Novel mechanisms of the conformational transformations of the biologically important G·C nucleobase pairs in Watson–Crick, Hoogsteen and wobble configurations via the mutual rotations of the bases around the intermolecular H-bonds: a QM/QTAIM study

It was established conformational transformations of the G·C nucleobase pairs, occurring via the mutual rotation of the G and C bases around the intermolecular H-bonds.

A Hidden Side of the Conformational Mobility of the Quercetin Molecule Caused by the Rotations of the O3H, O5H and O7H Hydroxyl Groups: In Silico Scrupulous Study

In this study at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of quantum-mechanical theory it was explored conformational variety of the isolated quercetin molecule due to the mirror-symmetrical hindered turnings of the O3H, O5H and O7H hydroxyl groups, belonging to the A and C rings, around the exocyclic C–O bonds. These dipole active conformational transformations proceed through the 72 transition states (TSs; C1 point symmetry) with non-orthogonal orientation of the hydroxyl groups relatively the plane of the A or C rings of the molecule (HO7C7C8/HO7C7C6 = ±(89.9–93.3), HO5C5C10 = ±(108.9–114.4) and HO3C3C4 = ±(113.6–118.8 degrees) (here and below signs ‘±’ corresponds to the enantiomers)) with Gibbs free energy barrier of activation ΔΔGTS in the range 3.51–16.17 kcal·mol−1 under the standard conditions (T = 298.1 K and pressure 1 atm): ΔΔGTSO7H (3.51–4.27) < ΔΔGTSO3H (9.04–11.26) < ΔΔGTSO5H (12.34–16.17 kcal mol−1). Conformational dynamics of the O3H and O5H groups is partially controlled by the intramolecular specific interactions O3H…O4, C2′/C6′H…O3, O3H…C2′/C6′, O5H…O4 and O4…O5, which are flexible and cooperative. Dipole-active interconversions of the enantiomers of the non-planar conformers of the quercetin molecule (C1 point symmetry) is realized via the 24 TSs with C1 point symmetry (HO3C3C2C1 = ±(11.0–19.1), HC2′/C6′C1′C2 = ±(0.6–2.9) and C3C2C1′C2′/C3C2C1′C6′ = ±(1.7–9.1) degree; ΔΔGTS = 1.65–5.59 kcal·mol−1), which are stabilized by the participation of the intramolecular C2′/C6′H…O1 and O3H…HC2′/C6′ H-bonds. Investigated conformational rearrangements are rather quick processes, since the time, which is necessary to acquire thermal equilibrium does not exceed 6.5 ns.

A conceptual approach to the formation of paramagnetic nanospecies of noble metals

The general concepts are analyzed regarding the approach for the formation of paramagnetic species of noble metals, with a non-rigid (labile) molecule being used as a supporting matrix. The formation of the metal nanospecies follows three stages: (i) the metal ions are captured by the matrix, (ii) the reducing agent causes formation of individual atoms separated by the matrix fragments, (iii) the individual atoms agglomerate due to conformational transformations of the labile molecule-matrix. This algorithm is realized in two distinct systems: Ag-containing nanospecies embedded within the system of polyacrylic acid (PAA) chains grafted to the film of fluorinated ethylene propylene copolymer (FEP) and Au-containing nanospecies in the free matrix of tannin-citrate- oxo-hydroxo aluminate. The evolution of the electron paramagnetic resonance (EPR) spectra while cooling down demonstrates the appearance of the exchange interaction which is suppressed at higher temperatures by the vibrational modes of the molecule-matrix. The role of the oxo-hydroxo aluminate form is one of a molecular motor sorting the individual nanospecies by their size and charge state.

USE OF MECHANICAL ACTIVATION OF POLYVINYL CHLORIDE IN THE PRODUCTION OF TENT MATERIALS

Physical and mechanical characteristics of tent materials depend on the quality of raw materials, which varies depending on its mechanical processing. A mathematical model of the process of dispersed materials activation is proposed, which describes the kinetics of change both during processing and dur-ing the further storage of the product of one or a number of factors characterizing physicochemical prop-erties of the material. The process of mechanical activation and verification of the adequacy of mathe-matical model proposed was carried out on emulsion polyvinyl chloride in a disintegrator unit. When processing PVC-E in a disintegrator, physicochemical processes take place, leading both to an increase and to a decrease in the viscosity of PVC-E solutions. The processes of dehydrochlorination breaking molecules, lead to a decrease in viscosity, and the formation of organic acids and copolymers - to in-crease. And these processes are irreversible. Conformational transformations of macromolecules con-tribute to the growth of viscosity of PVC-E solutions and are reversible. The adequacy of the proposed mathematical model describing the process of mechanical activation of dispersed materials is shown on the example of viscosity change of PVC-E solutions. Calculations show that increasing the loading speed, it is possible to maximize viscosity of PVC-E solutions in the minimum number of treatment cycles. If the number of processing cycles is more than one, then the rate of each subsequent loading should increase. The use of PVC-E, treated once in a disintegrator at a speed of 140 m / s, allows increasing physical and mechanical parameters of tent materials.

Comparative Studies of the Dynamics Effects of BAY60-2770 and BAY58-2667 Binding with Human and Bacterial H-NOX Domains

Soluble guanylate cyclase (sGC) is a key enzyme implicated in various physiological processes such as vasodilation, thrombosis and platelet aggregation. The enzyme’s Heme-Nitric oxide/Oxygen (H-NOX) binding domain is the only sensor of nitric oxide (NO) in humans, which on binding with NO activates sGC to produce the second messenger cGMP. H-NOX is thus a hot target for drug design programs. BAY60-2770 and BAY58-2667 are two widely studied activators of sGC. Here we present comparative molecular dynamics studies to understand the molecular details characterizing the binding of BAY60-2770 and BAY58-2667 with the human H-NOX (hH-NOX) and bacterial H-NOX (bH-NOX) domains. HartreeFock method was used for parametrization of both the activators. A 50 ns molecular dynamics (MD) simulation was run to identify the functionally critical regions of the H-NOX domains. The CPPTRAJ module was used for analysis. BAY60-2770 on binding with bH-NOX, triggered rotational movement in signaling helix F and significant dynamicity in loops α and β, but in hH-NOX domain the compound showed relatively lesser aforementioned structural fluctuations. Conversely, hH-NOX ligated BAY58-2667 experienced highest transitions in its helix F due to electrostatic interactions with D84, T85 and R88 residues which are not conserved in bH-NOX. These conformational transformations might be essential to communicate with downstream PAS, CC and cyclase domains of sGC. Comparative MD studies revealed that BAY bound bHNOX dynamics varied from that of hH-NOX, plausibly due to some key residues such as R40, F74 and Y112 which are not conserved in bacteria. These findings will help to the design of novel drug leads to cure diseases associated to human sGC.