Deformation behavior of an amorphous zeolitic imidazolate framework - from a supersoft material to a complex organometallic alloy

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.

Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex

The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.

First-Principles Simulation of Dielectric Function in Biomolecules

The dielectric spectra of complex biomolecules reflect the molecular heterogeneity of the proteins and are particularly important for the calculations of electrostatic (Coulomb) and electrodynamic (van der Waals) interactions in protein physics. The dielectric response of the proteins can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. We present a new robust simulation method anchored in rigorous ab initio quantum mechanical calculations of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the dielectric spectra of small proteins under different conditions. We implement this methodology to a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the spike protein of SARS-COV-2. Two peaks at 5.2-5.7 eV and 14.4-15.2 eV in the dielectric absorption spectra are observed for 1FUV and SD1 in vacuum as well as in their solvated and salted models.

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

Cement and concrete have been important construction materials throughout human history. There is an urgent need to explore novel and untraditional cementitious materials to enhance the durability of building materials and structures in response to increased infrastructure demand worldwide. We report an exploratory study on a biocomposite cement based on a large-scale computational study using density functional theory. An explicitly solvated mixture of a mineral calcium silicate hydrate (C-S-H) crystal suolunite (Ca₂Si₂O₅(OH)₂·H₂O) and a silicon binding peptide with amino acid sequence PRO-PRO-PRO-TRP-LEU-PRO-TYR-MET-PRO-PRO-TRP-SER is constructed using ab initio molecular dynamics (AIMD). Detailed analysis on the interface structure, interatomic bonding, mechanical properties, and solvent effect of this model reveals a complex interplay of different types of covalent and ionic bonding, including ubiquitous hydrogen bonding which plays a crucial role in their properties. The use of the total bond order density (TBOD), a single quantum mechanical metric, for assessing the interfacial cohesion for this composite biocement is proposed. We find that the solvated model has a slightly larger TBOD than the dried one. These results could lead to a systematic search and rational design for different types of bioinspired and hybrid functional materials with other inorganic minerals and organic peptides.

Atomic-Scale Understanding of Structure and Properties of Complex Pyrophosphate Crystals by First-Principles Calculations

The electronic structure and mechanical and optical properties of five pyrophosphate crystals with very complex structures are studied by first principles density functional theory calculations. The results show the complex interplay of the minor differences in specific local structures and compositions can result in large differences in reactivity and interaction that are rare in other classes of inorganic crystals. These are discussed by dividing the pyrophosphate crystals into three structural units. H2P2O7 is the most important and dominating unit in pyrophosphates. The other two are the influential cationic group with metals and water molecules. The strongest P-O bond in P2O5 is the strongest bond for crystal cohesion, but O-H and N-H bonds also play an important part. Different type of bonding between O and H atoms such as O-H, hydrogen bonding, and bridging bonds are present. Metallic cations such as Mg, Zn, and Cu form octahedral bonding with O. The water molecule provides the unique H∙∙∙O bonds, and metallic elements can influence the structure and bonding to a certain extent. The two Cu-containing phosphates show the presence of narrow metallic bands near the valence band edge. All this complex bonding affects their physical properties, indicating that fundamental understanding remains an open question.