Polarization experiments with the SPIN setup at the ITEP synchrotron

New experimental data on the spin-rotation parameters A and R measured for elastic π ^± p scattering in the resonance region and on the asymmetry in pC scattering at primary momenta in the range 1.35–2.02 GeV/c, as well as in quasielastic proton scattering on nuclei in the same momentum range, are summarized. All these data were recently obtained by using the proton synchrotron installed at the Institute of Theoretical and Experimental Physics (ITEP, Moscow). The spectrum and features of seven isospin-3/2 baryon resonances that form a peak in the total cross section at a c.m. energy of 1.9 GeV are analyzed on the basis of new data on the parameters A and R, and the results of this analysis are presented. The experiments surveyed in this article were performed by a collaboration of researchers from ITEP and the Petersburg Nuclear Physics Institute (PNPI, Gatchina), the ITEP-PNPI collaboration.     

Formation of Cyclic Oligomers in Concentrated Aqueous Solutions of Formaldehyde

An MNDO calculation gave the formation enthalpies of the components of equilibrium mixtures in concentrated aqueous acid solutions of formaldehyde. The results of this study suggest that intramolecular cyclization of linear oligomers with 5 and 9 CH₂O units, respectively, is the most plausible mechanism of formation of cyclic oligomers of formaldehyde — trioxane and tetraoxane. Ring protonation by the hydroxonium ion with ring opening is the most energetically favorable route of cyclic acetal decomposition.     

Novel Inhibitors of 2′-O-Methyltransferase of the SARS-CoV-2 Coronavirus

The COVID-19 pandemic is still affecting many people worldwide and causing a heavy burden to global health. To eliminate the disease, SARS-CoV-2, the virus responsible for the pandemic, can be targeted in several ways. One of them is to inhibit the 2′-O-methyltransferase (nsp16) enzyme that is crucial for effective translation of viral RNA and virus replication. For methylation of substrates, nsp16 utilizes S-adenosyl methionine (SAM). Binding of a small molecule in the protein site where SAM binds can disrupt the synthesis of viral proteins and, as a result, the replication of the virus. Here, we performed high-throughput docking into the SAM-binding site of nsp16 for almost 40 thousand structures, prepared for compounds from three libraries: Enamine Coronavirus Library, Enamine Nucleoside Mimetics Library, and Chemdiv Nucleoside Analogue Library. For the top scoring ligands, semi-empirical quantum-chemical calculations were performed, to better estimate protein–ligand binding enthalpy. Relying upon the calculated binding energies and predicted docking poses, we selected 21 compounds for experimental testing.     

New Blood Coagulation Factor XIIa Inhibitors: Molecular Modeling,Synthesis, and Experimental Confirmation

In the modern world, complications caused by disorders in the blood coagulation system are found in almost all areas of medicine. Thus, the development of new, more advanced drugs that can prevent pathological conditions without disrupting normal hemostasis is an urgent task. The blood coagulation factor XIIa is one of the most promising therapeutic targets for the development of anticoagulants based on its inhibitors. The initial stage of drug development is directly related to computational methods of searching for a lead compound. In this study, docking followed by quantum chemical calculations was used to search for noncovalent low-molecular-weight factor XIIa inhibitors in a focused library of druglike compounds. As a result of the study, four low-molecular-weight compounds were experimentally confirmed as factor XIIa inhibitors. Selectivity testing revealed that two of the identified factor XIIa inhibitors were selective over the coagulation factors Xa and XIa.     

Computation of hydration free energies of organic solutes with an implicit water model

A new approach for computing hydration free energies DeltaG(solv) of organic solutes is formulated and parameterized. The method combines a conventional PCM (polarizable continuum model) computation for the electrostatic component DeltaG(el) of DeltaG(solv) and a specially detailed algorithm for treating the complementary nonelectrostatic contributions (DeltaG(nel)). The novel features include the following: (a) two different cavities are used for treating DeltaG(el) and DeltaG(nel). For the latter case the cavity is larger and based on thermal atomic radii (i.e., slightly reduced van der Waals radii). (b) The cavitation component of DeltaG(nel) is taken to be proportional to the volume of the large cavity. (c) In the treatment of van der Waals interactions, all solute atoms are counted explicitly. The corresponding interaction energies are computed as integrals over the surface of the larger cavity; they are based on Lennard Jones (LJ) type potentials for individual solute atoms. The weighting coefficients of these LJ terms are considered as fitting parameters. Testing this method on a collection of 278 uncharged organic solutes gave satisfactory results. The average error (RMSD) between calculated and experimental free energy values varies between 0.15 and 0.5 kcal/mol for different classes of solutes. The larger deviations found for the case of oxygen compounds are probably due to a poor approximation of H-bonding in terms of LJ potentials. For the seven compounds with poorest fit to experiment, the error exceeds 1.5 kcal/mol; these outlier points were not included in the parameterization procedure. Several possible origins of these errors are discussed.     

