Multilevel and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer

Five multilevel model chemistries (CBS-QB3, G3B3, G3MP2B3, MCG3/3, and MC-QCISD/3) and seven hybrid density functional methods (PBE0, B1B95, B3LYP, MPW1KCIS, PBE1KCIS, and MPW1B95) have been applied to the calculation of gas-phase basicity and proton affinity values for a series of 17 molecules relevant to the study of biological phosphoryl transfer. In addition, W1 calculations were performed on a subset of molecules. The accuracy of the methods was assessed and the nature of systematic errors was explored, leading to the introduction of a set of effective bond enthalpy and entropy correction terms. The multicoefficient correlation methods (MCG3/3 and MC-QCISD), with inclusion of specific zero-point scale factors, slightly outperform the other multilevel methods tested (CBS-QB3, G3B3, and G3MP2B3), with significantly less computational cost, and in the case of MC-QCISD, slightly less severe scaling. Four density functional methods, PBE1KCIS, MPW1B95, PBE0, and B1B95 perform nearly as well as the multilevel methods. These results provide an important set of benchmarks relevant to biological phosphoryl transfer reactions.     

Fluorous phase-transfer activation of catalysts: application of a new rate-enhancement strategy to alkene metathesis

Reactions of the bis(pyridine) complex (H2IMes)(Py)2(Cl)2Ru(=CHPh) and fluorous phosphines P(CH2CH2R(fn))3 (n = a, 6; b, 8; c, 10; R(fn) = (CF2)(n-1)CF3) give (H2IMes)(P(CH2CH2R(fn))3)(Cl)2Ru(=CHPh) (2a-c, 64-73%), which are analogs of Grubbs' second generation catalyst and effective alkene metathesis catalysts under organic monophasic and fluorous/organic biphasic conditions. The latter give rate accelerations, which are believed to arise from phase transfer of the dissociated fluorous phosphine.     

Sparkle/AM1 structure modeling of lanthanum (III) and lutetium (III) complexes

The sparkle/AM1 model for the quantum chemical prediction of coordination polyhedron crystallographic geometries from isolated lanthanide complex ion calculations, defined recently for Eu(III), Gd(III), and Tb(III) (Inorg. Chem. 2005, 44, 3299) is now extended to La(III) and Lu(III). Thus, for each of the metal ions we chose a training set of 15 complexes that possess various representative ligands of high crystallographic quality (R factor < 0.05 Angstroms) and oxygen and/or nitrogen as coordinating atoms. In the validation procedure we used a set of 60 more La(III) coordination compound structures, as well as 15 more Lu(III) coordination compound structures, all of high crystallographic quality. For both the 75 La(III) compounds and the 30 Lu(III) compounds, the Sparkle/AM1 unsigned mean error, for all interatomic distances between the metal ions and the ligand atoms of the first sphere of coordination, is 0.08 Angstroms, thus comparable to the accuracy normally achievable by present day ab initio/ECP calculations, while being hundreds of times faster.     

Computational study on the bond dissociation enthalpies in the enolic and ketonic forms of beta-diketones: their influence on metal-ligand bond enthalpies

A computational study on the thermodynamic properties of 13 beta-diketones is presented. The B3LYP//6-311+G(2d,2p)//B3LYP/6-31G(d) theoretical approach was employed to compute the O-H and C-H bond dissociation enthalpies and enthalpy of tautomerization and to estimate standard gas-phase enthalpies of formation for the radicals and for the parent molecules. The gas-phase enthalpies of formation for the neutral molecules are in excellent agreement with available experimental data, supporting the estimates made for the radicals. The latter are very important for the clarification of the thermochemistry of many beta-diketonato metal complexes previously reported in the literature. Importantly, when substituents R = -CHR' are attached to the beta-diketone's scaffold, C-H homolytic bond cleavage is always favored with respect to O-H bond scission.     

On a lemma due to Ladyzhenskaya and Solonnikov and some applications

We present some applications of a lemma by Ladyzhenskaya and Solonnikov [Determination of solutions of boundary value problems for stationary Stokes and Navier–Stokes equations having an unbounded Dirichlet integral, Zap. Nauchn. Sem. Leningrad. Otdel. Mat. Inst. Steklov. (LOMI) 96 (1980) 117–160 (English Transl.: J. Soviet Math. 21 (1983) 728–761)]. Some other results in that paper referring to stationary Navier–Stokes equations are extended to a non-Newtonian fluid, the so-called micropolar fluid. This model depends on the microrotational viscosity _νr${\nu }_{\mathrm{r}}$ which vanishes for a Navier–Stokes fluid. We use the lemma in full to show that, as _νr${\nu }_{\mathrm{r}}$ tends to zero, the solutions of the Ladyzhenskaya–Solonnikov problem converge to the solutions of the corresponding problem for Navier–Stokes equations. In addition, we obtain a similar convergence regarding the Leray problem for micropolar fluids.     

