Electronic and adsorption properties of Ce‐Ag layers

Silver has rarely been considered as the catalyst for CO oxidation, although it has been recognized to be very active in several partial oxidation reactions such as ethylene epoxidation and formaldehyde synthesis. It is generally believed that a metal support interaction plays an important role in catalytic processes. Therefore in our study, we examined electronic and adsorption properties of cerium deposited onto a polycrystalline silver substrate. Layers of approximately one monolayer of cerium deposited on a clean silver substrate were examined in situ using surface‐sensitive techniques—by XPS, ultraviolet photoelectron spectroscopy (UPS) and low energy ion scattering (LEIS). CO molecular adsorption was observed by UPS and LEIS; experimental results exhibited CO adsorption on Ce atoms sites. Oxygen adsorption on deposited layers led to a strong oxidation; stoichiometry of oxidized layers was given by amount of adsorbed oxygen and by temperature. Copyright © 2011 John Wiley & Sons, Ltd.     

Tautomerism of xanthine: The second-order MØller-Plesset study

Four 9H and four 7H tautomers of DNA base xanthine were studied by the ab initio LCAO-MO method at the MP2/6-311G^**//HF/6-31G^** and MP2/6-31G^**//HF/6-31G^** approximations. All calculated structures are minima at the HF/6-31G^** potential energy surface with the dioxo 7H tautomer (A1) being the global minimum. The second most stable tautomer, dioxo-9H (B1) is by 9 kcal/mol less stable. For the A1 B1 transition the calculated MP2 energy gap corresponds to the equilibrium constant of 2 × 10^–7. Therefore, only the major tautomeric form A1 is predicted to be detectable in the gas phase. The 7H and 9H groups of tautomers are discussed separately. Within both groups, the dioxo form (A1-7H, B1-9H) is the most stable one and is succeeded by the 2-dihydroxy (A2, B2) form. However, while the energy difference between A1 and A2 is 10 kcal/mol, the energy difference between B1 a B2 is only 2 kcal/mol. The effect of polar environment was estimated by the SCRF method, using a spherical cavity, at the HF/6-31G^** level. These calculations did not change the gas phase stability order of the tautomers. However, the energy difference between A1 and B1 decreased from 9 kcal/mol at the HF/6-31G^** level to 4 kcal/mol at the SCRF HF/6-31G^** level.     

Thermal analysis methods in the characterization of photocatalytic titania precursors

A new method for the preparation of titania photocatalyst was proposed. Precursors of the photoactive titania were prepared from TiOSO₄·nH₂O solution by precipitation with ammonia and addition of H₂O₂ or HNO₃, respectively. Methods of TG, DTA, ETA, EGA/MS detection and FTIR were used to characterize the thermal degradation of the titania precursor and to determine the optimal temperature to obtain the photoactive titania. ETA made it possible to characterize the microstructure development of the samples in the heating conditions.     

Expression and Structure/Function Relationships of Human Defensin 5

The innate immunity utilizes a battery of broad-spectrum antibacterial cationic polypeptides (3–5 kDa), among them defensins. In humans, defensins are the first line of defense against pathogens and their expression has been implicated in several diseases. The antibacterial activity of defensins is generally ascribed to their overall positive charge, which enables them to disrupt bacterial membrane integrity and function, but their active surface has not been fully elucidated. To perform structural and functional assays, an efficient, high-yield, easy-to-use expression and purification system must be established. Up to now, most efforts to obtain larger quantities of active recombinant defensins have been only moderately successful. Herein, we report the establishment of an efficient, high-yield expression and purification system for human defensin 5 (HD-5). Using site-directed mutagenesis, we pinpoint several arginine residues and Y27 as important for HD-5 antibacterial activity. Our expression and purification system can be harnessed for structure/activity relationship studies of defensins in particular and small polypeptides in general.     

