This approach could be easily applied to many other proteins of biomedical interest in life sciences.

Chalcogenide crystals are a unique class of materials very different from semiconductors or metallic alloys. They also have many practical applications, especially in relation to their optical properties. However, the fundamental understanding of their electronic structure and physical properties is rather scattered and incomplete. We present a detailed study using first-principles calculations on the electronic structure, interatomic bonding, and optical and mechanical properties for 32 chalcogenide crystals. They consist of 22 binary (A_nB_m) and 10 ternary (A_nA′B_m) crystals with A = Ag, As, Cu, Ge, Sb, Sn, Cd, Zn; A′ = In, Ge, Sn; and B = S, Se, Te with n = 1, 2, 4 and m = 1, 2, 3, 4, 9. We use the novel concept of total bond order density as a single quantum mechanical metric to characterize the internal cohesion of these crystals and correlate them with the calculated properties, especially the mechanical properties. Based on this large database, we are able to identify some new and conspicuous observations to reach some useful conclusions related to the chemical composition of the chalcogenide compounds and their complex interatomic interactions. Specific examples from crystals and their unique properties in relation to the elements A and A′ and chalcogenide element B (S, Se, and Te) are discussed and highlighted. Finally, generalization of the observed trends and empirical rules can be extended to much larger classes of ternary and quaternary chalcogenide crystals and glasses so far unexplored.

The rapid evolution in materials science has resulted in a significant interest in high-entropy alloys (HEAs) for their unique properties. This study focuses on understanding both quaternary and quinary body-centered cubic (BCC) of 12 refractory-based HEAs, and on analysis of their electronic structures, lattice distortions, mechanical, and thermal properties. A comprehensive assessment is undertaken by means of density functional theory (DFT)-based first principles calculations. It is well known that multiple constituents lead to notable lattice distortions, especially in quinary HEAs. This distortion, in turn, has significant implications on the electronic structure that ultimately affect mechanical and thermal behaviors of these alloys such as ductility, lattice thermal conductivity, and toughness. Our in-depth analysis of their electronic structures revealed the role of valence electron concentration and its correlation with bond order and mechanical properties. Local lattice distortion (LD) was investigated for these 12 HEA models. M1 (WTiVZrHf), M7 (TiZrHfW), and M12 (TiZrHfVNb) have the highest LD whereas the models M3 (MoTaTiV), M5 (WTaCrV), M6 (MoNbTaW), and M9 (NbTaTiV) have the less LD. Furthermore, we investigated the thermal properties focusing on Debye temperature (Θ_D), thermal conductivity (κ), Grüneisen parameter (γ_α), and dominant phonon wavelength (λ_dom). The NbTaTiV(M9) and TiVNbHf(M10) models have significantly reduced lattice thermal conductivities (κ_L). This reduction is due to the mass increase and strain fluctuations, which in turn signify lattice distortion. The findings not only provide an understanding of these promising materials but also offer guidance for the design of next-generation HEAs with properties tailored for potential specific applications.