A double-stranded molecular probe for homogeneous nucleic acid analysis

This paper reports the design and optimization of a double-stranded molecular probe for homogeneous detection of specific nucleotide sequences. The probes are labeled with either a fluorophore or a quencher such that the probe hybridization brings the two labels into close proximity, and this diminishes the fluorescence signal in the absence of a target. In the presence of a target, the fluorophore probe is thermodynamically driven to unzip from its hybridized form and bind with the target. An equilibrium analysis, which successfully describes all the major features of the assay without any fitting parameter, is performed to generalize the design of the probe. Several key parameters affecting the performance of the assay are examined. We show that the dynamic range and the signal-to-noise ratio of the assay can be optimized by the probe concentration, the quencher-to-fluorophore ratio, and the probe strand sequence. By proper design of the sequence, the probe discriminates single nucleotide mismatches in a single step without any separation step or measurement of melting profile.     

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...     

Full spin-orbit configuration interaction calculations on electronic states of LiBe

Ab initio calculations are reported for the simplest heteronuclear metal cluster, LiBe. Full spin-orbit configuration interaction calculations in the context of relativistic effective core potentials lead to accurate potential energy curves for low-lying states. Results are compared with recent experimental observations and with all electron multi-reference configuration interaction calculations.     

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.     

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.     

Mechanochemical Modification of Deoxypeganine Hydrochloride by Polyampholite

The solubility and dialysis of deoxypeganine hydrochloride and natural polyampholite were studied by IR spectra and x-ray diffraction analysis. Inclusion complexes form during mechanical treatment of a 1:1 mixture of deoxypeganine hydrochloride and natural polyampholite