NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains

Polymers of N-substituted glycines (“peptoids”) containing chiral centers at the α position of their side chains can form stable structures in solution. We studied a prototypical peptoid, consisting of five para-substituted (S)-N-(1-phenylethyl)glycine residues, by NMR spectroscopy. Multiple configurational isomers were observed, but because of extensive signal overlap, only the major isomer containing all cis-amide bonds was examined in detail. The NMR data for this molecule, in conjunction with previous CD spectroscopic results, indicate that the major species in methanol is a right-handed helix with cis-amide bonds. The periodicity of the helix is three residues per turn, with a pitch of ≈6 Å. This conformation is similar to that anticipated by computational studies of a chiral peptoid octamer. The helical repeat orients the amide bond chromophores in a manner consistent with the intensity of the CD signal exhibited by this molecule. Many other chiral polypeptoids have similar CD spectra, suggesting that a whole family of peptoids containing chiral side chains is capable of adopting this secondary structure motif. Taken together, our experimental and theoretical studies of the structural properties of chiral peptoids lay the groundwork for the rational design of more complex polypeptoid molecules, with a variety of applications, ranging from nanostructures to nonviral gene delivery systems.

NMR investigation of ferricytochrome c unfolding: Detection of an equilibrium unfolding intermediate and residual structure in the denatured state

Horse ferricytochrome c (cyt c) undergoes exchange of one of its axial heme ligands (Met-80) for one or more non-native ligands under denaturing conditions. We have used 1H NMR spectroscopy to detect two conformations of paramagnetic cyt c with non-native heme ligation through a range of urea concentrations. One non-native form is an equilibrium unfolding intermediate observed under partially denaturing conditions and is attributed to replacement of Met-80 with one or more Lys side chains. The second non-native form, in which the native Met ligand is replaced by a His, is observed under strongly denaturing conditions. Thermodynamic analysis of these data indicates a relatively small ΔG (17 kJ/mol) for the transition from native to the Lys-ligated intermediate and a significantly larger ΔG (47 kJ/mol) for the transition from native to the His-ligated species. Although CD and fluorescence data indicate that the equilibrium unfolding of cyt c is a two-state process, these NMR results implicate an intermediate with His-Lys ligation.

Observation via one-dimensional 13Calpha NMR of local conformational substates in thermal unfolding equilibria of a synthetic analog of the GCN4 leucine zipper.

Synthesis of a 33-residue, capped leucine zipper analogous to that in GCN4 is reported. Histidine and arginine residues are mutated to lysine to reduce the unfolding temperature. CD and ultracentrifugation studies indicate that the molecule is a two-stranded coiled coil under benign conditions. Versions of the same peptide are made with 99% 13Calpha at selected sites. One-dimensional 13C NMR spectra are assigned by inspection and used to study thermal unfolding equilibria over the entire transition from 8 to 73 degrees C. Spectra at the temperature extremes establish the approximate chemical shifts for folded and unfolded forms at each labeled site. Resonances for each amino acid appear at both locations at intermediate T, indicating that folded and unfolded forms interconvert slowly (> >2 ms) on the NMR time scale. Moreover, near room temperature, the structured form's resonance is double at several, but not all, sites, indicating at least two slowly interconverting, structured, local conformational substates. Analysis of the dynamics is possible. For example, near room temperature at the Val-9, Ala-24, and Gly-31 positions, the equilibrium constant for interconversion of the two structured forms is near unity and the time scale is > or= 10-20 ms.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Authenticity study of Phyllanthus species by NMR and FT-IR Techniques coupled with chemometric methods

The importance of medicinal plants and their use in industrial applications is increasing worldwide, especially in Brazil. Phyllanthus species, popularly known as quebra-pedras in Brazil, are used in folk medicine for treating urinary infections and renal calculus. This paper reports an authenticity study, based on herbal drugs from Phyllanthus species, involving commercial and authentic samples using spectroscopic techniques: FT-IR, ¹H HR-MAS NMR and ¹H NMR in solution, combined with chemometric analysis. The spectroscopic techniques evaluated, coupled with chemometric methods, have great potential in the investigation of complex matrices. Furthermore, several metabolites were identified by the NMR techniques.

Synthesis of novel O-acylated-D-ribono-1,5-lactones and structural assignment supported by conventional NOESY-NMR and x-ray analysis

A practical method for the structural assignment of 3,4-O-benzylidene-D-ribono-1,5-lactones and analogues using conventional NMR techniques and NOESY measurements in solution is described. 2-O-Acyl-3,4-O-benzylidene-D-ribono-1,5-lactones were prepared in good yields by acylation of Zinner’s lactone with acyl chlorides under mildly basic conditions. Structural determination of 2-O-(4-nitrobenzoyl)-3,4-O-benzylidene-D-ribono-1,5-lactone was achieved by single crystal x-ray diffraction, which supports the results based on spectroscopic data.