The thermodynamic characteristics of formation of organic molecule complexes with the magnesium ion in water: The results of quantum-chemical modeling

The Gibbs energy ΔG _b of formation of organic molecule complexes with the Mg²⁺ ion in water was calculated on the basis of a two-stage scheme for the complex formation reaction. The first stage is ligand transfer from infinity into the second coordination sphere of the Mg²⁺ ion, and the second stage is the dissociation of bonds between water molecules and the Mg²⁺ ion and the formation of bonds between the ligand and Mg²⁺. The contribution of the first reaction stage to ΔG _b was calculated on the assumption that the ligand was a solid body with a charge or dipole moment (if the ligand was neutral). The contribution of the second stage to ΔG _b was calculated using quantum-chemical modeling. The major contribution to ΔG _b was made by a change in the internal energy of the complex as a result of the dissociation/formation of coordination bonds and a change in the electric component of the Gibbs energy of interaction between the magnesium ion and molecule with water when they formed a complex. The contribution of the nonpolar component of complex interaction with water was comparatively small. Accurate calculations of the contribution of vibrational degrees of freedom to ΔG _b were also of importance.     

Absorption of light by a ferromagnetic semiconductor

The coefficient of absorption of light by a ferromagnetic semiconductor is calculated for indirect transitions with allowance for the electron-magnon interaction. The absorption coefficient is obtained as a function of the external magnetic field. The magnetic red shift of the absorption edge is considered.     

Differential inhibition of postnatal brain,spinal cord and body growth by a growth hormone antagonist

Background  

Growth hormone (GH) plays an incompletely understood role in the development of the central nervous system (CNS). In this study, we use transgenic mice expressing a growth hormone antagonist (GHA) to explore the role of GH in regulating postnatal brain, spinal cord and body growth into adulthood. The GHA transgene encodes a protein that inhibits the binding of GH to its receptor, specifically antagonizing the trophic effects of endogenous GH.     

Excluded volume effect for large and small solutes in water

The cavitation effect, i.e., the process of the creation of a void of excluded volume in bulk solvent (a cavity), is considered. The cavitation free energy is treated in terms of the information theory (IT) approach [Hummer, G.; Garde, S.; Garcia, A. E.; Paulaitis, M. E.; Pratt, L. R. J. Phys. Chem. B 1998, 102, 10469]. The binomial cell model suggested earlier is applied as the IT default distribution p(m) for the number m of solute (water) particles occupying a cavity of given size and shape. In the present work, this model is extended to cover the entire range of cavity size between small ordinary molecular solutes and bulky biomolecular structures. The resulting distribution consists of two binomial peaks responsible for producing the free energy contributions, which are proportional respectively to the volume and to the surface area of a cavity. The surface peak dominates in the large cavity limit, when the two peaks are well separated. The volume effects become decisive in the opposite limit of small cavities, when the two peaks reduce to a single-peak distribution as considered in our earlier work. With a proper interpolation procedure connecting these two regimes, the MC simulation results for model spherical solutes with radii increasing up to R = 10 A [Huang, D. H.; Geissler, P. L.; Chandler, D. J. Phys. Chem. B 2001, 105, 6704] are well reproduced. The large cavity limit conforms to macroscopic properties of bulk water solvent, such as surface tension, isothermal compressibility and Tolman length. The computations are extended to include nonspherical solutes (hydrocarbons C1-C6).     

Localization of the complex roots of a certain quasi-polynomial

The problem of localization of the zeros of the function w(z) = sinz + μsin(z/λ) on the complex plane is considered. Effective bounds for the imaginary parts |?(ζ)| on nonreal zeros ζ of w(.) are obtained. It is demonstrated that, in the case of rational λ, ?(ζ) is quasiuniformly distributed.