Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations.

NMR chemical shielding anisotropy (CSA) relaxation is an important tool in the study of dynamical processes in proteins and nucleic acids in solution. Herein, we investigate how dynamical variations in local geometry affect the chemical shielding anisotropy relaxation of the carbonyl carbon nucleus, using the following protocol: 1) Using density functional theory, the carbonyl (13)C' CSA is computed for 103 conformations of the model peptide group N-methylacetamide (NMA). 2) The variations in computed (13)C' CSA parameters are fitted against quadratic hypersurfaces containing cross terms between the variables. 3) The predictive quality of the CSA hypersurfaces is validated by comparing the predicted and de novo calculated (13)C' CSAs for 20 molecular dynamics snapshots. 4) The CSA fluctuations and their autocorrelation and cross correlation functions due to bond-length and bond-angle distortions are predicted for a chemistry Harvard molecular mechanics (CHARMM) molecular dynamics trajectory of Ca(2+)-saturated calmodulin and GB3 from the hypersurfaces, as well as for a molecular dynamics (MD) simulation of an NMA trimer using a quantum mechanically correct forcefield. We find that the fluctuations can be represented by a 0.93 scaling factor of the CSA tensor for both R(1) and R(2) relaxations for residues in helix, coil, and sheet alike. This result is important, as it establishes that (13)C' relaxation is a valid tool for measurement of interesting dynamical events in proteins.     

Multistep energy transfer in single molecular photonic wires

We demonstrate the synthesis and spectroscopic characterization of an unidirectional photonic wire based on four highly efficient fluorescence energy-transfer steps (FRET) between five spectrally different chromophores covalently attached to double-stranded DNA. The DNA-based modular conception enables the introduction of various chromophores at well-defined positions and arbitrary interchromophore distances. While ensemble fluorescence measurements show overall FRET efficiencies between 15 and 30%, single-molecule spectroscopy performed on four spectrally separated detectors easily uncovers subpopulations that exhibit overall FRET efficiencies of up to approximately 90% across a distance of 13.6 nm and a spectral range of approximately 200 nm. Fluorescence trajectories of individual photonic wires show five different fluorescence intensity patterns which can be ascribed to successive photobleaching events.     

Energetic and topological analysis of the reaction of Mo and Mo2 with NH3, C2H2, and C2H4 molecules

The Density functional theory has been applied to characterize the structural features of Mo(1,2)-NH(3),-C(2)H(4), and -C(2)H(2) compounds. Coordination modes, geometrical structures, and binding energies have been calculated for several spin multiplets. It has been shown that in contrast to the conserved spin cases (Mo(1,2)-NH(3)), the interaction between Mo (or Mo(2)) and C(2)H(4) (or C(2)H(2)) are the low-spin (Mo-C(2)H(4) and -C(2)H(2)) and high-spin (Mo(2)-C(2)H(4) and -C(2)H(2)) complexes. In the ground state of Mo(1,2)-C(2)H(4) and -C(2)H(2), the metal-center always reacts with the C-C center. The spontaneous formation of the global minima is found to be possible due to the crossing between the potential energy surfaces (ground and excited states with respect to the metallic center). The bonding characterization has been performed using the topological analysis of the Electron Localization Function. It has been shown that the most stable electronic structure for a pi-acceptor ligand correlates with a maximum charge transfer from the metal center to the C-C bond of the unsaturated hydrocarbons, resulting in the formation of two new basins located on the carbon atoms (away from hydrogen atoms) and the reduction of the number of attractors of the C-C basin. The interaction between Mo(1,2) and C(2)H(4) (or C(2)H(2)) should be considered as a chemical reaction, which causes the multiplicity change. Contrarily, there is no charge transfer between Mo(1,2) and NH(3), and the partners are bound by an electrostatic interaction.     

Ascorbate-induced oxidation of formate by peroxodisulfate: product yields,kinetics and mechanism

The slow reaction between peroxodisulfate and formate is significantly accelerated by ascorbate at room temperature. The products of this induced oxidation, CO₂ and oxalate (C₂O^2– ₄), were analyzed by several methods and the kinetics of this reaction were measured. The overall mechanism involves free radical species. Ascorbate reacts with peroxodisulfate to initiate production of the sulfate radical ion (SO^– ₄), which reacts with formate to produce carbon dioxide radical ion (CO^– ₂) and sulfate. The carbon dioxide radical reacts with peroxodisulfate to form CO₂ or self-combines to form oxalate. Competition occurring between these two processes determines the overall fate of the carbon dioxide radical species. As pH decreases, protonation of the carbon dioxide radical ion tends to favor production of CO₂.     

Efficient RNase H-directed cleavage of RNA promoted by antisense DNA or 2'F-ANA constructs containing acyclic nucleotide inserts

The ability of modified antisense oligonucleotides (AONs) containing acyclic interresidue units to support RNase H-promoted cleavage of complementary RNA is described. Manipulation of the backbone and sugar geometries in these conformationally labile monomers shows great benefits in the enzymatic recognition of the nucleic acid hybrids, while highlighting the importance of local strand conformation on the hydrolytic efficiency of the enzyme more conclusively. Our results demonstrate that the duplexes support remarkably high levels of enzymatic degradation when treated with human RNase HII, making them efficient mimics of the native substrates. Furthermore, interesting linker-dependent modulation of enzymatic activity is observed during in vitro assays, suggesting a potential role for this AON class in an RNase H-dependent pathway of controlling RNA expression. Additionally, the butyl-modified 2'F-ANA AONs described in this work constitute the first examples of a nucleic acid species capable of eliciting high RNase H activity while possessing a highly flexible molecular architecture at predetermined sites along the AON.     

