The potential energy surfaces corresponding to the dehydrogenation reaction of H2O, NH3, and CH4 molecules
by Fe+(6D, 4F) cation have been investigated in the framework of the density functional theory in its B3LYP
formulation and employing a new optimized basis set for iron. In all cases, the low-spin ion−dipole complex,
which is the most stable species on the respective potential energy hypersurfaces, is initially formed. In the
second step, a hydrogen shift process leads to the formation of the insertion products, which are more stable
in a low-spin state. From these intermediates, three dissociation channels have been considered. All of the
results have been compared with existing experimental and theoretical data. Results show that the three insertion
pathways are significantly different, although spin crossings between high- and low-spin surfaces are observed
in all cases. The topological analysis of the electron localization function has been used to characterize the
nature of the bonds for all of the minima and transition states along the paths.
An approach to quantum mechanical investigation of interactions in protein-ligand complexes has been developed that treats the solvation effect in a mixed scheme combining implicit and explicit solvent models. In this approach, the first solvation shell of the solvent around the solute is modeled with a limited number of hydrogen bonded explicit solvent molecules. The influence of the remaining bulk solvent is treated as a surrounding continuum in the conductor-like screening model (COSMO). The enthalpy term of the binding free energy for the protein-ligand complexes was calculated using the semiempirical PM3 method implemented in the MOPAC package, applied to a trimmed model of the protein-ligand complex constructed with special rules. The dependence of the accuracy of binding enthalpy calculations on size of the trimmed model and number of optimized parameters was evaluated. Testing of the approach was performed for 12 complexes of different ligands with trypsin, thrombin, and ribonuclease with experimentally known binding enthalpies. The root-mean-square deviation (RMSD) of the calculated binding enthalpies from experimental data was found as ϳ1 kcal/mol over a large range.
A recombinant vaccine candidate has been developed based on the major coronaviruses’ antigen (S protein) fragments and a novel adjuvant—spherical particles (SPs) formed during tobacco mosaic virus thermal remodeling. The receptor-binding domain and the highly conserved antigenic fragments of the S2 protein subunit were chosen for the design of recombinant coronavirus antigens. The set of three antigens (Co1, CoF, and PE) was developed and used to create a vaccine candidate composed of antigens and SPs (SPs + 3AG). Recognition of SPs + 3AG compositions by commercially available antibodies against spike proteins of SARS-CoV and SARS-CoV-2 was confirmed. The immunogenicity testing of these compositions in a mouse model showed that SPs improved immune response to the CoF and PE antigens. Total IgG titers against both proteins were 9–16 times higher than those to SPs. Neutralizing activity against SARS-CoV-2 in serum samples collected from hamsters immunized with the SPs + 3AG was demonstrated.
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