Nitrogen defects in wide band gap oxides: defect equilibria and electronic structure from first principles calculations

The nitrogen related defect chemistry and electronic structure of wide band gap oxides are investigated by density functional theory defect calculations of N, NH, and as well as and in MgO, CaO, SrO, Al(2)O(3), In(2)O(3), Sc(2)O(3), Y(2)O(3), La(2)O(3), TiO(2), SnO(2), ZrO(2), BaZrO(3), and SrZrO(3). The N acceptor level is found to be deep and the binding energy of NH with respect to and is found to be significantly negative, i.e. binding, in all of the investigated oxides. The defect structure of the oxides was found to be remarkably similar under reducing and nitriding conditions (1 bar N(2), 1 bar H(2) and 1 × 10(-7) bar H(2)O): NH predominates at low temperatures and predominates at higher temperatures (>900 K for most of the oxides). Furthermore, we evaluate how the defect structure is affected by non-equilibrium conditions such as doping and quenching. In terms of electronic structure, is found to introduce isolated N-2p states within the band gap, while the N-2p states of NH are shifted towards, or overlap with the VBM. Finally, we assess the effect of nitrogen incorporation on the proton conducting properties of oxides and comment on their corrosion resistance in nitriding atmospheres in light of the calculated defect structures.     

Synthesis of 2,6-Dideoxy-6-Thio Derivatives of KDO

ABSTRACT

Ammonium 2,3,6-trideoxy-2,6-epithio-D-manno-2-octenoate (8), ammonium 2,3,6-trideoxy-2,6-epithio-D-glycero-D-talo-octanoate (10a), ammonium 2,3,6-trideoxy-2,6-epithio-D-glycero-D-galacto-octanoate (10b) and ammonium 2,3,6-trideoxy-2,6-epithio-oxa-D-glycero-D-galacto-octanoate (13) have been synthesised as potential inhibitors of the enzyme CMP-KDO synthetase. The key step in the synthesis of 8 was the elimination of water from methyl 3,6-dideoxy-4,5:7,8-di-O-isopropylidene-6-thio-D-manno-2-octulosonate (4) using chlorodiphenylphosphine, imidazole and bromine to give the unsaturated methyl 2,3,6-trideoxy-2,6-epithio-4,5:7,8-di-O-isopropylidene-D-manno-2-octenoate (5). For the synthesis of 10a and 10b, zinc reduction of methyl 3,6-dideoxy-4,5:7,8-di-O-isopropylidene-6-S-(4-methoxybenzyl)-6-thio-2-O-(trichloro-tert-butoxycarbonyl)-D-manno-2-octenoate (2) gave an epimeric mixture of an α-hydroxyester 6 which was ring closed by in situ activation of the hydroxyl group using triphenylphosphine and tri-iodoimidazole followed by cleavage of the p-methoxybenzyl group to give 7a and 7b, which then were deprotected to give 10a and 10b.     

Synthesis of C 2 Symmetric Potential Inhibitors of HIV-1 Protease From D-Mannitol

ABSTRACT

D-Mannitol was used as precursor for the synthesis of acyclic C ₂ symmetric potential HIV-1 protease inhibitors. The 1- and 6-hydroxy groups of D-mannitol were substituted by -NHBoc, -NHValZ, -SAr, -SOAr and -SO₂Ar and the 2-and 5-hydroxy groups were benzylated. In some products one of the central hydroxyl groups was either inverted or deoxygenated. Despite a close structural similarity to previously published inhibitors none of the products showed significant inhibitory activity against HIV-1 protease.

     

Quadracyclic adenine: a non-perturbing fluorescent adenine analogue

Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300?nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8?% with an emission maximum at 456?nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.     

Cyclodextrin-surfactant coassembly depends on the cyclodextrin ability to crystallize

Full equilibrium phase diagrams are presented for two ternary systems composed of the cationic surfactant dodecyltrimethylammonium bromide (DTAB), water (D(2)O), and a cyclodextrin, either β-cyclodextrin (β-CD) or (2-hydroypropyl)-β-cyclodextrin (2HPβCD). (2)H NMR, SAXS, WAXS, and visual examination were used to determine the phase boundaries and characterize the nature of the phases formed. Additionally, diffusion (1)H NMR was used to investigate parts of the diagrams. The water solubility of 2HPβCD is 80% (w/w), whereas it is only 1.85% (w/w) for β-CD. Solubility increases for both species upon complexation with DTAB; while the increase is minute for 2HPβCD, it is dramatic for β-CD. Both systems displayed an isotropic liquid solution (L(1)) one-phase region, the extension of which differs extensively between the two systems. Additionally, the DTAB:2HPβCD:water system also comprised a normal hexagonal (H(1)) area, which was not found for the DTAB:β-CD:water system. In the DTAB:β-CD:water system, on the other hand, we found cocrystallization of DTAB and β-CD. From this work we conclude that DTAB and CD molecules form 1:1 inclusion complexes with high affinities. Moreover, we observed indications of an association of 2HPβCD to DTAB micelles in the isotropic solution phase, which was not the case for β-CD and DTAB micelles. This is, to our knowledge, the first complete phase diagrams of surfactant-CD mixtures; as a novel feature it includes the observation of cocrystallization at high concentrations.     

Rigid orthogonal bis-TEMPO biradicals with improved solubility for dynamic nuclear polarization

The synthesis and characterization of oxidized bis-thioketal-trispiro dinitroxide biradicals that orient the nitroxides in a rigid, approximately orthogonal geometry are reported. The biradicals show better performance as polarizing agents in dynamic nuclear polarization (DNP) NMR experiments as compared to biradicals lacking the constrained geometry. In addition, the biradicals display improved solubility in aqueous media due to the presence of polar sulfoxides. The results suggest that the orientation of the radicals is not dramatically affected by the oxidation state of the sulfur atoms in the biradical, and we conclude that a biradical polarizing agent containing a mixture of oxidation states can be used for improved solubility without a loss in performance.     

Cyclic Ketones in Spiroannulation

Conversion of a cyclic carbonyl carbon into a quaternary carbon has been effected by a Wittig–Horner reaction with diethyl (N-benzyliden)aminomethylphosphonate and a subsequent alkylation with a protected vinyl ketone. The product was a substrate for spiroannulation after initial hydrolysis. The reaction sequence was carried out as a one-pot reaction.     

A theoretical determination of the electronic spectrum of formaldehyde

Summary The electronically excited states of formaldehyde are examined by means of multiconfigurational second-order perturbation (CASPT2) theory with extended ANO-type basis sets. The calculations comprised five valence excited states plus all singlet 3s, 3p, and 3d members of the Rydberg series converging on the first ionization. The computed vertical excitation energies were found to be within 0.2 eV of the available experimental energies. Full geometry optimization has been performed for five valence excited states. Assuming a planar geometry, the 0-0 transition for the valence¹A₁( *) state is calculated to appear near 7.9 eV, close to the (n _y 3p) region. This state is, however, not planar and the true adiabatic energy is 7.4 eV, which is 2.3 eV below the corresponding vertical transition.