Niobian iron oxides as heterogeneous Fenton catalysts for environmental remediation

Heterogeneous Fenton or Fenton-like reagents consist of a mixture of an iron-containing solid matrix and a liquid medium with H₂O₂. The Fenton system is based on the reaction between Fe^2?+? and H₂O₂ to produce highly reactive intermediate hydroxyl radicals (^???OH), which are able to oxidize organic contaminants, whereas the Fenton-like reaction is based on the reaction between Fe^3?+? and H₂O₂. These heterogeneous systems offer several advantages over their homogeneous counterparts, such as no sludge formation, operation at near-neutral pH and the possibility of recycling the iron promoter. Some doping transition cations in the iron oxide structure are believed to enhance the catalytic efficiency for the oxidation of organic substrates in water. In this work, goethites synthesized in presence of niobium served as precursors for the preparation of magnetites (niobian magnetites) via chemical reduction with hydrogen at 400°C. These materials were used as Fenton-like catalysts. Both groups of (Nb, Fe)-oxide samples were characterized by ⁵⁷Fe Mössbauer spectroscopy at 298 K. The results show that increasing niobium contents raise the catalytic potential for decomposition of methylene blue, which was, in this work, used as a model molecule for organic substrates in water.     

Effects of pressure on maghemite nanoparticles with a core/shell structure

The magnetic property and intraparticle structure of the γ phase of Fe₂O₃ (maghemite) nanoparticles with a diameter (D) of 5.1±0.5 nm were investigated through AC and DC magnetic measurements and powder X-ray diffraction (XRD) measurements at pressures (P) up to 27.7 kbar. Maghemite originally exhibits ferrimagnetic ordering below 918 K, and has an inverse-spinel structure with vacancies. Maghemite nanoparticles studied here consist of a core with structural periodicity and a disordered shell without the periodicity, and core shows superparamagnetism. The DC and AC susceptibilities reveal that the anisotropy energy barrier (ΔE/k_B) and the effective value of the core moment decrease against the initial pressure (P≤3.8 kbar), recovering at P≥3.8 kbar. The change of ΔE/k_B with P is qualitatively identical with that of the core moment, suggesting a down-and-up fluctuation of the number of Fe³⁺ ions constituting the core at the pressure threshold of about 4 kbar. This phenomenon was confirmed by the analysis of the XRD measurement using Scherrer’s formula. The core volume decreased for P≤2.5 kbar, whereas at higher pressure the core was restructured. For 2.5≤P≤10.7 kbar, the volume shrinkage of particle hardly occurs. There, ΔE/k_B is approximately proportional to the volume associated to the ordered fraction of the nanoparticles as seen from XRD, V_core. From this dependence it is possible to separate the core/shell contribution to ΔE/k_B and estimate core and surface anisotropy constants. As for the structural experiments, similar experimental data have been obtained for D=12.8±3.2 nm as well.     

Negative c-axis magnetoresistance in graphite

We have studied the c-axis interlayer magnetoresistance (ILMR), Rc(B) in graphite. The measurements have been performed on strongly anisotropic highly oriented pyrolytic graphite (HOPG) and single crystalline Kish graphite samples in magnetic field up to B=9 T, and the temperature interval 2 K?T?300 K. We have observed negative magnetoresistance, dRc/dB<0, for B‖c-axis for both samples above a certain field Bm(T)>5.4 T and 0.2 T for HOPG and Kish graphite, respectively. The results can be understood consistently by assuming that ILMR is related to a tunneling between zero-energy Landau levels of quasi-two-dimensional Dirac fermions, in a close analogy with the behavior reported for α-(BEDT-TTF)₂I₃ [N. Tajima, et al., Phys. Rev. Lett. 102 (2009) 176403], another multilayer Dirac electron system.     

Confirming the lattice contraction in CdSe nanocrystals grown in a glass matrix by Raman scattering

This work gives the evidence of the lattice contraction in CdSe nanocrystals (NCs) grown in a glass matrix. The CdSe NCs were investigated by atomic force microscopy (AFM), optical absorption (OA), and Raman spectroscopy. The average size of CdSe NCs can be estimated by AFM images. Using the OA spectra and the effective‐mass approximation, it was also possible to estimate the average sizes of CdSe NCs, which agree very well with the AFM data. These results showed that the CdSe NCs grow with increasing time of heat treatment. The blue shift of the longitudinal optical (LO) modes and surface optical (SO) phonon modes with an increase in the average radius of the NCs, shown in the Raman spectra, was explained by the lattice contraction in CdSe NCs caused by thermodynamic interactions at the interface with the host glass matrix. Copyright © 2010 John Wiley & Sons, Ltd.