Determining the absolute configuration of two marine compounds using vibrational chiroptical spectroscopy

Chiroptical techniques are increasingly employed for assigning the absolute configuration of chiral molecules through comparison of experimental spectra with theoretical predictions. For assignment of natural products, electronic chiroptical spectroscopies such as electronic circular dichroism (ECD) are routinely applied. However, the sensitivity of electronic spectral parameters to experimental conditions and the theoretical methods employed can lead to incorrect assignments. Vibrational chiroptical methods (vibrational circular dichroism, VCD, and Raman optical activity, ROA) provide more reliable assignments, although they, in particular ROA, have been little explored for assignments of natural products. In this study, the ECD, VCD, and ROA chiroptical spectroscopies are evaluated for the assignment of the absolute configuration of a highly flexible natural compound with two stereocenters and an asymmetrically substituted double bond, the marine antibiotic Synoxazolidinone A (SynOxA), recently isolated from the sub-Arctic ascidian Synoicum pulmonaria. Conformationally averaged nuclear magnetic resonance (NMR), ECD, Raman, ROA, infrared (IR) and VCD spectral parameters are computed for the eight possible stereoisomers of SynOxA and compared to experimental results. In contrast to previously reported results, the stereochemical assignment of SynOxA based on ECD spectral bands is found to be unreliable. On the other hand, ROA spectra allow for a reliable determination of the configuration at the double bond and the ring stereocenter. However, ROA is not able to resolve the chlorine-substituted stereogenic center on the guanidinium side chain of SynOxA. Application of the third chiroptical method, VCD, indicates unique spectral features for all eight SynOxA isomers in the theoretical spectra. Although the experimental VCD is weak and restricted by the limited amount of sample, it allows for a tentative assignment of the elusive chlorine-substituted stereocenter. VCD chiroptical analysis of a SynOxA derivative with three stereocenters, SynOxC, results in the same absolute configuration as for SynOxA. Despite the experimental challenges, the results convincingly prove that the assignment of absolute configuration based on vibrational chiroptical methods is more reliable than for ECD.     

Determination of 1-hydroxypyrene in human urine by HPLC with electrochemical detection at a boron-doped diamond film electrode

A high-performance liquid chromatographic method with electrochemical detection (HPLC-ED) at a boron-doped diamond film electrode with preliminary separation and preconcentration by solid-phase extraction (SPE) has been developed for the determination of 1-hydroxypyrene (1-HP) in human urine. 1-HP is among the most widely used biomarkers of exposure to polycyclic aromatic hydrocarbons. Optimal HPLC-ED conditions have been found: mobile phase methanol-0.05 mol L(-1) phosphate buffer pH 5.0 (80:20, v/v), detection potential +1,000 mV versus Ag/AgCl (3 mol L(-1) KCl), and flow rate 0.8 mL min(-1). For SPE, LiChrolut(?) RP-18 E cartridges were used. The extraction yield was (87.0 ± 5.8)% (n = 5). The concentration dependence of 1-HP was measured in the concentration range from 0.01 to 10 μmol L(-1) (2.18-2,180 μg L(-1)) using methanolic solutions resulting from the SPE pretreatment of spiked human urine samples. The limit of detection (signal-to-noise ratio 3) and the limit of quantification (signal-to-noise ratio 10) of the biomarker were 0.013 μmol L(-1) (2.84 μg L(-1)) and 0.043 μmol L(-1) (9.39 μg L(-1)), respectively, which is sufficient for its determination in the urine of persons exposed to polycyclic aromatic hydrocarbons.     

Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment

NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1) H and (13) C?NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13) C and (1) H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.     

