Vibrational spectrum of BiH3: Six-dimensional variational calculations on high-level ab initio potential energy surfaces

We report a theoretical study of the ground electronic state of BiH₃. The potential energy surface (PES) is obtained from coupled cluster CCSD(T) calculations with a large basis set (289 contracted Gaussian functions). The previously available quartic force field (P4) is extended by adding the dominant quintic and sextic stretching terms to yield improved potential functions in symmetry coordinates (P6) and Morse-type coordinates (M4). Second-order rovibrational perturbation calculations on the P4-PES and full variational calculations on the P6-PES and M4-PES yield almost identical vibrational term values which is rationalized by considering the local mode behavior of BiH₃ and the Morse-type character of the M4-PES. The remaining deviations between the computed and observed vibrational term values must thus be caused by imperfections in the CCSD(T) surface. A refinement of this ab initio surface by a restrained fit to experimental data allows an essentially perfect reproduction of the observed vibrational term values. Variational calculations on this refined surface provide predictions for several overtone and combination bands that have not yet been observed. Dedicated to Hermann Stoll on the occasion of his 60th birthday     

Density functional energy decomposition into one- and two-atom contributions

The present work provides a generalization of Mayer's energy decomposition for the density-functional theory (DFT) case. It is shown that one- and two-atom Hartree-Fock energy components in Mayer's approach can be represented as an action of a one-atom potential V(A) on a one-atom density rho(A) or rho(B). To treat the exchange-correlation term in the DFT energy expression in a similar way, the exchange-correlation energy density per electron is expanded into a linear combination of basis functions. Calculations carried out for a number of density functionals demonstrate that the DFT and Hartree-Fock two-atom energies agree to a reasonable extent with each other. The two-atom energies for strong covalent bonds are within the range of typical bond dissociation energies and are therefore a convenient computational tool for assessment of individual bond strength in polyatomic molecules. For nonspecific nonbonding interactions, the two-atom energies are low. They can be either repulsive or slightly attractive, but the DFT results more frequently yield small attractive values compared to the Hartree-Fock case. The hydrogen bond in the water dimer is calculated to be between the strong covalent and nonbonding interactions on the energy scale.     

Fast centroid molecular dynamics: a force-matching approach for the predetermination of the effective centroid forces

A fast centroid molecular dynamics (CMD) methodology is proposed in which the effective centroid forces are predetermined through a force-matching algorithm applied to a standard path integral molecular dynamics simulation. The resulting method greatly reduces the computational cost of generating centroid trajectories, thus extending the applicability of CMD. The method is applied to the study of liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point. The static and dynamical results are compared to those obtained from full adiabatic CMD simulations and found to be in excellent agreement for all three systems; the transport properties are also compared to experiment and found to have a similar level of agreement.     

NMR studies of solid state—solvent and H/D isotope effects on hydrogen bond geometries of 1:1 complexes of collidine with carboxylic acids

¹H and ¹⁵N NMR spectra of 10 complexes exhibiting strong OHN hydrogen bonds formed by ¹⁵N-labeled collidine and different proton donors, partially deuterated in mobile proton sites, have been observed by low-temperature NMR spectroscopy using a low-freezing CDF₃/CDF₂Cl mixture as polar aprotic solvent. The following proton donors have been used: HCl, formic acid, acetic acid, various substituted benzoic acids and HBF₄. The slow hydrogen bond exchange regime could be reached below 140 K, which allowed us to resolve ¹⁵N signal splittings due to H/D isotopic substitution. The valence bond order model is used to link the observed NMR parameters to hydrogen bond geometries. The results are compared to those obtained previously [Magn. Reson. Chem. 39 (2001) S18] for the same complexes in the organic solids. The increase of the dielectric constant from the organic solids to the solution (30 at 130 K) leads to a change of the hydrogen bond geometries along the geometric correlation line towards the zwitterionic structures, where the proton is partially transferred from oxygen to nitrogen. Whereas the changes of spectroscopic and, hence, geometric parameters are small for the systems which are already zwitterionic in the solid state, large changes are observed for molecular complexes which exhibit almost a full proton transfer from oxygen to nitrogen in the polar liquid solvent.     

