All-atom level direct folding simulation of a betabetaalpha miniprotein

We performed ab initio folding simulation for a betabetaalpha peptide BBA5 (PDB code 1T8J) with a modified param99 force field using the generalized Born solvation model (param99MOD5/GBSA). For efficient conformational sampling, we extended a previously developed novel Q-replica exchange molecular dynamics (Q-REMD) into a multiplexed Q-REMD. Starting from a fully extended conformation, we were able to locate the nativelike structure in the global free minimum region at 280 K. The current approach, which combines the more balanced force field with the efficient sampling scheme, demonstrates a clear advantage in direct folding simulation at all-atom level.     

Rheological properties of sulfur-containing hyperbranched polycarbosilanes and related magnetic compositions

Russian Chemical Bulletin - The rheological properties of hyperbranched polycarbosilanes with butyl and decyl terminal groups and their sulfur-containing analogs were compared. The use of various...     

Fluoropropenoates as dienophiles in the Diels-Alder reaction

Several fluorinated alkenes were prepared from known ethyl (R)-2-fluoro-4,5-dihydroxyisopropylidine-2-pentenoate (1). The fluoroalkenoates were tested as dienophiles with several dienes and showed cycloaddition only with the very reactive diene, 1,3-diphenylisobenzofuran (5). Fluorobutenolide 2 reacted with 5 to produce the endo-syn adduct 9 in a highly stereoselective manner.     

Three-dimensional coupled numerical model of creeping flow of viscous fluid

A three-dimensional coupled numerical model is developed to describe creeping flow in a computational domain that consists of a thick viscous layer overlaid with a thin multilayered viscous sheet. The density of the sheet is assumed to be lower than that of the layer. The model couples the Stokes equations describing the flow in the layer and the Reynolds equations describing the flow in the sheet. We investigate the long-time behavior of the flow in the sheet by using an asymptotic method and derive an ordinary differential equation for the sheet boundary displacements and the velocities at the interface between the sheet and the layer. The Stokes and Reynolds equations are coupled by applying the resulting equation as an internal boundary condition. Numerical implementation is based on a modified finite element method combined with the projection gradient method. The computational domain is discretized into rectangular hexahedra. Piecewise square basis functions are used. The model proposed enables different-type hydrodynamic equations to be coupled without any iterative improvements. As a result, the computational costs are reduced significantly in comparison with available coupled models. Numerical experiments confirm that the three-dimensional coupled model developed is of good accuracy.     

Nuclear Spin relaxation mediated by Fermi-edge electrons in n-type GaAs

A method based on the optical orientation technique was developed to measure the nuclear-spin lattice relaxation time T ₁ in semiconductors. It was applied to bulk n-type GaAs, where T ₁ was measured after switching off the optical excitation in magnetic fields from 400 to 1200 G at low (< 30 K) temperatures. The spin-lattice relaxation of nuclei in the studied sample with n _D = 9 × 10¹⁶ cm^?3 was found to be determined by hyperfine scattering of itinerant electrons (Korringa mechanism) which predicts invariability of T ₁ with the change in magnetic field and linear dependence of the relaxation rate on temperature. This result extends the experimentally verified applicability of the Korringa relaxation law in degenerate semiconductors, previously studied in strong magnetic fields (several Tesla), to the moderate field range.     

Large tunneling effect on the hydrogen transfer in bis(μ-oxo)dicopper enzyme: a theoretical study

Type-III copper-containing enzymes have dicopper centers in their active sites and exhibit a novel capacity for activating aliphatic C-H bonds in various substrates by taking molecular oxygen. Dicopper enzyme models developed by Tolman and co-workers reveal exceptionally large kinetic isotope effects (KIEs) for the hydrogen transfer process, indicating a significant tunneling effect. In this work, we demonstrate that variational transition state theory allows accurate prediction of the KIEs and Arrhenius parameters for such model systems. This includes multidimensional tunneling based on state-of-the-art quantum-mechanical calculations of the minimum-energy path (MEP). The computational model of bis(μ-oxo)dicopper enzyme consists of 70 atoms, resulting in a 204-dimensional potential energy surface. The calculated values of E(a)(H) - E(a)(D), A(H)/A(D), and the KIE at 233 K are -1.86 kcal/mol, 0.51, and 28.1, respectively, for the isopropyl ligand system. These values agree very well with experimental values within the limits of experimental error. For the representative tunneling path (RTP) at 233 K, the pre- and post-tunneling configurations are 3.3 kcal/mol below the adiabatic energy maximum, where the hydrogen travels 0.54 ? by tunneling. We found that tunneling is very efficient for hydrogen transfer and that the RTP is very different from the MEP. It is mainly heavy atoms that move as the reaction proceeds from the reactant complex to the pretunneling configuration, and the hydrogen atom suddenly hops at that point.     

Magnetic properties of porous glass-CuO nanocomposites

The magnetization of the porous glass nanocomposite with CuO nanoparticles embedded in the pores has been studied in the temperature range from 1.8 to 350 K for different pore fillings. It has been shown that the magnetic properties of these nanocomposites depend significantly on pore filling. It has been found that, in the low-temperature range for the nanocomposite with a pore filling of 55% and for pressed CuO, the ZFC and FC susceptibilities diverge, a feature which has been almost absent in the nanocomposite with 21% filling. It has been demonstrated that the kink in the temperature dependence of magnetization, which corresponds to the paramagnetic-multiferroic phase transition, does not shift in the sample with a larger pore filling as compared to that observed in the bulk sample.     

Formation of copper(II) oxide nanostructures in porous glass as revealed by electrical conductivity measurements

Copper(II) oxide was synthesized in a glass matrix by multiple cycles of impregnation of porous glass with an aqueous solution of copper nitrate, followed by dehydration and thermal decomposition of the salt. The electrical conductivity and its temperature dependences, measured during the progressive accumulation of copper(II) oxide in porous glass, are indicative of a gradual change from chains to 2D structures, eventually resulting in a conductive oxide monolayer.