Structural insights into ACE2 interactions and immune activation of SARS-CoV-2 and its variants: an in-silico study

The initial interaction between COVID-19 and the human body involves the receptor-binding domain (RBD) of the viral spike protein with the angiotensin-converting enzyme 2 (ACE2) receptor. Likewise, the spike protein can engage with immune-related proteins, such as toll-like receptors (TLRs) and pulmonary surfactant proteins A (SP-A) and D (SP-D), thereby triggering immune responses. In this study, we utilize computational methods to investigate the interactions between the spike protein and TLRs (specifically TLR2 and TLR4), as well as (SP-A) and (SP-D). The study is conducted on four variants of concern (VOC) to differentiate and identify common virus behaviours. An assessment of the structural stability of various variants indicates slight changes attributed to mutations, yet overall structural integrity remains preserved. Our findings reveal the spike protein's ability to bind with TLR4 and TLR2, prompting immune activation. In addition, our in-silico results reveal almost similar docking scores and therefore affinity for both ACE2-spike and TLR4-spike complexes. We demonstrate that even minor changes due to mutations in all variants, surfactant A and D proteins can function as inhibitors against the spike in all variants, hindering the ACE2-RBD interaction.Communicated by Ramaswamy H. Sarma.

Carbon nanotubes and nanobelts as potential materials for biosensor

We investigate the electronic response of single-walled carbon nanotubes (SWCNTs) and a carbon nanobelt (CNB) to N-linked and O-linked SARS-CoV-2 spike glycoproteins, using ab initio quantum mechanical approach. The CNTs are selected from three zigzag, armchair, and chiral groups. We examine the effect of carbon nanotube (CNT) chirality on the interaction between CNTs and glycoproteins. Results indicate that the chiral semiconductor CNTs clearly response to the presence of the glycoproteins by changing the electronic band gaps and electron density of states (DOS). Since the changes in the CNTs band gaps in the presence of N-linked are about two times larger than the changes in the presence of the O-linked glycoprotein, chiral CNT may distinguish different types of the glycoproteins. The same results are obtained from CNBs. Thereby, we predict CNBs and chiral CNTs have suitable potential in sequential analysis of N- and O-linked glycosylation of the spike protein.

Predicting the new carbon nanocages, fullerynes: a DFT study

In this study, based on density functional theory, we propose a new branch of pseudo-fullerenes which contain triple bonds with sp hybridization. We call these new nanostructures fullerynes, according to IUPAC. We present four samples with the chemical formula of C4nHn, and the structures derived from fulleranes. We compare the structural and electronic properties of these structures with those of two common fullerenes and fulleranes systems. The calculated electron affinities of the sampled fullerynes are negative, and much smaller than those of fullerenes, so they should be chemically more stable than fullerenes. Although fulleranes also exhibit higher chemical stability than fullerynes, but pentagon or hexagon of the fullerane structures cannot pass ions and molecules. Applications of fullerynes can be included in the storage of ions and gases at the nanoscale. On the other hand, they can also be used as cathode/anode electrodes in lithium-ion batteries.

Graphene-induced band gap renormalization in polythiophene: a many-body perturbation study

Density functional theory and many-body perturbation theory at the G₀W₀ level are employed to study the electronic properties of polythiophene (PT) adsorbed on the graphene surface. Analysis of the charge density difference shows that substrate-adsorbate interaction leads to a strong physisorption and interfacial electric dipole moment formation. The electrostatic potential displays a  -0.19 eV shift in the graphene work function from its initial value of 4.53 eV, as the result of the interaction. The LDA band gap of the polymer does not show any change. However, the band structure exhibits weak orbital hybridizations resulting from slight overlapping between the polymer and graphene states wave functions. The interfacial polarization effects on the band gap and levels alignment are investigated at the G₀W₀ level and show a notable reduction of PT band gap compared to that of the isolated chain.

