Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in π-stacking and hydrogen-bonding behavior

We have investigated the performance of the dispersion-corrected density functionals (BLYP-D, BP86-D and PBE-D) and the widely used B3LYP functional for describing the hydrogen bonds and the stacking interactions in DNA base dimers. For the gas-phase situation, the bonding energies have been compared to the best ab initio results available in the literature. All dispersion-corrected functionals reproduce well the ab initio results, whereas B3LYP fails completely for the stacked systems. The use of the proper functional leads us to find minima for the adenine quartets, which are energetically and structurally very different from the C_4h structures, and might explain why adenine has to be sandwiched between guanine quartets to form planar adenine quartets.     

Identification of isomeric spin adducts of Leu-Tyr and Tyr-Leu free radicals using liquid chromatography-tandem mass spectrometry

Free radical species are generally short-lived due to their high reactivity and thus direct measurement and identification are often impossible. In this study we used a spin trap, 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), to trap radical intermediates formed during the oxidation of isomeric dipeptides tyrosine-leucine (Tyr-Leu) and leucine-tyrosine (Leu-Tyr), induced by the hydroxyl radical. To investigate the influence of the amino acid position in the peptide chain on the oxidation and free radical generation, the spin adducts were characterized using LC-MS and MS(n) . We detected carbon and oxygen DMPO adducts and adducts bearing two DMPO, which were analyzed by MS(n) . Both alkoxyl and peroxyl radicals were identified. Radical intermediates were localized in Tyr during oxidation of Tyr-Leu, while radicals were identified in Leu and Tyr during oxidation of Leu-Tyr. DMPO adducts of acyl radical species formed from cleavage of the peptide backbone, promoted by the alkoxyl radical in α carbon of the N-terminal amino acid were observed. The results show that the amino acid position has an influence in the oxidation process, at least on small peptides, and that the α carbon of the N-terminal amino acid is more vulnerable to the attack of the electrophilic hydroxyl radical.     

The use of imidazolium ionic liquids for the formation and stabilization of ir0 and rh0 nanoparticles: efficient catalysts for the hydrogenation of arenes

Stable transition-metal nanoparticles of the type [M(0)](n) are easily accessible through the reduction of Ir(I) or Rh(III) compounds dissolved in "dry" 1-n-butyl-3-methylimidazolium hexafluorophosphate ionic liquid by molecular hydrogen. The formation of these [M(0)](n) nanoparticles is straightforward; they are prepared in dry ionic liquid whereas the presence of the water causes the partial decomposition of ionic liquid with the formation of phosphates, HF and transition-metal fluorides. Transmission electron microscopy (TEM) observations and X-ray diffraction analysis (XRD) show the formation of [Ir(0)](n) and [Rh(0)](n) nanoparticles with 2.0-2.5 nm in diameter. The isolated [M(0)](n) nanoparticles can be redispersed in the ionic liquid, in acetone or used in solventless conditions for the liquid-liquid biphasic, homogeneous or heterogeneous hydrogenation of arenes under mild reaction conditions (75 degrees C and 4 atm). The recovered iridium nanoparticles can be reused several times without any significant loss in catalytic activity. Unprecedented total turnover numbers (TTO) of 3509 in 32 h, for arene hydrogenation by nanoparticles catalysts, have been achieved in the reduction of benzene by the [Ir(0)](n) in solventless conditions. Contrarily, the recovered Rh(0) nanoparticles show significant agglomeration into large particles with a loss of catalytic activity. The hydrogenation of arenes containing functional groups, such as anisole, by the [Ir(0)](n) nanoparticles occurs with concomitant hydrogenolysis of the C-O bond, suggesting that these nanoparticles behave as "heterogeneous catalysts" rather than "homogeneous catalysts".     