Formation of a stable cyano-bridged dinuclear iron cluster following oxidation of the superoxide reductases from Treponema pallidum and Desulfovibrio vulgaris with K(3)Fe(CN)(6)

Superoxide reductases catalyze the monovalent reduction of superoxide anion to hydrogen peroxide. Spectroscopic evidence for the formation of a dinuclear cyano-bridged adduct after K(3)Fe(CN)(6) oxidation of the superoxide reductases neelaredoxin from Treponema pallidum and desulfoferrodoxin from Desulfovibrio vulgaris was reported. Oxidation with K(3)Fe(CN)(6) reveals a band in the near-IR with lambda(max) at 1020 nm, coupled with an increase of the iron content by almost 2-fold. Fourier transform infrared spectroscopy provided additional evidence with CN-stretching vibrations at 2095, 2025-2030, and 2047 cm(-)(1), assigned to a ferrocyanide adduct of the enzyme. Interestingly, the low-temperature electronic paramagnetic resonance (EPR) spectra of oxidized TpNlr reveal at least three different species indicating structural heterogeneity in the coordination environment of the active site Fe ion. Given the likely 6-coordinate geometry of the active site Fe(3+) ion in the ferrocyanide adduct, we propose that the rhombic EPR species can serve as a model of a hexacoordinate form of the active site.     

New Derivatives of 5-Substituted Uracils: Potential Agents with a Wide Spectrum of Biological Activity

Pyrimidine nucleoside analogues are widely used to treat infections caused by the human immunodeficiency virus (HIV) and DNA viruses from the herpes family. It has been shown that 5-substituted uracil derivatives can inhibit HIV-1, herpes family viruses, mycobacteria and other pathogens through various mechanisms. Among the 5-substituted pyrimidine nucleosides, there are not only the classical nucleoside inhibitors of the herpes family viruses, 2′-deoxy-5-iodocytidine and 5-bromovinyl-2′-deoxyuridine, but also derivatives of 1-(benzyl)-5-(phenylamino)uracil, which proved to be non-nucleoside inhibitors of HIV-1 and EBV. It made this modification of nucleoside analogues very promising in connection with the emergence of new viruses and the crisis of drug resistance when the task of creating effective antiviral agents of new types that act on other targets or exhibit activity by other mechanisms is very urgent. In this paper, we present the design, synthesis and primary screening of the biological activity of new nucleoside analogues, namely, 5′-norcarbocyclic derivatives of substituted 5-arylamino- and 5-aryloxyuracils, against RNA viruses.     

Dynamics of charge transfer at Au/Si metal-semiconductor nano-interface

An ab initio analysis of the periodic array of Au/Si nanostructure composed of gold clusters linked to silicon quantum dot (QD) co-doped by aluminium and phosphorus along [111] direction is presented in this paper. The density functional theory (DFT) is used to compute the electronic structure of the simulated system. Non-adiabatic coupling implemented in the form of dissipative equation of motion for reduced density matrix is used to study the phonon-induced relaxation in the simulated system. The density of states clearly shows that the formation of Au–Si bonds contributes states to the band gap of the model. Dynamics of selected photo-excitations shows that hole relaxation in energy and in space is much faster than electron relaxation, which is due to the higher density of states of the valence band.     

Mechanistic studies on the reaction between glutathionylcobalamin and selenocysteine

Abstract

The reaction between glutathionylcobalamin (GSCbl), a complex of Co(III)-cobalamin with glutathione, and selenocysteine (Sec) was investigated using ultraviolet-visible (UV–vis) spectroscopy. The interaction results in the formation of cob(II)alamin and proceeds via two pathways: (i) a rapid formation of complex between GSCbl and Sec followed by the rate-determining substitution of glutathionyl-ligand by Sec and rapid electron-transfer from Se-atom to Co(III)-ion and (ii) a nucleophilic attack of Co(III)-S bond by Sec.     

Sonochemical reactions with mesoporous alumina

Herein, we report the sonochemical reactions with MSU-X mesoporous alumina (m-Al₂O₃) in aqueous solutions. Sonication (f = 20 kHz, I = 30 W cm^?2, W_aq = 0.67 W mL^?1, T = 36–38 °C, Ar) causes significant acceleration of m-Al₂O₃ dissolution in the pH range of 4–11. Moreover, power ultrasound has a dramatic effect on the textural properties and phase composition of m-Al₂O₃. Short-time sonication at pH = 4 leads to the formation of nanorods and nanofibers of boehmite, AlO(OH). Prolonged ultrasonic treatment causes high aspect morphology transformation to aggregated nanosheets in weakly acid solutions or plated nanocrystals in alkaline solutions. Sonochemical products in alkaline medium are composed principally from boehmite and small amounts of bayerite, Al(OH)₃. Silent hydrolysis of m-Al₂O₃ yields boehmite at pH = 4 and bayerite at pH = 11. The effect of ultrasound on the textural properties of mesoporous alumina as well as on the transformation of nanosized bayerite to boehmite can be consistently attributed to the transient strong heating of the liquid shell surrounding the cavitation bubble which caused the chemical processes similar to those occurred during hydrothermal treatment.     

Stacking-Conformations in Functionally Substituted Phosphines

The methods of synthesis and space structure of phosphorus-containing compounds, in which stacking conformation is realized, are considered. It is shown that intramolecular stacking can be observed in monoheterocyclic compounds, bi-and polycyclic compounds, complexes of metals and acyclic compounds.