Interfacial Interaction between Suolunite Crystal and Silica Binding Peptide for Novel Bioinspired Cement

Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory

The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid-amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.

First-Principles Calculations of Thermoelectric Transport Properties of Quaternary and Ternary Bulk Chalcogenide Crystals

Chalcogenide crystals have a wide range of applications, especially as thermoelectric materials for energy conversion. Thermoelectric materials can be used to generate an electric current from a temperature gradient based on the Seebeck effect and based on the Peltier effect, and they can be used in cooling applications. Using first-principles calculations and semiclassical Boltzmann theory, we have computed the Seebeck coefficient, electrical conductivity, electronic thermal conductivity, power factor, and figure of merit of 30 chalcogenide crystals. A Quantum Espresso package is used to calculate the electronic properties and locate the Fermi level. The transport properties are then calculated using the BoltzTraP code. The 30 crystals are divided into two groups. The first group has four crystals with quaternary composition (A₂BCQ₄) (A = Tl; B = Cd, Hg; C = Si, Ge, Sn; Q = S, Se, Te). The second group contains 26 crystals with the ternary composition (A’B’Q₂) (A’ = Ag, Cu, Au, Na; B’ = B, Al, Ga, In; Q = S, Se, Te). Among these 30 chalcogenide crystals, the results for 11 crystals: Tl₂CdGeSe₄, Tl₂CdSnSe₄, Tl₂HgSiSe₄, Tl₂HgSnS₄, AuBSe₂, AuBTe₂, AuAlTe₂, AuGaTe₂, AuInTe₂, AgAlSe₂, and AgAlTe₂ are revealed for the first time. In addition, temperature-dependent transport properties of pure and doped AgSbSe₂ and AgSbTe₂ crystals with dopant compositions of AgSb_0.94Cd_0.06Te₂ and AgSbTe_1.85Se_0.15 were explored. These results provide an excellent database for bulk chalcogenides crucial for a wide range of potential applications in renewable energy fields.

Molecular Dynamics Study on Mechanical Properties of Interface between Urea-Formaldehyde Resin and Calcium-Silicate-Hydrates

Microcapsule based self-healing concrete can automatically repair damage and improve the durability of concrete structures, the performance of which depends on the binding behavior between the microcapsule wall and cement matrix. However, conventional experimental methods could not provide detailed information on a microscopic level. In this paper, through molecular dynamics simulation, three composite models of Tobermorite (Tobermorite 9 Å, Tobermorite 11 Å, Tobermorite 14 Å), a mineral similar to Calcium-Silicate-Hydrate (C-S-H) gel, with the linear urea-formaldehyde (UF), the shell of the microcapsule, were established to investigate the mechanical properties and interface binding behaviour of the Tobermorite/UF composite. The results showed that the Young's modulus, shear modulus and bulk modulus of Tobermorite/UF were lower than that of 'pure' Tobermorite, whereas the tensile strength and failure strain of Tobermorite/UF were higher than that of 'pure' Tobermorite. Moreover, through radial distribution function (RDF) analysis, the connection between Tobermorite and UF found a strong interaction between Ca, N, and O, whereas Si from Tobermorite and N from UF did not contribute to the interface binding strength. Finally, high binding energy between the Tobermorite and UF was observed. The research results should provide insights into the interface behavior between the microcapsule wall and the cement matrix.