Multiresidue determination of fluoroquinolones in shrimp by liquid chromatography-fluorescence-mass spectrometry

An efficient multiresidue method for analysis of fluoroquinolones in shrimp has been developed in which quantitation by fluorescence and confirmation by Multiple Stage Mass Spectrometry (MS) is achieved simultaneously. In this method, shrimp tissue is extracted with ammoniacal acetonitrile and the extract is defatted and then evaporated. After dissolution in basic phosphate buffer, fluoroquinolones in the extract are separated by liquid chromatography and quantitated, taking advantage of their intense fluorescence. Eluate from the fluorescence detector enters the MS, which allows for confirmation by monitoring ratios of 2 prominent product ions in the MS3 or MS2 spectrum. Using this method, 8 fluoroquinolones have been analyzed in shrimp samples fortified at 10, 25, 50, or 100 ppb levels. Recoveries for desethyleneciprofloxacin, norfloxacin, ciprofloxacin, danofloxacin, enrofloxacin, orbifloxacin, sarafloxacin, and difloxacin ranged from 75 to 92%, with relative standard deviation values of <6%. The limits of quantitation ranged from 0.1 to 1 ng/g. Enrofloxacin and ciprofloxacin were also successfully determined in enrofloxacin-incurred shrimp using this method.     

Radical copolymerization of citraconic acid with styrene in dioxane solution

Styrene and citraconic acid (CA) were copolymerized in the dioxane solution ranging mole fraction of CA in feed from 0.1 to 0.9 at 70 °C. The terminal and penultimate models were used to fit the copolymer composition equation. Curve fitting, Mayo-Lewis, Joshi-Joshi, Fineman-Ross, Ezrielev-Brokhina-Roskin, Kellen-Tüd?s methods were used to solve the copolymer equation in terminal model. Besides these methods Solver in Excel 97 was used to solve copolymer equation in terminal and penultimate models of copolymerization. Experimental mole fractions of CA and those predicted from both models are agreed within the precision of the method used for the copolymer analysis, so the copolymer composition does not permit a definite choice of the adequate copolymerization model.     

On the synthesis of 3(5)-carbomethoxy-4-hetarylpyrazoles

3(5)-Carbomethoxy-4-hetarylpyrazoles 3 can be obtained by the aromatization of the corresponding cis-3-benzamido-3-carbomethoxy-4-hetaryl-Δ¹-pyrazolines 2 obtained by 1,3-dipolar cycloaddition of diazo-methane with methyl Z-2-benzamido-3-hetarylpropenoates 1. An explanation, based on FMO theory, for the different reactivity of the dipolarophiles with diazomethane is given.     

Lipase from a Brazilian StrainPenicillium citrinum Cultured in a Simple and Inexpensive Medium st]Heat-Denaturation, Kinetics, and pH Stability

This work is a study of lipase production by a Brazilian strain ofPenicillium citrinum using an inexpensive and simple medium without organic nitrogen sources and of some important industrial properties, including thermostability in relation to ionic strength. The maximal lipase activity (1585 U/L) was obtained whenPenicillium citrinum was cultured on 0.75% ammonium sulfate complemented with minerals salts instead of yeast extract. Although this activity was about 55% lower than that produced in medium with yeast extract (2850 U/L), the specific activity (7.8 U/mg proteins) was higher than that obtained with the yeast extract (4.9 U/mg proteins). The morphology of fungus changed totally, with yeast extract there are smooth, solid, and spherical pellets whereas on ammonium sulfate there are small “hairy” pellets uniformly suspended in the medium. The effect of ferrous (Fe⁺⁺) ions was carried out using medium MA with and without Fe⁺⁺ ions. Lipase production byPenicillium citrinum in medium MA requires Fe⁺⁺ ions, the absence of which caused a decreased of about 50% in the specific activity (3.5 U/mg proteins). The utilization of commercial, locally available oils as carbon sources, such as soybean oil (236 U/L) and corn oil (74 U/L) resulted in lower activity compared to olive oil, showing that lipase production byPenicillium citrinum is specifically induced by olive oil. Potassium concentration in the medium can effects the production of lipase (1 mM (1585 U/L), 10 mM (1290 U/L), and 30 mM (1238 U/L), 50 mM (195 U/L), and 100 mM (2 U/L). The crude culture filtered was susceptable to thermal deactivation. It was stable at pH 6.0, but was not stable at the optimum pH (8.0-8.5) at 50 mM. At the low ionic concentration (1-25 mM) this lipase was stable at low pH (3.5-4.0). The activation energy was 22.4 ±2.2 Kcal. mol 1.     

Simultaneous determination of N-butylscopolamine and oxazepam in pharmaceutical formulations by first-order digital derivative spectrophotometry

A simple method has been developed for the simultaneous determination of N-butylscopolamine bromide and oxazepam in pharmaceutical formulations using first-order digital derivative spectrophotometry. Acetonitrile was selected as the solvent in which both compounds showed well-defined bands. Both analytes showed good stability in this solvent when solutions of the analytes were exposed to light and temperatures between 20 degrees and 80 degrees C. The simultaneous determination of both drugs was performed by the zero-crossing method at 226.0 and 257.0 nm for N-butylscopolamine and oxazepam, respectively. The linear range of determination was found to be 2.5 x 10(-7) to 8.0 x 10(-5) mol/L for N-butylscopolamine and 7.1 x 10(-8) to 8.0 x 10(-5) mol/L for oxazepam. A very good level of repeatability (relative standard deviation) of 0.2% was observed for N-butylscopolamine and oxazepam. The ingredients commonly found in pharmaceutical formulations do not interfere. The proposed method was applied to the determination of these drugs in pharmaceutical formulations (capsules).