Theoretical study of thieno-thiophene based low band gap copolymers and substituent effect on the optoelectronic properties of them

This paper studies donor-acceptor systems which incorporate benzodithiophene (BDT), benzodifuran (BDF) and benzodipyrrole (BDP) units as the electron-rich monomer with TT unit representing the electron-deficient monomer. This research is based on employing density functional theory (DFT) and time-dependent DFT (TD-DFT). The highest occupied molecular orbitals (HOMO) and the lowest unoccupied molecular orbitals (LUMO), HOMO-LUMO gaps and dihedral-angles of these copolymers were calculated using oligomer extrapolation technique and periodic boundary condition (PBC) method. The optical band gaps and UV-vis absorption spectra of aforementioned copolymers were obtained by TD-DFT at the same level of theory. Based on the fair agreement between PBC-DFT calculated results and experimental data, the substituent effects of Cl, Br, CCH, COH, NO₂, OH, SH and NH₂ groups were investigated by PBC-DFT method. The difference between the ground and excited-states dipole moment (Δμ_ge) of all derivatives were also calculated. Taking these results into account, a better understanding of the substituent effects on the photo-physical properties of the copolymers under study was achieved. Due to the shift of HOMO and LUMO energy levels, smaller band gaps and higher Δμ_ge are observed in some derivatives. The calculation results demonstrate that the substitution of COH and NO₂ by fluorine in BDF-TT and BDP-TT leads to higher maximum theoretical efficiencies (η).

Sila-fulleranes: promising chemically active fullerene analogs

Density-functional theory (DFT) was applied to investigate the geometry and electronic properties of bare Si60 and H-terminated Si-fullerene. DFT predicts outward sites on a bare Si60 cage. By using π-orbital axis analysis (POAV), it is shown that these sites result from a strong tendency of silicon atoms to form sp(3) hybridization bonds. Natural bond orbital (NBO) analysis confirms the sp(3) hybridization nature of Si-Si bonds in Si-fulleranes. The quantum confinement effect (QCE) does not affect band gap (BG) so strongly in the size between 1 and 1.7 nm. In contrast, the geometry and symmetry of the cage have a significant influence on the BG. In contrast to their carbon analogs, pentagon rings increase the stability of the cages. Functionalized Si-cages are stable and can be chemically very active. The electronic properties are highly sensitive to the surface chemistry via functionalization with different chemical groups. As a result, BGs and chemical activities of these cages can be drastically tuned through the chemistry of the surface.

Density functional theory investigation of opto-electronic properties of thieno[3,4-b]thiophene and benzodithiophene polymer and derivatives and their applications in solar cell

PTBs polymers with thieno[3,4-b]thiophene [TT] and benzodithiophene [BDT] units have particular properties, which demonstrate it as one of the best group of donor materials in organic solar cells. In the present work, density functional theory (DFT) is applied to investigate the optimized structure, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), band gap and dihedral angle of PTB7 at B3LYP/6-31G(d). Two different approaches are applied to carry out these investigations: Oligomer extrapolation technique and periodic boundary condition (PBC) method. The results obtained from PBC-DFT method are in fair agreement with experiments. Based on these reliable outcomes; the investigations continued to perform some derivatives of PTB7. In this study, sulfur is substituted by nitrogen, oxygen, silicon, phosphor or selenium atoms in pristine PTB7. Due to the shift of HOMO and LUMO levels, smaller band gaps are predicted to appear in some derivatives in comparison with PTB7. Maximum theoretical efficiencies, η, of the mentioned derivatives as well as local difference of dipole moments between the ground and excited states (Δμge) are computed. The results indicate that substitution of sulfur by nitrogen or oxygen in BDT unit, and silicon or phosphor in TT unit of pristine PTB7 leads to a higher η as well as Δμge.

Altering the electronic properties of diamondoids through encapsulating small particles

The stability, optimized structure, and electronic gap of four diamondoid complexes, adamantane, C(10)H(16), diamantane, C(14)H(20), triamantane, C(18)H(24) and the T(d)-symmetry isomer of pentamantane, C(26)H(32), incorporating cage-centered small atoms and ions (X@cage, where X = H(+), Li(0,+), Be(0,+,2+), Na(0,+), Mg(0,2+), He, Ne, and F(-)) have been studied at the B3LYP hybrid level of theory. All adamantane complexes, except those encapsulating H(+) and Mg, are endohedral minima. In contrast no diamantane complexes are minima. A wide variety of atoms and ions can be encapsulated by triamantane and pentamantane molecules. The complexes are more stable for smaller and more highly charged metallic guest species. The electronic HOMO-LUMO gaps of diamondoid complexes are significantly affected by the inclusion of charged particles. The stability of the structures, the amount of the charges which are transferred between small particles and diamondoids cages, and the change in the HOMO-LUMO gaps of diamondoids are nearly the same for the corresponding possible complexes. All these features mostly depend on the charge, the size and the type of the encapsulated particle, and not on the type of diamondoid.