Preparação de membranas de acetato de celulose organomodificadas para adsorção dos íons Cu(II), Cd(II), Mn(II) e Ni(II)

Cellulose acetate polymeric membranes had been prepared by a procedure of two steps, combining the method of phase inversion and the technique of hydrolysis-deposition. The first step was the preparation of the membrane, and together was organomodified with tetraethylortosilicate and 3-aminopropyltrietoxysilane. Parameters that exert influence in the complexation of the metallic ion, as pH, time of complexation, metal concentration, had been studied in laboratory using tests of metal removal. The membranes had presented resistance mechanics and reactivity to cations, being able to be an alternative for the removal, daily pay-concentration or in the study of the lability of metals complexed.

Determinação de As, Cd e Pb em amêndoas e mesocarpo de babaçu, sapucaia, xixá e castanha-do-pará por espectrometria de absorção atômica

This work describes methods for the simultaneous determination of Cd and Pb by graphite furnace atomic absorption spectrometry and As by hydride generation atomic absorption spectrometry in Brazilian nuts. The samples (~ 0.300 g) were digested to clear solutions in a closed vessel microwave oven. The pyrolysis and atomization temperatures for simultaneous determinations of Cd and Pb were 1100 and 2100 °C, respectively, using 0.5% (w v-1) NH4H2PO4 + 0.03% (w v-1) Mg(NO3)2 as chemical modifier. The limits of detection (3Δ) were 3.8 μg kg-1 for As, 0.86 μg kg-1 for Cd and 13 μg kg-1 for Pb. The reliability of the entire procedures was confirmed by peach leaves (No. 1547 - NIST) certified reference material analysis and addition and recovery tests. The found concentrations presented no statistical differences at the 95% confidence level.

Utilização de pelos de animais silvestres para monitoramento ambiental de Cd, Cr, Cu, Fe, Mn, Pb e Zn

This study investigates the use of wild animal hair of C. brachyurus, C. thous and L. pardalis as biomonitors of trace metal at Parque Nacional das Emas, Brazil. Results reveal a strong correlation between Cd and Pb as well as Cu and Zn, which suggests a single source of emission. Most metals showed a lower or equal concentration than those obtained in previous studies. The research shows that monitoring may be performed only with Zn, Pb, Cd, and Cr because of statistical similarity and of a non-natural occurrence of large amounts of the material under analysis.

Synthesis and total H-1- and C-13-NMR assignment of cephem derivatives for use in ADEPT approaches

We report the synthesis and total NMR characterization of 5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid-3-[[[(4''-nitrophenoxy)carbonyl]oxy]-methyl]-8-oxo-7[(2-thienyloxoacetyl)amino]-diphenylmethyl ester-5-dioxide (5), a new cephalosporin derivative. This compound can be used as the carrier of a wide range of drugs containing an amino group. The preparation of the intermediate product, 5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid-3-[methyl-4-(6-methoxyquinolin-8-ylamino) pentylcarbamate]-8-oxo-7-[(2-thienyloxoacetyl)amino]-diphenylmethyl ester-5-dioxide (6), as well as the synthesis of the antimalarial primaquine prodrug 5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid-3-[methyl-4-(6-methoxyquinolin-8-ylamino) pentylcarbamate]-8-oxo-7-[(2-thienyloxoacetyl)amino]-5-dioxide (7) are also described, together with their total H-1- and C-13-NMR assignments.

Resistively detected NMR of the nu=1 quantum Hall state: A tilted magnetic field study

Previous resistively detected NMR (RDNMR) studies on the nu approximate to 1 quantum Hall state have reported a ""dispersionlike"" line shape and extremely short nuclear-spin-lattice relaxation times, observations which have been attributed to the formation of a skyrme lattice. Here we examine the evolution of the RDNMR line shape and nuclear-spin relaxation for Zeeman: Coulomb energy ratios ranging from 0.012 to 0.036. According to theory, suppression of the skyrme crystal, along with the associated Goldstone mode nuclear-spin-relaxation mechanism, is expected at the upper end of this range. However, we find that the anomalous line shape persists at high Zeeman energy, and only a modest decrease in the RDNMR-detected nuclear-spin-relaxation rate is observed.