Bis[N,N′‐diisopropylbenzamidinato(−)]silicon(II): Lewis Acid/Base Reactions with Triorganylboranes

Reaction of the donor‐stabilized silylene 1 (which is three‐coordinate in the solid state and four‐coordinate in solution) with BEt₃ and BPh₃ leads to the formation of the Lewis acid/base complexes 2 and 3 , respectively, which are the first five‐coordinate silicon compounds with an Si?B bond. These compounds were structurally characterized by crystal structure analyses and by multinuclear NMR spectroscopic studies in the solid state and in solution. Additionally, the bonding situation in 2 and 3 was analyzed by quantum chemical studies.     

Kinetics of dehydration and textural characterizations of selectively leached vermiculites

Acid leaching of aluminosilicates is an interesting procedure for preparing high surface porous silica. Thermal behavior of vermiculite leached with a nitric acid solution at various concentrations was studied by thermogravimetry and differential scanning calorimetry. Activation energies of the dehydration process in selected temperature zones were determined by two different methods: Ozawa–Flynn–Wall and Friedman. The material obtained was characterized through Fourier transform infrared spectroscopy, X-ray diffraction, and nitrogen adsorption at 77 K to relate them to the estimated activation energies.     

Six‐Coordinate Group 13 Complexes: The Role of d Orbitals and Electron‐Rich Multi‐Center Bonding

Bonding in six‐coordinate complexes based on Group 13 elements (B, Al, Ga, In, Tl) is usually considered to be identical to that in transition‐metal analogues. We herein demonstrate through sophisticated electronic‐structure analyses that the bonding in these Group 13 element complexes is fundamentally different and better characterized as electron‐rich hypervalent bonding with essentially no role for the d orbitals. This characteristic is carried through to the molecular properties of the complex.     

A Highly Stabilizing Silver(I)‐Mediated Base Pair in Parallel‐Stranded DNA

The first parallel‐stranded DNA duplex with Hoogsteen base pairing that readily incorporates an Ag⁺ ion into an internal mispair to form a metal‐mediated base pair has been created. Towards this end, the highly stabilizing 6 FP ‐Ag⁺‐ 6 FP base pair comprising the artificial nucleobase 6‐furylpurine ( 6 FP ) was devised. A combination of temperature‐dependent UV spectroscopy, CD spectroscopy, and DFT calculations was used to confirm the formation of this base pair. The nucleobase 6 FP is capable of forming metal‐mediated base pairs both by the Watson–Crick edge (i.e. in regular antiparallel‐stranded DNA) and by the Hoogsteen edge (i.e. in parallel‐stranded DNA), depending on the oligonucleotide sequence and the experimental conditions. The 6 FP ‐Ag⁺‐ 6 FP base pair within parallel‐stranded DNA is the most strongly stabilizing Ag⁺‐mediated base pair reported to date for any type of nucleic acid, with an increase in melting temperature of almost 15 °C upon the binding of one Ag⁺ ion.     

On a new semi‐empirical electrotopological index for QSRR models

A new semi‐empirical electrotopological index, I_SET, for quantitative structure–retention relationships (QSRR) models was developed based on the refinement of the previously published semi‐empirical topological index, I_ET. We demonstrate that the values of C_i fragments that were firstly attributed from the experimental chromatographic retention and theoretical deductions have an excellent relationship with the net atomic charge of the carbon atoms. Thus, the values attributed to the vertices in the hydrogen‐suppressed graph of carbon atoms (C_i) are calculated from the correlation of the net atomic charge in each carbon atom, which is obtained from quantum chemical semi‐empirical calculations, and the C_i fragments for primary, secondary, tertiary and quaternary carbon atoms (1.0, 0.9, 0.8 and 0.7, respectively) obtained from the experimental values. This shows that I_ET encoded this quantum physical reality and that it is possible to calculate a new I_SET (the semi‐empirical electrotopological index) through the net atomic charge values obtained from a Mulliken population analysis using the semi‐empirical AM1 method and their correlation with the values attributed to the different types of carbon atoms. This demonstrates that the I_SET encodes information on the charge distribution of the solute on which dispersive and electrostatic interactions between the solute (alkanes and alkenes) and the stationary phase strongly depend. Thus, this new method can be considered as an initial step towards forthcoming QSRR/QSAR studies. Copyright © 2008 John Wiley & Sons, Ltd.