Platinum-modified adenines: unprecedented protonation behavior revealed by NMR spectroscopy and relativistic density-functional theory calculations

Two novel Pt(IV) complexes of aromatic cytokinins with possible antitumor properties were prepared by reaction of selected aminopurines with K(2)PtCl(6). The structures of both complexes, 9-[6-(benzylamino)purine] pentachloroplatinate (IV) and 9-[6-(furfurylamino)purine] pentachloroplatinate (IV), were characterized in detail by using two-dimensional NMR spectroscopy ((1)H, (13)C, (15)N, and (195)Pt) in solution and CP/MAS NMR techniques in the solid state. We report for the first time the X-ray structure of a nucleobase adenine derivative coordinated to Pt(IV) via the N9 atom. The protonation equilibria for the complexes in solution were characterized by using NMR spectroscopy (isotropic chemical shifts and indirect nuclear spin-spin coupling constants) and the structural conclusions drawn from the NMR analysis are supported by relativistic density-functional theory (DFT) calculations. Because of the presence of the Pt atom, hybrid GGA functionals and scalar-relativistic and spin-orbit corrections were employed for both the DFT calculations of the molecular structure and particularly for the NMR chemical shifts. In particular, the populations of the N7-protonated and neutral forms of the complexes in solution were characterized by correlating the experimental and the DFT-calculated NMR chemical shifts. In contrast to the chemical exchange process involving the N7-H group, the hydrogen atom at N3 was determined to be unexpectedly rigid, probably because of the presence of the stabilizing intramolecular interaction N3-H···Cl. The described methodology combining the NMR spectroscopy and relativistic DFT calculations can be employed for characterizing the tautomeric and protonation equilibria in a large family of transition-metal-modified purine bases.     

Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study

Molecular dynamics (MD) simulations of single-stranded (ss) and double-stranded (ds) oligonucleotides anchored via an aliphatic linker to a graphene surface were performed in order to investigate the role of the surface charge density in the structure and orientation of attached DNA. Two types of interactions of DNA with the surface are crucial for the stabilisation of the DNA-surface system. Whereas for a surface with a zero or low positive charge density the dispersion forces between the base(s) and the surface dominate, the higher charge densities applied on the surface lead to a strong electrostatic interaction between the phosphate groups of DNA, the surface and the ions. At high-charge densities, the interaction of the DNA with the surface is strongly affected by the formation of a low-mobility layer of counterions compensating for the charge of the surface. A considerable difference in the behaviour of the ds-DNA and ss-DNA anchored to the layer was observed. The ds-DNA interacts with the surface at low- and zero-charge densities exclusively by the nearest base pair. It keeps its geometry close to the canonical B-DNA form, even at surfaces with high-charge densities. The ss-DNA, owing to its much higher flexibility, has a tendency to maximise the attraction to the surface exploiting more bases for the interaction. The interaction of the polar amino group(s) of the base(s) of ss-DNA with a negatively charged surface also contributes significantly to the system stability.     

Synthesis and characterization of γ-Fe2O3/carbon hybrids and their application in removal of hexavalent chromium ions from aqueous solutions

Magnetic Fe(2)O(3)/carbon hybrids were prepared in a two-step process. First, acetic acid vapor interacted with iron cations dispersed on the surface of a nanocasted ordered mesoporous carbon (CMK-3). In the second step, the primarily created iron acetate species underwent pyrolysis and transformed to magnetic iron oxide nanoparticles. X-ray diffraction, Fourier-transform infrared, and Raman spectroscopies were used for the chemical and structural characterization of the hybrids, while surface area measurements, thermal analysis, and transmission electron microscopy were employed to determine their physical, surface, and textural properties. These results revealed the preservation of the host carbon structure, which was homogenously and controllably loaded (up to 27 wt %) with nanosized (ca. 20 nm) iron oxides inside the mesoporous system. M?ssbauer spectroscopy and magnetic measurements at low temperatures confirmed the formation of γ-Fe(2)O(3) nanoparticles exhibiting superparamagnetic behavior. The kinetic studies showed a rapid removal of Cr(VI) ions from the aqueous solutions in the presence of these magnetic mesoporous hybrids and a considerably increased adsorption capacity per unit mass of sorbent in comparison to that of pristine CMK-3 carbon. The results also indicate highly pH-dependent sorption efficiency of the hybrids, whereas their kinetics was described by a pseudo-second-order kinetic model. Taking into account the simplicity of the synthetic procedure and possibility of magnetic separation of hybrids with immobilized pollutant, the developed mesoporous nanomaterials have quite real potential for applications in water treatment technologies.