Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.     

Acoustic phonons in a quantum dot-matrix system: Hole-burning spectroscopy

A theory of burning spectral holes in an inhomogeneously broadened light absorption profile of quantum dots embedded in a dielectric matrix has been developed. The emphasis was on the possibility of using hole-burning spectroscopy to study the interaction of the electron subsystem of quantum dots with acoustic phonons. An analytical expression describing the shape of differential hole-burning spectra near the fundamental absorption edge for the cases of strong and weak confinement is obtained. The conditions under which the hole-burning spectra are most similar to the absorption spectra of a single quantum dot are determined.     

Kinetics of photoreactions in a regular porous nanostructure with cylindrical cells filled with activator-containing macromolecules

The kinetics of a two-stage laser-induced reaction between electronically excited molecules of two sorts (an organic luminophore and oxygen) in a regular porous nanostructure whose cells are filled with linear macromolecules is studied. A mathematical model of the process is proposed that takes into account an inhomogeneous distribution of polymer chain links in a nanopore, with this distribution determining the radial profile of reagents. One version of the theory considers a radial diffusion flux of activated oxygen molecules, while the other version considers a thermodiffusion flux of unexcited molecules. The numerical results of the model are compared to the data of molecular dynamic calculations and experiment.     

Change in the kinetics of delayed annihilation fluorescence during rearrangement of polymer-chain structure in a nanocavity of a solid adsorbent

Specially derived spatial density distributions of units of the polymer chain adsorbed by the surface of a nanosized spherical or cylindrical cavity were used to describe the kinetics of the bimolecular reaction of cross annihilation of electronic excitation in nanoporous media. The cases of marked attraction of the chain units by cavity walls and the lack of the attraction were considered. The formation of the radial profile of the density of the units was simulated by means of molecular dynamics to compare with the analytical expressions used.     

The Evolution of the Conductivity and Cathodoluminescence of the Films of Hafnium Oxide in the Case of a Change in the Concentration of Oxygen Vacancies

Physics of the Solid State - The dependence of the conductivity of the films of hafnium oxide HfO2 synthesized in different modes is studied. Depending on the modes of synthesis, the conductivity...     

Optical Properties of Nonstoichiometric Tantalum Oxide TaO<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript> (<Emphasis Type="Italic">x</Emphasis> &lt; 5/2) According to Spectral-Ellipsometry and Raman-Scattering Data

Optical properties of amorphous nonstoichiometric tantalum-oxide films of variable composition (TaO_x, x = 1.94–2.51) in the spectral range of 1.12–4.96 eV, obtained by ion-beam sputtering-deposition of metallic tantalum at different partial oxygen pressures (0.53–9.09 × 10^–3 Pa), have been investigated. It is shown by spectral ellipsometry that the character of dispersion of the absorption coefficient and refractive index in TaO_x of variable composition suggests that light-absorbing films with dispersion similar to that in metals are formed at oxygen pressures in the growth chamber below 2.21 × 10^–3 Pa, whereas transparent films with dielectric dispersion are formed at pressures above 2.81 × 10^–3 Pa. According to the data of quantumchemical simulation, the absorption peak at a photon energy of 4.6 eV in TaO_x observed in the absorptioncoefficient dispersion spectrum is due to oxygen vacancy. The peak in the Raman-scattering spectra of TaO_x films with metallic dispersion at frequencies of 200–230 cm^–1 is presumably related to tantalum nanoclusters.     

Short-Range Order in Amorphous and Crystalline Ferroelectric Hf<Subscript>0.5</Subscript>Zr<Subscript>0.5</Subscript>O<Subscript>2</Subscript>

The microstructures of amorphous and polycrystalline ferroelectric Hf_0.5Zr_0.5O₂ films are studied by X-ray spectroscopy and ellipsometry. EXAFS spectra demonstrate that the amorphous film consists of an “incompletely mixed” solid solution of metallic oxides HfO₂ and ZrO₂. After rapid thermal annealing, the mixed Hf_0.5Zr_0.5O₂ oxide films have a more ordered polycrystalline structure, and individual Hf and Zr monoxide islands are formed in the films. These islands are several nanometers in size and have a structure that is similar to the monoclinic structure of HfO₂ and ZrO₂. The presence of the HfO₂ and ZrO₂ phases in the Hf_0.5Zr_0.5O₂ films is also detected by ellipsometry.     

Atomic and Electronic Structures of a-SiNx:H

Journal of Experimental and Theoretical Physics - The atomic structure and the electronic spectrum of a-SiNx:H films, which are grown by plasmachemical deposition with varied ammonia and monosilane...     

Optical Properties of Nonstoichiometric Silicon Oxide SiOx (x < 2)

Optics and Spectroscopy - The optical properties of amorphous nonstoichiometric silicon oxide (SiOx) films of variable composition (x = 0.62–1.92) formed by plasma-enhanced chemical vapor...     

Relation between the shear and longitudinal viscosity coefficients for concentrated polymer solutions

A relation between the shear and longitudinal viscosity coefficients is obtained on the basis of the theory of flow of polymeric systems in the single relaxation time approximation. A comparison of the shear and longitudinal viscosity coefficients for polymer melts and solutions shows that the relation obtained is valid over a broad stress region.Institute of Chemical Physics, Academy of Sciences of the USSR, Moscow. Scientific-Research Institute of Synthetic Fibers, Moscow. Translated from Mekhanika Polimerov, No. 1, pp. 124–131, January–February, 1973.